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 f9152d3b38095a54cef8c5ac62cdb82f1d5c2462..c52737eaa3d983557429b636506e93f8dfdf6683 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
@@ -39,6 +39,7 @@ import org.apache.commons.codec.binary.Hex;
import org.apache.commons.collections4.map.MultiKeyMap;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.ArrayUtils;
+import org.apache.commons.lang.time.StopWatch;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.w3c.dom.Document;
@@ -84,6 +85,7 @@ import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronize
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.translator.INameTranslator;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.translator.PrefixBasedNameTranslator;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.util.DSPropertyUtils;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.util.Monitor;
import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.util.V3Utils;
import ch.systemsx.cisd.cifex.shared.basic.UserFailureException;
import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
@@ -198,6 +200,7 @@ public class EntitySynchronizer
private void registerDataSets(ResourceListParserData data, List<String> notSyncedAttachmentsHolders) throws IOException
{
+ Monitor monitor = new Monitor("Register data sets", operationLog);
// register physical data sets without any hierarchy
// Note that container/component and parent/child relationships are established post-reg.
// setParentDataSetsOnTheChildren(data);
@@ -237,10 +240,12 @@ public class EntitySynchronizer
skippedDataSets.addAll(notRegisteredDataSetCodes);
skippedDataSets.addAll(blackListedDataSetCodes);
establishDataSetRelationships(data.getDataSetsToProcess(), skippedDataSets, physicalDSMap);
+ monitor.log();
}
private List<String> registerAttachments(ResourceListParserData data, MultiKeyMap<String, String> newEntities)
{
+ Monitor monitor = new Monitor("Register attachments", operationLog);
operationLog.info("Processing attachments...");
List<IncomingEntity<?>> attachmentHoldersToProcess =
data.filterAttachmentHoldersByLastModificationDate(lastSyncTimestamp, attachmentHolderCodesToRetry);
@@ -262,12 +267,14 @@ public class EntitySynchronizer
: "synchronization of attachments for "
+ notSyncedAttachmentsHolders.size() + " entitities FAILED."));
}
+ monitor.log();
return notSyncedAttachmentsHolders;
}
private MultiKeyMap<String, String> registerEntities(ResourceListParserData data)
{
- AtomicEntityOperationDetails entityOperationDetails = createEntityOperationDetails(data);
+ Monitor monitor = new Monitor("Register entities", operationLog);
+ AtomicEntityOperationDetails entityOperationDetails = createEntityOperationDetails(data, monitor);
MultiKeyMap<String, String> newEntities = new MultiKeyMap<String, String>();
if (config.isDryRun() == false)
@@ -276,17 +283,18 @@ public class EntitySynchronizer
newEntities = getNewEntities(entityOperationDetails);
operationLog.info("Entity operation result: " + operationResult);
}
+ monitor.log();
return newEntities;
}
- private AtomicEntityOperationDetails createEntityOperationDetails(ResourceListParserData data)
+ private AtomicEntityOperationDetails createEntityOperationDetails(ResourceListParserData data, Monitor monitor)
{
AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
processSpaces(data, builder);
processProjects(data, builder);
processExperiments(data, builder);
- processSamples(data, builder);
+ processSamples(data, builder, monitor);
processMaterials(data, builder);
AtomicEntityOperationDetails entityOperationDetails = builder.getDetails();
@@ -311,24 +319,26 @@ public class EntitySynchronizer
private ResourceListParserData parseResourceList(Document doc) throws XPathExpressionException
{
+ Monitor monitor = new Monitor("Parsing resource list", operationLog);
// Parse the resource list: This sends back all projects,
// experiments, samples and data sets contained in the XML together with their last modification date to be used for filtering
operationLog.info("Parsing the resource list xml document...");
INameTranslator nameTranslator = new PrefixBasedNameTranslator(config.getDataSourceAlias());
ResourceListParser parser = ResourceListParser.create(nameTranslator, dataStoreCode);
- ResourceListParserData data = parser.parseResourceListDocument(doc);
+ ResourceListParserData data = parser.parseResourceListDocument(doc, monitor);
+ monitor.log();
return data;
}
private Document getResourceList() throws Exception
{
-
+ Monitor monitor = new Monitor("Retrieving resoure list", operationLog);
DataSourceConnector dataSourceConnector =
new DataSourceConnector(config.getDataSourceURI(), config.getAuthenticationCredentials(), operationLog);
- operationLog.info("\nRetrieving the resource list...");
+ operationLog.info("Retrieving the resource list...");
Document doc = dataSourceConnector.getResourceListAsXMLDoc(Arrays.asList(ArrayUtils.EMPTY_STRING_ARRAY));
-
+ monitor.log();
return doc;
}
@@ -736,6 +746,7 @@ public class EntitySynchronizer
private void registerMasterData(MasterData masterData)
{
+ Monitor monitor = new Monitor("Register master data", operationLog);
operationLog.info("Registering master data...");
if (config.isVerbose() == true)
{
@@ -753,6 +764,7 @@ public class EntitySynchronizer
MasterDataSynchronizer masterDataSyncronizer =
new MasterDataSynchronizer(config.getHarvesterUser(), config.getHarvesterPass(), config.isDryRun(), config.isVerbose(), operationLog);
masterDataSyncronizer.synchronizeMasterData(masterData);
+ monitor.log();
}
private void verboseLogMasterData(Set<String> types, String typeName)
@@ -769,6 +781,7 @@ public class EntitySynchronizer
private void processDeletions(ResourceListParserData data) throws NoSuchAlgorithmException, UnsupportedEncodingException
{
+ Monitor monitor = new Monitor("Delete entities", operationLog);
String sessionToken = ServiceProvider.getOpenBISService().getSessionToken();
IEntityRetriever entityRetriever =
SkinnyEntityRetriever.createWithSessionToken(ServiceProvider.getV3ApplicationService(), sessionToken);
@@ -899,6 +912,7 @@ public class EntitySynchronizer
if (config.isDryRun() == true)
{
+ monitor.log();
return;
}
@@ -980,6 +994,7 @@ public class EntitySynchronizer
getDirectoryProvider().getDataSetDirectory(physicalDS);
SegmentedStoreUtils.deleteDataSetInstantly(physicalDS.getCode(), datasetDir, new Log4jSimpleLogger(operationLog));
}
+ monitor.log();
}
private void verboseLogDeletions(Collection<String> identifiers, String entityKind)
@@ -1170,14 +1185,20 @@ public class EntitySynchronizer
return prjUpdate;
}
- private void processSamples(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder)
+ private void processSamples(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder, Monitor monitor)
{
// process samples
Map<String, IncomingSample> samplesToProcess = data.getSamplesToProcess();
Map<SampleIdentifier, NewSample> samplesToUpdate = new HashMap<SampleIdentifier, NewSample>();
Set<String> sampleWithUpdatedParents = new HashSet<String>();
+ int count = 0;
+ int n = samplesToProcess.size();
for (IncomingSample sample : samplesToProcess.values())
{
+ if (++count % 100 == 0)
+ {
+ monitor.log(String.format("%7d/%d sample: %s", count, n, sample.getIdentifer()));
+ }
NewSample incomingSample = sample.getSample();
if (sample.getLastModificationDate().after(lastSyncTimestamp))
{
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 cef2b91320e6a5a9af54eab8413bf78e3dd2046f..e55a13d8399de4f277bf0ef339e7f451e59b211e 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
@@ -26,7 +26,9 @@ import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
+import java.util.Map;
import java.util.TimeZone;
+import java.util.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -55,6 +57,7 @@ import ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronize
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.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.util.Monitor;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
@@ -112,7 +115,71 @@ public class ResourceListParser
return create(new DefaultNameTranslator(), dataStoreCode);
}
- public ResourceListParserData parseResourceListDocument(Document doc) throws XPathExpressionException
+ public ResourceListParserData parseResourceListDocument(Document doc, Monitor monitor) throws XPathExpressionException
+ {
+ XPath xpath = createXPath();
+ Date resourceListTimestamp = getResourceListTimestamp(doc, xpath);
+ data.setResourceListTimestamp(resourceListTimestamp);
+
+ monitor.log();
+ NodeList nodes = doc.getDocumentElement().getChildNodes();
+ for (int i = 0; i < nodes.getLength(); i++)
+ {
+ Node node = nodes.item(i);
+ Map<String, List<Node>> childrenByType = getChildrenByType(node);
+ List<Node> locNodes = childrenByType.get("loc");
+ if (locNodes == null)
+ {
+ continue;
+ }
+ String uri = locNodes.get(0).getTextContent();
+ if (uri.endsWith("MASTER_DATA/MASTER_DATA/M"))
+ {
+ parseMasterData(doc, xpath, uri);
+ }
+ }
+ for (int i = 0, n = nodes.getLength(); i < n; i++)
+ {
+ Node node = nodes.item(i);
+ Map<String, List<Node>> childrenByType = getChildrenByType(node);
+ List<Node> locNodes = childrenByType.get("loc");
+ if (locNodes == null)
+ {
+ continue;
+ }
+ String uri = locNodes.get(0).getTextContent();
+ if (uri.endsWith("MASTER_DATA/MASTER_DATA/M") == false && uri.endsWith("/M"))
+ {
+ List<Node> lastmodNodes = childrenByType.get("lastmod");
+ if (lastmodNodes == null)
+ {
+ continue;
+ }
+ String lastModDataStr = lastmodNodes.get(0).getTextContent().trim();
+ try
+ {
+ Date lastModificationDate = convertFromW3CDate(lastModDataStr);
+ List<Node> xdNodes = childrenByType.get("x:xd");
+ if (xdNodes == null)
+ {
+ continue;
+ }
+ if ((i + 1) % 10000 == 0)
+ {
+ monitor.log(String.format("%7d/%d uri: %s", i + 1, n, uri));
+ }
+ parseMetaData(uri, lastModificationDate, xdNodes.get(0));
+ } catch (ParseException e)
+ {
+ throw new XPathExpressionException("Last modification date cannot be parsed:" + lastModDataStr);
+ }
+ }
+ }
+
+ return data;
+ }
+
+ private XPath createXPath()
{
XPath xpath = XPathFactory.newInstance().newXPath();
xpath.setNamespaceContext(new NamespaceContext()
@@ -144,16 +211,7 @@ public class ResourceListParser
throw new UnsupportedOperationException("Not implemented!!!");
}
});
- Date resourceListTimestamp = getResourceListTimestamp(doc, xpath);
- data.setResourceListTimestamp(resourceListTimestamp);
-
- List<String> uris = getResourceLocations(doc, xpath);
- for (String uri : uris)
- {
- parseUriMetaData(doc, xpath, uri);
- }
-
- return data;
+ return xpath;
}
private Date getResourceListTimestamp(Document doc, XPath xpath) throws XPathExpressionException
@@ -170,27 +228,6 @@ public class ResourceListParser
}
}
- private List<String> getResourceLocations(Document doc, XPath xpath) throws XPathExpressionException
- {
- XPathExpression expr = xpath.compile("/s:urlset/s:url/s:loc");// "//*[local-name()='loc']/text()"); //"//s:loc/text()"
-
- Object result = expr.evaluate(doc, XPathConstants.NODESET);
- NodeList nodes = (NodeList) result;
- List<String> list = new ArrayList<String>();
- for (int i = 0; i < nodes.getLength(); i++)
- {
- String uri = nodes.item(i).getTextContent();
- if (uri.endsWith("MASTER_DATA/MASTER_DATA/M"))
- {
- parseMasterData(doc, xpath, uri);
- } else if (uri.endsWith("/M"))
- {
- list.add(uri);
- }
- }
- return list;
- }
-
private void parseMasterData(Document doc, XPath xpath, String uri) throws XPathExpressionException
{
MasterDataParser mdParser = MasterDataParser.create(nameTranslator);
@@ -207,48 +244,48 @@ public class ResourceListParser
masterData.setPropertyAssignmentsToProcess(mdParser.getEntityPropertyAssignments());
}
- private void parseUriMetaData(Document doc, XPath xpath, String uri) throws XPathExpressionException
+ private void parseMetaData(String uri, Date lastModificationDate, Node xdNode) throws XPathExpressionException
{
- Date lastModificationDate = extractLastModificationDate(doc, xpath, uri);
-
- Node xdNode = extractXdNode(doc, xpath, uri);
String entityKind = xdNode.getAttributes().getNamedItem("kind").getTextContent();
if (SyncEntityKind.PROJECT.getLabel().equals(entityKind))
{
- parseProjectMetaData(xpath, extractPermIdFromURI(uri), xdNode, lastModificationDate);
+ parseProjectMetaData(extractPermIdFromURI(uri), xdNode, lastModificationDate);
} else if (SyncEntityKind.EXPERIMENT.getLabel().equals(entityKind))
{
- parseExperimentMetaData(xpath, extractPermIdFromURI(uri), xdNode, lastModificationDate);
+ parseExperimentMetaData(extractPermIdFromURI(uri), xdNode, lastModificationDate);
} else if (SyncEntityKind.SAMPLE.getLabel().equals(entityKind))
{
- parseSampleMetaData(xpath, extractPermIdFromURI(uri), xdNode, lastModificationDate);
+ parseSampleMetaData(extractPermIdFromURI(uri), xdNode, lastModificationDate);
} else if (SyncEntityKind.DATA_SET.getLabel().equals(entityKind))
{
- parseDataSetMetaData(xpath, extractDataSetCodeFromURI(uri), xdNode, lastModificationDate);
+ parseDataSetMetaData(extractDataSetCodeFromURI(uri), xdNode, lastModificationDate);
} else if (SyncEntityKind.MATERIAL.getLabel().equals(entityKind))
{
- parseMaterialMetaData(xpath, extractMaterialCodeFromURI(uri), xdNode, lastModificationDate);
+ parseMaterialMetaData(extractMaterialCodeFromURI(uri), xdNode, lastModificationDate);
}
}
- private Date extractLastModificationDate(Document doc, XPath xpath, String uri) throws XPathExpressionException
+ private Map<String, List<Node>> getChildrenByType(Node node)
{
- XPathExpression expr = xpath.compile("//s:url/s:loc[normalize-space(.)='" + uri + "']//following-sibling::s:lastmod[1]");
- Node lastModNode = (Node) expr.evaluate(doc, XPathConstants.NODE);
- if (lastModNode == null)
+ Map<String, List<Node>> result = new TreeMap<>();
+ if (node.hasChildNodes())
{
- throw new XPathExpressionException("The resource list should contain 1 lastmod element per resource");
- }
-
- String lastModDataStr = lastModNode.getTextContent().trim();
- try
- {
- return convertFromW3CDate(lastModDataStr);
- } catch (ParseException e)
- {
- throw new XPathExpressionException("Last modification date cannot be parsed:" + lastModDataStr);
+ NodeList childNodes = node.getChildNodes();
+ for (int i = 0, n = childNodes.getLength(); i < n; i++)
+ {
+ Node childNode = childNodes.item(i);
+ String nodeName = childNode.getNodeName().toLowerCase();
+ List<Node> list = result.get(nodeName);
+ if (list == null)
+ {
+ list = new ArrayList<>();
+ result.put(nodeName, list);
+ }
+ list.add(childNode);
+ }
}
+ return result;
}
private Date convertFromW3CDate(String lastModDataStr) throws ParseException
@@ -258,19 +295,7 @@ public class ResourceListParser
return df1.parse(lastModDataStr);
}
- private Node extractXdNode(Document doc, XPath xpath, String uri) throws XPathExpressionException
- {
- // alternative expression: //s:url/s:loc[normalize-space(.)='" + uri + "']/../x:xd");
- XPathExpression expr = xpath.compile("//s:url/s:loc[normalize-space(.)='" + uri + "']//following-sibling::x:xd[1]");
- Node xdNode = (Node) expr.evaluate(doc, XPathConstants.NODE);
- if (xdNode == null)
- {
- throw new XPathExpressionException("The resource list should contain 1 xd element per resource");
- }
- return xdNode;
- }
-
- private void parseDataSetMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
+ private void parseDataSetMetaData(String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
String sampleIdentifier = extractAttribute(xdNode, "sample", true);
@@ -299,8 +324,8 @@ public class ResourceListParser
IncomingDataSet incomingDataSet = new IncomingDataSet(ds, lastModificationDate);
data.getDataSetsToProcess().put(permId, incomingDataSet);
- incomingDataSet.setConnections(parseConnections(xpath, xdNode));
- ds.setDataSetProperties(parseDataSetProperties(xpath, xdNode));
+ incomingDataSet.setConnections(parseConnections(xdNode));
+ ds.setDataSetProperties(parseDataSetProperties(xdNode));
}
private String extractAttribute(Node xdNode, String attrName, boolean nullAllowed)
@@ -366,7 +391,7 @@ public class ResourceListParser
expCode);
}
- private void parseProjectMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
+ private void parseProjectMetaData(String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
@@ -377,8 +402,8 @@ public class ResourceListParser
newProject.setPermID(permId);
IncomingProject incomingProject = new IncomingProject(newProject, lastModificationDate);
data.getProjectsToProcess().put(permId, incomingProject);
- incomingProject.setConnections(parseConnections(xpath, xdNode));
- incomingProject.setHasAttachments(hasAttachments(xpath, xdNode));
+ incomingProject.setConnections(parseConnections(xdNode));
+ incomingProject.setHasAttachments(hasAttachments(xdNode));
}
private ExperimentIdentifier createExperimentIdentifier(String spaceId, String prjCode, String expCode)
@@ -415,7 +440,7 @@ public class ResourceListParser
return new SpaceIdentifier(translatedSpaceId);
}
- private void parseMaterialMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
+ private void parseMaterialMetaData(String permId, Node xdNode, Date lastModificationDate)
{
String code = nameTranslator.translate(extractCode(xdNode));
String type = extractType(xdNode);
@@ -423,10 +448,10 @@ public class ResourceListParser
MaterialWithLastModificationDate materialWithLastModDate =
new MaterialWithLastModificationDate(newMaterial, lastModificationDate);
data.getMaterialsToProcess().put(code, type, materialWithLastModDate);
- newMaterial.setProperties(parseProperties(xpath, xdNode));
+ newMaterial.setProperties(parseProperties(xdNode));
}
- private List<Connection> parseConnections(XPath xpath, Node xdNode)
+ private List<Connection> parseConnections(Node xdNode)
{
List<Connection> conns = new ArrayList<Connection>();
Element docElement = (Element) xdNode;
@@ -445,21 +470,17 @@ public class ResourceListParser
return conns;
}
- private boolean hasAttachments(XPath xpath, Node xdNode)
+ private boolean hasAttachments(Node xdNode)
{
Element docElement = (Element) xdNode;
NodeList connsNode = docElement.getElementsByTagName("x:binaryData");
// if a sample/experiment/project node has binaryData element, it can only be because of attachments
- if (connsNode.getLength() == 1)
- {
- return true;
- }
- return false;
+ return connsNode.getLength() == 1;
}
- private List<NewProperty> parseDataSetProperties(XPath xpath, Node xdNode)
+ private List<NewProperty> parseDataSetProperties(Node xdNode)
{
- EntityProperty[] entityProperties = parseProperties(xpath, xdNode);
+ EntityProperty[] entityProperties = parseProperties(xdNode);
List<NewProperty> dsProperties = new ArrayList<NewProperty>();
for (EntityProperty entityProperty : entityProperties)
{
@@ -468,7 +489,7 @@ public class ResourceListParser
return dsProperties;
}
- private EntityProperty[] parseProperties(XPath xpath, Node xdNode)
+ private EntityProperty[] parseProperties(Node xdNode)
{
List<EntityProperty> entityProperties = new ArrayList<EntityProperty>();
@@ -533,7 +554,7 @@ public class ResourceListParser
return new MaterialIdentifier(code, typeCode).toString();
}
- private void parseExperimentMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
+ private void parseExperimentMetaData(String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
String type = extractType(xdNode);
@@ -544,12 +565,12 @@ public class ResourceListParser
newExp.setPermID(permId);
IncomingExperiment incomingExperiment = new IncomingExperiment(newExp, lastModificationDate);
data.getExperimentsToProcess().put(permId, incomingExperiment);
- incomingExperiment.setConnections(parseConnections(xpath, xdNode));
- incomingExperiment.setHasAttachments(hasAttachments(xpath, xdNode));
- newExp.setProperties(parseProperties(xpath, xdNode));
+ incomingExperiment.setConnections(parseConnections(xdNode));
+ incomingExperiment.setHasAttachments(hasAttachments(xdNode));
+ newExp.setProperties(parseProperties(xdNode));
}
- private void parseSampleMetaData(XPath xpath, String permId, Node xdNode, Date lastModificationDate)
+ private void parseSampleMetaData(String permId, Node xdNode, Date lastModificationDate)
{
String code = extractCode(xdNode);
String type = extractType(xdNode);
@@ -585,9 +606,9 @@ public class ResourceListParser
}
IncomingSample incomingSample = new IncomingSample(newSample, lastModificationDate);
data.getSamplesToProcess().put(permId, incomingSample);
- incomingSample.setHasAttachments(hasAttachments(xpath, xdNode));
- incomingSample.setConnections(parseConnections(xpath, xdNode));
- newSample.setProperties(parseProperties(xpath, xdNode));
+ incomingSample.setHasAttachments(hasAttachments(xdNode));
+ incomingSample.setConnections(parseConnections(xdNode));
+ newSample.setProperties(parseProperties(xdNode));
}
private String extractType(Node xdNode)
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/util/Monitor.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/util/Monitor.java
new file mode 100644
index 0000000000000000000000000000000000000000..36d8202f2cd02a0eea63938c765fbd9cb339b566
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/sync/harvester/synchronizer/util/Monitor.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2018 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.ethz.sis.openbis.generic.server.dss.plugins.sync.harvester.synchronizer.util;
+
+import java.util.concurrent.TimeUnit;
+
+import org.apache.commons.lang3.time.StopWatch;
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.logging.BufferedAppender;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.openbis.util.LogRecordingUtils;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class Monitor
+{
+ private String name;
+
+ private Logger operationLog;
+
+ private StopWatch stopWatch;
+
+ public Monitor(String name, Logger operationLog)
+ {
+ this.name = name;
+ this.operationLog = operationLog;
+ stopWatch = new StopWatch();
+ stopWatch.start();
+ operationLog.info("-------- monitoring started for '" + name + "'.");
+ }
+
+ public void log()
+ {
+ logInfo(createReport());
+ }
+
+ public void log(String message)
+ {
+ logInfo(createReport() + " " + message);
+ }
+
+ private void logInfo(String info)
+ {
+ operationLog.info("[" + name + "] " + info);
+ }
+
+ private String createReport()
+ {
+ Runtime runtime = Runtime.getRuntime();
+ String max = FileUtilities.byteCountToDisplaySize(runtime.maxMemory());
+ String free = FileUtilities.byteCountToDisplaySize(runtime.freeMemory());
+ String used = FileUtilities.byteCountToDisplaySize(runtime.maxMemory() - runtime.freeMemory());
+ long time = stopWatch.getTime(TimeUnit.SECONDS);
+ return String.format("[time: %5d sec, used: %9s, free: %9s, max: %9s]", time, used, free, max);
+ }
+}