diff --git a/openbis/source/java/ch/ethz/sis/openbis/generic/server/EntityRetriever.java b/openbis/source/java/ch/ethz/sis/openbis/generic/server/EntityRetriever.java
index 08fc895eb46dc09e2a33a2986892e92d6dc55c9e..cb9936d0c4d273e30642d5db86b719496fbe9e02 100644
--- a/openbis/source/java/ch/ethz/sis/openbis/generic/server/EntityRetriever.java
+++ b/openbis/source/java/ch/ethz/sis/openbis/generic/server/EntityRetriever.java
@@ -22,6 +22,7 @@ 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;
@@ -44,19 +45,16 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IAttachmentsHo
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.DataSetType;
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.ExperimentType;
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.MaterialType;
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;
@@ -66,7 +64,6 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.fetchoptions.ProjectFetc
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.SampleType;
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;
@@ -80,8 +77,13 @@ 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;
@@ -95,8 +97,6 @@ public class EntityRetriever
private final String sessionToken;
- private static final int TIMEOUT = 10000;
-
private EntityRetriever(IApplicationServerApi v3Api, String sessionToken, IMasterDataRegistrationTransaction masterDataRegistrationTransaction)
{
this.v3Api = v3Api;
@@ -410,7 +410,7 @@ public class EntityRetriever
return searchResult.getObjects();
}
- public String fetchMetaDataAsXML() throws ParserConfigurationException, TransformerException
+ public String fetchMasterDataAsXML() throws ParserConfigurationException, TransformerException
{
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
@@ -419,7 +419,7 @@ public class EntityRetriever
doc.appendChild(rootElement);
// append vocabularies
- List<IVocabularyImmutable> vocabularies = listVocabularies();
+ List<IVocabularyImmutable> vocabularies = masterDataRegistrationTransaction.listVocabularies();
if (vocabularies.size() > 0)
{
Element vocabsElement = doc.createElement("vocabularies");
@@ -430,7 +430,11 @@ public class EntityRetriever
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)
{
@@ -446,7 +450,7 @@ public class EntityRetriever
}
// append property types
- List<IPropertyTypeImmutable> propertyTypes = listPropertyTypes();
+ List<IPropertyTypeImmutable> propertyTypes = masterDataRegistrationTransaction.listPropertyTypes();
if (propertyTypes.size() > 0)
{
Element propertyTypesElement = doc.createElement("propertyTypes");
@@ -469,18 +473,18 @@ public class EntityRetriever
}
// append sample types
- List<SampleType> sampleTypes = this.getSampleTypes();
+ List<ISampleTypeImmutable> sampleTypes = masterDataRegistrationTransaction.listSampleTypes();
appendSampleTypes(doc, rootElement, sampleTypes);
// append experiment types
- List<ExperimentType> experimentTypes = this.getExperimentTypes();
+ List<IExperimentTypeImmutable> experimentTypes = masterDataRegistrationTransaction.listExperimentTypes();
appendExperimentTypes(doc, rootElement, experimentTypes);
// append data set types
- List<DataSetType> dataSetTypes = this.getDataSetTypes();
+ List<IDataSetTypeImmutable> dataSetTypes = masterDataRegistrationTransaction.listDataSetTypes();
appendDataSetTypes(doc, rootElement, dataSetTypes);
- List<MaterialType> materialTypes = this.getMaterialTypes();
+ List<IMaterialTypeImmutable> materialTypes = masterDataRegistrationTransaction.listMaterialTypes();
appendMaterialTypes(doc, rootElement, materialTypes);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
@@ -493,72 +497,82 @@ public class EntityRetriever
return writer.toString();
}
- private void appendMaterialTypes(Document doc, Element rootElement, List<MaterialType> materialTypes)
+ private void appendMaterialTypes(Document doc, Element rootElement, List<IMaterialTypeImmutable> materialTypes)
{
if (materialTypes.size() > 0)
{
Element materialTypesElement = doc.createElement("materialTypes");
rootElement.appendChild(materialTypesElement);
- for (MaterialType matType : materialTypes)
+ Map<String, List<PropertyAssignment>> materialTypeCodePropAssignmentMap = loadMaterialTypesUsingV3WithPropertyAssignments();
+ for (IMaterialTypeImmutable matType : materialTypes)
{
Element matTypeElement = getEntityTypeXML(doc, matType, "materialType");
materialTypesElement.appendChild(matTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, matType.getPropertyAssignments());
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, materialTypeCodePropAssignmentMap.get(matType.getCode()));
matTypeElement.appendChild(propertyAssignmentsElement);
}
}
}
- private void appendDataSetTypes(Document doc, Element rootElement, List<DataSetType> dataSetTypes)
+ private void appendDataSetTypes(Document doc, Element rootElement, List<IDataSetTypeImmutable> dataSetTypes)
{
if (dataSetTypes.size() > 0)
{
Element dataSetTypesElement = doc.createElement("dataSetTypes");
rootElement.appendChild(dataSetTypesElement);
- for (DataSetType dsType : dataSetTypes)
+ Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = loadDataSetTypesUsingV3WithPropertyAssignments();
+ for (IDataSetTypeImmutable dsType : dataSetTypes)
{
Element dsTypeElement = getEntityTypeXML(doc, dsType, "dataSetType");
dataSetTypesElement.appendChild(dsTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, dsType.getPropertyAssignments());
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, dsTypeCodePropAssignmentMap.get(dsType.getCode()));
dsTypeElement.appendChild(propertyAssignmentsElement);
}
}
}
-
- private void appendExperimentTypes(Document doc, Element rootElement, List<ExperimentType> experimentTypes)
+ private void appendExperimentTypes(Document doc, Element rootElement, List<IExperimentTypeImmutable> experimentTypes)
{
if (experimentTypes.size() > 0)
{
Element expTypesElement = doc.createElement("experimentTypes");
rootElement.appendChild(expTypesElement);
- for (ExperimentType expType : experimentTypes)
+ Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
+ for (IExperimentTypeImmutable expType : experimentTypes)
{
Element experimentTypeElement = getEntityTypeXML(doc, expType, "experimentType");
expTypesElement.appendChild(experimentTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, expType.getPropertyAssignments());
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, expTypeCodePropAssignmentMap.get(expType.getCode()));
experimentTypeElement.appendChild(propertyAssignmentsElement);
}
}
}
- private void appendSampleTypes(Document doc, Element rootElement, List<SampleType> sampleTypes)
+ private void appendSampleTypes(Document doc, Element rootElement, List<ISampleTypeImmutable> sampleTypes)
{
if (sampleTypes.size() > 0)
{
Element sampleTypesElement = doc.createElement("sampleTypes");
rootElement.appendChild(sampleTypesElement);
- for (SampleType sampleType : sampleTypes)
+
+ 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, sampleType.getPropertyAssignments());
+ Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, sampleTypeCodePropAssignmentMap.get(sampleType.getCode()));
sampleTypeElement.appendChild(propertyAssignmentsElement);
}
}
}
- private <E extends ICodeHolder> Element getEntityTypeXML(Document doc, E entityType,
+ private <E extends IEntityType> Element getEntityTypeXML(Document doc, E entityType,
String elementName)
{
Element typeElement = doc.createElement(elementName);
@@ -575,80 +589,92 @@ public class EntityRetriever
propertyAssignmentsElement.appendChild(propertyAssigmentElement);
propertyAssigmentElement.setAttribute("property_type_code", propAssignment.getPropertyType().getCode());
propertyAssigmentElement.setAttribute("data_type_code", propAssignment.getPropertyType().getDataType().toString());
- propertyAssigmentElement.setAttribute("mandatory", String.valueOf(propAssignment.isMandatory()));
- propertyAssigmentElement.setAttribute("section", propAssignment.getSection());
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;
}
- public void printSamples()
- {
- buildEntityGraph("SYNC");
- }
-
// @XmlRootElement
// @XmlAccessorType(XmlAccessType.FIELD)
private static class MasterData
{
// @XmlElement(name = "sampleType")
- List<SampleType> sampleTypes = new ArrayList<SampleType>();
-
- List<ExperimentType> experimentTypes = new ArrayList<ExperimentType>();
-
- List<DataSetType> dataSetTypes = new ArrayList<DataSetType>();
-
- List<MaterialType> materialTypes = new ArrayList<MaterialType>();
- }
-
- public List<IPropertyTypeImmutable> listPropertyTypes()
- {
- return masterDataRegistrationTransaction.listPropertyTypes();
}
- public List<IVocabularyImmutable> listVocabularies()
- {
- return masterDataRegistrationTransaction.listVocabularies();
- }
-
- private List<DataSetType> getDataSetTypes()
+ 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<DataSetType> searchResult = v3Api.searchDataSetTypes(sessionToken, searchCriteria, fetchOptions);
- return searchResult.getObjects();
+ 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 List<SampleType> getSampleTypes()
+ 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<SampleType> searchResult = v3Api.searchSampleTypes(sessionToken, searchCriteria, fetchOptions);
- return searchResult.getObjects();
+ 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 List<ExperimentType> getExperimentTypes()
+ 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<ExperimentType> searchResult = v3Api.searchExperimentTypes(sessionToken, searchCriteria, fetchOptions);
- return searchResult.getObjects();
+ 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 List<MaterialType> getMaterialTypes()
+ 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<MaterialType> searchResult = v3Api.searchMaterialTypes(sessionToken, searchCriteria, fetchOptions);
- return searchResult.getObjects();
+ 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;
}
protected List<String> extractCodes(List<? extends ICodeHolder> codeHolders)