diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
deleted file mode 100644
index b64004710779eb8ea2159639811c84c58272be26..0000000000000000000000000000000000000000
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/DataSetRegistrationTask.java
+++ /dev/null
@@ -1,1448 +0,0 @@
-/*
- * Copyright 2016 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.
- */
-//TODO should we use permId in hash tables instead of identifier, fore exp in samplesToUpdate
-//TODO try to implement sample relationship sync like DS rel. sync
-//TODO check if already loaded harvesterEntityGraph can be used in most cases
-//TODO check if harvesterEntityGraph can be partially loaded as required
-//TODO correctly handle saving of last sync timestamp
-//TODO different last sync timestamp files for different plugins -
-//this is actually handled by setting up different harvester plugins with different files
-//TODO when deleting make sure we are not emptying all the trash but just the ones we synchronized
-//TODO checksum checkss for data set files
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.UnsupportedEncodingException;
-import java.net.URI;
-import java.net.URISyntaxException;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.Paths;
-import java.security.MessageDigest;
-import java.security.NoSuchAlgorithmException;
-import java.text.DateFormat;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Comparator;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.Properties;
-import java.util.Set;
-import java.util.StringTokenizer;
-import java.util.concurrent.ExecutionException;
-import java.util.concurrent.TimeoutException;
-
-import javax.activation.DataHandler;
-import javax.activation.DataSource;
-import javax.mail.util.ByteArrayDataSource;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.xpath.XPathExpressionException;
-
-import org.apache.commons.codec.binary.Hex;
-import org.apache.log4j.DailyRollingFileAppender;
-import org.apache.log4j.Logger;
-import org.apache.log4j.PatternLayout;
-import org.eclipse.jetty.client.HttpClient;
-import org.eclipse.jetty.client.api.AuthenticationStore;
-import org.eclipse.jetty.client.api.ContentResponse;
-import org.eclipse.jetty.client.api.Request;
-import org.eclipse.jetty.client.util.BasicAuthentication;
-import org.eclipse.jetty.http.HttpStatus;
-import org.w3c.dom.Document;
-import org.xml.sax.SAXException;
-
-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.dataset.DataSetKind;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.delete.DataSetDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.deletion.id.IDeletionId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.delete.ExperimentDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.delete.MaterialDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.id.MaterialPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.delete.ProjectDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectPermId;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.delete.SampleDeletionOptions;
-import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
-import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.IDataSetFileId;
-import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
-import ch.ethz.sis.openbis.generic.server.EntityRetriever;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.Connection;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.DataSetWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ExperimentWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.MaterialWithLastModificationDate;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ProjectWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.SampleWithConnections;
-import ch.ethz.sis.openbis.generic.shared.entitygraph.EntityGraph;
-import ch.ethz.sis.openbis.generic.shared.entitygraph.Node;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
-import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.Status;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
-import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.mail.EMailAddress;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
-import ch.systemsx.cisd.common.parser.MemorySizeFormatter;
-import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
-import ch.systemsx.cisd.common.ssl.SslCertificateHelper;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.ConversionUtils;
-import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
-import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
-import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IngestionService;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskInfoProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistrationTransaction;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.EncapsulatedCommonServer;
-import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegistrationService;
-import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterialWithType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.PropertyBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.AtomicEntityOperationDetailsBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-
-/**
- * @author Ganime Betul Akin
- */
-public class DataSetRegistrationTask<T extends DataSetInformation> implements IMaintenanceTask
-{
- protected static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, DataSetRegistrationTask.class);
-
- // private static final String DATA_SOURCE_URI = "https://bs-mbpr121.d.ethz.ch:8444/datastore_server/re-sync"; //
- // "http://localhost:8889/datastore_server/re-sync";
-
- final DateFormat formater = new SimpleDateFormat("dd-MM-yy HH-mm-ss", Locale.ENGLISH);
-
- private static final String HARVESTER_CONFIG_FILE_PROPERTY_NAME = "harvester-config-file";
-
- private static final String DATA_SOURCE_URL_PROPERTY_NAME = "resource-list-url";
-
- private static final String DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME = "data-source-openbis-url";
-
- private static final String DATA_SOURCE_DSS_URL_PROPERTY_NAME = "data-source-dss-url";
-
- private static final String DATA_SOURCE_SPACES_PROPERTY_NAME = "data-source-spaces";
-
- private static final String DATA_SOURCE_PREFIX_PROPERTY_NAME = "data-source-prefix";
-
- private static final String DATA_SOURCE_AUTH_REALM_PROPERTY_NAME = "data-source-auth-realm";
-
- private static final String DATA_SOURCE_AUTH_USER_PROPERTY_NAME = "data-source-auth-user";
-
- private static final String DATA_SOURCE_AUTH_PASS_PROPERTY_NAME = "data-source-auth-pass";
-
- private static final String HARVESTER_SPACES_PROPERTY_NAME = "harvester-spaces";
-
- private static final String HARVESTER_TEMP_DIR_PROPERTY_NAME = "harvester-tmp-dir";
-
- private static final String DEFAULT_LAST_SYNC_TIMESTAMP_FILE = "last-sync-timestamp-file.txt";
-
- private static final String DEFAULT_LOG_FILE_NAME = "../../syncronization.log";
-
- private static final String HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME = "last-sync-timestamp-file";
-
- private static final String EMAIL_ADDRESSES_PROPERTY_NAME = "email-addresses";
-
- private static final String DEFAULT_DATA_SOURCE_SECTION = "DataSource1";
-
- private static final String HARVESTER_CONFIG_FILE_NAME = "harvester-config-file";
-
- private static final String LOG_FILE_PROPERTY_NAME = "log-file";
-
- private static final String SEPARATOR = ",";;
-
- private File lastSyncTimestampFile;
-
- private File newLastSyncTimeStampFile;
-
- private HashMap<String, String> spaceMappings = new HashMap<String, String>();
-
- private File storeRoot;
-
- private IEncapsulatedOpenBISService service;
-
- private DataSetProcessingContext context;
-
- private ResourceListParserData data;
-
- private Date lastSyncTimestamp;
-
- private File harvesterConfigFile;
-
- private SyncConfig config = null;
-
- private IMailClient mailClient;
-
- private void initializePluginProperties()
- {
- config = new SyncConfig();
- config.setDataSourceURI("https://localhost:8444/datastore_server/re-sync");
- config.setRealm("OAI-PMH");
- config.setUser("admin");
- config.setPass("aa");
- // dataSourceSpace = "DEFAULT";
- // harvesterSpace = "DST";
- }
-
- public static void main(String[] args)
- {
-
- DataSetRegistrationTask<DataSetInformation> dsrt = new DataSetRegistrationTask<DataSetInformation>();
-
- // File storeRoot = new File("targets/store");
- // File temp = new File(storeRoot, "harvester-tmp");
- // temp.mkdirs();
- // File file = new File(temp, "20160630103851669-100");
- // file.mkdirs();
- //
- // System.exit(0);
-
- Properties properties = new Properties();
- properties.put(PluginTaskInfoProvider.STOREROOT_DIR_KEY, "targets/store");
-
- Document doc;
- try
- {
- dsrt.initializePluginProperties();
- doc = dsrt.getResourceListAsXMLDoc();
- ResourceListParser parser = ResourceListParser.create(new HashMap<String, String>()); // , new Date(0L)
- parser.parseResourceListDocument(doc);
- } catch (XPathExpressionException | ParserConfigurationException | SAXException | IOException | URISyntaxException | InterruptedException
- | TimeoutException | ExecutionException e)
- {
- e.printStackTrace();
- }
- }
-
- private void createDataSourceToHarvesterSpaceMappings()
- {
- List<String> dataSourceSpaceList = extractSpaces(config.getDataSourceSpaces());
- List<String> harvesterSpaceList = extractSpaces(config.getHarvesterSpaces());
- if (dataSourceSpaceList.size() != harvesterSpaceList.size())
- {
- throw new ConfigurationFailureException("Please specify a harvester space for each data source space.");
- }
- for (int i = 0; i < dataSourceSpaceList.size(); i++)
- {
- String harvesterSpace = harvesterSpaceList.get(i);
- Space destSpace = ServiceProvider.getOpenBISService().tryGetSpace(new SpaceIdentifier(harvesterSpace));
- if (destSpace == null)
- {
- operationLog.error("Space " + harvesterSpace + " does not exist");
- throw new RuntimeException("Space " + harvesterSpace + " does not exist");
- }
- spaceMappings.put(dataSourceSpaceList.get(i), harvesterSpace);
- }
-
- operationLog.info("Syncing the following spaces:");
- for (String s : spaceMappings.keySet())
- {
- System.out.println(s + " : " + spaceMappings.get(s));
- }
- }
-
- private List<String> extractSpaces(String spaces)
- {
- StringTokenizer st = new StringTokenizer(spaces, SEPARATOR);
-
- List<String> harvesterSpaceList = new ArrayList<String>();
- while (st.hasMoreElements())
- {
- harvesterSpaceList.add(st.nextToken().trim());
- }
- return harvesterSpaceList;
- }
-
- private Document getResourceListAsXMLDoc() throws ParserConfigurationException, SAXException, IOException, XPathExpressionException,
- URISyntaxException,
- InterruptedException, TimeoutException, ExecutionException
- {
-
- HttpClient client = JettyHttpClientFactory.getHttpClient();
-
- // Add authentication credentials
- AuthenticationStore auth = client.getAuthenticationStore();
- auth.addAuthentication(new BasicAuthentication(new URI(config.getDataSourceURI()), config.getRealm(), config.getUser(), config.getPass()));
-
- String spacesParam = "";
- for (String dataSourceSpace : spaceMappings.keySet())
- {
- spacesParam += dataSourceSpace + ",";
- }
- if (spacesParam.isEmpty() == false)
- {
- spacesParam = spacesParam.substring(0, spacesParam.length() - 1);
- }
- Request requestEntity = client.newRequest(config.getDataSourceURI() + "?verb=resourcelist.xml&spaces=" + spacesParam).method("GET");
-
- ContentResponse contentResponse;
- contentResponse = requestEntity.send();
- int statusCode = contentResponse.getStatus();
-
- if (statusCode != HttpStatus.Code.OK.getCode())
- {
- throw new IOException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
- }
-
- byte[] content = contentResponse.getContent();
- ByteArrayInputStream bis = new ByteArrayInputStream(content);
-
- // System.out.println(new String(content));
- DocumentBuilderFactory domFactory =
- DocumentBuilderFactory.newInstance();
- domFactory.setNamespaceAware(true);
- DocumentBuilder builder = domFactory.newDocumentBuilder();
- return builder.parse(bis);
- }
-
- private final class DataSetRegistrationTaskExecutor implements ITaskExecutor<DataSetWithConnections>
- {
-
- private List<String> dataSetCodes;
-
- public DataSetRegistrationTaskExecutor(List<String> dataSetCodes)
- {
- this.dataSetCodes = dataSetCodes;
- }
-
- @Override
- public Status execute(DataSetWithConnections dataSet)
- {
- System.out.println("start " + dataSet.getDataSet().getCode());
-
- Properties props = setProperties();
-
- DataSetRegistrationIngestionService ingestionService =
- new DataSetRegistrationIngestionService(props, storeRoot, dataSetCodes, dataSet.getDataSet());
- ingestionService.createAggregationReport(new HashMap<String, Object>(), context);
- System.out.println("finished " + dataSet.getDataSet().getCode());
- dataSetCodes.add(dataSet.getDataSet().getCode());
- return Status.OK;
- }
-
- private Properties setProperties()
- {
- Properties props = new Properties();
- props.setProperty("user", DataSetRegistrationTask.this.config.getUser());
- props.setProperty("pass", DataSetRegistrationTask.this.config.getPass());
- props.setProperty("as-url", DataSetRegistrationTask.this.config.getDataSourceOpenbisURL());
- props.setProperty("dss-url", DataSetRegistrationTask.this.config.getDataSourceDSSURL());
- props.setProperty("harvester-temp-dir", DataSetRegistrationTask.this.config.getHarvesterTempDir());
- return props;
- }
- }
-
- private void registerMasterData()
- {
- EncapsulatedCommonServer encapsulatedServer = EncapsulatedCommonServer.create("http://localhost:8888/openbis/openbis", "admin", "a");
- MasterDataRegistrationService service = new MasterDataRegistrationService(encapsulatedServer);
- IMasterDataRegistrationTransaction transaction = service.transaction();
- transaction.getOrCreateNewDataSetType("test dataset type");
- // service.commit();
- }
-
- private static class DataSetRegistrationIngestionService extends IngestionService<DataSetInformation>
- {
-
- private static final long serialVersionUID = 1L;
-
- private List<String> dataSetCodes;
-
- private final NewExternalData dataSet;
-
- private final String loginUser;
-
- private final String loginPass;
-
- private final String asUrl;
-
- private final String dssUrl;
-
- private final String harvesterTempDir;
-
- public DataSetRegistrationIngestionService(Properties properties, File storeRoot, List<String> dataSetCodes, NewExternalData ds)
- {
- super(properties, storeRoot);
- this.dataSetCodes = dataSetCodes;
- this.dataSet = ds;
- this.loginUser = properties.getProperty("user");
- this.loginPass = properties.getProperty("pass");
- this.asUrl = properties.getProperty("as-url");
- this.dssUrl = properties.getProperty("dss-url");
- this.harvesterTempDir = properties.getProperty("harvester-temp-dir");
- }
-
- @Override
- protected TableModel process(IDataSetRegistrationTransactionV2 transaction, Map<String, Object> parameters, DataSetProcessingContext context)
- {
- IDataSetUpdatable dataSetForUpdate = transaction.getDataSetForUpdate(dataSet.getCode());
- ISampleImmutable sample = null;
-
- if (dataSet.getSampleIdentifierOrNull() != null)
- {
- sample = transaction.getSampleForUpdate(dataSet.getSampleIdentifierOrNull().toString());
- }
- IExperimentImmutable experiment = null;
- if (dataSet.getExperimentIdentifierOrNull() != null)
- {
- experiment = transaction.getExperimentForUpdate(dataSet.getExperimentIdentifierOrNull().toString());
- }
-
- List<NewProperty> dataSetProperties = dataSet.getDataSetProperties();
-
- if (dataSetForUpdate == null)
- {
- // REGISTER NEW DATA SET
- IDataSet ds = transaction.createNewDataSet(dataSet.getDataSetType().getCode(), dataSet.getCode());
- dataSetCodes.add(ds.getDataSetCode());
- ds.setSample(sample);
- ds.setExperiment(experiment);
- ds.setParentDatasets(dataSet.getParentDataSetCodes());
- for (NewProperty newProperty : dataSetProperties)
- {
- ds.setPropertyValue(newProperty.getPropertyCode(), newProperty.getValue());
- }
-
- File storeRoot = transaction.getGlobalState().getStoreRootDir();
- File temp = new File(storeRoot, this.harvesterTempDir);
- temp.mkdirs();
- File dir = new File(temp, ds.getDataSetCode());
- dir.mkdirs();
-
- downloadDataSetFiles(dir, ds.getDataSetCode());
-
- File dsPath = new File(dir, "original");
- for (File f : dsPath.listFiles())
- {
- transaction.moveFile(f.getAbsolutePath(), ds);
- }
- }
- else
- {
- // UPDATE data set meta data excluding the container/contained relationships
- dataSetForUpdate.setSample(sample);
- dataSetForUpdate.setExperiment(experiment);
- dataSetForUpdate.setParentDatasets(dataSet.getParentDataSetCodes());
- for (NewProperty newProperty : dataSetProperties)
- {
- dataSetForUpdate.setPropertyValue(newProperty.getPropertyCode(), newProperty.getValue());
- }
- }
- return null;
- }
-
- private void downloadDataSetFiles(File dir, String dataSetCode)
- {
- SslCertificateHelper.trustAnyCertificate(asUrl);
- SslCertificateHelper.trustAnyCertificate(dssUrl);
-
- IDataStoreServerApi dss =
- HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class,
- dssUrl + IDataStoreServerApi.SERVICE_URL, 10000);
- IApplicationServerApi as = HttpInvokerUtils
- .createServiceStub(IApplicationServerApi.class, asUrl
- + IApplicationServerApi.SERVICE_URL, 10000);
- String sessionToken = as.login(loginUser, loginPass);
-
- DataSetFileSearchCriteria criteria = new DataSetFileSearchCriteria();
- criteria.withDataSet().withCode().thatEquals(dataSetCode);
- SearchResult<DataSetFile> result = dss.searchFiles(sessionToken, criteria, new DataSetFileFetchOptions());
- List<DataSetFile> files = result.getObjects();
-
- List<IDataSetFileId> fileIds = new LinkedList<IDataSetFileId>();
- for (DataSetFile f : files)
- {
- fileIds.add(f.getPermId());
- }
- // Download the files & print the contents
- DataSetFileDownloadOptions options = new DataSetFileDownloadOptions();
- options.setRecursive(false);
- InputStream stream = dss.downloadFiles(sessionToken, fileIds, options);
- DataSetFileDownloadReader reader = new DataSetFileDownloadReader(stream);
- DataSetFileDownload fileDownload = null;
- while ((fileDownload = reader.read()) != null)
- {
- DataSetFile dsFile = fileDownload.getDataSetFile();
- if (dsFile.getPath().equals(""))
- continue;
- // if (dsFile.getPath().equals("original"))
- // continue;
- String filePath = dsFile.getPath();// .substring("original/".length());
- File output = new File(dir.getAbsolutePath(), filePath);
- if (dsFile.isDirectory())
- {
- output.mkdirs();
- }
- else
- {
- System.err.println("Downloaded " + dsFile.getPath() + " "
- + MemorySizeFormatter.format(dsFile.getFileLength()));
- Path path = Paths.get(dir.getAbsolutePath(), filePath);
- try
- {
- Files.copy(fileDownload.getInputStream(), path, java.nio.file.StandardCopyOption.REPLACE_EXISTING);
- } catch (IOException e)
- {
- // TODO Auto-generated catch block
- e.printStackTrace();
- }
- }
- }
- }
- }
-
- @Override
- public void setUp(String pluginName, Properties properties)
- {
- storeRoot = new File(DssPropertyParametersUtil.loadServiceProperties().getProperty(PluginTaskInfoProvider.STOREROOT_DIR_KEY));
- service = ServiceProvider.getOpenBISService();
- context = new DataSetProcessingContext(null, null, null, null, null, null);
- mailClient = ServiceProvider.getDataStoreService().createEMailClient();
-
- String configFileProperty = properties.getProperty(HARVESTER_CONFIG_FILE_PROPERTY_NAME);
- if (configFileProperty == null)
- {
- harvesterConfigFile =
- new File(ServiceProvider.getConfigProvider().getStoreRoot(), HARVESTER_CONFIG_FILE_NAME);
- } else
- {
- harvesterConfigFile = new File(configFileProperty);
- }
- // dbConfigurationContext = new SimpleDatabaseConfigurationContext(properties);
- // jdbcTemplate = new JdbcTemplate(dbConfigurationContext.getDataSource());
- }
-
- private void configureFileAppender()
- {
- DailyRollingFileAppender console = new DailyRollingFileAppender(); // create appender
- // configure the appender
- console.setName("bdfile");
- String PATTERN = "%d %-5p [%t] %c - %m%n";
- console.setLayout(new PatternLayout(PATTERN));
- // console.setThreshold(Level.FATAL);
- console.setAppend(false);
- console.setFile(config.getLogFilePath());
- console.activateOptions();
- // add appender to any Logger (here is root)
- operationLog.addAppender(console);
- operationLog.setAdditivity(false);
- }
-
- @Override
- public void execute()
- {
- try
- {
- operationLog.info(this.getClass() + " started.");
-
- initConfiguration();
-
- createDataSourceToHarvesterSpaceMappings();
-
- operationLog.info("Start synchronization from data source: " + config.getDataSourceOpenbisURL() + " spaces:" + spaceMappings.keySet());
-
- // operationLog.info("register master data");
- registerMasterData();
-
- if (lastSyncTimestampFile.exists())
- {
- String timeStr = FileUtilities.loadToString(lastSyncTimestampFile).trim();
- try
- {
- lastSyncTimestamp = formater.parse(timeStr);
- } catch (ParseException e)
- {
- operationLog.error("Cannot parse value as time:" + timeStr);
- return;
- }
- }
- else
- {
- lastSyncTimestamp = new Date(0L);
- }
- // save the current time into a temp file as last sync time
- FileUtilities.writeToFile(newLastSyncTimeStampFile, formater.format(new Date()));
-
- // retrieve the document from the data source
- operationLog.info("Retrieving the resource list..");
- Document doc = getResourceListAsXMLDoc();
-
- // 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");
- ResourceListParser parser = ResourceListParser.create(spaceMappings); // , lastSyncTimestamp
- data = parser.parseResourceListDocument(doc);
-
- // go through the resources returned by the parser and decide on add/update/delete operations
- Map<String, ProjectWithConnections> projectsToProcess = data.projectsToProcess;
- Map<String, ExperimentWithConnections> experimentsToProcess = data.experimentsToProcess;
- Map<String, SampleWithConnections> samplesToProcess = data.samplesToProcess;
- Map<String, DataSetWithConnections> dataSetsToProcess = data.datasetsToProcess;
- Map<String, MaterialWithLastModificationDate> materialsToProcess = data.materialsToProcess;
-
- operationLog.info("Processing deletions");
- processDeletions(data);
-
- AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
-
- processProjects(projectsToProcess, experimentsToProcess, builder);
-
- processExperiments(experimentsToProcess, samplesToProcess, dataSetsToProcess, builder);
-
- processSamples(samplesToProcess, builder);
-
- processMaterials(materialsToProcess, builder);
-
- operationLog.info("Registering meta data...");
- AtomicEntityOperationResult operationResult = service.performEntityOperations(builder.getDetails());
- System.err.println("entity operation result: " + operationResult);
- operationLog.info("entity operation result: " + operationResult);
-
- // register physical data sets
- operationLog.info("Registering data sets...");
- Map<String, DataSetWithConnections> physicalDSMap = data.filterPhysicalDataSetsByLastModificationDate(lastSyncTimestamp);
- List<DataSetWithConnections> dsList = new ArrayList<DataSetWithConnections>(physicalDSMap.values());
- List<String> dataSetCodes = Collections.synchronizedList(new ArrayList<String>());
-
- // TODO this parallelization needs to be revisited: In case of a data set appearing before DSs it is dependent on,
- // the parallelization will result in an error, i.e. The graph needs to be topologically sorted before it can be
- // parallelized
- ParallelizedExecutor.process(dsList, new DataSetRegistrationTaskExecutor(dataSetCodes), 0.5, 10, "register data sets", 0, false);
-
- // link physical data sets registered above to container data sets
- System.err.println("start linking/un-linking container and contained data sets");
- builder = new AtomicEntityOperationDetailsBuilder();
-
- builder.user(DataSetRegistrationTask.this.config.getUser());
- Map<String, NewExternalData> datasetsToUpdate = new HashMap<String, NewExternalData>();
-
- // set parent and container data set codes before everything else
- // container and physical data sets can both be parents/children of each other
- Map<String, Set<String>> dsToParents = new HashMap<String, Set<String>>();
- Map<String, Set<String>> dsToContained = new HashMap<String, Set<String>>();
- for (DataSetWithConnections dsWithConn : dataSetsToProcess.values())
- {
- for (Connection conn : dsWithConn.getConnections())
- {
- NewExternalData dataSet = dsWithConn.getDataSet();
- if (dataSetsToProcess.containsKey(conn.getToPermId()) && conn.getType().equals("Child"))
- {
- NewExternalData childDataSet = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
- List<String> parentDataSetCodes = childDataSet.getParentDataSetCodes();
- parentDataSetCodes.add(dataSet.getCode());
-
- // datasetsToUpdate.put(childDataSet.getCode(), childDataSet);
- dsToParents.put(childDataSet.getCode(), new HashSet<String>(parentDataSetCodes));
- }
- else if (dataSetsToProcess.containsKey(conn.getToPermId()) && conn.getType().equals("Component"))
- {
- NewExternalData componentDataSet = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
- NewContainerDataSet containerDataSet = (NewContainerDataSet) dataSet;
- List<String> containedDataSetCodes = containerDataSet.getContainedDataSetCodes();
- containedDataSetCodes.add(componentDataSet.getCode());
- dsToContained.put(dataSet.getCode(), new HashSet<String>(containedDataSetCodes));
- }
- }
- }
- // go through all the data sets, decide what needs to be updated
- for (DataSetWithConnections dsWithConn : dataSetsToProcess.values())
- {
- NewExternalData dataSet = (NewExternalData) dsWithConn.getDataSet();
- if (dsWithConn.getLastModificationDate().after(lastSyncTimestamp))
- {
- if (physicalDSMap.containsKey(dataSet.getCode()) == false && service.tryGetDataSet(dataSet.getCode()) == null)
- {
- builder.dataSet(dataSet);
- }
- else
- {
-
- datasetsToUpdate.put(dataSet.getCode(), dataSet);
- }
- }
- }
-
- // go thru to-be-updated DS list and establish/break relations
- for (NewExternalData dataSet : datasetsToUpdate.values())
- {
- DataSetBatchUpdatesDTO dsBatchUpdatesDTO = createDataSetBatchUpdateDTO(dataSet);
- if (dataSet instanceof NewContainerDataSet)
- {
- NewContainerDataSet containerDS = (NewContainerDataSet) dataSet;
- if (dsToContained.containsKey(containerDS.getCode()))
- {
- dsBatchUpdatesDTO.setModifiedContainedDatasetCodesOrNull(dsToContained.get(dataSet.getCode()).toArray(new
- String[containerDS.getContainedDataSetCodes().size()]));
- }
- else
- {
- dsBatchUpdatesDTO.setModifiedContainedDatasetCodesOrNull(new String[0]);
- }
- dsBatchUpdatesDTO.getDetails().setContainerUpdateRequested(true);
- }
- if (dsToParents.containsKey(dataSet.getCode()))
- {
- dsBatchUpdatesDTO.setModifiedParentDatasetCodesOrNull(dsToParents.get(dataSet.getCode()).toArray(
- new String[dataSet.getParentDataSetCodes().size()]));
- // TODO should this always be true or should we flag the ones that require parent update. Same for container
- }
- else
- {
- dsBatchUpdatesDTO.setModifiedParentDatasetCodesOrNull(new String[0]);
- }
- dsBatchUpdatesDTO.getDetails().setParentsUpdateRequested(true);
- SampleIdentifier sampleIdentifier = dataSet.getSampleIdentifierOrNull();
- if (sampleIdentifier != null)
- {
- Sample sampleWithExperiment = service.tryGetSampleWithExperiment(sampleIdentifier);
- dsBatchUpdatesDTO.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(sampleWithExperiment.getIdentifier()));
- dsBatchUpdatesDTO.getDetails().setSampleUpdateRequested(true);
- }
- else
- {
- dsBatchUpdatesDTO.setSampleIdentifierOrNull(null);
- dsBatchUpdatesDTO.getDetails().setSampleUpdateRequested(true);
- }
-
- ExperimentIdentifier expIdentifier = dataSet.getExperimentIdentifierOrNull();
- if (expIdentifier != null)
- {
- Experiment experiment = service.tryGetExperiment(expIdentifier);
- dsBatchUpdatesDTO.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(experiment.getIdentifier()));
- dsBatchUpdatesDTO.getDetails().setExperimentUpdateRequested(true);
- }
- else
- {
- dsBatchUpdatesDTO.setExperimentIdentifierOrNull(null);
- dsBatchUpdatesDTO.getDetails().setExperimentUpdateRequested(true);
- }
-
- builder.dataSetUpdate(dsBatchUpdatesDTO);
- }
- operationResult = service.performEntityOperations(builder.getDetails());
- System.err.println("entity operation result: " + operationResult);
- operationLog.info("entity operation result: " + operationResult);
-
- operationLog.info("Saving the timestamp of sync start to file");
- saveSyncTimestamp();
-
- operationLog.info("Done and dusted...");
- operationLog.info(this.getClass() + " finished executing.");
-
- } catch (Exception e)
- {
- operationLog.error("Sync failed: ", e);
- sendErrorEmail("Synchronization failed");
- }
- }
-
- private void sendErrorEmail(String subject)
- {
- if (config.getLogFilePath() != null)
- {
- // send the operation log as attachment
- DataSource dataSource = createDataSource(config.getLogFilePath()); // /Users/gakin/Documents/sync.log
- for (EMailAddress recipient : config.getEmailAddresses())
- {
- mailClient.sendEmailMessageWithAttachment(subject,
- "See the attached file for details.",
- "", new DataHandler(
- dataSource), null, null, recipient);
- }
- }
- else
- {
- for (EMailAddress recipient : config.getEmailAddresses())
- {
- mailClient.sendEmailMessage(subject,
- "See the data store server log for details.", null, null, recipient);
- }
- }
- }
-
- private DataSource createDataSource(final String filePath)
- {
- try
- {
- return new ByteArrayDataSource(new FileInputStream(filePath), "text/plain");
- } catch (IOException ex)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(ex);
- }
- }
-
- private void initConfiguration() throws IOException
- {
- ConfigReader reader = new ConfigReader(harvesterConfigFile);
-
- config = new SyncConfig();
- if (reader.sectionExists(DEFAULT_DATA_SOURCE_SECTION) == false)
- {
- throw new ConfigurationFailureException("Please specify at least one data source section.");
- }
-
- config.setEmailAddresses(reader.getString(DEFAULT_DATA_SOURCE_SECTION, EMAIL_ADDRESSES_PROPERTY_NAME, null, true));
- config.setLogFilePath(reader.getString(DEFAULT_DATA_SOURCE_SECTION, LOG_FILE_PROPERTY_NAME, DEFAULT_LOG_FILE_NAME, false));
- if (config.getLogFilePath() != null)
- {
- configureFileAppender();
- }
-
- config.setDataSourceURI(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_URL_PROPERTY_NAME, null, true));
- config.setDataSourceOpenbisURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME, null, true));
- config.setDataSourceDSSURL(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_DSS_URL_PROPERTY_NAME, null, true));
- config.setRealm(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_REALM_PROPERTY_NAME, null, true));
- config.setUser(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_USER_PROPERTY_NAME, null, true));
- config.setPass(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_AUTH_PASS_PROPERTY_NAME, null, true));
- config.setDataSourceSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_SPACES_PROPERTY_NAME, null, true));
- config.setHarvesterSpaces(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_SPACES_PROPERTY_NAME, null, true));
- config.setDataSourcePrefix(reader.getString(DEFAULT_DATA_SOURCE_SECTION, DATA_SOURCE_PREFIX_PROPERTY_NAME, null, false));
- config.setHarvesterTempDir(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_TEMP_DIR_PROPERTY_NAME, "targets/store", false));
- config.setLastSyncTimestampFileName(reader.getString(DEFAULT_DATA_SOURCE_SECTION, HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME,
- DEFAULT_LAST_SYNC_TIMESTAMP_FILE, false));
-
- String fileName = config.getLastSyncTimestampFileName();
- lastSyncTimestampFile = new File(fileName);
- newLastSyncTimeStampFile = new File(fileName + ".new");
-
- config.printConfig();
- }
-
- private void processDeletions(ResourceListParserData data) throws NoSuchAlgorithmException, UnsupportedEncodingException
- {
- String sessionToken = ServiceProvider.getOpenBISService().getSessionToken();
- EntityRetriever entityRetriever =
- EntityRetriever.createWithSessionToken(ServiceProvider.getV3ApplicationService(), sessionToken);
-
- Set<String> incomingProjectPermIds = data.projectsToProcess.keySet();
- Set<String> incomingExperimentPermIds = data.experimentsToProcess.keySet();
- Set<String> incomingSamplePermIds = data.samplesToProcess.keySet();
- Set<String> incomingDataSetCodes = data.datasetsToProcess.keySet();
- Set<String> incomingMaterialCodes = data.materialsToProcess.keySet();
-
- // find projects, experiments, samples and data sets to be deleted
- List<ProjectPermId> projectPermIds = new ArrayList<ProjectPermId>();
- List<ExperimentPermId> experimentPermIds = new ArrayList<ExperimentPermId>();
- List<SamplePermId> samplePermIds = new ArrayList<SamplePermId>();
- List<DataSetPermId> dsPermIds = new ArrayList<DataSetPermId>();
- List<MaterialPermId> matPermIds = new ArrayList<MaterialPermId>();
-
- Set<PhysicalDataSet> physicalDataSetsDelete = new HashSet<PhysicalDataSet>();
- // first find out the entities to be deleted
- for (String harvesterSpaceId : spaceMappings.values())
- {
- EntityGraph<Node<?>> harvesterEntityGraph = entityRetriever.getEntityGraph(harvesterSpaceId);
- List<Node<?>> entities = harvesterEntityGraph.getNodes();
- for (Node<?> entity : entities)
- {
- if (entity.getEntityKind().equals("PROJECT"))
- {
- if (incomingProjectPermIds.contains(entity.getPermId()) == false)
- {
- projectPermIds.add(new ProjectPermId(entity.getPermId()));
- }
- }
- else if (entity.getEntityKind().equals("EXPERIMENT"))
- {
- if (incomingExperimentPermIds.contains(entity.getPermId()) == false)
- {
- experimentPermIds.add(new ExperimentPermId(entity.getPermId()));
- }
- else {
- String typeCodeOrNull = entity.getTypeCodeOrNull();
- NewExperiment exp = data.experimentsToProcess.get(entity.getPermId()).getExperiment();
- if (typeCodeOrNull.equals(exp.getExperimentTypeCode()) == false)
- {
- experimentPermIds.add(new ExperimentPermId(entity.getPermId()));
- }
- }
- }
- else if (entity.getEntityKind().equals("SAMPLE"))
- {
- if (incomingSamplePermIds.contains(entity.getPermId()) == false)
- {
- samplePermIds.add(new SamplePermId(entity.getPermId()));
- }
- else
- {
- String typeCodeOrNull = entity.getTypeCodeOrNull();
- NewSample smp = data.samplesToProcess.get(entity.getPermId()).getSample();
- if (typeCodeOrNull.equals(smp.getSampleType().getCode()) == false)
- {
- samplePermIds.add(new SamplePermId(entity.getPermId()));
- }
- }
- }
- else if (entity.getEntityKind().equals("DATA_SET"))
- {
- if (incomingDataSetCodes.contains(entity.getPermId()) == false)
- {
- dsPermIds.add(new DataSetPermId(entity.getPermId()));
- }
- else
- {
- boolean sameDS = true;
- // if (ds.getKind() == DataSetKind.PHYSICAL && ds.lastModificationDate.after(lastSyncDate))
- String typeCodeOrNull = entity.getTypeCodeOrNull();
-
- DataSetWithConnections dsWithConns = data.datasetsToProcess.get(entity.getPermId());
- NewExternalData ds = dsWithConns.getDataSet();
- if (typeCodeOrNull.equals(ds.getDataSetType().getCode()) == false)
- {
- sameDS = false;
- }
- else
- {
- if (dsWithConns.getKind() == DataSetKind.PHYSICAL && dsWithConns.getLastModificationDate().after(lastSyncTimestamp))
- {
- PhysicalDataSet physicalDS = service.tryGetDataSet(entity.getPermId()).tryGetAsDataSet();
- sameDS = deepCompareDataSets(entity.getPermId());
- if (sameDS == false)
- physicalDataSetsDelete.add(physicalDS);
- }
- }
- if (sameDS == false)
- {
- dsPermIds.add(new DataSetPermId(entity.getPermId()));
- }
- }
- }
- }
- }
-
- List<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material> materials = entityRetriever.fetchMaterials();
-
- for (ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material material : materials)
- {
- if (incomingMaterialCodes.contains(material.getCode()) == false)
- {
- matPermIds.add(new MaterialPermId(material.getCode(), material.getType().getCode()));
- }
- }
-
- IApplicationServerApi v3Api = ServiceProvider.getV3ApplicationService();
-
- // delete data sets
- DataSetDeletionOptions dsDeletionOpts = new DataSetDeletionOptions();
- dsDeletionOpts.setReason("sync data set deletions"); // TODO maybe mention data source space id in the reason
-
- IDeletionId dsDeletionId =
- v3Api.deleteDataSets(sessionToken, dsPermIds, dsDeletionOpts);
-
- // delete samples
- SampleDeletionOptions sampleDeletionOptions = new SampleDeletionOptions();
- sampleDeletionOptions.setReason("sync sample deletions");
- IDeletionId smpDeletionId = v3Api.deleteSamples(sessionToken, samplePermIds, sampleDeletionOptions);
-
- // delete experiments
-
- ExperimentDeletionOptions expDeletionOpts = new ExperimentDeletionOptions();
- expDeletionOpts.setReason("sync experiment deletions");
- IDeletionId expDeletionId = v3Api.deleteExperiments(sessionToken, experimentPermIds, expDeletionOpts);
-
- // delete projects
- ProjectDeletionOptions prjDeletionOpts = new ProjectDeletionOptions();
- prjDeletionOpts.setReason("Sync projects");
- v3Api.deleteProjects(sessionToken, projectPermIds, prjDeletionOpts);
-
- // delete materials
- MaterialDeletionOptions matDeletionOptions = new MaterialDeletionOptions();
- matDeletionOptions.setReason("sync materials");
- v3Api.deleteMaterials(sessionToken, matPermIds, matDeletionOptions);
-
- // confirm deletions
- v3Api.confirmDeletions(sessionToken, Arrays.asList(expDeletionId, dsDeletionId, smpDeletionId));
-
- for (PhysicalDataSet physicalDS : physicalDataSetsDelete)
- {
- operationLog.info("Is going to delete the location: " + physicalDS.getLocation());
- File datasetDir =
- getDirectoryProvider().getDataSetDirectory(physicalDS);
- SegmentedStoreUtils.deleteDataSetInstantly(physicalDS.getCode(), datasetDir, new Log4jSimpleLogger(operationLog));
- }
- }
-
- private IDataSetDirectoryProvider getDirectoryProvider()
- {
- return new DataSetDirectoryProvider(getConfigProvider().getStoreRoot(), getShareIdManager());
- }
-
- private IConfigProvider getConfigProvider()
- {
- return ServiceProvider.getConfigProvider();
- }
-
- private IShareIdManager getShareIdManager()
- {
- return ServiceProvider.getShareIdManager();
- }
-
- private boolean deepCompareDataSets(String dataSetCode)
- throws NoSuchAlgorithmException, UnsupportedEncodingException
- {
- // get the file nodes in the incoming DS by querying the data source openbis
- String asUrl = config.getDataSourceOpenbisURL();
- String dssUrl = config.getDataSourceDSSURL();
-
- SslCertificateHelper.trustAnyCertificate(dssUrl);
- SslCertificateHelper.trustAnyCertificate(asUrl);
-
- IDataStoreServerApi dss =
- HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class,
- dssUrl + IDataStoreServerApi.SERVICE_URL, 10000);
- IApplicationServerApi as = HttpInvokerUtils
- .createServiceStub(IApplicationServerApi.class, asUrl
- + IApplicationServerApi.SERVICE_URL, 10000);
- String sessionToken = as.login(config.getUser(), config.getPass());
-
- DataSetFileSearchCriteria criteria = new DataSetFileSearchCriteria();
- criteria.withDataSet().withCode().thatEquals(dataSetCode);
- SearchResult<DataSetFile> result = dss.searchFiles(sessionToken, criteria, new DataSetFileFetchOptions());
-
- IDataStoreServerApi dssharvester = (IDataStoreServerApi) ServiceProvider.getDssServiceV3().getService();
- SearchResult<DataSetFile> resultHarvester =
- dssharvester.searchFiles(ServiceProvider.getOpenBISService().getSessionToken(), criteria, new DataSetFileFetchOptions());
- if (result.getTotalCount() != resultHarvester.getTotalCount())
- {
- return false;
- }
-
- List<DataSetFile> dsNodes = result.getObjects();
- List<DataSetFile> harvesterNodes = resultHarvester.getObjects();
- sortFileNodes(dsNodes);
- sortFileNodes(harvesterNodes);
- return calculateHash(dsNodes).equals(calculateHash(harvesterNodes));
- }
-
- private void sortFileNodes(List<DataSetFile> nodes)
- {
- Collections.sort(nodes, new Comparator<DataSetFile>()
- {
-
- @Override
- public int compare(DataSetFile dsFile1, DataSetFile dsFile2)
- {
- return dsFile1.getPath().compareTo(dsFile2.getPath());
- }
- });
- }
-
- private String calculateHash(List<DataSetFile> nodes) throws NoSuchAlgorithmException, UnsupportedEncodingException
- {
- StringBuffer sb = new StringBuffer();
- for (DataSetFile dataSetFile : nodes)
- {
- sb.append(dataSetFile.getPath());
- sb.append(dataSetFile.getChecksumCRC32());
- sb.append(dataSetFile.getFileLength());
- }
- byte[] digest = MessageDigest.getInstance("MD5").digest(new String(sb).getBytes("UTF-8"));
- return new String(Hex.encodeHex(digest));
- }
-
- private void saveSyncTimestamp()
- {
- newLastSyncTimeStampFile.renameTo(lastSyncTimestampFile);
- }
-
- private DataSetBatchUpdatesDTO createDataSetBatchUpdateDTO(NewExternalData childDS)
- {
- AbstractExternalData dsInHarvester = service.tryGetDataSet(childDS.getCode());
- ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetUpdatable updateUpdatable = new
- ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetUpdatable(dsInHarvester, service);
- DataSetBatchUpdatesDTO dsBatchUpdatesDTO = ConversionUtils.convertToDataSetBatchUpdatesDTO(updateUpdatable);
- //
- dsBatchUpdatesDTO.setDatasetId(TechId.create(dsInHarvester));
- List<IEntityProperty> entityProperties = new ArrayList<IEntityProperty>();
- for (NewProperty prop : childDS.getDataSetProperties())
- {
- String propertyCode = prop.getPropertyCode();
- String value = prop.getValue();
- entityProperties.add(new PropertyBuilder(propertyCode).value(value).getProperty());
- }
- dsBatchUpdatesDTO.setProperties(entityProperties);
- return dsBatchUpdatesDTO;
- }
-
- private void processMaterials(Map<String, MaterialWithLastModificationDate> materialsToProcess, AtomicEntityOperationDetailsBuilder builder)
- {
- // process materials
- for (MaterialWithLastModificationDate newMaterialWithType : materialsToProcess.values())
- {
- NewMaterialWithType newIncomingMaterial = newMaterialWithType.getMaterial();
- if (newMaterialWithType.getLastModificationDate().after(lastSyncTimestamp))
- {
- Material material = service.tryGetMaterial(new MaterialIdentifier(newIncomingMaterial.getCode(), newIncomingMaterial.getType()));
- if (material == null)
- {
- builder.material(newIncomingMaterial);
- }
- else
- {
- MaterialUpdateDTO update =
- new MaterialUpdateDTO(TechId.create(material), Arrays.asList(newIncomingMaterial.getProperties()),
- material.getModificationDate());
- builder.materialUpdate(update);
- }
- }
- }
- }
-
- private void processSamples(Map<String, SampleWithConnections> samplesToProcess, AtomicEntityOperationDetailsBuilder builder)
- {
- // process samples
- Map<SampleIdentifier, NewSample> samplesToUpdate = new HashMap<SampleIdentifier, NewSample>();
- Set<String> sampleWithUpdatedParents = new HashSet<String>();
- for (SampleWithConnections sample : samplesToProcess.values())
- {
- NewSample incomingSample = sample.getSample();
- if (sample.getLastModificationDate().after(lastSyncTimestamp))
- {
- SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(incomingSample);
- Sample sampleWithExperiment = null;
- try
- {
- sampleWithExperiment = service.tryGetSampleByPermId(incomingSample.getPermID());
- } catch (Exception e)
- {
- // TODO doing nothing because when the sample with the perm is not found
- // an exception will be thrown. See the same issue for projects
- }
- if (sampleWithExperiment == null)
- {
- // ADD SAMPLE
- builder.sample(incomingSample);
- }
- else
- {
- // defer creation of sample update objects until all samples have been gone through;
- samplesToUpdate.put(sampleIdentifier, incomingSample);
- List<Sample> childSamples = getChildSamples(sampleWithExperiment);
- for (Sample child : childSamples)
- {
- String childSampleIdentifier = child.getIdentifier();// edgeNodePair.getNode().getIdentifier();
- SampleWithConnections childSampleWithConns = findChildInSamplesToProcess(childSampleIdentifier, samplesToProcess);
- if (childSampleWithConns == null)
- {
- // TODO Handle sample delete
- }
- else
- {
- // the childSample will appear in the incoming samples list anyway
- // but we want to make sure its parent modification is handled
- NewSample childSample = childSampleWithConns.getSample();
- sampleWithUpdatedParents.add(childSample.getIdentifier());
- }
- }
- }
- }
- for (Connection conn : sample.getConnections())
- {
- if (conn.getType().equals("Component"))
- {
- NewSample containedSample = samplesToProcess.get(conn.getToPermId()).getSample();
- containedSample.setContainerIdentifier(incomingSample.getIdentifier());
- }
- else if (conn.getType().equals("Child"))
- {
- NewSample childSample = samplesToProcess.get(conn.getToPermId()).getSample();
- String[] parents = childSample.getParentsOrNull();
- List<String> parentIds = null;
- if (parents == null)
- {
- parentIds = new ArrayList<String>();
- }
- else
- {
- parentIds = new ArrayList<String>(Arrays.asList(parents));
- }
- parentIds.add(incomingSample.getIdentifier());
- childSample.setParentsOrNull(parentIds.toArray(new String[parentIds.size()]));
- }
- // TODO how about Connection Type
- // else if (conn.getType().equals("Connection")) // TODO not sure if this guarantees that we have a dataset in the toPermId
- // {
- // NewExternalData externalData = dataSetsToCreate.get(conn.getToPermId()).getDataSet();
- // externalData.setSampleIdentifierOrNull(new SampleIdentifier(newSmp.getIdentifier()));
- // }
- }
- }
-
- // create sample update dtos for the samples that need to be updated
- for (SampleIdentifier sampleIdentifier : samplesToUpdate.keySet())
- {
- NewSample newSmp = samplesToUpdate.get(sampleIdentifier);
- Sample sampleWithExperiment = service.tryGetSampleByPermId(newSmp.getPermID());
-
- TechId sampleId = TechId.create(sampleWithExperiment);
- String expIdentifier = newSmp
- .getExperimentIdentifier();
- String[] modifiedParentIds = newSmp.getParentsOrNull();
- if (modifiedParentIds == null)
- {
- if (sampleWithUpdatedParents.contains(newSmp.getIdentifier()))
- {
- modifiedParentIds = new String[0];
- }
- }
-
- SampleUpdatesDTO updates =
- new SampleUpdatesDTO(sampleId, Arrays.asList(newSmp.getProperties()), (expIdentifier == null) ? null
- : ExperimentIdentifierFactory.parse(expIdentifier),
- Collections.<NewAttachment> emptyList(), sampleWithExperiment.getVersion(),
- sampleIdentifier, newSmp.getContainerIdentifier() == null ? null : newSmp.getContainerIdentifier(),
- modifiedParentIds);
- builder.sampleUpdate(updates);
- }
- }
-
- private List<Sample> getChildSamples(Sample sampleWithExperiment)
- {
- ListSampleCriteria criteria = ListSampleCriteria.createForParent(new TechId(sampleWithExperiment.getId()));
- return service.listSamples(criteria);
- }
-
- private void processExperiments(Map<String, ExperimentWithConnections> experimentsToProcess,
- Map<String, SampleWithConnections> samplesToProcess, Map<String, DataSetWithConnections> dataSetsToProcess,
- AtomicEntityOperationDetailsBuilder builder)
- {
- // process experiments
- for (ExperimentWithConnections exp : experimentsToProcess.values())
- {
- NewExperiment newIncomingExp = exp.getExperiment();
- if (exp.getLastModificationDate().after(lastSyncTimestamp))
- {
- Experiment experiment = null;
- try
- {
- experiment = service.tryGetExperimentByPermId(newIncomingExp.getPermID());
- } catch (Exception e)
- {
- // TODO doing nothing because when the experiment with the perm id not found
- // an exception will be thrown. Seems to be the same with entity kinds
- }
-
- if (experiment == null)
- {
- // ADD EXPERIMENT
- builder.experiment(newIncomingExp);
- }
- else
- {
- // UPDATE EXPERIMENT
- ExperimentUpdatesDTO expUpdate = new ExperimentUpdatesDTO();
- expUpdate.setProjectIdentifier(ExperimentIdentifierFactory.parse(newIncomingExp.getIdentifier()));
- expUpdate.setVersion(experiment.getVersion());
- expUpdate.setProperties(Arrays.asList(newIncomingExp.getProperties()));
- expUpdate.setExperimentId(TechId.create(experiment));
- builder.experimentUpdate(expUpdate);
- // TODO attachments
- expUpdate.setAttachments(Collections.<NewAttachment> emptyList());
- }
- }
- for (Connection conn : exp.getConnections())
- {
- if (samplesToProcess.containsKey(conn.getToPermId()))
- {
- SampleWithConnections sample = samplesToProcess.get(conn.getToPermId());
- NewSample newSample = sample.getSample();
- newSample.setExperimentIdentifier(newIncomingExp.getIdentifier());
- }
- if (dataSetsToProcess.containsKey(conn.getToPermId()))
- {
- NewExternalData externalData = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
- externalData.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(newIncomingExp.getIdentifier()));
- }
- }
- }
- }
-
- private void processProjects(Map<String, ProjectWithConnections> projectsToProcess, Map<String, ExperimentWithConnections> experimentsToProcess,
- AtomicEntityOperationDetailsBuilder builder)
- {
- for (ProjectWithConnections prj : projectsToProcess.values())
- {
- NewProject incomingProject = prj.getProject();
- if (prj.getLastModificationDate().after(lastSyncTimestamp))
- {
- Project project = null;
- try
- {
- project = service.tryGetProjectByPermId(incomingProject.getPermID());
- } catch (Exception e)
- {
- // TODO doing nothing because when the project with the perm is not found
- // an exception will be thrown. See bug report SSDM-4108
- }
-
- if (project == null)
- {
- // ADD PROJECT
- builder.project(incomingProject);
- }
- else
- {
- // UPDATE PROJECT
- ProjectUpdatesDTO prjUpdate = new ProjectUpdatesDTO();
- prjUpdate.setVersion(project.getVersion());
- prjUpdate.setTechId(TechId.create(project));
- prjUpdate.setDescription(incomingProject.getDescription());
- // TODO attachments????
- prjUpdate.setAttachments(Collections.<NewAttachment> emptyList());
- ProjectIdentifier projectIdentifier = ProjectIdentifierFactory.parse(incomingProject.getIdentifier());
- prjUpdate.setSpaceCode(projectIdentifier.getSpaceCode());
- builder.projectUpdate(prjUpdate); // ConversionUtils.convertToProjectUpdateDTO(new
- // ch.systemsx.cisd.etlserver.registrator.api.v2.impl.Project(project))
- }
- }
- for (Connection conn : prj.getConnections())
- {
- String connectedExpPermId = conn.getToPermId();
- // TODO we need to do the same check for samples to support project samples
- if (experimentsToProcess.containsKey(connectedExpPermId))
- {
- // the project is connected to an experiment
- ExperimentWithConnections exp = experimentsToProcess.get(connectedExpPermId);
- NewExperiment newExp = exp.getExperiment();
- // check if our local graph has the same connection
- if (service.tryGetExperiment(ExperimentIdentifierFactory.parse(newExp.getIdentifier())) == null)
- {
- // add new edge
- String oldIdentifier = newExp.getIdentifier();
- int index = oldIdentifier.lastIndexOf('/');
- String expCode = oldIdentifier.substring(index + 1);
-
- newExp.setIdentifier(incomingProject.getIdentifier() + "/" + expCode);
- // add new experiment node
- }// TODO can the following happen. i.e. a project experiment connection is always of type Connection so we should be safe to
- // remove the following?
- // else
- // {
- // if (harvesterEntityGraph.edgeExists(incomingProject.getIdentifier(), newExp.getIdentifier(), conn.getType()) == false)
- // {
- // // add new edge
- // // String fullExpIdentifier = newExp.getIdentifier().replace("{1}", incomingProject.getIdentifier());
- // // newExp.setIdentifier(fullExpIdentifier);
- // }
- // else
- // {
- // // do nothing
- // }
- // }
- }
- else
- {
- // TODO This means the XML contains the connection but not the connected entity.
- // These sort of problems maybe recorded in a separate synchronization log?
- // ???????????????
- operationLog.info("Connected experiment with permid : " + connectedExpPermId + " is missing");
- }
- }
-
- // //check if we have existing edges in our harvester that are no longer in the data source
- // List<EdgeNodePair> existingEdges = harvesterEntityGraph.getNeighboursForEntity(incomingProject.getIdentifier());
- // for (EdgeNodePair edgeNodePair : existingEdges)
- // {
- // String experimentIdentifier = edgeNodePair.getNode().getIdentifier();
- // List<Connection> connections = prj.getConnections();
- // for (Connection conn : connections) {
- // if
- // }
- // }
- }
- }
-
- private SampleWithConnections findChildInSamplesToProcess(String childSampleIdentifier, Map<String, SampleWithConnections> samplesToProcess)
- {
- for (SampleWithConnections sample : samplesToProcess.values())
- {
- if (sample.getSample().getIdentifier().equals(childSampleIdentifier))
- {
- return sample;
- }
- }
- return null;
- }
-}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/DataSetRegistrationTask.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/DataSetRegistrationTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..9dd76658bbc8d97571478c742494e703cd2467f6
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/DataSetRegistrationTask.java
@@ -0,0 +1,218 @@
+/*
+ * Copyright 2016 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.
+ */
+//TODO should we use permId in hash tables instead of identifier, fore exp in samplesToUpdate
+//TODO try to implement sample relationship sync like DS rel. sync
+//TODO check if already loaded harvesterEntityGraph can be used in most cases
+//TODO check if harvesterEntityGraph can be partially loaded as required
+//TODO correctly handle saving of last sync timestamp
+//TODO different last sync timestamp files for different plugins -
+//this is actually handled by setting up different harvester plugins with different files
+//TODO when deleting make sure we are not emptying all the trash but just the ones we synchronized
+//TODO checksum checkss for data set files
+package ch.ethz.sis.openbis.generic.server.dss.plugins.harvester;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Properties;
+
+import javax.activation.DataHandler;
+import javax.activation.DataSource;
+import javax.mail.util.ByteArrayDataSource;
+
+import org.apache.log4j.Logger;
+
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.config.SyncConfig;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.config.SynchronizationConfigReader;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.EntitySynchronizer;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.mail.EMailAddress;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskInfoProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
+
+/**
+ * @author Ganime Betul Akin
+ */
+public class DataSetRegistrationTask<T extends DataSetInformation> implements IMaintenanceTask
+{
+ protected static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DataSetRegistrationTask.class);
+
+ // private static final String DATA_SOURCE_URI = "https://bs-mbpr121.d.ethz.ch:8444/datastore_server/re-sync"; //
+ // "http://localhost:8889/datastore_server/re-sync";
+
+ final DateFormat formater = new SimpleDateFormat("dd-MM-yy HH-mm-ss", Locale.ENGLISH);
+
+ private static final String HARVESTER_CONFIG_FILE_PROPERTY_NAME = "harvester-config-file";
+
+ private static final String DEFAULT_HARVESTER_CONFIG_FILE_NAME = "../../harvester-config.txt";
+
+ private HashMap<String, String> spaceMappings = new HashMap<String, String>();
+
+ private File storeRoot;
+
+ private IEncapsulatedOpenBISService service;
+
+ private DataSetProcessingContext context;
+
+ private Date lastSyncTimestamp;
+
+ private File harvesterConfigFile;
+
+ private IMailClient mailClient;
+
+ File lastSyncTimestampFile;
+
+ File newLastSyncTimeStampFile;
+
+ @Override
+ public void setUp(String pluginName, Properties properties)
+ {
+ storeRoot = new File(DssPropertyParametersUtil.loadServiceProperties().getProperty(PluginTaskInfoProvider.STOREROOT_DIR_KEY));
+ service = ServiceProvider.getOpenBISService();
+ context = new DataSetProcessingContext(null, null, null, null, null, null);
+ mailClient = ServiceProvider.getDataStoreService().createEMailClient();
+
+ String configFileProperty = properties.getProperty(HARVESTER_CONFIG_FILE_PROPERTY_NAME);
+ if (configFileProperty == null)
+ {
+ harvesterConfigFile =
+ new File(ServiceProvider.getConfigProvider().getStoreRoot(), DEFAULT_HARVESTER_CONFIG_FILE_NAME);
+ } else
+ {
+ harvesterConfigFile = new File(configFileProperty);
+ }
+ }
+
+ @Override
+ public void execute()
+ {
+ operationLog.info(this.getClass() + " started.");
+
+ SynchronizationConfigReader syncConfigReader = new SynchronizationConfigReader();
+ List<SyncConfig> configs;
+ try
+ {
+ configs = syncConfigReader.readConfiguration(harvesterConfigFile, operationLog);
+ } catch (Exception e)
+ {
+ operationLog.error("", e);
+ return;
+ }
+
+ for (SyncConfig config : configs)
+ {
+ try
+ {
+ operationLog
+ .info("Start synchronization from data source: " + config.getDataSourceOpenbisURL() + " spaces:" + spaceMappings.keySet());
+
+ String fileName = config.getLastSyncTimestampFileName();
+ lastSyncTimestampFile = new File(fileName);
+ newLastSyncTimeStampFile = new File(fileName + ".new");
+
+ if (lastSyncTimestampFile.exists())
+ {
+ String timeStr = FileUtilities.loadToString(lastSyncTimestampFile).trim();
+ try
+ {
+ lastSyncTimestamp = formater.parse(timeStr);
+ } catch (ParseException e)
+ {
+ operationLog.error("Cannot parse value as time:" + timeStr);
+ return;
+ }
+ }
+ else
+ {
+ lastSyncTimestamp = new Date(0L);
+ }
+ // save the current time into a temp file as last sync time
+ FileUtilities.writeToFile(newLastSyncTimeStampFile, formater.format(new Date()));
+
+ EntitySynchronizer synchronizer = new EntitySynchronizer(service, storeRoot, lastSyncTimestamp, context, config, operationLog);
+ synchronizer.syncronizeEntities();
+
+ operationLog.info("Saving the timestamp of sync start to file");
+ saveSyncTimestamp();
+
+ operationLog.info("Done and dusted...");
+ operationLog.info(this.getClass() + " finished executing.");
+
+ } catch (Exception e)
+ {
+ operationLog.error("Sync failed: ", e);
+ sendErrorEmail(config, "Synchronization failed");
+ }
+ }
+ }
+
+ private void sendErrorEmail(SyncConfig config, String subject)
+ {
+ if (config.getLogFilePath() != null)
+ {
+ // send the operation log as attachment
+ DataSource dataSource = createDataSource(config.getLogFilePath()); // /Users/gakin/Documents/sync.log
+ for (EMailAddress recipient : config.getEmailAddresses())
+ {
+ mailClient.sendEmailMessageWithAttachment(subject,
+ "See the attached file for details.",
+ "", new DataHandler(
+ dataSource), null, null, recipient);
+ }
+ }
+ else
+ {
+ for (EMailAddress recipient : config.getEmailAddresses())
+ {
+ mailClient.sendEmailMessage(subject,
+ "See the data store server log for details.", null, null, recipient);
+ }
+ }
+ }
+
+ private DataSource createDataSource(final String filePath)
+ {
+ try
+ {
+ return new ByteArrayDataSource(new FileInputStream(filePath), "text/plain");
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+ private void saveSyncTimestamp()
+ {
+ newLastSyncTimeStampFile.renameTo(lastSyncTimestampFile);
+ }
+}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/ConfigReader.java
similarity index 98%
rename from datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java
rename to datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/ConfigReader.java
index e291b4e5bf20856106db4795af86d1b8f52abd8f..db07d22280e411db2577ce0ad0adaa8005eb6591 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ConfigReader.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/ConfigReader.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
+package ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.config;
/**
*
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SyncConfig.java
similarity index 82%
rename from datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java
rename to datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SyncConfig.java
index 773b221ecffaea119c0eed22ac1f86795cd07119..3185266c67cbfd3b36f806c66bc60494b749b755 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/SyncConfig.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SyncConfig.java
@@ -14,10 +14,11 @@
* limitations under the License.
*/
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
+package ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.config;
import java.lang.reflect.Field;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.List;
import ch.systemsx.cisd.common.mail.EMailAddress;
@@ -27,7 +28,7 @@ import ch.systemsx.cisd.common.mail.EMailAddress;
*
* @author Ganime Betul Akin
*/
-class SyncConfig
+public class SyncConfig
{
private String dataSourceURI;
@@ -111,24 +112,30 @@ class SyncConfig
this.dataSourcePrefix = dataSourcePrefix;
}
- public String getDataSourceSpaces()
+ public List<String> getDataSourceSpaces()
{
return dataSourceSpaces;
}
public void setDataSourceSpaces(String dataSourceSpaces)
{
- this.dataSourceSpaces = dataSourceSpaces;
+ for (String token : dataSourceSpaces.split(SEPARATOR))
+ {
+ this.dataSourceSpaces.add(token.trim());
+ }
}
- public String getHarvesterSpaces()
+ public List<String> getHarvesterSpaces()
{
return harvesterSpaces;
}
public void setHarvesterSpaces(String harvesterSpaces)
{
- this.harvesterSpaces = harvesterSpaces;
+ for (String token : harvesterSpaces.split(SEPARATOR))
+ {
+ this.harvesterSpaces.add(token.trim());
+ }
}
public String getHarvesterTempDir()
@@ -178,9 +185,9 @@ class SyncConfig
private String dataSourcePrefix;
- private String dataSourceSpaces;
+ private List<String> dataSourceSpaces = new ArrayList<>();
- private String harvesterSpaces;
+ private List<String> harvesterSpaces = new ArrayList<>();
private String harvesterTempDir;
@@ -188,7 +195,14 @@ class SyncConfig
private String logFilePath;
- private static final String SEPARATOR = ",";;
+ private static final String SEPARATOR = ",";
+
+ private HashMap<String, String> spaceMappings = new HashMap<String, String>();
+
+ public HashMap<String, String> getSpaceMappings()
+ {
+ return spaceMappings;
+ }
public String getLogFilePath()
{
@@ -207,9 +221,7 @@ class SyncConfig
public void setEmailAddresses(String emailAddresses)
{
- String[] tokens =
- emailAddresses.split(SEPARATOR);
- for (String token : tokens)
+ for (String token : emailAddresses.split(SEPARATOR))
{
this.emailAddresses.add(new EMailAddress(token.trim()));
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SynchronizationConfigReader.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SynchronizationConfigReader.java
new file mode 100644
index 0000000000000000000000000000000000000000..79ded6289bf30fc19dfbc03e7db5d2a429a060a3
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/config/SynchronizationConfigReader.java
@@ -0,0 +1,142 @@
+/*
+ * Copyright 2016 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.harvester.config;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.log4j.DailyRollingFileAppender;
+import org.apache.log4j.Logger;
+import org.apache.log4j.PatternLayout;
+
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+
+/**
+ *
+ *
+ * @author Ganime Betul Akin
+ */
+public class SynchronizationConfigReader
+{
+ private static final String DATA_SOURCE_URL_PROPERTY_NAME = "resource-list-url";
+
+ private static final String DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME = "data-source-openbis-url";
+
+ private static final String DATA_SOURCE_DSS_URL_PROPERTY_NAME = "data-source-dss-url";
+
+ private static final String DATA_SOURCE_SPACES_PROPERTY_NAME = "data-source-spaces";
+
+ private static final String DATA_SOURCE_PREFIX_PROPERTY_NAME = "data-source-prefix";
+
+ private static final String DATA_SOURCE_AUTH_REALM_PROPERTY_NAME = "data-source-auth-realm";
+
+ private static final String DATA_SOURCE_AUTH_USER_PROPERTY_NAME = "data-source-auth-user";
+
+ private static final String DATA_SOURCE_AUTH_PASS_PROPERTY_NAME = "data-source-auth-pass";
+
+ private static final String HARVESTER_SPACES_PROPERTY_NAME = "harvester-spaces";
+
+ private static final String HARVESTER_TEMP_DIR_PROPERTY_NAME = "harvester-tmp-dir";
+
+ private static final String DEFAULT_LAST_SYNC_TIMESTAMP_FILE = "last-sync-timestamp-file.txt";
+
+ private static final String DEFAULT_LOG_FILE_NAME = "../../syncronization.log";
+
+ private static final String HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME = "last-sync-timestamp-file";
+
+ private static final String EMAIL_ADDRESSES_PROPERTY_NAME = "email-addresses";
+
+ private static final String LOG_FILE_PROPERTY_NAME = "log-file";
+
+ List<SyncConfig> configs = new ArrayList<>();
+
+ public List<SyncConfig> readConfiguration(File harvesterConfigFile, Logger logger) throws IOException
+ {
+ ConfigReader reader = new ConfigReader(harvesterConfigFile);
+ int sectionCount = reader.getSectionCount();
+ for (int i = 0; i < sectionCount; i++)
+ {
+ String section = reader.getSection(i);
+ SyncConfig config = new SyncConfig();
+ config.setEmailAddresses(reader.getString(section, EMAIL_ADDRESSES_PROPERTY_NAME, null, true));
+ config.setLogFilePath(reader.getString(section, LOG_FILE_PROPERTY_NAME, DEFAULT_LOG_FILE_NAME, false));
+ if (config.getLogFilePath() != null)
+ {
+ // configureFileAppender(config, logger);
+ }
+
+ config.setDataSourceURI(reader.getString(section, DATA_SOURCE_URL_PROPERTY_NAME, null, true));
+ config.setDataSourceOpenbisURL(reader.getString(section, DATA_SOURCE_OPENBIS_URL_PROPERTY_NAME, null, true));
+ config.setDataSourceDSSURL(reader.getString(section, DATA_SOURCE_DSS_URL_PROPERTY_NAME, null, true));
+ config.setRealm(reader.getString(section, DATA_SOURCE_AUTH_REALM_PROPERTY_NAME, null, true));
+ config.setUser(reader.getString(section, DATA_SOURCE_AUTH_USER_PROPERTY_NAME, null, true));
+ config.setPass(reader.getString(section, DATA_SOURCE_AUTH_PASS_PROPERTY_NAME, null, true));
+
+ config.setDataSourceSpaces(reader.getString(section, DATA_SOURCE_SPACES_PROPERTY_NAME, null, true));
+ config.setHarvesterSpaces(reader.getString(section, HARVESTER_SPACES_PROPERTY_NAME, null, true));
+ createDataSourceToHarvesterSpaceMappings(config);
+
+ config.setDataSourcePrefix(reader.getString(section, DATA_SOURCE_PREFIX_PROPERTY_NAME, null, false));
+ config.setHarvesterTempDir(reader.getString(section, HARVESTER_TEMP_DIR_PROPERTY_NAME, "targets/store", false));
+ config.setLastSyncTimestampFileName(reader.getString(section, HARVESTER_LAST_SYNC_TIMESTAMP_FILE_PROPERTY_NAME,
+ DEFAULT_LAST_SYNC_TIMESTAMP_FILE, false));
+ configs.add(config);
+ }
+ return configs;
+ }
+
+ private void configureFileAppender(SyncConfig config, Logger logger)
+ {
+ DailyRollingFileAppender console = new DailyRollingFileAppender(); // create appender
+ // configure the appender
+ console.setName("bdfile");
+ String PATTERN = "%d %-5p [%t] %c - %m%n";
+ console.setLayout(new PatternLayout(PATTERN));
+ // console.setThreshold(Level.FATAL);
+ console.setAppend(false);
+ console.setFile(config.getLogFilePath());
+ console.activateOptions();
+ // add appender to any Logger (here is root)
+ logger.addAppender(console);
+ logger.setAdditivity(false);
+ }
+
+ private void createDataSourceToHarvesterSpaceMappings(SyncConfig config)
+ {
+ List<String> dataSourceSpaceList = config.getDataSourceSpaces();
+ List<String> harvesterSpaceList = config.getHarvesterSpaces();
+ if (dataSourceSpaceList.size() != harvesterSpaceList.size())
+ {
+ throw new ConfigurationFailureException("Please specify a harvester space for each data source space.");
+ }
+ for (int i = 0; i < dataSourceSpaceList.size(); i++)
+ {
+ String harvesterSpace = harvesterSpaceList.get(i);
+ Space destSpace = ServiceProvider.getOpenBISService().tryGetSpace(new SpaceIdentifier(harvesterSpace));
+ if (destSpace == null)
+ {
+ throw new ConfigurationFailureException("Space " + harvesterSpace + " does not exist");
+ }
+ config.getSpaceMappings().put(dataSourceSpaceList.get(i), harvesterSpace);
+ }
+ }
+}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/DataSetRegistrationIngestionService.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/DataSetRegistrationIngestionService.java
new file mode 100644
index 0000000000000000000000000000000000000000..152b566053944e9c7dfdc329e644fb9798593bd0
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/DataSetRegistrationIngestionService.java
@@ -0,0 +1,203 @@
+/*
+ * Copyright 2016 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.harvester.synchronizer;
+
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+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.dssapi.v3.IDataStoreServerApi;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownload;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.download.DataSetFileDownloadReader;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.id.IDataSetFileId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
+import ch.systemsx.cisd.common.parser.MemorySizeFormatter;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.common.ssl.SslCertificateHelper;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
+import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetUpdatable;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IngestionService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+class DataSetRegistrationIngestionService extends IngestionService<DataSetInformation>
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private List<String> dataSetCodes;
+
+ private final NewExternalData dataSet;
+
+ private final String loginUser;
+
+ private final String loginPass;
+
+ private final String asUrl;
+
+ private final String dssUrl;
+
+ private final String harvesterTempDir;
+
+ public DataSetRegistrationIngestionService(Properties properties, File storeRoot, List<String> dataSetCodes, NewExternalData ds)
+ {
+ super(properties, storeRoot);
+ this.dataSetCodes = dataSetCodes;
+ this.dataSet = ds;
+ this.loginUser = properties.getProperty("user");
+ this.loginPass = properties.getProperty("pass");
+ this.asUrl = properties.getProperty("as-url");
+ this.dssUrl = properties.getProperty("dss-url");
+ this.harvesterTempDir = properties.getProperty("harvester-temp-dir");
+ }
+
+ @Override
+ protected TableModel process(IDataSetRegistrationTransactionV2 transaction, Map<String, Object> parameters, DataSetProcessingContext context)
+ {
+ IDataSetUpdatable dataSetForUpdate = transaction.getDataSetForUpdate(dataSet.getCode());
+ ISampleImmutable sample = null;
+
+ if (dataSet.getSampleIdentifierOrNull() != null)
+ {
+ sample = transaction.getSampleForUpdate(dataSet.getSampleIdentifierOrNull().toString());
+ }
+ IExperimentImmutable experiment = null;
+ if (dataSet.getExperimentIdentifierOrNull() != null)
+ {
+ experiment = transaction.getExperimentForUpdate(dataSet.getExperimentIdentifierOrNull().toString());
+ }
+
+ List<NewProperty> dataSetProperties = dataSet.getDataSetProperties();
+
+ if (dataSetForUpdate == null)
+ {
+ // REGISTER NEW DATA SET
+ IDataSet ds = transaction.createNewDataSet(dataSet.getDataSetType().getCode(), dataSet.getCode());
+ dataSetCodes.add(ds.getDataSetCode());
+ ds.setSample(sample);
+ ds.setExperiment(experiment);
+ ds.setParentDatasets(dataSet.getParentDataSetCodes());
+ for (NewProperty newProperty : dataSetProperties)
+ {
+ ds.setPropertyValue(newProperty.getPropertyCode(), newProperty.getValue());
+ }
+
+ File storeRoot = transaction.getGlobalState().getStoreRootDir();
+ File temp = new File(storeRoot, this.harvesterTempDir);
+ temp.mkdirs();
+ File dir = new File(temp, ds.getDataSetCode());
+ dir.mkdirs();
+
+ downloadDataSetFiles(dir, ds.getDataSetCode());
+
+ File dsPath = new File(dir, "original");
+ for (File f : dsPath.listFiles())
+ {
+ transaction.moveFile(f.getAbsolutePath(), ds);
+ }
+ }
+ else
+ {
+ // UPDATE data set meta data excluding the container/contained relationships
+ dataSetForUpdate.setSample(sample);
+ dataSetForUpdate.setExperiment(experiment);
+ dataSetForUpdate.setParentDatasets(dataSet.getParentDataSetCodes());
+ for (NewProperty newProperty : dataSetProperties)
+ {
+ dataSetForUpdate.setPropertyValue(newProperty.getPropertyCode(), newProperty.getValue());
+ }
+ }
+ return null;
+ }
+
+ private void downloadDataSetFiles(File dir, String dataSetCode)
+ {
+ SslCertificateHelper.trustAnyCertificate(asUrl);
+ SslCertificateHelper.trustAnyCertificate(dssUrl);
+
+ IDataStoreServerApi dss =
+ HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class,
+ dssUrl + IDataStoreServerApi.SERVICE_URL, 10000);
+ IApplicationServerApi as = HttpInvokerUtils
+ .createServiceStub(IApplicationServerApi.class, asUrl
+ + IApplicationServerApi.SERVICE_URL, 10000);
+ String sessionToken = as.login(loginUser, loginPass);
+
+ DataSetFileSearchCriteria criteria = new DataSetFileSearchCriteria();
+ criteria.withDataSet().withCode().thatEquals(dataSetCode);
+ SearchResult<DataSetFile> result = dss.searchFiles(sessionToken, criteria, new DataSetFileFetchOptions());
+ List<DataSetFile> files = result.getObjects();
+
+ List<IDataSetFileId> fileIds = new LinkedList<IDataSetFileId>();
+ for (DataSetFile f : files)
+ {
+ fileIds.add(f.getPermId());
+ }
+ // Download the files & print the contents
+ DataSetFileDownloadOptions options = new DataSetFileDownloadOptions();
+ options.setRecursive(false);
+ InputStream stream = dss.downloadFiles(sessionToken, fileIds, options);
+ DataSetFileDownloadReader reader = new DataSetFileDownloadReader(stream);
+ DataSetFileDownload fileDownload = null;
+ while ((fileDownload = reader.read()) != null)
+ {
+ DataSetFile dsFile = fileDownload.getDataSetFile();
+ if (dsFile.getPath().equals(""))
+ continue;
+ // if (dsFile.getPath().equals("original"))
+ // continue;
+ String filePath = dsFile.getPath();// .substring("original/".length());
+ File output = new File(dir.getAbsolutePath(), filePath);
+ if (dsFile.isDirectory())
+ {
+ output.mkdirs();
+ }
+ else
+ {
+ System.err.println("Downloaded " + dsFile.getPath() + " "
+ + MemorySizeFormatter.format(dsFile.getFileLength()));
+ Path path = Paths.get(dir.getAbsolutePath(), filePath);
+ try
+ {
+ Files.copy(fileDownload.getInputStream(), path, java.nio.file.StandardCopyOption.REPLACE_EXISTING);
+ } catch (IOException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/EntitySynchronizer.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/EntitySynchronizer.java
new file mode 100644
index 0000000000000000000000000000000000000000..6a49921a23e359b151d0575592a99c7fc7b9702d
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/EntitySynchronizer.java
@@ -0,0 +1,985 @@
+/*
+ * Copyright 2016 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.harvester.synchronizer;
+
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.UnsupportedEncodingException;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.Set;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.TimeoutException;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.xpath.XPathExpressionException;
+
+import org.apache.commons.codec.binary.Hex;
+import org.apache.log4j.Logger;
+import org.eclipse.jetty.client.HttpClient;
+import org.eclipse.jetty.client.api.AuthenticationStore;
+import org.eclipse.jetty.client.api.ContentResponse;
+import org.eclipse.jetty.client.api.Request;
+import org.eclipse.jetty.client.util.BasicAuthentication;
+import org.eclipse.jetty.http.HttpStatus;
+import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
+
+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.dataset.DataSetKind;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.delete.DataSetDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.DataSetPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.deletion.id.IDeletionId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.delete.ExperimentDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id.ExperimentPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.delete.MaterialDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.material.id.MaterialPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.delete.ProjectDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.project.id.ProjectPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.delete.SampleDeletionOptions;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
+import ch.ethz.sis.openbis.generic.dssapi.v3.IDataStoreServerApi;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.DataSetFile;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.fetchoptions.DataSetFileFetchOptions;
+import ch.ethz.sis.openbis.generic.dssapi.v3.dto.datasetfile.search.DataSetFileSearchCriteria;
+import ch.ethz.sis.openbis.generic.server.EntityRetriever;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.config.SyncConfig;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.Connection;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.DataSetWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.ExperimentWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.MaterialWithLastModificationDate;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.ProjectWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.SampleWithConnections;
+import ch.ethz.sis.openbis.generic.shared.entitygraph.EntityGraph;
+import ch.ethz.sis.openbis.generic.shared.entitygraph.Node;
+import ch.systemsx.cisd.common.concurrent.ITaskExecutor;
+import ch.systemsx.cisd.common.concurrent.ParallelizedExecutor;
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
+import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
+import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
+import ch.systemsx.cisd.common.ssl.SslCertificateHelper;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.ConversionUtils;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetDirectoryProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IDataSetDirectoryProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IShareIdManager;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.SegmentedStoreUtils;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.IMasterDataRegistrationTransaction;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.EncapsulatedCommonServer;
+import ch.systemsx.cisd.openbis.generic.server.jython.api.v1.impl.MasterDataRegistrationService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterialWithType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewProject;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PhysicalDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.PropertyBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetBatchUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.MaterialUpdateDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewContainerDataSet;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
+import ch.systemsx.cisd.openbis.generic.shared.dto.builders.AtomicEntityOperationDetailsBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+/**
+ *
+ *
+ * @author Ganime Betul Akin
+ */
+public class EntitySynchronizer
+{
+ private final File storeRoot;
+
+ private final IEncapsulatedOpenBISService service;
+
+ private final DataSetProcessingContext context;
+
+ private final Date lastSyncTimestamp;
+
+ private final SyncConfig config;
+
+ private final Logger operationLog;
+
+ public EntitySynchronizer(IEncapsulatedOpenBISService service, File storeRoot, Date lastSyncTimestamp, DataSetProcessingContext context,
+ SyncConfig config, Logger operationLog)
+ {
+ this.service = service;
+ this.storeRoot = storeRoot;
+ this.lastSyncTimestamp = lastSyncTimestamp;
+ this.context = context;
+ this.config = config;
+ this.operationLog = operationLog;
+ }
+
+ public void syncronizeEntities() throws XPathExpressionException, ParserConfigurationException, SAXException, IOException, URISyntaxException,
+ InterruptedException, TimeoutException, ExecutionException, NoSuchAlgorithmException
+ {
+ // operationLog.info("register master data");
+ registerMasterData();
+
+ // retrieve the document from the data source
+ operationLog.info("Retrieving the resource list..");
+ Document doc = getResourceListAsXMLDoc();
+
+ // 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");
+ ResourceListParser parser = ResourceListParser.create(config.getSpaceMappings()); // , lastSyncTimestamp
+ ResourceListParserData data = parser.parseResourceListDocument(doc);
+
+ operationLog.info("Processing deletions");
+ processDeletions(data);
+
+ AtomicEntityOperationDetailsBuilder builder = new AtomicEntityOperationDetailsBuilder();
+
+ processMetaData(data, builder);
+
+ operationLog.info("Registering meta data...");
+ AtomicEntityOperationResult operationResult = service.performEntityOperations(builder.getDetails());
+ operationLog.info("entity operation result: " + operationResult);
+
+ // register physical data sets
+ operationLog.info("Registering data sets...");
+
+ Map<String, DataSetWithConnections> physicalDSMap = data.filterPhysicalDataSetsByLastModificationDate(lastSyncTimestamp);
+
+ registerPhysicalDataSets(physicalDSMap);
+
+ // link physical data sets registered above to container data sets
+ operationLog.info("start linking/un-linking container and contained data sets");
+
+ processDataSetRelationships(data.getDataSetsToProcess(), physicalDSMap);
+ }
+
+ private void processDataSetRelationships(Map<String, DataSetWithConnections> dataSetsToProcess, Map<String, DataSetWithConnections> physicalDSMap)
+ {
+ AtomicEntityOperationDetailsBuilder builder;
+ AtomicEntityOperationResult operationResult;
+ builder = new AtomicEntityOperationDetailsBuilder();
+
+ builder.user(config.getUser());
+ Map<String, NewExternalData> datasetsToUpdate = new HashMap<String, NewExternalData>();
+
+ // set parent and container data set codes before everything else
+ // container and physical data sets can both be parents/children of each other
+ Map<String, Set<String>> dsToParents = new HashMap<String, Set<String>>();
+ Map<String, Set<String>> dsToContained = new HashMap<String, Set<String>>();
+ for (DataSetWithConnections dsWithConn : dataSetsToProcess.values())
+ {
+ for (Connection conn : dsWithConn.getConnections())
+ {
+ NewExternalData dataSet = dsWithConn.getDataSet();
+ if (dataSetsToProcess.containsKey(conn.getToPermId()) && conn.getType().equals("Child"))
+ {
+ NewExternalData childDataSet = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
+ List<String> parentDataSetCodes = childDataSet.getParentDataSetCodes();
+ parentDataSetCodes.add(dataSet.getCode());
+
+ // datasetsToUpdate.put(childDataSet.getCode(), childDataSet);
+ dsToParents.put(childDataSet.getCode(), new HashSet<String>(parentDataSetCodes));
+ }
+ else if (dataSetsToProcess.containsKey(conn.getToPermId()) && conn.getType().equals("Component"))
+ {
+ NewExternalData componentDataSet = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
+ NewContainerDataSet containerDataSet = (NewContainerDataSet) dataSet;
+ List<String> containedDataSetCodes = containerDataSet.getContainedDataSetCodes();
+ containedDataSetCodes.add(componentDataSet.getCode());
+ dsToContained.put(dataSet.getCode(), new HashSet<String>(containedDataSetCodes));
+ }
+ }
+ }
+ // go through all the data sets, decide what needs to be updated
+ for (DataSetWithConnections dsWithConn : dataSetsToProcess.values())
+ {
+ NewExternalData dataSet = (NewExternalData) dsWithConn.getDataSet();
+ if (dsWithConn.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ if (physicalDSMap.containsKey(dataSet.getCode()) == false && service.tryGetDataSet(dataSet.getCode()) == null)
+ {
+ builder.dataSet(dataSet);
+ }
+ else
+ {
+
+ datasetsToUpdate.put(dataSet.getCode(), dataSet);
+ }
+ }
+ }
+
+ // go thru to-be-updated DS list and establish/break relations
+ for (NewExternalData dataSet : datasetsToUpdate.values())
+ {
+ DataSetBatchUpdatesDTO dsBatchUpdatesDTO = createDataSetBatchUpdateDTO(dataSet);
+ if (dataSet instanceof NewContainerDataSet)
+ {
+ NewContainerDataSet containerDS = (NewContainerDataSet) dataSet;
+ if (dsToContained.containsKey(containerDS.getCode()))
+ {
+ dsBatchUpdatesDTO.setModifiedContainedDatasetCodesOrNull(dsToContained.get(dataSet.getCode()).toArray(new
+ String[containerDS.getContainedDataSetCodes().size()]));
+ }
+ else
+ {
+ dsBatchUpdatesDTO.setModifiedContainedDatasetCodesOrNull(new String[0]);
+ }
+ dsBatchUpdatesDTO.getDetails().setContainerUpdateRequested(true);
+ }
+ if (dsToParents.containsKey(dataSet.getCode()))
+ {
+ dsBatchUpdatesDTO.setModifiedParentDatasetCodesOrNull(dsToParents.get(dataSet.getCode()).toArray(
+ new String[dataSet.getParentDataSetCodes().size()]));
+ // TODO should this always be true or should we flag the ones that require parent update. Same for container
+ }
+ else
+ {
+ dsBatchUpdatesDTO.setModifiedParentDatasetCodesOrNull(new String[0]);
+ }
+ dsBatchUpdatesDTO.getDetails().setParentsUpdateRequested(true);
+ SampleIdentifier sampleIdentifier = dataSet.getSampleIdentifierOrNull();
+ if (sampleIdentifier != null)
+ {
+ Sample sampleWithExperiment = service.tryGetSampleWithExperiment(sampleIdentifier);
+ dsBatchUpdatesDTO.setSampleIdentifierOrNull(SampleIdentifierFactory.parse(sampleWithExperiment.getIdentifier()));
+ dsBatchUpdatesDTO.getDetails().setSampleUpdateRequested(true);
+ }
+ else
+ {
+ dsBatchUpdatesDTO.setSampleIdentifierOrNull(null);
+ dsBatchUpdatesDTO.getDetails().setSampleUpdateRequested(true);
+ }
+
+ ExperimentIdentifier expIdentifier = dataSet.getExperimentIdentifierOrNull();
+ if (expIdentifier != null)
+ {
+ Experiment experiment = service.tryGetExperiment(expIdentifier);
+ dsBatchUpdatesDTO.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(experiment.getIdentifier()));
+ dsBatchUpdatesDTO.getDetails().setExperimentUpdateRequested(true);
+ }
+ else
+ {
+ dsBatchUpdatesDTO.setExperimentIdentifierOrNull(null);
+ dsBatchUpdatesDTO.getDetails().setExperimentUpdateRequested(true);
+ }
+
+ builder.dataSetUpdate(dsBatchUpdatesDTO);
+ }
+ operationResult = service.performEntityOperations(builder.getDetails());
+ System.err.println("entity operation result: " + operationResult);
+ operationLog.info("entity operation result: " + operationResult);
+ }
+
+ private void registerPhysicalDataSets(Map<String, DataSetWithConnections> physicalDSMap)
+ {
+ List<DataSetWithConnections> dsList = new ArrayList<DataSetWithConnections>(physicalDSMap.values());
+ List<String> dataSetCodes = Collections.synchronizedList(new ArrayList<String>());
+
+ // TODO this parallelization needs to be revisited: In case of a data set appearing before DSs it is dependent on,
+ // the parallelization will result in an error, i.e. The graph needs to be topologically sorted before it can be
+ // parallelized
+ ParallelizedExecutor.process(dsList, new DataSetRegistrationTaskExecutor(dataSetCodes), 0.5, 10, "register data sets", 0, false);
+ }
+
+ private void processMetaData(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder)
+ {
+ processProjects(data, builder);
+
+ processExperiments(data, builder);
+
+ processSamples(data, builder);
+
+ processMaterials(data, builder);
+ }
+
+ private void registerMasterData()
+ {
+ EncapsulatedCommonServer encapsulatedServer = EncapsulatedCommonServer.create("http://localhost:8888/openbis/openbis", "admin", "a");
+ MasterDataRegistrationService service = new MasterDataRegistrationService(encapsulatedServer);
+ IMasterDataRegistrationTransaction transaction = service.transaction();
+ transaction.getOrCreateNewDataSetType("test dataset type");
+ // service.commit();
+ }
+
+ private Document getResourceListAsXMLDoc() throws ParserConfigurationException, SAXException, IOException, XPathExpressionException,
+ URISyntaxException,
+ InterruptedException, TimeoutException, ExecutionException
+ {
+
+ HttpClient client = JettyHttpClientFactory.getHttpClient();
+
+ // Add authentication credentials
+ AuthenticationStore auth = client.getAuthenticationStore();
+ auth.addAuthentication(new BasicAuthentication(new URI(config.getDataSourceURI()), config.getRealm(), config.getUser(), config.getPass()));
+
+ String spacesParam = "";
+ for (String dataSourceSpace : config.getSpaceMappings().keySet())
+ {
+ spacesParam += dataSourceSpace + ",";
+ }
+ if (spacesParam.isEmpty() == false)
+ {
+ spacesParam = spacesParam.substring(0, spacesParam.length() - 1);
+ }
+ Request requestEntity = client.newRequest(config.getDataSourceURI() + "?verb=resourcelist.xml&spaces=" + spacesParam).method("GET");
+
+ ContentResponse contentResponse;
+ contentResponse = requestEntity.send();
+ int statusCode = contentResponse.getStatus();
+
+ if (statusCode != HttpStatus.Code.OK.getCode())
+ {
+ throw new IOException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
+ }
+
+ byte[] content = contentResponse.getContent();
+ ByteArrayInputStream bis = new ByteArrayInputStream(content);
+
+ // System.out.println(new String(content));
+ DocumentBuilderFactory domFactory =
+ DocumentBuilderFactory.newInstance();
+ domFactory.setNamespaceAware(true);
+ DocumentBuilder builder = domFactory.newDocumentBuilder();
+ return builder.parse(bis);
+ }
+
+ private void processDeletions(ResourceListParserData data) throws NoSuchAlgorithmException, UnsupportedEncodingException
+ {
+ String sessionToken = ServiceProvider.getOpenBISService().getSessionToken();
+ EntityRetriever entityRetriever =
+ EntityRetriever.createWithSessionToken(ServiceProvider.getV3ApplicationService(), sessionToken);
+
+ Set<String> incomingProjectPermIds = data.getProjectsToProcess().keySet();
+ Set<String> incomingExperimentPermIds = data.getExperimentsToProcess().keySet();
+ Set<String> incomingSamplePermIds = data.getSamplesToProcess().keySet();
+ Set<String> incomingDataSetCodes = data.getDataSetsToProcess().keySet();
+ Set<String> incomingMaterialCodes = data.getMaterialsToProcess().keySet();
+
+ // find projects, experiments, samples and data sets to be deleted
+ List<ProjectPermId> projectPermIds = new ArrayList<ProjectPermId>();
+ List<ExperimentPermId> experimentPermIds = new ArrayList<ExperimentPermId>();
+ List<SamplePermId> samplePermIds = new ArrayList<SamplePermId>();
+ List<DataSetPermId> dsPermIds = new ArrayList<DataSetPermId>();
+ List<MaterialPermId> matPermIds = new ArrayList<MaterialPermId>();
+
+ Set<PhysicalDataSet> physicalDataSetsDelete = new HashSet<PhysicalDataSet>();
+ // first find out the entities to be deleted
+ for (String harvesterSpaceId : config.getSpaceMappings().values())
+ {
+ EntityGraph<Node<?>> harvesterEntityGraph = entityRetriever.getEntityGraph(harvesterSpaceId);
+ List<Node<?>> entities = harvesterEntityGraph.getNodes();
+ for (Node<?> entity : entities)
+ {
+ if (entity.getEntityKind().equals("PROJECT"))
+ {
+ if (incomingProjectPermIds.contains(entity.getPermId()) == false)
+ {
+ projectPermIds.add(new ProjectPermId(entity.getPermId()));
+ }
+ }
+ else if (entity.getEntityKind().equals("EXPERIMENT"))
+ {
+ if (incomingExperimentPermIds.contains(entity.getPermId()) == false)
+ {
+ experimentPermIds.add(new ExperimentPermId(entity.getPermId()));
+ }
+ else
+ {
+ String typeCodeOrNull = entity.getTypeCodeOrNull();
+ NewExperiment exp = data.getExperimentsToProcess().get(entity.getPermId()).getExperiment();
+ if (typeCodeOrNull.equals(exp.getExperimentTypeCode()) == false)
+ {
+ experimentPermIds.add(new ExperimentPermId(entity.getPermId()));
+ }
+ }
+ }
+ else if (entity.getEntityKind().equals("SAMPLE"))
+ {
+ if (incomingSamplePermIds.contains(entity.getPermId()) == false)
+ {
+ samplePermIds.add(new SamplePermId(entity.getPermId()));
+ }
+ else
+ {
+ String typeCodeOrNull = entity.getTypeCodeOrNull();
+ NewSample smp = data.getSamplesToProcess().get(entity.getPermId()).getSample();
+ if (typeCodeOrNull.equals(smp.getSampleType().getCode()) == false)
+ {
+ samplePermIds.add(new SamplePermId(entity.getPermId()));
+ }
+ }
+ }
+ else if (entity.getEntityKind().equals("DATA_SET"))
+ {
+ if (incomingDataSetCodes.contains(entity.getPermId()) == false)
+ {
+ dsPermIds.add(new DataSetPermId(entity.getPermId()));
+ }
+ else
+ {
+ boolean sameDS = true;
+ // if (ds.getKind() == DataSetKind.PHYSICAL && ds.lastModificationDate.after(lastSyncDate))
+ String typeCodeOrNull = entity.getTypeCodeOrNull();
+
+ DataSetWithConnections dsWithConns = data.getDataSetsToProcess().get(entity.getPermId());
+ NewExternalData ds = dsWithConns.getDataSet();
+ if (typeCodeOrNull.equals(ds.getDataSetType().getCode()) == false)
+ {
+ sameDS = false;
+ }
+ else
+ {
+ if (dsWithConns.getKind() == DataSetKind.PHYSICAL && dsWithConns.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ PhysicalDataSet physicalDS = service.tryGetDataSet(entity.getPermId()).tryGetAsDataSet();
+ sameDS = deepCompareDataSets(entity.getPermId());
+ if (sameDS == false)
+ physicalDataSetsDelete.add(physicalDS);
+ }
+ }
+ if (sameDS == false)
+ {
+ dsPermIds.add(new DataSetPermId(entity.getPermId()));
+ }
+ }
+ }
+ }
+ }
+
+ List<ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material> materials = entityRetriever.fetchMaterials();
+
+ for (ch.ethz.sis.openbis.generic.asapi.v3.dto.material.Material material : materials)
+ {
+ if (incomingMaterialCodes.contains(material.getCode()) == false)
+ {
+ matPermIds.add(new MaterialPermId(material.getCode(), material.getType().getCode()));
+ }
+ }
+
+ IApplicationServerApi v3Api = ServiceProvider.getV3ApplicationService();
+
+ // delete data sets
+ DataSetDeletionOptions dsDeletionOpts = new DataSetDeletionOptions();
+ dsDeletionOpts.setReason("sync data set deletions"); // TODO maybe mention data source space id in the reason
+
+ IDeletionId dsDeletionId =
+ v3Api.deleteDataSets(sessionToken, dsPermIds, dsDeletionOpts);
+
+ // delete samples
+ SampleDeletionOptions sampleDeletionOptions = new SampleDeletionOptions();
+ sampleDeletionOptions.setReason("sync sample deletions");
+ IDeletionId smpDeletionId = v3Api.deleteSamples(sessionToken, samplePermIds, sampleDeletionOptions);
+
+ // delete experiments
+
+ ExperimentDeletionOptions expDeletionOpts = new ExperimentDeletionOptions();
+ expDeletionOpts.setReason("sync experiment deletions");
+ IDeletionId expDeletionId = v3Api.deleteExperiments(sessionToken, experimentPermIds, expDeletionOpts);
+
+ // delete projects
+ ProjectDeletionOptions prjDeletionOpts = new ProjectDeletionOptions();
+ prjDeletionOpts.setReason("Sync projects");
+ v3Api.deleteProjects(sessionToken, projectPermIds, prjDeletionOpts);
+
+ // delete materials
+ MaterialDeletionOptions matDeletionOptions = new MaterialDeletionOptions();
+ matDeletionOptions.setReason("sync materials");
+ v3Api.deleteMaterials(sessionToken, matPermIds, matDeletionOptions);
+
+ // confirm deletions
+ v3Api.confirmDeletions(sessionToken, Arrays.asList(expDeletionId, dsDeletionId, smpDeletionId));
+
+ for (PhysicalDataSet physicalDS : physicalDataSetsDelete)
+ {
+ operationLog.info("Is going to delete the location: " + physicalDS.getLocation());
+ File datasetDir =
+ getDirectoryProvider().getDataSetDirectory(physicalDS);
+ SegmentedStoreUtils.deleteDataSetInstantly(physicalDS.getCode(), datasetDir, new Log4jSimpleLogger(operationLog));
+ }
+ }
+
+ private void processExperiments(ResourceListParserData data,
+ AtomicEntityOperationDetailsBuilder builder)
+ {
+ // process experiments
+ Map<String, ExperimentWithConnections> experimentsToProcess = data.getExperimentsToProcess();
+ for (ExperimentWithConnections exp : experimentsToProcess.values())
+ {
+ NewExperiment newIncomingExp = exp.getExperiment();
+ if (exp.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ Experiment experiment = null;
+ try
+ {
+ experiment = service.tryGetExperimentByPermId(newIncomingExp.getPermID());
+ } catch (Exception e)
+ {
+ // TODO doing nothing because when the experiment with the perm id not found
+ // an exception will be thrown. Seems to be the same with entity kinds
+ }
+
+ if (experiment == null)
+ {
+ // ADD EXPERIMENT
+ builder.experiment(newIncomingExp);
+ }
+ else
+ {
+ // UPDATE EXPERIMENT
+ ExperimentUpdatesDTO expUpdate = createExperimentUpdateDTOs(newIncomingExp, experiment);
+ builder.experimentUpdate(expUpdate);
+ }
+ }
+ handleSampleConnections(data, exp, newIncomingExp);
+ }
+ }
+
+ private void handleSampleConnections(ResourceListParserData data, ExperimentWithConnections exp, NewExperiment newIncomingExp)
+ {
+ Map<String, SampleWithConnections> samplesToProcess = data.getSamplesToProcess();
+ Map<String, DataSetWithConnections> dataSetsToProcess = data.getDataSetsToProcess();
+ for (Connection conn : exp.getConnections())
+ {
+ if (samplesToProcess.containsKey(conn.getToPermId()))
+ {
+ SampleWithConnections sample = samplesToProcess.get(conn.getToPermId());
+ NewSample newSample = sample.getSample();
+ newSample.setExperimentIdentifier(newIncomingExp.getIdentifier());
+ }
+ if (dataSetsToProcess.containsKey(conn.getToPermId()))
+ {
+ NewExternalData externalData = dataSetsToProcess.get(conn.getToPermId()).getDataSet();
+ externalData.setExperimentIdentifierOrNull(ExperimentIdentifierFactory.parse(newIncomingExp.getIdentifier()));
+ }
+ }
+ }
+
+ private ExperimentUpdatesDTO createExperimentUpdateDTOs(NewExperiment newIncomingExp, Experiment experiment)
+ {
+ ExperimentUpdatesDTO expUpdate = new ExperimentUpdatesDTO();
+ expUpdate.setProjectIdentifier(ExperimentIdentifierFactory.parse(newIncomingExp.getIdentifier()));
+ expUpdate.setVersion(experiment.getVersion());
+ expUpdate.setProperties(Arrays.asList(newIncomingExp.getProperties()));
+ expUpdate.setExperimentId(TechId.create(experiment));
+ // TODO attachments
+ expUpdate.setAttachments(Collections.<NewAttachment> emptyList());
+ return expUpdate;
+ }
+
+ private void processMaterials(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder)
+ {
+ // process materials
+ Map<String, MaterialWithLastModificationDate> materialsToProcess = data.getMaterialsToProcess();
+ for (MaterialWithLastModificationDate newMaterialWithType : materialsToProcess.values())
+ {
+ NewMaterialWithType newIncomingMaterial = newMaterialWithType.getMaterial();
+ if (newMaterialWithType.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ Material material = service.tryGetMaterial(new MaterialIdentifier(newIncomingMaterial.getCode(), newIncomingMaterial.getType()));
+ if (material == null)
+ {
+ builder.material(newIncomingMaterial);
+ }
+ else
+ {
+ MaterialUpdateDTO update =
+ new MaterialUpdateDTO(TechId.create(material), Arrays.asList(newIncomingMaterial.getProperties()),
+ material.getModificationDate());
+ builder.materialUpdate(update);
+ }
+ }
+ }
+ }
+
+ private void processProjects(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder)
+ {
+ Map<String, ProjectWithConnections> projectsToProcess = data.getProjectsToProcess();
+ for (ProjectWithConnections prj : projectsToProcess.values())
+ {
+ NewProject incomingProject = prj.getProject();
+ if (prj.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ Project project = null;
+ try
+ {
+ project = service.tryGetProjectByPermId(incomingProject.getPermID());
+ } catch (Exception e)
+ {
+ // TODO doing nothing because when the project with the perm is not found
+ // an exception will be thrown. See bug report SSDM-4108
+ }
+
+ if (project == null)
+ {
+ // ADD PROJECT
+ builder.project(incomingProject);
+ }
+ else
+ {
+ // UPDATE PROJECT
+ builder.projectUpdate(createProjectUpdateDTO(incomingProject, project));
+ }
+ }
+ handleProjectConnections(data, prj);
+ }
+ }
+
+ private void handleProjectConnections(ResourceListParserData data, ProjectWithConnections prj)
+ {
+ Map<String, ExperimentWithConnections> experimentsToProcess = data.getExperimentsToProcess();
+ for (Connection conn : prj.getConnections())
+ {
+ String connectedExpPermId = conn.getToPermId();
+ // TODO we need to do the same check for samples to support project samples
+ if (experimentsToProcess.containsKey(connectedExpPermId))
+ {
+ // the project is connected to an experiment
+ ExperimentWithConnections exp = experimentsToProcess.get(connectedExpPermId);
+ NewExperiment newExp = exp.getExperiment();
+ // check if our local graph has the same connection
+ if (service.tryGetExperiment(ExperimentIdentifierFactory.parse(newExp.getIdentifier())) == null)
+ {
+ // add new edge
+ String oldIdentifier = newExp.getIdentifier();
+ int index = oldIdentifier.lastIndexOf('/');
+ String expCode = oldIdentifier.substring(index + 1);
+
+ newExp.setIdentifier(prj.getProject().getIdentifier() + "/" + expCode);
+ // add new experiment node
+ }
+ }
+ else
+ {
+ // TODO This means the XML contains the connection but not the connected entity.
+ // These sort of problems maybe recorded in a separate synchronization log?
+ // ???????????????
+ operationLog.info("Connected experiment with permid : " + connectedExpPermId + " is missing");
+ }
+ }
+ }
+
+ private ProjectUpdatesDTO createProjectUpdateDTO(NewProject incomingProject, Project project)
+ {
+ ProjectUpdatesDTO prjUpdate = new ProjectUpdatesDTO();
+ prjUpdate.setVersion(project.getVersion());
+ prjUpdate.setTechId(TechId.create(project));
+ prjUpdate.setDescription(incomingProject.getDescription());
+ // TODO attachments????
+ prjUpdate.setAttachments(Collections.<NewAttachment> emptyList());
+ ProjectIdentifier projectIdentifier = ProjectIdentifierFactory.parse(incomingProject.getIdentifier());
+ prjUpdate.setSpaceCode(projectIdentifier.getSpaceCode());
+ return prjUpdate;
+ }
+
+ private void processSamples(ResourceListParserData data, AtomicEntityOperationDetailsBuilder builder)
+ {
+ // process samples
+ Map<String, SampleWithConnections> samplesToProcess = data.getSamplesToProcess();
+ Map<SampleIdentifier, NewSample> samplesToUpdate = new HashMap<SampleIdentifier, NewSample>();
+ Set<String> sampleWithUpdatedParents = new HashSet<String>();
+ for (SampleWithConnections sample : samplesToProcess.values())
+ {
+ NewSample incomingSample = sample.getSample();
+ if (sample.getLastModificationDate().after(lastSyncTimestamp))
+ {
+ SampleIdentifier sampleIdentifier = SampleIdentifierFactory.parse(incomingSample);
+ Sample sampleWithExperiment = null;
+ try
+ {
+ sampleWithExperiment = service.tryGetSampleByPermId(incomingSample.getPermID());
+ } catch (Exception e)
+ {
+ // TODO doing nothing because when the sample with the perm is not found
+ // an exception will be thrown. See the same issue for projects
+ }
+ if (sampleWithExperiment == null)
+ {
+ // ADD SAMPLE
+ builder.sample(incomingSample);
+ }
+ else
+ {
+ // defer creation of sample update objects until all samples have been gone through;
+ samplesToUpdate.put(sampleIdentifier, incomingSample);
+ List<Sample> childSamples = getChildSamples(sampleWithExperiment);
+ for (Sample child : childSamples)
+ {
+ String childSampleIdentifier = child.getIdentifier();// edgeNodePair.getNode().getIdentifier();
+ SampleWithConnections childSampleWithConns = findChildInSamplesToProcess(childSampleIdentifier, samplesToProcess);
+ if (childSampleWithConns == null)
+ {
+ // TODO Handle sample delete
+ }
+ else
+ {
+ // the childSample will appear in the incoming samples list anyway
+ // but we want to make sure its parent modification is handled
+ NewSample childSample = childSampleWithConns.getSample();
+ sampleWithUpdatedParents.add(childSample.getIdentifier());
+ }
+ }
+ }
+ }
+ for (Connection conn : sample.getConnections())
+ {
+ if (conn.getType().equals("Component"))
+ {
+ NewSample containedSample = samplesToProcess.get(conn.getToPermId()).getSample();
+ containedSample.setContainerIdentifier(incomingSample.getIdentifier());
+ }
+ else if (conn.getType().equals("Child"))
+ {
+ NewSample childSample = samplesToProcess.get(conn.getToPermId()).getSample();
+ String[] parents = childSample.getParentsOrNull();
+ List<String> parentIds = null;
+ if (parents == null)
+ {
+ parentIds = new ArrayList<String>();
+ }
+ else
+ {
+ parentIds = new ArrayList<String>(Arrays.asList(parents));
+ }
+ parentIds.add(incomingSample.getIdentifier());
+ childSample.setParentsOrNull(parentIds.toArray(new String[parentIds.size()]));
+ }
+ // TODO how about Connection Type
+ // else if (conn.getType().equals("Connection")) // TODO not sure if this guarantees that we have a dataset in the toPermId
+ // {
+ // NewExternalData externalData = dataSetsToCreate.get(conn.getToPermId()).getDataSet();
+ // externalData.setSampleIdentifierOrNull(new SampleIdentifier(newSmp.getIdentifier()));
+ // }
+ }
+ }
+
+ // create sample update dtos for the samples that need to be updated
+ for (SampleIdentifier sampleIdentifier : samplesToUpdate.keySet())
+ {
+ NewSample newSmp = samplesToUpdate.get(sampleIdentifier);
+ Sample sampleWithExperiment = service.tryGetSampleByPermId(newSmp.getPermID());
+
+ TechId sampleId = TechId.create(sampleWithExperiment);
+ String expIdentifier = newSmp
+ .getExperimentIdentifier();
+ String[] modifiedParentIds = newSmp.getParentsOrNull();
+ if (modifiedParentIds == null)
+ {
+ if (sampleWithUpdatedParents.contains(newSmp.getIdentifier()))
+ {
+ modifiedParentIds = new String[0];
+ }
+ }
+
+ SampleUpdatesDTO updates =
+ new SampleUpdatesDTO(sampleId, Arrays.asList(newSmp.getProperties()), (expIdentifier == null) ? null
+ : ExperimentIdentifierFactory.parse(expIdentifier),
+ Collections.<NewAttachment> emptyList(), sampleWithExperiment.getVersion(),
+ sampleIdentifier, newSmp.getContainerIdentifier() == null ? null : newSmp.getContainerIdentifier(),
+ modifiedParentIds);
+ builder.sampleUpdate(updates);
+ }
+ }
+
+ private List<Sample> getChildSamples(Sample sampleWithExperiment)
+ {
+ ListSampleCriteria criteria = ListSampleCriteria.createForParent(new TechId(sampleWithExperiment.getId()));
+ return service.listSamples(criteria);
+ }
+
+ private SampleWithConnections findChildInSamplesToProcess(String childSampleIdentifier, Map<String, SampleWithConnections> samplesToProcess)
+ {
+ for (SampleWithConnections sample : samplesToProcess.values())
+ {
+ if (sample.getSample().getIdentifier().equals(childSampleIdentifier))
+ {
+ return sample;
+ }
+ }
+ return null;
+ }
+
+ private final class DataSetRegistrationTaskExecutor implements ITaskExecutor<DataSetWithConnections>
+ {
+
+ private List<String> dataSetCodes;
+
+ public DataSetRegistrationTaskExecutor(List<String> dataSetCodes)
+ {
+ this.dataSetCodes = dataSetCodes;
+ }
+
+ @Override
+ public Status execute(DataSetWithConnections dataSet)
+ {
+ System.out.println("start " + dataSet.getDataSet().getCode());
+
+ Properties props = setProperties();
+
+ DataSetRegistrationIngestionService ingestionService =
+ new DataSetRegistrationIngestionService(props, storeRoot, dataSetCodes, dataSet.getDataSet());
+ ingestionService.createAggregationReport(new HashMap<String, Object>(), context);
+ System.out.println("finished " + dataSet.getDataSet().getCode());
+ dataSetCodes.add(dataSet.getDataSet().getCode());
+ return Status.OK;
+ }
+
+ private Properties setProperties()
+ {
+ Properties props = new Properties();
+ props.setProperty("user", EntitySynchronizer.this.config.getUser());
+ props.setProperty("pass", EntitySynchronizer.this.config.getPass());
+ props.setProperty("as-url", EntitySynchronizer.this.config.getDataSourceOpenbisURL());
+ props.setProperty("dss-url", EntitySynchronizer.this.config.getDataSourceDSSURL());
+ props.setProperty("harvester-temp-dir", EntitySynchronizer.this.config.getHarvesterTempDir());
+ return props;
+ }
+ }
+
+ private boolean deepCompareDataSets(String dataSetCode)
+ throws NoSuchAlgorithmException, UnsupportedEncodingException
+ {
+ // get the file nodes in the incoming DS by querying the data source openbis
+ String asUrl = config.getDataSourceOpenbisURL();
+ String dssUrl = config.getDataSourceDSSURL();
+
+ SslCertificateHelper.trustAnyCertificate(dssUrl);
+ SslCertificateHelper.trustAnyCertificate(asUrl);
+
+ IDataStoreServerApi dss =
+ HttpInvokerUtils.createStreamSupportingServiceStub(IDataStoreServerApi.class,
+ dssUrl + IDataStoreServerApi.SERVICE_URL, 10000);
+ IApplicationServerApi as = HttpInvokerUtils
+ .createServiceStub(IApplicationServerApi.class, asUrl
+ + IApplicationServerApi.SERVICE_URL, 10000);
+ String sessionToken = as.login(config.getUser(), config.getPass());
+
+ DataSetFileSearchCriteria criteria = new DataSetFileSearchCriteria();
+ criteria.withDataSet().withCode().thatEquals(dataSetCode);
+ SearchResult<DataSetFile> result = dss.searchFiles(sessionToken, criteria, new DataSetFileFetchOptions());
+
+ IDataStoreServerApi dssharvester = (IDataStoreServerApi) ServiceProvider.getDssServiceV3().getService();
+ SearchResult<DataSetFile> resultHarvester =
+ dssharvester.searchFiles(ServiceProvider.getOpenBISService().getSessionToken(), criteria, new DataSetFileFetchOptions());
+ if (result.getTotalCount() != resultHarvester.getTotalCount())
+ {
+ return false;
+ }
+
+ List<DataSetFile> dsNodes = result.getObjects();
+ List<DataSetFile> harvesterNodes = resultHarvester.getObjects();
+ sortFileNodes(dsNodes);
+ sortFileNodes(harvesterNodes);
+ return calculateHash(dsNodes).equals(calculateHash(harvesterNodes));
+ }
+
+ private void sortFileNodes(List<DataSetFile> nodes)
+ {
+ Collections.sort(nodes, new Comparator<DataSetFile>()
+ {
+
+ @Override
+ public int compare(DataSetFile dsFile1, DataSetFile dsFile2)
+ {
+ return dsFile1.getPath().compareTo(dsFile2.getPath());
+ }
+ });
+ }
+
+ private String calculateHash(List<DataSetFile> nodes) throws NoSuchAlgorithmException, UnsupportedEncodingException
+ {
+ StringBuffer sb = new StringBuffer();
+ for (DataSetFile dataSetFile : nodes)
+ {
+ sb.append(dataSetFile.getPath());
+ sb.append(dataSetFile.getChecksumCRC32());
+ sb.append(dataSetFile.getFileLength());
+ }
+ byte[] digest = MessageDigest.getInstance("MD5").digest(new String(sb).getBytes("UTF-8"));
+ return new String(Hex.encodeHex(digest));
+ }
+
+ private DataSetBatchUpdatesDTO createDataSetBatchUpdateDTO(NewExternalData childDS)
+ {
+ AbstractExternalData dsInHarvester = service.tryGetDataSet(childDS.getCode());
+ ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetUpdatable updateUpdatable = new
+ ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetUpdatable(dsInHarvester, service);
+ DataSetBatchUpdatesDTO dsBatchUpdatesDTO = ConversionUtils.convertToDataSetBatchUpdatesDTO(updateUpdatable);
+ //
+ dsBatchUpdatesDTO.setDatasetId(TechId.create(dsInHarvester));
+ List<IEntityProperty> entityProperties = new ArrayList<IEntityProperty>();
+ for (NewProperty prop : childDS.getDataSetProperties())
+ {
+ String propertyCode = prop.getPropertyCode();
+ String value = prop.getValue();
+ entityProperties.add(new PropertyBuilder(propertyCode).value(value).getProperty());
+ }
+ dsBatchUpdatesDTO.setProperties(entityProperties);
+ return dsBatchUpdatesDTO;
+ }
+
+ private IDataSetDirectoryProvider getDirectoryProvider()
+ {
+ return new DataSetDirectoryProvider(getConfigProvider().getStoreRoot(), getShareIdManager());
+ }
+
+ private IConfigProvider getConfigProvider()
+ {
+ return ServiceProvider.getConfigProvider();
+ }
+
+ private IShareIdManager getShareIdManager()
+ {
+ return ServiceProvider.getShareIdManager();
+ }
+
+}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParser.java
similarity index 94%
rename from datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java
rename to datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParser.java
index 2f11803a9bbebbca6dfcd989dedd592fdd9f4265..332e90a5e3bd9b1d1fb5467016ebb301149d1430 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParser.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParser.java
@@ -13,7 +13,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
+package ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer;
import java.text.DateFormat;
import java.text.ParseException;
@@ -42,12 +42,12 @@ import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.DataSetKind;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.Connection;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.DataSetWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ExperimentWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.MaterialWithLastModificationDate;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.ProjectWithConnections;
-import ch.ethz.sis.openbis.generic.server.dss.plugins.ResourceListParserData.SampleWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.Connection;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.DataSetWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.ExperimentWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.MaterialWithLastModificationDate;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.ProjectWithConnections;
+import ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer.ResourceListParserData.SampleWithConnections;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
@@ -292,7 +292,7 @@ public class ResourceListParser
}
}
DataSetWithConnections newDsWithConns = data.new DataSetWithConnections(ds, lastModificationDate);
- data.datasetsToProcess.put(permId, newDsWithConns);
+ data.getDataSetsToProcess().put(permId, newDsWithConns);
newDsWithConns.setConnections(parseConnections(xpath, xdNode));
ds.setDataSetProperties(parseDataSetProperties(xpath, xdNode));
}
@@ -325,7 +325,7 @@ public class ResourceListParser
newProject.setPermID(permId);
ProjectWithConnections newPrjWithConns =
data.new ProjectWithConnections(newProject, lastModificationDate);
- data.projectsToProcess.put(permId, newPrjWithConns);
+ data.getProjectsToProcess().put(permId, newPrjWithConns);
newPrjWithConns.setConnections(parseConnections(xpath, xdNode));
}
@@ -336,7 +336,7 @@ public class ResourceListParser
NewMaterialWithType newMaterial = new NewMaterialWithType(code, type);
MaterialWithLastModificationDate materialWithLastModDate =
data.new MaterialWithLastModificationDate(newMaterial, lastModificationDate);
- data.materialsToProcess.put(code, materialWithLastModDate);
+ data.getMaterialsToProcess().put(code, materialWithLastModDate);
newMaterial.setProperties(parseProperties(xpath, xdNode));
}
@@ -423,7 +423,7 @@ public class ResourceListParser
NewExperiment newExp = new NewExperiment("/" + spaceMappings.get(space) + "/" + project + "/" + code, type);
newExp.setPermID(permId);
ExperimentWithConnections newExpWithConns = data.new ExperimentWithConnections(newExp, lastModificationDate);
- data.experimentsToProcess.put(permId, newExpWithConns);
+ data.getExperimentsToProcess().put(permId, newExpWithConns);
newExpWithConns.setConnections(parseConnections(xpath, xdNode));
newExp.setProperties(parseProperties(xpath, xdNode));
}
@@ -442,7 +442,7 @@ public class ResourceListParser
new ArrayList<NewAttachment>());
newSample.setPermID(permId);
SampleWithConnections newSampleWithConns = data.new SampleWithConnections(newSample, lastModificationDate);
- data.samplesToProcess.put(permId, newSampleWithConns);
+ data.getSamplesToProcess().put(permId, newSampleWithConns);
newSampleWithConns.setConnections(parseConnections(xpath, xdNode));
newSample.setProperties(parseProperties(xpath, xdNode));
}
diff --git a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParserData.java
similarity index 82%
rename from datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java
rename to datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParserData.java
index c47b8e7672eb692d0b755b21ebfd935827feb7ee..59f5e3f8905ed41e082f662266f24161ed6fffd5 100644
--- a/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/ResourceListParserData.java
+++ b/datastore_server/source/java/ch/ethz/sis/openbis/generic/server/dss/plugins/harvester/synchronizer/ResourceListParserData.java
@@ -13,7 +13,7 @@
* See the License for the specific language governing permissions and
* limitations under the License.
*/
-package ch.ethz.sis.openbis.generic.server.dss.plugins;
+package ch.ethz.sis.openbis.generic.server.dss.plugins.harvester.synchronizer;
import java.io.Serializable;
import java.util.ArrayList;
@@ -36,22 +36,47 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewLinkDataSet;
*/
public class ResourceListParserData
{
- public Map<String, ProjectWithConnections> projectsToProcess = new HashMap<String, ResourceListParserData.ProjectWithConnections>();
+ private Map<String, ProjectWithConnections> projectsToProcess = new HashMap<String, ResourceListParserData.ProjectWithConnections>();
- public Map<String, ExperimentWithConnections> experimentsToProcess = new HashMap<String, ResourceListParserData.ExperimentWithConnections>();
+ private Map<String, ExperimentWithConnections> experimentsToProcess = new HashMap<String, ResourceListParserData.ExperimentWithConnections>();
- public Map<String, SampleWithConnections> samplesToProcess = new HashMap<String, ResourceListParserData.SampleWithConnections>();
+ private Map<String, SampleWithConnections> samplesToProcess = new HashMap<String, ResourceListParserData.SampleWithConnections>();
- public Map<String, DataSetWithConnections> datasetsToProcess = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
+ private Map<String, DataSetWithConnections> dataSetsToProcess = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- public Map<String, MaterialWithLastModificationDate> materialsToProcess = new HashMap<String, MaterialWithLastModificationDate>();
+ private Map<String, MaterialWithLastModificationDate> materialsToProcess = new HashMap<String, MaterialWithLastModificationDate>();
+
+ public Map<String, ProjectWithConnections> getProjectsToProcess()
+ {
+ return projectsToProcess;
+ }
+
+ public Map<String, ExperimentWithConnections> getExperimentsToProcess()
+ {
+ return experimentsToProcess;
+ }
+
+ public Map<String, SampleWithConnections> getSamplesToProcess()
+ {
+ return samplesToProcess;
+ }
+
+ public Map<String, DataSetWithConnections> getDataSetsToProcess()
+ {
+ return dataSetsToProcess;
+ }
+
+ public Map<String, MaterialWithLastModificationDate> getMaterialsToProcess()
+ {
+ return materialsToProcess;
+ }
public Map<String, DataSetWithConnections> filterPhysicalDataSetsByLastModificationDate(Date lastSyncDate)
{
Map<String, DataSetWithConnections> dsMap = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- for (String permId : datasetsToProcess.keySet())
+ for (String permId : dataSetsToProcess.keySet())
{
- DataSetWithConnections ds = datasetsToProcess.get(permId);
+ DataSetWithConnections ds = dataSetsToProcess.get(permId);
if (ds.getKind() == DataSetKind.PHYSICAL && ds.lastModificationDate.after(lastSyncDate))
{
dsMap.put(permId, ds);
@@ -64,9 +89,9 @@ public class ResourceListParserData
{
// List<NewDataSetWithConnections> dsList = new ArrayList<ResourceListParserData.NewDataSetWithConnections>();
Map<String, DataSetWithConnections> dsMap = new HashMap<String, ResourceListParserData.DataSetWithConnections>();
- for (String permId : datasetsToProcess.keySet())
+ for (String permId : dataSetsToProcess.keySet())
{
- DataSetWithConnections ds = datasetsToProcess.get(permId);
+ DataSetWithConnections ds = dataSetsToProcess.get(permId);
if (ds.getKind() == DataSetKind.CONTAINER)
{
dsMap.put(permId, ds);