From 036e058f092222ab17452f8e56de5f6fba288575 Mon Sep 17 00:00:00 2001
From: anttil <anttil>
Date: Wed, 8 Mar 2017 09:33:04 +0000
Subject: [PATCH] SSDM-4725: Get all copies of linked datasets through v3 api
SVN: 37863
---
.../server/dssapi/v3/DataStoreServerApi.java | 2 +-
.../dataset/ContentCopyBaseTranslator.java | 22 +++
... => ContentCopyExternalDmsTranslator.java} | 8 +-
.../translator/dataset/ContentCopyRecord.java | 12 ++
.../dataset/ContentCopyTranslator.java | 62 +++++++++
.../v3/translator/dataset/DataSetQuery.java | 10 +-
.../dataset/IContentCopyBaseTranslator.java | 8 ++
...=> IContentCopyExternalDmsTranslator.java} | 5 +-
.../dataset/IContentCopyTranslator.java | 10 ++
.../ILinkedDataContentCopiesTranslator.java | 6 +
.../IObjectToContentCopiesTranslator.java | 10 ++
.../dataset/LinkedDataBaseRecord.java | 4 +
.../LinkedDataContentCopiesTranslator.java | 21 +++
.../dataset/LinkedDataTranslator.java | 38 ++++--
.../ObjectToContentCopiesTranslator.java | 34 +++++
.../bo/datasetlister/DatasetLister.java | 11 +-
.../generic/server/dataaccess/db/DataDAO.java | 11 ++
.../generic/shared/dto/LinkDataPE.java | 2 +-
.../asapi/v3/AbstractExternalDmsTest.java | 15 +-
.../asapi/v3/AbstractLinkDataSetTest.java | 99 +++++++++-----
.../asapi/v3/CreateExternalDmsTest.java | 3 -
.../asapi/v3/CreateLinkDataSetTest.java | 129 ++++++++++++++++--
.../asapi/v3/GetExternalDmsTest.java | 3 -
.../asapi/v3/GetLinkDataSetTest.java | 98 +++++++++++++
.../asapi/v3/dto/dataset/LinkedData.java | 19 +++
.../generic/sharedapi/v3/dictionary.txt | 4 +-
26 files changed, 556 insertions(+), 90 deletions(-)
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyBaseTranslator.java
rename openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/{LinkedDataExternalDmsTranslator.java => ContentCopyExternalDmsTranslator.java} (91%)
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyRecord.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyTranslator.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyBaseTranslator.java
rename openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/{ILinkedDataExternalDmsTranslator.java => IContentCopyExternalDmsTranslator.java} (86%)
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyTranslator.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataContentCopiesTranslator.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IObjectToContentCopiesTranslator.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataContentCopiesTranslator.java
create mode 100644 openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ObjectToContentCopiesTranslator.java
create mode 100644 openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetLinkDataSetTest.java
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
index ba8b64783a5..b3f130aeaa5 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dssapi/v3/DataStoreServerApi.java
@@ -308,7 +308,7 @@ public class DataStoreServerApi extends AbstractDssServiceRpc<IDataStoreServerAp
List<DataSetFileCreation> files = newDataSets.get(i).getFileMetadata();
long dataSetId =
- dao.createDataSet(permId, newDataSets.get(i).getMetadataCreation().getLinkedData().getExternalDmsId().toString());
+ dao.createDataSet(permId, "External system(s)");
try
{
dao.createDataSetFiles(PathInfoDTOCreator.createPathEntries(dataSetId, permId, files));
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyBaseTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyBaseTranslator.java
new file mode 100644
index 00000000000..313623a91ee
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyBaseTranslator.java
@@ -0,0 +1,22 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import java.util.List;
+
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectBaseTranslator;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import net.lemnik.eodsql.QueryTool;
+
+@Component
+public class ContentCopyBaseTranslator extends ObjectBaseTranslator<ContentCopyRecord> implements IContentCopyBaseTranslator
+{
+
+ @Override
+ protected List<ContentCopyRecord> loadRecords(LongOpenHashSet objectIds)
+ {
+ DataSetQuery query = QueryTool.getManagedQuery(DataSetQuery.class);
+ return query.getContentCopies(new LongOpenHashSet(objectIds));
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataExternalDmsTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyExternalDmsTranslator.java
similarity index 91%
rename from openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataExternalDmsTranslator.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyExternalDmsTranslator.java
index 3c470989860..fabbe1d92a4 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataExternalDmsTranslator.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyExternalDmsTranslator.java
@@ -34,12 +34,9 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectRelat
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectToOneRelationTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.externaldms.IExternalDmsTranslator;
-/**
- * @author pkupczyk
- */
@Component
-public class LinkedDataExternalDmsTranslator extends ObjectToOneRelationTranslator<ExternalDms, ExternalDmsFetchOptions> implements
- ILinkedDataExternalDmsTranslator
+public class ContentCopyExternalDmsTranslator extends ObjectToOneRelationTranslator<ExternalDms, ExternalDmsFetchOptions> implements
+ IContentCopyExternalDmsTranslator
{
@Autowired
@@ -58,5 +55,4 @@ public class LinkedDataExternalDmsTranslator extends ObjectToOneRelationTranslat
{
return externalDmsTranslator.translate(context, relatedIds, relatedFetchOptions);
}
-
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyRecord.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyRecord.java
new file mode 100644
index 00000000000..fa40d1be357
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyRecord.java
@@ -0,0 +1,12 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectBaseRecord;
+
+public class ContentCopyRecord extends ObjectBaseRecord
+{
+ public String externalCode;
+
+ public String path;
+
+ public String gitCommitHash;
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyTranslator.java
new file mode 100644
index 00000000000..29d7a070a44
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ContentCopyTranslator.java
@@ -0,0 +1,62 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import java.util.Collection;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.AbstractCachingTranslator;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.TranslationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.TranslationResults;
+
+@Component
+public class ContentCopyTranslator extends AbstractCachingTranslator<Long, ContentCopy, LinkedDataFetchOptions> implements IContentCopyTranslator
+{
+
+ @Autowired
+ private IContentCopyBaseTranslator baseTranslator;
+
+ @Autowired
+ private IContentCopyExternalDmsTranslator externalDmsTranslator;
+
+ @Override
+ protected ContentCopy createObject(TranslationContext context, Long input, LinkedDataFetchOptions fetchOptions)
+ {
+ return new ContentCopy();
+ }
+
+ @Override
+ protected TranslationResults getObjectsRelations(TranslationContext context, Collection<Long> copyIds, LinkedDataFetchOptions fetchOptions)
+ {
+ TranslationResults relations = new TranslationResults();
+
+ relations.put(IContentCopyBaseTranslator.class, baseTranslator.translate(context, copyIds, null));
+
+ if (fetchOptions.hasExternalDms())
+ {
+ relations.put(IContentCopyExternalDmsTranslator.class, externalDmsTranslator.translate(context, copyIds, null));
+ }
+
+ return relations;
+ }
+
+ @Override
+ protected void updateObject(TranslationContext context, Long input, ContentCopy output, Object objectRelations,
+ LinkedDataFetchOptions fetchOptions)
+ {
+ TranslationResults relations = (TranslationResults) objectRelations;
+ ContentCopyRecord baseRecord = relations.get(IContentCopyBaseTranslator.class, input);
+ output.setExternalCode(baseRecord.externalCode);
+ output.setPath(baseRecord.path);
+ output.setGitCommitHash(baseRecord.gitCommitHash);
+ if (fetchOptions.hasExternalDms())
+ {
+ ExternalDms externalDms = relations.get(IContentCopyExternalDmsTranslator.class, input);
+ output.setExternalDms(externalDms);
+ }
+ }
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/DataSetQuery.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/DataSetQuery.java
index 69df673bf02..424a371e59e 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/DataSetQuery.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/DataSetQuery.java
@@ -25,6 +25,7 @@ import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.MaterialP
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.PropertyAssignmentRecord;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.property.PropertyRecord;
import ch.systemsx.cisd.common.db.mapper.LongSetMapper;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
import it.unimi.dsi.fastutil.longs.LongSet;
import net.lemnik.eodsql.Select;
@@ -66,7 +67,7 @@ public interface DataSetQuery extends ObjectQuery
LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<LinkedDataBaseRecord> getLinkedDatas(LongSet dataSetIds);
- @Select(sql = "select ld.data_id as objectId, cc.edms_id as relatedId from link_data ld, content_copies cc where cc.data_id = ld.data_id and ld.data_id = any(?{1})", parameterBindings = {
+ @Select(sql = "select cc.id as objectId, cc.edms_id as relatedId from content_copies cc where cc.id = any(?{1})", parameterBindings = {
LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<ObjectRelationRecord> getExternalDmsIds(LongSet dataSetIds);
@@ -193,4 +194,11 @@ public interface DataSetQuery extends ObjectQuery
LongSetMapper.class }, fetchSize = FETCH_SIZE)
public List<PropertyAssignmentRecord> getPropertyAssignments(LongSet dataSetTypePropertyTypeIds);
+ @Select(sql = "select d.id as objectId, cc.id as relatedId from data d, content_copies cc where cc.data_id = d.id and d.id = any(?{1})", parameterBindings = {
+ LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ObjectRelationRecord> getContentCopyIds(LongOpenHashSet dataSetIds);
+
+ @Select(sql = "select id, external_code as externalCode, path, git_commit_hash as gitCommitHash from content_copies where id = any(?{1})", parameterBindings = {
+ LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public List<ContentCopyRecord> getContentCopies(LongOpenHashSet longOpenHashSet);
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyBaseTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyBaseTranslator.java
new file mode 100644
index 00000000000..17dedb68e7a
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyBaseTranslator.java
@@ -0,0 +1,8 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.IObjectBaseTranslator;
+
+public interface IContentCopyBaseTranslator extends IObjectBaseTranslator<ContentCopyRecord>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataExternalDmsTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyExternalDmsTranslator.java
similarity index 86%
rename from openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataExternalDmsTranslator.java
rename to openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyExternalDmsTranslator.java
index 2c1da37164f..37f94ba7d22 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataExternalDmsTranslator.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyExternalDmsTranslator.java
@@ -20,10 +20,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.fetchoptions.ExternalDmsFetchOptions;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.IObjectToOneRelationTranslator;
-/**
- * @author pkupczyk
- */
-public interface ILinkedDataExternalDmsTranslator extends IObjectToOneRelationTranslator<ExternalDms, ExternalDmsFetchOptions>
+public interface IContentCopyExternalDmsTranslator extends IObjectToOneRelationTranslator<ExternalDms, ExternalDmsFetchOptions>
{
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyTranslator.java
new file mode 100644
index 00000000000..39c51f43fa1
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IContentCopyTranslator.java
@@ -0,0 +1,10 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.ITranslator;
+
+public interface IContentCopyTranslator extends ITranslator<Long, ContentCopy, LinkedDataFetchOptions>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataContentCopiesTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataContentCopiesTranslator.java
new file mode 100644
index 00000000000..18b2be647d3
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ILinkedDataContentCopiesTranslator.java
@@ -0,0 +1,6 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+public interface ILinkedDataContentCopiesTranslator extends IObjectToContentCopiesTranslator
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IObjectToContentCopiesTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IObjectToContentCopiesTranslator.java
new file mode 100644
index 00000000000..62a1a012521
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/IObjectToContentCopiesTranslator.java
@@ -0,0 +1,10 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.IObjectToManyRelationTranslator;
+
+public interface IObjectToContentCopiesTranslator extends IObjectToManyRelationTranslator<ContentCopy, LinkedDataFetchOptions>
+{
+
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataBaseRecord.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataBaseRecord.java
index c5c0f5ed7a3..a839d139d7a 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataBaseRecord.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataBaseRecord.java
@@ -16,6 +16,8 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+import java.util.List;
+
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectBaseRecord;
/**
@@ -26,4 +28,6 @@ public class LinkedDataBaseRecord extends ObjectBaseRecord
public String externalCode;
+ public List<ContentCopyRecord> copies;
+
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataContentCopiesTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataContentCopiesTranslator.java
new file mode 100644
index 00000000000..6ba395994fe
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataContentCopiesTranslator.java
@@ -0,0 +1,21 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import java.util.List;
+
+import org.springframework.stereotype.Component;
+
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectRelationRecord;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import net.lemnik.eodsql.QueryTool;
+
+@Component
+public class LinkedDataContentCopiesTranslator extends ObjectToContentCopiesTranslator implements ILinkedDataContentCopiesTranslator
+{
+
+ @Override
+ protected List<ObjectRelationRecord> loadRecords(LongOpenHashSet dataSetIds)
+ {
+ DataSetQuery query = QueryTool.getManagedQuery(DataSetQuery.class);
+ return query.getContentCopyIds(dataSetIds);
+ }
+}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataTranslator.java
index 5ed7409026d..270dfcf6275 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataTranslator.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/LinkedDataTranslator.java
@@ -16,13 +16,17 @@
package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+import java.util.ArrayList;
import java.util.Collection;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.LinkedData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressType;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.AbstractCachingTranslator;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.TranslationContext;
import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.TranslationResults;
@@ -36,10 +40,7 @@ public class LinkedDataTranslator extends AbstractCachingTranslator<Long, Linked
{
@Autowired
- private ILinkedDataBaseTranslator baseTranslator;
-
- @Autowired
- private ILinkedDataExternalDmsTranslator externalDmsTranslator;
+ private ILinkedDataContentCopiesTranslator contentCopiesTranslator;
@Override
protected LinkedData createObject(TranslationContext context, Long dataSetId, LinkedDataFetchOptions fetchOptions)
@@ -54,13 +55,7 @@ public class LinkedDataTranslator extends AbstractCachingTranslator<Long, Linked
{
TranslationResults relations = new TranslationResults();
- relations.put(ILinkedDataBaseTranslator.class, baseTranslator.translate(context, dataSetIds, null));
-
- if (fetchOptions.hasExternalDms())
- {
- relations.put(ILinkedDataExternalDmsTranslator.class,
- externalDmsTranslator.translate(context, dataSetIds, fetchOptions.withExternalDms()));
- }
+ relations.put(ILinkedDataContentCopiesTranslator.class, contentCopiesTranslator.translate(context, dataSetIds, fetchOptions));
return relations;
}
@@ -70,13 +65,28 @@ public class LinkedDataTranslator extends AbstractCachingTranslator<Long, Linked
LinkedDataFetchOptions fetchOptions)
{
TranslationResults relations = (TranslationResults) objectRelations;
- LinkedDataBaseRecord baseRecord = relations.get(ILinkedDataBaseTranslator.class, dataSetId);
+ Collection<ContentCopy> copies = relations.get(ILinkedDataContentCopiesTranslator.class, dataSetId);
+
+ ArrayList<ContentCopy> copyList = new ArrayList<>(copies);
+ result.setContentCopies(copyList);
+
+ String externalCode = LinkedData.NO_COPY_EXTERNAL_CODE;
+ ExternalDms externalDms = LinkedData.NO_COPY_EXTERNAL_DMS;
+ for (ContentCopy copy : copyList)
+ {
+ ExternalDmsAddressType type = copy.getExternalDms().getAddressType();
+ if (type.equals(ExternalDmsAddressType.OPENBIS) || type.equals(ExternalDmsAddressType.URL))
+ {
+ externalCode = copy.getExternalCode();
+ externalDms = copy.getExternalDms();
+ }
+ }
- result.setExternalCode(baseRecord.externalCode);
+ result.setExternalCode(externalCode);
if (fetchOptions.hasExternalDms())
{
- result.setExternalDms(relations.get(ILinkedDataExternalDmsTranslator.class, dataSetId));
+ result.setExternalDms(externalDms);
result.getFetchOptions().withExternalDmsUsing(fetchOptions.withExternalDms());
}
}
diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ObjectToContentCopiesTranslator.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ObjectToContentCopiesTranslator.java
new file mode 100644
index 00000000000..ee88df83d2b
--- /dev/null
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/asapi/v3/translator/dataset/ObjectToContentCopiesTranslator.java
@@ -0,0 +1,34 @@
+package ch.ethz.sis.openbis.generic.server.asapi.v3.translator.dataset;
+
+import java.util.Collection;
+import java.util.LinkedHashSet;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.TranslationContext;
+import ch.ethz.sis.openbis.generic.server.asapi.v3.translator.common.ObjectToManyRelationTranslator;
+
+public abstract class ObjectToContentCopiesTranslator extends ObjectToManyRelationTranslator<ContentCopy, LinkedDataFetchOptions>
+ implements IObjectToContentCopiesTranslator
+{
+
+ @Autowired
+ private IContentCopyTranslator contentCopyTranslator;
+
+ @Override
+ protected Map<Long, ContentCopy> translateRelated(TranslationContext context, Collection<Long> relatedIds,
+ LinkedDataFetchOptions relatedFetchOptions)
+ {
+
+ return contentCopyTranslator.translate(context, relatedIds, relatedFetchOptions);
+ }
+
+ @Override
+ protected Collection<ContentCopy> createCollection()
+ {
+ return new LinkedHashSet<ContentCopy>();
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index 057b9170286..846942c9354 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -1181,9 +1181,14 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
LinkDataSet linkDataSet = new LinkDataSet();
convertStandardAttributes(linkDataSet, record);
- linkDataSet.setExternalDataManagementSystem(externalDataManagementSystems
- .get(record.edms_id));
- linkDataSet.setExternalCode(record.external_code);
+
+ if (record.edms_id != null)
+ {
+
+ linkDataSet.setExternalDataManagementSystem(externalDataManagementSystems
+ .get(record.edms_id));
+ linkDataSet.setExternalCode(record.external_code);
+ }
return linkDataSet;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
index fd5edb1c0ed..17ae4aab17c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/DataDAO.java
@@ -827,6 +827,7 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
sqls.insertEvent = SQLBuilder.createInsertEventSQL();
// data set specific queries
sqls.deleteExternalData = createDeleteExternalDataSQL();
+ sqls.deleteContentCopies = createDeleteContentCopiesSQL();
Long relationshipTypeId = RelationshipUtils.getParentChildRelationshipType(relationshipTypeDAO).getId();
sqls.deleteChildrenConnections = createDeleteChildrenConnectionsSQL(relationshipTypeId);
sqls.deleteParentConnections = createDeleteParentConnectionsSQL(relationshipTypeId);
@@ -851,6 +852,8 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
public String deleteExternalData;
+ public String deleteContentCopies;
+
public String deleteChildrenConnections;
public String deleteParentConnections;
@@ -896,6 +899,12 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
+ SQLBuilder.inEntityIds();
}
+ private static String createDeleteContentCopiesSQL()
+ {
+ return "DELETE FROM " + TableNames.CONTENT_COPIES_TABLE + " WHERE data_id "
+ + SQLBuilder.inEntityIds();
+ }
+
private static String createDeleteChildrenConnectionsSQL(long relationshipTypeId)
{
return "DELETE FROM " + TableNames.DATA_SET_RELATIONSHIPS_ALL_TABLE
@@ -1048,6 +1057,7 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
final SQLQuery deleteEntities = session.createSQLQuery(sqls.deleteDataSets);
final SQLQuery insertEvent = session.createSQLQuery(sqls.insertEvent);
final SQLQuery deleteExternalData = session.createSQLQuery(sqls.deleteExternalData);
+ final SQLQuery deleteContentCopies = session.createSQLQuery(sqls.deleteContentCopies);
final SQLQuery deleteChildrenConnections = session.createSQLQuery(sqls.deleteChildrenConnections);
final SQLQuery deleteParentConnections = session.createSQLQuery(sqls.deleteParentConnections);
@@ -1065,6 +1075,7 @@ final class DataDAO extends AbstractGenericEntityWithPropertiesDAO<DataPE> imple
executeUpdate(deleteProperties, entityIdsToDelete);
executeUpdate(deleteExternalData, entityIdsToDelete);
+ executeUpdate(deleteContentCopies, entityIdsToDelete);
executeUpdate(deleteChildrenConnections, entityIdsToDelete);
executeUpdate(deleteParentConnections, entityIdsToDelete);
executeUpdate(deleteEntities, entityIdsToDelete);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LinkDataPE.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LinkDataPE.java
index 9cbae55e4c5..6762659d79c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LinkDataPE.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/LinkDataPE.java
@@ -49,7 +49,7 @@ public class LinkDataPE extends DataPE
private Set<ContentCopyPE> contentCopies;
- @OneToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL, mappedBy = "dataSet")
+ @OneToMany(fetch = FetchType.EAGER, cascade = CascadeType.ALL, mappedBy = "dataSet", orphanRemoval = true)
@Fetch(FetchMode.SUBSELECT)
@IndexedEmbedded(prefix = SearchFieldConstants.PREFIX_CONTENT_COPY)
public Set<ContentCopyPE> getContentCopies()
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractExternalDmsTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractExternalDmsTest.java
index 7c8df4b2879..6dcc95b2a38 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractExternalDmsTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractExternalDmsTest.java
@@ -10,6 +10,7 @@ import org.apache.commons.lang.builder.ToStringBuilder;
import org.hamcrest.Description;
import org.hamcrest.Matcher;
import org.hamcrest.TypeSafeDiagnosingMatcher;
+import org.testng.annotations.BeforeClass;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressType;
@@ -21,19 +22,25 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.IExternalDmsId;
public abstract class AbstractExternalDmsTest extends AbstractTest
{
+ protected String session;
+
+ @BeforeClass
+ protected void login()
+ {
+ session = v3api.login(TEST_USER, PASSWORD);
+ }
+
protected ExternalDmsPermId create(ExternalDmsCreationBuilder creation)
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
List<ExternalDmsPermId> ids =
- v3api.createExternalDataManagementSystems(sessionToken, Collections.singletonList(creation.build()));
+ v3api.createExternalDataManagementSystems(session, Collections.singletonList(creation.build()));
return ids.get(0);
}
protected ExternalDms get(ExternalDmsPermId id)
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
Map<IExternalDmsId, ExternalDms> result =
- v3api.getExternalDataManagementSystems(sessionToken, Collections.singletonList(id), new ExternalDmsFetchOptions());
+ v3api.getExternalDataManagementSystems(session, Collections.singletonList(id), new ExternalDmsFetchOptions());
return result.get(id);
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractLinkDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractLinkDataSetTest.java
index 08d258e835d..308a2266f60 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractLinkDataSetTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/AbstractLinkDataSetTest.java
@@ -1,90 +1,105 @@
package ch.ethz.sis.openbis.systemtest.asapi.v3;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;
+import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.ContentCopy;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.ContentCopyCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.DataSetTypeCreation;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.create.LinkedDataCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.delete.DataSetDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.IDataSetId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.deletion.id.IDeletionId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.IEntityTypeId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentCreation;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.create.ExperimentTypeCreation;
+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.externaldms.ExternalDmsAddressType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.IExternalDmsId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.create.ProjectCreation;
+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.space.create.SpaceCreation;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.delete.SpaceDeletionOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.SpacePermId;
public abstract class AbstractLinkDataSetTest extends AbstractExternalDmsTest
{
- private IEntityTypeId linkDataSetType;
-
private ExperimentPermId experiment;
+ private SpacePermId space;
+
+ private ProjectPermId project;
+
+ private List<DataSetPermId> datasets = new ArrayList<DataSetPermId>();
+
@BeforeClass
protected void createData()
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
- DataSetTypeCreation datasetTypeCreation = new DataSetTypeCreation();
- datasetTypeCreation.setCode("linked-" + uuid());
- datasetTypeCreation.setKind(DataSetKind.LINK);
-
- this.linkDataSetType = v3api.createDataSetTypes(sessionToken, Collections.singletonList(datasetTypeCreation)).get(0);
-
SpaceCreation spaceCreation = new SpaceCreation();
spaceCreation.setCode("space-" + uuid());
- SpacePermId space = v3api.createSpaces(sessionToken, Collections.singletonList(spaceCreation)).get(0);
+ space = v3api.createSpaces(session, Collections.singletonList(spaceCreation)).get(0);
ProjectCreation projectCreation = new ProjectCreation();
projectCreation.setCode("project-" + uuid());
projectCreation.setSpaceId(space);
- ProjectPermId project = v3api.createProjects(sessionToken, Collections.singletonList(projectCreation)).get(0);
-
- ExperimentTypeCreation experimentTypeCreation = new ExperimentTypeCreation();
- experimentTypeCreation.setCode("experiment-type-" + uuid());
- EntityTypePermId experimentType = v3api.createExperimentTypes(sessionToken, Collections.singletonList(experimentTypeCreation)).get(0);
+ project = v3api.createProjects(session, Collections.singletonList(projectCreation)).get(0);
ExperimentCreation experimentCreation = new ExperimentCreation();
experimentCreation.setCode("experiment-" + uuid());
- experimentCreation.setTypeId(experimentType);
+ experimentCreation.setProperty("DESCRIPTION", "DESCRIPTION");
+ experimentCreation.setTypeId(new EntityTypePermId("SIRNA_HCS"));
experimentCreation.setProjectId(project);
+ experiment = v3api.createExperiments(session, Collections.singletonList(experimentCreation)).get(0);
+ }
- this.experiment = v3api.createExperiments(sessionToken, Collections.singletonList(experimentCreation)).get(0);
-
+ @AfterClass
+ protected void deleteData()
+ {
+ DataSetDeletionOptions dd = new DataSetDeletionOptions();
+ dd.setReason("test");
+ ExperimentDeletionOptions ed = new ExperimentDeletionOptions();
+ ed.setReason("test");
+ ProjectDeletionOptions pd = new ProjectDeletionOptions();
+ pd.setReason("test");
+ SpaceDeletionOptions sd = new SpaceDeletionOptions();
+ sd.setReason("test");
+
+ IDeletionId delDataSets = v3api.deleteDataSets(session, datasets, dd);
+ IDeletionId delExperiments = v3api.deleteExperiments(session, Collections.singletonList(experiment), ed);
+ v3api.confirmDeletions(session, Collections.singletonList(delDataSets));
+ v3api.confirmDeletions(session, Collections.singletonList(delExperiments));
+ v3api.deleteProjects(session, Collections.singletonList(project), pd);
+ v3api.deleteSpaces(session, Collections.singletonList(space), sd);
}
protected DataSetPermId create(LinkDataCreationBuilder creation)
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
- List<DataSetPermId> ids = v3api.createDataSets(sessionToken, Collections.singletonList(creation.build()));
+ List<DataSetPermId> ids = v3api.createDataSets(session, Collections.singletonList(creation.build()));
+ datasets.addAll(ids);
return ids.get(0);
}
protected DataSet get(DataSetPermId id)
{
- final String sessionToken = v3api.login(TEST_USER, PASSWORD);
DataSetFetchOptions fo = new DataSetFetchOptions();
LinkedDataFetchOptions lfo = new LinkedDataFetchOptions();
lfo.withExternalDms();
fo.withLinkedDataUsing(lfo);
- Map<IDataSetId, DataSet> result = v3api.getDataSets(sessionToken, Collections.singletonList(id), fo);
+ Map<IDataSetId, DataSet> result = v3api.getDataSets(session, Collections.singletonList(id), fo);
return result.get(id);
}
@@ -159,24 +174,26 @@ public abstract class AbstractLinkDataSetTest extends AbstractExternalDmsTest
protected class LinkDataCreationBuilder
{
- private List<ContentCopyCreation> copies;
+ private List<ContentCopyCreation> copies = new ArrayList<>();
private String externalCode;
private IExternalDmsId edms;
- public LinkDataCreationBuilder with(ContentCopyCreationBuilder copy)
+ public LinkDataCreationBuilder with(ContentCopyCreationBuilder copy1, ContentCopyCreationBuilder... rest)
{
- return with(copy.build());
+ LinkDataCreationBuilder result = with(copy1.build());
+ for (ContentCopyCreationBuilder b : rest)
+ {
+ result = result.with(b.build());
+ }
+ return result;
}
- public LinkDataCreationBuilder with(ContentCopyCreation copy)
+ public LinkDataCreationBuilder with(ContentCopyCreation first, ContentCopyCreation... rest)
{
- if (copies == null)
- {
- copies = new ArrayList<>();
- }
- copies.add(copy);
+ copies.add(first);
+ copies.addAll(Arrays.asList(rest));
return this;
}
@@ -200,11 +217,21 @@ public abstract class AbstractLinkDataSetTest extends AbstractExternalDmsTest
linkData.setExternalDmsId(edms);
DataSetCreation creation = new DataSetCreation();
creation.setLinkedData(linkData);
- creation.setTypeId(linkDataSetType);
+ creation.setTypeId(new EntityTypePermId("LINK_TYPE"));
creation.setExperimentId(experiment);
creation.setAutoGeneratedCode(true);
creation.setDataStoreId(new DataStorePermId("STANDARD"));
return creation;
}
}
+
+ protected String stringify(ContentCopyCreation c)
+ {
+ return c.getExternalId() + " / " + c.getPath() + " / " + c.getGitCommitHash() + " / " + c.getExternalDmsId();
+ }
+
+ protected String stringify(ContentCopy c)
+ {
+ return c.getExternalCode() + " / " + c.getPath() + " / " + c.getGitCommitHash() + " / " + c.getExternalDms().getCode();
+ }
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExternalDmsTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExternalDmsTest.java
index 8af18317149..cec5f019891 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExternalDmsTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateExternalDmsTest.java
@@ -28,9 +28,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressTy
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
-/**
- * @author anttil
- */
public class CreateExternalDmsTest extends AbstractExternalDmsTest
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateLinkDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateLinkDataSetTest.java
index f351f33f55f..8293a9c79d4 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateLinkDataSetTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/CreateLinkDataSetTest.java
@@ -3,8 +3,12 @@ package ch.ethz.sis.openbis.systemtest.asapi.v3;
import static org.hamcrest.CoreMatchers.is;
import static org.hamcrest.MatcherAssert.assertThat;
+import java.util.Arrays;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
+import org.hamcrest.collection.IsIterableContainingInAnyOrder;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
@@ -18,8 +22,8 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
public class CreateLinkDataSetTest extends AbstractLinkDataSetTest
{
- @Test(enabled = false)
- void copiesInOpenBISWork()
+ @Test
+ void copyInOpenBIS()
{
ExternalDmsPermId openbis = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
ContentCopyCreation creation = copyAt(openbis).build();
@@ -35,15 +39,115 @@ public class CreateLinkDataSetTest extends AbstractLinkDataSetTest
assertThat(copy.getExternalDms(), isSimilarTo(get(openbis)));
}
- // this goes to GetLinkDataSetTest, look for problems in legacy fields
- // @Test
- // void copiesInOpenBISWork()
- // {
- // ExternalDmsPermId openbis = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
- // DataSetPermId id = create(linkDataSet().with(copyAt(openbis)));
- // DataSet dataSet = get(id);
- // assertThat(dataSet.getLinkedData().getExternalDms(), isSimilarTo(get(openbis)));
- // }
+ @Test
+ void copyInURL()
+ {
+ ExternalDmsPermId url = create(externalDms().withType(ExternalDmsAddressType.URL));
+ ContentCopyCreation creation = copyAt(url).build();
+ DataSetPermId id = create(linkDataSet().with(creation));
+ List<ContentCopy> contentCopies = get(id).getLinkedData().getContentCopies();
+
+ assertThat(contentCopies.size(), is(1));
+
+ ContentCopy copy = contentCopies.get(0);
+ assertThat(copy.getExternalCode(), is(creation.getExternalId()));
+ assertThat(copy.getPath(), is(creation.getPath()));
+ assertThat(copy.getGitCommitHash(), is(creation.getGitCommitHash()));
+ assertThat(copy.getExternalDms(), isSimilarTo(get(url)));
+ }
+
+ @Test
+ void copyInPlainFileSystem()
+ {
+ ExternalDmsPermId fs = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ ContentCopyCreation creation = copyAt(fs).withPath("/path/to/dir").build();
+ DataSetPermId id = create(linkDataSet().with(creation));
+ List<ContentCopy> contentCopies = get(id).getLinkedData().getContentCopies();
+
+ assertThat(contentCopies.size(), is(1));
+
+ ContentCopy copy = contentCopies.get(0);
+ assertThat(copy.getExternalCode(), is(creation.getExternalId()));
+ assertThat(copy.getPath(), is(creation.getPath()));
+ assertThat(copy.getGitCommitHash(), is(creation.getGitCommitHash()));
+ assertThat(copy.getExternalDms(), isSimilarTo(get(fs)));
+ }
+
+ @Test
+ void copyInGit()
+ {
+ ExternalDmsPermId fs = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ ContentCopyCreation creation = copyAt(fs).withPath("/path/to/dir").withGitCommitHash("asdfasfa").build();
+ DataSetPermId id = create(linkDataSet().with(creation));
+ List<ContentCopy> contentCopies = get(id).getLinkedData().getContentCopies();
+
+ assertThat(contentCopies.size(), is(1));
+
+ ContentCopy copy = contentCopies.get(0);
+ assertThat(copy.getExternalCode(), is(creation.getExternalId()));
+ assertThat(copy.getPath(), is(creation.getPath()));
+ assertThat(copy.getGitCommitHash(), is(creation.getGitCommitHash()));
+ assertThat(copy.getExternalDms(), isSimilarTo(get(fs)));
+ }
+
+ @Test
+ void noCopies()
+ {
+ DataSetPermId id = create(linkDataSet());
+ List<ContentCopy> contentCopies = get(id).getLinkedData().getContentCopies();
+
+ assertThat(contentCopies.size(), is(0));
+ }
+
+ @Test
+ void multipleCopies()
+ {
+ ExternalDmsPermId openbis1 = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
+ ExternalDmsPermId openbis2 = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
+
+ ExternalDmsPermId url1 = create(externalDms().withType(ExternalDmsAddressType.URL));
+ ExternalDmsPermId url2 = create(externalDms().withType(ExternalDmsAddressType.URL));
+
+ ExternalDmsPermId fs1 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ ExternalDmsPermId fs2 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+
+ ContentCopyCreation creation1 = copyAt(openbis1).build();
+ ContentCopyCreation creation2 = copyAt(openbis1).build();
+
+ ContentCopyCreation creation3 = copyAt(openbis2).build();
+ ContentCopyCreation creation4 = copyAt(openbis2).build();
+
+ ContentCopyCreation creation5 = copyAt(url1).build();
+ ContentCopyCreation creation6 = copyAt(url1).build();
+
+ ContentCopyCreation creation7 = copyAt(url2).build();
+ ContentCopyCreation creation8 = copyAt(url2).build();
+
+ ContentCopyCreation creation9 = copyAt(fs1).withPath("/path/to/dir").withGitCommitHash("asdf").build();
+ ContentCopyCreation creation10 = copyAt(fs1).withPath("/path/to/dir2").build();
+
+ ContentCopyCreation creation11 = copyAt(fs2).withPath("/path/to/dir").withGitCommitHash("asdf").build();
+ ContentCopyCreation creation12 = copyAt(fs2).withPath("/path/to/dir2").build();
+
+ DataSetPermId id = create(linkDataSet().with(creation1, creation2, creation3, creation4, creation5, creation6, creation7, creation8,
+ creation9, creation10, creation11, creation12));
+ List<ContentCopy> contentCopies = get(id).getLinkedData().getContentCopies();
+
+ Set<String> expected = new HashSet<String>();
+ for (ContentCopyCreation c : Arrays.asList(creation1, creation2, creation3, creation4, creation5, creation6, creation7, creation8,
+ creation9, creation10, creation11, creation12))
+ {
+ expected.add(stringify(c));
+ }
+
+ Set<String> actual = new HashSet<String>();
+ for (ContentCopy c : contentCopies)
+ {
+ actual.add(stringify(c));
+ }
+ assertThat(contentCopies.size(), is(12));
+ assertThat(actual, IsIterableContainingInAnyOrder.<String> containsInAnyOrder(expected.toArray(new String[0])));
+ }
@DataProvider(name = "InvalidLocationCombinations")
public static Object[][] invalidLocationCombinations()
@@ -73,7 +177,7 @@ public class CreateLinkDataSetTest extends AbstractLinkDataSetTest
};
}
- @Test(enabled = false, dataProvider = "InvalidLocationCombinations", expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = ".*Invalid arguments.*")
+ @Test(dataProvider = "InvalidLocationCombinations", expectedExceptions = UserFailureException.class, expectedExceptionsMessageRegExp = ".*Invalid arguments.*")
void cannotLinkToExternalDmsOfWrongType(ExternalDmsAddressType dmsType, String externalCode, String path, String gitCommitHash)
{
ExternalDmsPermId edms = create(externalDms().withType(dmsType));
@@ -82,5 +186,4 @@ public class CreateLinkDataSetTest extends AbstractLinkDataSetTest
.withPath(path)
.withGitCommitHash(gitCommitHash)));
}
-
}
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExternalDmsTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExternalDmsTest.java
index 528d8401dd2..adccc67bf8f 100644
--- a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExternalDmsTest.java
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetExternalDmsTest.java
@@ -25,9 +25,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressType;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
-/**
- * @author anttil
- */
public class GetExternalDmsTest extends AbstractExternalDmsTest
{
diff --git a/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetLinkDataSetTest.java b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetLinkDataSetTest.java
new file mode 100644
index 00000000000..d853671e4fe
--- /dev/null
+++ b/openbis/sourceTest/java/ch/ethz/sis/openbis/systemtest/asapi/v3/GetLinkDataSetTest.java
@@ -0,0 +1,98 @@
+package ch.ethz.sis.openbis.systemtest.asapi.v3;
+
+import static org.hamcrest.CoreMatchers.anyOf;
+import static org.hamcrest.CoreMatchers.is;
+import static org.hamcrest.MatcherAssert.assertThat;
+
+import org.testng.annotations.Test;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.LinkedData;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
+
+public class GetLinkDataSetTest extends AbstractLinkDataSetTest
+{
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWithOpenBISBasedDataSets()
+ {
+ String externalCode = uuid();
+ ExternalDmsPermId openbis = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
+ DataSetPermId id = create(linkDataSet().with(copyAt(openbis).withExternalCode(externalCode)));
+ DataSet dataSet = get(id);
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(externalCode));
+ assertThat(dataSet.getLinkedData().getExternalDms(), isSimilarTo(get(openbis)));
+ }
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWithURLBasedDataSets()
+ {
+ String externalCode = uuid();
+ ExternalDmsPermId url = create(externalDms().withType(ExternalDmsAddressType.URL));
+ DataSetPermId id = create(linkDataSet().with(copyAt(url).withExternalCode(externalCode)));
+ DataSet dataSet = get(id);
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(externalCode));
+ assertThat(dataSet.getLinkedData().getExternalDms(), isSimilarTo(get(url)));
+ }
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWithFileSystemBasedDataSets()
+ {
+ ExternalDmsPermId fs = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ DataSetPermId id = create(linkDataSet().with(copyAt(fs).withPath("/path/to/dir")));
+ DataSet dataSet = get(id);
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(LinkedData.NO_COPY_EXTERNAL_CODE));
+ assertThat(dataSet.getLinkedData().getExternalDms(), is(LinkedData.NO_COPY_EXTERNAL_DMS));
+ }
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWhenThereAreNoCopies()
+ {
+ DataSetPermId id = create(linkDataSet());
+ DataSet dataSet = get(id);
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(LinkedData.NO_COPY_EXTERNAL_CODE));
+ assertThat(dataSet.getLinkedData().getExternalDms(), is(LinkedData.NO_COPY_EXTERNAL_DMS));
+ }
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWithMultipleCopiesThatAreAllFileBased()
+ {
+ ExternalDmsPermId fs1 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ ExternalDmsPermId fs2 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+
+ DataSetPermId id = create(linkDataSet().with(
+ copyAt(fs1).withPath("/path/to/dir"),
+ copyAt(fs1).withPath("/path/to/dir2"),
+ copyAt(fs2).withPath("/path/to/dir")));
+ DataSet dataSet = get(id);
+
+ assertThat(dataSet.getLinkedData().getContentCopies().size(), is(3));
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(LinkedData.NO_COPY_EXTERNAL_CODE));
+ assertThat(dataSet.getLinkedData().getExternalDms(), is(LinkedData.NO_COPY_EXTERNAL_DMS));
+ }
+
+ @Test
+ void legacyFieldsAreProperlyPopulatedWithMultipleCopiesSomeOfWhichResideInOpenBISOrInUrl()
+ {
+ String code = uuid();
+ ExternalDmsPermId openbis = create(externalDms().withType(ExternalDmsAddressType.OPENBIS));
+ ExternalDmsPermId url = create(externalDms().withType(ExternalDmsAddressType.URL));
+ ExternalDmsPermId fs1 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+ ExternalDmsPermId fs2 = create(externalDms().withType(ExternalDmsAddressType.FILE_SYSTEM));
+
+ DataSetPermId id = create(linkDataSet().with(
+ copyAt(fs1).withPath("/path/to/dir"),
+ copyAt(fs1).withPath("/path/to/dir2"),
+ copyAt(fs2).withPath("/path/to/dir"),
+ copyAt(openbis).withExternalCode(code),
+ copyAt(url).withExternalCode(code)));
+ DataSet dataSet = get(id);
+
+ assertThat(dataSet.getLinkedData().getContentCopies().size(), is(5));
+ assertThat(dataSet.getLinkedData().getExternalCode(), is(code));
+ assertThat(dataSet.getLinkedData().getExternalDms(), anyOf(isSimilarTo(get(url)), isSimilarTo(get(openbis))));
+ }
+
+}
diff --git a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/dataset/LinkedData.java b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/dataset/LinkedData.java
index 6c21c94f2e2..5e27beea33a 100644
--- a/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/dataset/LinkedData.java
+++ b/openbis_api/source/java/ch/ethz/sis/openbis/generic/asapi/v3/dto/dataset/LinkedData.java
@@ -23,6 +23,7 @@ import com.fasterxml.jackson.annotation.JsonProperty;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.LinkedDataFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDms;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.ExternalDmsAddressType;
import ch.ethz.sis.openbis.generic.asapi.v3.exceptions.NotFetchedException;
import ch.systemsx.cisd.base.annotation.JsonObject;
import ch.systemsx.cisd.common.annotation.TechPreview;
@@ -35,6 +36,22 @@ public class LinkedData implements Serializable
{
private static final long serialVersionUID = 1L;
+ public static final String NO_COPY_EXTERNAL_CODE = "no copies";
+
+ public static final ExternalDms NO_COPY_EXTERNAL_DMS;
+
+ static
+ {
+ ExternalDms nced = new ExternalDms();
+ nced.setAddress("");
+ nced.setAddressType(ExternalDmsAddressType.URL);
+ nced.setCode("no copies");
+ nced.setLabel("");
+ nced.setOpenbis(false);
+ nced.setUrlTemplate("");
+ NO_COPY_EXTERNAL_DMS = nced;
+ }
+
@JsonProperty
private LinkedDataFetchOptions fetchOptions;
@@ -44,6 +61,7 @@ public class LinkedData implements Serializable
@JsonProperty
private ExternalDms externalDms;
+ @JsonIgnore
private List<ContentCopy> contentCopies;
// Method automatically generated with DtoGenerator
@@ -92,6 +110,7 @@ public class LinkedData implements Serializable
}
@TechPreview
+ @JsonIgnore
public List<ContentCopy> getContentCopies()
{
return contentCopies;
diff --git a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
index cb6b4c3e3f1..398f2c95560 100644
--- a/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
+++ b/openbis_api/sourceTest/java/ch/ethz/sis/openbis/generic/sharedapi/v3/dictionary.txt
@@ -1550,4 +1550,6 @@ getSerialversionuid
setContentCopies
setExternalId
setGitCommitHash
-ContentCopy
\ No newline at end of file
+ContentCopy
+NO_COPY_EXTERNAL_CODE
+NO_COPY_EXTERNAL_DMS
\ No newline at end of file
--
GitLab