GitHub 895: Search: Over indexing Assay Batch

api/src/org/labkey/api/exp/api/ExpProtocol.java

@@ -99,7 +99,7 @@ enum Status
     String getContact();
 
     List<? extends ExpProtocol> getChildProtocols();
-    List<? extends ExpExperiment> getBatches();
+    List<? extends ExpExperiment> getBatches(@Nullable Container c);
 
     void setEntityId(String entityId);
     String getEntityId();

assay/src/org/labkey/assay/AssayManager.java

@@ -378,10 +378,16 @@ public AssaySchema createSchema(User user, Container container, @Nullable Contai
 
     @Override
     public @NotNull List<ExpProtocol> getAssayProtocols(Container container)
+    {
+        return getAssayProtocols(container, false);
+    }
+
+    private @NotNull List<ExpProtocol> getAssayProtocols(Container container, boolean currentOnly)
     {
         List<ExpProtocol> allProtocols = new ArrayList<>();
 
-        for (Container containerInScope : container.getContainersFor(ContainerType.DataType.protocol))
+        Collection<Container> containerScopes = currentOnly ? List.of(container) : container.getContainersFor(ContainerType.DataType.protocol);
+        for (Container containerInScope : containerScopes)
         {
             List<ExpProtocol> ids = PROTOCOL_CACHE.get(containerInScope);
             allProtocols.addAll(ids);
@@ -622,14 +628,14 @@ public ExpExperiment findBatch(ExpRun run)
     }
 
     /**
-     * Creates a single document per assay design/folder combo, with some simple assay info (name, description), plus
-     * the names and comments from all the runs.
+     * Creates a single document per assay design, with some simple assay info (name, description).
+     * Note: the document for an assay protocol will just be associated with the protocol's container
      */
     @Override
     public void indexAssays(SearchService.TaskIndexingQueue queue)
     {
-        List<ExpProtocol> protocols = getAssayProtocols(queue.getContainer());
-
+        // GitHub Issue 895: for the assay protocol search document just user the current container's protocols
+        List<ExpProtocol> protocols = getAssayProtocols(queue.getContainer(), true);
         for (ExpProtocol protocol : protocols)
             indexAssay(queue, protocol);
     }
@@ -661,22 +667,6 @@ public void indexAssay(SearchService.TaskIndexingQueue queue, ExpProtocol protoc
         m.put(SearchService.PROPERTY.keywordsMed.toString(), keywords);
         m.put(SearchService.PROPERTY.categories.toString(), ASSAY_CATEGORY.getName());
 
-        ExperimentService.get().getExpRuns(c, protocol, null)
-            .forEach(run -> {
-                StringBuilder runKeywords = new StringBuilder();
-
-                runKeywords.append(" ");
-                runKeywords.append(run.getName());
-
-                if (null != run.getComments())
-                {
-                    runKeywords.append(" ");
-                    runKeywords.append(run.getComments());
-                }
-
-                body.append(runKeywords);
-            });
-
         String docId = protocol.getDocumentId();
         WebdavResource r = new SimpleDocumentResource(new Path(docId), docId, c.getEntityId(), "text/plain", body.toString(), assayBeginURL, createdBy, created, modifiedBy, modified, m);
         queue.addResource(r);
@@ -728,7 +718,7 @@ private void indexAssayBatches(SearchService.TaskIndexingQueue queue, ExpProtoco
     {
         if (shouldIndexProtocolBatches(protocol))
         {
-            for (ExpExperiment batch : protocol.getBatches())
+            for (ExpExperiment batch : protocol.getBatches(queue.getContainer()))
             {
                 if (modifiedSince == null || modifiedSince.before(batch.getModified()))
                     indexAssayBatch(queue, batch);

experiment/src/org/labkey/experiment/api/ExpProtocolImpl.java

@@ -21,7 +21,6 @@
 import org.labkey.api.assay.AssayProvider;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.ContainerManager;
-import org.labkey.api.data.Filter;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.SqlSelector;
@@ -329,9 +328,12 @@ public List<ExpProtocolImpl> getChildProtocols()
     }
 
     @Override
-    public List<ExpExperimentImpl> getBatches()
+    public List<ExpExperimentImpl> getBatches(@Nullable Container c)
     {
-        Filter filter = new SimpleFilter(FieldKey.fromParts("BatchProtocolId"), getRowId());
+        SimpleFilter filter = new SimpleFilter(FieldKey.fromParts("BatchProtocolId"), getRowId());
+        // GitHub Issue 895: add param option to get just the assay batches for a specific container
+        if (c != null)
+            filter.addCondition(FieldKey.fromParts("container"), c);
         return ExpExperimentImpl.fromExperiments(new TableSelector(ExperimentServiceImpl.get().getTinfoExperiment(), filter, null).getArray(Experiment.class));
     }
 

experiment/src/org/labkey/experiment/api/ExperimentServiceImpl.java

@@ -4528,7 +4528,7 @@ public void deleteProtocolByRowIds(Container c, User user, @Nullable String audi
 
             for (ExpProtocol protocolToDelete : expProtocols)
             {
-                for (ExpExperiment batch : protocolToDelete.getBatches())
+                for (ExpExperiment batch : protocolToDelete.getBatches(null))
                 {
                     batch.delete(user);
                 }