Use correct container when updating replaced readsets

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java

@@ -221,7 +221,10 @@ public class FastqcReportAction extends SimpleViewAction<FastqcForm>
         public ModelAndView getView(FastqcForm form, BindException errors) throws Exception
         {
             if (form.getFilenames() == null && form.getDataIds() == null)
-                errors.reject("Must provide a filename or Exp data Ids");
+            {
+                errors.reject(ERROR_MSG, "Must provide a filename or Exp data Ids");
+                return null;
+            }
 
             //resolve files
             List<File> files = new ArrayList<>();
@@ -597,20 +600,20 @@ public void validateCommand(DeleteForm form, Errors errors)
         {
             if (form.getSchema() == null)
             {
-                errors.reject("No schema provided");
+                errors.reject(ERROR_MSG, "No schema provided");
                 return;
             }
 
             if (form.getQueryName() == null)
             {
-                errors.reject("No queryName provided");
+                errors.reject(ERROR_MSG, "No queryName provided");
                 return;
             }
 
             _table = SequenceAnalysisSchema.getInstance().getSchema().getTable(form.getQueryName());
             if (_table == null)
             {
-                errors.reject("Unknown table: " + form.getQueryName());
+                errors.reject(ERROR_MSG, "Unknown table: " + form.getQueryName());
                 return;
             }
 
@@ -2220,7 +2223,7 @@ public ApiResponse execute(CreateReferenceLibraryForm form, BindException errors
                             String[] coordinates = t.split("-");
                             if (coordinates.length != 2)
                             {
-                                errors.reject("Inproper interval: [" + t + "]");
+                                errors.reject(ERROR_MSG, "Inproper interval: [" + t + "]");
                                 return null;
                             }
 
@@ -3143,7 +3146,7 @@ public void exec(ResultSet object) throws SQLException
                             String wholeSequence = model.getSequence();
                             if (wholeSequence == null)
                             {
-                                errors.reject("Unable to find sequence for: " + rowId);
+                                errors.reject(ERROR_MSG, "Unable to find sequence for: " + rowId);
                                 return;
                             }
 
@@ -3152,21 +3155,21 @@ public void exec(ResultSet object) throws SQLException
                                 String[] coordinates = t.split("-");
                                 if (coordinates.length != 2)
                                 {
-                                    errors.reject("Inproper interval: [" + t + "]");
+                                    errors.reject(ERROR_MSG, "Inproper interval: [" + t + "]");
                                     return;
                                 }
 
                                 Integer start = StringUtils.trimToNull(coordinates[0]) == null ? null : ConvertHelper.convert(coordinates[0], Integer.class);
                                 if (wholeSequence.length() < start)
                                 {
-                                    errors.reject("Start is beyond the length of the sequence.  Length: " + wholeSequence.length());
+                                    errors.reject(ERROR_MSG, "Start is beyond the length of the sequence.  Length: " + wholeSequence.length());
                                     return;
                                 }
 
                                 Integer stop = StringUtils.trimToNull(coordinates[1]) == null ? null : ConvertHelper.convert(coordinates[1], Integer.class);
                                 if (wholeSequence.length() < stop)
                                 {
-                                    errors.reject("Stop is beyond the length of the sequence.  Length: " + wholeSequence.length());
+                                    errors.reject(ERROR_MSG, "Stop is beyond the length of the sequence.  Length: " + wholeSequence.length());
                                     return;
                                 }
 
@@ -3274,7 +3277,7 @@ public ApiResponse execute(RecreateReferenceLibraryForm form, BindException erro
         {
             if (form.getLibraryIds() == null || form.getLibraryIds().length == 0)
             {
-                errors.reject("Must provide a list of reference genomes to re-process");
+                errors.reject(ERROR_MSG, "Must provide a list of reference genomes to re-process");
                 return null;
             }
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetCreationTask.java

@@ -173,20 +173,18 @@ private void importReadsets() throws PipelineJobException
                 SequenceReadsetImpl r = (SequenceReadsetImpl)rs;
                 getJob().getLogger().info("Starting readset " + r.getName());
 
-                boolean readsetExists = r.getReadsetId() != null && r.getReadsetId() > 0;
-                List<ReadDataImpl> preexistingReadData;
-                if (readsetExists)
+                List<ReadDataImpl> preexistingReadData = ((SequenceReadsetImpl)SequenceAnalysisService.get().getReadset(r.getReadsetId(), getJob().getUser())).getReadDataImpl();
+                boolean readsetExistsWithData = !preexistingReadData.isEmpty();
+                if (readsetExistsWithData)
                 {
+                    getJob().getLogger().info("Readset has existing data: " + r.getName());
+
                     readsetsToDeactivate.put(r.getReadsetId(), r.getContainer());
-                    preexistingReadData = ((SequenceReadsetImpl)SequenceAnalysisService.get().getReadset(r.getReadsetId(), getJob().getUser())).getReadDataImpl();
-                }
-                else
-                {
-                    preexistingReadData = Collections.emptyList();
                 }
 
                 SequenceReadsetImpl row;
-                if (!readsetExists)
+                boolean readsetWillBeCreated = true;
+                if (!readsetExistsWithData)
                 {
                     row = new SequenceReadsetImpl();
 
@@ -237,7 +235,10 @@ private void importReadsets() throws PipelineJobException
                         row.setCreated(new Date());
                         row.setModifiedBy(getJob().getUser().getUserId());
                         row.setModified(new Date());
-                        readsetExists = false;
+                    }
+                    else
+                    {
+                        readsetWillBeCreated = false;
                     }
                 }
 
@@ -360,7 +361,7 @@ private void importReadsets() throws PipelineJobException
                 row.setReadData(readDatasToCreate);
 
                 SequenceReadsetImpl newRow;
-                if (!readsetExists)
+                if (!readsetWillBeCreated)
                 {
                     newRow = Table.insert(getJob().getUser(), readsetTable, row);
                     getJob().getLogger().info("Created readset: " + newRow.getReadsetId());