diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
index e3a590c3b243391d980b4fe8980e2cc14b2c410a..8a340cb501b6a1e3a6112f86f2becfe7b9eab6f6 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
@@ -69,6 +69,15 @@ import org.xml.sax.SAXException;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.delete.DataSetDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.deletion.id.IDeletionId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.delete.ExperimentDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.delete.ProjectDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.delete.SampleDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
@@ -77,12 +86,15 @@ import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFil
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.IDataSetFileId;
import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
+import ch.ethz.sis.openbis.generic.server.EntityRetriever;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.Connection;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.DataSetWithConnections;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ExperimentWithConnections;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.MaterialWithLastModificationDate;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ProjectWithConnections;
import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.SampleWithConnections;
+import ch.ethz.sis.openbis.generic.shared.entitygraph.EntityGraph;
+import ch.ethz.sis.openbis.generic.shared.entitygraph.Node;
import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
@@ -625,18 +637,13 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
data = parser.parseResourceListDocument(doc);
// go through the resources returned by the parser and decide on add/update/delete operations
- Map<String, ProjectWithConnections> projectsToProcess = data.projectsToCreate;
- Map<String, ExperimentWithConnections> experimentsToProcess = data.experimentsToCreate;
- Map<String, SampleWithConnections> samplesToProcess = data.samplesToCreate;
- Map<String, DataSetWithConnections> dataSetsToProcess = data.datasetsToCreate;
- List<MaterialWithLastModificationDate> materialsToProcess = data.materialsToCreate;
+ Map<String, ProjectWithConnections> projectsToProcess = data.projectsToProcess;
+ Map<String, ExperimentWithConnections> experimentsToProcess = data.experimentsToProcess;
+ Map<String, SampleWithConnections> samplesToProcess = data.samplesToProcess;
+ Map<String, DataSetWithConnections> dataSetsToProcess = data.datasetsToProcess;
+ List<MaterialWithLastModificationDate> materialsToProcess = data.materialsToProcess;
AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
-
- // EntityRetriever entityRetriever =
- // EntityRetriever.createWithSessionToken(ServiceProvider.getV3ApplicationService(), ServiceProvider.getOpenBISService()
- // .getSessionToken());
- // EntityGraph<Node<?>> harvesterEntityGraph = entityRetriever.getEntityGraph(harvesterSpace);
processProjects(projectsToProcess, experimentsToProcess, builder);
@@ -772,7 +779,10 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
operationResult = service.performEntityOperations(builder.getDetails());
System.err.println("entity operation result: " + operationResult);
- operationLog.info("Saving the timestamp of synn start into file");
+ operationLog.info("Processing deletions");
+ processDeletions(data);
+
+ operationLog.info("Saving the timestamp of sync start to file");
saveSyncTimestamp();
operationLog.info("Done and dusted...");
@@ -785,6 +795,92 @@ public class DataSetRegistrationTask<T extends DataSetInformation> implements IM
}
}
+ private void processDeletions(ResourceListParserData data)
+ {
+ String sessionToken = ServiceProvider.getOpenBISService().getSessionToken();
+ EntityRetriever entityRetriever =
+ EntityRetriever.createWithSessionToken(ServiceProvider.getV3ApplicationService(), sessionToken);
+
+ Set<String> incomingProjectPermIds = data.projectsToProcess.keySet();
+ Set<String> incomingExperimentPermIds = data.experimentsToProcess.keySet();
+ Set<String> incomingSamplePermIds = data.samplesToProcess.keySet();
+ Set<String> incomingDataSetCodes = data.datasetsToProcess.keySet();
+
+ // find projects, experiments, samples and data sets to be deleted
+ List<ProjectPermId> projectPermIds = new ArrayList<ProjectPermId>();
+ List<ExperimentPermId> experimentPermIds = new ArrayList<ExperimentPermId>();
+ List<SamplePermId> samplePermIds = new ArrayList<SamplePermId>();
+ List<DataSetPermId> dsPermIds = new ArrayList<DataSetPermId>();
+
+ for (String harvesterSpaceId : spaceMappings.values())
+ {
+ EntityGraph<Node<?>> harvesterEntityGraph = entityRetriever.getEntityGraph(harvesterSpaceId);
+ List<Node<?>> entities = harvesterEntityGraph.getNodes();
+ for (Node<?> entity : entities)
+ {
+ if (entity.getEntityKind().equals("PROJECT"))
+ {
+ if (incomingProjectPermIds.contains(entity.getPermId()) == false)
+ {
+ projectPermIds.add(new ProjectPermId(entity.getPermId()));
+ }
+ }
+ else if (entity.getEntityKind().equals("EXPERIMENT"))
+ {
+ if (incomingExperimentPermIds.contains(entity.getPermId()) == false)
+ {
+ experimentPermIds.add(new ExperimentPermId(entity.getPermId()));
+ }
+ }
+ else if (entity.getEntityKind().equals("SAMPLE"))
+ {
+ if (incomingSamplePermIds.contains(entity.getPermId()) == false)
+ {
+ samplePermIds.add(new SamplePermId(entity.getPermId()));
+ }
+ }
+ else if (entity.getEntityKind().equals("DATA_SET"))
+ {
+ if (incomingDataSetCodes.contains(entity.getPermId()) == false)
+ {
+ dsPermIds.add(new DataSetPermId(entity.getPermId()));
+ }
+ }
+ }
+ }
+
+ IApplicationServerApi v3Api = ServiceProvider.getV3ApplicationService();
+
+ // delete data sets
+ DataSetDeletionOptions dsDeletionOpts = new DataSetDeletionOptions();
+ dsDeletionOpts.setReason("sync data set deletions"); // TODO maybe mention data source space id in the reason
+
+ IDeletionId dsDeletionId =
+ v3Api.deleteDataSets(sessionToken, dsPermIds, dsDeletionOpts);
+
+ // delete samples
+ SampleDeletionOptions deletionOptions = new SampleDeletionOptions();
+ deletionOptions.setReason("sync sample deletions");
+ IDeletionId smpDeletionId = v3Api.deleteSamples(sessionToken, samplePermIds, deletionOptions);
+
+ // delete experiments
+
+ ExperimentDeletionOptions expDeletionOpts = new ExperimentDeletionOptions();
+ expDeletionOpts.setReason("sync experiment deletions");
+ IDeletionId expDeletionId = v3Api.deleteExperiments(sessionToken, experimentPermIds, expDeletionOpts);
+
+ // delete projects
+ ProjectDeletionOptions prjDeletionOpts = new ProjectDeletionOptions();
+ prjDeletionOpts.setReason("Sync projects");
+ v3Api.deleteProjects(sessionToken, projectPermIds, prjDeletionOpts);
+
+ // confirm deletions
+ // TODO confirm
+ // v3Api.confirmDeletions(sessionToken, Arrays.asList(expDeletionId, dsDeletionId, smpDeletionId));
+
+ // TODO sync material deletions
+ }
+
private void saveSyncTimestamp()
{
newLastSyncTimeStampFile.renameTo(lastSyncTimestampFile);
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java
index 296b79fa4dd18875de22c61e2446632777e51f04..ffa4720b0d50cc0a4dcd396ba33dc9b1a07cd596 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java
@@ -292,7 +292,7 @@ public class ResourceListParser
}
}
DataSetWithConnections newDsWithConns = data.new DataSetWithConnections(ds, lastModificationDate);
- data.datasetsToCreate.put(permId, newDsWithConns);
+ data.datasetsToProcess.put(permId, newDsWithConns);
newDsWithConns.setConnections(parseConnections(xpath, xdNode));
ds.setDataSetProperties(parseDataSetProperties(xpath, xdNode));
}
@@ -325,7 +325,7 @@ public class ResourceListParser
newProject.setPermID(permId);
ProjectWithConnections newPrjWithConns =
data.new ProjectWithConnections(newProject, lastModificationDate);
- data.projectsToCreate.put(permId, newPrjWithConns);
+ data.projectsToProcess.put(permId, newPrjWithConns);
newPrjWithConns.setConnections(parseConnections(xpath, xdNode));
}
@@ -336,7 +336,7 @@ public class ResourceListParser
NewMaterialWithType newMaterial = new NewMaterialWithType(code, type);
MaterialWithLastModificationDate materialWithLastModDate =
data.new MaterialWithLastModificationDate(newMaterial, lastModificationDate);
- data.materialsToCreate.add(materialWithLastModDate);
+ data.materialsToProcess.add(materialWithLastModDate);
newMaterial.setProperties(parseProperties(xpath, xdNode));
}
@@ -423,7 +423,7 @@ public class ResourceListParser
NewExperiment newExp = new NewExperiment("/" + spaceMappings.get(space) + "/" + project + "/" + code, type);
newExp.setPermID(permId);
ExperimentWithConnections newExpWithConns = data.new ExperimentWithConnections(newExp, lastModificationDate);
- data.experimentsToCreate.put(permId, newExpWithConns);
+ data.experimentsToProcess.put(permId, newExpWithConns);
newExpWithConns.setConnections(parseConnections(xpath, xdNode));
newExp.setProperties(parseProperties(xpath, xdNode));
}
@@ -442,7 +442,7 @@ public class ResourceListParser
new ArrayList<NewAttachment>());
newSample.setPermID(permId);
SampleWithConnections newSampleWithConns = data.new SampleWithConnections(newSample, lastModificationDate);
- data.samplesToCreate.put(permId, newSampleWithConns);
+ data.samplesToProcess.put(permId, newSampleWithConns);
newSampleWithConns.setConnections(parseConnections(xpath, xdNode));
newSample.setProperties(parseProperties(xpath, xdNode));
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java
index ef073481bb6f059dc3abcb1c767bab8c0d164351..eef5a44ed6db78ca0840efe34c5510b8869d1005 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java
@@ -30,31 +30,28 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewLinkDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
/**
* @author Ganime Betul Akin
*/
public class ResourceListParserData
{
- public Map<String, ProjectWithConnections> projectsToCreate = new HashMap<String, ResourceListParserData.ProjectWithConnections>();
+ public Map<String, ProjectWithConnections> projectsToProcess = new HashMap<String, ResourceListParserData.ProjectWithConnections>();
- public Map<String, ProjectUpdatesDTO> projectUpdates = new HashMap<String, ProjectUpdatesDTO>();
+ public Map<String, ExperimentWithConnections> experimentsToProcess = new HashMap<String, ResourceListParserData.ExperimentWithConnections>();
- public Map<String, ExperimentWithConnections> experimentsToCreate = new HashMap<String, ResourceListParserData.ExperimentWithConnections>();
+ public Map<String, SampleWithConnections> samplesToProcess = new HashMap<String, ResourceListParserData.SampleWithConnections>();
- public Map<String, SampleWithConnections> samplesToCreate = new HashMap<String, ResourceListParserData.SampleWithConnections>();
+ public Map<String, DataSetWithConnections> datasetsToProcess = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- public Map<String, DataSetWithConnections> datasetsToCreate = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
-
- public List<MaterialWithLastModificationDate> materialsToCreate = new ArrayList<MaterialWithLastModificationDate>();
+ public List<MaterialWithLastModificationDate> materialsToProcess = new ArrayList<MaterialWithLastModificationDate>();
public Map<String, DataSetWithConnections> filterPhysicalDataSetsByLastModificationDate(Date lastSyncDate)
{
Map<String, DataSetWithConnections> dsMap = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- for (String permId : datasetsToCreate.keySet())
+ for (String permId : datasetsToProcess.keySet())
{
- DataSetWithConnections ds = datasetsToCreate.get(permId);
+ DataSetWithConnections ds = datasetsToProcess.get(permId);
if (ds.getKind() == DataSetKind.PHYSICAL && ds.lastModificationDate.after(lastSyncDate))
{
dsMap.put(permId, ds);
@@ -67,9 +64,9 @@ public class ResourceListParserData
{
// List<NewDataSetWithConnections> dsList = new ArrayList<ResourceListParserData.NewDataSetWithConnections>();
Map<String, DataSetWithConnections> dsMap = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- for (String permId : datasetsToCreate.keySet())
+ for (String permId : datasetsToProcess.keySet())
{
- DataSetWithConnections ds = datasetsToCreate.get(permId);
+ DataSetWithConnections ds = datasetsToProcess.get(permId);
if (ds.getKind() == DataSetKind.CONTAINER)
{
dsMap.put(permId, ds);
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/shared/entitygraph/EntityGraph.java b/openbis/source/java/ch/ethz/sis/openbis/generic/shared/entitygraph/EntityGraph.java
index be39a04a156c453ed79e00ad06165cfb52cfd9f6..10f16e5383e379572f8c700f80d14b0c09f61455 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/shared/entitygraph/EntityGraph.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/shared/entitygraph/EntityGraph.java
@@ -121,7 +121,7 @@ public class EntityGraph<N extends Node<?>>
for (EdgeNodePair edgeNodePair : list)
{
Node<?> neighbourNode = edgeNodePair.getNode();
- sb.append("\"" + node.getCode() + "(" + node.getEntityKind().charAt(0) + getDifferentiatorStr(node) + ")\" -> "
+ sb.append("\"" + node.getCode() + "(" + getDifferentiatorStr(node) + ")\" -> "
+ getRightHandNodeRep(neighbourNode));
sb.append(System.getProperty("line.separator"));
}
@@ -131,7 +131,7 @@ public class EntityGraph<N extends Node<?>>
private String getRightHandNodeRep(Node<?> node)
{
- return "\"" + node.getCode() + "(" + node.getEntityKind().charAt(0) + getDifferentiatorStr(node) + ")\";";
+ return "\"" + node.getCode() + "(" + getDifferentiatorStr(node) + ")\";";
}
private String getDifferentiatorStr(Node<?> node)
@@ -139,9 +139,12 @@ public class EntityGraph<N extends Node<?>>
String differentiatorStr = "";
if (node.getEntityKind().equals("EXPERIMENT")) // in order to differentiate between experiments in the same space but under different projects
{
- differentiatorStr =
+ differentiatorStr = "-" +
node.getPermId().substring(node.getPermId().indexOf('-') + 1);
}
+ else {
+ differentiatorStr = "" + node.getEntityKind().charAt(0);
+ }
return differentiatorStr;
}