Allow insert of records using query API into outputfiles to automatically create ExpData IDs

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/outputfiles.js

@@ -14,3 +14,17 @@ function beforeDelete(row, errors){
         errors._form = 'You cannot directly delete analyses.  To delete these records, use the delete button above the analysis grid.';
     }
 }
+
+function beforeInsert(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpdate(row, errors){
+    beforeUpsert(row, errors);
+}
+
+function beforeUpsert(row, errors) {
+    if (row.dataid && typeof row.dataid == 'string') {
+        row.dataid = triggerHelper.createExpData(row.dataid);
+    }
+}

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java

@@ -18,13 +18,19 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
+import org.labkey.api.exp.api.DataType;
+import org.labkey.api.exp.api.ExpData;
+import org.labkey.api.exp.api.ExperimentService;
+import org.labkey.api.pipeline.PipeRoot;
+import org.labkey.api.pipeline.PipelineService;
 import org.labkey.api.query.FieldKey;
 import org.labkey.api.query.QueryService;
 import org.labkey.api.security.User;
 import org.labkey.api.security.UserManager;
 import org.labkey.api.sequenceanalysis.RefNtSequenceModel;
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.StringWriter;
 import java.util.Arrays;
@@ -221,4 +227,31 @@ public void testTranslation() {
             }
         }
     }
+    
+    public int createExpData(String relPath) {
+        PipeRoot pr = PipelineService.get().getPipelineRootSetting(getContainer());
+        if (pr == null)
+        {
+            throw new IllegalArgumentException("Unable to find pipeline root");
+        }
+
+        File f = new File(pr.getRootPath(), relPath);
+        if (!f.exists())
+        {
+            throw new IllegalArgumentException("Unable to find file: " + f.getPath());
+        }
+
+        ExpData d = ExperimentService.get().getExpDataByURL(f, getContainer());
+        if (d != null)
+        {
+            return d.getRowId();
+        }
+        
+        d = ExperimentService.get().createData(getContainer(), new DataType("Output"));
+        d.setDataFileURI(f.toURI());
+        d.setName(f.getName());
+        d.save(getUser());
+
+        return d.getRowId();
+    }
 }