From f0dab14bad7229b51c9553a1f6988c7143366fcf Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 17 May 2011 15:47:30 +0000
Subject: [PATCH] [LMS-2104]: initial implementation of deletion for virtual
data sets
SVN: 21347
---
.../systemsx/cisd/common/collections/DAG.java | 109 ++++++++++++++++++
.../cisd/common/collections/DAGTest.java | 80 +++++++++++++
.../server/business/bo/DataSetTable.java | 83 ++++++++++---
.../shared/basic/dto/ExternalData.java | 1 -
.../openbis/generic/shared/dto/DataPE.java | 28 +++++
.../generic/shared/dto/ExternalDataPE.java | 20 ++++
.../shared/translator/DataSetTranslator.java | 1 -
.../translator/ExternalDataTranslator.java | 1 -
.../server/business/bo/DataSetTableTest.java | 1 +
9 files changed, 307 insertions(+), 17 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/collections/DAG.java
create mode 100644 common/sourceTest/java/ch/systemsx/cisd/common/collections/DAGTest.java
diff --git a/common/source/java/ch/systemsx/cisd/common/collections/DAG.java b/common/source/java/ch/systemsx/cisd/common/collections/DAG.java
new file mode 100644
index 00000000000..5f42de715f4
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/collections/DAG.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.collections;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * Directed acyclic graph.
+ *
+ * @author Kaloyan Enimanev
+ */
+public abstract class DAG<T>
+{
+ protected Collection<T> nodes;
+
+ /**
+ * constructs a {@link DAG} for a given set of nodes.
+ *
+ * @param nodes
+ */
+ public DAG(Collection<T> nodes)
+ {
+ this.nodes = Collections.unmodifiableCollection(nodes);
+ }
+
+ /**
+ * Return the graph's nodes.
+ */
+ public Collection<T> getNodes()
+ {
+ return nodes;
+ }
+
+ /**
+ * For a given node returns the list of its successors.
+ */
+ public abstract Collection<T> getSuccessors(T node);
+
+ /**
+ * @return a topological sort of the graph's nodes.
+ */
+ public List<T> sortTopologically()
+ {
+ HashSet<T> nodesCopy = new HashSet<T>(nodes);
+ ArrayList<T> sorted = new ArrayList<T>();
+ while (nodesCopy.isEmpty() == false)
+ {
+ T nextNode = getNextNodeForTopologicalSort(nodesCopy);
+ if (nextNode == null)
+ {
+ throw new UserFailureException(
+ "Graph cycle detected. Cannot execute topological sort.");
+ }
+ sorted.add(nextNode);
+ nodesCopy.remove(nextNode);
+ }
+
+ return sorted;
+ }
+
+ /**
+ * helper method for topological sorting.
+ */
+ private T getNextNodeForTopologicalSort(Collection<T> nodesCollection)
+ {
+ for (T node : nodesCollection)
+ {
+ Collection<T> successors = getSuccessors(node);
+ boolean hasDependencies = false;
+ if (successors != null)
+ {
+ for (T successor : successors)
+ {
+ if (nodesCollection.contains(successor))
+ {
+ hasDependencies = true;
+ }
+ }
+
+ }
+ if (hasDependencies == false)
+ {
+ return node;
+ }
+ }
+ return null;
+ }
+
+}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/collections/DAGTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/collections/DAGTest.java
new file mode 100644
index 00000000000..87682931ff6
--- /dev/null
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/collections/DAGTest.java
@@ -0,0 +1,80 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.common.collections;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * @author Kaloyan Enimanev
+ */
+public class DAGTest extends AssertJUnit
+{
+
+ @Test
+ public void testTopologicalSort()
+ {
+ HashMap<String, List<String>> adjacencyMap = new HashMap<String, List<String>>();
+
+ adjacencyMap.put("A", new ArrayList<String>());
+ adjacencyMap.put("B", Arrays.asList("A"));
+ adjacencyMap.put("C", Arrays.asList("A", "B"));
+ adjacencyMap.put("D", Arrays.asList("C", "B", "A"));
+ adjacencyMap.put("E", Arrays.asList("C", "D"));
+
+ Collection<String> sorted = sortTopologically(adjacencyMap);
+
+ assertEquals(Arrays.asList("A", "B", "C", "D", "E"), sorted);
+
+ }
+
+ @Test(expectedExceptions = UserFailureException.class)
+ public void testCyclicGraph()
+ {
+ HashMap<String, List<String>> adjacencyMap = new HashMap<String, List<String>>();
+
+ adjacencyMap.put("A", Arrays.asList("B"));
+ adjacencyMap.put("B", Arrays.asList("C"));
+ adjacencyMap.put("C", Arrays.asList("A"));
+
+ sortTopologically(adjacencyMap);
+ }
+
+ private Collection<String> sortTopologically(final Map<String, List<String>> adjacencyMap)
+ {
+ DAG<String> dag = new DAG<String>(adjacencyMap.keySet())
+ {
+ @Override
+ public Collection<String> getSuccessors(String node)
+ {
+ return adjacencyMap.get(node);
+ }
+ };
+
+ return dag.sortTopologically();
+ }
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
index f0faf24754a..66d29d7b487 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTable.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collection;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
@@ -36,6 +37,7 @@ import org.springframework.dao.DataIntegrityViolationException;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.collections.DAG;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -240,19 +242,22 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
public void deleteLoadedDataSets(String reason)
{
+ dataSets = loadContainedDataSetsRecursively();
assertDatasetsAreDeletable(dataSets);
- Map<DataStorePE, List<ExternalDataPE>> allToBeDeleted = groupExternalDataByDataStores();
+ dataSets = sortTopologicallyByContainerRelationship(dataSets);
+
+ Map<DataStorePE, List<DataPE>> allToBeDeleted = groupDataSetsByDataStores();
Map<DataStorePE, List<ExternalDataPE>> availableDatasets =
filterAvailableDatasets(allToBeDeleted);
assertDataSetsAreKnown(availableDatasets);
- for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : allToBeDeleted.entrySet())
+ for (Map.Entry<DataStorePE, List<DataPE>> entry : allToBeDeleted.entrySet())
{
DataStorePE dataStore = entry.getKey();
- List<ExternalDataPE> allDataSets = entry.getValue();
+ List<DataPE> allDataSets = entry.getValue();
// delete locally from DB
- for (ExternalDataPE dataSet : allDataSets)
+ for (DataPE dataSet : allDataSets)
{
deleteDataSetLocally(dataSet, reason);
}
@@ -262,19 +267,63 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
}
+ private List<DataPE> loadContainedDataSetsRecursively()
+ {
+ Map<Long, DataPE> loadCache = new HashMap<Long, DataPE>();
+ for (DataPE dataSet : dataSets)
+ {
+ loadContainedDataSetsInternal(dataSet, loadCache);
+ }
+
+ return new ArrayList<DataPE>(loadCache.values());
+ }
+
+ private void loadContainedDataSetsInternal(DataPE dataSet, Map<Long /* id */, DataPE> loaded)
+ {
+ Long id = dataSet.getId();
+ if (false == loaded.containsKey(id))
+ {
+ loaded.put(id, dataSet);
+ if (dataSet.getContainedDataSets() != null)
+ {
+ for (DataPE containedDataSet : dataSet.getContainedDataSets())
+ {
+ loadContainedDataSetsInternal(containedDataSet, loaded);
+ }
+ }
+
+ }
+ }
+
+ private List<DataPE> sortTopologicallyByContainerRelationship(List<DataPE> datasets)
+ {
+ DAG<DataPE> dag = new DAG<DataPE>(datasets)
+ {
+ @Override
+ public Collection<DataPE> getSuccessors(DataPE node)
+ {
+ return node.getContainedDataSets();
+ }
+ };
+
+ return dag.sortTopologically();
+ }
+
private Map<DataStorePE, List<ExternalDataPE>> filterAvailableDatasets(
- Map<DataStorePE, List<ExternalDataPE>> map)
+ Map<DataStorePE, List<DataPE>> map)
{
Map<DataStorePE, List<ExternalDataPE>> result =
new HashMap<DataStorePE, List<ExternalDataPE>>();
- for (Map.Entry<DataStorePE, List<ExternalDataPE>> entry : map.entrySet())
+ for (Map.Entry<DataStorePE, List<DataPE>> entry : map.entrySet())
{
ArrayList<ExternalDataPE> available = new ArrayList<ExternalDataPE>();
- for (ExternalDataPE data : entry.getValue())
+ for (DataPE data : entry.getValue())
{
- if (data.getStatus().isAvailable())
+ ExternalDataPE externalData = data.tryAsExternalData();
+ if (externalData != null && externalData.isAvailable())
{
- available.add(data);
+
+ available.add(externalData);
}
}
result.put(entry.getKey(), available);
@@ -282,7 +331,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return result;
}
- private void deleteDataSetLocally(ExternalDataPE dataSet, String reason)
+ private void deleteDataSetLocally(DataPE dataSet, String reason)
throws UserFailureException
{
try
@@ -301,7 +350,7 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
}
}
- public static EventPE createDeletionEvent(ExternalDataPE dataSet, PersonPE registrator,
+ public static EventPE createDeletionEvent(DataPE dataSet, PersonPE registrator,
String reason)
{
EventPE event = new EventPE();
@@ -315,9 +364,16 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
return event;
}
- private static String getDeletionDescription(ExternalDataPE dataSet)
+ private static String getDeletionDescription(DataPE dataSet)
{
- return dataSet.getLocation();
+ if (dataSet.isExternalData())
+ {
+ return dataSet.tryAsExternalData().getLocation();
+
+ } else
+ {
+ return StringUtils.EMPTY;
+ }
}
public String uploadLoadedDataSetsToCIFEX(DataSetUploadContext uploadContext)
@@ -451,7 +507,6 @@ public final class DataSetTable extends AbstractDataSetBusinessObject implements
/** groups all data sets (both virtual and non-virtual) by data stores */
// TODO 2011-05-17, Piotr Buczek: use this instead of groupExternalDataByDataStores in places
// where we want to support virtual data sets
- @SuppressWarnings("unused")
private Map<DataStorePE, List<DataPE>> groupDataSetsByDataStores()
{
Map<DataStorePE, List<DataPE>> map = new LinkedHashMap<DataStorePE, List<DataPE>>();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
index b2ce1cf8077..92a20655689 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ExternalData.java
@@ -62,7 +62,6 @@ public class ExternalData extends CodeWithRegistration<ExternalData> implements
private Collection<ExternalData> parents;
- // TODO KE: 2011-05-06 Implement a logic in ContainerDataSets to calculate the size
private Long size;
private Sample sample;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
index 26bb5f19683..ef8e31f3cc5 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/DataPE.java
@@ -642,4 +642,32 @@ public class DataPE extends AbstractIdAndCodeHolder<DataPE> implements
return (this instanceof ExternalDataPE) ? (ExternalDataPE) this : null;
}
+ /**
+ * return true if the data set if available in the data store.
+ */
+ @Transient
+ public boolean isAvailable()
+ {
+ return false;
+ }
+
+ /**
+ * return true if the data set can be deleted.
+ */
+ @Transient
+ public boolean isDeletable()
+ {
+ if (containedDataSets != null)
+ {
+ for (DataPE containedDataSet : containedDataSets)
+ {
+ if (containedDataSet.isDeletable() == false)
+ {
+ return false;
+ }
+ }
+
+ }
+ return true;
+ }
}
\ No newline at end of file
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
index 3622089df33..f26e7454381 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/ExternalDataPE.java
@@ -234,4 +234,24 @@ public final class ExternalDataPE extends DataPE
this.speedHint = speedHint == null ? Constants.DEFAULT_SPEED_HINT : speedHint;
}
+ /**
+ * return true if the data set if available in the data store.
+ */
+ @Transient
+ @Override
+ public boolean isAvailable()
+ {
+ return getStatus().isAvailable();
+ }
+
+ /**
+ * return true if the data set can be deleted.
+ */
+ @Transient
+ @Override
+ public boolean isDeletable()
+ {
+ return getStatus().isDeletable();
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
index 6b8ed36280d..6e0e1cb9179 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/DataSetTranslator.java
@@ -67,7 +67,6 @@ public class DataSetTranslator
DataSet dataSet = data.tryGetAsDataSet();
if (dataSet != null)
{
- // TODO KE: 2011-05-06 make sure this other classes handle NULL correctly
description.setDataSetLocation(dataSet.getLocation());
description.setSpeedHint(dataSet.getSpeedHint());
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
index 5f25ef920e7..c1a589d54ba 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/translator/ExternalDataTranslator.java
@@ -67,7 +67,6 @@ public class ExternalDataTranslator
DataSet dataSet = data.tryGetAsDataSet();
if (dataSet != null)
{
- // TODO KE: 2011-05-06 make sure this other classes handle NULL correctly
description.setDataSetLocation(dataSet.getLocation());
description.setSpeedHint(dataSet.getSpeedHint());
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
index 51386c46939..b640b92556b 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/DataSetTableTest.java
@@ -481,6 +481,7 @@ public final class DataSetTableTest extends AbstractBOTest
private ExternalDataPE createDataSet(String code, DataStorePE dataStore)
{
ExternalDataPE data = new ExternalDataPE();
+ data.setId((long) code.hashCode());
data.setCode(code);
data.setDataStore(dataStore);
data.setLocation("here/" + code);
--
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