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 cdadf650d1b4d90d34138c24e83be8cf141f2fd2..a7b6c42e32a675ebdd23dc6d940e47057b999c0f 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
@@ -56,13 +56,12 @@ import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistra
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.CodeConverter;
/**
- *
- *
* @author Ganime Betul Akin
*/
public class MasterDataExtractor
@@ -91,9 +90,15 @@ public class MasterDataExtractor
DocumentBuilderFactory docFactory = DocumentBuilderFactory.newInstance();
DocumentBuilder docBuilder = docFactory.newDocumentBuilder();
Document doc = docBuilder.newDocument();
- Element rootElement = doc.createElement("masterData");
+ docFactory.setNamespaceAware(true);
+ Element rootElement = doc.createElementNS("https://sis.id.ethz.ch/software/#openbis/xmdterms/", "xmd:masterData");
+ 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);
+
// append file format types
List<IFileFormatTypeImmutable> fileFormatTypes = masterDataRegistrationTransaction.listFileFormatTypes();
appendFileFormatTypes(doc, rootElement, fileFormatTypes);
@@ -124,6 +129,12 @@ public class MasterDataExtractor
TransformerFactory transformerFactory = TransformerFactory.newInstance();
Transformer transformer = transformerFactory.newTransformer();
transformer.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
+ transformer.setOutputProperty(OutputKeys.METHOD, "xml");
+ transformer.setOutputProperty(OutputKeys.ENCODING, "UTF-8");
+ transformer.setOutputProperty(OutputKeys.CDATA_SECTION_ELEMENTS,
+ "validationPlugin");
+ transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+
DOMSource source = new DOMSource(doc);
StringWriter writer = new StringWriter();
StreamResult result = new StreamResult(writer);
@@ -131,15 +142,36 @@ public class MasterDataExtractor
return writer.toString();
}
+ private void appendValidationPlugins(Document doc, Element rootElement, List<IScriptImmutable> scripts)
+ {
+ if (scripts.size() > 0)
+ {
+ Element pluginsElement = doc.createElement("xmd:validationPlugins");
+ rootElement.appendChild(pluginsElement);
+ for (IScriptImmutable script : scripts)
+ {
+ 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());
+
+ pluginElement.appendChild(doc.createCDATASection(script.getScript()));
+ pluginsElement.appendChild(pluginElement);
+ }
+ }
+ }
+
private void appendFileFormatTypes(Document doc, Element rootElement, List<IFileFormatTypeImmutable> fileFormatTypes)
{
if (fileFormatTypes.size() > 0)
{
- Element fileFormatTypesElement = doc.createElement("fileFormatTypes");
+ Element fileFormatTypesElement = doc.createElement("xmd:fileFormatTypes");
rootElement.appendChild(fileFormatTypesElement);
for (IFileFormatTypeImmutable fileFormatType : fileFormatTypes)
{
- Element fileFormatTypeElement = doc.createElement("fileFormatType");
+ Element fileFormatTypeElement = doc.createElement("xmd:fileFormatType");
fileFormatTypeElement.setAttribute("code", fileFormatType.getCode());
fileFormatTypeElement.setAttribute("description", fileFormatType.getDescription());
fileFormatTypesElement.appendChild(fileFormatTypeElement);
@@ -151,7 +183,7 @@ public class MasterDataExtractor
{
if (propertyTypes.size() > 0)
{
- Element propertyTypesElement = doc.createElement("propertyTypes");
+ Element propertyTypesElement = doc.createElement("xmd:propertyTypes");
rootElement.appendChild(propertyTypesElement);
for (IPropertyTypeImmutable propertyTypeImmutable : propertyTypes)
{
@@ -159,7 +191,7 @@ public class MasterDataExtractor
(propertyTypeImmutable.isInternalNamespace()
&& propertyTypeImmutable.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX)) ? CodeConverter.tryToDatabase(propertyTypeImmutable
.getCode()) : propertyTypeImmutable.getCode();
- Element propertyTypeElement = doc.createElement("propertyType");
+ Element propertyTypeElement = doc.createElement("xmd:propertyType");
propertyTypeElement.setAttribute("code", code);
propertyTypeElement.setAttribute("label", propertyTypeImmutable.getLabel());
propertyTypeElement.setAttribute("dataType", propertyTypeImmutable.getDataType().name());
@@ -170,7 +202,8 @@ public class MasterDataExtractor
{
propertyTypeElement.setAttribute("vocabulary", propertyTypeImmutable.getVocabulary().getCode());
}
- else if (propertyTypeImmutable.getDataType().name().equals(DataType.MATERIAL.name())) {
+ else if (propertyTypeImmutable.getDataType().name().equals(DataType.MATERIAL.name()))
+ {
if (propertyTypeImmutable.getMaterialType() != null)
{
propertyTypeElement.setAttribute("material", propertyTypeImmutable.getMaterialType().getCode());
@@ -190,14 +223,14 @@ public class MasterDataExtractor
{
if (vocabularies.size() > 0)
{
- Element vocabsElement = doc.createElement("controlledVocabularies");
+ Element vocabsElement = doc.createElement("xmd:controlledVocabularies");
rootElement.appendChild(vocabsElement);
for (IVocabularyImmutable vocabImmutable : vocabularies)
{
- Element vocabElement = doc.createElement("controlledVocabulary");
+ Element vocabElement = doc.createElement("xmd:controlledVocabulary");
String code = vocabImmutable.isInternalNamespace()
&& vocabImmutable.getCode().startsWith(INTERNAL_NAMESPACE_PREFIX) ? CodeConverter.tryToDatabase(vocabImmutable.getCode())
- : vocabImmutable.getCode();
+ : vocabImmutable.getCode();
vocabElement.setAttribute("code", code);
vocabElement.setAttribute("description", vocabImmutable.getDescription());
vocabElement.setAttribute("urlTemplate", vocabImmutable.getUrlTemplate());
@@ -225,12 +258,12 @@ public class MasterDataExtractor
{
if (materialTypes.size() > 0)
{
- Element materialTypesElement = doc.createElement("materialTypes");
+ Element materialTypesElement = doc.createElement("xmd:materialTypes");
rootElement.appendChild(materialTypesElement);
Map<String, List<PropertyAssignment>> materialTypeCodePropAssignmentMap = loadMaterialTypesUsingV3WithPropertyAssignments();
for (IMaterialTypeImmutable matType : materialTypes)
{
- Element matTypeElement = getEntityTypeXML(doc, matType, "materialType");
+ Element matTypeElement = getEntityTypeXML(doc, matType, "xmd:materialType");
matTypeElement.setAttribute("description", matType.getDescription());
// TODO validation script
materialTypesElement.appendChild(matTypeElement);
@@ -244,12 +277,12 @@ public class MasterDataExtractor
{
if (dataSetTypes.size() > 0)
{
- Element dataSetTypesElement = doc.createElement("dataSetTypes");
+ Element dataSetTypesElement = doc.createElement("xmd:dataSetTypes");
rootElement.appendChild(dataSetTypesElement);
Map<String, List<PropertyAssignment>> dsTypeCodePropAssignmentMap = loadDataSetTypesUsingV3WithPropertyAssignments();
for (IDataSetTypeImmutable dsType : dataSetTypes)
{
- Element dsTypeElement = getEntityTypeXML(doc, dsType, "dataSetType");
+ Element dsTypeElement = getEntityTypeXML(doc, dsType, "xmd:dataSetType");
dsTypeElement.setAttribute("description", dsType.getDescription());
dsTypeElement.setAttribute("dataSetKind", dsType.getDataSetKind());
dsTypeElement.setAttribute("mainDataSetPattern", dsType.getMainDataSetPattern());
@@ -267,12 +300,12 @@ public class MasterDataExtractor
{
if (experimentTypes.size() > 0)
{
- Element experimentTypesElement = doc.createElement("collectionTypes");
+ Element experimentTypesElement = doc.createElement("xmd:collectionTypes");
rootElement.appendChild(experimentTypesElement);
Map<String, List<PropertyAssignment>> expTypeCodePropAssignmentMap = loadExperimentTypesUsingV3WithPropertyAssignments();
for (IExperimentTypeImmutable expType : experimentTypes)
{
- Element experimentTypeElement = getEntityTypeXML(doc, expType, "collectionType");
+ Element experimentTypeElement = getEntityTypeXML(doc, expType, "xmd:collectionType");
experimentTypeElement.setAttribute("description", expType.getDescription());
// TODO validation script?
experimentTypesElement.appendChild(experimentTypeElement);
@@ -286,13 +319,13 @@ public class MasterDataExtractor
{
if (sampleTypes.size() > 0)
{
- Element sampleTypesElement = doc.createElement("objectTypes");
+ Element sampleTypesElement = doc.createElement("xmd:objectTypes");
rootElement.appendChild(sampleTypesElement);
Map<String, List<PropertyAssignment>> sampleTypeCodePropAssignmentMap = loadSampleTypesUsingV3WithPropertyAssignments();
for (ISampleTypeImmutable sampleType : sampleTypes)
{
- Element sampleTypeElement = getEntityTypeXML(doc, sampleType, "objectType");
+ 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()));
@@ -318,10 +351,10 @@ public class MasterDataExtractor
private Element getPropertyAssignmentXML(Document doc, List<PropertyAssignment> propertyAssignments)
{
- Element propertyAssignmentsElement = doc.createElement("propertyAssignments");
+ Element propertyAssignmentsElement = doc.createElement("xmd:propertyAssignments");
for (PropertyAssignment propAssignment : propertyAssignments)
{
- Element propertyAssignmentElement = doc.createElement("propertyAssignment");
+ Element propertyAssignmentElement = doc.createElement("xmd:propertyAssignment");
propertyAssignmentsElement.appendChild(propertyAssignmentElement);
propertyAssignmentElement.setAttribute("propertyTypeCode", CodeConverter.tryToBusinessLayer(propAssignment.getPropertyType().getCode(),
propAssignment.getPropertyType().isInternalNameSpace()));