From 5d2efc2e9da9f051cd8146b8b76eea8d8b19d3fe Mon Sep 17 00:00:00 2001
From: felmer <franz-josef.elmer@id.ethz.ch>
Date: Thu, 24 Jan 2019 13:50:28 +0100
Subject: [PATCH] SSDM-7204: External Data Management Systems added as master
data. MasterDataExtractor refactored.
---
.../plugins/sync/common/EntityRetriever.java | 14 +
.../sync/common/MasterDataExtractor.java | 531 +++++++++---------
.../plugins/sync/common/entitygraph/Node.java | 6 +-
3 files changed, 277 insertions(+), 274 deletions(-)
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 7b716af44ff..5d1edc68ec2 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
@@ -33,10 +33,13 @@ import org.apache.log4j.Logger;
import ch.ethz.sis.openbis.generic.asapi.v3.IApplicationServerApi;
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.ContentCopy;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.LinkedData;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.fetchoptions.DataSetFetchOptions;
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.externaldms.ExternalDms;
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.search.MaterialSearchCriteria;
@@ -305,6 +308,16 @@ public class EntityRetriever implements IEntityRetriever
{
Node<DataSet> dataSetNode = new Node<DataSet>(dataSet);
graph.addEdge(expNode, dataSetNode, new Edge(CONNECTION));
+ LinkedData linkedData = dataSet.getLinkedData();
+ if (linkedData != null)
+ {
+ List<ContentCopy> contentCopies = linkedData.getContentCopies();
+ for (ContentCopy contentCopy : contentCopies)
+ {
+ ExternalDms externalDms = contentCopy.getExternalDms();
+// Node<ExternalDms> dmsNode = new Node<ExternalDms>(externalDms);
+ }
+ }
addChildAndContainedDataSets(dataSetNode);
}
}
@@ -507,6 +520,7 @@ public class EntityRetriever implements IEntityRetriever
fo.withProperties();
fo.withChildrenUsing(fo);
fo.withComponentsUsing(fo);
+ fo.withLinkedData().withExternalDms();
return fo;
}
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 8094e9b051b..420e6ee2589 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
@@ -19,9 +19,8 @@ package ch.ethz.sis.openbis.generic.server.dss.plugins.sync.common;
import static ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant.INTERNAL_NAMESPACE_PREFIX;
import java.io.StringWriter;
-import java.util.HashMap;
import java.util.List;
-import java.util.Map;
+import java.util.Set;
import javax.xml.parsers.DocumentBuilder;
import javax.xml.parsers.DocumentBuilderFactory;
@@ -37,29 +36,41 @@ 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.common.interfaces.ICodeHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IDescriptionHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertyAssignmentsHolder;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetType;
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.entitytype.EntityKind;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.ExperimentType;
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.externaldms.ExternalDms;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.fetchoptions.ExternalDmsFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.search.ExternalDmsSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.MaterialType;
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.plugin.Plugin;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.fetchoptions.PluginFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.plugin.search.PluginSearchCriteria;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyAssignment;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.PropertyType;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.fetchoptions.PropertyTypeFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.property.search.PropertyTypeSearchCriteria;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.SampleType;
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.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.Vocabulary;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.VocabularyTerm;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.fetchoptions.VocabularyFetchOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.vocabulary.search.VocabularySearchCriteria;
+import ch.systemsx.cisd.common.shared.basic.string.CommaSeparatedListBuilder;
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.IFileFormatTypeImmutable;
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.IScriptImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyImmutable;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IVocabularyTermImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.BasicConstant;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
/**
@@ -67,6 +78,18 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.CodeConverter;
*/
public class MasterDataExtractor
{
+ private static final VocabularySearchCriteria VOCABULARY_SEARCH_CRITERIA = new VocabularySearchCriteria();
+
+ private static final PropertyTypeSearchCriteria PROPERTY_TYPE_SEARCH_CRITERIA = new PropertyTypeSearchCriteria();
+
+ private static final ExperimentTypeSearchCriteria EXPERIMENT_TYPE_SEARCH_CRITERIA = new ExperimentTypeSearchCriteria();
+
+ private static final MaterialTypeSearchCriteria MATERIAL_TYPE_SEARCH_CRITERIA = new MaterialTypeSearchCriteria();
+
+ private static final SampleTypeSearchCriteria SAMPLE_TYPE_SEARCH_CRITERIA = new SampleTypeSearchCriteria();
+
+ private static final DataSetTypeSearchCriteria DATA_SET_TYPE_SEARCH_CRITERIA = new DataSetTypeSearchCriteria();
+
private final IMasterDataRegistrationTransaction masterDataRegistrationTransaction;
private final IApplicationServerApi v3Api;
@@ -96,36 +119,18 @@ public class MasterDataExtractor
rootElement.setAttribute("xmlns:xmd", "https://sis.id.ethz.ch/software/#openbis/xmdterms/");
doc.appendChild(rootElement);
- // append scripts
- List<IScriptImmutable> scripts = masterDataRegistrationTransaction.listScripts();
- appendValidationPlugins(doc, rootElement, scripts);
+ appendFileFormatTypes(doc, rootElement);
- // append file format types
- List<IFileFormatTypeImmutable> fileFormatTypes = masterDataRegistrationTransaction.listFileFormatTypes();
- appendFileFormatTypes(doc, rootElement, fileFormatTypes);
-
- // append vocabularies
- List<IVocabularyImmutable> vocabularies = masterDataRegistrationTransaction.listVocabularies();
- appendVocabularies(doc, rootElement, vocabularies);
-
- // append property types
- List<IPropertyTypeImmutable> propertyTypes = masterDataRegistrationTransaction.listPropertyTypes();
- appendPropertyTypes(doc, rootElement, propertyTypes);
+ appendValidationPlugins(doc, rootElement);
+ appendVocabularies(doc, rootElement);
- // append sample types
- List<ISampleTypeImmutable> sampleTypes = masterDataRegistrationTransaction.listSampleTypes();
- appendSampleTypes(doc, rootElement, sampleTypes);
+ appendPropertyTypes(doc, rootElement);
+ appendSampleTypes(doc, rootElement);
+ appendExperimentTypes(doc, rootElement);
+ appendDataSetTypes(doc, rootElement);
+ appendMaterialTypes(doc, rootElement);
- // 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);
+ appendExternalDataManagementSystems(doc, rootElement);
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
@@ -143,30 +148,71 @@ public class MasterDataExtractor
return writer.toString();
}
- private void appendValidationPlugins(Document doc, Element rootElement, List<IScriptImmutable> scripts)
+ protected void appendExternalDataManagementSystems(Document doc, Element rootElement)
{
- if (scripts.size() > 0)
+ ExternalDmsSearchCriteria searchCriteria = new ExternalDmsSearchCriteria();
+ ExternalDmsFetchOptions fetchOptions = new ExternalDmsFetchOptions();
+ List<ExternalDms> externalDataManagementSystems =
+ v3Api.searchExternalDataManagementSystems(sessionToken, searchCriteria, fetchOptions).getObjects();
+ if (externalDataManagementSystems.isEmpty() == false)
{
- Element pluginsElement = doc.createElement("xmd:validationPlugins");
- rootElement.appendChild(pluginsElement);
- for (IScriptImmutable script : scripts)
+ Element externalDataManagementSystemsElement = doc.createElement("xmd:externalDataManagementSystems");
+ rootElement.appendChild(externalDataManagementSystemsElement);
+ for (ExternalDms externalDms : externalDataManagementSystems)
{
- Element pluginElement = doc.createElement("xmd:validationPlugin");
- // pluginElement.setAttribute("code", script.getCode());
- pluginElement.setAttribute("name", script.getName());
- pluginElement.setAttribute("description", script.getDescription());
- pluginElement.setAttribute("type", script.getScriptType());
- pluginElement.setAttribute("entityKind", script.getEntity() == null ? "All" : script.getEntity());
- // TODO isAvailable? Maybe to be gotten from the internal API?
-
- pluginElement.appendChild(doc.createCDATASection(script.getScript()));
- pluginsElement.appendChild(pluginElement);
+ Element externalDmsElement = doc.createElement("xmd:externalDataManagementSystem");
+ externalDmsElement.setAttribute("code", externalDms.getCode());
+ externalDmsElement.setAttribute("label", externalDms.getLabel());
+ externalDmsElement.setAttribute("address", externalDms.getAddress());
+ externalDmsElement.setAttribute("addressType", externalDms.getAddressType().toString());
+ externalDataManagementSystemsElement.appendChild(externalDmsElement);
}
}
}
- private void appendFileFormatTypes(Document doc, Element rootElement, List<IFileFormatTypeImmutable> fileFormatTypes)
+ private void appendValidationPlugins(Document doc, Element rootElement)
{
+ PluginFetchOptions fetchOptions = new PluginFetchOptions();
+ fetchOptions.withScript();
+ List<Plugin> plugins = v3Api.searchPlugins(sessionToken, new PluginSearchCriteria(), fetchOptions).getObjects();
+ if (plugins.isEmpty())
+ {
+ return;
+ }
+ Element pluginsElement = doc.createElement("xmd:validationPlugins");
+ rootElement.appendChild(pluginsElement);
+ for (Plugin plugin : plugins)
+ {
+ Element pluginElement = doc.createElement("xmd:validationPlugin");
+ pluginElement.setAttribute("name", plugin.getName());
+ pluginElement.setAttribute("description", plugin.getDescription());
+ pluginElement.setAttribute("type", plugin.getPluginType().toString());
+ pluginElement.setAttribute("entityKind", getEntityKind(plugin));
+ pluginElement.setAttribute("isAvailable", String.valueOf(plugin.isAvailable()));
+ pluginElement.appendChild(doc.createCDATASection(plugin.getScript()));
+ pluginsElement.appendChild(pluginElement);
+ }
+ }
+
+ protected String getEntityKind(Plugin plugin)
+ {
+ String entityKind = "All";
+ Set<EntityKind> entityKinds = plugin.getEntityKinds();
+ if (entityKinds != null)
+ {
+ CommaSeparatedListBuilder builder = new CommaSeparatedListBuilder();
+ for (EntityKind kind : entityKinds)
+ {
+ builder.append(kind.toString());
+ }
+ entityKind = builder.toString();
+ }
+ return entityKind;
+ }
+
+ private void appendFileFormatTypes(Document doc, Element rootElement)
+ {
+ List<IFileFormatTypeImmutable> fileFormatTypes = masterDataRegistrationTransaction.listFileFormatTypes();
if (fileFormatTypes.size() > 0)
{
Element fileFormatTypesElement = doc.createElement("xmd:fileFormatTypes");
@@ -181,274 +227,221 @@ public class MasterDataExtractor
}
}
- private void appendPropertyTypes(Document doc, Element rootElement, List<IPropertyTypeImmutable> propertyTypes)
+ private void appendPropertyTypes(Document doc, Element rootElement)
{
- if (propertyTypes.size() > 0)
+ PropertyTypeFetchOptions fetchOptions = new PropertyTypeFetchOptions();
+ fetchOptions.withMaterialType();
+ fetchOptions.withVocabulary();
+ List<PropertyType> propertyTypes = v3Api.searchPropertyTypes(sessionToken, PROPERTY_TYPE_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (propertyTypes.isEmpty())
{
- Element propertyTypesElement = doc.createElement("xmd:propertyTypes");
- rootElement.appendChild(propertyTypesElement);
- for (IPropertyTypeImmutable propertyTypeImmutable : propertyTypes)
- {
- String code =
- (propertyTypeImmutable.isInternalNamespace()
- && propertyTypeImmutable.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX))
- ? CodeConverter.tryToDatabase(propertyTypeImmutable
- .getCode())
- : propertyTypeImmutable.getCode();
- Element propertyTypeElement = doc.createElement("xmd:propertyType");
- propertyTypeElement.setAttribute("code", code);
- 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());
- } else if (propertyTypeImmutable.getDataType().name().equals(DataType.MATERIAL.name()))
- {
- if (propertyTypeImmutable.getMaterialType() != null)
- {
- propertyTypeElement.setAttribute("material", propertyTypeImmutable.getMaterialType().getCode());
- } else
- {
- // for properties like "inhibitor_of" where it is of Material of Any Type
- propertyTypeElement.setAttribute("material", "");
- }
- }
- propertyTypesElement.appendChild(propertyTypeElement);
- }
+ return;
}
- }
-
- private void appendVocabularies(Document doc, Element rootElement, List<IVocabularyImmutable> vocabularies)
- {
- if (vocabularies.size() > 0)
+ Element propertyTypesElement = doc.createElement("xmd:propertyTypes");
+ rootElement.appendChild(propertyTypesElement);
+ for (PropertyType propertyType : propertyTypes)
{
- Element vocabsElement = doc.createElement("xmd:controlledVocabularies");
- rootElement.appendChild(vocabsElement);
- for (IVocabularyImmutable vocabImmutable : vocabularies)
+ Boolean internalNameSpace = propertyType.isInternalNameSpace();
+ String code =
+ (internalNameSpace && propertyType.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX))
+ ? CodeConverter.tryToDatabase(propertyType.getCode())
+ : propertyType.getCode();
+ Element typeElement = doc.createElement("xmd:propertyType");
+ typeElement.setAttribute("code", code);
+ typeElement.setAttribute("label", propertyType.getLabel());
+ typeElement.setAttribute("dataType", propertyType.getDataType().name());
+ typeElement.setAttribute("internalNamespace", String.valueOf(internalNameSpace));
+ typeElement.setAttribute("managedInternally", String.valueOf(propertyType.isManagedInternally()));
+ typeElement.setAttribute("description", propertyType.getDescription());
+ if (propertyType.getDataType().name().equals(DataType.CONTROLLEDVOCABULARY.name()))
{
- Element vocabElement = doc.createElement("xmd:controlledVocabulary");
- String code = vocabImmutable.isInternalNamespace()
- && vocabImmutable.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX) ? CodeConverter.tryToDatabase(vocabImmutable.getCode())
- : vocabImmutable.getCode();
- vocabElement.setAttribute("code", code);
- 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)
+ typeElement.setAttribute("vocabulary", propertyType.getVocabulary().getCode());
+ } else if (propertyType.getDataType().name().equals(DataType.MATERIAL.name()))
+ {
+ if (propertyType.getMaterialType() != null)
+ {
+ typeElement.setAttribute("material", propertyType.getMaterialType().getCode());
+ } else
{
- 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);
+ // for properties like "inhibitor_of" where it is of Material of Any Type
+ typeElement.setAttribute("material", "");
}
}
+ propertyTypesElement.appendChild(typeElement);
}
}
- private void appendMaterialTypes(Document doc, Element rootElement, List<IMaterialTypeImmutable> materialTypes)
+ private void appendVocabularies(Document doc, Element rootElement)
{
- if (materialTypes.size() > 0)
+ VocabularyFetchOptions fetchOptions = new VocabularyFetchOptions();
+ fetchOptions.withTerms();
+ List<Vocabulary> vocabularies = v3Api.searchVocabularies(sessionToken, VOCABULARY_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (vocabularies.isEmpty())
{
- Element materialTypesElement = doc.createElement("xmd:materialTypes");
- rootElement.appendChild(materialTypesElement);
- Map<String, List<PropertyAssignment>> materialTypeCodePropAssignmentMap = loadMaterialTypesUsingV3WithPropertyAssignments();
- for (IMaterialTypeImmutable matType : materialTypes)
- {
- Element matTypeElement = getEntityTypeXML(doc, matType, "xmd:materialType");
- matTypeElement.setAttribute("description", matType.getDescription());
- matTypeElement.setAttribute("validationPlugin", matType.getValidationScript() != null ? matType.getValidationScript().getName() : "");
- materialTypesElement.appendChild(matTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, materialTypeCodePropAssignmentMap.get(matType.getCode()));
- matTypeElement.appendChild(propertyAssignmentsElement);
- }
+ return;
}
- }
-
- private void appendDataSetTypes(Document doc, Element rootElement, List<IDataSetTypeImmutable> dataSetTypes)
- {
- if (dataSetTypes.size() > 0)
+ Element vocabsElement = doc.createElement("xmd:controlledVocabularies");
+ rootElement.appendChild(vocabsElement);
+ for (Vocabulary vocabulary : vocabularies)
{
- Element dataSetTypesElement = doc.createElement("xmd:dataSetTypes");
- rootElement.appendChild(dataSetTypesElement);
- Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = loadDataSetTypesUsingV3WithPropertyAssignments();
- for (IDataSetTypeImmutable dsType : dataSetTypes)
+ Element vocabElement = doc.createElement("xmd:controlledVocabulary");
+ String code = vocabulary.isInternalNameSpace()
+ && vocabulary.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX) ? CodeConverter.tryToDatabase(vocabulary.getCode())
+ : vocabulary.getCode();
+ vocabElement.setAttribute("code", code);
+ vocabElement.setAttribute("description", vocabulary.getDescription());
+ String urlTemplate = vocabulary.getUrlTemplate();
+ vocabElement.setAttribute("urlTemplate", urlTemplate);
+ vocabElement.setAttribute("managedInternally", String.valueOf(vocabulary.isManagedInternally()));
+ vocabElement.setAttribute("internalNamespace", String.valueOf(vocabulary.isInternalNameSpace()));
+ vocabElement.setAttribute("chosenFromList", String.valueOf(vocabulary.isChosenFromList()));
+ vocabsElement.appendChild(vocabElement);
+
+ for (VocabularyTerm term : vocabulary.getTerms())
{
- Element dsTypeElement = getEntityTypeXML(doc, dsType, "xmd:dataSetType");
- dsTypeElement.setAttribute("description", dsType.getDescription());
- dsTypeElement.setAttribute("mainDataSetPattern", dsType.getMainDataSetPattern());
- dsTypeElement.setAttribute("mainDataSetPath", dsType.getMainDataSetPath());
- dsTypeElement.setAttribute("deletionDisallowed", String.valueOf(dsType.isDeletionDisallowed()));
- dsTypeElement.setAttribute("validationPlugin", dsType.getValidationScript() != null ? dsType.getValidationScript().getName() : "");
- dataSetTypesElement.appendChild(dsTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, dsTypeCodePropAssignmentMap.get(dsType.getCode()));
- dsTypeElement.appendChild(propertyAssignmentsElement);
+ Element termElement = doc.createElement("term");
+ termElement.setAttribute("code", term.getCode());
+ termElement.setAttribute("label", term.getLabel());
+ termElement.setAttribute("description", term.getDescription());
+ termElement.setAttribute("ordinal", String.valueOf(term.getOrdinal()));
+ termElement.setAttribute("url", createUrl(urlTemplate, term.getCode()));
+ vocabElement.appendChild(termElement);
}
}
}
- private void appendExperimentTypes(Document doc, Element rootElement, List<IExperimentTypeImmutable> experimentTypes)
+ private String createUrl(String urlTemplate, String code)
{
- if (experimentTypes.size() > 0)
+ if (urlTemplate == null)
{
- Element experimentTypesElement = doc.createElement("xmd:collectionTypes");
- rootElement.appendChild(experimentTypesElement);
- Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
- for (IExperimentTypeImmutable expType : experimentTypes)
- {
- Element experimentTypeElement = getEntityTypeXML(doc, expType, "xmd:collectionType");
- experimentTypeElement.setAttribute("description", expType.getDescription());
- experimentTypesElement.setAttribute("validationPlugin",
- expType.getValidationScript() != null ? expType.getValidationScript().getName() : "");
- experimentTypesElement.appendChild(experimentTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, expTypeCodePropAssignmentMap.get(expType.getCode()));
- experimentTypeElement.appendChild(propertyAssignmentsElement);
- }
+ return null;
}
+ String url = urlTemplate.replaceAll(BasicConstant.DEPRECATED_VOCABULARY_URL_TEMPLATE_TERM_PATTERN, code);
+ return url.replaceAll(BasicConstant.VOCABULARY_URL_TEMPLATE_TERM_PATTERN, code);
}
- private void appendSampleTypes(Document doc, Element rootElement, List<ISampleTypeImmutable> sampleTypes)
+ private void appendMaterialTypes(Document doc, Element rootElement)
{
- if (sampleTypes.size() > 0)
+ MaterialTypeFetchOptions fetchOptions = new MaterialTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType();
+ fetchOptions.withPropertyAssignments().withPlugin();
+ fetchOptions.withValidationPlugin();
+ List<MaterialType> types = v3Api.searchMaterialTypes(sessionToken, MATERIAL_TYPE_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (types.isEmpty())
{
- Element sampleTypesElement = doc.createElement("xmd:objectTypes");
- rootElement.appendChild(sampleTypesElement);
-
- Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = loadSampleTypesUsingV3WithPropertyAssignments();
- for (ISampleTypeImmutable sampleType : sampleTypes)
- {
- Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "xmd:objectType");
- 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());
- sampleTypeElement.setAttribute("validationPlugin", sampleType.getValidationScript() != null ? sampleType.getValidationScript()
- .getName() : "");
- sampleTypesElement.appendChild(sampleTypeElement);
- Element propertyAssignmentsElement = getPropertyAssignmentXML(doc, sampleTypeCodePropAssignmentMap.get(sampleType.getCode()));
- sampleTypeElement.appendChild(propertyAssignmentsElement);
- }
+ return;
}
- }
-
- 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("xmd:propertyAssignments");
- for (PropertyAssignment propAssignment : propertyAssignments)
+ Element typesElement = doc.createElement("xmd:materialTypes");
+ rootElement.appendChild(typesElement);
+ for (MaterialType type : types)
{
- Element propertyAssignmentElement = doc.createElement("xmd:propertyAssignment");
- propertyAssignmentsElement.appendChild(propertyAssignmentElement);
- propertyAssignmentElement.setAttribute("propertyTypeCode", propAssignment.getPropertyType().getCode());
- propertyAssignmentElement.setAttribute("ordinal", String.valueOf(propAssignment.getOrdinal()));
- propertyAssignmentElement.setAttribute("section", propAssignment.getSection());
- propertyAssignmentElement.setAttribute("showInEdit", String.valueOf(propAssignment.isShowInEditView()));
- propertyAssignmentElement.setAttribute("mandatory", String.valueOf(propAssignment.isMandatory()));
- propertyAssignmentElement.setAttribute("showRawValueInForms", String.valueOf(propAssignment.isShowRawValueInForms()));
- Plugin plugin = propAssignment.getPlugin();
- if (plugin != null)
- {
- propertyAssignmentElement.setAttribute("plugin", plugin.getPermId().getPermId());
- propertyAssignmentElement.setAttribute("pluginType", plugin.getPluginType().toString());
- }
+ Element typeElement = createTypeElement(doc, typesElement, "xmd:materialType", type);
+ typeElement.setAttribute("validationPlugin", type.getValidationPlugin() != null ? type.getValidationPlugin().getName() : null);
}
- return propertyAssignmentsElement;
}
- private Map<String, List<PropertyAssignment>> loadDataSetTypesUsingV3WithPropertyAssignments()
+ private void appendExperimentTypes(Document doc, Element rootElement)
{
- // 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();
+ ExperimentTypeFetchOptions fetchOptions = new ExperimentTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType();
fetchOptions.withPropertyAssignments().withPlugin();
-
- 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)
+ fetchOptions.withValidationPlugin();
+ List<ExperimentType> types = v3Api.searchExperimentTypes(sessionToken, EXPERIMENT_TYPE_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (types.isEmpty())
+ {
+ return;
+ }
+ Element typesElement = doc.createElement("xmd:collectionTypes");
+ rootElement.appendChild(typesElement);
+ for (ExperimentType type : types)
{
- dsTypeCodePropAssignmentMap.put(dataSetType.getCode(), dataSetType.getPropertyAssignments());
+ Element typeElement = createTypeElement(doc, typesElement, "xmd:collectionType", type);
+ typeElement.setAttribute("validationPlugin", type.getValidationPlugin() != null ? type.getValidationPlugin().getName() : null);
}
- return dsTypeCodePropAssignmentMap;
}
- private Map<String, List<PropertyAssignment>> loadSampleTypesUsingV3WithPropertyAssignments()
+ private void appendSampleTypes(Document doc, Element rootElement)
{
- // 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();
+ fetchOptions.withPropertyAssignments().withPropertyType();
fetchOptions.withPropertyAssignments().withPlugin();
-
- 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)
+ fetchOptions.withValidationPlugin();
+ List<SampleType> types = v3Api.searchSampleTypes(sessionToken, SAMPLE_TYPE_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (types.isEmpty())
+ {
+ return;
+ }
+ Element typesElement = doc.createElement("xmd:objectTypes");
+ rootElement.appendChild(typesElement);
+ for (SampleType type : types)
{
- sampleTypeCodePropAssignmentMap.put(sampleType.getCode(), sampleType.getPropertyAssignments());
+ Element typeElement = createTypeElement(doc, typesElement, "xmd:objectType", type);
+ typeElement.setAttribute("listable", String.valueOf(type.isListable()));
+ typeElement.setAttribute("showContainer", String.valueOf(type.isShowContainer()));
+ typeElement.setAttribute("showParents", String.valueOf(type.isShowParents()));
+ typeElement.setAttribute("showParentMetadata", String.valueOf(type.isShowParentMetadata()));
+ typeElement.setAttribute("subcodeUnique", String.valueOf(type.isSubcodeUnique()));
+ typeElement.setAttribute("autoGeneratedCode", String.valueOf(type.isAutoGeneratedCode()));
+ typeElement.setAttribute("generatedCodePrefix", type.getGeneratedCodePrefix());
+ typeElement.setAttribute("validationPlugin", type.getValidationPlugin() != null ? type.getValidationPlugin().getName() : null);
}
- return sampleTypeCodePropAssignmentMap;
}
- private Map<String, List<PropertyAssignment>> loadExperimentTypesUsingV3WithPropertyAssignments()
+ private void appendDataSetTypes(Document doc, Element rootElement)
{
- // 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();
+ DataSetTypeFetchOptions fetchOptions = new DataSetTypeFetchOptions();
+ fetchOptions.withPropertyAssignments().withPropertyType();
fetchOptions.withPropertyAssignments().withPlugin();
-
- 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)
+ fetchOptions.withValidationPlugin();
+ List<DataSetType> types = v3Api.searchDataSetTypes(sessionToken, DATA_SET_TYPE_SEARCH_CRITERIA, fetchOptions).getObjects();
+ if (types.isEmpty())
{
- expTypeCodePropAssignmentMap.put(experimentType.getCode(), experimentType.getPropertyAssignments());
+ return;
+ }
+ Element typesElement = doc.createElement("xmd:dataSetTypes");
+ rootElement.appendChild(typesElement);
+ for (DataSetType type : types)
+ {
+ Element typeElement = createTypeElement(doc, typesElement, "xmd:dataSetType", type);
+ typeElement.setAttribute("mainDataSetPattern", type.getMainDataSetPattern());
+ typeElement.setAttribute("mainDataSetPath", type.getMainDataSetPath());
+ typeElement.setAttribute("deletionDisallowed", String.valueOf(type.isDisallowDeletion()));
+ typeElement.setAttribute("validationPlugin", type.getValidationPlugin() != null ? type.getValidationPlugin().getName() : null);
}
- return expTypeCodePropAssignmentMap;
}
- private Map<String, List<PropertyAssignment>> loadMaterialTypesUsingV3WithPropertyAssignments()
+ private <T extends ICodeHolder & IDescriptionHolder & IPropertyAssignmentsHolder> Element createTypeElement(
+ Document doc, Element rootElement, String elementType, T type)
{
- // 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();
- fetchOptions.withPropertyAssignments().withPlugin();
+ Element typeElement = doc.createElement(elementType);
+ rootElement.appendChild(typeElement);
+ typeElement.setAttribute("code", type.getCode());
+ typeElement.setAttribute("description", type.getDescription());
+ appendPropertyAssignments(doc, typeElement, type.getPropertyAssignments());
+ return typeElement;
+ }
- 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)
+ private void appendPropertyAssignments(Document doc, Element rootElement, List<PropertyAssignment> propertyAssignments)
+ {
+ Element propertyAssignmentsElement = doc.createElement("xmd:propertyAssignments");
+ rootElement.appendChild(propertyAssignmentsElement);
+ for (PropertyAssignment propertyAssignment : propertyAssignments)
{
- matTypeCodePropAssignmentMap.put(materialType.getCode(), materialType.getPropertyAssignments());
+ Element propertyAssignmentElement = doc.createElement("xmd:propertyAssignment");
+ propertyAssignmentsElement.appendChild(propertyAssignmentElement);
+ propertyAssignmentElement.setAttribute("propertyTypeCode", propertyAssignment.getPropertyType().getCode());
+ propertyAssignmentElement.setAttribute("ordinal", String.valueOf(propertyAssignment.getOrdinal()));
+ propertyAssignmentElement.setAttribute("section", propertyAssignment.getSection());
+ propertyAssignmentElement.setAttribute("showInEdit", String.valueOf(propertyAssignment.isShowInEditView()));
+ propertyAssignmentElement.setAttribute("mandatory", String.valueOf(propertyAssignment.isMandatory()));
+ propertyAssignmentElement.setAttribute("showRawValueInForms", String.valueOf(propertyAssignment.isShowRawValueInForms()));
+ Plugin plugin = propertyAssignment.getPlugin();
+ if (plugin != null)
+ {
+ propertyAssignmentElement.setAttribute("plugin", plugin.getPermId().getPermId());
+ propertyAssignmentElement.setAttribute("pluginType", plugin.getPluginType().toString());
+ }
}
- return matTypeCodePropAssignmentMap;
}
+
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/entitygraph/Node.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/entitygraph/Node.java
index 46d08fda539..557be0af64c 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/entitygraph/Node.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/common/entitygraph/Node.java
@@ -24,13 +24,10 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.attachment.Attachment;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IAttachmentsHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.ICodeHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IExperimentHolder;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IModificationDateHolder;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IModifierHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPermIdHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IProjectHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IPropertiesHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IRegistrationDateHolder;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.IRegistratorHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.ISampleHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.common.interfaces.ISpaceHolder;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSet;
@@ -40,8 +37,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.Sample;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.space.Space;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.common.SyncEntityKind;
-public class Node<T extends IModificationDateHolder & IModifierHolder & IRegistrationDateHolder & IRegistratorHolder & IPermIdHolder & ICodeHolder>
- implements INode
+public class Node<T extends IRegistrationDateHolder & IPermIdHolder & ICodeHolder> implements INode
{
private final List<EdgeNodePair> connections;
--
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