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Posted to commits@taverna.apache.org by st...@apache.org on 2016/06/08 12:40:51 UTC
[10/15] incubator-taverna-common-activities git commit: add CWL icon
add CWL icon
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/17cdbdd0
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/tree/17cdbdd0
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/diff/17cdbdd0
Branch: refs/heads/cwl-browse
Commit: 17cdbdd08fe3e9f0ad19700919fbf048172b7d85
Parents: 00dd951
Author: ThilinaManamgoda <ma...@gmail.com>
Authored: Mon Jun 6 09:09:15 2016 +0530
Committer: ThilinaManamgoda <ma...@gmail.com>
Committed: Mon Jun 6 09:09:15 2016 +0530
----------------------------------------------------------------------
.../CWLFiles/customtool1.cwl | 42 +++++++++
.../CWLFiles/customtoolrecord.cwl | 41 +++++++++
.../Icon/cwl-logo-header.png | Bin 0 -> 4344 bytes
taverna-cwl-activity-ui/pom.xml | 92 +++++++++++++++++++
.../cwl/ui/serviceprovider/CwlServiceDesc.java | 13 +--
.../cwl/ui/serviceprovider/CwlServiceIcon.java | 49 ++++++++++
.../ui/serviceprovider/CwlServiceProvider.java | 13 ++-
.../taverna/cwl/ui/serviceprovider/Testing.java | 60 ++++++------
.../apache/taverna/cwl/ui/TestWorkBench.java | 11 +++
9 files changed, 276 insertions(+), 45 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl b/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl
new file mode 100644
index 0000000..762f9d0
--- /dev/null
+++ b/taverna-cwl-activity-ui/CWLFiles/customtool1.cwl
@@ -0,0 +1,42 @@
+################################################################################
+# 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.
+#################################################################################
+
+
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: cwl:draft-3
+
+inputs:
+ - id: input_1
+ type: int
+
+ - id: input_2
+ type:
+ type: array
+ items: int
+ - id: input_3
+ type: String
+
+outputs:
+ - id: output_1
+ type: int
+
+ - id: ouput_2
+ type: String
+
+basecommand: echo
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/CWLFiles/customtoolrecord.cwl
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/CWLFiles/customtoolrecord.cwl b/taverna-cwl-activity-ui/CWLFiles/customtoolrecord.cwl
new file mode 100644
index 0000000..f008bdb
--- /dev/null
+++ b/taverna-cwl-activity-ui/CWLFiles/customtoolrecord.cwl
@@ -0,0 +1,41 @@
+################################################################################
+# 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.
+#################################################################################
+
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: cwl:draft-3
+
+inputs:
+ - id: input_1
+ type: record
+
+ - id: input_2
+ type:
+ type: array
+ items: int
+ - id: input_3
+ type: String
+
+outputs:
+ - id: output_1
+ type: int
+
+ - id: ouput_2
+ type: String
+
+basecommand: echo
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/Icon/cwl-logo-header.png
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/Icon/cwl-logo-header.png b/taverna-cwl-activity-ui/Icon/cwl-logo-header.png
new file mode 100644
index 0000000..c24484e
Binary files /dev/null and b/taverna-cwl-activity-ui/Icon/cwl-logo-header.png differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/pom.xml b/taverna-cwl-activity-ui/pom.xml
index e14b203..70e436c 100644
--- a/taverna-cwl-activity-ui/pom.xml
+++ b/taverna-cwl-activity-ui/pom.xml
@@ -81,6 +81,97 @@
<groupId>${project.groupId}</groupId>
<version>${project.version}</version>
</dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.taverna-workbench</groupId>
+ <artifactId>workbench-dev</artifactId>
+ <version>${t2.workbench.version}</version>
+ <scope>test</scope>
+
+ <exclusions>
+
+ <!-- Disable various activities that are not relevant to testing our
+ example activity. If you want to re-enable for instance WSDL activity, remember
+ to comment out the exclusion for both wsdl-activity-ui and wsdl-activity
+ further down. -->
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>apiconsumer-activity-ui</artifactId>
+ </exclusion>
+
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>biomoby-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>biomart-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>soaplab-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>ncbi-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>rshell-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>spreadsheet-import-activity-ui</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>wsdl-activity-ui</artifactId>
+ </exclusion>
+
+ <!-- .. and the t2.activities counterparts -->
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>apiconsumer-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomoby-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>biomart-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>soaplab-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>ncbi-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>rshell-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>spreadsheet-import-activity</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ </exclusion>
+ <!-- Perspectives pulling in too many dependencies -->
+ <exclusion>
+ <!-- fails due to direct dependency to WSDL -->
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>perspective-biocatalogue</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.sf.taverna.t2.ui-exts</groupId>
+ <artifactId>perspective-myexperiment</artifactId>
+ </exclusion>
+ </exclusions>
+ </dependency>
<!-- ==================================================================================================== -->
</dependencies>
@@ -88,6 +179,7 @@
<!-- Added these properties to configure new dependencies -->
<properties>
<t2.ui.api.version>1.5</t2.ui.api.version>
+ <t2.workbench.version>2.5.0</t2.workbench.version>
</properties>
<repositories>
<repository>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
index 6dc4879..dc6a969 100644
--- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
+++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceDesc.java
@@ -16,12 +16,14 @@
*******************************************************************************/
package org.apache.taverna.cwl.ui.serviceprovider;
+import java.util.Arrays;
import java.util.List;
import java.util.Map;
import javax.swing.Icon;
import org.apache.taverna.cwl.CwlActivityConfigurationBean;
+import org.apache.taverna.cwl.CwlDumyActivity;
import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
@@ -32,8 +34,7 @@ public class CwlServiceDesc extends ServiceDescription<CwlActivityConfigurationB
private String toolName;
@Override
public Class<? extends Activity<CwlActivityConfigurationBean>> getActivityClass() {
- // TODO Auto-generated method stub
- return null;
+ return (Class<? extends Activity<CwlActivityConfigurationBean>>) CwlDumyActivity.class;
}
@Override
@@ -54,26 +55,22 @@ public class CwlServiceDesc extends ServiceDescription<CwlActivityConfigurationB
@Override
public Icon getIcon() {
- // TODO Auto-generated method stub
- return null;
+ return CwlServiceIcon.getIcon();
}
@Override
public String getName() {
- // TODO Auto-generated method stub
return toolName;
}
@Override
public List<? extends Comparable> getPath() {
- // TODO Auto-generated method stub
return null;
}
@Override
protected List<? extends Object> getIdentifyingData() {
- // TODO Auto-generated method stub
- return null;
+ return Arrays.asList("CWL Services " + toolName);
}
public String getToolName() {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceIcon.java
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceIcon.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceIcon.java
new file mode 100644
index 0000000..46ab810
--- /dev/null
+++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceIcon.java
@@ -0,0 +1,49 @@
+/*******************************************************************************
+ * 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.cwl.ui.serviceprovider;
+
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+
+import org.apache.taverna.cwl.CwlDumyActivity;
+
+import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
+import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
+
+public class CwlServiceIcon implements ActivityIconSPI {
+ private static Icon icon;
+
+ @Override
+ public int canProvideIconScore(Activity<?> activity) {
+ if (activity instanceof CwlDumyActivity) {
+ return DEFAULT_ICON;
+ }
+ return NO_ICON;
+ }
+
+ @Override
+ public Icon getIcon(Activity<?> arg0) {
+ return getIcon();
+ }
+
+ public static Icon getIcon() {
+ if (icon == null) {
+ icon = new ImageIcon("/Icon/cwl-logo-header.png");
+ }
+ return icon;
+ }
+}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
index 1e5193b..0fd36d4 100644
--- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
+++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/CwlServiceProvider.java
@@ -20,6 +20,7 @@ import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FilenameFilter;
+import java.net.URI;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@@ -37,7 +38,9 @@ public class CwlServiceProvider extends AbstractConfigurableServiceProvider<CwlS
CwlServiceProvider() {
super(new CwlServiceProviderConfig());
}
-
+ private static final String providerName ="CWL Services";
+ private static final URI providerId = URI
+ .create("http://cwl.com/2016/service-provider/cwlcommandlinetools");
private File cwlFilesLocation;
@Override
@@ -82,20 +85,17 @@ public class CwlServiceProvider extends AbstractConfigurableServiceProvider<CwlS
@Override
public Icon getIcon() {
- // TODO Auto-generated method stub
return null;
}
@Override
public String getId() {
- // TODO Auto-generated method stub
- return null;
+ return providerId.toASCIIString();
}
@Override
public String getName() {
- // TODO Auto-generated method stub
- return null;
+ return providerName;
}
private File[] getCwlFiles() {
@@ -125,7 +125,6 @@ public class CwlServiceProvider extends AbstractConfigurableServiceProvider<CwlS
@Override
protected List<? extends Object> getIdentifyingData() {
- // TODO Auto-generated method stub
return null;
}
}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
index ef03f5b..92deb34 100644
--- a/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
+++ b/taverna-cwl-activity-ui/src/main/java/org/apache/taverna/cwl/ui/serviceprovider/Testing.java
@@ -42,36 +42,36 @@ public class Testing {
private static final int DEPTH_1 = 1;
private static final int DEPTH_2 = 2;
- public static void main(String[] args) {
- File[] cwlFiles = getCwlFiles();
-
- for (File file : cwlFiles) {
-
- Map cwlFile = null;
- // Load the CWL file using SnakeYaml lib
- Yaml cwlReader = new Yaml();
- try {
- cwlFile = (Map) cwlReader.load(new FileInputStream(file));
- System.out.println(file.getName().split("\\.")[0]);
- HashMap<String, Integer> map =processInputs(cwlFile);
- for (String s : map.keySet()) {
- //System.out.println(map.get(s));
- }
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- if (cwlFile != null) {
- // Creating the CWL configuration bean
- CwlActivityConfigurationBean configurationBean = new CwlActivityConfigurationBean();
- configurationBean.setCwlConfigurations(cwlFile);
-
-
- }
-
- }
-
-
- }
+// public static void main(String[] args) {
+// File[] cwlFiles = getCwlFiles();
+//
+// for (File file : cwlFiles) {
+//
+// Map cwlFile = null;
+// // Load the CWL file using SnakeYaml lib
+// Yaml cwlReader = new Yaml();
+// try {
+// cwlFile = (Map) cwlReader.load(new FileInputStream(file));
+// System.out.println(file.getName().split("\\.")[0]);
+// HashMap<String, Integer> map =processInputs(cwlFile);
+// for (String s : map.keySet()) {
+// //System.out.println(map.get(s));
+// }
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
+// if (cwlFile != null) {
+// // Creating the CWL configuration bean
+// CwlActivityConfigurationBean configurationBean = new CwlActivityConfigurationBean();
+// configurationBean.setCwlConfigurations(cwlFile);
+//
+//
+// }
+//
+// }
+//
+//
+// }
private static HashMap<String, Integer> processInputs(Map cwlFile) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-common-activities/blob/17cdbdd0/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
----------------------------------------------------------------------
diff --git a/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java b/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
new file mode 100644
index 0000000..e36a6e0
--- /dev/null
+++ b/taverna-cwl-activity-ui/src/test/java/org/apache/taverna/cwl/ui/TestWorkBench.java
@@ -0,0 +1,11 @@
+package org.apache.taverna.cwl.ui;
+
+import java.net.URISyntaxException;
+
+import net.sf.taverna.t2.workbench.dev.DeveloperWorkbench;
+
+public class TestWorkBench {
+public static void main(String[] args) throws URISyntaxException {
+ DeveloperWorkbench.main(args);
+}
+}