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 510b319354f25287fbfd3e93349e52376f4c6c51..9b0bb4e473eacffa3b3b2543db745027367e3e84 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
@@ -112,6 +112,11 @@ public class EntityRetriever
graph = new EntityGraph<Node<?>>();
// add shared samples
+ /*
+ * adding shared samples to the entity graph for a space means if we are synching from multiple spaces, each entity graph (for each space)
+ * will have the shared entity. When we add them to the RL (Resource List) in the data source servlet, any duplicate will throw an error when
+ * using the Resync library. To work around this we catch the duplicate exceptions where a shared sample is involved.
+ */
findSharedSamples();
// build the graph for the space from top-down starting from projects
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/config/ConfigReader.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/config/ConfigReader.java
index 6c8009cceae905fa8e6dda6459c62f846150f27a..eb969e940d48c315f3ac91563f9e756ed4d19ac7 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/config/ConfigReader.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/config/ConfigReader.java
@@ -31,6 +31,8 @@ import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
+import org.apache.commons.lang3.StringUtils;
+
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
public class ConfigReader
@@ -155,15 +157,11 @@ public class ConfigReader
throw new ConfigurationFailureException("Section '" + section + " does not exist.");
}
String val = map.get(key);
- if (val == null)
- {
- return null;
- }
- if (val.trim().equals("") == true)
+ if (StringUtils.isBlank(val) == true)
{
return null;
}
- return val;
+ return val.trim();
}
public int getInt(String section, String key, int defaultvalue, boolean mandatory)
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
index ab0aaaa30e191bde84f75df3ce6a6339db6ef711..54524d4f48d78b735f959d70097dfca063048631 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/EntitySynchronizer.java
@@ -37,6 +37,7 @@ import java.util.Set;
import org.apache.commons.codec.binary.Hex;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.w3c.dom.Document;
@@ -188,7 +189,7 @@ public class EntitySynchronizer
operationLog.info("parsing the resource list xml document");
String dataSourcePrefix = config.getDataSourceAlias();
INameTranslator nameTranslator = null;
- if (dataSourcePrefix != null && dataSourcePrefix.trim().equals("") == false)
+ if (StringUtils.isBlank(dataSourcePrefix) == false)
{
nameTranslator = new PrefixBasedNameTranslator(dataSourcePrefix);
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
index 891a44c4cc31e978929fa433c18aafca26f81031..4e4756b2ed9a8877ab18a528f2a7a271c6ffdefd 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/ResourceListParser.java
@@ -35,6 +35,7 @@ import javax.xml.xpath.XPathExpression;
import javax.xml.xpath.XPathExpressionException;
import javax.xml.xpath.XPathFactory;
+import org.apache.commons.lang.StringUtils;
import org.w3c.dom.Document;
import org.w3c.dom.Element;
import org.w3c.dom.Node;
@@ -44,10 +45,10 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.Connection;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.IncomingDataSet;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.IncomingExperiment;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.MasterData;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.MaterialWithLastModificationDate;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.IncomingProject;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.IncomingSample;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.MasterData;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.ResourceListParserData.MaterialWithLastModificationDate;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.translator.DefaultNameTranslator;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.translator.INameTranslator;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
@@ -273,49 +274,63 @@ public class ResourceListParser
private void parseDataSetMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
- String sample = extractAttribute(xdNode, "sample");
- String experiment = extractAttribute(xdNode, "experiment");
+ String sample = extractAttribute(xdNode, "sample", true);
+ String experiment = extractAttribute(xdNode, "experiment", true);
String type = extractType(xdNode);
String dsKind = extractAttribute(xdNode, "dsKind");
- NewExternalData ds = new NewExternalData();
+ NewExternalData ds = null;
if (dsKind.equals(DataSetKind.CONTAINER.toString()))
{
ds = new NewContainerDataSet();
- ds.setCode(code);
- ds.setDataSetType(new DataSetType(type));
- ds.setDataStoreCode(this.dataStoreCode);
- if (sample.trim().equals("") == false)
- {
- ds.setSampleIdentifierOrNull(getSampleIdentifier(sample));
- }
- if (experiment.trim().equals("") == false)
- {
- ds.setExperimentIdentifierOrNull(getExperimentIdentifier(experiment));
- }
}
else if (dsKind.equals(DataSetKind.PHYSICAL.toString()))
{
- ds.setCode(code);
- ds.setDataSetType(new DataSetType(type));
- ds.setDataStoreCode(this.dataStoreCode);
- if (sample.trim().equals("") == false)
- {
- ds.setSampleIdentifierOrNull(getSampleIdentifier(sample));
- }
- if (experiment.trim().equals("") == false)
- {
- ds.setExperimentIdentifierOrNull(getExperimentIdentifier(experiment));
- }
+ ds = new NewExternalData();
}
+ // else if (dsKind.equals(DataSetKind.LINK.toString())) {
+ // ds = new NewLinkDataSet();
+ // ((NewLinkDataSet)ds).
+ // }
+ else
+ {
+ throw new IllegalArgumentException(dsKind + " data sets are currently not supported");
+ }
+ ds.setCode(code);
+ ds.setDataSetType(new DataSetType(type));
+ ds.setDataStoreCode(this.dataStoreCode);
+
+ ds.setSampleIdentifierOrNull(getSampleIdentifier(sample));
+ ds.setExperimentIdentifierOrNull(getExperimentIdentifier(experiment));
+
IncomingDataSet incomingDataSet = data.new IncomingDataSet(ds, lastModificationDate);
data.getDataSetsToProcess().put(permId, incomingDataSet);
incomingDataSet.setConnections(parseConnections(xpath, xdNode));
ds.setDataSetProperties(parseDataSetProperties(xpath, xdNode));
}
- private String extractAttribute(Node xdNode, String attrName)
+ private String extractAttribute(Node xdNode, String attrName, boolean nullAllowed)
+ {
+ String val = xdNode.getAttributes().getNamedItem(attrName).getTextContent();
+ if (StringUtils.isBlank(val) == true)
+ {
+ if (nullAllowed == false)
+ {
+ throw new IllegalArgumentException(attrName + " cannot be empty in Resource List");
+ }
+ else
+ {
+ return null;
+ }
+ }
+ else
+ {
+ return val.trim();
+ }
+ }
+
+ private String extractAttribute(Node xdNode, String attrName) throws IllegalArgumentException
{
- return xdNode.getAttributes().getNamedItem(attrName).getTextContent();
+ return extractAttribute(xdNode, attrName, false);
}
private String extractCode(Node xdNode)
@@ -325,15 +340,23 @@ public class ResourceListParser
private SampleIdentifier getSampleIdentifier(String sampleIdentifierStr)
{
+ if (sampleIdentifierStr == null)
+ {
+ return null;
+ }
SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(sampleIdentifierStr);
SpaceIdentifier spaceLevel = sampleIdentifier.getSpaceLevel();
String originalSpaceCode = spaceLevel.getSpaceCode();
return new SampleIdentifier(new SpaceIdentifier(nameTranslator.translate(originalSpaceCode)), sampleIdentifier.getSampleCode());
}
- private ExperimentIdentifier getExperimentIdentifier(String experiment)
+ private ExperimentIdentifier getExperimentIdentifier(String experimentIdentifierStr)
{
- ExperimentIdentifier experimentIdentifier = ExperimentIdentifierFactory.parse(experiment);
+ if (experimentIdentifierStr == null)
+ {
+ return null;
+ }
+ ExperimentIdentifier experimentIdentifier = ExperimentIdentifierFactory.parse(experimentIdentifierStr);
String originalSpaceCode = experimentIdentifier.getSpaceCode();
String projectCode = experimentIdentifier.getProjectCode();
String expCode = experimentIdentifier.getExperimentCode();
@@ -345,9 +368,9 @@ public class ResourceListParser
String code = extractCode(xdNode);
String desc = xdNode.getAttributes().getNamedItem("desc").getTextContent();
- String space = extractSpace(xdNode);
- // TODO is there a better way to create project identifier below?
- NewProject newProject = new NewProject("/" + nameTranslator.translate(space) + "/" + code, desc);
+ String space = extractSpace(xdNode, false);
+ ProjectIdentifier projectIdentifier = createProjectIdentifier(code, space);
+ NewProject newProject = new NewProject(projectIdentifier.toString(), desc);
newProject.setPermID(permId);
IncomingProject incomingProject =
data.new IncomingProject(newProject, lastModificationDate);
@@ -356,6 +379,26 @@ public class ResourceListParser
incomingProject.setHasAttachments(hasAttachments(xpath, xdNode));
}
+ private ProjectIdentifier createProjectIdentifier(String code, String space)
+ {
+ return new ProjectIdentifier(createSpaceIdentifier(space), code);
+ }
+
+ private SampleIdentifier createSampleIdentifier(String code, String space)
+ {
+ if (space == null)
+ {
+ return new SampleIdentifier(nameTranslator.translate(code));
+ }
+ SpaceIdentifier spaceIdentifier = createSpaceIdentifier(space);
+ return new SampleIdentifier(spaceIdentifier, code);
+ }
+
+ private SpaceIdentifier createSpaceIdentifier(String space)
+ {
+ return new SpaceIdentifier(nameTranslator.translate(space));
+ }
+
private void parseMaterialMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
@@ -457,7 +500,7 @@ public class ResourceListParser
String code = extractCode(xdNode);
String type = extractType(xdNode);
String project = extractAttribute(xdNode, "project");
- String space = extractSpace(xdNode);
+ String space = extractSpace(xdNode, false);
NewExperiment newExp = new NewExperiment("/" + nameTranslator.translate(space) + "/" + project + "/" + code, type);
newExp.setPermID(permId);
IncomingExperiment incomingExperiment = data.new IncomingExperiment(newExp, lastModificationDate);
@@ -471,15 +514,20 @@ public class ResourceListParser
{
String code = extractCode(xdNode);
String type = extractType(xdNode);
- String experiment = extractAttribute(xdNode, "experiment");
- String space = extractSpace(xdNode);
+ String experiment = extractAttribute(xdNode, "experiment", true);
+ String space = extractSpace(xdNode, true);
SampleType sampleType = new SampleType();
sampleType.setCode(type);
- NewSample newSample = new NewSample("/" + nameTranslator.translate(space) + "/" + code, sampleType, null, null,
- experiment.trim().equals("") ? null : experiment, null, null, new IEntityProperty[0],
+ SampleIdentifier identifier = createSampleIdentifier(code, space);
+ NewSample newSample = new NewSample(identifier.toString(), sampleType, null, null,
+ experiment, null, null, new IEntityProperty[0],
new ArrayList<NewAttachment>());
newSample.setPermID(permId);
+ if (space == null)
+ {
+ newSample.setDefaultSpaceIdentifier(null);
+ }
IncomingSample incomingSample = data.new IncomingSample(newSample, lastModificationDate);
data.getSamplesToProcess().put(permId, incomingSample);
incomingSample.setHasAttachments(hasAttachments(xpath, xdNode));
@@ -492,10 +540,13 @@ public class ResourceListParser
return extractAttribute(xdNode, "type");
}
- private String extractSpace(Node xdNode)
+ private String extractSpace(Node xdNode, boolean nullAllowed)
{
- String space = extractAttribute(xdNode, "space");
- data.getHarvesterSpaceList().add(nameTranslator.translate(space));
+ String space = extractAttribute(xdNode, "space", nullAllowed);
+ if (space != null)
+ {
+ data.getHarvesterSpaceList().add(nameTranslator.translate(space));
+ }
return space;
}