Allow PlinkPcaStep to limit to specific sample sets

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/PlinkPcaStep.java

@@ -81,6 +81,7 @@ public Provider()
                         put("sortField", "application");
                     }}, null),
                     ToolParameterDescriptor.create("allowMissingSamples", "Allow Missing Samples", "When using split by application, this controls whether or not the job should fail if a matching readset cannot be found for specific samples.", "checkbox", null, false),
+                    ToolParameterDescriptor.create("fileSets", "File Set(s) For Readset Query", "If Split By Application is used, the system needs to query each sample name in the VCF and find the corresponding readset. If this is provided, this query will be limited to redsets where a gVCF exists and is tagged as one of these file sets", "sequenceanalysis-trimmingtextarea", null, null),
                     ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_INCLUDE, "Sample(s) Include", "Only the following samples will be included in the analysis.", "sequenceanalysis-trimmingtextarea", null, null),
                     ToolParameterDescriptor.create(SelectSamplesStep.SAMPLE_EXCLUDE, "Samples(s) To Exclude", "The following samples will be excluded from the analysis.", "sequenceanalysis-trimmingtextarea", null, null)
             ), List.of("sequenceanalysis/field/TrimmingTextArea.js"), "https://zzz.bwh.harvard.edu/plink/");
@@ -249,16 +250,31 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Seque
                             throw new PipelineJobException("Expected VCF to have samples: " + so.getFile().getPath());
                         }
 
+                        List<Integer> allowableReadsets = null;
+                        Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbook() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer();
+                        String fileSetsText = StringUtils.trimToNull(getProvider().getParameterByName("fileSets").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class));
+                        if (fileSetsText != null)
+                        {
+                            SimpleFilter fileSetFilter = new SimpleFilter(FieldKey.fromString("fileSets"), Arrays.asList(fileSetsText.split(";")), CompareType.CONTAINS_ONE_OF);
+                            fileSetFilter.addCondition(FieldKey.fromString("category"), "gVCF File");
+                            allowableReadsets = new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_OUTPUTFILES), PageFlowUtil.set("readset"), fileSetFilter, null).getArrayList(Integer.class);
+                            getPipelineCtx().getLogger().debug("Limiting to file sets: " + fileSetsText + ", found " + allowableReadsets.size() + " readsets");
+                        }
+
                         for (String sample : header.getSampleNamesInOrder())
                         {
                             // Find readset:
-                            Container targetContainer = getPipelineCtx().getJob().getContainer().isWorkbook() ? getPipelineCtx().getJob().getContainer().getParent() : getPipelineCtx().getJob().getContainer();
                             SimpleFilter filter = new SimpleFilter(FieldKey.fromString("name"), sample).addCondition(FieldKey.fromString("status"), null, CompareType.ISBLANK);
                             if (allowableApplications != null)
                             {
                                 filter.addCondition(FieldKey.fromString("application"), allowableApplications, CompareType.IN);
                             }
 
+                            if (allowableReadsets != null)
+                            {
+                                filter.addCondition(FieldKey.fromString("rowid"), allowableReadsets, CompareType.IN);
+                            }
+
                             Collection<Map<String, Object>> results = new TableSelector(QueryService.get().getUserSchema(getPipelineCtx().getJob().getUser(), targetContainer, SequenceAnalysisSchema.SCHEMA_NAME).getTable(SequenceAnalysisSchema.TABLE_READSETS), PageFlowUtil.set("application", "rowid"), filter, null).getMapCollection();
                             if (results.size() == 1)
                             {