Merge pull request #118 from SeqWare/feature/SEQWARE_1750_input_file_overwrite

Feature/seqware 1750 input file overwrite

Former-commit-id: ff0867a

Author: ataggart

seqware-pipeline/src/main/java/net/sourceforge/seqware/pipeline/plugin/WorkflowPlugin.java

@@ -143,12 +143,17 @@ public ReturnValue init() {
     }
 
     if (options.has("workflow-engine")){
-      if (!ENGINES.contains(options.valueOf("workflow-engine"))){
+      if (!ENGINES.contains((String)options.valueOf("workflow-engine"))){
         Log.error("Invalid workflow-engine value. Must be one of: "+ENGINES_LIST);
         ret.setExitStatus(ReturnValue.INVALIDARGUMENT);
         return ret;
       }
     }
+    if (options.has(WAIT) && options.has(LAUNCH_SCHEDULED)){
+        Log.error("Cannot launch scheduled workflows with wait");
+        ret.setExitStatus(ReturnValue.INVALIDARGUMENT);
+        return ret;
+    }
 
     // wrong assumption here I think, --host is possible even when not
     // scheduling or waiting

seqware-webservice/src/main/java/net/sourceforge/seqware/webservice/resources/tables/WorkflowRunIDResource.java

@@ -203,7 +203,6 @@ public WorkflowRun updateWorkflowRun(WorkflowRun newWR) throws ResourceException
         wr.setWorkflowEngine(newWR.getWorkflowEngine());
         if (newWR.getInputFileAccessions() != null){
             Log.debug("Saving " + wr.getInputFileAccessions().size() + " input files");
-            wr.getInputFileAccessions().clear();
             wr.getInputFileAccessions().addAll(newWR.getInputFileAccessions());
         }
 

seqware-webservice/src/test/java/net/sourceforge/seqware/common/metadata/MetadataWSTest.java

@@ -761,9 +761,9 @@ public void testGetInputFilesForExistingWorkflowRun(){
 
     @Test
     public void testUpdateWorkflowRunWithInputFiles() {
-        final int wr_sw_accession = 863;
+        final int wr_sw_accession = 6603;
         WorkflowRun wr = instance.getWorkflowRun(wr_sw_accession);
-        // try emptying it and asking for it back
+        // should already be blank
         instance.update_workflow_run(wr.getWorkflowRunId(), wr.getCommand(), wr.getTemplate(), wr.getStatus(),
                 wr.getStatusCmd(), wr.getCurrentWorkingDir(), wr.getDax(), wr.getIniFile(),
                 wr.getHost(), wr.getStdOut(), wr.getStdErr(), wr.getWorkflowEngine(), new HashSet<Integer>());
@@ -794,20 +794,6 @@ public void testUpdateWorkflowRunWithInputFiles() {
                 wr.getHost(), wr.getStdOut(), wr.getStdErr(), wr.getWorkflowEngine(), wr.getInputFileAccessions());
         wr = instance.getWorkflowRun(wr_sw_accession);
         Assert.assertTrue("updated  input file set  should be size 4, was " + wr.getInputFileAccessions().size(), wr.getInputFileAccessions().size() == 4);
-        // try deleting the set and asking for it back (protects against cascading error as well)
-        wr.getInputFileAccessions().clear();
-        instance.update_workflow_run(wr.getWorkflowRunId(), wr.getCommand(), wr.getTemplate(), wr.getStatus(),
-                wr.getStatusCmd(), wr.getCurrentWorkingDir(), wr.getDax(), wr.getIniFile(),
-                wr.getHost(), wr.getStdOut(), wr.getStdErr(), wr.getWorkflowEngine(), wr.getInputFileAccessions());
-        wr = instance.getWorkflowRun(wr_sw_accession);
-        Assert.assertTrue("final size zero input file set should be blank", wr.getInputFileAccessions().isEmpty());
-        // make sure we didn't cascade any deletes
-        File f1 = instance.getFile(f1_sw_accession);
-        File f2 = instance.getFile(f2_sw_accession);
-        File f3 = instance.getFile(f3_sw_accession);
-        File f4 = instance.getFile(f4_sw_accession);
-        Assert.assertTrue("workflowrun was cascade deleted!", wr.getSwAccession() == wr_sw_accession);
-        Assert.assertTrue("files were cascade deleted!", f1.getSwAccession() == f1_sw_accession && f2.getSwAccession() == f2_sw_accession && f3.getSwAccession() == f3_sw_accession && f4.getSwAccession() == f4_sw_accession);
     }
 
     @Test