Add code to automatically update luceneIndex of release record

Author: bbimber

mGAP/src/org/labkey/mgap/pipeline/IndexVariantsForMgapStep.java

@@ -5,12 +5,16 @@
 import org.json.JSONObject;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.SimpleFilter;
+import org.labkey.api.data.TableInfo;
 import org.labkey.api.data.TableSelector;
 import org.labkey.api.jbrowse.JBrowseService;
 import org.labkey.api.pipeline.PipelineJob;
 import org.labkey.api.pipeline.PipelineJobException;
+import org.labkey.api.query.BatchValidationException;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.InvalidKeyException;
 import org.labkey.api.query.QueryService;
+import org.labkey.api.query.QueryUpdateServiceException;
 import org.labkey.api.security.User;
 import org.labkey.api.sequenceanalysis.SequenceOutputFile;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractVariantProcessingStepProvider;
@@ -28,8 +32,11 @@
 
 import javax.annotation.Nullable;
 import java.io.File;
+import java.sql.SQLException;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
+import java.util.Map;
 
 public class IndexVariantsForMgapStep extends AbstractCommandPipelineStep<SelectVariantsWrapper> implements VariantProcessingStep
 {
@@ -97,4 +104,41 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
 
         return output;
     }
+
+    @Override
+    public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
+    {
+        String releaseVersion = getProvider().getParameterByName("releaseVersion").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class);
+
+        List<SequenceOutputFile> of = outputsCreated.stream().filter(x -> CATEGORY.equals(x.getCategory())).toList();
+        if (of.size() != 1)
+        {
+            throw new PipelineJobException("Expected a single output, found: " + of.size());
+        }
+
+        Container target = job.getContainer().isWorkbook() ? job.getContainer().getParent() : job.getContainer();
+        TableInfo ti = QueryService.get().getUserSchema(job.getUser(), target, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES);
+        TableSelector ts = new TableSelector(ti, PageFlowUtil.set("rowId", "container"), new SimpleFilter(FieldKey.fromString("version"), releaseVersion), null);
+        if (ts.exists())
+        {
+            job.getLogger().info("Updating release record");
+            Map<String, Object> row = ts.getValueMap();
+            row.put("luceneIndex", of.get(0).getRowid());
+
+            try
+            {
+                BatchValidationException bve = new BatchValidationException();
+                Map<String, Object> oldKeys = Map.of("rowId", row.get("rowId"));
+                ti.getUpdateService().updateRows(job.getUser(), target, Collections.singletonList(row), Collections.singletonList(oldKeys), bve, null, null);
+            }
+            catch (BatchValidationException | InvalidKeyException | QueryUpdateServiceException | SQLException e)
+            {
+                throw new PipelineJobException(e);
+            }
+        }
+        else
+        {
+            job.getLogger().info("No release record found, will not update");
+        }
+    }
 }