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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/23 11:19:00 UTC
[8/8] incubator-taverna-commandline git commit: Revert "temporarily
empty repository"
Revert "temporarily empty repository"
This reverts commit d57ed128cd36e12f5cc1e3304f67bd5c10f0735c.
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/commit/53c8a6c1
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/tree/53c8a6c1
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/diff/53c8a6c1
Branch: refs/heads/master
Commit: 53c8a6c1de9f892cc516afa2919ef32322abad32
Parents: d57ed12
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Mon Feb 23 10:17:05 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Mon Feb 23 10:17:05 2015 +0000
----------------------------------------------------------------------
.gitignore | 24 +
.travis.yml | 1 +
README.md | 6 +
pom.xml | 40 ++
taverna-commandline-api/pom.xml | 12 +
.../exceptions/ArgumentsParsingException.java | 34 +
.../CommandLineMasterPasswordException.java | 34 +
.../DatabaseConfigurationException.java | 43 ++
.../exceptions/InputMismatchException.java | 61 ++
.../exceptions/InvalidOptionException.java | 30 +
.../exceptions/OpenDataflowException.java | 44 ++
.../exceptions/ReadInputException.java | 35 +
.../exceptions/SaveResultsException.java | 34 +
.../commandline/options/CommandLineOptions.java | 119 ++++
taverna-commandline-common/pom.xml | 88 +++
.../CommandLineMasterPasswordProvider.java | 184 ++++++
.../taverna/t2/commandline/CommandLineTool.java | 437 +++++++++++++
.../data/DatabaseConfigurationHandler.java | 154 +++++
.../t2/commandline/data/ErrorValueHandler.java | 72 +++
.../t2/commandline/data/InputsHandler.java | 280 ++++++++
.../t2/commandline/data/SaveResultsHandler.java | 87 +++
.../taverna-commandline-common-context-osgi.xml | 22 +
.../taverna-commandline-common-context.xml | 21 +
.../main/resources/database-defaults.properties | 11 +
.../src/main/resources/help.txt | 87 +++
.../TestDatabaseConfigurationHandler.java | 21 +
taverna-commandline-launcher/pom.xml | 83 +++
.../commandline/CommandLineOptionsImpl.java | 445 +++++++++++++
.../taverna/commandline/TavernaCommandLine.java | 143 ++++
.../src/main/resources/help.txt | 87 +++
.../TestCommandLineOptionsHandler.java | 267 ++++++++
taverna-commandline-product/pom.xml | 529 +++++++++++++++
.../main/assembly/dependencies-component.xml | 21 +
.../src/main/assembly/developer-assembly.xml | 13 +
.../src/main/assembly/nightly-assembly.xml | 15 +
.../src/main/assembly/release-assembly.xml | 15 +
.../src/main/etc/conf/log4j.properties | 14 +
.../src/main/etc/conf/logging.properties | 10 +
.../src/main/etc/conf/taverna.app.properties | 2 +
.../src/main/etc/executeworkflow.bat | 17 +
.../src/main/etc/executeworkflow.sh | 25 +
taverna-commandline-tests/pom.xml | 71 ++
.../commandline/TavernaCommandLineTest.java | 485 ++++++++++++++
.../taverna/commandline/WorkflowTestRunner.java | 70 ++
.../taverna/commandline/WorkflowTestSuite.java | 79 +++
.../biomartandembossanalysis.url | 1 +
.../biomartandembossanalysis/ignorePort | 1 +
.../biomoby_tutorial_workflow.url | 1 +
.../biomoby_tutorial_workflow/ignorePort | 1 +
.../biomoby_tutorial_workflow/inputs/id | 1 +
.../biomoby_tutorial_workflow/inputs/namespace | 1 +
.../demonstration_of_configurable_iteration.url | 1 +
.../ebi_interproscan_newservices.url | 1 +
.../ebi_interproscan_newservices/ignorePort | 1 +
.../ebi_interproscan_newservices/inputs/email | 1 +
.../inputs/sequence | 8 +
.../example_of_conditional_invocation.url | 1 +
.../inputs/condition | 1 +
.../example_of_explicit_looping.url | 1 +
.../example_of_explicit_looping/inputs/end | 1 +
.../example_of_explicit_looping/inputs/start | 1 +
.../example_of_explicit_looping/inputs/step | 1 +
...e_workflow_for_rest_and_xpath_activities.url | 1 +
.../Name_Of_Location_for_Weather_Forecast | 1 +
.../fetch_dragon_images_from_biomoby.url | 1 +
.../fetch_pdb_flatfile_from_rcsb_server.url | 1 +
.../inputs/pdbID | 1 +
.../fetch_today_s_xkcd_comic.url | 1 +
.../myexperiment/gbseq_test/gbseq_test.url | 1 +
.../myexperiment/hello_anyone/hello_anyone.url | 1 +
.../myexperiment/hello_anyone/inputs/name | 1 +
.../myexperiment/hello_world/hello_world.url | 1 +
.../pipelined_list_iteration/inputs/input | 1 +
.../pipelined_list_iteration.url | 1 +
.../retrieve_sequence_in_embl_format.url | 1 +
.../secure_rest_service_call_example.url | 1 +
.../secure_web_service_call_example.url | 1 +
.../spreadsheed_data_import_example.url | 1 +
.../unix_external_tools_with_zip_and_unzip.url | 1 +
.../unix_numerically_adding_two_values/inputs/a | 1 +
.../unix_numerically_adding_two_values/inputs/b | 1 +
.../unix_numerically_adding_two_values.url | 1 +
...ix_tool_service_using_string_replacement.url | 1 +
.../src/test/resources/security/t2keystore.ubr | Bin 0 -> 3312 bytes
.../test/resources/security/t2truststore.ubr | Bin 0 -> 213408 bytes
.../resources/security/taverna-keystore.ubr | Bin 0 -> 3312 bytes
.../resources/security/taverna-truststore.ubr | Bin 0 -> 213408 bytes
.../workflows/apiconsumer/apiconsumer.t2flow | 178 +++++
.../resources/workflows/apiconsumer/inputs/in | 1 +
.../workflows/beanshell/beanshell.t2flow | 137 ++++
.../resources/workflows/beanshell/inputs/in | 1 +
.../resources/workflows/biomart/biomart.t2flow | 30 +
.../workflows/dataflow/dataflow.t2flow | 217 +++++++
.../test/resources/workflows/dataflow/inputs/in | 1 +
.../resources/workflows/in-out/in-out.t2flow | 12 +
.../test/resources/workflows/in-out/inputs/in | 1 +
.../resources/workflows/iteration/inputs/in | 1 +
.../workflows/iteration/iteration.t2flow | 474 ++++++++++++++
.../resources/workflows/localworker/inputs/in | 1 +
.../workflows/localworker/localworker.t2flow | 67 ++
.../test/resources/workflows/rest/rest.t2flow | 154 +++++
.../secure-basic-authentication-https.t2flow | 74 +++
.../secure-basic-authentication.t2flow | 74 +++
...cure-client-cert-authentication-https.t2flow | 162 +++++
.../secure-digest-authentication-https.t2flow | 107 +++
.../secure-digest-authentication.t2flow | 129 ++++
.../secure-ws-https/secure-ws-https.t2flow | 180 ++++++
.../workflows/secure-ws/secure-ws.t2flow | 180 ++++++
.../workflows/secure-wsdl/secure-wsdl.t2flow | 131 ++++
.../resources/workflows/soaplab/soaplab.t2flow | 84 +++
.../spreadsheetimport/spreadsheetimport.t2flow | 646 +++++++++++++++++++
.../stringconstant/stringconstant.t2flow | 32 +
.../test/resources/workflows/tool/tool.t2flow | 158 +++++
.../test/resources/workflows/wsdl/wsdl.t2flow | 22 +
.../resources/workflows/xmlSplitter/inputs/age | 1 +
.../workflows/xmlSplitter/inputs/firstName | 1 +
.../workflows/xmlSplitter/inputs/lastName | 1 +
.../workflows/xmlSplitter/xmlSplitter.t2flow | 339 ++++++++++
.../test/resources/workflows/xpath/xpath.t2flow | 127 ++++
119 files changed, 8140 insertions(+)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/.gitignore
----------------------------------------------------------------------
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..ebe0e5b
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,24 @@
+# ignore project files #
+.classpath
+.project
+.settings/
+catalog-v001.xml
+
+# ignore target files #
+target/
+bin/
+build/
+dist/
+apidoc/
+*.swp
+
+# ignore svn files if there
+.svn
+
+# ignore log files #
+*.log
+/logs/*
+*/logs/*
+
+
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/.travis.yml
----------------------------------------------------------------------
diff --git a/.travis.yml b/.travis.yml
new file mode 100644
index 0000000..dff5f3a
--- /dev/null
+++ b/.travis.yml
@@ -0,0 +1 @@
+language: java
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/README.md
----------------------------------------------------------------------
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..bcd653c
--- /dev/null
+++ b/README.md
@@ -0,0 +1,6 @@
+# Apache Taverna Commandline
+
+[](https://travis-ci.org/taverna-incubator/incubator-taverna-commandline)
+
+After building, see taverna-commandline-product/target/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT-dev/apache-taverna-commandline-3.1.0-incubating-SNAPSHOT/ or equivalent
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
new file mode 100644
index 0000000..0355623
--- /dev/null
+++ b/pom.xml
@@ -0,0 +1,40 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>1-incubating-SNAPSHOT</version>
+ </parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ <packaging>pom</packaging>
+ <name>Apache Taverna Command Line</name>
+ <properties>
+ <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
+ <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
+ <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
+ <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
+ </properties>
+ <modules>
+ <module>taverna-commandline-api</module>
+ <module>taverna-commandline-common</module>
+ <module>taverna-commandline-launcher</module>
+ <module>taverna-commandline-product</module>
+ <!--
+ <module>taverna-commandline-tests</module>
+ -->
+ </modules>
+ <repositories>
+ <repository>
+ <id>taverna-incubating</id>
+ <name>Apache Taverna incubating Repository</name>
+ <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ </repository>
+ </repositories>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/pom.xml b/taverna-commandline-api/pom.xml
new file mode 100644
index 0000000..98ae247
--- /dev/null
+++ b/taverna-commandline-api/pom.xml
@@ -0,0 +1,12 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <packaging>bundle</packaging>
+ <artifactId>taverna-commandline-api</artifactId>
+ <name>Apache Taverna Commandline API</name>
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
new file mode 100644
index 0000000..eb21cd7
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ArgumentsParsingException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+@SuppressWarnings("serial")
+public class ArgumentsParsingException extends Exception {
+
+ public ArgumentsParsingException(String message) {
+ super(message);
+ }
+
+ public ArgumentsParsingException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
new file mode 100644
index 0000000..0714275
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/CommandLineMasterPasswordException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+@SuppressWarnings("serial")
+public class CommandLineMasterPasswordException extends Exception {
+
+ public CommandLineMasterPasswordException(String message) {
+ super(message);
+ }
+
+ public CommandLineMasterPasswordException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
new file mode 100644
index 0000000..616fb70
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/DatabaseConfigurationException.java
@@ -0,0 +1,43 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+public class DatabaseConfigurationException extends Exception {
+
+ private static final long serialVersionUID = -4128248547532355697L;
+
+ public DatabaseConfigurationException() {
+
+ }
+
+ public DatabaseConfigurationException(String message) {
+ super(message);
+ }
+
+ public DatabaseConfigurationException(Throwable cause) {
+ super(cause);
+ }
+
+ public DatabaseConfigurationException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
new file mode 100644
index 0000000..da03891
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InputMismatchException.java
@@ -0,0 +1,61 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+import java.util.Set;
+
+public class InputMismatchException extends InvalidOptionException {
+
+ private static final long serialVersionUID = -5368068332397293706L;
+ private final Set<String> expectedInputNames;
+ private final Set<String> providedInputNames;
+
+ public InputMismatchException(String msg, Set<String> expectedInputNames, Set<String> providedInputNames) {
+ super(msg);
+ this.expectedInputNames = expectedInputNames;
+ this.providedInputNames = providedInputNames;
+ }
+
+ public String getMessage() {
+ String result = super.getMessage();
+
+ if (expectedInputNames != null){
+ result += "\n" + expectedInputNames.size() + " inputs were expected";
+ if (expectedInputNames.size()>0) result += " which are:\n";
+ for (String name : expectedInputNames) {
+ result += "'"+name+"' ";
+ }
+ }
+
+ if (providedInputNames != null){
+ result += "\n" + providedInputNames.size()
+ + " inputs were provided";
+ if (providedInputNames.size() > 0)
+ result += " which are:\n";
+ for (String name : providedInputNames) {
+ result += "'" + name + "' ";
+ }
+ }
+ return result;
+ }
+
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
new file mode 100644
index 0000000..c07a19f
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/InvalidOptionException.java
@@ -0,0 +1,30 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+public class InvalidOptionException extends Exception {
+
+ private static final long serialVersionUID = 2467409785164223258L;
+
+ public InvalidOptionException(String message) {
+ super(message);
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
new file mode 100644
index 0000000..664ab71
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/OpenDataflowException.java
@@ -0,0 +1,44 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+public class OpenDataflowException extends Exception {
+
+
+ private static final long serialVersionUID = 4778578311101082197L;
+
+ public OpenDataflowException() {
+
+ }
+
+ public OpenDataflowException(String message) {
+ super(message);
+ }
+
+ public OpenDataflowException(Throwable cause) {
+ super(cause);
+ }
+
+ public OpenDataflowException(String message, Throwable cause) {
+ super(message, cause);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
new file mode 100644
index 0000000..226d6ea
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/ReadInputException.java
@@ -0,0 +1,35 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+public class ReadInputException extends Exception {
+
+ private static final long serialVersionUID = -3494432791254643055L;
+
+ public ReadInputException(String msg) {
+ super(msg);
+ }
+
+ public ReadInputException(String msg, Throwable e) {
+ super(msg,e);
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
new file mode 100644
index 0000000..7ad460d
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/exceptions/SaveResultsException.java
@@ -0,0 +1,34 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.exceptions;
+
+@SuppressWarnings("serial")
+public class SaveResultsException extends Exception {
+
+ public SaveResultsException(String message) {
+ super(message);
+ }
+
+ public SaveResultsException(String message, Throwable cause) {
+ super(message, cause);
+ }
+}
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
new file mode 100644
index 0000000..dd8e20f
--- /dev/null
+++ b/taverna-commandline-api/src/main/java/net/sf/taverna/t2/commandline/options/CommandLineOptions.java
@@ -0,0 +1,119 @@
+/*******************************************************************************
+ * Copyright (C) 2013 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.options;
+
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+
+/**
+ *
+ *
+ * @author David Withers
+ */
+public interface CommandLineOptions {
+
+ public static final String CREDENTIAL_MANAGER_DIR_OPTION = "cmdir";
+ public static final String CREDENTIAL_MANAGER_PASSWORD_OPTION = "cmpassword";
+
+ public boolean askedForHelp();
+
+ public boolean isProvenanceEnabled();
+
+ public void displayHelp();
+
+ public void displayHelp(boolean showFullText);
+
+ public String[] getArgs();
+
+ /**
+ *
+ * @return the port that the database should run on
+ */
+ public String getDatabasePort();
+
+ /**
+ *
+ * @return a path to a properties file that contains database configuration
+ * settings
+ */
+ public String getDatabaseProperties();
+
+ /**
+ * Returns an array that alternates between a portname and path to a file
+ * containing the input values. Therefore the array will always contain an
+ * even number of elements
+ *
+ * @return an array of portname and path to files containing individual
+ * inputs.
+ */
+ public String[] getInputFiles();
+
+ public String[] getInputValues();
+
+ public String getLogFile();
+
+ /**
+ *
+ * @return the directory to write the results to
+ */
+ public String getOutputDirectory();
+
+ public boolean getStartDatabase();
+
+ /**
+ * @return the directory with Credential Manager's files
+ */
+ public String getCredentialManagerDir();
+
+ public boolean getStartDatabaseOnly() throws InvalidOptionException;
+
+ public String getWorkflow() throws InvalidOptionException;
+
+ public boolean hasDelimiterFor(String inputName);
+
+ public boolean hasInputFiles();
+
+ public boolean hasInputValues();
+
+ public boolean hasLogFile();
+
+ public boolean hasOption(String option);
+
+ public boolean hasSaveResultsToBundle() ;
+
+ public String inputDelimiter(String inputName);
+
+ public boolean isClientServer();
+
+ public boolean isEmbedded();
+
+ public boolean isInMemory();
+
+ /**
+ * Save the results to a directory if -outputdir has been explicitly defined,
+ * or if -outputdoc has not been defined.
+ *
+ * @return boolean
+ */
+ public boolean saveResultsToDirectory();
+
+ public String saveResultsToBundle();
+
+}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/pom.xml b/taverna-commandline-common/pom.xml
new file mode 100644
index 0000000..17c6a42
--- /dev/null
+++ b/taverna-commandline-common/pom.xml
@@ -0,0 +1,88 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>org.apache.taverna.commandline</groupId>
+ <artifactId>taverna-commandline</artifactId>
+ <version>3.1.0.incubating-SNAPSHOT</version>
+ </parent>
+ <artifactId>taverna-commandline-common</artifactId>
+ <packaging>bundle</packaging>
+ <name>Apache Taverna Commandline Common</name>
+ <dependencies>
+ <dependency>
+ <groupId>${project.parent.groupId}</groupId>
+ <artifactId>taverna-commandline-api</artifactId>
+ <version>${project.parent.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-run-api</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-database-configuration-api</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-api</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-structural</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-scufl2-validation-correctness</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.taverna.language</groupId>
+ <artifactId>taverna-databundle</artifactId>
+ <version>${taverna.language.version}</version>
+ </dependency>
+
+<!--
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>provenanceconnector</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+ -->
+ <dependency>
+ <groupId>org.apache.taverna.engine</groupId>
+ <artifactId>taverna-credential-manager</artifactId>
+ <version>${taverna.engine.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>commons-io</groupId>
+ <artifactId>commons-io</artifactId>
+ <version>${commons.io.version}</version>
+ </dependency>
+
+ <!-- <dependency> <groupId>uk.org.mygrid.resources.mimeutil</groupId> <artifactId>mime-util</artifactId>
+ <version>2.1.2-2</version> </dependency> -->
+
+ <!-- TEST -->
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+
+ </dependencies>
+
+</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
new file mode 100644
index 0000000..048e582
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineMasterPasswordProvider.java
@@ -0,0 +1,184 @@
+/*******************************************************************************
+ * Copyright (C) 2008-2010 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline;
+
+import java.io.BufferedReader;
+import java.io.Console;
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+
+import net.sf.taverna.t2.commandline.exceptions.CommandLineMasterPasswordException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+import net.sf.taverna.t2.security.credentialmanager.MasterPasswordProvider;
+
+import org.apache.log4j.Logger;
+
+/**
+ * An implementation of {@link MasterPasswordProvider} that reads Credential Manager's
+ * master password from stdin (pipe or terminal) is -cmpassword option is present in command
+ * line arguments. Otherwise it tries to read it from a special file password.txt in a special
+ * directory specified by -cmdir option, if present.
+ *
+ * @author Alex Nenadic
+ */
+public class CommandLineMasterPasswordProvider implements MasterPasswordProvider {
+
+ private static final String CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION = "cmpassword";
+ private static final String CREDENTIAL_MANAGER_DIRECTORY_OPTION = "cmdir";
+
+ private static Logger logger = Logger.getLogger(CommandLineMasterPasswordProvider.class);
+
+ private String masterPassword = null;
+ private int priority = 200;
+
+ private boolean finishedReadingPassword = false;
+ private final CommandLineOptions commandLineOptions;
+
+ public CommandLineMasterPasswordProvider(CommandLineOptions commandLineOptions) {
+ this.commandLineOptions = commandLineOptions;
+ }
+
+ @Override
+ public String getMasterPassword(boolean firstTime) {
+ if (!finishedReadingPassword) {
+ // -cmpassword option was present in the command line arguments
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_MASTER_PASSWORD_OPTION)) {
+ // Try to read the password from stdin (terminal or pipe)
+ try {
+ masterPassword = getCredentialManagerPasswordFromStdin();
+ } catch (CommandLineMasterPasswordException e) {
+ masterPassword = null;
+ }
+ }
+ // -cmpassword option was not present in the command line arguments
+ // and -cmdir option was there - try to get the master password from
+ // the "special" password file password.txt inside the Cred. Manager directory.
+ else {
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
+ // Try to read the password from a special file located in
+ // Credential Manager directory (if the dir was not null)
+ try {
+ masterPassword = getCredentialManagerPasswordFromFile();
+ } catch (CommandLineMasterPasswordException ex) {
+ masterPassword = null;
+ }
+ }
+ }
+ finishedReadingPassword = true; // we do not want to attempt to read from stdin several
+ // times
+ }
+ return masterPassword;
+ }
+
+ public void setMasterPassword(String masterPassword) {
+ this.masterPassword = masterPassword;
+ finishedReadingPassword = true;
+ }
+
+ @Override
+ public int getProviderPriority() {
+ return priority;
+ }
+
+ private String getCredentialManagerPasswordFromStdin()
+ throws CommandLineMasterPasswordException {
+
+ String password = null;
+
+ Console console = System.console();
+
+ if (console == null) { // password is being piped in, not entered in the terminal by user
+ BufferedReader buffReader = null;
+ try {
+ buffReader = new BufferedReader(new InputStreamReader(System.in));
+ password = buffReader.readLine();
+ } catch (IOException ex) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error(
+ "An error occured while trying to read Credential Manager's password that was piped in: "
+ + ex.getMessage(), ex);
+ throw new CommandLineMasterPasswordException(
+ "An error occured while trying to read Credential Manager's password that was piped in: "
+ + ex.getMessage(), ex);
+ } finally {
+ try {
+ buffReader.close();
+ } catch (Exception ioe1) {
+ // Ignore
+ }
+ }
+ } else { // read the password from the terminal as entered by the user
+ try {
+ // Block until user enters password
+ char passwordArray[] = console.readPassword("Password for Credential Manager: ");
+ if (passwordArray != null) { // user did not abort input
+ password = new String(passwordArray);
+ } // else password will be null
+
+ } catch (Exception ex) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error(
+ "An error occured while trying to read Credential Manager's password from the terminal: "
+ + ex.getMessage(), ex);
+ throw new CommandLineMasterPasswordException(
+ "An error occured while trying to read Credential Manager's password from the terminal: "
+ + ex.getMessage(), ex);
+ }
+ }
+ return password;
+ }
+
+ private String getCredentialManagerPasswordFromFile() throws CommandLineMasterPasswordException {
+ String password = null;
+ if (commandLineOptions.hasOption(CREDENTIAL_MANAGER_DIRECTORY_OPTION)) {
+ String cmDir = commandLineOptions.getCredentialManagerDir();
+
+ File passwordFile = new File(cmDir, "password.txt");
+ BufferedReader buffReader = null;
+ try {
+ buffReader = new BufferedReader(new FileReader(passwordFile));
+ password = buffReader.readLine();
+ } catch (IOException ioe) {
+ // For some reason the error of the exception thrown
+ // does not get printed from the Launcher so print it here as
+ // well as it gives more clue as to what is going wrong.
+ logger.error("There was an error reading the Credential Manager password from "
+ + passwordFile.toString() + ": " + ioe.getMessage(), ioe);
+ throw new CommandLineMasterPasswordException(
+ "There was an error reading the Credential Manager password from "
+ + passwordFile.toString() + ": " + ioe.getMessage(), ioe);
+ } finally {
+ try {
+ buffReader.close();
+ } catch (Exception ioe1) {
+ // Ignore
+ }
+ }
+ }
+ return password;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
new file mode 100644
index 0000000..368527d
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/CommandLineTool.java
@@ -0,0 +1,437 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Set;
+
+import javax.naming.NamingException;
+
+import net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler;
+import net.sf.taverna.t2.commandline.data.InputsHandler;
+import net.sf.taverna.t2.commandline.data.SaveResultsHandler;
+import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
+import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.exceptions.OpenDataflowException;
+import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+import net.sf.taverna.t2.security.credentialmanager.CMException;
+import net.sf.taverna.t2.security.credentialmanager.CredentialManager;
+
+import org.apache.log4j.Level;
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+import org.apache.log4j.PropertyConfigurator;
+import org.apache.log4j.RollingFileAppender;
+import org.purl.wf4ever.robundle.Bundle;
+
+import uk.org.taverna.configuration.database.DatabaseConfiguration;
+import uk.org.taverna.configuration.database.DatabaseManager;
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.platform.execution.api.ExecutionEnvironment;
+import uk.org.taverna.platform.execution.api.InvalidExecutionIdException;
+import uk.org.taverna.platform.execution.api.InvalidWorkflowException;
+import uk.org.taverna.platform.report.State;
+import uk.org.taverna.platform.report.WorkflowReport;
+import uk.org.taverna.platform.run.api.InvalidRunIdException;
+import uk.org.taverna.platform.run.api.RunProfile;
+import uk.org.taverna.platform.run.api.RunProfileException;
+import uk.org.taverna.platform.run.api.RunService;
+import uk.org.taverna.platform.run.api.RunStateException;
+import uk.org.taverna.scufl2.api.common.NamedSet;
+import uk.org.taverna.scufl2.api.container.WorkflowBundle;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.io.ReaderException;
+import uk.org.taverna.scufl2.api.io.WorkflowBundleIO;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+import uk.org.taverna.scufl2.api.port.OutputWorkflowPort;
+import uk.org.taverna.scufl2.validation.ValidationException;
+import uk.org.taverna.scufl2.validation.correctness.CorrectnessValidator;
+import uk.org.taverna.scufl2.validation.correctness.ReportCorrectnessValidationListener;
+import uk.org.taverna.scufl2.validation.structural.ReportStructuralValidationListener;
+import uk.org.taverna.scufl2.validation.structural.StructuralValidator;
+
+/**
+ * A utility class that wraps the process of executing a workflow, allowing workflows to be easily
+ * executed independently of the GUI.
+ *
+ * @author Stuart Owen
+ * @author Alex Nenadic
+ */
+public class CommandLineTool {
+ private static boolean BOOTSTRAP_LOGGING = false;
+ private static Logger logger = Logger.getLogger(CommandLineTool.class);
+
+ private RunService runService;
+ private CredentialManager credentialManager;
+ private CommandLineOptions commandLineOptions;
+ private WorkflowBundle workflowBundle;
+ private WorkflowBundleIO workflowBundleIO;
+ private DatabaseConfiguration databaseConfiguration;
+ private DatabaseManager databaseManager;
+
+ public void run() {
+ try {
+ if (BOOTSTRAP_LOGGING)
+ initialiseLogging();
+ int result = setupAndExecute();
+ System.exit(result);
+ } catch (InvalidOptionException | IOException | ReadInputException
+ | InvalidRunIdException | RunStateException
+ | InvalidExecutionIdException | OpenDataflowException
+ | RunProfileException e) {
+ error(e.getMessage());
+ } catch (CMException e) {
+ error("There was an error initializing Taverna's SSLSocketFactory from Credential Manager. "
+ + e.getMessage());
+ } catch (ReaderException e) {
+ error("There was an error reading the workflow: " + e.getMessage());
+ } catch (ValidationException e) {
+ error("There was an error validating the workflow: " + e.getMessage());
+ } catch (InvalidWorkflowException e) {
+ error("There was an error validating the workflow: " + e.getMessage());
+ } catch (DatabaseConfigurationException e) {
+ error("There was an error configuring the database: " + e.getMessage());
+ }
+ System.exit(1);
+ }
+
+ private void initialiseLogging() {
+ LogManager.resetConfiguration();
+
+ if (System.getProperty("log4j.configuration") == null) {
+ try {
+ PropertyConfigurator.configure(CommandLineTool.class.getClassLoader()
+ .getResource("cl-log4j.properties").toURI().toURL());
+ } catch (MalformedURLException e) {
+ logger.error("There was a serious error reading the default logging configuration",
+ e);
+ } catch (URISyntaxException e) {
+ logger.error("There was a serious error reading the default logging configuration",
+ e);
+ }
+
+ } else {
+ PropertyConfigurator.configure(System.getProperty("log4j.configuration"));
+ }
+
+ if (commandLineOptions.hasLogFile()) {
+ RollingFileAppender appender;
+ try {
+
+ PatternLayout layout = new PatternLayout("%-5p %d{ISO8601} (%c:%L) - %m%n");
+ appender = new RollingFileAppender(layout, commandLineOptions.getLogFile());
+ appender.setMaxFileSize("1MB");
+ appender.setEncoding("UTF-8");
+ appender.setMaxBackupIndex(4);
+ // Let root logger decide level
+ appender.setThreshold(Level.ALL);
+ LogManager.getRootLogger().addAppender(appender);
+ } catch (IOException e) {
+ System.err.println("Could not log to " + commandLineOptions.getLogFile());
+ }
+ }
+ }
+
+ public int setupAndExecute() throws InputMismatchException, InvalidOptionException,
+ CMException, OpenDataflowException, ReaderException, IOException, ValidationException,
+ ReadInputException, InvalidWorkflowException, RunProfileException,
+ InvalidRunIdException, RunStateException, InvalidExecutionIdException, DatabaseConfigurationException {
+
+ if (!commandLineOptions.askedForHelp()) {
+ setupDatabase(commandLineOptions);
+
+ if (commandLineOptions.getWorkflow() != null) {
+
+ /* Set context class loader to us,
+ * so that things such as JSON-LD caching of
+ * robundle works.
+ */
+
+ Thread.currentThread().setContextClassLoader(getClass().getClassLoader());
+
+
+ /*
+ * Initialise Credential Manager and SSL stuff quite early as
+ * parsing and validating the workflow may require it
+ */
+ String credentialManagerDirPath = commandLineOptions.getCredentialManagerDir();
+
+ /*
+ * If credentialManagerDirPath is null, the Credential Manager
+ * will be initialized from the default location in
+ * <TAVERNA_HOME>/security somewhere inside user's home
+ * directory. This should not be used when running command line
+ * tool on a server and the Credential Manager dir path should
+ * always be passed in as we do not want to store the security
+ * files in user's home directory on the server (we do not even
+ * know which user the command line tool will be running as).
+ */
+ if (credentialManagerDirPath != null) {
+ credentialManager.setConfigurationDirectoryPath(new File(
+ credentialManagerDirPath));
+ }
+
+ // Initialise the SSL stuff - set the SSLSocketFactory
+ // to use Taverna's Keystore and Truststore.
+ credentialManager.initializeSSL();
+
+ URL workflowURL = readWorkflowURL(commandLineOptions.getWorkflow());
+
+ workflowBundle = workflowBundleIO.readBundle(workflowURL, null);
+
+ logger.debug("Read the wf bundle");
+
+ validateWorkflowBundle(workflowBundle);
+ logger.debug("Validated the wf bundle");
+
+
+ Set<ExecutionEnvironment> executionEnvironments = runService
+ .getExecutionEnvironments();
+
+ ExecutionEnvironment executionEnvironment = null;
+
+ /*
+ * Find the right execution environment, e.g. local execution
+ * with the correct reference service based on command line
+ * options
+ */
+ while (executionEnvironments.iterator().hasNext()) {
+ // TODO Choose the right one
+ // take the fist one for now
+ executionEnvironment = executionEnvironments.iterator().next();
+ break;
+ }
+
+ logger.debug("Got the execution environment");
+
+ InputsHandler inputsHandler = new InputsHandler();
+ Map<String, InputWorkflowPort> portMap = new HashMap<String, InputWorkflowPort>();
+
+ Workflow workflow = workflowBundle.getMainWorkflow();
+
+ for (InputWorkflowPort port : workflow.getInputPorts()) {
+ portMap.put(port.getName(), port);
+ }
+ inputsHandler.checkProvidedInputs(portMap, commandLineOptions);
+ logger.debug("Checked inputs");
+
+ Bundle inputs = inputsHandler.registerInputs(portMap, commandLineOptions, null);
+ logger.debug("Registered inputs");
+
+ RunProfile runProfile = new RunProfile(executionEnvironment, workflowBundle, inputs);
+
+ String runId = runService.createRun(runProfile);
+
+ runService.start(runId);
+ logger.debug("Started wf run");
+
+ WorkflowReport report = runService.getWorkflowReport(runId);
+
+ while (!workflowFinished(report)) {
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException e) {
+ System.err.println("Interrupted while waiting for workflow to finish");
+ return 1;
+ }
+ }
+
+ NamedSet<OutputWorkflowPort> workflowOutputPorts = workflow.getOutputPorts();
+ if (!workflowOutputPorts.isEmpty()) {
+ File outputDir = null;
+
+ if (commandLineOptions.saveResultsToDirectory()) {
+ outputDir = determineOutputDir(commandLineOptions, workflowBundle.getName());
+ outputDir.mkdirs();
+ }
+
+ Path outputs = DataBundles.getOutputs(runService.getDataBundle(runId));
+
+ if (outputDir != null) {
+ SaveResultsHandler saveResultsHandler = new SaveResultsHandler(outputDir);
+
+ for (OutputWorkflowPort outputWorkflowPort : workflowOutputPorts) {
+ String workflowOutputPortName = outputWorkflowPort.getName();
+ Path output = DataBundles.getPort(outputs, workflowOutputPortName);
+ if (!DataBundles.isMissing(output)) {
+ saveResultsHandler.saveResultsForPort(workflowOutputPortName, output);
+ }
+ }
+ }
+ }
+ if (commandLineOptions.saveResultsToBundle() != null) {
+ Path bundlePath = Paths.get(commandLineOptions.saveResultsToBundle());
+ DataBundles.closeAndSaveBundle(runService.getDataBundle(runId), bundlePath);
+ System.out.println("Workflow Run Bundle saved to: " + bundlePath.toAbsolutePath());
+ } else {
+ System.out.println("Workflow Run Bundle: " + runService.getDataBundle(runId).getSource());
+ // For debugging we'll leave it in /tmp for now
+ runService.getDataBundle(runId).setDeleteOnClose(false);
+ DataBundles.closeBundle(runService.getDataBundle(runId));
+ }
+
+ if (report.getState().equals(State.FAILED)) {
+ System.out.println("Workflow failed - see report below.");
+ System.out.println(report);
+ } else if (report.getState().equals(State.COMPLETED)) {
+ System.out.println("Workflow completed.");
+ }
+
+ }
+ } else {
+ commandLineOptions.displayHelp();
+ }
+
+ // wait until user hits CTRL-C before exiting
+ if (commandLineOptions.getStartDatabaseOnly()) {
+ // FIXME: need to do this more gracefully.
+ while (true) {
+ try {
+ Thread.sleep(500);
+ } catch (InterruptedException e) {
+ return 0;
+ }
+ }
+ }
+
+ return 0;
+ }
+
+ private boolean workflowFinished(WorkflowReport report) {
+ State state = report.getState();
+ if (state == State.CANCELLED || state == State.COMPLETED || state == State.FAILED) {
+ return true;
+ }
+ return false;
+ }
+
+ protected void validateWorkflowBundle(WorkflowBundle workflowBundle) throws ValidationException {
+ CorrectnessValidator cv = new CorrectnessValidator();
+ ReportCorrectnessValidationListener rcvl = new ReportCorrectnessValidationListener();
+ cv.checkCorrectness(workflowBundle, true, rcvl);
+ if (rcvl.detectedProblems()) {
+ throw rcvl.getException();
+ }
+
+ StructuralValidator sv = new StructuralValidator();
+ ReportStructuralValidationListener rsvl = new ReportStructuralValidationListener();
+ sv.checkStructure(workflowBundle, rsvl);
+ if (rsvl.detectedProblems()) {
+ throw rcvl.getException();
+ }
+ }
+
+ private void setupDatabase(CommandLineOptions options)
+ throws DatabaseConfigurationException {
+ DatabaseConfigurationHandler dbHandler = new DatabaseConfigurationHandler(
+ options, databaseConfiguration, databaseManager);
+ dbHandler.configureDatabase();
+ try {
+ if (!options.isInMemory())
+ dbHandler.testDatabaseConnection();
+ } catch (NamingException e) {
+ throw new DatabaseConfigurationException(
+ "There was an error trying to setup the database datasource: "
+ + e.getMessage(), e);
+ } catch (SQLException e) {
+ if (options.isClientServer())
+ throw new DatabaseConfigurationException(
+ "There was an error whilst making a test database connection. If running with -clientserver you should check that a server is running (check -startdb or -dbproperties)",
+ e);
+ if (options.isEmbedded())
+ throw new DatabaseConfigurationException(
+ "There was an error whilst making a test database connection. If running with -embedded you should make sure that another process isn't using the database, or a server running through -startdb",
+ e);
+ }
+ }
+
+ private File determineOutputDir(CommandLineOptions options, String dataflowName) {
+ File result = new File(dataflowName + "_output");
+ int x = 1;
+ while (result.exists()) {
+ result = new File(dataflowName + "_output_" + x);
+ x++;
+ }
+ System.out.println("Outputs will be saved to the directory: "
+ + result.getAbsolutePath());
+ return result;
+ }
+
+ protected void error(String msg) {
+ System.err.println(msg);
+ }
+
+ private URL readWorkflowURL(String workflowOption) throws OpenDataflowException {
+ try {
+ return new URL(new URL("file:"), workflowOption);
+ } catch (MalformedURLException e) {
+ throw new OpenDataflowException("The was an error processing the URL to the workflow: "
+ + e.getMessage(), e);
+ }
+ }
+
+ public void setCommandLineOptions(CommandLineOptions commandLineOptions){
+ this.commandLineOptions = commandLineOptions;
+ }
+
+ public void setRunService(RunService runService) {
+ this.runService = runService;
+ }
+
+ public void setCredentialManager(CredentialManager credentialManager) {
+ this.credentialManager = credentialManager;
+ }
+
+ public void setWorkflowBundleIO(WorkflowBundleIO workflowBundleIO) {
+ this.workflowBundleIO = workflowBundleIO;
+ }
+
+ /**
+ * Sets the databaseConfiguration.
+ *
+ * @param databaseConfiguration the new value of databaseConfiguration
+ */
+ public void setDatabaseConfiguration(DatabaseConfiguration databaseConfiguration) {
+ this.databaseConfiguration = databaseConfiguration;
+ }
+
+ /**
+ * Sets the databaseManager.
+ *
+ * @param databaseManager the new value of databaseManager
+ */
+ public void setDatabaseManager(DatabaseManager databaseManager) {
+ this.databaseManager = databaseManager;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
new file mode 100644
index 0000000..46b6c92
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/DatabaseConfigurationHandler.java
@@ -0,0 +1,154 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.data;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.util.Properties;
+
+import javax.naming.NamingException;
+
+import net.sf.taverna.t2.commandline.exceptions.DatabaseConfigurationException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+
+import org.apache.log4j.Logger;
+
+import uk.org.taverna.configuration.database.DatabaseConfiguration;
+import uk.org.taverna.configuration.database.DatabaseManager;
+
+/**
+ * Handles the initialisation and configuration of the data source according to
+ * the command line arguments, or a properties file.
+ * This also handles starting a network based instance of a Derby server, if requested.
+ *
+ * @author Stuart Owen
+ *
+ */
+public class DatabaseConfigurationHandler {
+
+ private static Logger logger = Logger.getLogger(DatabaseConfigurationHandler.class);
+ private final CommandLineOptions options;
+ private final DatabaseConfiguration dbConfig;
+ private final DatabaseManager databaseManager;
+
+ public DatabaseConfigurationHandler(CommandLineOptions options, DatabaseConfiguration databaseConfiguration, DatabaseManager databaseManager) {
+ this.options = options;
+ this.dbConfig = databaseConfiguration;
+ this.databaseManager = databaseManager;
+ databaseConfiguration.disableAutoSave();
+ }
+
+ public void configureDatabase() throws DatabaseConfigurationException {
+ overrideDefaults();
+ useOptions();
+ if (dbConfig.getStartInternalDerbyServer()) {
+ databaseManager.startDerbyNetworkServer();
+ System.out.println("Started Derby Server on Port: "
+ + dbConfig.getCurrentPort());
+ }
+ }
+
+ public DatabaseConfiguration getDBConfig() {
+ return dbConfig;
+ }
+
+ private void importConfigurationFromStream(InputStream inStr)
+ throws IOException {
+ Properties p = new Properties();
+ p.load(inStr);
+ for (Object key : p.keySet()) {
+ dbConfig.setProperty((String)key, p.getProperty((String)key).trim());
+ }
+ }
+
+ protected void overrideDefaults() throws DatabaseConfigurationException {
+
+ InputStream inStr = DatabaseConfigurationHandler.class.getClassLoader().getResourceAsStream("database-defaults.properties");
+ try {
+ importConfigurationFromStream(inStr);
+ } catch (IOException e) {
+ throw new DatabaseConfigurationException("There was an error reading the default database configuration settings: "+e.getMessage(),e);
+ }
+ }
+
+ protected void readConfigirationFromFile(String filename) throws IOException {
+ FileInputStream fileInputStream = new FileInputStream(filename);
+ importConfigurationFromStream(fileInputStream);
+ fileInputStream.close();
+ }
+
+ public void testDatabaseConnection()
+ throws DatabaseConfigurationException, NamingException, SQLException {
+ //try and get a connection
+ Connection con = null;
+ try {
+ con = databaseManager.getConnection();
+ } finally {
+ if (con!=null)
+ try {
+ con.close();
+ } catch (SQLException e) {
+ logger.warn("There was an SQL error whilst closing the test connection: "+e.getMessage(),e);
+ }
+ }
+ }
+
+ public void useOptions() throws DatabaseConfigurationException {
+
+ if (options.hasOption("port")) {
+ dbConfig.setPort(options.getDatabasePort());
+ }
+
+ if (options.hasOption("startdb")) {
+ dbConfig.setStartInternalDerbyServer(true);
+ }
+
+ if (options.hasOption("inmemory")) {
+ dbConfig.setInMemory(true);
+ }
+
+ if (options.hasOption("embedded")) {
+ dbConfig.setInMemory(false);
+ dbConfig.setDriverClassName("org.apache.derby.jdbc.EmbeddedDriver");
+ }
+
+ if (options.isProvenanceEnabled()) {
+ dbConfig.setProvenanceEnabled(true);
+ }
+
+ if (options.hasOption("clientserver")) {
+ dbConfig.setInMemory(false);
+ dbConfig.setDriverClassName("org.apache.derby.jdbc.ClientDriver");
+ dbConfig.setJDBCUri("jdbc:derby://localhost:" + dbConfig.getPort() + "/t2-database;create=true;upgrade=true");
+ }
+
+ if (options.hasOption("dbproperties")) {
+ try {
+ readConfigirationFromFile(options.getDatabaseProperties());
+ } catch (IOException e) {
+ throw new DatabaseConfigurationException("There was an error reading the database configuration options at "+options.getDatabaseProperties()+" : "+e.getMessage(),e);
+ }
+ }
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
new file mode 100644
index 0000000..44faea5
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/ErrorValueHandler.java
@@ -0,0 +1,72 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.data;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.util.List;
+
+import javax.swing.tree.DefaultMutableTreeNode;
+
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.databundle.ErrorDocument;
+
+/**
+ * Handles ErrorValues and transforming them into String representations
+ * that can be stored as a file, or within a Baclava document.
+ *
+ * @author Stuart Owen
+ * @author David Withers
+ */
+public class ErrorValueHandler {
+
+ /**
+ * Creates a string representation of the ErrorValue.
+ * @throws IOException
+ */
+ public static String buildErrorValueString(ErrorDocument errorValue) throws IOException {
+
+ String errDocumentString = errorValue.getMessage() + "\n";
+
+ String exceptionMessage = errorValue.getMessage();
+ if (exceptionMessage != null && !exceptionMessage.equals("")) {
+ DefaultMutableTreeNode exceptionMessageNode = new DefaultMutableTreeNode(
+ exceptionMessage);
+ errDocumentString += exceptionMessageNode + "\n";
+ errDocumentString += errorValue.getTrace();
+ }
+
+ List<Path> errorReferences = errorValue.getCausedBy();
+ if (!errorReferences.isEmpty()) {
+ errDocumentString += "Set of cause errors to follow." + "\n";
+ }
+ int errorCounter = 1;
+ for (Path cause : errorReferences) {
+ if (DataBundles.isError(cause)) {
+ errDocumentString += "ErrorValue " + (errorCounter++) + "\n";
+ errDocumentString += buildErrorValueString(DataBundles.getError(cause)) + "\n";
+ }
+ }
+
+ return errDocumentString;
+ }
+
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
new file mode 100644
index 0000000..bcaa7fb
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/InputsHandler.java
@@ -0,0 +1,280 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.data;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URISyntaxException;
+import java.net.URL;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import net.sf.taverna.t2.commandline.exceptions.InputMismatchException;
+import net.sf.taverna.t2.commandline.exceptions.InvalidOptionException;
+import net.sf.taverna.t2.commandline.exceptions.ReadInputException;
+import net.sf.taverna.t2.commandline.options.CommandLineOptions;
+import net.sf.taverna.t2.invocation.InvocationContext;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Logger;
+import org.jdom.JDOMException;
+import org.purl.wf4ever.robundle.Bundle;
+
+import uk.org.taverna.databundle.DataBundles;
+import uk.org.taverna.scufl2.api.port.InputWorkflowPort;
+
+/**
+ * Handles the reading, or processing, or input values according to arguments provided to the
+ * commandline.
+ * The may be either as direct values, from a file, or from a Baclava document.
+ * Also handles registering the input values with the Data Service, ready to initiate
+ * the workflow run.
+ *
+ * @author Stuart Owen
+ */
+public class InputsHandler {
+
+ private static Logger logger = Logger.getLogger(InputsHandler.class);
+
+ public void checkProvidedInputs(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options) throws InputMismatchException {
+ // we dont check for the document
+ Set<String> providedInputNames = new HashSet<String>();
+ for (int i = 0; i < options.getInputFiles().length; i += 2) {
+ // If it already contains a value for the input port, e.g
+ // two inputs are provided for the same port
+ if (providedInputNames.contains(options.getInputFiles()[i])) {
+ throw new InputMismatchException(
+ "Two input values were provided for the same input port "
+ + options.getInputFiles()[i] + ".", null, null);
+ }
+ providedInputNames.add(options.getInputFiles()[i]);
+ }
+
+ for (int i = 0; i < options.getInputValues().length; i += 2) {
+ // If it already contains a value for the input port, e.g
+ // two inputs are provided for the same port
+ if (providedInputNames.contains(options.getInputValues()[i])) {
+ throw new InputMismatchException(
+ "Two input values were provided for the same input port "
+ + options.getInputValues()[i] + ".", null, null);
+ }
+ providedInputNames.add(options.getInputValues()[i]);
+ }
+
+ if (portMap.size() * 2 != (options.getInputFiles().length + options.getInputValues().length)) {
+ throw new InputMismatchException(
+ "The number of inputs provided does not match the number of input ports.",
+ portMap.keySet(), providedInputNames);
+ }
+
+ for (String portName : portMap.keySet()) {
+ if (!providedInputNames.contains(portName)) {
+ throw new InputMismatchException(
+ "The provided inputs does not contain an input for the port '"
+ + portName + "'", portMap.keySet(), providedInputNames);
+ }
+ }
+ }
+
+ public Bundle registerInputs(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, InvocationContext context) throws InvalidOptionException,
+ ReadInputException, IOException {
+ Bundle inputDataBundle;
+ inputDataBundle = DataBundles.createBundle();
+ inputDataBundle.setDeleteOnClose(false);
+ System.out.println("Bundle: " + inputDataBundle.getSource());
+
+ Path inputs = DataBundles.getInputs(inputDataBundle);
+
+ URL url;
+ try {
+ url = new URL("file:");
+ } catch (MalformedURLException e1) {
+ // Should never happen, but just in case:
+ throw new ReadInputException(
+ "The was an internal error setting up the URL to open the inputs. You should contact Taverna support.",
+ e1);
+ }
+
+ if (options.hasInputFiles()) {
+ regesterInputsFromFiles(portMap, options, inputs, url);
+ }
+
+ if (options.hasInputValues()) {
+ registerInputsFromValues(portMap, options, inputs);
+
+ }
+
+ return inputDataBundle;
+ }
+
+ private void registerInputsFromValues(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, Path inputs) throws InvalidOptionException {
+ String[] inputParams = options.getInputValues();
+ for (int i = 0; i < inputParams.length; i = i + 2) {
+ String inputName = inputParams[i];
+ try {
+ String inputValue = inputParams[i + 1];
+ InputWorkflowPort port = portMap.get(inputName);
+
+ if (port == null) {
+ throw new InvalidOptionException("Cannot find an input port named '"
+ + inputName + "'");
+ }
+
+ Path portPath = DataBundles.getPort(inputs, inputName);
+ if (options.hasDelimiterFor(inputName)) {
+ String delimiter = options.inputDelimiter(inputName);
+ Object value = checkForDepthMismatch(1, port.getDepth(), inputName,
+ inputValue.split(delimiter));
+ setValue(portPath, value);
+ } else {
+ Object value = checkForDepthMismatch(0, port.getDepth(), inputName, inputValue);
+ setValue(portPath, value);
+ }
+
+ } catch (IndexOutOfBoundsException e) {
+ throw new InvalidOptionException("Missing input value for input " + inputName);
+ } catch (IOException e) {
+ throw new InvalidOptionException("Error creating value for input " + inputName);
+ }
+ }
+ }
+
+ private void regesterInputsFromFiles(Map<String, InputWorkflowPort> portMap,
+ CommandLineOptions options, Path inputs, URL url) throws InvalidOptionException {
+ String[] inputParams = options.getInputFiles();
+ for (int i = 0; i < inputParams.length; i = i + 2) {
+ String inputName = inputParams[i];
+ try {
+ URL inputURL = new URL(url, inputParams[i + 1]);
+ InputWorkflowPort port = portMap.get(inputName);
+
+ if (port == null) {
+ throw new InvalidOptionException("Cannot find an input port named '"
+ + inputName + "'");
+ }
+
+ Path portPath = DataBundles.getPort(inputs, inputName);
+ if (options.hasDelimiterFor(inputName)) {
+ String delimiter = options.inputDelimiter(inputName);
+ Object value = IOUtils.toString(inputURL.openStream()).split(delimiter);
+ value = checkForDepthMismatch(1, port.getDepth(), inputName, value);
+ setValue(portPath, value);
+ } else {
+ Object value = IOUtils.toByteArray(inputURL.openStream());
+ value = checkForDepthMismatch(0, port.getDepth(), inputName, value);
+ setValue(portPath, value);
+ }
+ } catch (IndexOutOfBoundsException e) {
+ throw new InvalidOptionException("Missing input filename for input " + inputName);
+ } catch (IOException e) {
+ throw new InvalidOptionException("Could not read input " + inputName + ": "
+ + e.getMessage());
+ }
+ }
+ }
+
+ private void setValue(Path port, Object userInput) throws IOException {
+ if (userInput instanceof File) {
+ DataBundles.setReference(port, ((File) userInput).toURI());
+ } else if (userInput instanceof URL) {
+ try {
+ DataBundles.setReference(port, ((URL) userInput).toURI());
+ } catch (URISyntaxException e) {
+ logger.warn(String.format("Error converting %1$s to URI", userInput), e);
+ }
+ } else if (userInput instanceof String) {
+ DataBundles.setStringValue(port, (String) userInput);
+ } else if (userInput instanceof byte[]) {
+ Files.write(port, (byte[]) userInput, StandardOpenOption.TRUNCATE_EXISTING, StandardOpenOption.CREATE);
+ } else if (userInput instanceof List<?>) {
+ DataBundles.createList(port);
+ List<?> list = (List<?>) userInput;
+ for (Object object : list) {
+ setValue(DataBundles.newListItem(port), object);
+ }
+ } else {
+ logger.warn("Unknown input type : " + userInput.getClass().getName());
+ }
+ }
+
+ private Object checkForDepthMismatch(int inputDepth, int portDepth, String inputName,
+ Object inputValue) throws InvalidOptionException {
+ if (inputDepth != portDepth) {
+ if (inputDepth < portDepth) {
+ logger.warn("Wrapping input for '" + inputName + "' from a depth of " + inputDepth
+ + " to the required depth of " + portDepth);
+ while (inputDepth < portDepth) {
+ List<Object> l = new ArrayList<Object>();
+ l.add(inputValue);
+ inputValue = l;
+ inputDepth++;
+ }
+ } else {
+ String msg = "There is a mismatch between depth of the list for the input port '"
+ + inputName + "' and the data presented. The input port requires a "
+ + depthToString(portDepth) + " and the data presented is a "
+ + depthToString(inputDepth);
+ throw new InvalidOptionException(msg);
+ }
+ }
+
+ return inputValue;
+ }
+
+ private String depthToString(int depth) {
+ switch (depth) {
+ case 0:
+ return "single item";
+ case 1:
+ return "list";
+ case 2:
+ return "list of lists";
+ default:
+ return "list of depth " + depth;
+ }
+ }
+
+ private int getObjectDepth(Object o) {
+ int result = 0;
+ if (o instanceof Iterable) {
+ result++;
+ Iterator i = ((Iterable) o).iterator();
+
+ if (i.hasNext()) {
+ Object child = i.next();
+ result = result + getObjectDepth(child);
+ }
+ }
+ return result;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-commandline/blob/53c8a6c1/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
----------------------------------------------------------------------
diff --git a/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
new file mode 100644
index 0000000..1df05c2
--- /dev/null
+++ b/taverna-commandline-common/src/main/java/net/sf/taverna/t2/commandline/data/SaveResultsHandler.java
@@ -0,0 +1,87 @@
+/*******************************************************************************
+ * Copyright (C) 2007 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program 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 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program 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 program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+package net.sf.taverna.t2.commandline.data;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.Map;
+
+import uk.org.taverna.databundle.DataBundles;
+
+/**
+ * Handles all recording of results as they are received by the {@link CommandLineResultListener} or
+ * when the workflow enactment has completed.
+ * This includes saving as a Baclava Document, or storing individual results.
+ *
+ * @author Stuart Owen
+ * @see BaclavaHandler
+ * @see CommandLineResultListener
+ */
+public class SaveResultsHandler {
+
+ private final File outputDirectory;
+
+ public SaveResultsHandler(File rootOutputDir) {
+ this.outputDirectory = rootOutputDir;
+ }
+
+ /**
+ * Given the Data on an output port, saves the data on a disk in the
+ * output directory.
+ *
+ * @param portName
+ * @param data
+ * @throws IOException
+ */
+ public void saveResultsForPort(String portName, Path data) throws IOException {
+ if (DataBundles.isList(data)) {
+ Path outputPath = outputDirectory.toPath().resolve(portName);
+ Files.createDirectories(outputPath);
+ saveList(DataBundles.getList(data), outputPath);
+ } else if (DataBundles.isError(data)) {
+ Files.copy(data, outputDirectory.toPath().resolve(portName + ".error"));
+ } else {
+ Files.copy(data, outputDirectory.toPath().resolve(portName));
+ }
+ }
+
+ private void saveList(List<Path> list, Path destination) throws IOException {
+ int index = 1;
+ for (Path data : list) {
+ if (data != null) {
+ if (DataBundles.isList(data)) {
+ Path outputPath = destination.resolve(String.valueOf(index));
+ Files.createDirectories(outputPath);
+ saveList(DataBundles.getList(data), outputPath);
+ } else if (DataBundles.isError(data)) {
+ Files.copy(data, destination.resolve(String.valueOf(index) + ".error"));
+ } else {
+ Files.copy(data, destination.resolve(String.valueOf(index)));
+ }
+ }
+ index++;
+ }
+ }
+
+}