SSDM-8342: data source: AbstractEntityWithPermIdDeliverer.getAllEntities() in...

SSDM-8342: data source: AbstractEntityWithPermIdDeliverer.getAllEntities() in order to get only those samples which in the requested spaces. This fixes a HTTP timeout bug caused by filtering a huge number of samples where only a few are passing the filter

datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/datasource/AbstractEntityDeliverer.java

@@ -81,13 +81,12 @@ abstract class AbstractEntityDeliverer<T> implements IDeliverer
     @Override
     public void deliverEntities(DeliveryExecutionContext context) throws XMLStreamException
     {
-        IDataSourceQueryService queryService = context.getQueryService();
         String sessionToken = context.getSessionToken();
-        List<T> allEntities = getAllEntities(queryService, sessionToken);
+        List<T> allEntities = getAllEntities(context, sessionToken);
         executeInBatches(allEntities, entities -> deliverEntities(context, entities));
     }
     
-    protected List<T> getAllEntities(IDataSourceQueryService queryService, String sessionToken)
+    protected List<T> getAllEntities(DeliveryExecutionContext executionContext, String sessionToken)
     {
         return Collections.emptyList();
     }

datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/datasource/AbstractEntityWithPermIdDeliverer.java

@@ -45,11 +45,17 @@ abstract class AbstractEntityWithPermIdDeliverer extends AbstractEntityDeliverer
     }
 
     @Override
-    protected List<String> getAllEntities(IDataSourceQueryService queryService, String sessionToken)
+    protected List<String> getAllEntities(DeliveryExecutionContext executionContext, String sessionToken)
     {
+        return getAllEntities(executionContext, sessionToken, sql);
+    }
+
+    protected List<String> getAllEntities(DeliveryExecutionContext executionContext, String sessionToken, String query)
+    {
+        IDataSourceQueryService queryService = executionContext.getQueryService();
         List<String> permIds = new ArrayList<>();
         String dataSourceName = context.getOpenBisDataSourceName();
-        DataSet<Map<String, Object>> select = queryService.select(dataSourceName, sql);
+        DataSet<Map<String, Object>> select = queryService.select(dataSourceName, query);
         for (Map<String, Object> row : select)
         {
             permIds.add((String) row.get(databasePermIdColumn));

datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/datasource/DataSetDeliverer.java

@@ -33,6 +33,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetc
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
+import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContent;
 import ch.systemsx.cisd.openbis.common.io.hierarchical_content.api.IHierarchicalContentNode;
 
 /**
@@ -121,7 +122,11 @@ public class DataSetDeliverer extends AbstractEntityWithPermIdDeliverer
                 addAttribute(writer, "path", contentCopy.getPath());
                 writer.writeEndElement();
             }
-            addFileNodes(writer, code, context.getContentProvider().asContent(code).getRootNode());
+            IHierarchicalContent content = context.getContentProvider().asContent(code);
+            if (content != null)
+            {
+                addFileNodes(writer, code, content.getRootNode());
+            }
             writer.writeEndElement();
         }
     }

datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/datasource/MaterialDeliverer.java

@@ -32,7 +32,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.fetchoptions.MaterialFetchOptions;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.id.MaterialPermId;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.search.MaterialSearchCriteria;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.IDataSourceQueryService;
 
 /**
  * @author Franz-Josef Elmer
@@ -46,7 +45,7 @@ public class MaterialDeliverer extends AbstractEntityDeliverer<Material>
     }
 
     @Override
-    protected List<Material> getAllEntities(IDataSourceQueryService queryService, String sessionToken)
+    protected List<Material> getAllEntities(DeliveryExecutionContext executionContext, String sessionToken)
     {
 
         MaterialSearchCriteria searchCriteria = new MaterialSearchCriteria();

datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/datasource/SampleDeliverer.java

@@ -29,6 +29,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.EntityKind;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
 import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.systemsx.cisd.common.shared.basic.string.CommaSeparatedListBuilder;
 
 /**
  * @author Franz-Josef Elmer
@@ -88,6 +89,20 @@ public class SampleDeliverer extends AbstractEntityWithPermIdDeliverer
         operationLog.info(count + " of " + samplePermIds.size() + " samples have been delivered.");
     }
 
+    @Override
+    protected List<String> getAllEntities(DeliveryExecutionContext executionContext, String sessionToken)
+    {
+        String sql = "select perm_id from samples where space_id is null";
+        Set<String> spaces = executionContext.getSpaces();
+        if (spaces.isEmpty() == false)
+        {
+            CommaSeparatedListBuilder builder = new CommaSeparatedListBuilder();
+            spaces.stream().forEach(space -> builder.append("'" + space + "'"));
+            sql += " or space_id in (select id from spaces where code in (" + builder + "))";
+        }
+        return super.getAllEntities(executionContext, sessionToken, sql);
+    }
+
     private SampleFetchOptions createFullFetchOptions()
     {
             SampleFetchOptions fo = new SampleFetchOptions();