diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/EntityRetriever.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/EntityRetriever.java
index 35a5e2431b331a996bf699545906def700d02b0e..ee41b4daa3e7a05f2509c8000c8c056101e4330b 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/EntityRetriever.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/EntityRetriever.java
@@ -19,25 +19,13 @@ import static ch.ethz.sis.openbis.generic.shared.entitygraph.Edge.CHILD;
import static ch.ethz.sis.openbis.generic.shared.entitygraph.Edge.COMPONENT;
import static ch.ethz.sis.openbis.generic.shared.entitygraph.Edge.CONNECTION;
-import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashMap;
import java.util.List;
import java.util.Map;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.attachment.Attachment;
@@ -46,28 +34,19 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.ICodeHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.Experiment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.fetchoptions.MaterialFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.fetchoptions.MaterialTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.search.MaterialSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.search.MaterialTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.Project;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.search.ProjectSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleFetchOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleSearchCriteria;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleTypeSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.fetchoptions.SpaceFetchOptions;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.id.ISpaceId;
@@ -76,16 +55,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.search.SpaceSearchCriteria
import ch.ethz.sis.openbis.generic.shared.entitygraph.Edge;
import ch.ethz.sis.openbis.generic.shared.entitygraph.EntityGraph;
import ch.ethz.sis.openbis.generic.shared.entitygraph.Node;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IDataSetTypeImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IEntityType;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IExperimentTypeImmutable;
import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistrationTransaction;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMaterialTypeImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IPropertyTypeImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.ISampleTypeImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyTermImmutable;
public class EntityRetriever
{
@@ -412,269 +382,8 @@ public class EntityRetriever
public String fetchMasterDataAsXML() throws ParserConfigurationException, TransformerException
{
- DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
- DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
- Document doc = docBuilder.newDocument();
- Element rootElement = doc.createElement("masterData");
- doc.appendChild(rootElement);
-
- // append vocabularies
- List<IVocabularyImmutable> vocabularies = masterDataRegistrationTransaction.listVocabularies();
- if (vocabularies.size() > 0)
- {
- Element vocabsElement = doc.createElement("vocabularies");
- rootElement.appendChild(vocabsElement);
- for (IVocabularyImmutable vocabImmutable : vocabularies)
- {
- Element vocabElement = doc.createElement("vocabulary");
- vocabElement.setAttribute("code", vocabImmutable.getCode());
- vocabElement.setAttribute("description", vocabImmutable.getDescription());
- vocabElement.setAttribute("urlTemplate", vocabImmutable.getUrlTemplate());
- vocabElement.setAttribute("managedInternally", String.valueOf(vocabImmutable.isManagedInternally()));
- vocabElement.setAttribute("internalNamespace", String.valueOf(vocabImmutable.isInternalNamespace()));
- vocabElement.setAttribute("chosenFromList", String.valueOf(vocabImmutable.isChosenFromList()));
- vocabsElement.appendChild(vocabElement);
-
- List<IVocabularyTermImmutable> terms = vocabImmutable.getTerms();
- for (IVocabularyTermImmutable vocabTermImmutable : terms)
- {
- Element termElement = doc.createElement("term");
- termElement.setAttribute("code", vocabTermImmutable.getCode());
- termElement.setAttribute("label", vocabTermImmutable.getLabel());
- termElement.setAttribute("description", vocabTermImmutable.getDescription());
- termElement.setAttribute("ordinal", String.valueOf(vocabTermImmutable.getOrdinal()));
- termElement.setAttribute("url", vocabTermImmutable.getUrl());
- vocabElement.appendChild(termElement);
- }
- }
- }
-
- // append property types
- List<IPropertyTypeImmutable> propertyTypes = masterDataRegistrationTransaction.listPropertyTypes();
- if (propertyTypes.size() > 0)
- {
- Element propertyTypesElement = doc.createElement("propertyTypes");
- rootElement.appendChild(propertyTypesElement);
- for (IPropertyTypeImmutable propertyTypeImmutable : propertyTypes)
- {
- Element propertyTypeElement = doc.createElement("propertyType");
- propertyTypeElement.setAttribute("code", propertyTypeImmutable.getCode());
- propertyTypeElement.setAttribute("label", propertyTypeImmutable.getLabel());
- propertyTypeElement.setAttribute("dataType", propertyTypeImmutable.getDataType().name());
- propertyTypeElement.setAttribute("internalNamespace", String.valueOf(propertyTypeImmutable.isInternalNamespace()));
- propertyTypeElement.setAttribute("managedInternally", String.valueOf(propertyTypeImmutable.isManagedInternally()));
- propertyTypeElement.setAttribute("description", propertyTypeImmutable.getDescription());
- if (propertyTypeImmutable.getDataType().name().equals(DataType.CONTROLLEDVOCABULARY.name()))
- {
- propertyTypeElement.setAttribute("vocabulary", propertyTypeImmutable.getVocabulary().getCode());
- }
- propertyTypesElement.appendChild(propertyTypeElement);
- }
- }
-
- // append sample types
- List<ISampleTypeImmutable> sampleTypes = masterDataRegistrationTransaction.listSampleTypes();
- appendSampleTypes(doc, rootElement, sampleTypes);
-
- // append experiment types
- List<IExperimentTypeImmutable> experimentTypes = masterDataRegistrationTransaction.listExperimentTypes();
- appendExperimentTypes(doc, rootElement, experimentTypes);
-
- // append data set types
- List<IDataSetTypeImmutable> dataSetTypes = masterDataRegistrationTransaction.listDataSetTypes();
- appendDataSetTypes(doc, rootElement, dataSetTypes);
-
- List<IMaterialTypeImmutable> materialTypes = masterDataRegistrationTransaction.listMaterialTypes();
- appendMaterialTypes(doc, rootElement, materialTypes);
-
- TransformerFactory transformerFactory = TransformerFactory.newInstance();
- Transformer transformer = transformerFactory.newTransformer();
- transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- DOMSource source = new DOMSource(doc);
- StringWriter writer = new StringWriter();
- StreamResult result = new StreamResult(writer);
- transformer.transform(source, result);
- return writer.toString();
- }
-
- private void appendMaterialTypes(Document doc, Element rootElement, List<IMaterialTypeImmutable> materialTypes)
- {
- if (materialTypes.size() > 0)
- {
- Element materialTypesElement = doc.createElement("materialTypes");
- rootElement.appendChild(materialTypesElement);
- Map<String, List<PropertyAssignment>> materialTypeCodePropAssignmentMap = loadMaterialTypesUsingV3WithPropertyAssignments();
- for (IMaterialTypeImmutable matType : materialTypes)
- {
- Element matTypeElement = getEntityTypeXML(doc, matType, "materialType");
- materialTypesElement.appendChild(matTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, materialTypeCodePropAssignmentMap.get(matType.getCode()));
- matTypeElement.appendChild(propertyAssignmentsElement);
- }
- }
- }
-
- private void appendDataSetTypes(Document doc, Element rootElement, List<IDataSetTypeImmutable> dataSetTypes)
- {
- if (dataSetTypes.size() > 0)
- {
- Element dataSetTypesElement = doc.createElement("dataSetTypes");
- rootElement.appendChild(dataSetTypesElement);
- Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = loadDataSetTypesUsingV3WithPropertyAssignments();
- for (IDataSetTypeImmutable dsType : dataSetTypes)
- {
- Element dsTypeElement = getEntityTypeXML(doc, dsType, "dataSetType");
- dataSetTypesElement.appendChild(dsTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, dsTypeCodePropAssignmentMap.get(dsType.getCode()));
- dsTypeElement.appendChild(propertyAssignmentsElement);
- }
- }
- }
- private void appendExperimentTypes(Document doc, Element rootElement, List<IExperimentTypeImmutable> experimentTypes)
- {
- if (experimentTypes.size() > 0)
- {
- Element expTypesElement = doc.createElement("experimentTypes");
- rootElement.appendChild(expTypesElement);
- Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
- for (IExperimentTypeImmutable expType : experimentTypes)
- {
- Element experimentTypeElement = getEntityTypeXML(doc, expType, "experimentType");
- expTypesElement.appendChild(experimentTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, expTypeCodePropAssignmentMap.get(expType.getCode()));
- experimentTypeElement.appendChild(propertyAssignmentsElement);
- }
- }
- }
-
- private void appendSampleTypes(Document doc, Element rootElement, List<ISampleTypeImmutable> sampleTypes)
- {
- if (sampleTypes.size() > 0)
- {
- Element sampleTypesElement = doc.createElement("sampleTypes");
- rootElement.appendChild(sampleTypesElement);
-
- Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = loadSampleTypesUsingV3WithPropertyAssignments();
- for (ISampleTypeImmutable sampleType : sampleTypes)
- {
- Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "sampleType");
- sampleTypeElement.setAttribute("description", sampleType.getDescription());
- sampleTypeElement.setAttribute("listable", String.valueOf(sampleType.isListable()));
- sampleTypeElement.setAttribute("showContainer", String.valueOf(sampleType.isShowContainer()));
- sampleTypeElement.setAttribute("showParents", String.valueOf(sampleType.isShowParents()));
- sampleTypeElement.setAttribute("showParentMetadata", String.valueOf(sampleType.isShowParentMetadata()));
- sampleTypeElement.setAttribute("generatedCodePrefix", sampleType.getGeneratedCodePrefix());
- sampleTypeElement.setAttribute("subcodeUnique", String.valueOf(sampleType.isSubcodeUnique()));
- sampleTypesElement.appendChild(sampleTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, sampleTypeCodePropAssignmentMap.get(sampleType.getCode()));
- sampleTypeElement.appendChild(propertyAssignmentsElement);
- }
- }
- }
-
- private <E extends IEntityType> Element getEntityTypeXML(Document doc, E entityType,
- String elementName)
- {
- Element typeElement = doc.createElement(elementName);
- typeElement.setAttribute("code", entityType.getCode());
- return typeElement;
- }
-
- private Element getPropertyAssignmentXML(Document doc, List<PropertyAssignment> propertyAssignments)
- {
- Element propertyAssignmentsElement = doc.createElement("propertyAssignments");
- for (PropertyAssignment propAssignment : propertyAssignments)
- {
- Element propertyAssigmentElement = doc.createElement("propertyAssigment");
- propertyAssignmentsElement.appendChild(propertyAssigmentElement);
- propertyAssigmentElement.setAttribute("property_type_code", propAssignment.getPropertyType().getCode());
- propertyAssigmentElement.setAttribute("data_type_code", propAssignment.getPropertyType().getDataType().toString());
- propertyAssigmentElement.setAttribute("ordinal", String.valueOf(propAssignment.getOrdinal()));
- propertyAssigmentElement.setAttribute("section", propAssignment.getSection());
- propertyAssigmentElement.setAttribute("showInEdit", String.valueOf(propAssignment.isShowInEditView()));
- propertyAssigmentElement.setAttribute("mandatory", String.valueOf(propAssignment.isMandatory()));
- propertyAssigmentElement.setAttribute("showRawValueInForms", String.valueOf(propAssignment.isShowRawValueInForms()));
- }
- return propertyAssignmentsElement;
- }
-
- // @XmlRootElement
- // @XmlAccessorType(XmlAccessType.FIELD)
- private static class MasterData
- {
- // @XmlElement(name = "sampleType")
- }
-
- private Map<String, List<PropertyAssignment>> loadDataSetTypesUsingV3WithPropertyAssignments()
- {
- // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
- Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
- DataSetTypeSearchCriteria searchCriteria = new DataSetTypeSearchCriteria();
- DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
- fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
-
- SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType> searchResult =
- v3Api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
- List<ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType> objects = searchResult.getObjects();
- for (ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType dataSetType : objects)
- {
- dsTypeCodePropAssignmentMap.put(dataSetType.getCode(), dataSetType.getPropertyAssignments());
- }
- return dsTypeCodePropAssignmentMap;
- }
-
- private Map<String, List<PropertyAssignment>> loadSampleTypesUsingV3WithPropertyAssignments()
- {
- // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
- Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
- SampleTypeSearchCriteria searchCriteria = new SampleTypeSearchCriteria();
- SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
- fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
-
- SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType> searchResult =
- v3Api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
- List<ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType> objects = searchResult.getObjects();
- for (ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType sampleType : objects)
- {
- sampleTypeCodePropAssignmentMap.put(sampleType.getCode(), sampleType.getPropertyAssignments());
- }
- return sampleTypeCodePropAssignmentMap;
- }
-
- private Map<String, List<PropertyAssignment>> loadExperimentTypesUsingV3WithPropertyAssignments()
- {
- // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
- Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
- ExperimentTypeSearchCriteria searchCriteria = new ExperimentTypeSearchCriteria();
- ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
- fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
-
- SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType> searchResult =
- v3Api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
- List<ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType> objects = searchResult.getObjects();
- for (ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType experimentType : objects)
- {
- expTypeCodePropAssignmentMap.put(experimentType.getCode(), experimentType.getPropertyAssignments());
- }
- return expTypeCodePropAssignmentMap;
- }
-
- private Map<String, List<PropertyAssignment>> loadMaterialTypesUsingV3WithPropertyAssignments()
- {
- // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
- Map<String, List<PropertyAssignment>> matTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
- MaterialTypeSearchCriteria searchCriteria = new MaterialTypeSearchCriteria();
- MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
- fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
-
- SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType> searchResult =
- v3Api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
- List<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType> objects = searchResult.getObjects();
- for (ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType materialType : objects)
- {
- matTypeCodePropAssignmentMap.put(materialType.getCode(), materialType.getPropertyAssignments());
- }
- return matTypeCodePropAssignmentMap;
+ MasterDataExtractor masterDataExtractor = new MasterDataExtractor(v3Api, sessionToken, masterDataRegistrationTransaction);
+ return masterDataExtractor.fetchAsXmlString();
}
protected List<String> extractCodes(List<? extends ICodeHolder> codeHolders)
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
new file mode 100644
index 0000000000000000000000000000000000000000..62d9010fa04f2a2845b838cfc998d55dec109dd0
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/MasterDataExtractor.java
@@ -0,0 +1,363 @@
+/*
+ * Copyright 2017 ETH Zuerich, SIS
+ *
+ * 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.ethz.sis.openbis.generic.server.dss.plugins.sync.common;
+
+import java.io.StringWriter;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.OutputKeys;
+import javax.xml.transform.Transformer;
+import javax.xml.transform.TransformerException;
+import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+
+import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search.SearchResult;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.search.DataSetTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.fetchoptions.ExperimentTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.search.ExperimentTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.fetchoptions.MaterialTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.search.MaterialTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions.SampleTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search.SampleTypeSearchCriteria;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.DataType;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IDataSetTypeImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IEntityType;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IExperimentTypeImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistrationTransaction;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMaterialTypeImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IPropertyTypeImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.ISampleTypeImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyImmutable;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyTermImmutable;
+
+/**
+ *
+ *
+ * @author Ganime Betul Akin
+ */
+public class MasterDataExtractor
+{
+ private final IMasterDataRegistrationTransaction masterDataRegistrationTransaction;
+
+ private final IApplicationServerApi v3Api;
+
+ private final String sessionToken;
+
+ /**
+ * @param v3Api
+ * @param sessionToken
+ * @param masterDataRegistrationTransaction
+ */
+ public MasterDataExtractor(IApplicationServerApi v3Api, String sessionToken,
+ IMasterDataRegistrationTransaction masterDataRegistrationTransaction)
+ {
+ this.v3Api = v3Api;
+ this.sessionToken = sessionToken;
+ this.masterDataRegistrationTransaction = masterDataRegistrationTransaction;
+ }
+
+ public String fetchAsXmlString() throws ParserConfigurationException, TransformerException
+ {
+ DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
+ DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
+ Document doc = docBuilder.newDocument();
+ Element rootElement = doc.createElement("masterData");
+ doc.appendChild(rootElement);
+
+ // append vocabularies
+ List<IVocabularyImmutable> vocabularies = masterDataRegistrationTransaction.listVocabularies();
+ if (vocabularies.size() > 0)
+ {
+ Element vocabsElement = doc.createElement("vocabularies");
+ rootElement.appendChild(vocabsElement);
+ for (IVocabularyImmutable vocabImmutable : vocabularies)
+ {
+ Element vocabElement = doc.createElement("vocabulary");
+ vocabElement.setAttribute("code", vocabImmutable.getCode());
+ vocabElement.setAttribute("description", vocabImmutable.getDescription());
+ vocabElement.setAttribute("urlTemplate", vocabImmutable.getUrlTemplate());
+ vocabElement.setAttribute("managedInternally", String.valueOf(vocabImmutable.isManagedInternally()));
+ vocabElement.setAttribute("internalNamespace", String.valueOf(vocabImmutable.isInternalNamespace()));
+ vocabElement.setAttribute("chosenFromList", String.valueOf(vocabImmutable.isChosenFromList()));
+ vocabsElement.appendChild(vocabElement);
+
+ List<IVocabularyTermImmutable> terms = vocabImmutable.getTerms();
+ for (IVocabularyTermImmutable vocabTermImmutable : terms)
+ {
+ Element termElement = doc.createElement("term");
+ termElement.setAttribute("code", vocabTermImmutable.getCode());
+ termElement.setAttribute("label", vocabTermImmutable.getLabel());
+ termElement.setAttribute("description", vocabTermImmutable.getDescription());
+ termElement.setAttribute("ordinal", String.valueOf(vocabTermImmutable.getOrdinal()));
+ termElement.setAttribute("url", vocabTermImmutable.getUrl());
+ vocabElement.appendChild(termElement);
+ }
+ }
+ }
+
+ // append property types
+ List<IPropertyTypeImmutable> propertyTypes = masterDataRegistrationTransaction.listPropertyTypes();
+ if (propertyTypes.size() > 0)
+ {
+ Element propertyTypesElement = doc.createElement("propertyTypes");
+ rootElement.appendChild(propertyTypesElement);
+ for (IPropertyTypeImmutable propertyTypeImmutable : propertyTypes)
+ {
+ Element propertyTypeElement = doc.createElement("propertyType");
+ propertyTypeElement.setAttribute("code", propertyTypeImmutable.getCode());
+ propertyTypeElement.setAttribute("label", propertyTypeImmutable.getLabel());
+ propertyTypeElement.setAttribute("dataType", propertyTypeImmutable.getDataType().name());
+ propertyTypeElement.setAttribute("internalNamespace", String.valueOf(propertyTypeImmutable.isInternalNamespace()));
+ propertyTypeElement.setAttribute("managedInternally", String.valueOf(propertyTypeImmutable.isManagedInternally()));
+ propertyTypeElement.setAttribute("description", propertyTypeImmutable.getDescription());
+ if (propertyTypeImmutable.getDataType().name().equals(DataType.CONTROLLEDVOCABULARY.name()))
+ {
+ propertyTypeElement.setAttribute("vocabulary", propertyTypeImmutable.getVocabulary().getCode());
+ }
+ propertyTypesElement.appendChild(propertyTypeElement);
+ }
+ }
+
+ // append sample types
+ List<ISampleTypeImmutable> sampleTypes = masterDataRegistrationTransaction.listSampleTypes();
+ appendSampleTypes(doc, rootElement, sampleTypes);
+
+ // append experiment types
+ List<IExperimentTypeImmutable> experimentTypes = masterDataRegistrationTransaction.listExperimentTypes();
+ appendExperimentTypes(doc, rootElement, experimentTypes);
+
+ // append data set types
+ List<IDataSetTypeImmutable> dataSetTypes = masterDataRegistrationTransaction.listDataSetTypes();
+ appendDataSetTypes(doc, rootElement, dataSetTypes);
+
+ List<IMaterialTypeImmutable> materialTypes = masterDataRegistrationTransaction.listMaterialTypes();
+ appendMaterialTypes(doc, rootElement, materialTypes);
+
+ TransformerFactory transformerFactory = TransformerFactory.newInstance();
+ Transformer transformer = transformerFactory.newTransformer();
+ transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ DOMSource source = new DOMSource(doc);
+ StringWriter writer = new StringWriter();
+ StreamResult result = new StreamResult(writer);
+ transformer.transform(source, result);
+ return writer.toString();
+ }
+
+ private void appendMaterialTypes(Document doc, Element rootElement, List<IMaterialTypeImmutable> materialTypes)
+ {
+ if (materialTypes.size() > 0)
+ {
+ Element materialTypesElement = doc.createElement("materialTypes");
+ rootElement.appendChild(materialTypesElement);
+ Map<String, List<PropertyAssignment>> materialTypeCodePropAssignmentMap = loadMaterialTypesUsingV3WithPropertyAssignments();
+ for (IMaterialTypeImmutable matType : materialTypes)
+ {
+ Element matTypeElement = getEntityTypeXML(doc, matType, "materialType");
+ matTypeElement.setAttribute("description", matType.getDescription());
+ // TODO validation script
+ materialTypesElement.appendChild(matTypeElement);
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, materialTypeCodePropAssignmentMap.get(matType.getCode()));
+ matTypeElement.appendChild(propertyAssignmentsElement);
+ }
+ }
+ }
+
+ private void appendDataSetTypes(Document doc, Element rootElement, List<IDataSetTypeImmutable> dataSetTypes)
+ {
+ if (dataSetTypes.size() > 0)
+ {
+ Element dataSetTypesElement = doc.createElement("dataSetTypes");
+ rootElement.appendChild(dataSetTypesElement);
+ Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = loadDataSetTypesUsingV3WithPropertyAssignments();
+ for (IDataSetTypeImmutable dsType : dataSetTypes)
+ {
+ Element dsTypeElement = getEntityTypeXML(doc, dsType, "dataSetType");
+ dsTypeElement.setAttribute("description", dsType.getDescription());
+ dsTypeElement.setAttribute("dataSetKind", dsType.getDataSetKind());
+ dsTypeElement.setAttribute("mainDataSetPattern", dsType.getMainDataSetPattern());
+ dsTypeElement.setAttribute("mainDataSetPath", dsType.getMainDataSetPath());
+ dsTypeElement.setAttribute("deletionDisallowed", String.valueOf(dsType.isDeletionDisallowed()));
+ // TODO validation script?
+ dataSetTypesElement.appendChild(dsTypeElement);
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, dsTypeCodePropAssignmentMap.get(dsType.getCode()));
+ dsTypeElement.appendChild(propertyAssignmentsElement);
+ }
+ }
+ }
+
+ private void appendExperimentTypes(Document doc, Element rootElement, List<IExperimentTypeImmutable> experimentTypes)
+ {
+ if (experimentTypes.size() > 0)
+ {
+ Element experimentTypesElement = doc.createElement("experimentTypes");
+ rootElement.appendChild(experimentTypesElement);
+ Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
+ for (IExperimentTypeImmutable expType : experimentTypes)
+ {
+ Element experimentTypeElement = getEntityTypeXML(doc, expType, "experimentType");
+ experimentTypeElement.setAttribute("description", expType.getDescription());
+ // TODO validation script?
+ experimentTypesElement.appendChild(experimentTypeElement);
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, expTypeCodePropAssignmentMap.get(expType.getCode()));
+ experimentTypeElement.appendChild(propertyAssignmentsElement);
+ }
+ }
+ }
+
+ private void appendSampleTypes(Document doc, Element rootElement, List<ISampleTypeImmutable> sampleTypes)
+ {
+ if (sampleTypes.size() > 0)
+ {
+ Element sampleTypesElement = doc.createElement("sampleTypes");
+ rootElement.appendChild(sampleTypesElement);
+
+ Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = loadSampleTypesUsingV3WithPropertyAssignments();
+ for (ISampleTypeImmutable sampleType : sampleTypes)
+ {
+ Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "sampleType");
+ sampleTypeElement.setAttribute("description", sampleType.getDescription());
+ sampleTypeElement.setAttribute("listable", String.valueOf(sampleType.isListable()));
+ sampleTypeElement.setAttribute("showContainer", String.valueOf(sampleType.isShowContainer()));
+ sampleTypeElement.setAttribute("showParents", String.valueOf(sampleType.isShowParents()));
+ sampleTypeElement.setAttribute("showParentMetadata", String.valueOf(sampleType.isShowParentMetadata()));
+ sampleTypeElement.setAttribute("subcodeUnique", String.valueOf(sampleType.isSubcodeUnique()));
+ sampleTypeElement.setAttribute("autoGeneratedCode", String.valueOf(sampleType.isAutoGeneratedCode()));
+ sampleTypeElement.setAttribute("generatedCodePrefix", sampleType.getGeneratedCodePrefix());
+ sampleTypesElement.appendChild(sampleTypeElement);
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, sampleTypeCodePropAssignmentMap.get(sampleType.getCode()));
+ sampleTypeElement.appendChild(propertyAssignmentsElement);
+ }
+ }
+ }
+
+ private <E extends IEntityType> Element getEntityTypeXML(Document doc, E entityType,
+ String elementName)
+ {
+ Element typeElement = doc.createElement(elementName);
+ typeElement.setAttribute("code", entityType.getCode());
+ return typeElement;
+ }
+
+ private Element getPropertyAssignmentXML(Document doc, List<PropertyAssignment> propertyAssignments)
+ {
+ Element propertyAssignmentsElement = doc.createElement("propertyAssignments");
+ for (PropertyAssignment propAssignment : propertyAssignments)
+ {
+ Element propertyAssigmentElement = doc.createElement("propertyAssigment");
+ propertyAssignmentsElement.appendChild(propertyAssigmentElement);
+ propertyAssigmentElement.setAttribute("property_type_code", propAssignment.getPropertyType().getCode());
+ // propertyAssigmentElement.setAttribute("data_type_code", propAssignment.getPropertyType().getDataType().toString());
+ propertyAssigmentElement.setAttribute("ordinal", String.valueOf(propAssignment.getOrdinal()));
+ propertyAssigmentElement.setAttribute("section", propAssignment.getSection());
+ propertyAssigmentElement.setAttribute("showInEdit", String.valueOf(propAssignment.isShowInEditView()));
+ propertyAssigmentElement.setAttribute("mandatory", String.valueOf(propAssignment.isMandatory()));
+ propertyAssigmentElement.setAttribute("showRawValueInForms", String.valueOf(propAssignment.isShowRawValueInForms()));
+ }
+ return propertyAssignmentsElement;
+ }
+
+ // @XmlRootElement
+ // @XmlAccessorType(XmlAccessType.FIELD)
+ private static class MasterData
+ {
+ // @XmlElement(name = "sampleType")
+ }
+
+ private Map<String, List<PropertyAssignment>> loadDataSetTypesUsingV3WithPropertyAssignments()
+ {
+ // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
+ Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
+ DataSetTypeSearchCriteria searchCriteria = new DataSetTypeSearchCriteria();
+ DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
+
+ SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType> searchResult =
+ v3Api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
+ List<ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType> objects = searchResult.getObjects();
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType dataSetType : objects)
+ {
+ dsTypeCodePropAssignmentMap.put(dataSetType.getCode(), dataSetType.getPropertyAssignments());
+ }
+ return dsTypeCodePropAssignmentMap;
+ }
+
+ private Map<String, List<PropertyAssignment>> loadSampleTypesUsingV3WithPropertyAssignments()
+ {
+ // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
+ Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
+ SampleTypeSearchCriteria searchCriteria = new SampleTypeSearchCriteria();
+ SampleTypeFetchOptions fetchOptions = new SampleTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
+
+ SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType> searchResult =
+ v3Api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
+ List<ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType> objects = searchResult.getObjects();
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType sampleType : objects)
+ {
+ sampleTypeCodePropAssignmentMap.put(sampleType.getCode(), sampleType.getPropertyAssignments());
+ }
+ return sampleTypeCodePropAssignmentMap;
+ }
+
+ private Map<String, List<PropertyAssignment>> loadExperimentTypesUsingV3WithPropertyAssignments()
+ {
+ // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
+ Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
+ ExperimentTypeSearchCriteria searchCriteria = new ExperimentTypeSearchCriteria();
+ ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
+
+ SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType> searchResult =
+ v3Api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
+ List<ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType> objects = searchResult.getObjects();
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType experimentType : objects)
+ {
+ expTypeCodePropAssignmentMap.put(experimentType.getCode(), experimentType.getPropertyAssignments());
+ }
+ return expTypeCodePropAssignmentMap;
+ }
+
+ private Map<String, List<PropertyAssignment>> loadMaterialTypesUsingV3WithPropertyAssignments()
+ {
+ // We are mixing up v1 and v3 here because using v3 api to get property assignments is easier
+ Map<String, List<PropertyAssignment>> matTypeCodePropAssignmentMap = new HashMap<String, List<PropertyAssignment>>();
+ MaterialTypeSearchCriteria searchCriteria = new MaterialTypeSearchCriteria();
+ MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType().withVocabulary();
+
+ SearchResult<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType> searchResult =
+ v3Api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
+ List<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType> objects = searchResult.getObjects();
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType materialType : objects)
+ {
+ matTypeCodePropAssignmentMap.put(materialType.getCode(), materialType.getPropertyAssignments());
+ }
+ return matTypeCodePropAssignmentMap;
+ }
+}