diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/MasterDataExtractor.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/MasterDataExtractor.java
index a4cc92b22870673cc0134e337eb2dc161e835cbb..cdadf650d1b4d90d34138c24e83be8cf141f2fd2 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/MasterDataExtractor.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/MasterDataExtractor.java
@@ -190,11 +190,11 @@ public class MasterDataExtractor
{
if (vocabularies.size() > 0)
{
- Element vocabsElement = doc.createElement("vocabularies");
+ Element vocabsElement = doc.createElement("controlledVocabularies");
rootElement.appendChild(vocabsElement);
for (IVocabularyImmutable vocabImmutable : vocabularies)
{
- Element vocabElement = doc.createElement("vocabulary");
+ Element vocabElement = doc.createElement("controlledVocabulary");
String code = vocabImmutable.isInternalNamespace()
&& vocabImmutable.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX) ? CodeConverter.tryToDatabase(vocabImmutable.getCode())
: vocabImmutable.getCode();
@@ -267,12 +267,12 @@ public class MasterDataExtractor
{
if (experimentTypes.size() > 0)
{
- Element experimentTypesElement = doc.createElement("experimentTypes");
+ Element experimentTypesElement = doc.createElement("collectionTypes");
rootElement.appendChild(experimentTypesElement);
Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
for (IExperimentTypeImmutable expType : experimentTypes)
{
- Element experimentTypeElement = getEntityTypeXML(doc, expType, "experimentType");
+ Element experimentTypeElement = getEntityTypeXML(doc, expType, "collectionType");
experimentTypeElement.setAttribute("description", expType.getDescription());
// TODO validation script?
experimentTypesElement.appendChild(experimentTypeElement);
@@ -286,13 +286,13 @@ public class MasterDataExtractor
{
if (sampleTypes.size() > 0)
{
- Element sampleTypesElement = doc.createElement("sampleTypes");
+ Element sampleTypesElement = doc.createElement("objectTypes");
rootElement.appendChild(sampleTypesElement);
Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = loadSampleTypesUsingV3WithPropertyAssignments();
for (ISampleTypeImmutable sampleType : sampleTypes)
{
- Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "sampleType");
+ Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "objectType");
sampleTypeElement.setAttribute("description", sampleType.getDescription());
sampleTypeElement.setAttribute("listable", String.valueOf(sampleType.isListable()));
sampleTypeElement.setAttribute("showContainer", String.valueOf(sampleType.isShowContainer()));
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
index a1dd6caab805d4de312fdfa5feeb6bdef5251b25..8a5533855cdbe8b249ecf123cfbe4074eb8b312a 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
@@ -584,7 +584,14 @@ public class EntitySynchronizer
// delete materials
MaterialDeletionOptions matDeletionOptions = new MaterialDeletionOptions();
matDeletionOptions.setReason("sync materials");
- v3Api.deleteMaterials(sessionToken, matPermIds, matDeletionOptions);
+
+ try
+ {
+ v3Api.deleteMaterials(sessionToken, matPermIds, matDeletionOptions);
+ } catch (Exception e)
+ {
+ operationLog.warn("One or more materials could not be deleted due to: " + e.getMessage());
+ }
// confirm deletions
ArrayList<IDeletionId> deletionIds = new ArrayList<IDeletionId>();
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataParser.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataParser.java
index 65fb0e249c989ccc0be68f980cb2e814e6dca9bd..30b7a11486a40940b27dec6e7c9c7a68f5633747 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataParser.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataParser.java
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewETPTAssignment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewVocabulary;
@@ -59,6 +60,8 @@ public class MasterDataParser
{
private final INameTranslator nameTranslator;
+ private Map<String, FileFormatType> fileFormatTypes = new HashMap<String, FileFormatType>();
+
private Map<String, PropertyType> propertyTypes = new HashMap<String, PropertyType>();
private Map<String, SampleType> sampleTypes = new HashMap<String, SampleType>();
@@ -68,17 +71,11 @@ public class MasterDataParser
private Map<String, ExperimentType> experimentTypes = new HashMap<String, ExperimentType>();
private Map<String, MaterialType> materialTypes = new HashMap<String, MaterialType>();
- private Map<String, NodeList> materialTypePropertyAssignmentsMap = new HashMap<String, NodeList>();
private Map<String, NewVocabulary> vocabularies = new HashMap<String, NewVocabulary>();
MultiKeyMap<String, List<NewETPTAssignment>> entityPropertyAssignments = new MultiKeyMap<String, List<NewETPTAssignment>>();
- public Map<String, NewVocabulary> getVocabularies()
- {
- return vocabularies;
- }
-
private MasterDataParser(INameTranslator nameTranslator)
{
this.nameTranslator = nameTranslator;
@@ -108,12 +105,23 @@ public class MasterDataParser
throw new XPathExpressionException("The master data resurce list should contain 1 master data element");
}
Element docElement = (Element) xdNode;
- parseVocabularies(docElement.getElementsByTagName("vocabularies"));
+ parseFileFormatTypes(docElement.getElementsByTagName("fileFormatTypes"));
+ parseVocabularies(docElement.getElementsByTagName("controlledVocabularies"));
parseMaterialTypes(docElement.getElementsByTagName("materialTypes"));
parsePropertyTypes(docElement.getElementsByTagName("propertyTypes"));
- parseSampleTypes(docElement.getElementsByTagName("sampleTypes"));
+ parseSampleTypes(docElement.getElementsByTagName("objectTypes"));
parseDataSetTypes(docElement.getElementsByTagName("dataSetTypes"));
- parseExperimentTypes(docElement.getElementsByTagName("experimentTypes"));
+ parseExperimentTypes(docElement.getElementsByTagName("collectionTypes"));
+ }
+
+ public Map<String, FileFormatType> getFileFormatTypes()
+ {
+ return fileFormatTypes;
+ }
+
+ public Map<String, NewVocabulary> getVocabularies()
+ {
+ return vocabularies;
}
public Map<String, PropertyType> getPropertyTypes()
@@ -146,28 +154,47 @@ public class MasterDataParser
return materialTypes;
}
- private void parseVocabularies(NodeList vocabulariesNode)
+ private void parseFileFormatTypes(NodeList fileFormatTypesNode)
{
- if (vocabulariesNode.getLength() == 1)
+ assert fileFormatTypesNode.getLength() == 1 : "Resource List should contain a single 'fileFormatTypes' node";
+
+ Element fileFormatTypesElement = (Element) fileFormatTypesNode.item(0);
+ NodeList fileFormatTypeNodes = fileFormatTypesElement.getElementsByTagName("fileFormatType");
+
+ for (int i = 0; i < fileFormatTypeNodes.getLength(); i++)
{
- Element vocabsElement = (Element) vocabulariesNode.item(0);
- NodeList vocabNodes = vocabsElement.getElementsByTagName("vocabulary");
+ Element typeElement = (Element) fileFormatTypeNodes.item(i);
+
+ FileFormatType type = new FileFormatType();
+ String code = getAttribute(typeElement, "code");
+ type.setCode(code);
+ type.setDescription(getAttribute(typeElement, "description"));
+
+ fileFormatTypes.put(code, type);
+ }
+ }
- for (int i = 0; i < vocabNodes.getLength(); i++)
- {
- Element vocabElement = (Element) vocabNodes.item(i);
- String code = getAttribute(vocabElement, "code");
-
- NewVocabulary newVocabulary = new NewVocabulary();
- newVocabulary.setCode(code);
- newVocabulary.setDescription(getAttribute(vocabElement, "description"));
- newVocabulary.setURLTemplate(getAttribute(vocabElement, "urlTemplate"));
- newVocabulary.setManagedInternally(Boolean.valueOf(getAttribute(vocabElement, "managedInternally")));
- newVocabulary.setInternalNamespace(Boolean.valueOf(getAttribute(vocabElement, "internalNamespace")));
- newVocabulary.setChosenFromList(Boolean.valueOf(getAttribute(vocabElement, "chosenFromList")));
- vocabularies.put(CodeConverter.tryToBusinessLayer(newVocabulary.getCode(), newVocabulary.isInternalNamespace()), newVocabulary);
- parseVocabularyTerms(vocabElement, newVocabulary);
- }
+ private void parseVocabularies(NodeList vocabulariesNode)
+ {
+ assert vocabulariesNode.getLength() == 1 : "Resource List should contain a single 'controlledVocabularies' node";
+
+ Element vocabsElement = (Element) vocabulariesNode.item(0);
+ NodeList vocabNodes = vocabsElement.getElementsByTagName("controlledVocabulary");
+
+ for (int i = 0; i < vocabNodes.getLength(); i++)
+ {
+ Element vocabElement = (Element) vocabNodes.item(i);
+ String code = getAttribute(vocabElement, "code");
+
+ NewVocabulary newVocabulary = new NewVocabulary();
+ newVocabulary.setCode(code);
+ newVocabulary.setDescription(getAttribute(vocabElement, "description"));
+ newVocabulary.setURLTemplate(getAttribute(vocabElement, "urlTemplate"));
+ newVocabulary.setManagedInternally(Boolean.valueOf(getAttribute(vocabElement, "managedInternally")));
+ newVocabulary.setInternalNamespace(Boolean.valueOf(getAttribute(vocabElement, "internalNamespace")));
+ newVocabulary.setChosenFromList(Boolean.valueOf(getAttribute(vocabElement, "chosenFromList")));
+ vocabularies.put(CodeConverter.tryToBusinessLayer(newVocabulary.getCode(), newVocabulary.isInternalNamespace()), newVocabulary);
+ parseVocabularyTerms(vocabElement, newVocabulary);
}
}
@@ -194,172 +221,166 @@ public class MasterDataParser
private void parseMaterialTypes(NodeList matTypesNode)
{
- if (matTypesNode.getLength() == 1)
+ assert matTypesNode.getLength() == 1 : "Resource List should contain a single 'materialTypes' node";
+
+ Element matTypesElement = (Element) matTypesNode.item(0);
+ NodeList matTypeNodes = matTypesElement.getElementsByTagName("materialType");
+ for (int i = 0; i < matTypeNodes.getLength(); i++)
{
- Element matTypesElement = (Element) matTypesNode.item(0);
- NodeList matTypeNodes = matTypesElement.getElementsByTagName("materialType");
- for (int i = 0; i < matTypeNodes.getLength(); i++)
- {
- Element materialTypeElement = (Element) matTypeNodes.item(i);
- MaterialType materialType = new MaterialType();
- materialType.setCode(getAttribute(materialTypeElement, "code"));
- materialType.setDescription(getAttribute(materialTypeElement, "description"));
- materialTypes.put(materialType.getCode(), materialType);
+ Element materialTypeElement = (Element) matTypeNodes.item(i);
+ MaterialType materialType = new MaterialType();
+ materialType.setCode(getAttribute(materialTypeElement, "code"));
+ materialType.setDescription(getAttribute(materialTypeElement, "description"));
+ materialTypes.put(materialType.getCode(), materialType);
- parsePropertyAssignments(EntityKind.MATERIAL, materialType, materialTypeElement.getElementsByTagName("propertyAssignments"));
- }
+ parsePropertyAssignments(EntityKind.MATERIAL, materialType, materialTypeElement.getElementsByTagName("propertyAssignments"));
}
}
private void parseExperimentTypes(NodeList expTypesNode)
{
- if (expTypesNode.getLength() == 1)
+ assert expTypesNode.getLength() == 1 : "Resource List should contain a single 'collectionTypes' node";
+
+ Element expTypesElement = (Element) expTypesNode.item(0);
+ NodeList expTypeNodes = expTypesElement.getElementsByTagName("collectionType");
+ for (int i = 0; i < expTypeNodes.getLength(); i++)
{
- Element expTypesElement = (Element) expTypesNode.item(0);
- NodeList expTypeNodes = expTypesElement.getElementsByTagName("experimentType");
- for (int i = 0; i < expTypeNodes.getLength(); i++)
- {
- Element expTypeElement = (Element) expTypeNodes.item(i);
- String code = getAttribute(expTypeElement, "code");
- ExperimentType expType = new ExperimentType();
- expType.setCode(code);
- expType.setDescription(getAttribute(expTypeElement, "description"));
- experimentTypes.put(expType.getCode(), expType);
-
- parsePropertyAssignments(EntityKind.EXPERIMENT, expType, expTypeElement.getElementsByTagName("propertyAssignments"));
- }
+ Element expTypeElement = (Element) expTypeNodes.item(i);
+ String code = getAttribute(expTypeElement, "code");
+ ExperimentType expType = new ExperimentType();
+ expType.setCode(code);
+ expType.setDescription(getAttribute(expTypeElement, "description"));
+ experimentTypes.put(expType.getCode(), expType);
+
+ parsePropertyAssignments(EntityKind.EXPERIMENT, expType, expTypeElement.getElementsByTagName("propertyAssignments"));
}
}
private void parseSampleTypes(NodeList sampleTypesNode)
{
- if (sampleTypesNode.getLength() == 1)
+ assert sampleTypesNode.getLength() == 1 : "Resource List should contain a single 'objectTypes' node";
+
+ Element sampleTypesElement = (Element) sampleTypesNode.item(0);
+ NodeList sampleTypeNodes = sampleTypesElement.getElementsByTagName("objectType");
+ for (int i = 0; i < sampleTypeNodes.getLength(); i++)
{
- Element sampleTypesElement = (Element) sampleTypesNode.item(0);
- NodeList sampleTypeNodes = sampleTypesElement.getElementsByTagName("sampleType");
- for (int i = 0; i < sampleTypeNodes.getLength(); i++)
- {
- Element sampleTypeElement = (Element) sampleTypeNodes.item(i);
- SampleType sampleType = new SampleType();
- sampleType.setCode(getAttribute(sampleTypeElement, "code"));
- sampleType.setDescription(getAttribute(sampleTypeElement, "description"));
- sampleType.setListable(Boolean.valueOf(getAttribute(sampleTypeElement, "listable")));
- sampleType.setShowContainer(Boolean.valueOf(getAttribute(sampleTypeElement, "showContainer")));
- sampleType.setShowParents(Boolean.valueOf(getAttribute(sampleTypeElement, "showParents")));
- sampleType.setShowParentMetadata(Boolean.valueOf(getAttribute(sampleTypeElement, "showParentMetadata")));
- sampleType.setSubcodeUnique(Boolean.valueOf(getAttribute(sampleTypeElement, "subcodeUnique")));
- sampleType.setAutoGeneratedCode(Boolean.valueOf(getAttribute(sampleTypeElement, "autoGeneratedCode")));
- sampleType.setGeneratedCodePrefix(getAttribute(sampleTypeElement, "generatedCodePrefix"));
- sampleTypes.put(sampleType.getCode(), sampleType);
-
- parsePropertyAssignments(EntityKind.SAMPLE, sampleType, sampleTypeElement.getElementsByTagName("propertyAssignments"));
- }
+ Element sampleTypeElement = (Element) sampleTypeNodes.item(i);
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(getAttribute(sampleTypeElement, "code"));
+ sampleType.setDescription(getAttribute(sampleTypeElement, "description"));
+ sampleType.setListable(Boolean.valueOf(getAttribute(sampleTypeElement, "listable")));
+ sampleType.setShowContainer(Boolean.valueOf(getAttribute(sampleTypeElement, "showContainer")));
+ sampleType.setShowParents(Boolean.valueOf(getAttribute(sampleTypeElement, "showParents")));
+ sampleType.setShowParentMetadata(Boolean.valueOf(getAttribute(sampleTypeElement, "showParentMetadata")));
+ sampleType.setSubcodeUnique(Boolean.valueOf(getAttribute(sampleTypeElement, "subcodeUnique")));
+ sampleType.setAutoGeneratedCode(Boolean.valueOf(getAttribute(sampleTypeElement, "autoGeneratedCode")));
+ sampleType.setGeneratedCodePrefix(getAttribute(sampleTypeElement, "generatedCodePrefix"));
+ sampleTypes.put(sampleType.getCode(), sampleType);
+
+ parsePropertyAssignments(EntityKind.SAMPLE, sampleType, sampleTypeElement.getElementsByTagName("propertyAssignments"));
}
}
private void parseDataSetTypes(NodeList dataSetTypesNode)
{
- if (dataSetTypesNode.getLength() == 1)
+ assert dataSetTypesNode.getLength() == 1 : "Resource List should contain a single 'dataSetTypes' node";
+
+ Element dataSetTypesElement = (Element) dataSetTypesNode.item(0);
+ NodeList dataSetTypeNodes = dataSetTypesElement.getElementsByTagName("dataSetType");
+ for (int i = 0; i < dataSetTypeNodes.getLength(); i++)
{
- Element dataSetTypesElement = (Element) dataSetTypesNode.item(0);
- NodeList dataSetTypeNodes = dataSetTypesElement.getElementsByTagName("dataSetType");
- for (int i = 0; i < dataSetTypeNodes.getLength(); i++)
+ Element dataSetTypeElement = (Element) dataSetTypeNodes.item(i);
+ String code = getAttribute(dataSetTypeElement, "code");
+ DataSetType dataSetType = new DataSetType();
+ dataSetType.setCode(code);
+ dataSetType.setDescription(getAttribute(dataSetTypeElement, "description"));
+ dataSetType.setDataSetKind(DataSetKind.valueOf(getAttribute(dataSetTypeElement, "dataSetKind")));
+ String mainDataSetPattern = getAttribute(dataSetTypeElement, "mainDataSetPattern");
+ if (mainDataSetPattern.length() < 1)
{
- Element dataSetTypeElement = (Element) dataSetTypeNodes.item(i);
- String code = getAttribute(dataSetTypeElement, "code");
- DataSetType dataSetType = new DataSetType();
- dataSetType.setCode(code);
- dataSetType.setDescription(getAttribute(dataSetTypeElement, "description"));
- dataSetType.setDataSetKind(DataSetKind.valueOf(getAttribute(dataSetTypeElement, "dataSetKind")));
- String mainDataSetPattern = getAttribute(dataSetTypeElement, "mainDataSetPattern");
- if (mainDataSetPattern.length() < 1)
- {
- dataSetType.setMainDataSetPattern(null);
- }
- else
- {
- dataSetType.setMainDataSetPattern(mainDataSetPattern);
- }
- if (mainDataSetPattern.length() < 1)
- {
- dataSetType.setMainDataSetPath(null);
- }
- else
- {
- dataSetType.setMainDataSetPath(mainDataSetPattern);
- }
- dataSetType.setDeletionDisallow(Boolean.valueOf(getAttribute(dataSetTypeElement, "deletionDisallowed")));
- dataSetTypes.put(dataSetType.getCode(), dataSetType);
-
- parsePropertyAssignments(EntityKind.DATA_SET, dataSetType, dataSetTypeElement.getElementsByTagName("propertyAssignments"));
+ dataSetType.setMainDataSetPattern(null);
}
+ else
+ {
+ dataSetType.setMainDataSetPattern(mainDataSetPattern);
+ }
+ if (mainDataSetPattern.length() < 1)
+ {
+ dataSetType.setMainDataSetPath(null);
+ }
+ else
+ {
+ dataSetType.setMainDataSetPath(mainDataSetPattern);
+ }
+ dataSetType.setDeletionDisallow(Boolean.valueOf(getAttribute(dataSetTypeElement, "deletionDisallowed")));
+ dataSetTypes.put(dataSetType.getCode(), dataSetType);
+
+ parsePropertyAssignments(EntityKind.DATA_SET, dataSetType, dataSetTypeElement.getElementsByTagName("propertyAssignments"));
}
}
private void parsePropertyAssignments(EntityKind entityKind, EntityType entityType, NodeList propertyAssignmentsNode)
{
- if (propertyAssignmentsNode.getLength() == 1)
+ assert propertyAssignmentsNode.getLength() == 1 : "Resource List should contain a single property assignments node";
+
+ List<NewETPTAssignment> list = new ArrayList<NewETPTAssignment>();
+ Element propertyAssignmentsElement = (Element) propertyAssignmentsNode.item(0);
+ NodeList propertyAssignmentNodes = propertyAssignmentsElement.getElementsByTagName("propertyAssignment");
+ for (int i = 0; i < propertyAssignmentNodes.getLength(); i++)
{
- List<NewETPTAssignment> list = new ArrayList<NewETPTAssignment>();
- Element propertyAssignmentsElement = (Element) propertyAssignmentsNode.item(0);
- NodeList propertyAssignmentNodes = propertyAssignmentsElement.getElementsByTagName("propertyAssignment");
- for (int i = 0; i < propertyAssignmentNodes.getLength(); i++)
- {
- Element propertyAssignmentElement = (Element) propertyAssignmentNodes.item(i);
- String propertyTypeCode = getAttribute(propertyAssignmentElement, "property_type_code");
- NewETPTAssignment assignment = new NewETPTAssignment();
- assignment.setPropertyTypeCode(propertyTypeCode);
- assignment.setEntityKind(entityType.getEntityKind());
- assignment.setEntityTypeCode(entityType.getCode());
- assignment.setMandatory(Boolean.valueOf(getAttribute(propertyAssignmentElement, "mandatory")));
- assignment.setDefaultValue(ERROR_PROPERTY_PREFIX);
- assignment.setSection(getAttribute(propertyAssignmentElement, "section"));
- assignment.setOrdinal(Long.valueOf(getAttribute(propertyAssignmentElement, "ordinal")));
- assignment.setShownInEditView(Boolean.valueOf(getAttribute(propertyAssignmentElement, "showInEdit")));
- list.add(assignment);
- }
- entityPropertyAssignments.put(entityType.getEntityKind().name(), entityType.getCode(), list);
+ Element propertyAssignmentElement = (Element) propertyAssignmentNodes.item(i);
+ String propertyTypeCode = getAttribute(propertyAssignmentElement, "propertyTypeCode");
+ NewETPTAssignment assignment = new NewETPTAssignment();
+ assignment.setPropertyTypeCode(propertyTypeCode);
+ assignment.setEntityKind(entityType.getEntityKind());
+ assignment.setEntityTypeCode(entityType.getCode());
+ assignment.setMandatory(Boolean.valueOf(getAttribute(propertyAssignmentElement, "mandatory")));
+ assignment.setDefaultValue(ERROR_PROPERTY_PREFIX);
+ assignment.setSection(getAttribute(propertyAssignmentElement, "section"));
+ assignment.setOrdinal(Long.valueOf(getAttribute(propertyAssignmentElement, "ordinal")));
+ assignment.setShownInEditView(Boolean.valueOf(getAttribute(propertyAssignmentElement, "showInEdit")));
+ list.add(assignment);
}
+ entityPropertyAssignments.put(entityType.getEntityKind().name(), entityType.getCode(), list);
}
private void parsePropertyTypes(NodeList propertyTypesNode)
{
- if (propertyTypesNode.getLength() == 1)
+ assert propertyTypesNode.getLength() == 1 : "Resource List should contain a single 'propertyTypes' node";
+
+ Element propertyTypesElement = (Element) propertyTypesNode.item(0);
+ NodeList propertyTypeNodes = propertyTypesElement.getElementsByTagName("propertyType");
+ for (int i = 0; i < propertyTypeNodes.getLength(); i++)
{
- Element propertyTypesElement = (Element) propertyTypesNode.item(0);
- NodeList propertyTypeNodes = propertyTypesElement.getElementsByTagName("propertyType");
- for (int i = 0; i < propertyTypeNodes.getLength(); i++)
+ Element propertyTypeElement = (Element) propertyTypeNodes.item(i);
+ PropertyType newPropertyType = new PropertyType();
+
+ String code = getAttribute(propertyTypeElement, "code");
+ newPropertyType.setLabel(getAttribute(propertyTypeElement, "label"));
+ DataTypeCode dataTypeCode = DataTypeCode.valueOf(getAttribute(propertyTypeElement, "dataType"));
+ newPropertyType.setDataType(new DataType(dataTypeCode));
+ newPropertyType.setDescription(getAttribute(propertyTypeElement, "description"));
+ newPropertyType.setManagedInternally(Boolean.valueOf(getAttribute(propertyTypeElement, "managedInternally")));
+ newPropertyType.setInternalNamespace(Boolean.valueOf(getAttribute(propertyTypeElement, "internalNamespace")));
+ newPropertyType.setCode(CodeConverter.tryToBusinessLayer(code, newPropertyType.isInternalNamespace()));
+
+ propertyTypes.put(newPropertyType.getCode(), newPropertyType);
+ if (dataTypeCode.equals(DataTypeCode.CONTROLLEDVOCABULARY))
{
- Element propertyTypeElement = (Element) propertyTypeNodes.item(i);
- PropertyType newPropertyType = new PropertyType();
-
- String code = getAttribute(propertyTypeElement, "code");
- newPropertyType.setLabel(getAttribute(propertyTypeElement, "label"));
- DataTypeCode dataTypeCode = DataTypeCode.valueOf(getAttribute(propertyTypeElement, "dataType"));
- newPropertyType.setDataType(new DataType(dataTypeCode));
- newPropertyType.setDescription(getAttribute(propertyTypeElement, "description"));
- newPropertyType.setManagedInternally(Boolean.valueOf(getAttribute(propertyTypeElement, "managedInternally")));
- newPropertyType.setInternalNamespace(Boolean.valueOf(getAttribute(propertyTypeElement, "internalNamespace")));
- newPropertyType.setCode(CodeConverter.tryToBusinessLayer(code, newPropertyType.isInternalNamespace()));
-
- propertyTypes.put(newPropertyType.getCode(), newPropertyType);
- if (dataTypeCode.equals(DataTypeCode.CONTROLLEDVOCABULARY))
+ String vocabularyCode = getAttribute(propertyTypeElement, "vocabulary");
+ newPropertyType.setVocabulary(vocabularies.get(vocabularyCode));
+ }
+ else if (dataTypeCode.equals(DataTypeCode.MATERIAL))
+ {
+ String materialCode = getAttribute(propertyTypeElement, "material");
+ if (materialCode.trim().length() < 1)
{
- String vocabularyCode = getAttribute(propertyTypeElement, "vocabulary");
- newPropertyType.setVocabulary(vocabularies.get(vocabularyCode));
+ newPropertyType.setMaterialType(null); // material of any type
}
- else if (dataTypeCode.equals(DataTypeCode.MATERIAL))
+ else
{
- String materialCode = getAttribute(propertyTypeElement, "material");
- if (materialCode.trim().length() < 1)
- {
- newPropertyType.setMaterialType(null); // material of any type
- }
- else
- {
- newPropertyType.setMaterialType(materialTypes.get(materialCode));
- }
- }
+ newPropertyType.setMaterialType(materialTypes.get(materialCode));
+ }
}
}
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataSynchronizer.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataSynchronizer.java
index 3bd0f9d96c04b71caf60f1161a853ec7bf22d754..5aa900f229c7d0bdcc587a73afcce6c5b92ab8ed 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataSynchronizer.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/MasterDataSynchronizer.java
@@ -35,6 +35,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityTypePropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewETPTAssignment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewVocabulary;
@@ -69,6 +70,7 @@ public class MasterDataSynchronizer
public void synchronizeMasterData() {
MultiKeyMap<String, List<NewETPTAssignment>> propertyAssignmentsToProcess = masterData.getPropertyAssignmentsToProcess();
+ processFileFormatTypes(masterData.getFileFormatTypesToProcess());
processVocabularies(masterData.getVocabulariesToProcess());
// materials are registered but their property assignments are deferred until after property types are processed
processEntityTypes(masterData.getMaterialTypesToProcess(), propertyAssignmentsToProcess);
@@ -102,6 +104,31 @@ public class MasterDataSynchronizer
}
}
+ private void processFileFormatTypes(Map<String, FileFormatType> fileFormatTypesToProcess)
+ {
+ List<FileFormatType> fileFormatTypes = commonServer.listFileFormatTypes(sessionToken);
+ Map<String, FileFormatType> typeMap = new HashMap<String, FileFormatType>();
+ for (FileFormatType type : fileFormatTypes)
+ {
+ typeMap.put(type.getCode(), type);
+ }
+
+ for (String typeCode : fileFormatTypesToProcess.keySet())
+ {
+ FileFormatType incomingType = fileFormatTypesToProcess.get(typeCode);
+ FileFormatType existingTypeOrNull = typeMap.get(typeCode);
+ if (existingTypeOrNull != null)
+ {
+ existingTypeOrNull.setDescription(incomingType.getDescription());
+ commonServer.updateFileFormatType(sessionToken, existingTypeOrNull);
+ }
+ else
+ {
+ commonServer.registerFileFormatType(sessionToken, incomingType);
+ }
+ }
+ }
+
private void processVocabularies(Map<String, NewVocabulary> vocabulariesToProcess)
{
List<Vocabulary> existingVocabularies = commonServer.listVocabularies(sessionToken, true, false);
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
index f846888e5d87f4d7eab7e57111ba21dac48cab1e..f25c3eed3734e7a56ed9ad1a15733a645047abbe 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
@@ -192,6 +192,7 @@ public class ResourceListParser
MasterDataParser mdParser = MasterDataParser.create(nameTranslator);
mdParser.parseMasterData(doc, xpath, uri);
MasterData masterData = data.getMasterData();
+ masterData.setFileFormatTypesToProcess(mdParser.getFileFormatTypes());
masterData.setVocabulariesToProcess(mdParser.getVocabularies());
masterData.setPropertyTypesToProcess(mdParser.getPropertyTypes());
masterData.setSampleTypesToProcess(mdParser.getSampleTypes());
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParserData.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParserData.java
index 165f5585263fd4eb337b825bb58c9f19faa1b52f..7f383e89f6c20073b1fd0c606707007083c5eb0b 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParserData.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParserData.java
@@ -29,6 +29,7 @@ import org.apache.commons.collections.map.MultiKeyMap;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewETPTAssignment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
@@ -307,6 +308,8 @@ public class ResourceListParserData
class MasterData
{
+ private Map<String, FileFormatType> fileFormatTypesToProcess = new HashMap<String, FileFormatType>();
+
private Map<String, NewVocabulary> vocabulariesToProcess = new HashMap<String, NewVocabulary>();
private Map<String, PropertyType> propertyTypesToProcess = new HashMap<String, PropertyType>();
@@ -356,6 +359,16 @@ public class ResourceListParserData
return vocabulariesToProcess;
}
+ public Map<String, FileFormatType> getFileFormatTypesToProcess()
+ {
+ return fileFormatTypesToProcess;
+ }
+
+ public void setFileFormatTypesToProcess(Map<String, FileFormatType> fileFormatTypesToProcess)
+ {
+ this.fileFormatTypesToProcess = fileFormatTypesToProcess;
+ }
+
public void setVocabulariesToProcess(Map<String, NewVocabulary> vocabulariesToProcess)
{
this.vocabulariesToProcess = vocabulariesToProcess;