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Commit 66a5b98f authored by gakin's avatar gakin
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SSDM-4559 : Extract further master data using MasterDataExtractor class 

SVN: 37586
parent 1c904fbb
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datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/EntityRetriever.java
+ 2
− 293
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......@@ -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)
......
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