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Posted to commits@taverna.apache.org by st...@apache.org on 2018/08/06 14:46:10 UTC
[06/14] incubator-taverna-language git commit: Fix conflicts and
merge branch 'cwlparser' into cwl
Fix conflicts and merge branch 'cwlparser' into cwl
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/commit/a4e79d49
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/tree/a4e79d49
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/diff/a4e79d49
Branch: refs/heads/cwlparser
Commit: a4e79d4976213b95fc3461277f7d2eba0d97779a
Parents: b56f451 87fa1c1
Author: Majdi Haouech <m....@criteo.com>
Authored: Mon Jul 16 20:20:22 2018 +0200
Committer: Majdi Haouech <m....@criteo.com>
Committed: Mon Jul 16 20:20:22 2018 +0200
----------------------------------------------------------------------
.../apache/taverna/scufl2/cwl/CWLParser.java | 3 +-
.../taverna/scufl2/cwl/WorkflowParser.java | 28 +++---------
.../scufl2/cwl/components/CommandLineTool.java | 7 ++-
.../scufl2/cwl/components/WorkflowProcess.java | 45 ++++----------------
.../taverna/scufl2/cwl/TestWorkflowProcess.java | 36 ++++++++++++++++
5 files changed, 55 insertions(+), 64 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a4e79d49/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
----------------------------------------------------------------------
diff --cc taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
index b41d054,b8902e7..481c93f
--- a/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/main/java/org/apache/taverna/scufl2/cwl/components/WorkflowProcess.java
@@@ -31,8 -29,6 +31,7 @@@ import org.apache.taverna.scufl2.api.co
import org.apache.taverna.scufl2.api.core.DataLink;
import org.apache.taverna.scufl2.api.core.Workflow;
+import org.apache.taverna.scufl2.api.container.WorkflowBundle;
-
import org.apache.taverna.scufl2.api.port.InputWorkflowPort;
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
@@@ -85,35 -71,15 +77,14 @@@ public class WorkflowProcess implement
workflow.setInputPorts(inputs);
workflow.setOutputPorts(outputs);
workflow.setProcessors(processors);
-- workflow.setDataLinks(dataLinks);
+
- // System.out.println(workflow);
- // writeWorkflowToFile(workflow);
- //
+
// System.out.println("DEBUG WORKFLOW");
// System.out.println(workflow.getInputPorts());
// System.out.println(workflow.getOutputPorts());
// System.out.println(workflow.getProcessors());
}
-
- public void writeWorkflowToFile(Workflow workflow) {
- try {
- WorkflowBundleIO io = new WorkflowBundleIO();
- File scufl2File = new File("workflow.wfbundle");
- WorkflowBundle bundle = io.createBundle();
- Set<Workflow> workflowSet = new HashSet<>();
- workflowSet.add(workflow);
- bundle.setWorkflows(workflowSet);
- bundle.setMainWorkflow(workflow);
- io.writeBundle(bundle, scufl2File, "text/vnd.taverna.scufl2.structure");
- } catch(WriterException e) {
- System.out.println("Exception writing the workflow bundle");
- } catch(IOException e) {
- System.out.println("IOException");
- }
- }
--
public void parseInputs() {
Set<PortDetail> cwlInputs = cwlParser.parseInputs();
for (PortDetail port: cwlInputs) {
http://git-wip-us.apache.org/repos/asf/incubator-taverna-language/blob/a4e79d49/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
----------------------------------------------------------------------
diff --cc taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
index 015ded4,10604b1..97d944f
--- a/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
+++ b/taverna-scufl2-cwl/src/test/java/org/apache/taverna/scufl2/cwl/TestWorkflowProcess.java
@@@ -18,7 -18,8 +18,12 @@@
*/
package org.apache.taverna.scufl2.cwl;
++<<<<<<< HEAD
+
++=======
+ import java.io.File;
+ import java.io.IOException;
++>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
import java.util.Set;
import java.util.HashSet;
import java.util.Map;
@@@ -45,6 -46,11 +50,14 @@@ import org.apache.taverna.scufl2.api.po
import org.apache.taverna.scufl2.api.port.OutputWorkflowPort;
import org.apache.taverna.scufl2.api.port.InputProcessorPort;
++<<<<<<< HEAD
++=======
+ import org.apache.taverna.scufl2.api.io.WorkflowBundleIO;
+ import org.apache.taverna.scufl2.api.io.WriterException;
+
+ import org.apache.taverna.scufl2.api.container.WorkflowBundle;
+
++>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
public class TestWorkflowProcess {
private static final String HELLO_WORLD_CWL = "/hello_world.cwl";
@@@ -92,8 -98,26 +105,31 @@@
@Test
public void testWorkflowSteps() {
cwlFile = loadYamlFile(WORKFLOW_WITH_COMMAND);
++<<<<<<< HEAD
+ WorkflowProcess workflow = new WorkflowProcess(cwlFile);
+
++=======
+ Process workflow = ProcessFactory.createProcess(cwlFile);
+
+ assert(workflow instanceof WorkflowProcess);
+ }
+
+ public void writeWorkflowToFile(Workflow workflow) {
+ try {
+ WorkflowBundleIO io = new WorkflowBundleIO();
+ File scufl2File = new File("workflow.wfbundle");
+ WorkflowBundle bundle = io.createBundle();
+ Set<Workflow> workflowSet = new HashSet<>();
+ workflowSet.add(workflow);
+ bundle.setWorkflows(workflowSet);
+ bundle.setMainWorkflow(workflow);
+ io.writeBundle(bundle, scufl2File, "text/vnd.taverna.scufl2.structure");
+ } catch(WriterException e) {
+ System.out.println("Exception writing the workflow bundle");
+ } catch(IOException e) {
+ System.out.println("IOException");
+ }
++>>>>>>> 87fa1c18d2b7aa210db3d238905234bf4f52b491
}
}