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Posted to commits@taverna.apache.org by st...@apache.org on 2016/05/04 01:56:48 UTC
[1/6] incubator-taverna-common-activities git commit: TAVERNA-963 ASF
license header
Repository: incubator-taverna-common-activities
Updated Branches:
refs/heads/cwl-browse 545856641 -> 4e64abd8e
TAVERNA-963 ASF license header
> Hajo Krabbenhoeft and Steffen Moelller have both signed ICLAs for pre-Apache
> Taverna. That licensed their work to Manchester University and should be
> covered by the University's transfer to Apache.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/5eea144c
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/5eea144c
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/5eea144c
Branch: refs/heads/cwl-browse
Commit: 5eea144c058c8d60c0ebd3029d1a49cb08913a13
Parents: 5458566
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed May 4 00:47:12 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed May 4 00:47:12 2016 +0100
----------------------------------------------------------------------
.../inb/knowarc/gui/AskUserForPwPopup.java | 31 +++++++++-----------
.../inb/knowarc/gui/PleaseWaitDialog.java | 30 +++++++++----------
.../knowarc/usecases/RuntimeEnvironment.java | 30 +++++++++----------
.../usecases/RuntimeEnvironmentConstraint.java | 30 +++++++++----------
.../inb/knowarc/usecases/ScriptInput.java | 30 +++++++++----------
.../inb/knowarc/usecases/ScriptInputStatic.java | 30 +++++++++----------
.../inb/knowarc/usecases/ScriptInputUser.java | 30 +++++++++----------
.../inb/knowarc/usecases/ScriptOutput.java | 30 +++++++++----------
.../knowarc/usecases/UseCaseDescription.java | 30 +++++++++----------
.../knowarc/usecases/UseCaseEnumeration.java | 30 +++++++++----------
.../usecases/invocation/AskUserForPw.java | 30 +++++++++----------
.../invocation/InvocationException.java | 23 +++++++++++----
.../usecases/invocation/UseCaseInvocation.java | 30 +++++++++----------
.../local/LocalUseCaseInvocation.java | 30 +++++++++----------
.../ssh/SshAutoLoginTrustEveryone.java | 30 +++++++++----------
.../usecases/invocation/ssh/SshNode.java | 30 +++++++++----------
.../usecases/invocation/ssh/SshNodeFactory.java | 22 ++++++++++----
.../usecases/invocation/ssh/SshPool.java | 22 ++++++++++----
.../usecases/invocation/ssh/SshReference.java | 16 +++++++++-
.../knowarc/usecases/invocation/ssh/SshUrl.java | 22 ++++++++++----
.../invocation/ssh/SshUrlToSshReference.java | 21 +++++++++----
.../invocation/ssh/SshUseCaseInvocation.java | 30 +++++++++----------
22 files changed, 320 insertions(+), 287 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
index e2ae7e1..0ce0460 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
@@ -1,23 +1,20 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
-
package de.uni_luebeck.inb.knowarc.gui;
import javax.swing.JOptionPane;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
index a6bf707..2a643eb 100755
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.gui;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
index ea49079..c7fd889 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
index baa68d2..ce7e055 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
index 305564c..50747b5 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
index 989c59a..749e104 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
index 59ead67..715c13e 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
index 066c88a..d824ad4 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
index 58bfa93..1c5914e 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
index 08069e5..d5c5d2c 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
index 9c54b1d..e912db1 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
index d714ab1..2f4485f 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
@@ -1,12 +1,23 @@
-/**
- *
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
+
package de.uni_luebeck.inb.knowarc.usecases.invocation;
-/**
- * @author alanrw
- *
- */
public class InvocationException extends Exception {
/**
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
index 17b90c3..d6b2502 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
index f4ae273..612a487 100755
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.local;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
index 60d3bec..ec9c15c 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
index 7cd0f90..6bc122a 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
index 2d8f4bb..bb9a16e 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
@@ -1,5 +1,19 @@
-/**
- *
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
@@ -7,10 +21,6 @@ import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
-/**
- * @author alanrw
- *
- */
public class SshNodeFactory {
private Map<String, SshNode> nodeMap = Collections.synchronizedMap(new HashMap<String, SshNode> ());
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
index c6a5851..3eac767 100755
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
@@ -1,5 +1,19 @@
-/**
- *
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
@@ -18,10 +32,6 @@ import com.jcraft.jsch.Session;
import de.uni_luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint;
import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-/**
- * @author alanrw
- *
- */
public class SshPool {
private static Logger logger = Logger.getLogger(SshPool.class);
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
index c226e8a..b401c0f 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
*
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
index 601735b..ae40ead 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
@@ -1,14 +1,24 @@
-/**
- *
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
import org.apache.taverna.reference.ReferencedDataNature;
-/**
- * @author alanrw
- *
- */
public class SshUrl {
private SshNode sshNode;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
index 3e89f38..7ab4cc6 100644
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
@@ -1,6 +1,21 @@
-/**
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
+
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
import org.apache.taverna.reference.ExternalReferenceSPI;
@@ -9,10 +24,6 @@ import org.apache.taverna.reference.ValueToReferenceConversionException;
import org.apache.taverna.reference.ValueToReferenceConverterSPI;
import org.apache.taverna.security.credentialmanager.CredentialManager;
-/**
- * @author alanrw
- *
- */
public class SshUrlToSshReference implements ValueToReferenceConverterSPI {
private CredentialManager credentialManager;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/5eea144c/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
index 9d01e08..5f77364 100755
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
+++ b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
@@ -1,21 +1,19 @@
-/* Part of the KnowARC Janitor Use-case processor for taverna
- * written 2007-2010 by Hajo Nils Krabbenhoeft and Steffen Moeller
- * University of Luebeck, Institute for Neuro- and Bioinformatics
- * University of Luebeck, Institute for Dermatolgy
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
*
- * This package is free software; you can redistribute it and/or modify
- * it under the terms of the GNU Lesser General Public License as published by
- * the Free Software Foundation; either version 3 of the License, or
- * (at your option) any later version.
+ * http://www.apache.org/licenses/LICENSE-2.0
*
- * This package is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public License
- * along with this package; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
*/
package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
[4/6] incubator-taverna-common-activities git commit: TAVERNA-963
package taverna.externaltool.*
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
deleted file mode 100755
index 612a487..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/local/LocalUseCaseInvocation.java
+++ /dev/null
@@ -1,561 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.local;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.io.OutputStreamWriter;
-import java.io.Reader;
-import java.io.UnsupportedEncodingException;
-import java.io.Writer;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.charset.Charset;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Matcher;
-
-import org.apache.taverna.reference.AbstractExternalReference;
-import org.apache.taverna.reference.ErrorDocument;
-import org.apache.taverna.reference.ExternalReferenceSPI;
-import org.apache.taverna.reference.Identified;
-import org.apache.taverna.reference.ReferenceService;
-import org.apache.taverna.reference.ReferenceSet;
-import org.apache.taverna.reference.ReferencedDataNature;
-import org.apache.taverna.reference.T2Reference;
-import org.apache.taverna.reference.impl.external.file.FileReference;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrl;
-
-/**
- * The job is executed locally, i.e. not via the grid.
- * @author Hajo Krabbenhoeft
- */
-public class LocalUseCaseInvocation extends UseCaseInvocation {
-
- private static Logger logger = Logger.getLogger(LocalUseCaseInvocation.class);
-
- private final File tempDir;
-
- public static String LOCAL_USE_CASE_INVOCATION_TYPE = "789663B8-DA91-428A-9F7D-B3F3DA185FD4";
-
- private Process running;
-
- private final String shellPrefix;
-
- private final String linkCommand;
-
- private Reader stdInReader = null;
-
- private static Map<String, Set<String>> runIdToTempDir = Collections.synchronizedMap(new HashMap<String, Set<String>> ());
-
- private static String LOCAL_INVOCATION_FILE = "localInvocations";
-
- public LocalUseCaseInvocation(UseCaseDescription desc, boolean retrieveData, String mainTempDirectory, String shellPrefix, String linkCommand) throws IOException {
-
- usecase = desc;
- setRetrieveData(retrieveData);
- this.shellPrefix = shellPrefix;
- this.linkCommand = linkCommand;
-
- if (mainTempDirectory != null) {
-
- File mainTempDir = new File(mainTempDirectory);
-
- tempDir = File.createTempFile("usecase", "dir", mainTempDir);
- } else {
- tempDir = File.createTempFile("usecase", "dir");
- }
- tempDir.delete();
- tempDir.mkdir();
- logger.info("mainTempDirectory is " + mainTempDirectory);
- logger.info("Using tempDir " + tempDir.getAbsolutePath());
-
- }
-
- void recDel(File c) {
- File[] files = c.listFiles();
- if (files != null) {
- for (File cc : files)
- recDel(cc);
- }
- c.delete();
- }
-
- private String setOneBinaryInput(ReferenceService referenceService,
- T2Reference t2Reference, ScriptInput input, String targetSuffix)
- throws InvocationException {
-
- if (input.isFile() || input.isTempFile()) {
- // Try to get it as a file
- String target = tempDir.getAbsolutePath() + "/" + targetSuffix;
- FileReference fileRef = getAsFileReference(referenceService,
- t2Reference);
- if (fileRef != null) {
-
- if (!input.isForceCopy()) {
- if (linkCommand != null) {
- String source = fileRef.getFile().getAbsolutePath();
- String actualLinkCommand = getActualOsCommand(
- linkCommand, source, targetSuffix, target);
- logger.info("Link command is " + actualLinkCommand);
- String[] splitCmds = actualLinkCommand.split(" ");
- ProcessBuilder builder = new ProcessBuilder(splitCmds);
- builder.directory(tempDir);
- try {
- int code = builder.start().waitFor();
- if (code == 0) {
- return target;
- } else {
- logger.error("Link command gave errorcode: "
- + code);
- }
-
- } catch (InterruptedException e) {
- // go through
- } catch (IOException e) {
- // go through
- }
-
- }
- }
- }
-
- InputStream is = null;
- OutputStream os = null;
- is = getAsStream(referenceService, t2Reference);
-
- try {
- os = new FileOutputStream(target);
- } catch (FileNotFoundException e) {
- throw new InvocationException(e);
- }
-
- try {
- IOUtils.copyLarge(is, os);
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- try {
- is.close();
- os.close();
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- return target;
- } else {
- String value = (String) referenceService.renderIdentifier(
- t2Reference, String.class, this.getContext());
- return value;
- }
- }
-
- @Override
- public String setOneInput(ReferenceService referenceService,
- T2Reference t2Reference, ScriptInput input)
- throws InvocationException {
-
- if (input.getCharsetName() == null) {
- input.setCharsetName(Charset.defaultCharset().name());
- }
- String target = null;
- String targetSuffix = null;
- if (input.isFile()) {
- targetSuffix = input.getTag();
- } else if (input.isTempFile()) {
- targetSuffix = "tempfile." + (nTempFiles++) + ".tmp";
- }
-
- if (input.isBinary()) {
- return setOneBinaryInput(referenceService, t2Reference, input,
- targetSuffix);
- }
-
- logger.info("Target is " + target);
- if (input.isFile() || input.isTempFile()) {
- target = tempDir.getAbsolutePath() + "/" + targetSuffix;
- // Try to get it as a file
- Reader r;
- Writer w;
- FileReference fileRef = getAsFileReference(referenceService,
- t2Reference);
- if (fileRef != null) {
-
- if (!input.isForceCopy()) {
- if (linkCommand != null) {
- String source = fileRef.getFile().getAbsolutePath();
- String actualLinkCommand = getActualOsCommand(
- linkCommand, source, targetSuffix, target);
- logger.info("Link command is " + actualLinkCommand);
- String[] splitCmds = actualLinkCommand.split(" ");
- ProcessBuilder builder = new ProcessBuilder(splitCmds);
- builder.directory(tempDir);
- try {
- int code = builder.start().waitFor();
- if (code == 0) {
- return target;
- } else {
- logger.error("Link command gave errorcode: "
- + code);
- }
-
- } catch (InterruptedException e) {
- // go through
- } catch (IOException e) {
- // go through
- }
-
- }
- }
-
- if (fileRef.getDataNature().equals(ReferencedDataNature.TEXT)) {
- r = new InputStreamReader(fileRef.openStream(this
- .getContext()), Charset.forName(fileRef
- .getCharset()));
- } else {
- try {
- r = new FileReader(fileRef.getFile());
- } catch (FileNotFoundException e) {
- throw new InvocationException(e);
- }
- }
- } else {
- r = new InputStreamReader(getAsStream(referenceService,
- t2Reference));
- }
- try {
- w = new OutputStreamWriter(new FileOutputStream(target), input
- .getCharsetName());
- } catch (UnsupportedEncodingException e) {
- throw new InvocationException(e);
- } catch (FileNotFoundException e) {
- throw new InvocationException(e);
- }
- try {
- IOUtils.copyLarge(r, w);
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- try {
- r.close();
- w.close();
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- return target;
- } else {
- String value = (String) referenceService.renderIdentifier(
- t2Reference, String.class, this.getContext());
- return value;
- }
- }
-
- private void forgetRun() {
- Set<String> directories = runIdToTempDir.get(getRunId());
- try {
- directories.remove(tempDir.getCanonicalPath());
- } catch (IOException e) {
- logger.error(e);
- }
- }
-
- private static void deleteDirectory(String location) {
- try {
- FileUtils.deleteDirectory(new File(location));
- } catch (IOException e) {
- logger.error("Problem deleting " + location, e);
- }
- }
-
- public static void cleanup(String runId) {
- Set<String> tempDirectories = runIdToTempDir.get(runId);
- if (tempDirectories != null) {
- for (String tempDir : tempDirectories) {
- deleteDirectory(tempDir);
- }
- runIdToTempDir.remove(runId);
- }
- }
-
- @Override
- protected void submit_generate_job_inner() throws InvocationException {
- tags.put("uniqueID", "" + getSubmissionID());
- String command = usecase.getCommand();
- for (String cur : tags.keySet()) {
- command = command.replaceAll("\\Q%%" + cur + "%%\\E", Matcher.quoteReplacement(tags.get(cur)));
- }
-
- List<String> cmds = new ArrayList<String>();
- if ((shellPrefix != null) && !shellPrefix.isEmpty()) {
- String[] prefixCmds = shellPrefix.split(" ");
- for (int i = 0; i < prefixCmds.length; i++) {
- cmds.add(prefixCmds[i]);
- }
- cmds.add(command);
- } else {
- String[] splitCmds = command.split(" ");
- for (int i = 0; i < splitCmds.length; i++) {
- cmds.add(splitCmds[i]);
- }
- }
-
- ProcessBuilder builder = new ProcessBuilder(cmds);
- builder.directory(tempDir);
-
- for (int i = 0; i < cmds.size(); i++) {
- logger.info("cmds[" + i + "] = " + cmds.get(i));
- }
- logger.info("Command is " + command + " in directory " + tempDir);
- try {
- running = builder.start();
- if (stdInReader != null) {
- BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(running.getOutputStream()));
- IOUtils.copyLarge(stdInReader, writer);
- writer.close();
- }
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- }
-
- private void copy_stream(InputStream read, OutputStream write) throws IOException {
- int a = read.available();
- if (a > 0) {
- byte[] buf = new byte[a];
- read.read(buf);
- write.write(buf);
- }
- }
-
- @Override
- public HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException {
- ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
- ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
- while (true) {
- try {
- copy_stream(running.getInputStream(), stdout_buf);
- copy_stream(running.getErrorStream(), stderr_buf);
- } catch (IOException e1) {
- throw new InvocationException(e1);
- }
- try {
- int exitcode = running.exitValue();
- if (!usecase.getValidReturnCodes().contains(exitcode)) {
- try {
- throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString("US-ASCII"));
- } catch (UnsupportedEncodingException e) {
- throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString());
- }
- }
- else
- break;
- } catch (IllegalThreadStateException e) {
-
- try {
- Thread.sleep(100);
- } catch (InterruptedException e1) {
- throw new InvocationException(e);
- }
-
- }
- }
-
- HashMap<String, Object> results = new HashMap<String, Object>();
- results.put("STDOUT", stdout_buf.toByteArray());
- results.put("STDERR", stderr_buf.toByteArray());
-
- for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs().entrySet()) {
- ScriptOutput scriptOutput = cur.getValue();
- File result = new File(tempDir.getAbsoluteFile() + "/" + cur.getValue().getPath());
- if (result.exists()) {
- AbstractExternalReference ref;
- if (isRetrieveData()) {
- FileInputStream is;
- try {
- is = new FileInputStream(result);
- } catch (FileNotFoundException e) {
- throw new InvocationException(e);
- }
- if (scriptOutput.isBinary()) {
- ref = inlineByteArrayReferenceBuilder.createReference(is, null);
- } else {
- ref = inlineStringReferenceBuilder.createReference(is, null);
- }
- try {
- is.close();
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- }
- else {
- ref = new FileReference(result);
- if (scriptOutput.isBinary()) {
- ((FileReference) ref)
- .setDataNature(ReferencedDataNature.BINARY);
- } else {
- ((FileReference) ref)
- .setDataNature(ReferencedDataNature.TEXT);
- ((FileReference) ref).setCharset("UTF-8");
- }
- }
- results.put(cur.getKey(), ref);
- } else {
- ErrorDocument ed = referenceService.getErrorDocumentService().registerError("No result for " + cur.getKey(), 0, getContext());
- results.put(cur.getKey(), ed);
- }
- }
-
- if (isRetrieveData()) {
- forgetRun();
- try {
- deleteDirectory(tempDir.getCanonicalPath());
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- }
-
- return results;
- }
-
- private FileReference getAsFileReference(ReferenceService referenceService, T2Reference t2Reference) {
- Identified identified = referenceService.resolveIdentifier(t2Reference, null, null);
- if (identified instanceof ReferenceSet) {
- for (ExternalReferenceSPI ref : ((ReferenceSet) identified).getExternalReferences()) {
- if (ref instanceof FileReference) {
- return (FileReference) ref;
- }
- }
- }
- return null;
- }
-
- @Override
- public void setStdIn(ReferenceService referenceService,
- T2Reference t2Reference) {
- stdInReader = new BufferedReader(new InputStreamReader(getAsStream(referenceService, t2Reference)));
- }
-
- @Override
- public void rememberRun(String runId) {
- this.setRunId(runId);
- Set<String> directories = runIdToTempDir.get(runId);
- if (directories == null) {
- directories = Collections.synchronizedSet(new HashSet<String> ());
- runIdToTempDir.put(runId, directories);
- }
- try {
- directories.add(tempDir.getCanonicalPath());
- } catch (IOException e) {
- logger.error("Unable to record temporary directory: " + tempDir, e);
- }
- }
-
- public static void load(File directory) {
- File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
- if (!invocationsFile.exists()) {
- return;
- }
- BufferedReader reader = null;
- try {
- reader = new BufferedReader(new FileReader(invocationsFile));
- String line = reader.readLine();
- while (line != null) {
- String[] parts = line.split(" ");
- if (parts.length != 2) {
- break;
- }
- String runId = parts[0];
- String tempDirString = parts[1];
- Set<String> tempDirs = runIdToTempDir.get(runId);
- if (tempDirs == null) {
- tempDirs = new HashSet<String>();
- runIdToTempDir.put(runId, tempDirs);
- }
- tempDirs.add(tempDirString);
- line = reader.readLine();
- }
- } catch (FileNotFoundException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- } finally {
- if (reader != null) {
- try {
- reader.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
- }
- }
-
- public static void persist(File directory) {
- File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
- BufferedWriter writer = null;
- try {
- writer = new BufferedWriter(new FileWriter(invocationsFile));
- for (String runId : runIdToTempDir.keySet()) {
- for (String tempDir : runIdToTempDir.get(runId)) {
- writer.write(runId);
- writer.write(" ");
- writer.write(tempDir);
- writer.newLine();
- }
- }
- } catch (IOException e) {
- logger.error(e);
- } finally {
- if (writer != null) {
- try {
- writer.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
deleted file mode 100644
index ec9c15c..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshAutoLoginTrustEveryone.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.UIKeyboardInteractive;
-import com.jcraft.jsch.UserInfo;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-
-final class SshAutoLoginTrustEveryone implements UserInfo, UIKeyboardInteractive {
-
- private static Logger logger = Logger.getLogger(SshAutoLoginTrustEveryone.class);
-
- private final AskUserForPw askUserForPw;
-
- public SshAutoLoginTrustEveryone(AskUserForPw askUserForPw) {
- super();
- this.askUserForPw = askUserForPw;
- }
-
- public void showMessage(String arg0) {
- logger.info(arg0);
- }
-
- public boolean promptYesNo(String arg0) {
- if (arg0.startsWith("The authenticity of host"))
- return true;
- return false;
- }
-
- public boolean promptPassword(String arg0) {
- return true;
- }
-
- public boolean promptPassphrase(String arg0) {
- return true;
- }
-
- public String getPassword() {
- return askUserForPw.getPassword();
- }
-
- public String getPassphrase() {
- return askUserForPw.getPassphrase();
- }
-
- public String[] promptKeyboardInteractive(String destination, String name, String instruction, String[] prompt, boolean[] echo) {
- if (prompt.length >= 1 && prompt[0].toLowerCase().startsWith("password"))
- return new String[] { askUserForPw.getPassword() };
- return null;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
deleted file mode 100644
index 6bc122a..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNode.java
+++ /dev/null
@@ -1,157 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
-
-public class SshNode {
-
- public static String DEFAULT_HOST = "127.0.0.1";
- public static int DEFAULT_PORT = 22;
- public static String DEFAULT_DIRECTORY = "/tmp/";
-
- private String host = DEFAULT_HOST;
- private int port = DEFAULT_PORT;
- private String directory = DEFAULT_DIRECTORY;
-
- private SshUrl url;
-
- private String linkCommand = null;
- private String copyCommand = null;
- private boolean retrieveData = false;
-
- /**
- *
- */
- SshNode() {
- super();
- linkCommand = InvocationMechanism.UNIX_LINK;
- copyCommand = InvocationMechanism.UNIX_COPY;
-
- }
- /**
- * @param directory the directory to set
- */
- public void setDirectory(String directory) {
- if ((directory != null) && !directory.isEmpty()) {
- if (!directory.endsWith("/")) {
- directory = directory + "/";
- }
- this.directory = directory;
- }
- }
-
- /**
- * @return the directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param host the host to set
- */
- public void setHost(String host) {
- this.host = host;
- }
-
- /**
- * @return the host
- */
- public String getHost() {
- return host;
- }
-
- /**
- * @param port the port to set
- */
- public void setPort(int port) {
- this.port = port;
- }
-
- /**
- * @return the port
- */
- public int getPort() {
- return port;
- }
-
- SshUrl getUrl() {
- if (url == null) {
- url = new SshUrl(this);
- }
- return url;
- }
-
- public int hashCode() {
- return getUrl().hashCode();
- }
-
- public boolean equals(Object obj) {
- if ((obj == null) || !(obj instanceof SshNode)) {
- return false;
- }
- return (this.hashCode() == obj.hashCode());
- }
- /**
- * @return the linkCommand
- */
- public String getLinkCommand() {
- return linkCommand;
- }
- /**
- * @param linkCommand the linkCommand to set
- */
- public void setLinkCommand(String linkCommand) {
- if ((linkCommand != null) && linkCommand.isEmpty()) {
- this.linkCommand = null;
- } else {
- this.linkCommand = linkCommand;
- } }
- /**
- * @return the copyCommand
- */
- public String getCopyCommand() {
- return copyCommand;
- }
- /**
- * @param copyCommand the copyCommand to set
- */
- public void setCopyCommand(String copyCommand) {
- if ((copyCommand != null) && copyCommand.isEmpty()) {
- this.copyCommand = null;
- } else {
- this.copyCommand = copyCommand;
- }
- }
-
- /**
- * @return the retrieveData
- */
- public boolean isRetrieveData() {
- return retrieveData;
- }
- /**
- * @param retrieveData the retrieveData to set
- */
- public void setRetrieveData(boolean retrieveData) {
- this.retrieveData = retrieveData;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
deleted file mode 100644
index bb9a16e..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshNodeFactory.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-public class SshNodeFactory {
-
- private Map<String, SshNode> nodeMap = Collections.synchronizedMap(new HashMap<String, SshNode> ());
-
- private static SshNodeFactory INSTANCE = new SshNodeFactory();
-
- private SshNode defaultNode;
-
- private SshNodeFactory() {
- defaultNode = getSshNode(SshNode.DEFAULT_HOST, SshNode.DEFAULT_PORT, SshNode.DEFAULT_DIRECTORY);
- }
-
- public SshNode getDefaultNode() {
- return defaultNode;
- }
-
- public static SshNodeFactory getInstance() {
- return INSTANCE;
- }
-
- public SshNode getSshNode(String host, int port, String directory) {
- String url = makeUrl(host, port, directory);
- if (nodeMap.containsKey(url)) {
- return nodeMap.get(url);
- }
- else {
- SshNode newNode = new SshNode();
- newNode.setHost(host);
- newNode.setPort(port);
- newNode.setDirectory(directory);
- nodeMap.put(url, newNode);
- return newNode;
- }
- }
-
- public boolean containsSshNode(String host, int port, String directory) {
- return nodeMap.containsKey(makeUrl(host, port, directory));
- }
-
- public static String makeUrl(String host, int port, String directory) {
- return ("ssh://" + host + ":" + port + directory);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
deleted file mode 100755
index 3eac767..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshPool.java
+++ /dev/null
@@ -1,158 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSch;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-
-import de.uni_luebeck.inb.knowarc.usecases.RuntimeEnvironmentConstraint;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-
-public class SshPool {
-
- private static Logger logger = Logger.getLogger(SshPool.class);
-
-
- private static JSch jsch = new JSch();
-
- private static int CONNECT_TIMEOUT = 10000; // milliseconds
-
- private static Map<SshNode, Session> sessionMap = Collections.synchronizedMap(new HashMap<SshNode, Session> ());
- private static Map<Session, ChannelSftp> sftpGetMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
- private static Map<Session, ChannelSftp> sftpPutMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
-
- public static Session getSshSession(final SshUrl sshUrl, final AskUserForPw askUserForPw) throws JSchException {
- return getSshSession(sshUrl.getSshNode(), askUserForPw);
- }
-
- public static synchronized Session getSshSession(final SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
-
- Session s = sessionMap.get(sshNode);
- if ((s != null) && s.isConnected()) {
- logger.info("Reusing session");
- return s;
- }
- if (s != null) {
- logger.info("Session was not connected");
- }
- if (s == null) {
- logger.info("No session found for " + sshNode.toString());
- }
-
- if (askUserForPw.getKeyfile().length() > 0) {
- jsch.addIdentity(askUserForPw.getKeyfile());
- }
- logger.info("Using host is " + sshNode.getHost() + " and port " + sshNode.getPort());
- Session sshSession = jsch.getSession(askUserForPw.getUsername(), sshNode.getHost(), sshNode.getPort());
- sshSession.setUserInfo(new SshAutoLoginTrustEveryone(askUserForPw));
- sshSession.connect(CONNECT_TIMEOUT);
-
- askUserForPw.authenticationSucceeded();
- sessionMap.put(sshNode, sshSession);
- if (sshSession == null) {
- logger.error("Returning a null session");
- }
- return sshSession;
- }
-
- public static ChannelSftp getSftpGetChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
- return getSftpGetChannel(getSshSession(sshNode, askUserForPw));
- }
-
- private static synchronized ChannelSftp getSftpGetChannel(Session session) throws JSchException {
- ChannelSftp result = sftpGetMap.get(session);
- if (!session.isConnected()) {
- logger.warn("Session is not connected");
- }
- if (result == null) {
- logger.info("Creating new sftp channel");
- result = (ChannelSftp) session.openChannel("sftp");
- sftpGetMap.put(session, result);
- }
- else {
- logger.info("Reusing sftp channel");
- }
- if (!result.isConnected()) {
- logger.info("Connecting");
- result.connect();
- } else {
- logger.info("Already connected");
- }
- return result;
- }
-
- public static ChannelSftp getSftpPutChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
- return getSftpPutChannel(getSshSession(sshNode, askUserForPw));
- }
-
- private static synchronized ChannelSftp getSftpPutChannel(Session session) throws JSchException {
- ChannelSftp result = null;
- synchronized(sftpPutMap) {
- result = sftpPutMap.get(session);
- if (!session.isConnected()) {
- logger.info("Session is not connected");
- }
- if (result == null) {
- logger.info("Creating new sftp channel");
- result = (ChannelSftp) session.openChannel("sftp");
- sftpPutMap.put(session, result);
- }
- else {
- logger.info("Reusing sftp channel");
- }
- }
- if (!result.isConnected()) {
- logger.info("Connecting");
- result.connect(CONNECT_TIMEOUT);
- } else {
- logger.info("Already connected");
- }
- return result;
- }
-
- public static synchronized ChannelExec openExecChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
- return (ChannelExec) getSshSession(sshNode, askUserForPw).openChannel("exec");
- }
-
- private static synchronized ChannelExec openExecChannel(Session session) throws JSchException {
- return (ChannelExec) session.openChannel("exec");
- }
-
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
deleted file mode 100644
index b401c0f..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.java
+++ /dev/null
@@ -1,222 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.io.InputStream;
-
-import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna;
-import org.apache.taverna.reference.AbstractExternalReference;
-import org.apache.taverna.reference.DereferenceException;
-import org.apache.taverna.reference.ExternalReferenceSPI;
-import org.apache.taverna.reference.ReferenceContext;
-import org.apache.taverna.security.credentialmanager.CredentialManager;
-import org.apache.taverna.reference.ReferencedDataNature;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.SftpException;
-
-/**
- * @author alanrw
- *
- */
-public class SshReference extends AbstractExternalReference implements
- ExternalReferenceSPI {
-
- private static Logger logger = Logger.getLogger(SshReference.class);
-
-
- private String host = "127.0.0.1";
- private int port = 22;
- private String directory = "/tmp/";
- private String subDirectory;
- private String fileName;
-
- private CredentialManager credentialManager;
-
- private int dataNatureInteger = ReferencedDataNature.UNKNOWN.ordinal();
- private String charset = "UTF-8";
-
- public SshReference() {
- super();
- }
-
- public SshReference(SshUrl url) {
- super();
- this.host = url.getSshNode().getHost();
- this.port = url.getSshNode().getPort();
- this.directory = url.getSshNode().getDirectory();
- this.subDirectory = url.getSubDirectory();
- this.fileName = url.getFileName();
- this.setDataNature(url.getDataNature());
- this.setCharset(url.getCharset());
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#getApproximateSizeInBytes()
- */
- @Override
- public Long getApproximateSizeInBytes() {
- return 10000L;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#openStream(net.sf.taverna.t2.reference.ReferenceContext)
- */
- @Override
- public InputStream openStream(ReferenceContext context)
- throws DereferenceException {
- try {
- SshNode node = SshNodeFactory.getInstance().getSshNode(this.getHost(), this.getPort(), this.getDirectory());
- String fullPath = getDirectory() + getSubDirectory() + "/" + getFileName();
- ChannelSftp channel = SshPool.getSftpGetChannel(node, new RetrieveLoginFromTaverna(new SshUrl(node).toString(), credentialManager));
- logger.info("Opening stream on " + fullPath);
- return (channel.get(fullPath));
- } catch (JSchException e) {
- //TODO
- logger.error(e);
- } catch (SftpException e) {
- // TODO Auto-generated catch block
- logger.error(e);
- }
- return null;
- }
-
- /**
- * @return the host
- */
- public String getHost() {
- return host;
- }
-
- /**
- * @param host the host to set
- */
- public void setHost(String host) {
- this.host = host;
- }
-
- /**
- * @return the port
- */
- public int getPort() {
- return port;
- }
-
- /**
- * @param port the port to set
- */
- public void setPort(int port) {
- this.port = port;
- }
-
- /**
- * @return the directory
- */
- public String getDirectory() {
- return directory;
- }
-
- /**
- * @param directory the directory to set
- */
- public void setDirectory(String directory) {
- this.directory = directory;
- }
-
- /**
- * @return the subDirectory
- */
- public String getSubDirectory() {
- return subDirectory;
- }
-
- /**
- * @param subDirectory the subDirectory to set
- */
- public void setSubDirectory(String subDirectory) {
- this.subDirectory = subDirectory;
- }
-
- /**
- * @return the fileName
- */
- public String getFileName() {
- return fileName;
- }
-
- /**
- * @param fileName the fileName to set
- */
- public void setFileName(String fileName) {
- this.fileName = fileName;
- }
-
- public String getFullPath() {
- return getDirectory() + "/" + getSubDirectory() + "/" + getFileName();
- }
-
- public ReferencedDataNature getDataNature() {
- return ReferencedDataNature.values()[dataNatureInteger];
- }
-
- public void setDataNature(ReferencedDataNature dataNature) {
- this.dataNatureInteger = dataNature.ordinal();
- }
-
- public String getCharset() {
- return charset;
- }
-
- public void setCredentialManager(CredentialManager credentialManager) {
- this.credentialManager = credentialManager;
- }
-
- public void setCharset(String charset) {
- this.charset = charset;
- }
-
- /**
- * @return the dataNatureInteger
- */
- public int getDataNatureInteger() {
- return dataNatureInteger;
- }
-
- /**
- * @param dataNatureInteger the dataNatureInteger to set
- */
- public void setDataNatureInteger(int dataNatureInteger) {
- this.dataNatureInteger = dataNatureInteger;
- }
-
- public SshReference clone() {
- SshReference result = new SshReference();
- result.setHost(this.getHost());
- result.setPort(this.getPort());
- result.setDirectory(this.getDirectory());
- result.setSubDirectory(this.getSubDirectory());
- result.setFileName(this.getFileName());
- result.setDataNature(this.getDataNature());
- result.setCharset(this.getCharset());
- return result;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
deleted file mode 100644
index ae40ead..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrl.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import org.apache.taverna.reference.ReferencedDataNature;
-
-public class SshUrl {
-
- private SshNode sshNode;
- private String subDirectory;
- private String fileName;
-
- private ReferencedDataNature dataNature = ReferencedDataNature.UNKNOWN;
- private String charset = "UTF-8";
-
-
- public SshUrl(SshNode sshNode) {
- this.setSshNode(sshNode);
- }
-
-
- /**
- * @return the host
- */
- public String getHost() {
- return getSshNode().getHost();
- }
- /**
- * @param host the host to set
- */
- public void setHost(String host) {
- getSshNode().setHost(host);
- }
- /**
- * @return the port
- */
- public int getPort() {
- return getSshNode().getPort();
- }
- /**
- * @param port the port to set
- */
- public void setPort(int port) {
- getSshNode().setPort(port);
- }
- /**
- * @return the directory
- */
- public String getDirectory() {
- return getSshNode().getDirectory();
- }
- /**
- * @param directory the directory to set
- */
- public void setDirectory(String directory) {
- getSshNode().setDirectory(directory);
- }
- /**
- * @return the subDirectory
- */
- public String getSubDirectory() {
- return subDirectory;
- }
- /**
- * @param subDirectory the subDirectory to set
- */
- public void setSubDirectory(String subDirectory) {
- this.subDirectory = subDirectory;
- }
- /**
- * @return the fileName
- */
- public String getFileName() {
- return fileName;
- }
- /**
- * @param fileName the fileName to set
- */
- public void setFileName(String fileName) {
- this.fileName = fileName;
- }
-
- public String toString() {
- String result = SshNodeFactory.makeUrl(getHost(), getPort(), getDirectory());
- if (getSubDirectory() != null) {
- result += getSubDirectory();
- }
- if (getFileName() != null) {
- result += "/" + getFileName();
- }
- return result;
- }
-
- public int hashCode() {
- return toString().hashCode();
-
- }
-
- public boolean equals(Object obj) {
- if ((obj == null) || !(obj instanceof SshUrl)) {
- return false;
- }
- return (this.hashCode() == obj.hashCode());
- }
-
- public SshUrl getBaseUrl() {
- SshUrl result = new SshUrl(this.getSshNode());
- return result;
- }
-
-
- /**
- * @return the sshNode
- */
- public SshNode getSshNode() {
- return sshNode;
- }
-
-
- /**
- * @param sshNode the sshNode to set
- */
- public void setSshNode(SshNode sshNode) {
- this.sshNode = sshNode;
- }
-
- public ReferencedDataNature getDataNature() {
- return dataNature;
- }
-
-
- public void setDataNature(ReferencedDataNature dataNature) {
- this.dataNature = dataNature;
- }
-
-
- public String getCharset() {
- return charset;
- }
-
-
- public void setCharset(String charset) {
- this.charset = charset;
- }
-
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
deleted file mode 100644
index 7ab4cc6..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUrlToSshReference.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import org.apache.taverna.reference.ExternalReferenceSPI;
-import org.apache.taverna.reference.ReferenceContext;
-import org.apache.taverna.reference.ValueToReferenceConversionException;
-import org.apache.taverna.reference.ValueToReferenceConverterSPI;
-import org.apache.taverna.security.credentialmanager.CredentialManager;
-
-public class SshUrlToSshReference implements ValueToReferenceConverterSPI {
-
- private CredentialManager credentialManager;
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#canConvert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
- */
- @Override
- public boolean canConvert(Object o, ReferenceContext context) {
- return (o instanceof SshUrl);
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#convert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
- */
- @Override
- public ExternalReferenceSPI convert(Object o, ReferenceContext context)
- throws ValueToReferenceConversionException {
- SshReference result = new SshReference((SshUrl) o);
- result.setCredentialManager(credentialManager);
- return result;
- }
-
- public void setCredentialManager(CredentialManager credentialManager) {
- this.credentialManager = credentialManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
deleted file mode 100755
index 5f77364..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshUseCaseInvocation.java
+++ /dev/null
@@ -1,561 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation.ssh;
-
-import java.io.BufferedInputStream;
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Random;
-import java.util.Set;
-import java.util.Vector;
-import java.util.regex.Matcher;
-
-import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna;
-import org.apache.taverna.reference.AbstractExternalReference;
-import org.apache.taverna.reference.ErrorDocument;
-import org.apache.taverna.reference.ErrorDocumentServiceException;
-import org.apache.taverna.reference.ExternalReferenceSPI;
-import org.apache.taverna.reference.Identified;
-import org.apache.taverna.reference.ReferenceService;
-import org.apache.taverna.reference.ReferenceSet;
-import org.apache.taverna.reference.ReferencedDataNature;
-import org.apache.taverna.reference.T2Reference;
-import org.apache.taverna.security.credentialmanager.CredentialManager;
-
-import org.apache.log4j.Logger;
-
-import com.jcraft.jsch.ChannelExec;
-import com.jcraft.jsch.ChannelSftp;
-import com.jcraft.jsch.JSchException;
-import com.jcraft.jsch.Session;
-import com.jcraft.jsch.SftpException;
-import com.jcraft.jsch.ChannelSftp.LsEntry;
-
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-
-/**
- * The job is executed by connecting to a worker pc using ssh, i.e. not via the
- * grid.
- *
- * @author Hajo Krabbenhoeft
- */
-public class SshUseCaseInvocation extends UseCaseInvocation {
-
- private static Logger logger = Logger.getLogger(SshUseCaseInvocation.class);
-
- private SshUrl location = null;
-
- private InputStream stdInputStream = null;
-
- public static final String SSH_USE_CASE_INVOCATION_TYPE = "D0A4CDEB-DD10-4A8E-A49C-8871003083D8";
- private String tmpname;
- private final SshNode workerNode;
- private final AskUserForPw askUserForPw;
-
- private ChannelExec running;
-
- private List<String> precedingCommands = new ArrayList<String>();
-
- private final ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
- private final ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
-
- private static Map<String, Object> nodeLock = Collections
- .synchronizedMap(new HashMap<String, Object>());
-
- private static Map<String, Set<SshUrl>> runIdToTempDir = Collections
- .synchronizedMap(new HashMap<String, Set<SshUrl>>());
-
- private static String SSH_INVOCATION_FILE = "sshInvocations";
-
- private final CredentialManager credentialManager;
-
- public static String test(final SshNode workerNode,
- final AskUserForPw askUserForPw) {
- try {
- Session sshSession = SshPool
- .getSshSession(workerNode, askUserForPw);
-
- ChannelSftp sftpTest = (ChannelSftp) sshSession.openChannel("sftp");
- sftpTest.connect();
- sftpTest.cd(workerNode.getDirectory());
- sftpTest.disconnect();
- sshSession.disconnect();
- } catch (JSchException e) {
- return e.toString();
- } catch (SftpException e) {
- return e.toString();
- }
- return null;
- }
-
- public SshUseCaseInvocation(UseCaseDescription desc, SshNode workerNodeA,
- AskUserForPw askUserForPwA, CredentialManager credentialManager)
- throws JSchException, SftpException {
- this.workerNode = workerNodeA;
- this.credentialManager = credentialManager;
-
- setRetrieveData(workerNodeA.isRetrieveData());
- this.askUserForPw = askUserForPwA;
- usecase = desc;
-
- ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode, askUserForPw);
- synchronized (getNodeLock(workerNode)) {
-
- logger.info("Changing remote directory to "
- + workerNode.getDirectory());
- sftp.cd(workerNode.getDirectory());
- Random rnd = new Random();
- while (true) {
- tmpname = "usecase" + rnd.nextLong();
- try {
- sftp.lstat(workerNode.getDirectory() + tmpname);
- continue;
- } catch (Exception e) {
- // file seems to not exist :)
- }
- sftp.mkdir(workerNode.getDirectory() + tmpname);
- sftp.cd(workerNode.getDirectory() + tmpname);
- break;
- }
- }
- }
-
- private static void recursiveDelete(ChannelSftp sftp, String path)
- throws SftpException, JSchException {
- Vector<?> entries = sftp.ls(path);
- for (Object object : entries) {
- LsEntry entry = (LsEntry) object;
- if (entry.getFilename().equals(".")
- || entry.getFilename().equals("..")) {
- continue;
- }
- if (entry.getAttrs().isDir()) {
- recursiveDelete(sftp, path + entry.getFilename() + "/");
- } else {
- sftp.rm(path + entry.getFilename());
- }
- }
- sftp.rmdir(path);
- }
-
- private static void deleteDirectory(SshUrl directory,
- CredentialManager credentialManager) throws InvocationException {
- URI uri;
- try {
- uri = new URI(directory.toString());
-
- ChannelSftp sftp;
- SshNode workerNode;
- String fullPath = uri.getPath();
- String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
- String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
- try {
- workerNode = SshNodeFactory.getInstance().getSshNode(
- uri.getHost(), uri.getPort(), path);
-
- sftp = SshPool.getSftpPutChannel(workerNode,
- new RetrieveLoginFromTaverna(workerNode.getUrl()
- .toString(), credentialManager));
- } catch (JSchException e) {
- throw new InvocationException(e);
- }
- synchronized (getNodeLock(workerNode)) {
- try {
- sftp.cd(path);
- recursiveDelete(sftp, path + "/" + tempDir + "/");
- } catch (SftpException e) {
- throw new InvocationException(e);
- } catch (JSchException e) {
- throw new InvocationException(e);
- }
- }
- } catch (URISyntaxException e1) {
- throw new InvocationException(e1);
- }
- }
-
- public static void cleanup(String runId, CredentialManager credentialManager)
- throws InvocationException {
- Set<SshUrl> tempDirectories = runIdToTempDir.get(runId);
- if (tempDirectories != null) {
- for (SshUrl tempUrl : tempDirectories) {
- deleteDirectory(tempUrl, credentialManager);
- }
- runIdToTempDir.remove(runId);
- }
- }
-
- @Override
- protected void submit_generate_job_inner() throws InvocationException {
- tags.put("uniqueID", "" + getSubmissionID());
- String command = usecase.getCommand();
- for (String cur : tags.keySet()) {
- command = command.replaceAll("\\Q%%" + cur + "%%\\E",
- Matcher.quoteReplacement(tags.get(cur)));
- }
- String fullCommand = "cd " + workerNode.getDirectory() + tmpname;
- for (String preceding : precedingCommands) {
- fullCommand += " && " + preceding;
- }
- fullCommand += " && " + command;
-
- logger.info("Full command is " + fullCommand);
-
- try {
- running = SshPool.openExecChannel(workerNode, askUserForPw);
- running.setCommand(fullCommand);
- running.setOutputStream(stdout_buf);
- running.setErrStream(stderr_buf);
- if (stdInputStream != null) {
- running.setInputStream(stdInputStream);
- }
- running.connect();
- } catch (JSchException e) {
- throw new InvocationException(e);
- }
-
- }
-
- @Override
- public HashMap<String, Object> submit_wait_fetch_results(
- ReferenceService referenceService) throws InvocationException {
- while (!running.isClosed()) {
- try {
- Thread.sleep(1000);
- } catch (InterruptedException e) {
- throw new InvocationException("Invocation interrupted:"
- + e.getMessage());
- }
- }
-
- int exitcode = running.getExitStatus();
- if (!usecase.getValidReturnCodes().contains(exitcode)) {
- try {
- throw new InvocationException("Invalid exit code " + exitcode
- + ":" + stderr_buf.toString("US-ASCII"));
- } catch (UnsupportedEncodingException e) {
- throw new InvocationException("Invalid exit code " + exitcode
- + ":" + stderr_buf.toString());
- }
- }
-
- HashMap<String, Object> results = new HashMap<String, Object>();
-
- results.put("STDOUT", stdout_buf.toByteArray());
- results.put("STDERR", stderr_buf.toByteArray());
- try {
- stdout_buf.close();
- stderr_buf.close();
- } catch (IOException e2) {
- throw new InvocationException(e2);
- }
-
- try {
- ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
- askUserForPw);
- synchronized (getNodeLock(workerNode)) {
- for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs()
- .entrySet()) {
- ScriptOutput scriptOutput = cur.getValue();
- String fullPath = workerNode.getDirectory() + tmpname + "/"
- + scriptOutput.getPath();
- try {
- if (sftp.stat(fullPath) != null) {
- SshUrl url = new SshUrl(workerNode);
- url.setSubDirectory(tmpname);
- url.setFileName(scriptOutput.getPath());
- if (scriptOutput.isBinary()) {
- url.setDataNature(ReferencedDataNature.BINARY);
- } else {
- url.setDataNature(ReferencedDataNature.TEXT);
- url.setCharset("UTF-8");
- }
- if (isRetrieveData()) {
- SshReference urlRef = new SshReference(url);
- InputStream is = urlRef.openStream(null);
- AbstractExternalReference ref;
- if (scriptOutput.isBinary()) {
- ref = inlineByteArrayReferenceBuilder
- .createReference(is, null);
- } else {
- ref = inlineStringReferenceBuilder
- .createReference(is, null);
- }
- try {
- is.close();
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- results.put(cur.getKey(), ref);
- } else {
- results.put(cur.getKey(), url);
- }
- } else {
- ErrorDocument ed = referenceService
- .getErrorDocumentService().registerError(
- "No result for " + cur.getKey(), 0,
- getContext());
- results.put(cur.getKey(), ed);
- }
- } catch (SftpException e) {
- ErrorDocument ed = referenceService
- .getErrorDocumentService().registerError(
- "No result for " + cur.getKey(), 0,
- getContext());
- results.put(cur.getKey(), ed);
-
- }
- }
- }
- } catch (JSchException e1) {
- throw new InvocationException(e1);
- } catch (ErrorDocumentServiceException e) {
- throw new InvocationException(e);
- }
-
- if (running != null) {
- running.disconnect();
- }
- if (stdInputStream != null) {
- try {
- stdInputStream.close();
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- }
-
- if (isRetrieveData()) {
- forgetRun();
- deleteDirectory(location, credentialManager);
-
- }
- return results;
- }
-
- @Override
- public String setOneInput(ReferenceService referenceService,
- T2Reference t2Reference, ScriptInput input)
- throws InvocationException {
- String target = null;
- String remoteName = null;
- if (input.isFile()) {
- remoteName = input.getTag();
- } else if (input.isTempFile()) {
- remoteName = "tempfile." + (nTempFiles++) + ".tmp";
-
- }
- if (input.isFile() || input.isTempFile()) {
- SshReference sshRef = getAsSshReference(referenceService,
- t2Reference, workerNode);
- target = workerNode.getDirectory() + tmpname + "/" + remoteName;
- logger.info("Target is " + target);
- if (sshRef != null) {
- if (!input.isForceCopy()) {
- String linkCommand = workerNode.getLinkCommand();
- if (linkCommand != null) {
- String actualLinkCommand = getActualOsCommand(
- linkCommand, sshRef.getFullPath(), remoteName,
- target);
- precedingCommands.add(actualLinkCommand);
- return target;
-
- }
- }
- String copyCommand = workerNode.getCopyCommand();
- if (copyCommand != null) {
- String actualCopyCommand = getActualOsCommand(copyCommand,
- sshRef.getFullPath(), remoteName, target);
- precedingCommands.add(actualCopyCommand);
- return target;
- }
- }
- try {
- ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
- askUserForPw);
- synchronized (getNodeLock(workerNode)) {
- InputStream r = getAsStream(referenceService, t2Reference);
- sftp.put(r, target);
- r.close();
- }
- } catch (SftpException e) {
- throw new InvocationException(e);
- } catch (JSchException e) {
- throw new InvocationException(e);
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- return target;
- } else {
- String value = (String) referenceService.renderIdentifier(
- t2Reference, String.class, this.getContext());
- return value;
-
- }
- }
-
- public SshReference getAsSshReference(ReferenceService referenceService,
- T2Reference t2Reference, SshNode workerNode) {
- Identified identified = referenceService.resolveIdentifier(t2Reference,
- null, null);
- if (identified instanceof ReferenceSet) {
- for (ExternalReferenceSPI ref : ((ReferenceSet) identified)
- .getExternalReferences()) {
- if (ref instanceof SshReference) {
- SshReference sshRef = (SshReference) ref;
- if (sshRef.getHost().equals(workerNode.getHost())) {
- return sshRef;
- }
- }
- }
- }
- return null;
- }
-
- private static Object getNodeLock(final SshNode node) {
- return getNodeLock(node.getHost());
- }
-
- private static synchronized Object getNodeLock(String hostName) {
- if (!nodeLock.containsKey(hostName)) {
- nodeLock.put(hostName, new Object());
- }
- return nodeLock.get(hostName);
- }
-
- @Override
- public void setStdIn(ReferenceService referenceService,
- T2Reference t2Reference) {
- stdInputStream = new BufferedInputStream(getAsStream(referenceService,
- t2Reference));
- }
-
- @Override
- public void rememberRun(String runId) {
- this.setRunId(runId);
- Set<SshUrl> directories = runIdToTempDir.get(runId);
- if (directories == null) {
- directories = Collections.synchronizedSet(new HashSet<SshUrl>());
- runIdToTempDir.put(runId, directories);
- }
- location = new SshUrl(workerNode);
- location.setSubDirectory(tmpname);
- directories.add(location);
- }
-
- private void forgetRun() {
- Set<SshUrl> directories = runIdToTempDir.get(getRunId());
- directories.remove(location);
- }
-
- public static void load(File directory) {
- File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
- if (!invocationsFile.exists()) {
- return;
- }
- BufferedReader reader = null;
- try {
- reader = new BufferedReader(new FileReader(invocationsFile));
- String line = reader.readLine();
- while (line != null) {
- String[] parts = line.split(" ");
- if (parts.length != 2) {
- break;
- }
- String runId = parts[0];
- String urlString = parts[1];
- Set<SshUrl> urls = runIdToTempDir.get(runId);
- if (urls == null) {
- urls = new HashSet<SshUrl>();
- runIdToTempDir.put(runId, urls);
- }
- URI uri = new URI(urlString);
- String fullPath = uri.getPath();
- String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
- String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
- SshNode node = SshNodeFactory.getInstance().getSshNode(
- uri.getHost(), uri.getPort(), path);
- SshUrl newUrl = new SshUrl(node);
- newUrl.setSubDirectory(tempDir);
- urls.add(newUrl);
- line = reader.readLine();
- }
- } catch (FileNotFoundException e) {
- logger.error(e);
- } catch (URISyntaxException e) {
- logger.error(e);
- } catch (IOException e) {
- logger.error(e);
- } finally {
- if (reader != null) {
- try {
- reader.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
- }
- }
-
- public static void persist(File directory) {
- File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
- BufferedWriter writer = null;
- try {
- writer = new BufferedWriter(new FileWriter(invocationsFile));
- for (String runId : runIdToTempDir.keySet()) {
- for (SshUrl url : runIdToTempDir.get(runId)) {
- writer.write(runId);
- writer.write(" ");
- writer.write(url.toString());
- writer.newLine();
- }
- }
- } catch (IOException e) {
- logger.error(e);
- } finally {
- if (writer != null) {
- try {
- writer.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java
index fb903c8..167f424 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivity.java
@@ -24,6 +24,12 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import org.apache.taverna.activities.externaltool.desc.ScriptInput;
+import org.apache.taverna.activities.externaltool.desc.ScriptInputUser;
+import org.apache.taverna.activities.externaltool.desc.ScriptOutput;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.InvocationException;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationGroup;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.annotation.Annotated;
@@ -41,13 +47,6 @@ import org.apache.taverna.workflowmodel.processor.activity.AsynchronousActivityC
import org.apache.log4j.Logger;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-
/**
* This is the main class of the use case activity plugin. Here we store the
* configuration and the description of a use case activity, configure the input
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java
index 5e6fd23..74c9070 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityConfigurationBean.java
@@ -21,12 +21,12 @@ package org.apache.taverna.activities.externaltool;
import java.util.List;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
import org.apache.taverna.activities.externaltool.manager.InvocationGroup;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.activities.externaltool.manager.MechanismCreator;
import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
@ConfigurationBean(uri = ExternalToolActivity.URI + "#Config")
public final class ExternalToolActivityConfigurationBean {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityMimeTypeChecker.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityMimeTypeChecker.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityMimeTypeChecker.java
index 641b60d..051b69b 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityMimeTypeChecker.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ExternalToolActivityMimeTypeChecker.java
@@ -27,6 +27,8 @@ import java.util.List;
import java.util.Set;
import java.util.Map.Entry;
+import org.apache.taverna.activities.externaltool.desc.ScriptInputUser;
+import org.apache.taverna.activities.externaltool.desc.ScriptOutput;
import org.apache.taverna.visit.VisitReport;
import org.apache.taverna.visit.VisitReport.Status;
import org.apache.taverna.workflowmodel.Dataflow;
@@ -49,9 +51,6 @@ import org.apache.taverna.workflowmodel.utils.Tools;
import org.apache.log4j.Logger;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptOutput;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java
index 6697ed6..6bf729c 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/InvocationCreator.java
@@ -21,9 +21,8 @@ package org.apache.taverna.activities.externaltool;
import java.util.Map;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.reference.ReferenceService;
import org.apache.taverna.reference.T2Reference;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/RetrieveLoginFromTaverna.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/RetrieveLoginFromTaverna.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/RetrieveLoginFromTaverna.java
index 3dcfd0f..dff298a 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/RetrieveLoginFromTaverna.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/RetrieveLoginFromTaverna.java
@@ -21,10 +21,10 @@ package org.apache.taverna.activities.externaltool;
import java.net.URI;
+import org.apache.taverna.activities.externaltool.invocation.AskUserForPw;
import org.apache.taverna.security.credentialmanager.CMException;
import org.apache.taverna.security.credentialmanager.CredentialManager;
import org.apache.taverna.security.credentialmanager.UsernamePassword;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
public class RetrieveLoginFromTaverna implements AskUserForPw {
private final String url;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
new file mode 100644
index 0000000..ad58eea
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
@@ -0,0 +1,251 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Representation of information about a single runtime environment. It is used
+ * to decide if one runtime environment is possibly compatible with another one
+ * for the selection of queues to commit to.
+ *
+ * To experiment/test these functions, run the following java -cp
+ * target/taverna-knowarc-processor-0.1.7.jar
+ * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 foo-1 java -cp
+ * target/taverna-knowarc-processor-0.1.7.jar
+ * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 bla-2 java -cp
+ * target/taverna-knowarc-processor-0.1.7.jar
+ * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1.2 bla-1
+ *
+ * @author Steffen Moeller
+ */
+@SuppressWarnings("unchecked")
+public class RuntimeEnvironment implements Comparable {
+
+ private static Logger logger = Logger.getLogger(RuntimeEnvironment.class);
+
+
+ /**
+ * Unique identification of the runtime environment - the full name
+ */
+ protected String id;
+
+ /**
+ * Accessor function for the complete identifier of the runtime environment
+ */
+ public String getID() {
+ return id;
+ }
+
+ protected String name;
+
+ /**
+ * Accessor function for the RE's name
+ */
+ public String getName() {
+ return name;
+ }
+
+ protected String version;
+
+ /**
+ * Accessfor function for the version
+ */
+ public String getVersion() {
+ return version;
+ }
+
+ /**
+ * for those busy fellows who don't have the time to convert the String into
+ * a RuntimeEnvironment object.
+ *
+ * @author Steffen Moeller
+ */
+ public boolean atLeastAsCapableAs(String s) {
+ RuntimeEnvironment tmpRE = new RuntimeEnvironment(s);
+ return this.atLeastAsCapableAs(tmpRE);
+ }
+
+ /**
+ * Indicates if a runtime environment has the same name, and if so, if the
+ * given RE has the same or a later version.
+ *
+ * @author Steffen Moeller
+ */
+ public boolean atLeastAsCapableAs(RuntimeEnvironment re) {
+ if (!name.equals(re.name))
+ return false;
+ int c = compareVersions(getVersion(), re.getVersion());
+ if (c >= 0) {
+ return true;
+ } else {
+ return false;
+ }
+ }
+
+ /**
+ * Indicates if this runtimeEnvironment is the same version or later as any
+ * in that list.
+ *
+ * @author Steffen Moeller
+ */
+ public boolean atLeastAsCapableAsAnyOf(Iterable<RuntimeEnvironment> res) {
+ boolean compatibleOneFound = false;
+ Iterator<RuntimeEnvironment> i = res.iterator();
+ while (i.hasNext() && !compatibleOneFound) {
+ RuntimeEnvironment r = i.next();
+ compatibleOneFound = atLeastAsCapableAs(r);
+ }
+ return compatibleOneFound;
+ }
+
+ /**
+ * Indicates if any of the runtime environments listed is the same version
+ * as this or later.
+ *
+ * @author Steffen Moeller
+ */
+ public boolean isInferiorToAtLeastOneIn(Iterable<RuntimeEnvironment> res) {
+ boolean compatibleOneFound = false;
+ Iterator<RuntimeEnvironment> i = res.iterator();
+ while (i.hasNext() && !compatibleOneFound) {
+ RuntimeEnvironment r = i.next();
+ compatibleOneFound = r.atLeastAsCapableAs(this);
+ }
+ return compatibleOneFound;
+ }
+
+ /**
+ * Parses a string as commonly presented by the infosystem
+ *
+ * @author Steffen Moeller
+ */
+ public RuntimeEnvironment(String raw) {
+ id = raw;
+ int dashpos = raw.indexOf("-");
+ if (-1 == dashpos) {
+ version = "";
+ name = raw;
+ } else {
+ name = raw.substring(0, dashpos);
+ if (dashpos + 1 <= raw.length()) {
+ version = raw.substring(dashpos + 1, raw.length());
+ } else {
+ version = "";
+ }
+ }
+ }
+
+ /**
+ * to make it behave like a string at time, as it was originally implemented
+ */
+ @Override
+ public String toString() {
+ return id;
+ }
+
+ /**
+ * Implementation of Comparable interface. It comes handy albeit this
+ * function says nothing about the compatibility of two runtime environments
+ * unless their names are identical and the relation of the constraint was
+ * taken into account. It just sorts them in lists.
+ */
+ public int compareTo(Object o) throws ClassCastException {
+ RuntimeEnvironment r = (RuntimeEnvironment) o;
+ if (getName().equals(r.getName())) {
+ return RuntimeEnvironment.compareVersions(getVersion(), r.getVersion());
+ } else {
+ return id.compareTo(r.getID());
+ }
+ }
+
+ /**
+ * FIXME: For the sake of simplicity, this implementation makes an error in
+ * treating . and - in the versions equally. Versions, if numerical, are
+ * treated numerically. Otherwise it is lexicographical, which is error
+ * prone, though. Should the 'Scanner' class should be tapped into?
+ *
+ * @author Steffen Moeller
+ */
+ public static int compareVersions(String a, String b) {
+
+ // null pointer exceptions are not risked .. we are nice
+ if (null == a)
+ a = "";
+ if (null == b)
+ b = "";
+
+ // catching the dumb case first
+ if (a.equals(b))
+ return 0;
+
+ List as = Arrays.asList(a.split("[.-]"));
+ List bs = Arrays.asList(b.split("[.-]"));
+
+ // both lists have the empty element as members at least
+ Iterator aIterator = as.iterator();
+ Iterator bIterator = bs.iterator();
+
+ while (aIterator.hasNext()) {
+ String aa = (String) aIterator.next();
+ if (!bIterator.hasNext()) {
+ // a is longer while equal so far
+ return 1; // a > b
+ }
+ String bb = (String) bIterator.next();
+ if (!aa.equals(bb)) {
+ // a and b differ
+ try {
+ Integer aInt = Integer.parseInt(aa);
+ Integer bInt = Integer.parseInt(bb);
+ return aInt.compareTo(bInt);
+ } catch (Exception e) {
+ return aa.compareTo(bb);
+ }
+ }
+ }
+ if (bIterator.hasNext()) {
+ // b is longer while equal so far
+ return -1; // a < b
+ }
+ return 0; // a == b
+ }
+
+ /**
+ * For testing purposes
+ */
+ public static void main(String argv[]) {
+ if ("compare".equals(argv[0])) {
+ RuntimeEnvironment r1 = new RuntimeEnvironment(argv[1]);
+ RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]);
+ logger.info("r1.getName(): " + r1.getName());
+ logger.info("r1.getVersion(): " + r1.getVersion());
+ logger.info("r2.getName(): " + r2.getName());
+ logger.info("r2.getVersion(): " + r2.getVersion());
+ logger.info("r1.atLeastAsCapableAs(r2): " + String.valueOf(r1.atLeastAsCapableAs(r2)));
+ } else {
+ logger.info("Don't know how to '" + argv[0] + "'");
+ }
+ }
+
+}
[2/6] incubator-taverna-common-activities git commit: TAVERNA-963
package taverna.externaltool.*
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalUseCaseInvocation.java
new file mode 100755
index 0000000..b57be14
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalUseCaseInvocation.java
@@ -0,0 +1,560 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.local;
+
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.Reader;
+import java.io.UnsupportedEncodingException;
+import java.io.Writer;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.charset.Charset;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Matcher;
+
+import org.apache.taverna.activities.externaltool.desc.ScriptInput;
+import org.apache.taverna.activities.externaltool.desc.ScriptOutput;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.InvocationException;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
+import org.apache.taverna.activities.externaltool.ssh.SshNode;
+import org.apache.taverna.activities.externaltool.ssh.SshNodeFactory;
+import org.apache.taverna.activities.externaltool.ssh.SshUrl;
+import org.apache.taverna.reference.AbstractExternalReference;
+import org.apache.taverna.reference.ErrorDocument;
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.reference.Identified;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.ReferenceSet;
+import org.apache.taverna.reference.ReferencedDataNature;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.reference.impl.external.file.FileReference;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+
+/**
+ * The job is executed locally, i.e. not via the grid.
+ * @author Hajo Krabbenhoeft
+ */
+public class LocalUseCaseInvocation extends UseCaseInvocation {
+
+ private static Logger logger = Logger.getLogger(LocalUseCaseInvocation.class);
+
+ private final File tempDir;
+
+ public static String LOCAL_USE_CASE_INVOCATION_TYPE = "789663B8-DA91-428A-9F7D-B3F3DA185FD4";
+
+ private Process running;
+
+ private final String shellPrefix;
+
+ private final String linkCommand;
+
+ private Reader stdInReader = null;
+
+ private static Map<String, Set<String>> runIdToTempDir = Collections.synchronizedMap(new HashMap<String, Set<String>> ());
+
+ private static String LOCAL_INVOCATION_FILE = "localInvocations";
+
+ public LocalUseCaseInvocation(UseCaseDescription desc, boolean retrieveData, String mainTempDirectory, String shellPrefix, String linkCommand) throws IOException {
+
+ usecase = desc;
+ setRetrieveData(retrieveData);
+ this.shellPrefix = shellPrefix;
+ this.linkCommand = linkCommand;
+
+ if (mainTempDirectory != null) {
+
+ File mainTempDir = new File(mainTempDirectory);
+
+ tempDir = File.createTempFile("usecase", "dir", mainTempDir);
+ } else {
+ tempDir = File.createTempFile("usecase", "dir");
+ }
+ tempDir.delete();
+ tempDir.mkdir();
+ logger.info("mainTempDirectory is " + mainTempDirectory);
+ logger.info("Using tempDir " + tempDir.getAbsolutePath());
+
+ }
+
+ void recDel(File c) {
+ File[] files = c.listFiles();
+ if (files != null) {
+ for (File cc : files)
+ recDel(cc);
+ }
+ c.delete();
+ }
+
+ private String setOneBinaryInput(ReferenceService referenceService,
+ T2Reference t2Reference, ScriptInput input, String targetSuffix)
+ throws InvocationException {
+
+ if (input.isFile() || input.isTempFile()) {
+ // Try to get it as a file
+ String target = tempDir.getAbsolutePath() + "/" + targetSuffix;
+ FileReference fileRef = getAsFileReference(referenceService,
+ t2Reference);
+ if (fileRef != null) {
+
+ if (!input.isForceCopy()) {
+ if (linkCommand != null) {
+ String source = fileRef.getFile().getAbsolutePath();
+ String actualLinkCommand = getActualOsCommand(
+ linkCommand, source, targetSuffix, target);
+ logger.info("Link command is " + actualLinkCommand);
+ String[] splitCmds = actualLinkCommand.split(" ");
+ ProcessBuilder builder = new ProcessBuilder(splitCmds);
+ builder.directory(tempDir);
+ try {
+ int code = builder.start().waitFor();
+ if (code == 0) {
+ return target;
+ } else {
+ logger.error("Link command gave errorcode: "
+ + code);
+ }
+
+ } catch (InterruptedException e) {
+ // go through
+ } catch (IOException e) {
+ // go through
+ }
+
+ }
+ }
+ }
+
+ InputStream is = null;
+ OutputStream os = null;
+ is = getAsStream(referenceService, t2Reference);
+
+ try {
+ os = new FileOutputStream(target);
+ } catch (FileNotFoundException e) {
+ throw new InvocationException(e);
+ }
+
+ try {
+ IOUtils.copyLarge(is, os);
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ try {
+ is.close();
+ os.close();
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ return target;
+ } else {
+ String value = (String) referenceService.renderIdentifier(
+ t2Reference, String.class, this.getContext());
+ return value;
+ }
+ }
+
+ @Override
+ public String setOneInput(ReferenceService referenceService,
+ T2Reference t2Reference, ScriptInput input)
+ throws InvocationException {
+
+ if (input.getCharsetName() == null) {
+ input.setCharsetName(Charset.defaultCharset().name());
+ }
+ String target = null;
+ String targetSuffix = null;
+ if (input.isFile()) {
+ targetSuffix = input.getTag();
+ } else if (input.isTempFile()) {
+ targetSuffix = "tempfile." + (nTempFiles++) + ".tmp";
+ }
+
+ if (input.isBinary()) {
+ return setOneBinaryInput(referenceService, t2Reference, input,
+ targetSuffix);
+ }
+
+ logger.info("Target is " + target);
+ if (input.isFile() || input.isTempFile()) {
+ target = tempDir.getAbsolutePath() + "/" + targetSuffix;
+ // Try to get it as a file
+ Reader r;
+ Writer w;
+ FileReference fileRef = getAsFileReference(referenceService,
+ t2Reference);
+ if (fileRef != null) {
+
+ if (!input.isForceCopy()) {
+ if (linkCommand != null) {
+ String source = fileRef.getFile().getAbsolutePath();
+ String actualLinkCommand = getActualOsCommand(
+ linkCommand, source, targetSuffix, target);
+ logger.info("Link command is " + actualLinkCommand);
+ String[] splitCmds = actualLinkCommand.split(" ");
+ ProcessBuilder builder = new ProcessBuilder(splitCmds);
+ builder.directory(tempDir);
+ try {
+ int code = builder.start().waitFor();
+ if (code == 0) {
+ return target;
+ } else {
+ logger.error("Link command gave errorcode: "
+ + code);
+ }
+
+ } catch (InterruptedException e) {
+ // go through
+ } catch (IOException e) {
+ // go through
+ }
+
+ }
+ }
+
+ if (fileRef.getDataNature().equals(ReferencedDataNature.TEXT)) {
+ r = new InputStreamReader(fileRef.openStream(this
+ .getContext()), Charset.forName(fileRef
+ .getCharset()));
+ } else {
+ try {
+ r = new FileReader(fileRef.getFile());
+ } catch (FileNotFoundException e) {
+ throw new InvocationException(e);
+ }
+ }
+ } else {
+ r = new InputStreamReader(getAsStream(referenceService,
+ t2Reference));
+ }
+ try {
+ w = new OutputStreamWriter(new FileOutputStream(target), input
+ .getCharsetName());
+ } catch (UnsupportedEncodingException e) {
+ throw new InvocationException(e);
+ } catch (FileNotFoundException e) {
+ throw new InvocationException(e);
+ }
+ try {
+ IOUtils.copyLarge(r, w);
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ try {
+ r.close();
+ w.close();
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ return target;
+ } else {
+ String value = (String) referenceService.renderIdentifier(
+ t2Reference, String.class, this.getContext());
+ return value;
+ }
+ }
+
+ private void forgetRun() {
+ Set<String> directories = runIdToTempDir.get(getRunId());
+ try {
+ directories.remove(tempDir.getCanonicalPath());
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+
+ private static void deleteDirectory(String location) {
+ try {
+ FileUtils.deleteDirectory(new File(location));
+ } catch (IOException e) {
+ logger.error("Problem deleting " + location, e);
+ }
+ }
+
+ public static void cleanup(String runId) {
+ Set<String> tempDirectories = runIdToTempDir.get(runId);
+ if (tempDirectories != null) {
+ for (String tempDir : tempDirectories) {
+ deleteDirectory(tempDir);
+ }
+ runIdToTempDir.remove(runId);
+ }
+ }
+
+ @Override
+ protected void submit_generate_job_inner() throws InvocationException {
+ tags.put("uniqueID", "" + getSubmissionID());
+ String command = usecase.getCommand();
+ for (String cur : tags.keySet()) {
+ command = command.replaceAll("\\Q%%" + cur + "%%\\E", Matcher.quoteReplacement(tags.get(cur)));
+ }
+
+ List<String> cmds = new ArrayList<String>();
+ if ((shellPrefix != null) && !shellPrefix.isEmpty()) {
+ String[] prefixCmds = shellPrefix.split(" ");
+ for (int i = 0; i < prefixCmds.length; i++) {
+ cmds.add(prefixCmds[i]);
+ }
+ cmds.add(command);
+ } else {
+ String[] splitCmds = command.split(" ");
+ for (int i = 0; i < splitCmds.length; i++) {
+ cmds.add(splitCmds[i]);
+ }
+ }
+
+ ProcessBuilder builder = new ProcessBuilder(cmds);
+ builder.directory(tempDir);
+
+ for (int i = 0; i < cmds.size(); i++) {
+ logger.info("cmds[" + i + "] = " + cmds.get(i));
+ }
+ logger.info("Command is " + command + " in directory " + tempDir);
+ try {
+ running = builder.start();
+ if (stdInReader != null) {
+ BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(running.getOutputStream()));
+ IOUtils.copyLarge(stdInReader, writer);
+ writer.close();
+ }
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ }
+
+ private void copy_stream(InputStream read, OutputStream write) throws IOException {
+ int a = read.available();
+ if (a > 0) {
+ byte[] buf = new byte[a];
+ read.read(buf);
+ write.write(buf);
+ }
+ }
+
+ @Override
+ public HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException {
+ ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
+ ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
+ while (true) {
+ try {
+ copy_stream(running.getInputStream(), stdout_buf);
+ copy_stream(running.getErrorStream(), stderr_buf);
+ } catch (IOException e1) {
+ throw new InvocationException(e1);
+ }
+ try {
+ int exitcode = running.exitValue();
+ if (!usecase.getValidReturnCodes().contains(exitcode)) {
+ try {
+ throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString("US-ASCII"));
+ } catch (UnsupportedEncodingException e) {
+ throw new InvocationException("Invalid exit code " + exitcode + ":" + stderr_buf.toString());
+ }
+ }
+ else
+ break;
+ } catch (IllegalThreadStateException e) {
+
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException e1) {
+ throw new InvocationException(e);
+ }
+
+ }
+ }
+
+ HashMap<String, Object> results = new HashMap<String, Object>();
+ results.put("STDOUT", stdout_buf.toByteArray());
+ results.put("STDERR", stderr_buf.toByteArray());
+
+ for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs().entrySet()) {
+ ScriptOutput scriptOutput = cur.getValue();
+ File result = new File(tempDir.getAbsoluteFile() + "/" + cur.getValue().getPath());
+ if (result.exists()) {
+ AbstractExternalReference ref;
+ if (isRetrieveData()) {
+ FileInputStream is;
+ try {
+ is = new FileInputStream(result);
+ } catch (FileNotFoundException e) {
+ throw new InvocationException(e);
+ }
+ if (scriptOutput.isBinary()) {
+ ref = inlineByteArrayReferenceBuilder.createReference(is, null);
+ } else {
+ ref = inlineStringReferenceBuilder.createReference(is, null);
+ }
+ try {
+ is.close();
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ }
+ else {
+ ref = new FileReference(result);
+ if (scriptOutput.isBinary()) {
+ ((FileReference) ref)
+ .setDataNature(ReferencedDataNature.BINARY);
+ } else {
+ ((FileReference) ref)
+ .setDataNature(ReferencedDataNature.TEXT);
+ ((FileReference) ref).setCharset("UTF-8");
+ }
+ }
+ results.put(cur.getKey(), ref);
+ } else {
+ ErrorDocument ed = referenceService.getErrorDocumentService().registerError("No result for " + cur.getKey(), 0, getContext());
+ results.put(cur.getKey(), ed);
+ }
+ }
+
+ if (isRetrieveData()) {
+ forgetRun();
+ try {
+ deleteDirectory(tempDir.getCanonicalPath());
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ }
+
+ return results;
+ }
+
+ private FileReference getAsFileReference(ReferenceService referenceService, T2Reference t2Reference) {
+ Identified identified = referenceService.resolveIdentifier(t2Reference, null, null);
+ if (identified instanceof ReferenceSet) {
+ for (ExternalReferenceSPI ref : ((ReferenceSet) identified).getExternalReferences()) {
+ if (ref instanceof FileReference) {
+ return (FileReference) ref;
+ }
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void setStdIn(ReferenceService referenceService,
+ T2Reference t2Reference) {
+ stdInReader = new BufferedReader(new InputStreamReader(getAsStream(referenceService, t2Reference)));
+ }
+
+ @Override
+ public void rememberRun(String runId) {
+ this.setRunId(runId);
+ Set<String> directories = runIdToTempDir.get(runId);
+ if (directories == null) {
+ directories = Collections.synchronizedSet(new HashSet<String> ());
+ runIdToTempDir.put(runId, directories);
+ }
+ try {
+ directories.add(tempDir.getCanonicalPath());
+ } catch (IOException e) {
+ logger.error("Unable to record temporary directory: " + tempDir, e);
+ }
+ }
+
+ public static void load(File directory) {
+ File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
+ if (!invocationsFile.exists()) {
+ return;
+ }
+ BufferedReader reader = null;
+ try {
+ reader = new BufferedReader(new FileReader(invocationsFile));
+ String line = reader.readLine();
+ while (line != null) {
+ String[] parts = line.split(" ");
+ if (parts.length != 2) {
+ break;
+ }
+ String runId = parts[0];
+ String tempDirString = parts[1];
+ Set<String> tempDirs = runIdToTempDir.get(runId);
+ if (tempDirs == null) {
+ tempDirs = new HashSet<String>();
+ runIdToTempDir.put(runId, tempDirs);
+ }
+ tempDirs.add(tempDirString);
+ line = reader.readLine();
+ }
+ } catch (FileNotFoundException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ } finally {
+ if (reader != null) {
+ try {
+ reader.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+ }
+ }
+
+ public static void persist(File directory) {
+ File invocationsFile = new File(directory, LOCAL_INVOCATION_FILE);
+ BufferedWriter writer = null;
+ try {
+ writer = new BufferedWriter(new FileWriter(invocationsFile));
+ for (String runId : runIdToTempDir.keySet()) {
+ for (String tempDir : runIdToTempDir.get(runId)) {
+ writer.write(runId);
+ writer.write(" ");
+ writer.write(tempDir);
+ writer.newLine();
+ }
+ }
+ } catch (IOException e) {
+ logger.error(e);
+ } finally {
+ if (writer != null) {
+ try {
+ writer.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/ExternalToolSshInvocationMechanism.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/ExternalToolSshInvocationMechanism.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/ExternalToolSshInvocationMechanism.java
index c373879..94cc466 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/ExternalToolSshInvocationMechanism.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/ExternalToolSshInvocationMechanism.java
@@ -24,13 +24,8 @@ import java.util.List;
import org.jdom.Element;
import org.jdom.Text;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshAutoLoginTrustEveryone.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshAutoLoginTrustEveryone.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshAutoLoginTrustEveryone.java
new file mode 100644
index 0000000..dfee8bb
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshAutoLoginTrustEveryone.java
@@ -0,0 +1,69 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.ssh;
+
+import org.apache.log4j.Logger;
+import org.apache.taverna.activities.externaltool.invocation.AskUserForPw;
+
+import com.jcraft.jsch.UIKeyboardInteractive;
+import com.jcraft.jsch.UserInfo;
+
+final class SshAutoLoginTrustEveryone implements UserInfo, UIKeyboardInteractive {
+
+ private static Logger logger = Logger.getLogger(SshAutoLoginTrustEveryone.class);
+
+ private final AskUserForPw askUserForPw;
+
+ public SshAutoLoginTrustEveryone(AskUserForPw askUserForPw) {
+ super();
+ this.askUserForPw = askUserForPw;
+ }
+
+ public void showMessage(String arg0) {
+ logger.info(arg0);
+ }
+
+ public boolean promptYesNo(String arg0) {
+ if (arg0.startsWith("The authenticity of host"))
+ return true;
+ return false;
+ }
+
+ public boolean promptPassword(String arg0) {
+ return true;
+ }
+
+ public boolean promptPassphrase(String arg0) {
+ return true;
+ }
+
+ public String getPassword() {
+ return askUserForPw.getPassword();
+ }
+
+ public String getPassphrase() {
+ return askUserForPw.getPassphrase();
+ }
+
+ public String[] promptKeyboardInteractive(String destination, String name, String instruction, String[] prompt, boolean[] echo) {
+ if (prompt.length >= 1 && prompt[0].toLowerCase().startsWith("password"))
+ return new String[] { askUserForPw.getPassword() };
+ return null;
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java
index 88f6ceb..b876ec8 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationCreator.java
@@ -25,20 +25,13 @@ import java.util.Map;
import org.apache.taverna.activities.externaltool.InvocationCreator;
import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna;
-
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
import org.apache.log4j.Logger;
import com.jcraft.jsch.JSchException;
import com.jcraft.jsch.SftpException;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrl;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation;
-
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.reference.ExternalReferenceSPI;
import org.apache.taverna.reference.Identified;
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationPersister.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationPersister.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationPersister.java
index 1884cbe..bad5c2e 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationPersister.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshInvocationPersister.java
@@ -21,6 +21,7 @@ package org.apache.taverna.activities.externaltool.ssh;
import java.io.File;
+import org.apache.taverna.activities.externaltool.invocation.InvocationException;
import org.apache.taverna.activities.externaltool.manager.InvocationPersister;
/*
* Licensed to the Apache Software Foundation (ASF) under one
@@ -45,9 +46,6 @@ import org.apache.taverna.security.credentialmanager.CredentialManager;
import org.apache.log4j.Logger;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.InvocationException;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshMechanismCreator.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshMechanismCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshMechanismCreator.java
index 2a15d38..097f8db 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshMechanismCreator.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshMechanismCreator.java
@@ -27,10 +27,6 @@ import org.apache.taverna.activities.externaltool.manager.MechanismCreator;
import org.apache.log4j.Logger;
import org.jdom.Element;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNodeFactory;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUseCaseInvocation;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNode.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNode.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNode.java
new file mode 100644
index 0000000..378696f
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNode.java
@@ -0,0 +1,157 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.ssh;
+
+import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
+
+public class SshNode {
+
+ public static String DEFAULT_HOST = "127.0.0.1";
+ public static int DEFAULT_PORT = 22;
+ public static String DEFAULT_DIRECTORY = "/tmp/";
+
+ private String host = DEFAULT_HOST;
+ private int port = DEFAULT_PORT;
+ private String directory = DEFAULT_DIRECTORY;
+
+ private SshUrl url;
+
+ private String linkCommand = null;
+ private String copyCommand = null;
+ private boolean retrieveData = false;
+
+ /**
+ *
+ */
+ SshNode() {
+ super();
+ linkCommand = InvocationMechanism.UNIX_LINK;
+ copyCommand = InvocationMechanism.UNIX_COPY;
+
+ }
+ /**
+ * @param directory the directory to set
+ */
+ public void setDirectory(String directory) {
+ if ((directory != null) && !directory.isEmpty()) {
+ if (!directory.endsWith("/")) {
+ directory = directory + "/";
+ }
+ this.directory = directory;
+ }
+ }
+
+ /**
+ * @return the directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param host the host to set
+ */
+ public void setHost(String host) {
+ this.host = host;
+ }
+
+ /**
+ * @return the host
+ */
+ public String getHost() {
+ return host;
+ }
+
+ /**
+ * @param port the port to set
+ */
+ public void setPort(int port) {
+ this.port = port;
+ }
+
+ /**
+ * @return the port
+ */
+ public int getPort() {
+ return port;
+ }
+
+ SshUrl getUrl() {
+ if (url == null) {
+ url = new SshUrl(this);
+ }
+ return url;
+ }
+
+ public int hashCode() {
+ return getUrl().hashCode();
+ }
+
+ public boolean equals(Object obj) {
+ if ((obj == null) || !(obj instanceof SshNode)) {
+ return false;
+ }
+ return (this.hashCode() == obj.hashCode());
+ }
+ /**
+ * @return the linkCommand
+ */
+ public String getLinkCommand() {
+ return linkCommand;
+ }
+ /**
+ * @param linkCommand the linkCommand to set
+ */
+ public void setLinkCommand(String linkCommand) {
+ if ((linkCommand != null) && linkCommand.isEmpty()) {
+ this.linkCommand = null;
+ } else {
+ this.linkCommand = linkCommand;
+ } }
+ /**
+ * @return the copyCommand
+ */
+ public String getCopyCommand() {
+ return copyCommand;
+ }
+ /**
+ * @param copyCommand the copyCommand to set
+ */
+ public void setCopyCommand(String copyCommand) {
+ if ((copyCommand != null) && copyCommand.isEmpty()) {
+ this.copyCommand = null;
+ } else {
+ this.copyCommand = copyCommand;
+ }
+ }
+
+ /**
+ * @return the retrieveData
+ */
+ public boolean isRetrieveData() {
+ return retrieveData;
+ }
+ /**
+ * @param retrieveData the retrieveData to set
+ */
+ public void setRetrieveData(boolean retrieveData) {
+ this.retrieveData = retrieveData;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNodeFactory.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNodeFactory.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNodeFactory.java
new file mode 100644
index 0000000..a697bd7
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshNodeFactory.java
@@ -0,0 +1,66 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.taverna.activities.externaltool.ssh;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+public class SshNodeFactory {
+
+ private Map<String, SshNode> nodeMap = Collections.synchronizedMap(new HashMap<String, SshNode> ());
+
+ private static SshNodeFactory INSTANCE = new SshNodeFactory();
+
+ private SshNode defaultNode;
+
+ private SshNodeFactory() {
+ defaultNode = getSshNode(SshNode.DEFAULT_HOST, SshNode.DEFAULT_PORT, SshNode.DEFAULT_DIRECTORY);
+ }
+
+ public SshNode getDefaultNode() {
+ return defaultNode;
+ }
+
+ public static SshNodeFactory getInstance() {
+ return INSTANCE;
+ }
+
+ public SshNode getSshNode(String host, int port, String directory) {
+ String url = makeUrl(host, port, directory);
+ if (nodeMap.containsKey(url)) {
+ return nodeMap.get(url);
+ }
+ else {
+ SshNode newNode = new SshNode();
+ newNode.setHost(host);
+ newNode.setPort(port);
+ newNode.setDirectory(directory);
+ nodeMap.put(url, newNode);
+ return newNode;
+ }
+ }
+
+ public boolean containsSshNode(String host, int port, String directory) {
+ return nodeMap.containsKey(makeUrl(host, port, directory));
+ }
+
+ public static String makeUrl(String host, int port, String directory) {
+ return ("ssh://" + host + ":" + port + directory);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshPool.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshPool.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshPool.java
new file mode 100755
index 0000000..e7f9787
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshPool.java
@@ -0,0 +1,157 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.taverna.activities.externaltool.ssh;
+
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.log4j.Logger;
+import org.apache.taverna.activities.externaltool.desc.RuntimeEnvironmentConstraint;
+import org.apache.taverna.activities.externaltool.invocation.AskUserForPw;
+
+import com.jcraft.jsch.ChannelExec;
+import com.jcraft.jsch.ChannelSftp;
+import com.jcraft.jsch.JSch;
+import com.jcraft.jsch.JSchException;
+import com.jcraft.jsch.Session;
+
+public class SshPool {
+
+ private static Logger logger = Logger.getLogger(SshPool.class);
+
+
+ private static JSch jsch = new JSch();
+
+ private static int CONNECT_TIMEOUT = 10000; // milliseconds
+
+ private static Map<SshNode, Session> sessionMap = Collections.synchronizedMap(new HashMap<SshNode, Session> ());
+ private static Map<Session, ChannelSftp> sftpGetMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
+ private static Map<Session, ChannelSftp> sftpPutMap = Collections.synchronizedMap(new HashMap<Session, ChannelSftp> ());
+
+ public static Session getSshSession(final SshUrl sshUrl, final AskUserForPw askUserForPw) throws JSchException {
+ return getSshSession(sshUrl.getSshNode(), askUserForPw);
+ }
+
+ public static synchronized Session getSshSession(final SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
+
+ Session s = sessionMap.get(sshNode);
+ if ((s != null) && s.isConnected()) {
+ logger.info("Reusing session");
+ return s;
+ }
+ if (s != null) {
+ logger.info("Session was not connected");
+ }
+ if (s == null) {
+ logger.info("No session found for " + sshNode.toString());
+ }
+
+ if (askUserForPw.getKeyfile().length() > 0) {
+ jsch.addIdentity(askUserForPw.getKeyfile());
+ }
+ logger.info("Using host is " + sshNode.getHost() + " and port " + sshNode.getPort());
+ Session sshSession = jsch.getSession(askUserForPw.getUsername(), sshNode.getHost(), sshNode.getPort());
+ sshSession.setUserInfo(new SshAutoLoginTrustEveryone(askUserForPw));
+ sshSession.connect(CONNECT_TIMEOUT);
+
+ askUserForPw.authenticationSucceeded();
+ sessionMap.put(sshNode, sshSession);
+ if (sshSession == null) {
+ logger.error("Returning a null session");
+ }
+ return sshSession;
+ }
+
+ public static ChannelSftp getSftpGetChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
+ return getSftpGetChannel(getSshSession(sshNode, askUserForPw));
+ }
+
+ private static synchronized ChannelSftp getSftpGetChannel(Session session) throws JSchException {
+ ChannelSftp result = sftpGetMap.get(session);
+ if (!session.isConnected()) {
+ logger.warn("Session is not connected");
+ }
+ if (result == null) {
+ logger.info("Creating new sftp channel");
+ result = (ChannelSftp) session.openChannel("sftp");
+ sftpGetMap.put(session, result);
+ }
+ else {
+ logger.info("Reusing sftp channel");
+ }
+ if (!result.isConnected()) {
+ logger.info("Connecting");
+ result.connect();
+ } else {
+ logger.info("Already connected");
+ }
+ return result;
+ }
+
+ public static ChannelSftp getSftpPutChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
+ return getSftpPutChannel(getSshSession(sshNode, askUserForPw));
+ }
+
+ private static synchronized ChannelSftp getSftpPutChannel(Session session) throws JSchException {
+ ChannelSftp result = null;
+ synchronized(sftpPutMap) {
+ result = sftpPutMap.get(session);
+ if (!session.isConnected()) {
+ logger.info("Session is not connected");
+ }
+ if (result == null) {
+ logger.info("Creating new sftp channel");
+ result = (ChannelSftp) session.openChannel("sftp");
+ sftpPutMap.put(session, result);
+ }
+ else {
+ logger.info("Reusing sftp channel");
+ }
+ }
+ if (!result.isConnected()) {
+ logger.info("Connecting");
+ result.connect(CONNECT_TIMEOUT);
+ } else {
+ logger.info("Already connected");
+ }
+ return result;
+ }
+
+ public static synchronized ChannelExec openExecChannel(SshNode sshNode, final AskUserForPw askUserForPw) throws JSchException {
+ return (ChannelExec) getSshSession(sshNode, askUserForPw).openChannel("exec");
+ }
+
+ private static synchronized ChannelExec openExecChannel(Session session) throws JSchException {
+ return (ChannelExec) session.openChannel("exec");
+ }
+
+}
+
+
+
+
+
+
+
+
+
+
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshReference.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshReference.java
new file mode 100644
index 0000000..091bd0c
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshReference.java
@@ -0,0 +1,222 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.taverna.activities.externaltool.ssh;
+
+import java.io.InputStream;
+
+import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna;
+import org.apache.taverna.reference.AbstractExternalReference;
+import org.apache.taverna.reference.DereferenceException;
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.reference.ReferenceContext;
+import org.apache.taverna.security.credentialmanager.CredentialManager;
+import org.apache.taverna.reference.ReferencedDataNature;
+
+import org.apache.log4j.Logger;
+
+import com.jcraft.jsch.ChannelSftp;
+import com.jcraft.jsch.JSchException;
+import com.jcraft.jsch.SftpException;
+
+/**
+ * @author alanrw
+ *
+ */
+public class SshReference extends AbstractExternalReference implements
+ ExternalReferenceSPI {
+
+ private static Logger logger = Logger.getLogger(SshReference.class);
+
+
+ private String host = "127.0.0.1";
+ private int port = 22;
+ private String directory = "/tmp/";
+ private String subDirectory;
+ private String fileName;
+
+ private CredentialManager credentialManager;
+
+ private int dataNatureInteger = ReferencedDataNature.UNKNOWN.ordinal();
+ private String charset = "UTF-8";
+
+ public SshReference() {
+ super();
+ }
+
+ public SshReference(SshUrl url) {
+ super();
+ this.host = url.getSshNode().getHost();
+ this.port = url.getSshNode().getPort();
+ this.directory = url.getSshNode().getDirectory();
+ this.subDirectory = url.getSubDirectory();
+ this.fileName = url.getFileName();
+ this.setDataNature(url.getDataNature());
+ this.setCharset(url.getCharset());
+ }
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#getApproximateSizeInBytes()
+ */
+ @Override
+ public Long getApproximateSizeInBytes() {
+ return 10000L;
+ }
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.reference.ExternalReferenceSPI#openStream(net.sf.taverna.t2.reference.ReferenceContext)
+ */
+ @Override
+ public InputStream openStream(ReferenceContext context)
+ throws DereferenceException {
+ try {
+ SshNode node = SshNodeFactory.getInstance().getSshNode(this.getHost(), this.getPort(), this.getDirectory());
+ String fullPath = getDirectory() + getSubDirectory() + "/" + getFileName();
+ ChannelSftp channel = SshPool.getSftpGetChannel(node, new RetrieveLoginFromTaverna(new SshUrl(node).toString(), credentialManager));
+ logger.info("Opening stream on " + fullPath);
+ return (channel.get(fullPath));
+ } catch (JSchException e) {
+ //TODO
+ logger.error(e);
+ } catch (SftpException e) {
+ // TODO Auto-generated catch block
+ logger.error(e);
+ }
+ return null;
+ }
+
+ /**
+ * @return the host
+ */
+ public String getHost() {
+ return host;
+ }
+
+ /**
+ * @param host the host to set
+ */
+ public void setHost(String host) {
+ this.host = host;
+ }
+
+ /**
+ * @return the port
+ */
+ public int getPort() {
+ return port;
+ }
+
+ /**
+ * @param port the port to set
+ */
+ public void setPort(int port) {
+ this.port = port;
+ }
+
+ /**
+ * @return the directory
+ */
+ public String getDirectory() {
+ return directory;
+ }
+
+ /**
+ * @param directory the directory to set
+ */
+ public void setDirectory(String directory) {
+ this.directory = directory;
+ }
+
+ /**
+ * @return the subDirectory
+ */
+ public String getSubDirectory() {
+ return subDirectory;
+ }
+
+ /**
+ * @param subDirectory the subDirectory to set
+ */
+ public void setSubDirectory(String subDirectory) {
+ this.subDirectory = subDirectory;
+ }
+
+ /**
+ * @return the fileName
+ */
+ public String getFileName() {
+ return fileName;
+ }
+
+ /**
+ * @param fileName the fileName to set
+ */
+ public void setFileName(String fileName) {
+ this.fileName = fileName;
+ }
+
+ public String getFullPath() {
+ return getDirectory() + "/" + getSubDirectory() + "/" + getFileName();
+ }
+
+ public ReferencedDataNature getDataNature() {
+ return ReferencedDataNature.values()[dataNatureInteger];
+ }
+
+ public void setDataNature(ReferencedDataNature dataNature) {
+ this.dataNatureInteger = dataNature.ordinal();
+ }
+
+ public String getCharset() {
+ return charset;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+ public void setCharset(String charset) {
+ this.charset = charset;
+ }
+
+ /**
+ * @return the dataNatureInteger
+ */
+ public int getDataNatureInteger() {
+ return dataNatureInteger;
+ }
+
+ /**
+ * @param dataNatureInteger the dataNatureInteger to set
+ */
+ public void setDataNatureInteger(int dataNatureInteger) {
+ this.dataNatureInteger = dataNatureInteger;
+ }
+
+ public SshReference clone() {
+ SshReference result = new SshReference();
+ result.setHost(this.getHost());
+ result.setPort(this.getPort());
+ result.setDirectory(this.getDirectory());
+ result.setSubDirectory(this.getSubDirectory());
+ result.setFileName(this.getFileName());
+ result.setDataNature(this.getDataNature());
+ result.setCharset(this.getCharset());
+ return result;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrl.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrl.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrl.java
new file mode 100644
index 0000000..4c39d66
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrl.java
@@ -0,0 +1,163 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.taverna.activities.externaltool.ssh;
+
+import org.apache.taverna.reference.ReferencedDataNature;
+
+public class SshUrl {
+
+ private SshNode sshNode;
+ private String subDirectory;
+ private String fileName;
+
+ private ReferencedDataNature dataNature = ReferencedDataNature.UNKNOWN;
+ private String charset = "UTF-8";
+
+
+ public SshUrl(SshNode sshNode) {
+ this.setSshNode(sshNode);
+ }
+
+
+ /**
+ * @return the host
+ */
+ public String getHost() {
+ return getSshNode().getHost();
+ }
+ /**
+ * @param host the host to set
+ */
+ public void setHost(String host) {
+ getSshNode().setHost(host);
+ }
+ /**
+ * @return the port
+ */
+ public int getPort() {
+ return getSshNode().getPort();
+ }
+ /**
+ * @param port the port to set
+ */
+ public void setPort(int port) {
+ getSshNode().setPort(port);
+ }
+ /**
+ * @return the directory
+ */
+ public String getDirectory() {
+ return getSshNode().getDirectory();
+ }
+ /**
+ * @param directory the directory to set
+ */
+ public void setDirectory(String directory) {
+ getSshNode().setDirectory(directory);
+ }
+ /**
+ * @return the subDirectory
+ */
+ public String getSubDirectory() {
+ return subDirectory;
+ }
+ /**
+ * @param subDirectory the subDirectory to set
+ */
+ public void setSubDirectory(String subDirectory) {
+ this.subDirectory = subDirectory;
+ }
+ /**
+ * @return the fileName
+ */
+ public String getFileName() {
+ return fileName;
+ }
+ /**
+ * @param fileName the fileName to set
+ */
+ public void setFileName(String fileName) {
+ this.fileName = fileName;
+ }
+
+ public String toString() {
+ String result = SshNodeFactory.makeUrl(getHost(), getPort(), getDirectory());
+ if (getSubDirectory() != null) {
+ result += getSubDirectory();
+ }
+ if (getFileName() != null) {
+ result += "/" + getFileName();
+ }
+ return result;
+ }
+
+ public int hashCode() {
+ return toString().hashCode();
+
+ }
+
+ public boolean equals(Object obj) {
+ if ((obj == null) || !(obj instanceof SshUrl)) {
+ return false;
+ }
+ return (this.hashCode() == obj.hashCode());
+ }
+
+ public SshUrl getBaseUrl() {
+ SshUrl result = new SshUrl(this.getSshNode());
+ return result;
+ }
+
+
+ /**
+ * @return the sshNode
+ */
+ public SshNode getSshNode() {
+ return sshNode;
+ }
+
+
+ /**
+ * @param sshNode the sshNode to set
+ */
+ public void setSshNode(SshNode sshNode) {
+ this.sshNode = sshNode;
+ }
+
+ public ReferencedDataNature getDataNature() {
+ return dataNature;
+ }
+
+
+ public void setDataNature(ReferencedDataNature dataNature) {
+ this.dataNature = dataNature;
+ }
+
+
+ public String getCharset() {
+ return charset;
+ }
+
+
+ public void setCharset(String charset) {
+ this.charset = charset;
+ }
+
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrlToSshReference.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrlToSshReference.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrlToSshReference.java
new file mode 100644
index 0000000..74b01e1
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUrlToSshReference.java
@@ -0,0 +1,54 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.ssh;
+
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.reference.ReferenceContext;
+import org.apache.taverna.reference.ValueToReferenceConversionException;
+import org.apache.taverna.reference.ValueToReferenceConverterSPI;
+import org.apache.taverna.security.credentialmanager.CredentialManager;
+
+public class SshUrlToSshReference implements ValueToReferenceConverterSPI {
+
+ private CredentialManager credentialManager;
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#canConvert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
+ */
+ @Override
+ public boolean canConvert(Object o, ReferenceContext context) {
+ return (o instanceof SshUrl);
+ }
+
+ /* (non-Javadoc)
+ * @see net.sf.taverna.t2.reference.ValueToReferenceConverterSPI#convert(java.lang.Object, net.sf.taverna.t2.reference.ReferenceContext)
+ */
+ @Override
+ public ExternalReferenceSPI convert(Object o, ReferenceContext context)
+ throws ValueToReferenceConversionException {
+ SshReference result = new SshReference((SshUrl) o);
+ result.setCredentialManager(credentialManager);
+ return result;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUseCaseInvocation.java
new file mode 100755
index 0000000..fcbc33f
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/ssh/SshUseCaseInvocation.java
@@ -0,0 +1,560 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.ssh;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedReader;
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Random;
+import java.util.Set;
+import java.util.Vector;
+import java.util.regex.Matcher;
+
+import org.apache.taverna.activities.externaltool.RetrieveLoginFromTaverna;
+import org.apache.taverna.activities.externaltool.desc.ScriptInput;
+import org.apache.taverna.activities.externaltool.desc.ScriptOutput;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.AskUserForPw;
+import org.apache.taverna.activities.externaltool.invocation.InvocationException;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
+import org.apache.taverna.reference.AbstractExternalReference;
+import org.apache.taverna.reference.ErrorDocument;
+import org.apache.taverna.reference.ErrorDocumentServiceException;
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.reference.Identified;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.ReferenceSet;
+import org.apache.taverna.reference.ReferencedDataNature;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.security.credentialmanager.CredentialManager;
+
+import org.apache.log4j.Logger;
+
+import com.jcraft.jsch.ChannelExec;
+import com.jcraft.jsch.ChannelSftp;
+import com.jcraft.jsch.JSchException;
+import com.jcraft.jsch.Session;
+import com.jcraft.jsch.SftpException;
+import com.jcraft.jsch.ChannelSftp.LsEntry;
+
+/**
+ * The job is executed by connecting to a worker pc using ssh, i.e. not via the
+ * grid.
+ *
+ * @author Hajo Krabbenhoeft
+ */
+public class SshUseCaseInvocation extends UseCaseInvocation {
+
+ private static Logger logger = Logger.getLogger(SshUseCaseInvocation.class);
+
+ private SshUrl location = null;
+
+ private InputStream stdInputStream = null;
+
+ public static final String SSH_USE_CASE_INVOCATION_TYPE = "D0A4CDEB-DD10-4A8E-A49C-8871003083D8";
+ private String tmpname;
+ private final SshNode workerNode;
+ private final AskUserForPw askUserForPw;
+
+ private ChannelExec running;
+
+ private List<String> precedingCommands = new ArrayList<String>();
+
+ private final ByteArrayOutputStream stdout_buf = new ByteArrayOutputStream();
+ private final ByteArrayOutputStream stderr_buf = new ByteArrayOutputStream();
+
+ private static Map<String, Object> nodeLock = Collections
+ .synchronizedMap(new HashMap<String, Object>());
+
+ private static Map<String, Set<SshUrl>> runIdToTempDir = Collections
+ .synchronizedMap(new HashMap<String, Set<SshUrl>>());
+
+ private static String SSH_INVOCATION_FILE = "sshInvocations";
+
+ private final CredentialManager credentialManager;
+
+ public static String test(final SshNode workerNode,
+ final AskUserForPw askUserForPw) {
+ try {
+ Session sshSession = SshPool
+ .getSshSession(workerNode, askUserForPw);
+
+ ChannelSftp sftpTest = (ChannelSftp) sshSession.openChannel("sftp");
+ sftpTest.connect();
+ sftpTest.cd(workerNode.getDirectory());
+ sftpTest.disconnect();
+ sshSession.disconnect();
+ } catch (JSchException e) {
+ return e.toString();
+ } catch (SftpException e) {
+ return e.toString();
+ }
+ return null;
+ }
+
+ public SshUseCaseInvocation(UseCaseDescription desc, SshNode workerNodeA,
+ AskUserForPw askUserForPwA, CredentialManager credentialManager)
+ throws JSchException, SftpException {
+ this.workerNode = workerNodeA;
+ this.credentialManager = credentialManager;
+
+ setRetrieveData(workerNodeA.isRetrieveData());
+ this.askUserForPw = askUserForPwA;
+ usecase = desc;
+
+ ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode, askUserForPw);
+ synchronized (getNodeLock(workerNode)) {
+
+ logger.info("Changing remote directory to "
+ + workerNode.getDirectory());
+ sftp.cd(workerNode.getDirectory());
+ Random rnd = new Random();
+ while (true) {
+ tmpname = "usecase" + rnd.nextLong();
+ try {
+ sftp.lstat(workerNode.getDirectory() + tmpname);
+ continue;
+ } catch (Exception e) {
+ // file seems to not exist :)
+ }
+ sftp.mkdir(workerNode.getDirectory() + tmpname);
+ sftp.cd(workerNode.getDirectory() + tmpname);
+ break;
+ }
+ }
+ }
+
+ private static void recursiveDelete(ChannelSftp sftp, String path)
+ throws SftpException, JSchException {
+ Vector<?> entries = sftp.ls(path);
+ for (Object object : entries) {
+ LsEntry entry = (LsEntry) object;
+ if (entry.getFilename().equals(".")
+ || entry.getFilename().equals("..")) {
+ continue;
+ }
+ if (entry.getAttrs().isDir()) {
+ recursiveDelete(sftp, path + entry.getFilename() + "/");
+ } else {
+ sftp.rm(path + entry.getFilename());
+ }
+ }
+ sftp.rmdir(path);
+ }
+
+ private static void deleteDirectory(SshUrl directory,
+ CredentialManager credentialManager) throws InvocationException {
+ URI uri;
+ try {
+ uri = new URI(directory.toString());
+
+ ChannelSftp sftp;
+ SshNode workerNode;
+ String fullPath = uri.getPath();
+ String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
+ String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
+ try {
+ workerNode = SshNodeFactory.getInstance().getSshNode(
+ uri.getHost(), uri.getPort(), path);
+
+ sftp = SshPool.getSftpPutChannel(workerNode,
+ new RetrieveLoginFromTaverna(workerNode.getUrl()
+ .toString(), credentialManager));
+ } catch (JSchException e) {
+ throw new InvocationException(e);
+ }
+ synchronized (getNodeLock(workerNode)) {
+ try {
+ sftp.cd(path);
+ recursiveDelete(sftp, path + "/" + tempDir + "/");
+ } catch (SftpException e) {
+ throw new InvocationException(e);
+ } catch (JSchException e) {
+ throw new InvocationException(e);
+ }
+ }
+ } catch (URISyntaxException e1) {
+ throw new InvocationException(e1);
+ }
+ }
+
+ public static void cleanup(String runId, CredentialManager credentialManager)
+ throws InvocationException {
+ Set<SshUrl> tempDirectories = runIdToTempDir.get(runId);
+ if (tempDirectories != null) {
+ for (SshUrl tempUrl : tempDirectories) {
+ deleteDirectory(tempUrl, credentialManager);
+ }
+ runIdToTempDir.remove(runId);
+ }
+ }
+
+ @Override
+ protected void submit_generate_job_inner() throws InvocationException {
+ tags.put("uniqueID", "" + getSubmissionID());
+ String command = usecase.getCommand();
+ for (String cur : tags.keySet()) {
+ command = command.replaceAll("\\Q%%" + cur + "%%\\E",
+ Matcher.quoteReplacement(tags.get(cur)));
+ }
+ String fullCommand = "cd " + workerNode.getDirectory() + tmpname;
+ for (String preceding : precedingCommands) {
+ fullCommand += " && " + preceding;
+ }
+ fullCommand += " && " + command;
+
+ logger.info("Full command is " + fullCommand);
+
+ try {
+ running = SshPool.openExecChannel(workerNode, askUserForPw);
+ running.setCommand(fullCommand);
+ running.setOutputStream(stdout_buf);
+ running.setErrStream(stderr_buf);
+ if (stdInputStream != null) {
+ running.setInputStream(stdInputStream);
+ }
+ running.connect();
+ } catch (JSchException e) {
+ throw new InvocationException(e);
+ }
+
+ }
+
+ @Override
+ public HashMap<String, Object> submit_wait_fetch_results(
+ ReferenceService referenceService) throws InvocationException {
+ while (!running.isClosed()) {
+ try {
+ Thread.sleep(1000);
+ } catch (InterruptedException e) {
+ throw new InvocationException("Invocation interrupted:"
+ + e.getMessage());
+ }
+ }
+
+ int exitcode = running.getExitStatus();
+ if (!usecase.getValidReturnCodes().contains(exitcode)) {
+ try {
+ throw new InvocationException("Invalid exit code " + exitcode
+ + ":" + stderr_buf.toString("US-ASCII"));
+ } catch (UnsupportedEncodingException e) {
+ throw new InvocationException("Invalid exit code " + exitcode
+ + ":" + stderr_buf.toString());
+ }
+ }
+
+ HashMap<String, Object> results = new HashMap<String, Object>();
+
+ results.put("STDOUT", stdout_buf.toByteArray());
+ results.put("STDERR", stderr_buf.toByteArray());
+ try {
+ stdout_buf.close();
+ stderr_buf.close();
+ } catch (IOException e2) {
+ throw new InvocationException(e2);
+ }
+
+ try {
+ ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
+ askUserForPw);
+ synchronized (getNodeLock(workerNode)) {
+ for (Map.Entry<String, ScriptOutput> cur : usecase.getOutputs()
+ .entrySet()) {
+ ScriptOutput scriptOutput = cur.getValue();
+ String fullPath = workerNode.getDirectory() + tmpname + "/"
+ + scriptOutput.getPath();
+ try {
+ if (sftp.stat(fullPath) != null) {
+ SshUrl url = new SshUrl(workerNode);
+ url.setSubDirectory(tmpname);
+ url.setFileName(scriptOutput.getPath());
+ if (scriptOutput.isBinary()) {
+ url.setDataNature(ReferencedDataNature.BINARY);
+ } else {
+ url.setDataNature(ReferencedDataNature.TEXT);
+ url.setCharset("UTF-8");
+ }
+ if (isRetrieveData()) {
+ SshReference urlRef = new SshReference(url);
+ InputStream is = urlRef.openStream(null);
+ AbstractExternalReference ref;
+ if (scriptOutput.isBinary()) {
+ ref = inlineByteArrayReferenceBuilder
+ .createReference(is, null);
+ } else {
+ ref = inlineStringReferenceBuilder
+ .createReference(is, null);
+ }
+ try {
+ is.close();
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ results.put(cur.getKey(), ref);
+ } else {
+ results.put(cur.getKey(), url);
+ }
+ } else {
+ ErrorDocument ed = referenceService
+ .getErrorDocumentService().registerError(
+ "No result for " + cur.getKey(), 0,
+ getContext());
+ results.put(cur.getKey(), ed);
+ }
+ } catch (SftpException e) {
+ ErrorDocument ed = referenceService
+ .getErrorDocumentService().registerError(
+ "No result for " + cur.getKey(), 0,
+ getContext());
+ results.put(cur.getKey(), ed);
+
+ }
+ }
+ }
+ } catch (JSchException e1) {
+ throw new InvocationException(e1);
+ } catch (ErrorDocumentServiceException e) {
+ throw new InvocationException(e);
+ }
+
+ if (running != null) {
+ running.disconnect();
+ }
+ if (stdInputStream != null) {
+ try {
+ stdInputStream.close();
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ }
+
+ if (isRetrieveData()) {
+ forgetRun();
+ deleteDirectory(location, credentialManager);
+
+ }
+ return results;
+ }
+
+ @Override
+ public String setOneInput(ReferenceService referenceService,
+ T2Reference t2Reference, ScriptInput input)
+ throws InvocationException {
+ String target = null;
+ String remoteName = null;
+ if (input.isFile()) {
+ remoteName = input.getTag();
+ } else if (input.isTempFile()) {
+ remoteName = "tempfile." + (nTempFiles++) + ".tmp";
+
+ }
+ if (input.isFile() || input.isTempFile()) {
+ SshReference sshRef = getAsSshReference(referenceService,
+ t2Reference, workerNode);
+ target = workerNode.getDirectory() + tmpname + "/" + remoteName;
+ logger.info("Target is " + target);
+ if (sshRef != null) {
+ if (!input.isForceCopy()) {
+ String linkCommand = workerNode.getLinkCommand();
+ if (linkCommand != null) {
+ String actualLinkCommand = getActualOsCommand(
+ linkCommand, sshRef.getFullPath(), remoteName,
+ target);
+ precedingCommands.add(actualLinkCommand);
+ return target;
+
+ }
+ }
+ String copyCommand = workerNode.getCopyCommand();
+ if (copyCommand != null) {
+ String actualCopyCommand = getActualOsCommand(copyCommand,
+ sshRef.getFullPath(), remoteName, target);
+ precedingCommands.add(actualCopyCommand);
+ return target;
+ }
+ }
+ try {
+ ChannelSftp sftp = SshPool.getSftpPutChannel(workerNode,
+ askUserForPw);
+ synchronized (getNodeLock(workerNode)) {
+ InputStream r = getAsStream(referenceService, t2Reference);
+ sftp.put(r, target);
+ r.close();
+ }
+ } catch (SftpException e) {
+ throw new InvocationException(e);
+ } catch (JSchException e) {
+ throw new InvocationException(e);
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ return target;
+ } else {
+ String value = (String) referenceService.renderIdentifier(
+ t2Reference, String.class, this.getContext());
+ return value;
+
+ }
+ }
+
+ public SshReference getAsSshReference(ReferenceService referenceService,
+ T2Reference t2Reference, SshNode workerNode) {
+ Identified identified = referenceService.resolveIdentifier(t2Reference,
+ null, null);
+ if (identified instanceof ReferenceSet) {
+ for (ExternalReferenceSPI ref : ((ReferenceSet) identified)
+ .getExternalReferences()) {
+ if (ref instanceof SshReference) {
+ SshReference sshRef = (SshReference) ref;
+ if (sshRef.getHost().equals(workerNode.getHost())) {
+ return sshRef;
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ private static Object getNodeLock(final SshNode node) {
+ return getNodeLock(node.getHost());
+ }
+
+ private static synchronized Object getNodeLock(String hostName) {
+ if (!nodeLock.containsKey(hostName)) {
+ nodeLock.put(hostName, new Object());
+ }
+ return nodeLock.get(hostName);
+ }
+
+ @Override
+ public void setStdIn(ReferenceService referenceService,
+ T2Reference t2Reference) {
+ stdInputStream = new BufferedInputStream(getAsStream(referenceService,
+ t2Reference));
+ }
+
+ @Override
+ public void rememberRun(String runId) {
+ this.setRunId(runId);
+ Set<SshUrl> directories = runIdToTempDir.get(runId);
+ if (directories == null) {
+ directories = Collections.synchronizedSet(new HashSet<SshUrl>());
+ runIdToTempDir.put(runId, directories);
+ }
+ location = new SshUrl(workerNode);
+ location.setSubDirectory(tmpname);
+ directories.add(location);
+ }
+
+ private void forgetRun() {
+ Set<SshUrl> directories = runIdToTempDir.get(getRunId());
+ directories.remove(location);
+ }
+
+ public static void load(File directory) {
+ File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
+ if (!invocationsFile.exists()) {
+ return;
+ }
+ BufferedReader reader = null;
+ try {
+ reader = new BufferedReader(new FileReader(invocationsFile));
+ String line = reader.readLine();
+ while (line != null) {
+ String[] parts = line.split(" ");
+ if (parts.length != 2) {
+ break;
+ }
+ String runId = parts[0];
+ String urlString = parts[1];
+ Set<SshUrl> urls = runIdToTempDir.get(runId);
+ if (urls == null) {
+ urls = new HashSet<SshUrl>();
+ runIdToTempDir.put(runId, urls);
+ }
+ URI uri = new URI(urlString);
+ String fullPath = uri.getPath();
+ String path = fullPath.substring(0, fullPath.lastIndexOf("/"));
+ String tempDir = fullPath.substring(fullPath.lastIndexOf("/"));
+ SshNode node = SshNodeFactory.getInstance().getSshNode(
+ uri.getHost(), uri.getPort(), path);
+ SshUrl newUrl = new SshUrl(node);
+ newUrl.setSubDirectory(tempDir);
+ urls.add(newUrl);
+ line = reader.readLine();
+ }
+ } catch (FileNotFoundException e) {
+ logger.error(e);
+ } catch (URISyntaxException e) {
+ logger.error(e);
+ } catch (IOException e) {
+ logger.error(e);
+ } finally {
+ if (reader != null) {
+ try {
+ reader.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+ }
+ }
+
+ public static void persist(File directory) {
+ File invocationsFile = new File(directory, SSH_INVOCATION_FILE);
+ BufferedWriter writer = null;
+ try {
+ writer = new BufferedWriter(new FileWriter(invocationsFile));
+ for (String runId : runIdToTempDir.keySet()) {
+ for (SshUrl url : runIdToTempDir.get(runId)) {
+ writer.write(runId);
+ writer.write(" ");
+ writer.write(url.toString());
+ writer.newLine();
+ }
+ }
+ } catch (IOException e) {
+ logger.error(e);
+ } finally {
+ if (writer != null) {
+ try {
+ writer.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI
index 6a18935..d63d896 100644
--- a/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI
+++ b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ExternalReferenceSPI
@@ -1,2 +1,2 @@
# Implementation classes of ExternalReferenceSPI go here, one per line
-de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference
+org.apache.taverna.activities.externaltool.invocation.ssh.SshReference
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI
index 53ca06c..50c5a16 100644
--- a/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI
+++ b/taverna-external-tool-activity/src/main/resources/META-INF/services/org.apache.taverna.reference.ValueToReferenceConverterSPI
@@ -1,3 +1,3 @@
# Implementation classes of ValueToReferenceConverterSPI go here, one per line
-de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrlToSshReference
+org.apache.taverna.activities.externaltool.invocation.ssh.SshUrlToSshReference
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/resources/META-INF/spring/external-tool-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/resources/META-INF/spring/external-tool-activity-context.xml b/taverna-external-tool-activity/src/main/resources/META-INF/spring/external-tool-activity-context.xml
index d933de9..297fc8d 100644
--- a/taverna-external-tool-activity/src/main/resources/META-INF/spring/external-tool-activity-context.xml
+++ b/taverna-external-tool-activity/src/main/resources/META-INF/spring/external-tool-activity-context.xml
@@ -21,7 +21,7 @@
xsi:schemaLocation="http://www.springframework.org/schema/beans
http://www.springframework.org/schema/beans/spring-beans.xsd">
- <bean id="SshReference" class="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference">
+ <bean id="SshReference" class="org.apache.taverna.activities.externaltool.invocation.ssh.SshReference">
<property name="credentialManager" ref="credentialManager" />
</bean>
@@ -37,7 +37,7 @@
<property name="invocationGroupManager" ref="invocationGroupManager" />
</bean>
- <bean id="SshUrlToSshReference" class="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshUrlToSshReference">
+ <bean id="SshUrlToSshReference" class="org.apache.taverna.activities.externaltool.invocation.ssh.SshUrlToSshReference">
<property name="credentialManager" ref="credentialManager" />
</bean>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml b/taverna-external-tool-activity/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
index 4f0a737..b67f6be 100644
--- a/taverna-external-tool-activity/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
+++ b/taverna-external-tool-activity/src/main/resources/de/uni_luebeck/inb/knowarc/usecases/invocation/ssh/SshReference.hbm.xml
@@ -23,7 +23,7 @@
<!-- Hibernate mapping for ssh reference bean -->
<hibernate-mapping>
<joined-subclass
- name="de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshReference"
+ name="org.apache.taverna.activities.externaltool.invocation.ssh.SshReference"
extends="org.apache.taverna.reference.AbstractExternalReference">
<!-- Link to primary key from abstract superclass -->
<key column="bean_id" />
[3/6] incubator-taverna-common-activities git commit: TAVERNA-963
package taverna.externaltool.*
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java
new file mode 100644
index 0000000..8324d61
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironmentConstraint.java
@@ -0,0 +1,160 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+import org.apache.log4j.Logger;
+
+
+/**
+ * When use cases present a runtime environment, then they don't want to express
+ * that these would provide such, but that these request such, i.e. they constrain
+ * lists of potentially eligible queues.
+ * @author Steffen Moeller
+ * @since 2008
+ */
+public class RuntimeEnvironmentConstraint extends RuntimeEnvironment {
+
+ private static Logger logger = Logger.getLogger(RuntimeEnvironmentConstraint.class);
+
+ private static String[] ACCEPTED_RELATIONS = new String[] {"=", ">=", "<=", ">", "<"};
+ /**
+ * If there is no relation specified, presume >=
+ */
+ private static String DEFAULT_RELATION = ">=";
+
+ public static String[] getAcceptedRelations() {
+ return ACCEPTED_RELATIONS;
+ }
+
+ public static String getDefaultRelation() {
+ return DEFAULT_RELATION;
+ }
+
+ /**
+ * Identifies the relation between runtime environments to be tested
+ */
+ protected String relation;
+
+ /**
+ * Accessor function for relation
+ */
+ public String getRelation() {
+ return this.relation;
+ }
+
+ /**
+ * Tests of a relation is supported
+ * @param relation
+ * @return true iff in <, > , <=, >=, =
+ */
+ public static boolean acceptedRelation(String relation) {
+ if ((null == relation) || relation.equals("")) {
+ return false;
+ }
+ return relation.equals("=")||relation.equals(">=")||relation.equals("<=")||relation.equals(">")||relation.equals("<");
+ }
+
+ /**
+ * Constructor
+ * @param id - expects the name of the runtime environment together with the version to which the
+ * @param relation - relates to (">","<","=",">=","<=")
+ */
+ public RuntimeEnvironmentConstraint(String id, String relation) {
+ super(id);
+ if (null == relation || relation.equals("")) {
+ relation=RuntimeEnvironmentConstraint.getDefaultRelation();
+ }
+ if (relation.equals("==")) {
+ relation="=";
+ }
+ else if (relation.equals("=<")) {
+ relation="<=";
+ }
+ else if (!RuntimeEnvironmentConstraint.acceptedRelation(relation)) {
+ logger.warn("Unknown relation '"+relation+"', presuming '"+RuntimeEnvironmentConstraint.getDefaultRelation()+"'");
+ relation=RuntimeEnvironmentConstraint.getDefaultRelation();
+ }
+ this.relation=relation;
+ }
+
+ /**
+ * Perfoms test if the RuntimeEnvironment (RE) passed as argument fulfills the requirements set by the constraint.
+ * @param re - RE to test
+ * @return true iff the RE fulfills this REconstraint.
+ */
+ public boolean isFulfilledBy(RuntimeEnvironment re) {
+ logger.info(re.getID()+" " + this.getRelation() + " "+this.getID() + " ?");
+ if (this.getRelation().equals("=")) {
+ logger.info("=");
+ return re.getID().equals(this.getID());
+ }
+ if (!re.getName().equals(this.getName())) {
+ logger.warn("Name match failed");
+ return false;
+ }
+ int c = RuntimeEnvironment.compareVersions(re.getVersion(),this.getVersion());
+ logger.info("c="+c);
+ if (this.getRelation().equals(">")) return c>0;
+ if (this.getRelation().equals(">=")) return c>=0;
+ if (this.getRelation().equals("<=")) return c<=0;
+ if (this.getRelation().equals("<")) return c<0;
+ throw new RuntimeException("Unknown/untreated releation '"+this.getRelation()+"'");
+ }
+
+ /**
+ * Iterates over all the RuntimeEnvironments passed as argument.
+ * @param REs - list of RuntimeEnvironments, mostly those offered at a particular queue
+ * @return true iff any RE among the REs passed as argument are fulfilling the constraint
+ */
+ public boolean isFulfilledByAtLeastOneIn(Collection<RuntimeEnvironment> REs) {
+ boolean fulfilled = false;
+ Iterator<RuntimeEnvironment> i = REs.iterator();
+ while(i.hasNext() && !fulfilled) {
+ RuntimeEnvironment r = i.next();
+ fulfilled = this.isFulfilledBy(r);
+ }
+ return fulfilled;
+ }
+ /**
+ * For testing purposes
+ */
+ public static void main(String argv[]) {
+ try {
+ if (argv[0].equals("--help") || argv.length != 3) {
+ logger.error("Expecting arguments (<|>|=|<=|>=) runtime1-version runtime2-version");
+ }
+ else {
+ RuntimeEnvironmentConstraint r1 = new RuntimeEnvironmentConstraint(argv[1], argv[0]);
+ RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]);
+ logger.info("r1.getName(): "+r1.getName());
+ logger.info("r1.getVersion(): "+r1.getVersion());
+ logger.info("r1.getRelation(): "+r1.getRelation());
+ logger.info("r2.getName(): "+r2.getName());
+ logger.info("r2.getVersion(): "+r2.getVersion());
+ logger.info("r1.isFulfilledBy(r2): "+String.valueOf(r1.isFulfilledBy(r2)));
+ }
+ }
+ catch (Exception e) {
+ logger.error(e);
+ }
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java
new file mode 100644
index 0000000..3d68272
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInput.java
@@ -0,0 +1,134 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import java.nio.charset.Charset;
+
+import org.apache.taverna.activities.externaltool.ExternalToolActivity;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Integrates inputs to the grid that come from the use case descriptions
+ * with those that are fed through the workflow.
+ *
+ * this class controls name and data storage of one input,
+ * no matter where the data comes from
+ */
+@ConfigurationBean(uri = ExternalToolActivity.URI + "#AbstractScriptInput")
+public abstract class ScriptInput {
+ /**
+ * This input can be referenced under the name 'tag'.
+ */
+ private String tag = null;
+ /**
+ * In most cases, the data will be stored under a specific
+ * filename.
+ */
+ private boolean file = false;
+ /**
+ * Set, if the name of the file to be executed is not
+ * explicitly set but prepared by some automatism and referenced
+ * via the tagging principle.
+ */
+ private boolean tempFile = false;
+ /**
+ * True if (!) the data is binary. (Text otherwise)
+ */
+ private boolean binary = false;
+
+ private String charsetName = Charset.defaultCharset().name();
+ private boolean forceCopy = false;
+
+ /**
+ * @return the tag
+ */
+ public final String getTag() {
+ return tag;
+ }
+ /**
+ * @param tag the tag to set
+ */
+ @ConfigurationProperty(name = "tag", label = "Tag")
+ public final void setTag(String tag) {
+ this.tag = tag;
+ }
+ /**
+ * @return the file
+ */
+ public final boolean isFile() {
+ return file;
+ }
+ /**
+ * @param file the file to set
+ */
+ @ConfigurationProperty(name = "file", label = "File")
+ public final void setFile(boolean file) {
+ this.file = file;
+ }
+ /**
+ * @return the tempFile
+ */
+ public final boolean isTempFile() {
+ return tempFile;
+ }
+ /**
+ * @param tempFile the tempFile to set
+ */
+ @ConfigurationProperty(name = "tempFile", label = "Temporary File")
+ public final void setTempFile(boolean tempFile) {
+ this.tempFile = tempFile;
+ }
+ /**
+ * @return the binary
+ */
+ public final boolean isBinary() {
+ return binary;
+ }
+ /**
+ * @param binary the binary to set
+ */
+ @ConfigurationProperty(name = "binary", label = "Binary")
+ public final void setBinary(boolean binary) {
+ this.binary = binary;
+ }
+
+ public String getCharsetName() {
+ return this.charsetName;
+ }
+ /**
+ * @param charsetName the charsetName to set
+ */
+ @ConfigurationProperty(name = "charsetName", label = "Chararter Set")
+ public void setCharsetName(String charsetName) {
+ this.charsetName = charsetName;
+ }
+
+ @ConfigurationProperty(name = "forceCopy", label = "Force Copy")
+ public final void setForceCopy(boolean forceCopy) {
+ this.forceCopy = forceCopy;
+
+ }
+ /**
+ * @return the forceCopy
+ */
+ public boolean isForceCopy() {
+ return forceCopy;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java
new file mode 100644
index 0000000..78b6c3b
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputStatic.java
@@ -0,0 +1,73 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import org.apache.taverna.activities.externaltool.ExternalToolActivity;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * This subclass of script input is used to manage static content
+ * which is embedded into the use case description.
+ */
+@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInputStatic")
+public class ScriptInputStatic extends ScriptInput {
+
+ public ScriptInputStatic() {
+ }
+
+ private String url = null; //if this is set, load content from remote URL
+ private String content = null;
+
+ @Override
+ public String toString() {
+ return "InputStatic[tag: " +
+ getTag() + (isFile() ? ", file" : "") + (isTempFile() ? ", tempfile" : "") + (isBinary() ? ", binary" : "") + ", content: " + content + "]";
+ }
+
+ /**
+ * @return the url
+ */
+ public final String getUrl() {
+ return url;
+ }
+
+ /**
+ * @param url the url to set
+ */
+ @ConfigurationProperty(name = "url", label = "URL", required=false)
+ public final void setUrl(String url) {
+ this.url = url;
+ }
+
+ /**
+ * @return the content
+ */
+ public final String getContent() {
+ return content;
+ }
+
+ /**
+ * @param content the content to set
+ */
+ @ConfigurationProperty(name = "content", label = "Content", required=false)
+ public final void setContent(String content) {
+ this.content = content;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java
new file mode 100644
index 0000000..a74bb5d
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptInputUser.java
@@ -0,0 +1,99 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+import java.util.ArrayList;
+
+import org.apache.taverna.activities.externaltool.ExternalToolActivity;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Internal description of output
+ */
+@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInput")
+public class ScriptInputUser extends ScriptInput {
+
+ /**
+ * This input may be fed from multiple ouputs.
+ */
+ private boolean list = false;
+ /**
+ * True if the data from a list input in taverna is concatenated into one single input file.
+ */
+ private boolean concatenate = false;
+
+ private ArrayList<String> mime = new ArrayList<String>();
+
+ @Override
+ public String toString() {
+ return "Input[tag: " + getTag() + (isFile() ? ", file" : "")
+ + (isTempFile() ? ", tempfile" : "")
+ + (isBinary() ? ", binary" : "") + (list ? ", list" : "")
+ + (concatenate ? ", concatenate" : "")
+ + " mime: " + mime.toString() + "]";
+ }
+
+ /**
+ * @return the list
+ */
+ public final boolean isList() {
+ return list;
+ }
+
+ /**
+ * @param list the list to set
+ */
+ @ConfigurationProperty(name = "list", label = "List")
+ public final void setList(boolean list) {
+ this.list = list;
+ }
+
+ /**
+ * @return the concatenate
+ */
+ public final boolean isConcatenate() {
+ return concatenate;
+ }
+
+ /**
+ * @param concatenate the concatenate to set
+ */
+ @ConfigurationProperty(name = "concatenate", label = "Concatenate")
+ public final void setConcatenate(boolean concatenate) {
+ this.concatenate = concatenate;
+ }
+
+ /**
+ * @return the mime
+ */
+ public final ArrayList<String> getMime() {
+ if (mime == null) {
+ mime = new ArrayList<String>();
+ }
+ return mime;
+ }
+
+ /**
+ * @param mime the mime to set
+ */
+ @ConfigurationProperty(name = "mime", label = "Mime Types", required=false)
+ public final void setMime(ArrayList<String> mime) {
+ this.mime = mime;
+ }
+};
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java
new file mode 100644
index 0000000..77bbc83
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/ScriptOutput.java
@@ -0,0 +1,88 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+import java.util.ArrayList;
+
+import org.apache.taverna.activities.externaltool.ExternalToolActivity;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+
+/**
+ * Internal description of input
+ */
+@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptOutput")
+public class ScriptOutput {
+ private String path;
+ private boolean binary;
+ private ArrayList<String> mime = new ArrayList<String>();
+
+ @Override
+ public String toString() {
+ return "Output[path: " + path + (binary ? ", binary" : "")
+ + " mime: " + mime.toString() + "]";
+ }
+
+ /**
+ * @return the path
+ */
+ public final String getPath() {
+ return path;
+ }
+
+ /**
+ * @param path the path to set
+ */
+ @ConfigurationProperty(name = "path", label = "Path")
+ public final void setPath(String path) {
+ this.path = path;
+ }
+
+ /**
+ * @return the binary
+ */
+ public final boolean isBinary() {
+ return binary;
+ }
+
+ /**
+ * @param binary the binary to set
+ */
+ @ConfigurationProperty(name = "binary", label = "Binary")
+ public final void setBinary(boolean binary) {
+ this.binary = binary;
+ }
+
+ /**
+ * @return the mime
+ */
+ public final ArrayList<String> getMime() {
+ if (mime == null) {
+ mime = new ArrayList<String>();
+ }
+ return mime;
+ }
+
+ /**
+ * @param mime the mime to set
+ */
+ @ConfigurationProperty(name = "mime", label = "Mime Types", required=false)
+ public final void setMime(ArrayList<String> mime) {
+ this.mime = mime;
+ }
+};
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java
new file mode 100644
index 0000000..934330f
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseDescription.java
@@ -0,0 +1,897 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import javax.swing.ImageIcon;
+
+import org.apache.taverna.activities.externaltool.ExternalToolActivity;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
+import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy;
+import org.apache.taverna.workflowmodel.serialization.DeserializationException;
+import org.apache.taverna.workflowmodel.utils.Tools;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+
+import org.apache.commons.lang.StringUtils;
+
+/**
+ * Class representation of XML-description of UseCases
+ */
+@ConfigurationBean(uri = ExternalToolActivity.URI + "#ToolDescription")
+public class UseCaseDescription {
+
+ private static Logger logger = Logger.getLogger(UseCaseDescription.class);
+
+ /**
+ * Identifier for the retrieval of this UseCase in the sharedRepository
+ * database, respectively its XML export.
+ */
+ private String usecaseid = "";
+ /**
+ * Workflow Elements now can get a group identifier. There may be subgroups
+ * divided by :
+ */
+ private String group = "";
+ /**
+ * Textual description of the use case itself. This description is very
+ * short to fit on the single line that is prepared for such descriptions in
+ * the Taverna workflow element list.
+ */
+ private String description = "";
+ /**
+ * What is actually executed on the shell.
+ */
+ private String command = "";
+
+ /**
+ * Accessor function of command
+ *
+ * @return shell-executable series of commands
+ */
+ public String getCommand() {
+ if (null == command) {
+ // FIXME: Is this possible?
+ return "";
+ } else {
+ return command;
+ }
+ }
+
+ /**
+ * Routine that may be executed as a first check if the program is indeed
+ * installed.
+ */
+ private String test_local = null;
+
+ /**
+ * URL of an icon that would help users to recognise the use case
+ */
+ private String icon_url = null;
+
+ private int preparingTimeoutInSeconds = 20 * 60; // 20 minutes
+ private int executionTimeoutInSeconds = 30 * 60; // 30 minutes
+
+ private List<String> tags = new ArrayList<String>();
+ private List<RuntimeEnvironmentConstraint> REs = new ArrayList<RuntimeEnvironmentConstraint>();
+ private ArrayList<String> queue_preferred = new ArrayList<String>();
+ private ArrayList<String> queue_deny = new ArrayList<String>();
+
+ private List<ScriptInputStatic> static_inputs = new ArrayList<ScriptInputStatic>();
+ private Map<String, ScriptInput> inputs = new HashMap<String, ScriptInput>();
+ private Map<String, ScriptOutput> outputs = new HashMap<String, ScriptOutput>();
+
+ private boolean includeStdIn = false;
+ private boolean includeStdOut = true;
+ private boolean includeStdErr = true;
+
+ private List<Integer> validReturnCodes = new ArrayList<Integer>();
+
+ /**
+ * Default constructor to make xstream happy
+ */
+ public UseCaseDescription() {
+
+ }
+
+ /**
+ * Constructor, for special purpose usecases.
+ *
+ * @param usecaseid
+ */
+ public UseCaseDescription(String usecaseid) {
+ this.setUsecaseid(usecaseid);
+ }
+
+ /**
+ * Constructor, expects an input stream containing the xml. for example, use
+ * getClass().getClassLoader().getResourceAsStream("..") to load a usecase
+ * from your program jar
+ */
+ public UseCaseDescription(InputStream programAsStream) throws DeserializationException {
+ SAXBuilder builder = new SAXBuilder();
+ Document doc;
+ try {
+ doc = builder.build(programAsStream);
+ programAsStream.close();
+ } catch (JDOMException e) {
+ throw new DeserializationException("Error deserializing usecase", e);
+ } catch (IOException e) {
+ throw new DeserializationException("Error deserializing usecase", e);
+ }
+ readFromXmlElement(doc.getRootElement());
+ }
+
+ /**
+ * Constructor, expects an XML-root to dissect.
+ */
+ public UseCaseDescription(Element programNode) throws DeserializationException {
+ readFromXmlElement(programNode);
+ }
+
+/**
+ * Produce an XML description of the UseCaseDescription
+ */
+ public Element writeToXMLElement() {
+ Element programNode = new Element("program");
+ programNode.setAttribute("name", getUsecaseid());
+ programNode.setAttribute("description", getDescription());
+ // Always use element version of command
+// programNode.setAttribute("command", getCommand());
+ Element commandNode = new Element("command");
+ commandNode.addContent(getCommand());
+ programNode.addContent(commandNode);
+ programNode.setAttribute("timeout", Integer.toString(getExecutionTimeoutInSeconds()));
+ programNode.setAttribute("preparing_timeout", Integer.toString(getPreparingTimeoutInSeconds()));
+ programNode.setAttribute("includeStdIn", Boolean.toString(isIncludeStdIn()));
+ programNode.setAttribute("includeStdOut", Boolean.toString(isIncludeStdOut()));
+ programNode.setAttribute("includeStdErr", Boolean.toString(isIncludeStdErr()));
+ for (ScriptInputStatic si : getStatic_inputs()) {
+ Element staticNode = new Element("static");
+ if (si.isBinary()) {
+ staticNode.setAttribute("binary", "true");
+ }
+ if (si.isForceCopy()) {
+ staticNode.setAttribute("forceCopy", "true");
+ }
+ if (si.isFile()) {
+ Element fileNode = new Element("file");
+ fileNode.setAttribute("path", si.getTag());
+ staticNode.addContent(fileNode);
+ } else if (si.isTempFile()) {
+ Element tempfileNode = new Element("tempfile");
+ tempfileNode.setAttribute("tag", si.getTag());
+ staticNode.addContent(tempfileNode);
+ } else {
+ Element replaceNode = new Element("replace");
+ replaceNode.setAttribute("tag", si.getTag());
+ staticNode.addContent(replaceNode);
+ }
+ if (si.getUrl() != null) {
+ Element contentNode = new Element("content");
+ contentNode.setAttribute("url", si.getUrl());
+ staticNode.addContent(contentNode);
+ } else {
+ Element contentNode = new Element("content");
+ contentNode.addContent((String) si.getContent());
+ staticNode.addContent(contentNode);
+ }
+ programNode.addContent(staticNode);
+ }
+ for (Entry<String, ScriptInput> entry : getInputs().entrySet()) {
+ String name = entry.getKey();
+ ScriptInputUser si = (ScriptInputUser) entry.getValue();
+ Element inputNode = new Element("input");
+ inputNode.setAttribute("name", name);
+ if (si.isBinary()) {
+ inputNode.setAttribute("binary", "true");
+ }
+ if (si.isForceCopy()) {
+ inputNode.setAttribute("forceCopy", "true");
+ }
+ if (si.isConcatenate()) {
+ inputNode.setAttribute("concatenate", "true");
+ }
+ if (si.isList()) {
+ inputNode.setAttribute("list", "true");
+ }
+ if (si.isFile()) {
+ Element fileNode = new Element("file");
+ fileNode.setAttribute("path", si.getTag());
+ inputNode.addContent(fileNode);
+ } else if (si.isTempFile()) {
+ Element tempfileNode = new Element("tempfile");
+ tempfileNode.setAttribute("tag", si.getTag());
+ inputNode.addContent(tempfileNode);
+ } else {
+ Element replaceNode = new Element("replace");
+ replaceNode.setAttribute("tag", si.getTag());
+ inputNode.addContent(replaceNode);
+ }
+ for (String mime : si.getMime()) {
+ Element mimeNode = new Element("mime");
+ mimeNode.setAttribute("type", mime);
+ inputNode.addContent(mimeNode);
+ }
+ programNode.addContent(inputNode);
+ }
+ for (Entry<String, ScriptOutput> entry : getOutputs().entrySet()) {
+ String name = entry.getKey();
+ ScriptOutput so = entry.getValue();
+ Element outputNode = new Element("output");
+ outputNode.setAttribute("name", name);
+ if (so.isBinary()) {
+ outputNode.setAttribute("binary", "true");
+ }
+ Element fromfileNode = new Element("fromfile");
+ fromfileNode.setAttribute("path", so.getPath());
+ outputNode.addContent(fromfileNode);
+ for (String mime : so.getMime()) {
+ Element mimeNode = new Element("mime");
+ mimeNode.setAttribute("type", mime);
+ outputNode.addContent(mimeNode);
+ }
+ programNode.addContent(outputNode);
+ }
+ for (RuntimeEnvironmentConstraint rec : getREs()) {
+ Element rteNode = new Element("rte");
+ rteNode.setAttribute("name", rec.getID());
+ rteNode.setAttribute("relation", rec.getRelation());
+ programNode.addContent(rteNode);
+ }
+ if ((group != null) && !group.isEmpty()) {
+ Element groupNode = new Element("group");
+ groupNode.setAttribute("name", group);
+ programNode.addContent(groupNode);
+ }
+ if ((test_local != null) && !test_local.isEmpty()) {
+ Element testNode = new Element("test");
+ testNode.setAttribute("local", test_local);
+ programNode.addContent(testNode);
+ }
+ if ((icon_url != null) && !icon_url.isEmpty()) {
+ Element iconNode = new Element("icon");
+ iconNode.setAttribute("url", icon_url);
+ programNode.addContent(iconNode);
+ }
+ if (!getQueue_preferred().isEmpty() || !getQueue_deny().isEmpty()) {
+ Element queueNode = new Element("queue");
+ for (String url : getQueue_preferred()) {
+ Element preferredNode = new Element("prefer");
+ preferredNode.setAttribute("url", url);
+ queueNode.addContent(preferredNode);
+ }
+ for (String url : getQueue_deny()) {
+ Element denyNode = new Element("deny");
+ denyNode.setAttribute("url", url);
+ queueNode.addContent(denyNode);
+ }
+ programNode.addContent(queueNode);
+ }
+ Element validReturnCodesNode = new Element("validReturnCodes");
+ validReturnCodesNode.setAttribute("codes", getReturnCodesAsText());
+ programNode.addContent(validReturnCodesNode);
+
+ return programNode;
+ }
+ /**
+ * Specifies the UseCaseDescription from the root of an XML description
+ * which is accessible online.
+ *
+ * @param programNode
+ * @throws DeserializationException
+ */
+ private void readFromXmlElement(Element programNode) throws DeserializationException {
+ if (programNode.getName().compareToIgnoreCase("program") != 0)
+ throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'");
+
+ setUsecaseid(programNode.getAttributeValue("name"));
+ setDescription(programNode.getAttributeValue("description"));
+ setCommand(programNode.getAttributeValue("command"));
+ String timeoutStr = programNode.getAttributeValue("timeout");
+ if (timeoutStr != null)
+ setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr));
+ timeoutStr = programNode.getAttributeValue("preparing_timeout");
+ if (timeoutStr != null)
+ setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr));
+
+ String includeStdInStr = programNode.getAttributeValue("includeStdIn");
+ if (includeStdInStr != null && !includeStdInStr.isEmpty()) {
+ setIncludeStdIn(includeStdInStr.equals("true"));
+ }
+
+ String includeStdOutStr = programNode.getAttributeValue("includeStdOut");
+ if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) {
+ setIncludeStdOut(includeStdOutStr.equals("true"));
+ }
+
+ String includeStdErrStr = programNode.getAttributeValue("includeStdErr");
+ if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) {
+ setIncludeStdErr(includeStdErrStr.equals("true"));
+ }
+
+ for (Object cur_ob : programNode.getChildren()) {
+ Element cur = (Element) cur_ob;
+
+ String name = cur.getAttributeValue("name");
+
+ String type = cur.getName();
+ boolean binary = false;
+ if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) {
+ binary = true;
+ }
+ boolean list = false;
+ if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) {
+ list = true;
+ }
+ boolean concatenate = false;
+ if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) {
+ concatenate = true;
+ }
+ boolean forceCopy = false;
+ if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) {
+ forceCopy = true;
+ }
+
+ Element inner = null;
+ String innerType = null, tag = null, path = null;
+ if (cur.getChildren().size() > 0) {
+ inner = (Element) cur.getChildren().get(0);
+ innerType = inner.getName();
+ tag = inner.getAttributeValue("tag");
+ path = inner.getAttributeValue("path");
+ }
+ // build mime type declaration list
+ ArrayList<String> mime = new ArrayList<String>();
+ for (Object child : cur.getChildren()) {
+ Element curChild = (Element) child;
+ if (curChild.getName().equalsIgnoreCase("mime")) {
+ mime.add(curChild.getAttributeValue("type"));
+ }
+ }
+ if (type.equalsIgnoreCase("static")) {
+ ScriptInputStatic si = new ScriptInputStatic();
+ Element content = cur.getChild("content");
+ if (content == null)
+ throw new DeserializationException("FIXME: script tag without embedded content tag");
+ si.setUrl(content.getAttributeValue("url"));
+ if (si.getUrl() == null)
+ si.setContent(content.getText());
+ fillInputDescription(si, binary, forceCopy, innerType, tag, path);
+ getStatic_inputs().add(si);
+ } else if (type.equalsIgnoreCase("input")) {
+ ScriptInputUser indesc = new ScriptInputUser();
+ indesc.setList(list);
+ indesc.setMime(mime);
+ indesc.setConcatenate(concatenate);
+ fillInputDescription(indesc, binary, forceCopy, innerType, tag, path);
+ getInputs().put(Tools.sanitiseName(name), indesc);
+ } else if (type.equalsIgnoreCase("output")) {
+ ScriptOutput outdesc = new ScriptOutput();
+ outdesc.setMime(mime);
+
+ boolean ok = true;
+ if (null == innerType) {
+ // don't know what to do
+ throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?");
+ } else if (innerType.equalsIgnoreCase("fromfile")) {
+ outdesc.setPath(path);
+ outdesc.setBinary(binary);
+ } else {
+ throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'");
+ }
+ if (ok) {
+ getOutputs().put(Tools.sanitiseName(name), outdesc);
+ }
+ } else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) {
+ getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation")));
+ } else if (type.equalsIgnoreCase("group")) {
+ group = name;
+ } else if (type.equalsIgnoreCase("test")) {
+ test_local = cur.getAttributeValue("local");
+ } else if (type.equalsIgnoreCase("icon")) {
+ icon_url = cur.getAttributeValue("url");
+ } else if (type.equalsIgnoreCase("queue")) {
+ for (Object child_ob : cur.getChildren()) {
+ Element child = (Element) child_ob;
+ if (child.getName().equalsIgnoreCase("prefer"))
+ getQueue_preferred().add(child.getAttributeValue("url"));
+ else if (child.getName().equalsIgnoreCase("deny"))
+ getQueue_deny().add(child.getAttributeValue("url"));
+ else
+ throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry");
+ }
+ } else if (type.equalsIgnoreCase("command")) {
+ // i like to have the ability to inject complete shell script
+ // fragments into the use case,
+ // so this should be replace and should allow multiple lines
+ if ((getCommand() != null) && !getCommand().isEmpty()) {
+ throw new DeserializationException("You have specified both command attribute and command tag.");
+ }
+ setCommand(cur.getText());
+ } else if (type.equalsIgnoreCase("validReturnCodes")) {
+ String codeString = cur.getAttributeValue("codes");
+ if (codeString != null) {
+ setReturnCodesAsText(codeString);
+ }
+ }
+ else {
+ throw new DeserializationException("Unexpected and uninterpreted attribute " + type);
+ }
+ }
+ }
+
+ private void fillInputDescription(ScriptInput fillMe, boolean binary, boolean forceCopy, String innerType, String tag, String path) throws DeserializationException {
+ fillMe.setBinary(binary);
+ fillMe.setForceCopy(forceCopy);
+ if (null == innerType) {
+ // don't know what to do
+ throw new DeserializationException("FIXME: Found null == innerType for input, is this the bug?");
+ } else if (innerType.equalsIgnoreCase("replace")) {
+ fillMe.setTag(tag);
+ fillMe.setTempFile(false);
+ fillMe.setFile(false);
+ getTags().add(tag);
+ } else if (innerType.equalsIgnoreCase("tempfile")) {
+ fillMe.setTag(tag);
+ fillMe.setTempFile(true);
+ fillMe.setFile(false);
+ getTags().add(tag);
+ } else if (innerType.equalsIgnoreCase("file")) {
+ fillMe.setTag(path);
+ fillMe.setTempFile(false);
+ fillMe.setFile(true);
+ } else {
+ throw new DeserializationException("Problem reading input port: unknown innerType '" + innerType + "'");
+ }
+ }
+
+ /**
+ * returns icon that is referenced in use case description
+ */
+ public ImageIcon getImageIcon() {
+ if (null == icon_url) return null;
+ try {
+ URL u = new URL(icon_url);
+ return new ImageIcon(u, getUsecaseid());
+ } catch (Exception e) {
+ logger.error(e);
+ return null;
+ }
+ }
+
+ /**
+ * String representation of the use case. It also contains interesting
+ * information on the availability of resources in the grid to actually
+ * execute that workflow element.
+ *
+ * @return String
+ */
+ @Override
+ public String toString() {
+ List<String> hlp = new ArrayList<String>();
+ hlp.add("usecaseid: " + getUsecaseid());
+ hlp.add("description: " + getDescription());
+ hlp.add("group: " + group);
+ hlp.add("test: " + test_local);
+ hlp.add("tags: " + getTags());
+ for (Map.Entry<String, ScriptInput> cur : getInputs().entrySet()) {
+ hlp.add(">" + cur.getKey() + ">: " + cur.getValue().toString());
+ }
+ for (Map.Entry<String, ScriptOutput> cur : getOutputs().entrySet()) {
+ hlp.add("<" + cur.getKey() + "<: " + cur.getValue().toString());
+ }
+ hlp.add("RE: " + getREs().toString());
+ hlp.add("preferred queues: " + getQueue_preferred());
+ hlp.add("denied queues: " + getQueue_deny());
+ String tos = super.toString() + "[";
+ for (int i = 0; i < hlp.size(); i++) {
+ if (i != 0)
+ tos += ", ";
+ tos += hlp.get(i);
+ }
+ return tos + " ]";
+ }
+
+ /**
+ * hajo's test just pass an url or file url to an xml file
+ *
+ * @throws IOException
+ * @throws MalformedURLException
+ * @throws DeserializationException
+ */
+ public static void main(String[] argv) throws MalformedURLException, IOException, DeserializationException {
+ UseCaseDescription d = new UseCaseDescription(new URL(argv[0]).openStream());
+ logger.info(d.getCommand());
+ }
+
+ /**
+ * @param command the command to set
+ */
+ @ConfigurationProperty(name = "command", label = "Command", description="What is actually executed on the shell")
+ public void setCommand(String command) {
+ this.command = command;
+ }
+
+ /**
+ * @param description the description to set
+ */
+ @ConfigurationProperty(name = "description", label = "Description", description="Textual description of the tool", required=false, uri="http://purl.org/dc/elements/1.1/description")
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the description
+ */
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param executionTimeoutInSeconds the executionTimeoutInSeconds to set
+ */
+ @ConfigurationProperty(name = "executionTimeoutInSeconds", label = "Execution Timeout In Seconds")
+ public void setExecutionTimeoutInSeconds(int executionTimeoutInSeconds) {
+ this.executionTimeoutInSeconds = executionTimeoutInSeconds;
+ }
+
+ /**
+ * @return the executionTimeoutInSeconds
+ */
+ public int getExecutionTimeoutInSeconds() {
+ return executionTimeoutInSeconds;
+ }
+
+ /**
+ * @param inputs the inputs to set
+ */
+ public void setInputs(Map<String, ScriptInput> inputs) {
+ this.inputs = inputs;
+ }
+
+ @ConfigurationProperty(name = "inputs", label = "Inputs", required=false)
+ public void setInputs(Set<InputMap> inputs) {
+ if (inputs != null) {
+ this.inputs = new HashMap<String, ScriptInput>();
+ for (InputMap inputMap : inputs) {
+ this.inputs.put(inputMap.getPort(), inputMap.getInput());
+ }
+ } else {
+ this.inputs = null;
+ }
+ }
+
+ /**
+ * @return the inputs
+ */
+ public Map<String, ScriptInput> getInputs() {
+ if (inputs == null) {
+ inputs = new HashMap<String, ScriptInput>();
+ }
+ return inputs;
+ }
+
+ /**
+ * @param outputs the outputs to set
+ */
+ public void setOutputs(Map<String, ScriptOutput> outputs) {
+ this.outputs = outputs;
+ }
+
+ @ConfigurationProperty(name = "outputs", label = "Outputs", required=false)
+ public void setOutputs(Set<OutputMap> outputs) {
+ if (outputs != null) {
+ this.outputs = new HashMap<String, ScriptOutput>();
+ for (OutputMap outputMap : outputs) {
+ this.outputs.put(outputMap.getPort(), outputMap.getOutput());
+ }
+ } else {
+ this.outputs = null;
+ }
+ }
+
+ /**
+ * @return the outputs
+ */
+ public Map<String, ScriptOutput> getOutputs() {
+ if (outputs == null) {
+ outputs = new HashMap<String, ScriptOutput>();
+ }
+ return outputs;
+ }
+
+ /**
+ * @param preparingTimeoutInSeconds the preparingTimeoutInSeconds to set
+ */
+ @ConfigurationProperty(name = "preparingTimeoutInSeconds", label = "Preparing Timeout In Seconds")
+ public void setPreparingTimeoutInSeconds(int preparingTimeoutInSeconds) {
+ this.preparingTimeoutInSeconds = preparingTimeoutInSeconds;
+ }
+
+ /**
+ * @return the preparingTimeoutInSeconds
+ */
+ public int getPreparingTimeoutInSeconds() {
+ return preparingTimeoutInSeconds;
+ }
+
+ /**
+ * @param queue_deny the queue_deny to set
+ */
+ public void setQueue_deny(ArrayList<String> queue_deny) {
+ this.queue_deny = queue_deny;
+ }
+
+ /**
+ * @return the queue_deny
+ */
+ public ArrayList<String> getQueue_deny() {
+ if (queue_deny == null) {
+ queue_deny = new ArrayList<String>();
+ }
+ return queue_deny;
+ }
+
+ /**
+ * @param queue_preferred the queue_preferred to set
+ */
+ public void setQueue_preferred(ArrayList<String> queue_preferred) {
+ this.queue_preferred = queue_preferred;
+ }
+
+ /**
+ * @return the queue_preferred
+ */
+ public ArrayList<String> getQueue_preferred() {
+ if (queue_preferred == null) {
+ queue_preferred = new ArrayList<String>();
+ }
+ return queue_preferred;
+ }
+
+ /**
+ * @param rEs the rEs to set
+ */
+ public void setREs(List<RuntimeEnvironmentConstraint> rEs) {
+ REs = rEs;
+ }
+
+ /**
+ * @return the rEs
+ */
+ public List<RuntimeEnvironmentConstraint> getREs() {
+ if (REs == null) {
+ REs = new ArrayList<RuntimeEnvironmentConstraint>();
+ }
+ return REs;
+ }
+
+ /**
+ * @param static_inputs the static_inputs to set
+ */
+ @ConfigurationProperty(name = "staticInputs", label = "Static Inputs", ordering=OrderPolicy.NON_ORDERED, required=false)
+ public void setStatic_inputs(List<ScriptInputStatic> static_inputs) {
+ this.static_inputs = static_inputs;
+ }
+
+ /**
+ * @return the static_inputs
+ */
+ public List<ScriptInputStatic> getStatic_inputs() {
+ if (static_inputs == null) {
+ static_inputs = new ArrayList<ScriptInputStatic>();
+ }
+ return static_inputs;
+ }
+
+ /**
+ * @param tags the tags to set
+ */
+ public void setTags(List<String> tags) {
+ this.tags = tags;
+ }
+
+ /**
+ * @return the tags
+ */
+ public List<String> getTags() {
+ if (tags == null) {
+ tags = new ArrayList<String>();
+ }
+ return tags;
+ }
+
+ /**
+ * @param usecaseid the usecaseid to set
+ */
+ @ConfigurationProperty(name = "usecaseid", label = "Title", uri="http://purl.org/dc/elements/1.1/title", required=false)
+ public void setUsecaseid(String usecaseid) {
+ this.usecaseid = usecaseid;
+ }
+
+ /**
+ * @return the usecaseid
+ */
+ public String getUsecaseid() {
+ return usecaseid;
+ }
+
+ public boolean isIncludeStdIn() {
+ return includeStdIn;
+ }
+
+ @ConfigurationProperty(name = "includeStdIn", label = "Include STDIN")
+ public void setIncludeStdIn(boolean includeStdIn) {
+ this.includeStdIn = includeStdIn;
+ }
+
+ public boolean isIncludeStdOut() {
+ return includeStdOut;
+ }
+
+ @ConfigurationProperty(name = "includeStdOut", label = "Include STDOUT")
+ public void setIncludeStdOut(boolean includeStdOut) {
+ this.includeStdOut = includeStdOut;
+ }
+
+ public boolean isIncludeStdErr() {
+ return includeStdErr;
+ }
+
+ @ConfigurationProperty(name = "includeStdErr", label = "Include STDERR")
+ public void setIncludeStdErr(boolean includeStdErr) {
+ this.includeStdErr = includeStdErr;
+ }
+
+ /**
+ * @return the validReturnCodes
+ */
+ public List<Integer> getValidReturnCodes() {
+ if (validReturnCodes == null) {
+ validReturnCodes = new ArrayList<Integer>();
+ }
+ if (validReturnCodes.isEmpty()) {
+ validReturnCodes.add(0);
+ }
+ return validReturnCodes;
+ }
+
+ /**
+ * @param validReturnCodes the validReturnCodes to set
+ */
+ public void setValidReturnCodes(List<Integer> validReturnCodes) {
+ this.validReturnCodes = validReturnCodes;
+ }
+
+ public String getReturnCodesAsText() {
+ return StringUtils.join(getValidReturnCodes(), ",");
+ }
+
+ public void setReturnCodesAsText(String text) {
+ if (getValidReturnCodes() == null) {
+ validReturnCodes = new ArrayList<Integer>();
+ }
+ validReturnCodes.clear();
+ String[] codes = text.split(",");
+ for (String code : codes) {
+ try {
+ Integer codeInt = new Integer(code);
+ if (!validReturnCodes.contains(codeInt)) {
+ validReturnCodes.add(codeInt);
+ }
+ }
+ catch (NumberFormatException e) {
+ logger.error(e);
+ }
+ }
+ if (validReturnCodes.isEmpty()) {
+ validReturnCodes.add(0);
+ }
+ Collections.sort(validReturnCodes);
+ }
+
+ /**
+ * @return the group
+ */
+ public String getGroup() {
+ return group;
+ }
+
+ /**
+ * @param group the group to set
+ */
+ public void setGroup(String group) {
+ this.group = group;
+ }
+
+ /**
+ * @return the icon_url
+ */
+ public String getIcon_url() {
+ return icon_url;
+ }
+
+ @ConfigurationBean(uri = ExternalToolActivity.URI + "#OutputMap")
+ public static class OutputMap {
+ private String port;
+
+ private ScriptOutput output;
+
+ public String getPort() {
+ return port;
+ }
+
+ @ConfigurationProperty(name = "port", label = "Port")
+ public void setPort(String port) {
+ this.port = port;
+ }
+
+ public ScriptOutput getOutput() {
+ return output;
+ }
+
+ @ConfigurationProperty(name = "output", label = "Output")
+ public void setOutput(ScriptOutput output) {
+ this.output = output;
+ }
+ }
+
+ @ConfigurationBean(uri = ExternalToolActivity.URI + "#InputMap")
+ public static class InputMap {
+ private String port;
+
+ private ScriptInputUser input;
+
+ public String getPort() {
+ return port;
+ }
+
+ @ConfigurationProperty(name = "port", label = "Port")
+ public void setPort(String port) {
+ this.port = port;
+ }
+
+ public ScriptInputUser getInput() {
+ return input;
+ }
+
+ @ConfigurationProperty(name = "input", label = "Input")
+ public void setInput(ScriptInputUser input) {
+ this.input = input;
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java
new file mode 100644
index 0000000..1a43461
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/UseCaseEnumeration.java
@@ -0,0 +1,111 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.desc;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URL;
+import java.net.URLConnection;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.taverna.workflowmodel.serialization.DeserializationException;
+
+import org.apache.log4j.Logger;
+import org.jdom.Document;
+import org.jdom.Element;
+import org.jdom.JDOMException;
+import org.jdom.input.SAXBuilder;
+
+public class UseCaseEnumeration {
+
+ private static Logger logger = Logger.getLogger(UseCaseEnumeration.class);
+
+ public static List<UseCaseDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException {
+
+ List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>();
+ URLConnection con = null;
+ try {
+ URL url = new URL(xmlFileUrl);
+
+ con = url.openConnection();
+ con.setConnectTimeout(4000);
+ ret = readDescriptionsFromStream(con.getInputStream());
+
+ } catch (IOException ioe) {
+ logger.error("Problem retrieving from " + xmlFileUrl);
+ logger.error(ioe);
+ throw ioe;
+ }
+ finally {
+
+ }
+
+ return ret;
+
+ }
+
+ public static List<UseCaseDescription> readDescriptionsFromStream(InputStream is) {
+
+ List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>();
+
+ SAXBuilder builder = new SAXBuilder();
+ Document doc = null;
+ try {
+ doc = builder.build(is);
+ is.close();
+ } catch (JDOMException e1) {
+ logger.error(e1);
+ return ret;
+ } catch (IOException e1) {
+ logger.error(e1);
+ return ret;
+ } finally {
+ try {
+ is.close();
+ } catch (IOException e) {
+ logger.error(e);
+ }
+ }
+
+ Element usecases = doc.getRootElement();
+ for (Object ochild : usecases.getChildren()) {
+ Element child = (Element) ochild;
+ if (child.getName().equalsIgnoreCase("program")) {
+ try {
+ ret.add(new UseCaseDescription(child));
+ } catch (DeserializationException e) {
+ logger.error(e);
+ }
+ }
+ }
+ return ret;
+ }
+
+ public static UseCaseDescription readDescriptionFromUrl(
+ String repositoryUrl, String id) throws IOException {
+ List<UseCaseDescription> descriptions = readDescriptionsFromUrl(repositoryUrl);
+ for (UseCaseDescription usecase : descriptions) {
+ if (usecase.getUsecaseid().equals(id)) {
+ return usecase;
+ }
+ }
+ return null;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java
new file mode 100644
index 0000000..9dbe959
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/AskUserForPwPopup.java
@@ -0,0 +1,74 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.taverna.activities.externaltool.gui;
+
+import javax.swing.JOptionPane;
+
+import org.apache.taverna.activities.externaltool.invocation.AskUserForPw;
+import org.apache.taverna.activities.externaltool.ssh.SshNode;
+
+public final class AskUserForPwPopup implements AskUserForPw {
+ private SshNode ret;
+ private String pw, pp, kf, us;
+
+ public static String ask(String message, String title) {
+ return (String) JOptionPane.showInputDialog(null, message, title, JOptionPane.QUESTION_MESSAGE, null, null, "");
+ }
+
+ public static boolean askYN(String message, String title) {
+ return JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION;
+ }
+
+ public String getPassword() {
+ getUsername();
+ if (pw != null)
+ return pw;
+ pw = ask("Please enter your password for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
+ return pw;
+ }
+
+ public String getPassphrase() {
+ getUsername();
+ if (pp != null)
+ return pp;
+ pp = ask("Please enter your passphrase for " + kf + " used for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
+ return pp;
+ }
+
+ public String getKeyfile() {
+ getUsername();
+ if (kf != null)
+ return kf;
+ kf = ask("Please enter the keyfile for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
+ return kf;
+ }
+
+ public String getUsername() {
+ if (us != null)
+ return us;
+ us = ask("Please enter the username for " + ret.getHost(), "Username for " + ret.getHost());
+ return us;
+ }
+
+ public void setSshNode(SshNode sshNode) {
+ this.ret = sshNode;
+ }
+
+ public void authenticationSucceeded() {
+ }
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java
new file mode 100755
index 0000000..9e265c8
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/gui/PleaseWaitDialog.java
@@ -0,0 +1,73 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.gui;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JDialog;
+import javax.swing.JLabel;
+
+public class PleaseWaitDialog extends JDialog {
+ private static final long serialVersionUID = 1L;
+
+ static PleaseWaitDialog instance = new PleaseWaitDialog();
+
+ public class WaitMessage{
+ public WaitMessage() {
+ }
+
+ String str;
+ public void set(String newstr) {
+ synchronized (PleaseWaitDialog.instance) {
+ if(this.str != null && this.str.equals(newstr)) return;
+ if(this.str != null) messages.remove(this.str);
+ this.str = newstr;
+ if(this.str != null) messages.add(this.str);
+ }
+ updateDialog();
+ }
+ public void done() {
+ set(null);
+ }
+ }
+
+ private void updateDialog() {
+ synchronized (PleaseWaitDialog.instance) {
+ if(messages.size() > 0) this.setVisible(true);
+ else this.setVisible(false);
+ String t = "";
+ for (String cur : messages) {
+ t += cur + "<br>";
+ }
+ l.setText("<html>"+t+"</html>");
+ }
+ }
+
+ List<String> messages = new ArrayList<String>();
+
+ JLabel l;
+ private PleaseWaitDialog() {
+ this.setAlwaysOnTop(true);
+ this.setTitle("Please wait");
+ l = new JLabel("");
+ this.add(l);
+ this.setSize(400, 100);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java
new file mode 100644
index 0000000..04bced0
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/AskUserForPw.java
@@ -0,0 +1,32 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.invocation;
+
+public interface AskUserForPw {
+
+ // we will try keyfile first
+ public String getKeyfile();
+ public String getPassphrase();
+
+ // then username+password
+ public String getUsername();
+ public String getPassword();
+
+ public void authenticationSucceeded();
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java
new file mode 100644
index 0000000..d9f6bce
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/InvocationException.java
@@ -0,0 +1,36 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.invocation;
+
+public class InvocationException extends Exception {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 437316164959631591L;
+
+ public InvocationException(String string) {
+ super(string);
+ }
+
+ public InvocationException(Exception e) {
+ super(e);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java
new file mode 100644
index 0000000..4d97030
--- /dev/null
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/invocation/UseCaseInvocation.java
@@ -0,0 +1,321 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements. See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership. The ASF licenses this file
+ * to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License. You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.apache.taverna.activities.externaltool.invocation;
+
+import java.io.BufferedWriter;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.taverna.activities.externaltool.desc.ScriptInput;
+import org.apache.taverna.activities.externaltool.desc.ScriptInputStatic;
+import org.apache.taverna.activities.externaltool.desc.ScriptInputUser;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.invocation.InvocationContext;
+import org.apache.taverna.reference.ExternalReferenceSPI;
+import org.apache.taverna.reference.Identified;
+import org.apache.taverna.reference.IdentifiedList;
+import org.apache.taverna.reference.ReferenceService;
+import org.apache.taverna.reference.ReferenceServiceException;
+import org.apache.taverna.reference.ReferenceSet;
+import org.apache.taverna.reference.T2Reference;
+import org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder;
+import org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder;
+
+/**
+ * An abstraction of various forms to bring job using the software that is
+ * referenced as a use case towards their execution.
+ *
+ * @author Hajo Nils Krabbenhoeft with some contribution by
+ * @author Steffen Moeller
+ */
+public abstract class UseCaseInvocation {
+
+ private String runId;
+
+
+ protected static String getActualOsCommand(String osCommand, String pathToOriginal,
+ String targetName, String pathTarget) {
+ String actualOsCommand = osCommand;
+ actualOsCommand = actualOsCommand.replace("%%PATH_TO_ORIGINAL%%", pathToOriginal);
+ actualOsCommand = actualOsCommand.replace("%%TARGET_NAME%%", targetName);
+ actualOsCommand = actualOsCommand.replace("%%PATH_TO_TARGET%%", pathTarget);
+ return actualOsCommand;
+ }
+
+ protected UseCaseDescription usecase;
+ protected final HashMap<String, String> tags = new HashMap<String, String>();
+ protected int nTempFiles = 0;
+ private static int submissionID = 0;
+ protected static InlineByteArrayReferenceBuilder inlineByteArrayReferenceBuilder = new InlineByteArrayReferenceBuilder();
+ protected static InlineStringReferenceBuilder inlineStringReferenceBuilder = new InlineStringReferenceBuilder();
+ private InvocationContext invocationContext;
+ private boolean retrieveData;
+
+ /*
+ * get the class of the data we expect for a given input
+ */
+ @SuppressWarnings("unchecked")
+ public Class getType(String inputName) {
+ if (!usecase.getInputs().containsKey(inputName))
+ return null;
+ ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName);
+ if (input.isList()) {
+ if (input.isBinary())
+ return List.class;
+ else
+ return List.class;
+ } else {
+ if (input.isBinary())
+ return byte[].class;
+ else
+ return String.class;
+ }
+ }
+
+ /*
+ * get a list of all the input port names
+ */
+ public Set<String> getInputs() {
+ return usecase.getInputs().keySet();
+ }
+
+
+ /*
+ * get a id, incremented with each job. thus, this should be thread-wide
+ * unique
+ */
+ public synchronized int getSubmissionID() {
+ return submissionID++;
+ }
+
+ /*
+ * set the data for the input port with given name
+ */
+ @SuppressWarnings("unchecked")
+ public void setInput(String inputName, ReferenceService referenceService, T2Reference t2Reference) throws InvocationException {
+ if (t2Reference == null) {
+ throw new InvocationException("No input specified for " + inputName);
+ }
+ ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName);
+ if (input.isList()) {
+ IdentifiedList<T2Reference> listOfReferences = (IdentifiedList<T2Reference>) referenceService
+ .getListService().getList(t2Reference);
+
+ if (!input.isConcatenate()) {
+ // this is a list input (not concatenated)
+ // so write every element to its own temporary file
+ // and create a filelist file
+
+ // we need to write the list elements to temporary files
+ ScriptInputUser listElementTemp = new ScriptInputUser();
+ listElementTemp.setBinary(input.isBinary());
+ listElementTemp.setTempFile(true);
+
+ String lineEndChar = "\n";
+ if (!input.isFile() && !input.isTempFile()) {
+ lineEndChar = " ";
+ }
+
+ String listFileContent = "";
+ String filenamesFileContent = "";
+ // create a list of all temp file names
+ for (T2Reference cur : listOfReferences) {
+ String tmp = setOneInput(referenceService, cur,
+ listElementTemp);
+ listFileContent += tmp + lineEndChar;
+ int ind = tmp.lastIndexOf('/');
+ if (ind == -1) {
+ ind = tmp.lastIndexOf('\\');
+ }
+ if (ind != -1) {
+ tmp = tmp.substring(ind + 1);
+ }
+ filenamesFileContent += tmp + lineEndChar;
+ }
+
+ // how do we want the listfile to be stored?
+ ScriptInputUser listFile = new ScriptInputUser();
+ listFile.setBinary(false); // since its a list file
+ listFile.setFile(input.isFile());
+ listFile.setTempFile(input.isTempFile());
+ listFile.setTag(input.getTag());
+ T2Reference listFileContentReference = referenceService
+ .register(listFileContent, 0, true, invocationContext);
+
+ tags.put(listFile.getTag(), setOneInput(referenceService,
+ listFileContentReference, listFile));
+
+ listFile.setTag(input.getTag() + "_NAMES");
+ T2Reference filenamesFileContentReference = referenceService
+ .register(filenamesFileContent, 0, true, null);
+ tags.put(listFile.getTag(), setOneInput(referenceService,
+ filenamesFileContentReference, listFile));
+ } else {
+ try {
+ // first, concatenate all data
+ if (input.isBinary()) {
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ BufferedWriter outputWriter = new BufferedWriter(
+ new OutputStreamWriter(outputStream));
+ for (T2Reference cur : listOfReferences) {
+ InputStreamReader inputReader = new InputStreamReader(
+ getAsStream(referenceService, cur));
+ IOUtils.copyLarge(inputReader, outputWriter);
+ inputReader.close();
+ }
+ outputWriter.close();
+ T2Reference binaryReference = referenceService
+ .register(outputStream.toByteArray(), 0, true,
+ invocationContext);
+ tags.put(input.getTag(), setOneInput(referenceService,
+ binaryReference, input));
+ } else {
+ ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
+ BufferedWriter outputWriter = new BufferedWriter(
+ new OutputStreamWriter(outputStream));
+ for (T2Reference cur : listOfReferences) {
+ InputStreamReader inputReader = new InputStreamReader(
+ getAsStream(referenceService, cur));
+ IOUtils.copyLarge(inputReader, outputWriter);
+ outputWriter.write(" ");
+ inputReader.close();
+ }
+ outputWriter.close();
+ T2Reference binaryReference = referenceService
+ .register(outputStream.toByteArray(), 0, true,
+ invocationContext);
+ tags.put(input.getTag(), setOneInput(referenceService,
+ binaryReference, input));
+ }
+ } catch (IOException e) {
+ throw new InvocationException(e);
+ }
+ }
+ } else {
+ tags.put(input.getTag(), setOneInput(referenceService, t2Reference,
+ input));
+ }
+ }
+
+ /*
+ * submit a grid job and wait for it to finish, then get the result as
+ * on-demand downloads or directly as data (in case of local execution)
+ */
+ public HashMap<String, Object> Submit(ReferenceService referenceService) throws InvocationException {
+ submit_generate_job(referenceService);
+ return submit_wait_fetch_results(referenceService);
+ }
+
+ /*
+ * just submit the job. useful if you want to wait for it to finish later on
+ *
+ * Can the statics be made more static?
+ */
+ public void submit_generate_job(ReferenceService referenceService) throws InvocationException {
+ for (ScriptInputStatic input : usecase.getStatic_inputs()) {
+ T2Reference ref;
+ if (input.getUrl() != null) {
+ // Does this work OK with binary
+ try {
+ ref = referenceService.register(new URL(input.getUrl()), 0, true, null);
+ } catch (ReferenceServiceException e) {
+ throw new InvocationException(e);
+ } catch (MalformedURLException e) {
+ throw new InvocationException(e);
+ }
+ } else {
+ ref = referenceService.register((String) input.getContent(), 0, true, null);
+ }
+ tags.put(input.getTag(), setOneInput(referenceService, ref, input));
+
+ }
+ submit_generate_job_inner();
+ }
+
+ protected abstract void submit_generate_job_inner() throws InvocationException;
+
+ /*
+ * wait for a submitted job to finish and fetch the results
+ */
+ public abstract HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException;
+
+ public abstract String setOneInput(ReferenceService referenceService, T2Reference t2Reference, ScriptInput input) throws InvocationException;
+
+ protected InputStream getAsStream(ReferenceService referenceService, T2Reference t2Reference) {
+ Identified identified = referenceService.resolveIdentifier(t2Reference, null, null);
+ if (identified instanceof ReferenceSet) {
+ ExternalReferenceSPI ref = ((ReferenceSet) identified).getExternalReferences().iterator().next();
+ return ref.openStream(invocationContext);
+ }
+ return null;
+ }
+
+ public void setContext(InvocationContext context) {
+ this.invocationContext = context;
+
+ }
+
+ public InvocationContext getContext() {
+ return this.invocationContext;
+ }
+
+ public abstract void setStdIn(ReferenceService referenceService,
+ T2Reference t2Reference);
+
+ public abstract void rememberRun(String runId);
+
+ /**
+ * @return the runId
+ */
+ protected String getRunId() {
+ return runId;
+ }
+
+ /**
+ * @param runId the runId to set
+ */
+ protected void setRunId(String runId) {
+ this.runId = runId;
+ }
+
+ /**
+ * @return the retrieveData
+ */
+ protected boolean isRetrieveData() {
+ return retrieveData;
+ }
+
+ /**
+ * @param retrieveData the retrieveData to set
+ */
+ protected void setRetrieveData(boolean retrieveData) {
+ this.retrieveData = retrieveData;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java
index f846d02..e921bc4 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/ExternalToolLocalInvocationMechanism.java
@@ -24,8 +24,6 @@ import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.jdom.Element;
import org.jdom.Text;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java
index 8c6234d..c340f0e 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationCreator.java
@@ -23,16 +23,14 @@ import java.io.IOException;
import java.util.Map;
import org.apache.taverna.activities.externaltool.InvocationCreator;
+import org.apache.taverna.activities.externaltool.desc.UseCaseDescription;
+import org.apache.taverna.activities.externaltool.invocation.UseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.reference.ReferenceService;
import org.apache.taverna.reference.T2Reference;
import org.apache.log4j.Logger;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.UseCaseInvocation;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation;
-
/**
* @author alanrw
*
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java
index b30a73b..8cc8201 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalInvocationPersister.java
@@ -22,8 +22,6 @@ package org.apache.taverna.activities.externaltool.local;
import java.io.File;
import org.apache.log4j.Logger;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationPersister;
/**
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java
index b92417c..3f95a2b 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/local/LocalMechanismCreator.java
@@ -20,8 +20,6 @@
package org.apache.taverna.activities.externaltool.local;
import org.jdom.Element;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.local.LocalUseCaseInvocation;
import org.apache.taverna.activities.externaltool.manager.InvocationMechanism;
import org.apache.taverna.activities.externaltool.manager.MechanismCreator;
[5/6] incubator-taverna-common-activities git commit: TAVERNA-963
package taverna.externaltool.*
Posted by st...@apache.org.
TAVERNA-963 package taverna.externaltool.*
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/1e35285b
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/1e35285b
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/1e35285b
Branch: refs/heads/cwl-browse
Commit: 1e35285b0c60962f81908fe16b7e268b28cb9a4f
Parents: 5eea144
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed May 4 00:53:18 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed May 4 00:53:18 2016 +0100
----------------------------------------------------------------------
.../inb/knowarc/gui/AskUserForPwPopup.java | 74 --
.../inb/knowarc/gui/PleaseWaitDialog.java | 73 --
.../knowarc/usecases/RuntimeEnvironment.java | 251 ------
.../usecases/RuntimeEnvironmentConstraint.java | 160 ----
.../inb/knowarc/usecases/ScriptInput.java | 134 ---
.../inb/knowarc/usecases/ScriptInputStatic.java | 73 --
.../inb/knowarc/usecases/ScriptInputUser.java | 99 --
.../inb/knowarc/usecases/ScriptOutput.java | 88 --
.../knowarc/usecases/UseCaseDescription.java | 897 -------------------
.../knowarc/usecases/UseCaseEnumeration.java | 111 ---
.../usecases/invocation/AskUserForPw.java | 32 -
.../invocation/InvocationException.java | 36 -
.../usecases/invocation/UseCaseInvocation.java | 322 -------
.../local/LocalUseCaseInvocation.java | 561 ------------
.../ssh/SshAutoLoginTrustEveryone.java | 70 --
.../usecases/invocation/ssh/SshNode.java | 157 ----
.../usecases/invocation/ssh/SshNodeFactory.java | 66 --
.../usecases/invocation/ssh/SshPool.java | 158 ----
.../usecases/invocation/ssh/SshReference.java | 222 -----
.../knowarc/usecases/invocation/ssh/SshUrl.java | 163 ----
.../invocation/ssh/SshUrlToSshReference.java | 54 --
.../invocation/ssh/SshUseCaseInvocation.java | 561 ------------
.../externaltool/ExternalToolActivity.java | 13 +-
.../ExternalToolActivityConfigurationBean.java | 2 +-
.../ExternalToolActivityMimeTypeChecker.java | 5 +-
.../externaltool/InvocationCreator.java | 5 +-
.../externaltool/RetrieveLoginFromTaverna.java | 2 +-
.../externaltool/desc/RuntimeEnvironment.java | 251 ++++++
.../desc/RuntimeEnvironmentConstraint.java | 160 ++++
.../externaltool/desc/ScriptInput.java | 134 +++
.../externaltool/desc/ScriptInputStatic.java | 73 ++
.../externaltool/desc/ScriptInputUser.java | 99 ++
.../externaltool/desc/ScriptOutput.java | 88 ++
.../externaltool/desc/UseCaseDescription.java | 897 +++++++++++++++++++
.../externaltool/desc/UseCaseEnumeration.java | 111 +++
.../externaltool/gui/AskUserForPwPopup.java | 74 ++
.../externaltool/gui/PleaseWaitDialog.java | 73 ++
.../externaltool/invocation/AskUserForPw.java | 32 +
.../invocation/InvocationException.java | 36 +
.../invocation/UseCaseInvocation.java | 321 +++++++
.../ExternalToolLocalInvocationMechanism.java | 2 -
.../local/LocalInvocationCreator.java | 6 +-
.../local/LocalInvocationPersister.java | 2 -
.../local/LocalMechanismCreator.java | 2 -
.../local/LocalUseCaseInvocation.java | 560 ++++++++++++
.../ssh/ExternalToolSshInvocationMechanism.java | 5 -
.../ssh/SshAutoLoginTrustEveryone.java | 69 ++
.../externaltool/ssh/SshInvocationCreator.java | 11 +-
.../ssh/SshInvocationPersister.java | 4 +-
.../externaltool/ssh/SshMechanismCreator.java | 4 -
.../activities/externaltool/ssh/SshNode.java | 157 ++++
.../externaltool/ssh/SshNodeFactory.java | 66 ++
.../activities/externaltool/ssh/SshPool.java | 157 ++++
.../externaltool/ssh/SshReference.java | 222 +++++
.../activities/externaltool/ssh/SshUrl.java | 163 ++++
.../externaltool/ssh/SshUrlToSshReference.java | 54 ++
.../externaltool/ssh/SshUseCaseInvocation.java | 560 ++++++++++++
...pache.taverna.reference.ExternalReferenceSPI | 2 +-
...verna.reference.ValueToReferenceConverterSPI | 2 +-
.../spring/external-tool-activity-context.xml | 4 +-
.../invocation/ssh/SshReference.hbm.xml | 2 +-
61 files changed, 4379 insertions(+), 4413 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
deleted file mode 100644
index 0ce0460..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/AskUserForPwPopup.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package de.uni_luebeck.inb.knowarc.gui;
-
-import javax.swing.JOptionPane;
-
-import de.uni_luebeck.inb.knowarc.usecases.invocation.AskUserForPw;
-import de.uni_luebeck.inb.knowarc.usecases.invocation.ssh.SshNode;
-
-public final class AskUserForPwPopup implements AskUserForPw {
- private SshNode ret;
- private String pw, pp, kf, us;
-
- public static String ask(String message, String title) {
- return (String) JOptionPane.showInputDialog(null, message, title, JOptionPane.QUESTION_MESSAGE, null, null, "");
- }
-
- public static boolean askYN(String message, String title) {
- return JOptionPane.showConfirmDialog(null, message, title, JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE) == JOptionPane.YES_OPTION;
- }
-
- public String getPassword() {
- getUsername();
- if (pw != null)
- return pw;
- pw = ask("Please enter your password for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return pw;
- }
-
- public String getPassphrase() {
- getUsername();
- if (pp != null)
- return pp;
- pp = ask("Please enter your passphrase for " + kf + " used for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return pp;
- }
-
- public String getKeyfile() {
- getUsername();
- if (kf != null)
- return kf;
- kf = ask("Please enter the keyfile for " + us + " @ " + ret.getHost(), us + " @ " + ret.getHost());
- return kf;
- }
-
- public String getUsername() {
- if (us != null)
- return us;
- us = ask("Please enter the username for " + ret.getHost(), "Username for " + ret.getHost());
- return us;
- }
-
- public void setSshNode(SshNode sshNode) {
- this.ret = sshNode;
- }
-
- public void authenticationSucceeded() {
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
deleted file mode 100755
index 2a643eb..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/gui/PleaseWaitDialog.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.gui;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-
-public class PleaseWaitDialog extends JDialog {
- private static final long serialVersionUID = 1L;
-
- static PleaseWaitDialog instance = new PleaseWaitDialog();
-
- public class WaitMessage{
- public WaitMessage() {
- }
-
- String str;
- public void set(String newstr) {
- synchronized (PleaseWaitDialog.instance) {
- if(this.str != null && this.str.equals(newstr)) return;
- if(this.str != null) messages.remove(this.str);
- this.str = newstr;
- if(this.str != null) messages.add(this.str);
- }
- updateDialog();
- }
- public void done() {
- set(null);
- }
- }
-
- private void updateDialog() {
- synchronized (PleaseWaitDialog.instance) {
- if(messages.size() > 0) this.setVisible(true);
- else this.setVisible(false);
- String t = "";
- for (String cur : messages) {
- t += cur + "<br>";
- }
- l.setText("<html>"+t+"</html>");
- }
- }
-
- List<String> messages = new ArrayList<String>();
-
- JLabel l;
- private PleaseWaitDialog() {
- this.setAlwaysOnTop(true);
- this.setTitle("Please wait");
- l = new JLabel("");
- this.add(l);
- this.setSize(400, 100);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
deleted file mode 100644
index c7fd889..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironment.java
+++ /dev/null
@@ -1,251 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.util.Arrays;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-
-/**
- * Representation of information about a single runtime environment. It is used
- * to decide if one runtime environment is possibly compatible with another one
- * for the selection of queues to commit to.
- *
- * To experiment/test these functions, run the following java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 foo-1 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 bla-2 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1.2 bla-1
- *
- * @author Steffen Moeller
- */
-@SuppressWarnings("unchecked")
-public class RuntimeEnvironment implements Comparable {
-
- private static Logger logger = Logger.getLogger(RuntimeEnvironment.class);
-
-
- /**
- * Unique identification of the runtime environment - the full name
- */
- protected String id;
-
- /**
- * Accessor function for the complete identifier of the runtime environment
- */
- public String getID() {
- return id;
- }
-
- protected String name;
-
- /**
- * Accessor function for the RE's name
- */
- public String getName() {
- return name;
- }
-
- protected String version;
-
- /**
- * Accessfor function for the version
- */
- public String getVersion() {
- return version;
- }
-
- /**
- * for those busy fellows who don't have the time to convert the String into
- * a RuntimeEnvironment object.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAs(String s) {
- RuntimeEnvironment tmpRE = new RuntimeEnvironment(s);
- return this.atLeastAsCapableAs(tmpRE);
- }
-
- /**
- * Indicates if a runtime environment has the same name, and if so, if the
- * given RE has the same or a later version.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAs(RuntimeEnvironment re) {
- if (!name.equals(re.name))
- return false;
- int c = compareVersions(getVersion(), re.getVersion());
- if (c >= 0) {
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Indicates if this runtimeEnvironment is the same version or later as any
- * in that list.
- *
- * @author Steffen Moeller
- */
- public boolean atLeastAsCapableAsAnyOf(Iterable<RuntimeEnvironment> res) {
- boolean compatibleOneFound = false;
- Iterator<RuntimeEnvironment> i = res.iterator();
- while (i.hasNext() && !compatibleOneFound) {
- RuntimeEnvironment r = i.next();
- compatibleOneFound = atLeastAsCapableAs(r);
- }
- return compatibleOneFound;
- }
-
- /**
- * Indicates if any of the runtime environments listed is the same version
- * as this or later.
- *
- * @author Steffen Moeller
- */
- public boolean isInferiorToAtLeastOneIn(Iterable<RuntimeEnvironment> res) {
- boolean compatibleOneFound = false;
- Iterator<RuntimeEnvironment> i = res.iterator();
- while (i.hasNext() && !compatibleOneFound) {
- RuntimeEnvironment r = i.next();
- compatibleOneFound = r.atLeastAsCapableAs(this);
- }
- return compatibleOneFound;
- }
-
- /**
- * Parses a string as commonly presented by the infosystem
- *
- * @author Steffen Moeller
- */
- public RuntimeEnvironment(String raw) {
- id = raw;
- int dashpos = raw.indexOf("-");
- if (-1 == dashpos) {
- version = "";
- name = raw;
- } else {
- name = raw.substring(0, dashpos);
- if (dashpos + 1 <= raw.length()) {
- version = raw.substring(dashpos + 1, raw.length());
- } else {
- version = "";
- }
- }
- }
-
- /**
- * to make it behave like a string at time, as it was originally implemented
- */
- @Override
- public String toString() {
- return id;
- }
-
- /**
- * Implementation of Comparable interface. It comes handy albeit this
- * function says nothing about the compatibility of two runtime environments
- * unless their names are identical and the relation of the constraint was
- * taken into account. It just sorts them in lists.
- */
- public int compareTo(Object o) throws ClassCastException {
- RuntimeEnvironment r = (RuntimeEnvironment) o;
- if (getName().equals(r.getName())) {
- return RuntimeEnvironment.compareVersions(getVersion(), r.getVersion());
- } else {
- return id.compareTo(r.getID());
- }
- }
-
- /**
- * FIXME: For the sake of simplicity, this implementation makes an error in
- * treating . and - in the versions equally. Versions, if numerical, are
- * treated numerically. Otherwise it is lexicographical, which is error
- * prone, though. Should the 'Scanner' class should be tapped into?
- *
- * @author Steffen Moeller
- */
- public static int compareVersions(String a, String b) {
-
- // null pointer exceptions are not risked .. we are nice
- if (null == a)
- a = "";
- if (null == b)
- b = "";
-
- // catching the dumb case first
- if (a.equals(b))
- return 0;
-
- List as = Arrays.asList(a.split("[.-]"));
- List bs = Arrays.asList(b.split("[.-]"));
-
- // both lists have the empty element as members at least
- Iterator aIterator = as.iterator();
- Iterator bIterator = bs.iterator();
-
- while (aIterator.hasNext()) {
- String aa = (String) aIterator.next();
- if (!bIterator.hasNext()) {
- // a is longer while equal so far
- return 1; // a > b
- }
- String bb = (String) bIterator.next();
- if (!aa.equals(bb)) {
- // a and b differ
- try {
- Integer aInt = Integer.parseInt(aa);
- Integer bInt = Integer.parseInt(bb);
- return aInt.compareTo(bInt);
- } catch (Exception e) {
- return aa.compareTo(bb);
- }
- }
- }
- if (bIterator.hasNext()) {
- // b is longer while equal so far
- return -1; // a < b
- }
- return 0; // a == b
- }
-
- /**
- * For testing purposes
- */
- public static void main(String argv[]) {
- if ("compare".equals(argv[0])) {
- RuntimeEnvironment r1 = new RuntimeEnvironment(argv[1]);
- RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]);
- logger.info("r1.getName(): " + r1.getName());
- logger.info("r1.getVersion(): " + r1.getVersion());
- logger.info("r2.getName(): " + r2.getName());
- logger.info("r2.getVersion(): " + r2.getVersion());
- logger.info("r1.atLeastAsCapableAs(r2): " + String.valueOf(r1.atLeastAsCapableAs(r2)));
- } else {
- logger.info("Don't know how to '" + argv[0] + "'");
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
deleted file mode 100644
index ce7e055..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/RuntimeEnvironmentConstraint.java
+++ /dev/null
@@ -1,160 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.util.Collection;
-import java.util.Iterator;
-
-import org.apache.log4j.Logger;
-
-
-/**
- * When use cases present a runtime environment, then they don't want to express
- * that these would provide such, but that these request such, i.e. they constrain
- * lists of potentially eligible queues.
- * @author Steffen Moeller
- * @since 2008
- */
-public class RuntimeEnvironmentConstraint extends RuntimeEnvironment {
-
- private static Logger logger = Logger.getLogger(RuntimeEnvironmentConstraint.class);
-
- private static String[] ACCEPTED_RELATIONS = new String[] {"=", ">=", "<=", ">", "<"};
- /**
- * If there is no relation specified, presume >=
- */
- private static String DEFAULT_RELATION = ">=";
-
- public static String[] getAcceptedRelations() {
- return ACCEPTED_RELATIONS;
- }
-
- public static String getDefaultRelation() {
- return DEFAULT_RELATION;
- }
-
- /**
- * Identifies the relation between runtime environments to be tested
- */
- protected String relation;
-
- /**
- * Accessor function for relation
- */
- public String getRelation() {
- return this.relation;
- }
-
- /**
- * Tests of a relation is supported
- * @param relation
- * @return true iff in <, > , <=, >=, =
- */
- public static boolean acceptedRelation(String relation) {
- if ((null == relation) || relation.equals("")) {
- return false;
- }
- return relation.equals("=")||relation.equals(">=")||relation.equals("<=")||relation.equals(">")||relation.equals("<");
- }
-
- /**
- * Constructor
- * @param id - expects the name of the runtime environment together with the version to which the
- * @param relation - relates to (">","<","=",">=","<=")
- */
- public RuntimeEnvironmentConstraint(String id, String relation) {
- super(id);
- if (null == relation || relation.equals("")) {
- relation=RuntimeEnvironmentConstraint.getDefaultRelation();
- }
- if (relation.equals("==")) {
- relation="=";
- }
- else if (relation.equals("=<")) {
- relation="<=";
- }
- else if (!RuntimeEnvironmentConstraint.acceptedRelation(relation)) {
- logger.warn("Unknown relation '"+relation+"', presuming '"+RuntimeEnvironmentConstraint.getDefaultRelation()+"'");
- relation=RuntimeEnvironmentConstraint.getDefaultRelation();
- }
- this.relation=relation;
- }
-
- /**
- * Perfoms test if the RuntimeEnvironment (RE) passed as argument fulfills the requirements set by the constraint.
- * @param re - RE to test
- * @return true iff the RE fulfills this REconstraint.
- */
- public boolean isFulfilledBy(RuntimeEnvironment re) {
- logger.info(re.getID()+" " + this.getRelation() + " "+this.getID() + " ?");
- if (this.getRelation().equals("=")) {
- logger.info("=");
- return re.getID().equals(this.getID());
- }
- if (!re.getName().equals(this.getName())) {
- logger.warn("Name match failed");
- return false;
- }
- int c = RuntimeEnvironment.compareVersions(re.getVersion(),this.getVersion());
- logger.info("c="+c);
- if (this.getRelation().equals(">")) return c>0;
- if (this.getRelation().equals(">=")) return c>=0;
- if (this.getRelation().equals("<=")) return c<=0;
- if (this.getRelation().equals("<")) return c<0;
- throw new RuntimeException("Unknown/untreated releation '"+this.getRelation()+"'");
- }
-
- /**
- * Iterates over all the RuntimeEnvironments passed as argument.
- * @param REs - list of RuntimeEnvironments, mostly those offered at a particular queue
- * @return true iff any RE among the REs passed as argument are fulfilling the constraint
- */
- public boolean isFulfilledByAtLeastOneIn(Collection<RuntimeEnvironment> REs) {
- boolean fulfilled = false;
- Iterator<RuntimeEnvironment> i = REs.iterator();
- while(i.hasNext() && !fulfilled) {
- RuntimeEnvironment r = i.next();
- fulfilled = this.isFulfilledBy(r);
- }
- return fulfilled;
- }
- /**
- * For testing purposes
- */
- public static void main(String argv[]) {
- try {
- if (argv[0].equals("--help") || argv.length != 3) {
- logger.error("Expecting arguments (<|>|=|<=|>=) runtime1-version runtime2-version");
- }
- else {
- RuntimeEnvironmentConstraint r1 = new RuntimeEnvironmentConstraint(argv[1], argv[0]);
- RuntimeEnvironment r2 = new RuntimeEnvironment(argv[2]);
- logger.info("r1.getName(): "+r1.getName());
- logger.info("r1.getVersion(): "+r1.getVersion());
- logger.info("r1.getRelation(): "+r1.getRelation());
- logger.info("r2.getName(): "+r2.getName());
- logger.info("r2.getVersion(): "+r2.getVersion());
- logger.info("r1.isFulfilledBy(r2): "+String.valueOf(r1.isFulfilledBy(r2)));
- }
- }
- catch (Exception e) {
- logger.error(e);
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
deleted file mode 100644
index 50747b5..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInput.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.nio.charset.Charset;
-
-import org.apache.taverna.activities.externaltool.ExternalToolActivity;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Integrates inputs to the grid that come from the use case descriptions
- * with those that are fed through the workflow.
- *
- * this class controls name and data storage of one input,
- * no matter where the data comes from
- */
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#AbstractScriptInput")
-public abstract class ScriptInput {
- /**
- * This input can be referenced under the name 'tag'.
- */
- private String tag = null;
- /**
- * In most cases, the data will be stored under a specific
- * filename.
- */
- private boolean file = false;
- /**
- * Set, if the name of the file to be executed is not
- * explicitly set but prepared by some automatism and referenced
- * via the tagging principle.
- */
- private boolean tempFile = false;
- /**
- * True if (!) the data is binary. (Text otherwise)
- */
- private boolean binary = false;
-
- private String charsetName = Charset.defaultCharset().name();
- private boolean forceCopy = false;
-
- /**
- * @return the tag
- */
- public final String getTag() {
- return tag;
- }
- /**
- * @param tag the tag to set
- */
- @ConfigurationProperty(name = "tag", label = "Tag")
- public final void setTag(String tag) {
- this.tag = tag;
- }
- /**
- * @return the file
- */
- public final boolean isFile() {
- return file;
- }
- /**
- * @param file the file to set
- */
- @ConfigurationProperty(name = "file", label = "File")
- public final void setFile(boolean file) {
- this.file = file;
- }
- /**
- * @return the tempFile
- */
- public final boolean isTempFile() {
- return tempFile;
- }
- /**
- * @param tempFile the tempFile to set
- */
- @ConfigurationProperty(name = "tempFile", label = "Temporary File")
- public final void setTempFile(boolean tempFile) {
- this.tempFile = tempFile;
- }
- /**
- * @return the binary
- */
- public final boolean isBinary() {
- return binary;
- }
- /**
- * @param binary the binary to set
- */
- @ConfigurationProperty(name = "binary", label = "Binary")
- public final void setBinary(boolean binary) {
- this.binary = binary;
- }
-
- public String getCharsetName() {
- return this.charsetName;
- }
- /**
- * @param charsetName the charsetName to set
- */
- @ConfigurationProperty(name = "charsetName", label = "Chararter Set")
- public void setCharsetName(String charsetName) {
- this.charsetName = charsetName;
- }
-
- @ConfigurationProperty(name = "forceCopy", label = "Force Copy")
- public final void setForceCopy(boolean forceCopy) {
- this.forceCopy = forceCopy;
-
- }
- /**
- * @return the forceCopy
- */
- public boolean isForceCopy() {
- return forceCopy;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
deleted file mode 100644
index 749e104..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputStatic.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import org.apache.taverna.activities.externaltool.ExternalToolActivity;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * This subclass of script input is used to manage static content
- * which is embedded into the use case description.
- */
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInputStatic")
-public class ScriptInputStatic extends ScriptInput {
-
- public ScriptInputStatic() {
- }
-
- private String url = null; //if this is set, load content from remote URL
- private String content = null;
-
- @Override
- public String toString() {
- return "InputStatic[tag: " +
- getTag() + (isFile() ? ", file" : "") + (isTempFile() ? ", tempfile" : "") + (isBinary() ? ", binary" : "") + ", content: " + content + "]";
- }
-
- /**
- * @return the url
- */
- public final String getUrl() {
- return url;
- }
-
- /**
- * @param url the url to set
- */
- @ConfigurationProperty(name = "url", label = "URL", required=false)
- public final void setUrl(String url) {
- this.url = url;
- }
-
- /**
- * @return the content
- */
- public final String getContent() {
- return content;
- }
-
- /**
- * @param content the content to set
- */
- @ConfigurationProperty(name = "content", label = "Content", required=false)
- public final void setContent(String content) {
- this.content = content;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
deleted file mode 100644
index 715c13e..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptInputUser.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-import java.util.ArrayList;
-
-import org.apache.taverna.activities.externaltool.ExternalToolActivity;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Internal description of output
- */
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptInput")
-public class ScriptInputUser extends ScriptInput {
-
- /**
- * This input may be fed from multiple ouputs.
- */
- private boolean list = false;
- /**
- * True if the data from a list input in taverna is concatenated into one single input file.
- */
- private boolean concatenate = false;
-
- private ArrayList<String> mime = new ArrayList<String>();
-
- @Override
- public String toString() {
- return "Input[tag: " + getTag() + (isFile() ? ", file" : "")
- + (isTempFile() ? ", tempfile" : "")
- + (isBinary() ? ", binary" : "") + (list ? ", list" : "")
- + (concatenate ? ", concatenate" : "")
- + " mime: " + mime.toString() + "]";
- }
-
- /**
- * @return the list
- */
- public final boolean isList() {
- return list;
- }
-
- /**
- * @param list the list to set
- */
- @ConfigurationProperty(name = "list", label = "List")
- public final void setList(boolean list) {
- this.list = list;
- }
-
- /**
- * @return the concatenate
- */
- public final boolean isConcatenate() {
- return concatenate;
- }
-
- /**
- * @param concatenate the concatenate to set
- */
- @ConfigurationProperty(name = "concatenate", label = "Concatenate")
- public final void setConcatenate(boolean concatenate) {
- this.concatenate = concatenate;
- }
-
- /**
- * @return the mime
- */
- public final ArrayList<String> getMime() {
- if (mime == null) {
- mime = new ArrayList<String>();
- }
- return mime;
- }
-
- /**
- * @param mime the mime to set
- */
- @ConfigurationProperty(name = "mime", label = "Mime Types", required=false)
- public final void setMime(ArrayList<String> mime) {
- this.mime = mime;
- }
-};
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
deleted file mode 100644
index d824ad4..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/ScriptOutput.java
+++ /dev/null
@@ -1,88 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-import java.util.ArrayList;
-
-import org.apache.taverna.activities.externaltool.ExternalToolActivity;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * Internal description of input
- */
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#ScriptOutput")
-public class ScriptOutput {
- private String path;
- private boolean binary;
- private ArrayList<String> mime = new ArrayList<String>();
-
- @Override
- public String toString() {
- return "Output[path: " + path + (binary ? ", binary" : "")
- + " mime: " + mime.toString() + "]";
- }
-
- /**
- * @return the path
- */
- public final String getPath() {
- return path;
- }
-
- /**
- * @param path the path to set
- */
- @ConfigurationProperty(name = "path", label = "Path")
- public final void setPath(String path) {
- this.path = path;
- }
-
- /**
- * @return the binary
- */
- public final boolean isBinary() {
- return binary;
- }
-
- /**
- * @param binary the binary to set
- */
- @ConfigurationProperty(name = "binary", label = "Binary")
- public final void setBinary(boolean binary) {
- this.binary = binary;
- }
-
- /**
- * @return the mime
- */
- public final ArrayList<String> getMime() {
- if (mime == null) {
- mime = new ArrayList<String>();
- }
- return mime;
- }
-
- /**
- * @param mime the mime to set
- */
- @ConfigurationProperty(name = "mime", label = "Mime Types", required=false)
- public final void setMime(ArrayList<String> mime) {
- this.mime = mime;
- }
-};
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
deleted file mode 100644
index 1c5914e..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseDescription.java
+++ /dev/null
@@ -1,897 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-
-import javax.swing.ImageIcon;
-
-import org.apache.taverna.activities.externaltool.ExternalToolActivity;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationBean;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty;
-import org.apache.taverna.workflowmodel.processor.config.ConfigurationProperty.OrderPolicy;
-import org.apache.taverna.workflowmodel.serialization.DeserializationException;
-import org.apache.taverna.workflowmodel.utils.Tools;
-
-import org.apache.log4j.Logger;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-import org.apache.commons.lang.StringUtils;
-
-/**
- * Class representation of XML-description of UseCases
- */
-@ConfigurationBean(uri = ExternalToolActivity.URI + "#ToolDescription")
-public class UseCaseDescription {
-
- private static Logger logger = Logger.getLogger(UseCaseDescription.class);
-
- /**
- * Identifier for the retrieval of this UseCase in the sharedRepository
- * database, respectively its XML export.
- */
- private String usecaseid = "";
- /**
- * Workflow Elements now can get a group identifier. There may be subgroups
- * divided by :
- */
- private String group = "";
- /**
- * Textual description of the use case itself. This description is very
- * short to fit on the single line that is prepared for such descriptions in
- * the Taverna workflow element list.
- */
- private String description = "";
- /**
- * What is actually executed on the shell.
- */
- private String command = "";
-
- /**
- * Accessor function of command
- *
- * @return shell-executable series of commands
- */
- public String getCommand() {
- if (null == command) {
- // FIXME: Is this possible?
- return "";
- } else {
- return command;
- }
- }
-
- /**
- * Routine that may be executed as a first check if the program is indeed
- * installed.
- */
- private String test_local = null;
-
- /**
- * URL of an icon that would help users to recognise the use case
- */
- private String icon_url = null;
-
- private int preparingTimeoutInSeconds = 20 * 60; // 20 minutes
- private int executionTimeoutInSeconds = 30 * 60; // 30 minutes
-
- private List<String> tags = new ArrayList<String>();
- private List<RuntimeEnvironmentConstraint> REs = new ArrayList<RuntimeEnvironmentConstraint>();
- private ArrayList<String> queue_preferred = new ArrayList<String>();
- private ArrayList<String> queue_deny = new ArrayList<String>();
-
- private List<ScriptInputStatic> static_inputs = new ArrayList<ScriptInputStatic>();
- private Map<String, ScriptInput> inputs = new HashMap<String, ScriptInput>();
- private Map<String, ScriptOutput> outputs = new HashMap<String, ScriptOutput>();
-
- private boolean includeStdIn = false;
- private boolean includeStdOut = true;
- private boolean includeStdErr = true;
-
- private List<Integer> validReturnCodes = new ArrayList<Integer>();
-
- /**
- * Default constructor to make xstream happy
- */
- public UseCaseDescription() {
-
- }
-
- /**
- * Constructor, for special purpose usecases.
- *
- * @param usecaseid
- */
- public UseCaseDescription(String usecaseid) {
- this.setUsecaseid(usecaseid);
- }
-
- /**
- * Constructor, expects an input stream containing the xml. for example, use
- * getClass().getClassLoader().getResourceAsStream("..") to load a usecase
- * from your program jar
- */
- public UseCaseDescription(InputStream programAsStream) throws DeserializationException {
- SAXBuilder builder = new SAXBuilder();
- Document doc;
- try {
- doc = builder.build(programAsStream);
- programAsStream.close();
- } catch (JDOMException e) {
- throw new DeserializationException("Error deserializing usecase", e);
- } catch (IOException e) {
- throw new DeserializationException("Error deserializing usecase", e);
- }
- readFromXmlElement(doc.getRootElement());
- }
-
- /**
- * Constructor, expects an XML-root to dissect.
- */
- public UseCaseDescription(Element programNode) throws DeserializationException {
- readFromXmlElement(programNode);
- }
-
-/**
- * Produce an XML description of the UseCaseDescription
- */
- public Element writeToXMLElement() {
- Element programNode = new Element("program");
- programNode.setAttribute("name", getUsecaseid());
- programNode.setAttribute("description", getDescription());
- // Always use element version of command
-// programNode.setAttribute("command", getCommand());
- Element commandNode = new Element("command");
- commandNode.addContent(getCommand());
- programNode.addContent(commandNode);
- programNode.setAttribute("timeout", Integer.toString(getExecutionTimeoutInSeconds()));
- programNode.setAttribute("preparing_timeout", Integer.toString(getPreparingTimeoutInSeconds()));
- programNode.setAttribute("includeStdIn", Boolean.toString(isIncludeStdIn()));
- programNode.setAttribute("includeStdOut", Boolean.toString(isIncludeStdOut()));
- programNode.setAttribute("includeStdErr", Boolean.toString(isIncludeStdErr()));
- for (ScriptInputStatic si : getStatic_inputs()) {
- Element staticNode = new Element("static");
- if (si.isBinary()) {
- staticNode.setAttribute("binary", "true");
- }
- if (si.isForceCopy()) {
- staticNode.setAttribute("forceCopy", "true");
- }
- if (si.isFile()) {
- Element fileNode = new Element("file");
- fileNode.setAttribute("path", si.getTag());
- staticNode.addContent(fileNode);
- } else if (si.isTempFile()) {
- Element tempfileNode = new Element("tempfile");
- tempfileNode.setAttribute("tag", si.getTag());
- staticNode.addContent(tempfileNode);
- } else {
- Element replaceNode = new Element("replace");
- replaceNode.setAttribute("tag", si.getTag());
- staticNode.addContent(replaceNode);
- }
- if (si.getUrl() != null) {
- Element contentNode = new Element("content");
- contentNode.setAttribute("url", si.getUrl());
- staticNode.addContent(contentNode);
- } else {
- Element contentNode = new Element("content");
- contentNode.addContent((String) si.getContent());
- staticNode.addContent(contentNode);
- }
- programNode.addContent(staticNode);
- }
- for (Entry<String, ScriptInput> entry : getInputs().entrySet()) {
- String name = entry.getKey();
- ScriptInputUser si = (ScriptInputUser) entry.getValue();
- Element inputNode = new Element("input");
- inputNode.setAttribute("name", name);
- if (si.isBinary()) {
- inputNode.setAttribute("binary", "true");
- }
- if (si.isForceCopy()) {
- inputNode.setAttribute("forceCopy", "true");
- }
- if (si.isConcatenate()) {
- inputNode.setAttribute("concatenate", "true");
- }
- if (si.isList()) {
- inputNode.setAttribute("list", "true");
- }
- if (si.isFile()) {
- Element fileNode = new Element("file");
- fileNode.setAttribute("path", si.getTag());
- inputNode.addContent(fileNode);
- } else if (si.isTempFile()) {
- Element tempfileNode = new Element("tempfile");
- tempfileNode.setAttribute("tag", si.getTag());
- inputNode.addContent(tempfileNode);
- } else {
- Element replaceNode = new Element("replace");
- replaceNode.setAttribute("tag", si.getTag());
- inputNode.addContent(replaceNode);
- }
- for (String mime : si.getMime()) {
- Element mimeNode = new Element("mime");
- mimeNode.setAttribute("type", mime);
- inputNode.addContent(mimeNode);
- }
- programNode.addContent(inputNode);
- }
- for (Entry<String, ScriptOutput> entry : getOutputs().entrySet()) {
- String name = entry.getKey();
- ScriptOutput so = entry.getValue();
- Element outputNode = new Element("output");
- outputNode.setAttribute("name", name);
- if (so.isBinary()) {
- outputNode.setAttribute("binary", "true");
- }
- Element fromfileNode = new Element("fromfile");
- fromfileNode.setAttribute("path", so.getPath());
- outputNode.addContent(fromfileNode);
- for (String mime : so.getMime()) {
- Element mimeNode = new Element("mime");
- mimeNode.setAttribute("type", mime);
- outputNode.addContent(mimeNode);
- }
- programNode.addContent(outputNode);
- }
- for (RuntimeEnvironmentConstraint rec : getREs()) {
- Element rteNode = new Element("rte");
- rteNode.setAttribute("name", rec.getID());
- rteNode.setAttribute("relation", rec.getRelation());
- programNode.addContent(rteNode);
- }
- if ((group != null) && !group.isEmpty()) {
- Element groupNode = new Element("group");
- groupNode.setAttribute("name", group);
- programNode.addContent(groupNode);
- }
- if ((test_local != null) && !test_local.isEmpty()) {
- Element testNode = new Element("test");
- testNode.setAttribute("local", test_local);
- programNode.addContent(testNode);
- }
- if ((icon_url != null) && !icon_url.isEmpty()) {
- Element iconNode = new Element("icon");
- iconNode.setAttribute("url", icon_url);
- programNode.addContent(iconNode);
- }
- if (!getQueue_preferred().isEmpty() || !getQueue_deny().isEmpty()) {
- Element queueNode = new Element("queue");
- for (String url : getQueue_preferred()) {
- Element preferredNode = new Element("prefer");
- preferredNode.setAttribute("url", url);
- queueNode.addContent(preferredNode);
- }
- for (String url : getQueue_deny()) {
- Element denyNode = new Element("deny");
- denyNode.setAttribute("url", url);
- queueNode.addContent(denyNode);
- }
- programNode.addContent(queueNode);
- }
- Element validReturnCodesNode = new Element("validReturnCodes");
- validReturnCodesNode.setAttribute("codes", getReturnCodesAsText());
- programNode.addContent(validReturnCodesNode);
-
- return programNode;
- }
- /**
- * Specifies the UseCaseDescription from the root of an XML description
- * which is accessible online.
- *
- * @param programNode
- * @throws DeserializationException
- */
- private void readFromXmlElement(Element programNode) throws DeserializationException {
- if (programNode.getName().compareToIgnoreCase("program") != 0)
- throw new DeserializationException("Expected <program>, read '" + programNode.getName() + "'");
-
- setUsecaseid(programNode.getAttributeValue("name"));
- setDescription(programNode.getAttributeValue("description"));
- setCommand(programNode.getAttributeValue("command"));
- String timeoutStr = programNode.getAttributeValue("timeout");
- if (timeoutStr != null)
- setExecutionTimeoutInSeconds(Integer.parseInt(timeoutStr));
- timeoutStr = programNode.getAttributeValue("preparing_timeout");
- if (timeoutStr != null)
- setPreparingTimeoutInSeconds(Integer.parseInt(timeoutStr));
-
- String includeStdInStr = programNode.getAttributeValue("includeStdIn");
- if (includeStdInStr != null && !includeStdInStr.isEmpty()) {
- setIncludeStdIn(includeStdInStr.equals("true"));
- }
-
- String includeStdOutStr = programNode.getAttributeValue("includeStdOut");
- if (includeStdOutStr != null && !includeStdOutStr.isEmpty()) {
- setIncludeStdOut(includeStdOutStr.equals("true"));
- }
-
- String includeStdErrStr = programNode.getAttributeValue("includeStdErr");
- if (includeStdErrStr != null && !includeStdErrStr.isEmpty()) {
- setIncludeStdErr(includeStdErrStr.equals("true"));
- }
-
- for (Object cur_ob : programNode.getChildren()) {
- Element cur = (Element) cur_ob;
-
- String name = cur.getAttributeValue("name");
-
- String type = cur.getName();
- boolean binary = false;
- if (null != cur.getAttributeValue("binary") && cur.getAttributeValue("binary").equalsIgnoreCase("true")) {
- binary = true;
- }
- boolean list = false;
- if (null != cur.getAttributeValue("list") && cur.getAttributeValue("list").equalsIgnoreCase("true")) {
- list = true;
- }
- boolean concatenate = false;
- if (null != cur.getAttributeValue("concatenate") && cur.getAttributeValue("concatenate").equalsIgnoreCase("true")) {
- concatenate = true;
- }
- boolean forceCopy = false;
- if (null != cur.getAttributeValue("forceCopy") && cur.getAttributeValue("forceCopy").equalsIgnoreCase("true")) {
- forceCopy = true;
- }
-
- Element inner = null;
- String innerType = null, tag = null, path = null;
- if (cur.getChildren().size() > 0) {
- inner = (Element) cur.getChildren().get(0);
- innerType = inner.getName();
- tag = inner.getAttributeValue("tag");
- path = inner.getAttributeValue("path");
- }
- // build mime type declaration list
- ArrayList<String> mime = new ArrayList<String>();
- for (Object child : cur.getChildren()) {
- Element curChild = (Element) child;
- if (curChild.getName().equalsIgnoreCase("mime")) {
- mime.add(curChild.getAttributeValue("type"));
- }
- }
- if (type.equalsIgnoreCase("static")) {
- ScriptInputStatic si = new ScriptInputStatic();
- Element content = cur.getChild("content");
- if (content == null)
- throw new DeserializationException("FIXME: script tag without embedded content tag");
- si.setUrl(content.getAttributeValue("url"));
- if (si.getUrl() == null)
- si.setContent(content.getText());
- fillInputDescription(si, binary, forceCopy, innerType, tag, path);
- getStatic_inputs().add(si);
- } else if (type.equalsIgnoreCase("input")) {
- ScriptInputUser indesc = new ScriptInputUser();
- indesc.setList(list);
- indesc.setMime(mime);
- indesc.setConcatenate(concatenate);
- fillInputDescription(indesc, binary, forceCopy, innerType, tag, path);
- getInputs().put(Tools.sanitiseName(name), indesc);
- } else if (type.equalsIgnoreCase("output")) {
- ScriptOutput outdesc = new ScriptOutput();
- outdesc.setMime(mime);
-
- boolean ok = true;
- if (null == innerType) {
- // don't know what to do
- throw new DeserializationException("FIXME: Found null == innerType for output, is this the bug?");
- } else if (innerType.equalsIgnoreCase("fromfile")) {
- outdesc.setPath(path);
- outdesc.setBinary(binary);
- } else {
- throw new DeserializationException("Problem reading output port: unknown innerType '" + innerType + "'");
- }
- if (ok) {
- getOutputs().put(Tools.sanitiseName(name), outdesc);
- }
- } else if (type.equalsIgnoreCase("rte") || type.equalsIgnoreCase("re")) {
- getREs().add(new RuntimeEnvironmentConstraint(name, cur.getAttributeValue("relation")));
- } else if (type.equalsIgnoreCase("group")) {
- group = name;
- } else if (type.equalsIgnoreCase("test")) {
- test_local = cur.getAttributeValue("local");
- } else if (type.equalsIgnoreCase("icon")) {
- icon_url = cur.getAttributeValue("url");
- } else if (type.equalsIgnoreCase("queue")) {
- for (Object child_ob : cur.getChildren()) {
- Element child = (Element) child_ob;
- if (child.getName().equalsIgnoreCase("prefer"))
- getQueue_preferred().add(child.getAttributeValue("url"));
- else if (child.getName().equalsIgnoreCase("deny"))
- getQueue_deny().add(child.getAttributeValue("url"));
- else
- throw new DeserializationException("Error while reading usecase " + this.getUsecaseid() + ": invalid queue entry");
- }
- } else if (type.equalsIgnoreCase("command")) {
- // i like to have the ability to inject complete shell script
- // fragments into the use case,
- // so this should be replace and should allow multiple lines
- if ((getCommand() != null) && !getCommand().isEmpty()) {
- throw new DeserializationException("You have specified both command attribute and command tag.");
- }
- setCommand(cur.getText());
- } else if (type.equalsIgnoreCase("validReturnCodes")) {
- String codeString = cur.getAttributeValue("codes");
- if (codeString != null) {
- setReturnCodesAsText(codeString);
- }
- }
- else {
- throw new DeserializationException("Unexpected and uninterpreted attribute " + type);
- }
- }
- }
-
- private void fillInputDescription(ScriptInput fillMe, boolean binary, boolean forceCopy, String innerType, String tag, String path) throws DeserializationException {
- fillMe.setBinary(binary);
- fillMe.setForceCopy(forceCopy);
- if (null == innerType) {
- // don't know what to do
- throw new DeserializationException("FIXME: Found null == innerType for input, is this the bug?");
- } else if (innerType.equalsIgnoreCase("replace")) {
- fillMe.setTag(tag);
- fillMe.setTempFile(false);
- fillMe.setFile(false);
- getTags().add(tag);
- } else if (innerType.equalsIgnoreCase("tempfile")) {
- fillMe.setTag(tag);
- fillMe.setTempFile(true);
- fillMe.setFile(false);
- getTags().add(tag);
- } else if (innerType.equalsIgnoreCase("file")) {
- fillMe.setTag(path);
- fillMe.setTempFile(false);
- fillMe.setFile(true);
- } else {
- throw new DeserializationException("Problem reading input port: unknown innerType '" + innerType + "'");
- }
- }
-
- /**
- * returns icon that is referenced in use case description
- */
- public ImageIcon getImageIcon() {
- if (null == icon_url) return null;
- try {
- URL u = new URL(icon_url);
- return new ImageIcon(u, getUsecaseid());
- } catch (Exception e) {
- logger.error(e);
- return null;
- }
- }
-
- /**
- * String representation of the use case. It also contains interesting
- * information on the availability of resources in the grid to actually
- * execute that workflow element.
- *
- * @return String
- */
- @Override
- public String toString() {
- List<String> hlp = new ArrayList<String>();
- hlp.add("usecaseid: " + getUsecaseid());
- hlp.add("description: " + getDescription());
- hlp.add("group: " + group);
- hlp.add("test: " + test_local);
- hlp.add("tags: " + getTags());
- for (Map.Entry<String, ScriptInput> cur : getInputs().entrySet()) {
- hlp.add(">" + cur.getKey() + ">: " + cur.getValue().toString());
- }
- for (Map.Entry<String, ScriptOutput> cur : getOutputs().entrySet()) {
- hlp.add("<" + cur.getKey() + "<: " + cur.getValue().toString());
- }
- hlp.add("RE: " + getREs().toString());
- hlp.add("preferred queues: " + getQueue_preferred());
- hlp.add("denied queues: " + getQueue_deny());
- String tos = super.toString() + "[";
- for (int i = 0; i < hlp.size(); i++) {
- if (i != 0)
- tos += ", ";
- tos += hlp.get(i);
- }
- return tos + " ]";
- }
-
- /**
- * hajo's test just pass an url or file url to an xml file
- *
- * @throws IOException
- * @throws MalformedURLException
- * @throws DeserializationException
- */
- public static void main(String[] argv) throws MalformedURLException, IOException, DeserializationException {
- UseCaseDescription d = new UseCaseDescription(new URL(argv[0]).openStream());
- logger.info(d.getCommand());
- }
-
- /**
- * @param command the command to set
- */
- @ConfigurationProperty(name = "command", label = "Command", description="What is actually executed on the shell")
- public void setCommand(String command) {
- this.command = command;
- }
-
- /**
- * @param description the description to set
- */
- @ConfigurationProperty(name = "description", label = "Description", description="Textual description of the tool", required=false, uri="http://purl.org/dc/elements/1.1/description")
- public void setDescription(String description) {
- this.description = description;
- }
-
- /**
- * @return the description
- */
- public String getDescription() {
- return description;
- }
-
- /**
- * @param executionTimeoutInSeconds the executionTimeoutInSeconds to set
- */
- @ConfigurationProperty(name = "executionTimeoutInSeconds", label = "Execution Timeout In Seconds")
- public void setExecutionTimeoutInSeconds(int executionTimeoutInSeconds) {
- this.executionTimeoutInSeconds = executionTimeoutInSeconds;
- }
-
- /**
- * @return the executionTimeoutInSeconds
- */
- public int getExecutionTimeoutInSeconds() {
- return executionTimeoutInSeconds;
- }
-
- /**
- * @param inputs the inputs to set
- */
- public void setInputs(Map<String, ScriptInput> inputs) {
- this.inputs = inputs;
- }
-
- @ConfigurationProperty(name = "inputs", label = "Inputs", required=false)
- public void setInputs(Set<InputMap> inputs) {
- if (inputs != null) {
- this.inputs = new HashMap<String, ScriptInput>();
- for (InputMap inputMap : inputs) {
- this.inputs.put(inputMap.getPort(), inputMap.getInput());
- }
- } else {
- this.inputs = null;
- }
- }
-
- /**
- * @return the inputs
- */
- public Map<String, ScriptInput> getInputs() {
- if (inputs == null) {
- inputs = new HashMap<String, ScriptInput>();
- }
- return inputs;
- }
-
- /**
- * @param outputs the outputs to set
- */
- public void setOutputs(Map<String, ScriptOutput> outputs) {
- this.outputs = outputs;
- }
-
- @ConfigurationProperty(name = "outputs", label = "Outputs", required=false)
- public void setOutputs(Set<OutputMap> outputs) {
- if (outputs != null) {
- this.outputs = new HashMap<String, ScriptOutput>();
- for (OutputMap outputMap : outputs) {
- this.outputs.put(outputMap.getPort(), outputMap.getOutput());
- }
- } else {
- this.outputs = null;
- }
- }
-
- /**
- * @return the outputs
- */
- public Map<String, ScriptOutput> getOutputs() {
- if (outputs == null) {
- outputs = new HashMap<String, ScriptOutput>();
- }
- return outputs;
- }
-
- /**
- * @param preparingTimeoutInSeconds the preparingTimeoutInSeconds to set
- */
- @ConfigurationProperty(name = "preparingTimeoutInSeconds", label = "Preparing Timeout In Seconds")
- public void setPreparingTimeoutInSeconds(int preparingTimeoutInSeconds) {
- this.preparingTimeoutInSeconds = preparingTimeoutInSeconds;
- }
-
- /**
- * @return the preparingTimeoutInSeconds
- */
- public int getPreparingTimeoutInSeconds() {
- return preparingTimeoutInSeconds;
- }
-
- /**
- * @param queue_deny the queue_deny to set
- */
- public void setQueue_deny(ArrayList<String> queue_deny) {
- this.queue_deny = queue_deny;
- }
-
- /**
- * @return the queue_deny
- */
- public ArrayList<String> getQueue_deny() {
- if (queue_deny == null) {
- queue_deny = new ArrayList<String>();
- }
- return queue_deny;
- }
-
- /**
- * @param queue_preferred the queue_preferred to set
- */
- public void setQueue_preferred(ArrayList<String> queue_preferred) {
- this.queue_preferred = queue_preferred;
- }
-
- /**
- * @return the queue_preferred
- */
- public ArrayList<String> getQueue_preferred() {
- if (queue_preferred == null) {
- queue_preferred = new ArrayList<String>();
- }
- return queue_preferred;
- }
-
- /**
- * @param rEs the rEs to set
- */
- public void setREs(List<RuntimeEnvironmentConstraint> rEs) {
- REs = rEs;
- }
-
- /**
- * @return the rEs
- */
- public List<RuntimeEnvironmentConstraint> getREs() {
- if (REs == null) {
- REs = new ArrayList<RuntimeEnvironmentConstraint>();
- }
- return REs;
- }
-
- /**
- * @param static_inputs the static_inputs to set
- */
- @ConfigurationProperty(name = "staticInputs", label = "Static Inputs", ordering=OrderPolicy.NON_ORDERED, required=false)
- public void setStatic_inputs(List<ScriptInputStatic> static_inputs) {
- this.static_inputs = static_inputs;
- }
-
- /**
- * @return the static_inputs
- */
- public List<ScriptInputStatic> getStatic_inputs() {
- if (static_inputs == null) {
- static_inputs = new ArrayList<ScriptInputStatic>();
- }
- return static_inputs;
- }
-
- /**
- * @param tags the tags to set
- */
- public void setTags(List<String> tags) {
- this.tags = tags;
- }
-
- /**
- * @return the tags
- */
- public List<String> getTags() {
- if (tags == null) {
- tags = new ArrayList<String>();
- }
- return tags;
- }
-
- /**
- * @param usecaseid the usecaseid to set
- */
- @ConfigurationProperty(name = "usecaseid", label = "Title", uri="http://purl.org/dc/elements/1.1/title", required=false)
- public void setUsecaseid(String usecaseid) {
- this.usecaseid = usecaseid;
- }
-
- /**
- * @return the usecaseid
- */
- public String getUsecaseid() {
- return usecaseid;
- }
-
- public boolean isIncludeStdIn() {
- return includeStdIn;
- }
-
- @ConfigurationProperty(name = "includeStdIn", label = "Include STDIN")
- public void setIncludeStdIn(boolean includeStdIn) {
- this.includeStdIn = includeStdIn;
- }
-
- public boolean isIncludeStdOut() {
- return includeStdOut;
- }
-
- @ConfigurationProperty(name = "includeStdOut", label = "Include STDOUT")
- public void setIncludeStdOut(boolean includeStdOut) {
- this.includeStdOut = includeStdOut;
- }
-
- public boolean isIncludeStdErr() {
- return includeStdErr;
- }
-
- @ConfigurationProperty(name = "includeStdErr", label = "Include STDERR")
- public void setIncludeStdErr(boolean includeStdErr) {
- this.includeStdErr = includeStdErr;
- }
-
- /**
- * @return the validReturnCodes
- */
- public List<Integer> getValidReturnCodes() {
- if (validReturnCodes == null) {
- validReturnCodes = new ArrayList<Integer>();
- }
- if (validReturnCodes.isEmpty()) {
- validReturnCodes.add(0);
- }
- return validReturnCodes;
- }
-
- /**
- * @param validReturnCodes the validReturnCodes to set
- */
- public void setValidReturnCodes(List<Integer> validReturnCodes) {
- this.validReturnCodes = validReturnCodes;
- }
-
- public String getReturnCodesAsText() {
- return StringUtils.join(getValidReturnCodes(), ",");
- }
-
- public void setReturnCodesAsText(String text) {
- if (getValidReturnCodes() == null) {
- validReturnCodes = new ArrayList<Integer>();
- }
- validReturnCodes.clear();
- String[] codes = text.split(",");
- for (String code : codes) {
- try {
- Integer codeInt = new Integer(code);
- if (!validReturnCodes.contains(codeInt)) {
- validReturnCodes.add(codeInt);
- }
- }
- catch (NumberFormatException e) {
- logger.error(e);
- }
- }
- if (validReturnCodes.isEmpty()) {
- validReturnCodes.add(0);
- }
- Collections.sort(validReturnCodes);
- }
-
- /**
- * @return the group
- */
- public String getGroup() {
- return group;
- }
-
- /**
- * @param group the group to set
- */
- public void setGroup(String group) {
- this.group = group;
- }
-
- /**
- * @return the icon_url
- */
- public String getIcon_url() {
- return icon_url;
- }
-
- @ConfigurationBean(uri = ExternalToolActivity.URI + "#OutputMap")
- public static class OutputMap {
- private String port;
-
- private ScriptOutput output;
-
- public String getPort() {
- return port;
- }
-
- @ConfigurationProperty(name = "port", label = "Port")
- public void setPort(String port) {
- this.port = port;
- }
-
- public ScriptOutput getOutput() {
- return output;
- }
-
- @ConfigurationProperty(name = "output", label = "Output")
- public void setOutput(ScriptOutput output) {
- this.output = output;
- }
- }
-
- @ConfigurationBean(uri = ExternalToolActivity.URI + "#InputMap")
- public static class InputMap {
- private String port;
-
- private ScriptInputUser input;
-
- public String getPort() {
- return port;
- }
-
- @ConfigurationProperty(name = "port", label = "Port")
- public void setPort(String port) {
- this.port = port;
- }
-
- public ScriptInputUser getInput() {
- return input;
- }
-
- @ConfigurationProperty(name = "input", label = "Input")
- public void setInput(ScriptInputUser input) {
- this.input = input;
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
deleted file mode 100644
index d5c5d2c..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/UseCaseEnumeration.java
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.taverna.workflowmodel.serialization.DeserializationException;
-
-import org.apache.log4j.Logger;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-public class UseCaseEnumeration {
-
- private static Logger logger = Logger.getLogger(UseCaseEnumeration.class);
-
- public static List<UseCaseDescription> readDescriptionsFromUrl(String xmlFileUrl) throws IOException {
-
- List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>();
- URLConnection con = null;
- try {
- URL url = new URL(xmlFileUrl);
-
- con = url.openConnection();
- con.setConnectTimeout(4000);
- ret = readDescriptionsFromStream(con.getInputStream());
-
- } catch (IOException ioe) {
- logger.error("Problem retrieving from " + xmlFileUrl);
- logger.error(ioe);
- throw ioe;
- }
- finally {
-
- }
-
- return ret;
-
- }
-
- public static List<UseCaseDescription> readDescriptionsFromStream(InputStream is) {
-
- List<UseCaseDescription> ret = new ArrayList<UseCaseDescription>();
-
- SAXBuilder builder = new SAXBuilder();
- Document doc = null;
- try {
- doc = builder.build(is);
- is.close();
- } catch (JDOMException e1) {
- logger.error(e1);
- return ret;
- } catch (IOException e1) {
- logger.error(e1);
- return ret;
- } finally {
- try {
- is.close();
- } catch (IOException e) {
- logger.error(e);
- }
- }
-
- Element usecases = doc.getRootElement();
- for (Object ochild : usecases.getChildren()) {
- Element child = (Element) ochild;
- if (child.getName().equalsIgnoreCase("program")) {
- try {
- ret.add(new UseCaseDescription(child));
- } catch (DeserializationException e) {
- logger.error(e);
- }
- }
- }
- return ret;
- }
-
- public static UseCaseDescription readDescriptionFromUrl(
- String repositoryUrl, String id) throws IOException {
- List<UseCaseDescription> descriptions = readDescriptionsFromUrl(repositoryUrl);
- for (UseCaseDescription usecase : descriptions) {
- if (usecase.getUsecaseid().equals(id)) {
- return usecase;
- }
- }
- return null;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
deleted file mode 100644
index e912db1..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/AskUserForPw.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation;
-
-public interface AskUserForPw {
-
- // we will try keyfile first
- public String getKeyfile();
- public String getPassphrase();
-
- // then username+password
- public String getUsername();
- public String getPassword();
-
- public void authenticationSucceeded();
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
deleted file mode 100644
index 2f4485f..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/InvocationException.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation;
-
-public class InvocationException extends Exception {
-
- /**
- *
- */
- private static final long serialVersionUID = 437316164959631591L;
-
- public InvocationException(String string) {
- super(string);
- }
-
- public InvocationException(Exception e) {
- super(e);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/1e35285b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java b/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
deleted file mode 100644
index d6b2502..0000000
--- a/taverna-external-tool-activity/src/main/java/de/uni_luebeck/inb/knowarc/usecases/invocation/UseCaseInvocation.java
+++ /dev/null
@@ -1,322 +0,0 @@
-/*
- * Licensed to the Apache Software Foundation (ASF) under one
- * or more contributor license agreements. See the NOTICE file
- * distributed with this work for additional information
- * regarding copyright ownership. The ASF licenses this file
- * to you under the Apache License, Version 2.0 (the
- * "License"); you may not use this file except in compliance
- * with the License. You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package de.uni_luebeck.inb.knowarc.usecases.invocation;
-
-import java.io.BufferedWriter;
-import java.io.ByteArrayOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.io.IOUtils;
-
-import org.apache.taverna.invocation.InvocationContext;
-import org.apache.taverna.reference.ExternalReferenceSPI;
-import org.apache.taverna.reference.Identified;
-import org.apache.taverna.reference.IdentifiedList;
-import org.apache.taverna.reference.ReferenceService;
-import org.apache.taverna.reference.ReferenceServiceException;
-import org.apache.taverna.reference.ReferenceSet;
-import org.apache.taverna.reference.T2Reference;
-import org.apache.taverna.reference.impl.external.object.InlineByteArrayReferenceBuilder;
-import org.apache.taverna.reference.impl.external.object.InlineStringReferenceBuilder;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInput;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInputStatic;
-import de.uni_luebeck.inb.knowarc.usecases.ScriptInputUser;
-import de.uni_luebeck.inb.knowarc.usecases.UseCaseDescription;
-
-/**
- * An abstraction of various forms to bring job using the software that is
- * referenced as a use case towards their execution.
- *
- * @author Hajo Nils Krabbenhoeft with some contribution by
- * @author Steffen Moeller
- */
-public abstract class UseCaseInvocation {
-
- private String runId;
-
-
- protected static String getActualOsCommand(String osCommand, String pathToOriginal,
- String targetName, String pathTarget) {
- String actualOsCommand = osCommand;
- actualOsCommand = actualOsCommand.replace("%%PATH_TO_ORIGINAL%%", pathToOriginal);
- actualOsCommand = actualOsCommand.replace("%%TARGET_NAME%%", targetName);
- actualOsCommand = actualOsCommand.replace("%%PATH_TO_TARGET%%", pathTarget);
- return actualOsCommand;
- }
-
- protected UseCaseDescription usecase;
- protected final HashMap<String, String> tags = new HashMap<String, String>();
- protected int nTempFiles = 0;
- private static int submissionID = 0;
- protected static InlineByteArrayReferenceBuilder inlineByteArrayReferenceBuilder = new InlineByteArrayReferenceBuilder();
- protected static InlineStringReferenceBuilder inlineStringReferenceBuilder = new InlineStringReferenceBuilder();
- private InvocationContext invocationContext;
- private boolean retrieveData;
-
- /*
- * get the class of the data we expect for a given input
- */
- @SuppressWarnings("unchecked")
- public Class getType(String inputName) {
- if (!usecase.getInputs().containsKey(inputName))
- return null;
- ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName);
- if (input.isList()) {
- if (input.isBinary())
- return List.class;
- else
- return List.class;
- } else {
- if (input.isBinary())
- return byte[].class;
- else
- return String.class;
- }
- }
-
- /*
- * get a list of all the input port names
- */
- public Set<String> getInputs() {
- return usecase.getInputs().keySet();
- }
-
-
- /*
- * get a id, incremented with each job. thus, this should be thread-wide
- * unique
- */
- public synchronized int getSubmissionID() {
- return submissionID++;
- }
-
- /*
- * set the data for the input port with given name
- */
- @SuppressWarnings("unchecked")
- public void setInput(String inputName, ReferenceService referenceService, T2Reference t2Reference) throws InvocationException {
- if (t2Reference == null) {
- throw new InvocationException("No input specified for " + inputName);
- }
- ScriptInputUser input = (ScriptInputUser) usecase.getInputs().get(inputName);
- if (input.isList()) {
- IdentifiedList<T2Reference> listOfReferences = (IdentifiedList<T2Reference>) referenceService
- .getListService().getList(t2Reference);
-
- if (!input.isConcatenate()) {
- // this is a list input (not concatenated)
- // so write every element to its own temporary file
- // and create a filelist file
-
- // we need to write the list elements to temporary files
- ScriptInputUser listElementTemp = new ScriptInputUser();
- listElementTemp.setBinary(input.isBinary());
- listElementTemp.setTempFile(true);
-
- String lineEndChar = "\n";
- if (!input.isFile() && !input.isTempFile()) {
- lineEndChar = " ";
- }
-
- String listFileContent = "";
- String filenamesFileContent = "";
- // create a list of all temp file names
- for (T2Reference cur : listOfReferences) {
- String tmp = setOneInput(referenceService, cur,
- listElementTemp);
- listFileContent += tmp + lineEndChar;
- int ind = tmp.lastIndexOf('/');
- if (ind == -1) {
- ind = tmp.lastIndexOf('\\');
- }
- if (ind != -1) {
- tmp = tmp.substring(ind + 1);
- }
- filenamesFileContent += tmp + lineEndChar;
- }
-
- // how do we want the listfile to be stored?
- ScriptInputUser listFile = new ScriptInputUser();
- listFile.setBinary(false); // since its a list file
- listFile.setFile(input.isFile());
- listFile.setTempFile(input.isTempFile());
- listFile.setTag(input.getTag());
- T2Reference listFileContentReference = referenceService
- .register(listFileContent, 0, true, invocationContext);
-
- tags.put(listFile.getTag(), setOneInput(referenceService,
- listFileContentReference, listFile));
-
- listFile.setTag(input.getTag() + "_NAMES");
- T2Reference filenamesFileContentReference = referenceService
- .register(filenamesFileContent, 0, true, null);
- tags.put(listFile.getTag(), setOneInput(referenceService,
- filenamesFileContentReference, listFile));
- } else {
- try {
- // first, concatenate all data
- if (input.isBinary()) {
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- BufferedWriter outputWriter = new BufferedWriter(
- new OutputStreamWriter(outputStream));
- for (T2Reference cur : listOfReferences) {
- InputStreamReader inputReader = new InputStreamReader(
- getAsStream(referenceService, cur));
- IOUtils.copyLarge(inputReader, outputWriter);
- inputReader.close();
- }
- outputWriter.close();
- T2Reference binaryReference = referenceService
- .register(outputStream.toByteArray(), 0, true,
- invocationContext);
- tags.put(input.getTag(), setOneInput(referenceService,
- binaryReference, input));
- } else {
- ByteArrayOutputStream outputStream = new ByteArrayOutputStream();
- BufferedWriter outputWriter = new BufferedWriter(
- new OutputStreamWriter(outputStream));
- for (T2Reference cur : listOfReferences) {
- InputStreamReader inputReader = new InputStreamReader(
- getAsStream(referenceService, cur));
- IOUtils.copyLarge(inputReader, outputWriter);
- outputWriter.write(" ");
- inputReader.close();
- }
- outputWriter.close();
- T2Reference binaryReference = referenceService
- .register(outputStream.toByteArray(), 0, true,
- invocationContext);
- tags.put(input.getTag(), setOneInput(referenceService,
- binaryReference, input));
- }
- } catch (IOException e) {
- throw new InvocationException(e);
- }
- }
- } else {
- tags.put(input.getTag(), setOneInput(referenceService, t2Reference,
- input));
- }
- }
-
- /*
- * submit a grid job and wait for it to finish, then get the result as
- * on-demand downloads or directly as data (in case of local execution)
- */
- public HashMap<String, Object> Submit(ReferenceService referenceService) throws InvocationException {
- submit_generate_job(referenceService);
- return submit_wait_fetch_results(referenceService);
- }
-
- /*
- * just submit the job. useful if you want to wait for it to finish later on
- *
- * Can the statics be made more static?
- */
- public void submit_generate_job(ReferenceService referenceService) throws InvocationException {
- for (ScriptInputStatic input : usecase.getStatic_inputs()) {
- T2Reference ref;
- if (input.getUrl() != null) {
- // Does this work OK with binary
- try {
- ref = referenceService.register(new URL(input.getUrl()), 0, true, null);
- } catch (ReferenceServiceException e) {
- throw new InvocationException(e);
- } catch (MalformedURLException e) {
- throw new InvocationException(e);
- }
- } else {
- ref = referenceService.register((String) input.getContent(), 0, true, null);
- }
- tags.put(input.getTag(), setOneInput(referenceService, ref, input));
-
- }
- submit_generate_job_inner();
- }
-
- protected abstract void submit_generate_job_inner() throws InvocationException;
-
- /*
- * wait for a submitted job to finish and fetch the results
- */
- public abstract HashMap<String, Object> submit_wait_fetch_results(ReferenceService referenceService) throws InvocationException;
-
- public abstract String setOneInput(ReferenceService referenceService, T2Reference t2Reference, ScriptInput input) throws InvocationException;
-
- protected InputStream getAsStream(ReferenceService referenceService, T2Reference t2Reference) {
- Identified identified = referenceService.resolveIdentifier(t2Reference, null, null);
- if (identified instanceof ReferenceSet) {
- ExternalReferenceSPI ref = ((ReferenceSet) identified).getExternalReferences().iterator().next();
- return ref.openStream(invocationContext);
- }
- return null;
- }
-
- public void setContext(InvocationContext context) {
- this.invocationContext = context;
-
- }
-
- public InvocationContext getContext() {
- return this.invocationContext;
- }
-
- public abstract void setStdIn(ReferenceService referenceService,
- T2Reference t2Reference);
-
- public abstract void rememberRun(String runId);
-
- /**
- * @return the runId
- */
- protected String getRunId() {
- return runId;
- }
-
- /**
- * @param runId the runId to set
- */
- protected void setRunId(String runId) {
- this.runId = runId;
- }
-
- /**
- * @return the retrieveData
- */
- protected boolean isRetrieveData() {
- return retrieveData;
- }
-
- /**
- * @param retrieveData the retrieveData to set
- */
- protected void setRetrieveData(boolean retrieveData) {
- this.retrieveData = retrieveData;
- }
-
-
-}
[6/6] incubator-taverna-common-activities git commit: classnames
Posted by st...@apache.org.
classnames
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/commit/4e64abd8
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/4e64abd8
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/4e64abd8
Branch: refs/heads/cwl-browse
Commit: 4e64abd8e7ad4062427ff8abfa21511523968c9a
Parents: 1e35285
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Wed May 4 00:56:19 2016 +0100
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Wed May 4 00:56:19 2016 +0100
----------------------------------------------------------------------
.../externaltool/desc/RuntimeEnvironment.java | 15 +++++++--------
1 file changed, 7 insertions(+), 8 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/4e64abd8/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
----------------------------------------------------------------------
diff --git a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
index ad58eea..97e946c 100644
--- a/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
+++ b/taverna-external-tool-activity/src/main/java/org/apache/taverna/activities/externaltool/desc/RuntimeEnvironment.java
@@ -29,15 +29,14 @@ import org.apache.log4j.Logger;
* to decide if one runtime environment is possibly compatible with another one
* for the selection of queues to commit to.
*
- * To experiment/test these functions, run the following java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 foo-1 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1 bla-2 java -cp
- * target/taverna-knowarc-processor-0.1.7.jar
- * de.uni_luebeck.janitor.ldap.RuntimeEnvironment compare bla-1.2 bla-1
+ * To experiment/test these functions, run the following:
+ * <pre>
+ * java -cp target/taverna-external-tool-activity-2.1.0-incubating-SNAPSHOT.jar org.apache.taverna.activities.externaltool.desc.RuntimeEnvironment compare bla-1 foo-1
*
- * @author Steffen Moeller
+ * java -cp target/taverna-external-tool-activity-2.1.0-incubating-SNAPSHOT.jar org.apache.taverna.activities.externaltool.desc.RuntimeEnvironment compare bla-1 bla-2
+ *
+ * java -cp target/taverna-external-tool-activity-2.1.0-incubating-SNAPSHOT.jar org.apache.taverna.activities.externaltool.desc.RuntimeEnvironment compare bla-1.2 bla-1
+ * </pre>
*/
@SuppressWarnings("unchecked")
public class RuntimeEnvironment implements Comparable {