Add column for RQG_alt_ID

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -126,7 +126,6 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Reads
             int totalArchivedPairs = 0;
 
             Map<String, List<ReadData>> readdataToSra = new HashMap<>();
-            HashSet<Integer> filesIdsDeleted = new HashSet<>();
             for (ReadData rd : rs.getReadData())
             {
                 String accession = rd.getSra_accession();
@@ -237,12 +236,6 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Reads
                                 writer.println("Condensing/merging readdata: " + r.getRowid() + ", " + r.getFileId1() + ", " + d1.getFile().getPath() + ", " + (r.getFileId2() == null ? "N/A" : r.getFileId2()) + ", " + (r.getFileId2() == null ? "N/A" : d2.getFile().getPath()));
 
                                 List<Map<String, Object>> toDelete = Arrays.asList(Map.of("rowid", r.getRowid()));
-                                filesIdsDeleted.add(r.getFileId1());
-                                if (r.getFileId2() != null)
-                                {
-                                    filesIdsDeleted.add(r.getFileId2());
-                                }
-
                                 QueryService.get().getUserSchema(job.getUser(), ContainerManager.getForId(r.getContainer()), SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_READ_DATA).getUpdateService().deleteRows(job.getUser(), ContainerManager.getForId(r.getContainer()), toDelete, null, null);
                             }
 
@@ -263,20 +256,13 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Reads
             support.cacheReadset(rs.getReadsetId(), job.getUser(), true);
             support.cacheObject(UPDATED_ACCESSIONS, StringUtils.join(updatedAccessions, ";"));
             support.cacheObject(ACCESSION_TO_READS, accessionToReads);
-            support.cacheObject(FILE_IDS_DELETED, filesIdsDeleted);
         }
 
         private Map<String, Integer> getCachedReadCounts(SequenceAnalysisJobSupport support) throws PipelineJobException
         {
             return support.getCachedObject(ACCESSION_TO_READS, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Map.class, String.class, Integer.class));
         }
 
-        private Set<Integer> getFilesIdsDeleted(SequenceAnalysisJobSupport support) throws PipelineJobException
-        {
-            return support.getCachedObject(FILE_IDS_DELETED, PipelineJob.createObjectMapper().getTypeFactory().constructParametricType(Set.class, Integer.class));
-        }
-
-        private static final String FILE_IDS_DELETED = "filesIdsDeleted";
         private static final String UPDATED_ACCESSIONS = "updatedAccessions";
         private static final String ACCESSION_TO_READS = "accessionToReads";
 
@@ -349,16 +335,6 @@ public void complete(PipelineJob job, List<Readset> readsets, List<SequenceOutpu
             {
                 throw new PipelineJobException(e);
             }
-
-            // Delete pre-existing metrics:
-            for (int dataId : getFilesIdsDeleted(((SequenceReadsetHandlerJob)job).getSequenceSupport()))
-            {
-                SimpleFilter filter = new SimpleFilter(FieldKey.fromString("readset"), rs.getRowId());
-                filter.addCondition(FieldKey.fromString("container"), rs.getContainer());
-                filter.addCondition(FieldKey.fromString("dataId"), dataId);
-                int deleted = Table.delete(SequenceAnalysisManager.get().getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS), filter);
-                job.getLogger().debug("existing metrics deleted: " + deleted);
-            }
         }
 
         @Override