diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ChainedDataSetMigrationTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ChainedDataSetMigrationTask.java
deleted file mode 100644
index 203d4b48bfa43e9e37d7c0c480a655abddd95bee..0000000000000000000000000000000000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/ChainedDataSetMigrationTask.java
+++ /dev/null
@@ -1,190 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * 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.systemsx.cisd.etlserver.plugins;
-
-import java.io.File;
-import java.io.FileFilter;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Properties;
-import java.util.regex.Pattern;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.maintenance.IMaintenanceTask;
-import ch.systemsx.cisd.common.utilities.ClassUtils;
-import ch.systemsx.cisd.common.utilities.PropertyParametersUtil;
-import ch.systemsx.cisd.common.utilities.PropertyUtils;
-import ch.systemsx.cisd.common.utilities.PropertyParametersUtil.SectionProperties;
-
-/**
- * Maintenance task migrating all data sets of a store by a chain of {@link IMigrator} instances.
- *
- * @author Franz-Josef Elmer
- */
-public class ChainedDataSetMigrationTask implements IMaintenanceTask
-{
- public static final String MIGRATORS_PROPERTY = "migrators";
-
- public static final String STORE_ROOT_PROPERTY = "storeRoot";
-
- private static final Pattern UUID_PATTERN =
- Pattern.compile("[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}");
-
- private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, ChainedDataSetMigrationTask.class);
-
- private File storeRoot;
-
- private List<IMigrator> migrators;
-
- public void setUp(String pluginName, Properties properties)
- {
- String storeRootPath = PropertyUtils.getMandatoryProperty(properties, STORE_ROOT_PROPERTY);
- storeRoot = new File(storeRootPath);
- if (storeRoot.isDirectory() == false)
- {
- throw new EnvironmentFailureException(storeRoot
- + " does not exist or is not a directory.");
- }
- SectionProperties[] sectionProperties =
- PropertyParametersUtil.extractSectionProperties(properties, MIGRATORS_PROPERTY,
- false);
- migrators = new ArrayList<IMigrator>();
- for (SectionProperties props : sectionProperties)
- {
- Properties migratorProperties = props.getProperties();
- IMigrator migrator =
- ClassUtils.create(IMigrator.class, PropertyUtils.getMandatoryProperty(
- migratorProperties, "class"), migratorProperties);
- migrators.add(migrator);
- }
- if (operationLog.isInfoEnabled())
- {
- StringBuilder builder = new StringBuilder();
- for (IMigrator migrator : migrators)
- {
- if (builder.length() > 0)
- {
- builder.append(", ");
- }
- builder.append(migrator.getDescription());
- }
- operationLog.info("Chain of migrators have been set up: " + builder);
- }
- }
-
- public void execute()
- {
- File dbInstanceDir = tryGetDatabaseInstanceDir(storeRoot);
- if (dbInstanceDir == null)
- {
- operationLog.warn("Store is empty, there is nothing to migrate");
- return;
- }
- for (IMigrator migrator : migrators)
- {
- boolean success = migrate(dbInstanceDir, migrator);
- if (success == false)
- {
- operationLog.error("Migration stopped at: " + migrator.getDescription());
- break;
- }
- }
- }
-
- /**
- * For a given datastore store directory returns the instance directory inside or null if it
- * does not exist.
- */
- public static File tryGetDatabaseInstanceDir(File storeRoot)
- {
- File[] files = storeRoot.listFiles(new FileFilter()
- {
- public boolean accept(File pathname)
- {
- String name = pathname.getName().toLowerCase();
- return pathname.isDirectory() && UUID_PATTERN.matcher(name).matches();
- }
- });
- if (files == null || files.length == 0)
- {
- return null;
- }
- if (files.length > 1)
- {
- throw new EnvironmentFailureException("At most one folder with UUID expected in "
- + storeRoot);
- }
- File dbInstanceDir = files[0];
- return dbInstanceDir;
- }
-
- private boolean migrate(File dbInstanceDir, IMigrator migrator)
- {
- List<File> migratedDataSets = new ArrayList<File>();
- List<File> failedDataSets = new ArrayList<File>();
- for (File l1 : dbInstanceDir.listFiles())
- {
- // The OS may put files into these folders (e.g., .DS_Store)
- if (false == l1.isDirectory())
- {
- continue;
- }
- for (File l2 : l1.listFiles())
- {
- if (false == l2.isDirectory())
- {
- continue;
- }
- for (File l3 : l2.listFiles())
- {
- if (false == l3.isDirectory())
- {
- continue;
- }
- for (File dataset : l3.listFiles())
- {
- boolean success = migrator.migrate(dataset);
- if (success)
- {
- migratedDataSets.add(dataset);
- } else
- {
- failedDataSets.add(dataset);
- }
- }
- }
- }
- }
- if (failedDataSets.isEmpty())
- {
- operationLog.info(migratedDataSets.size() + " data sets have been migrated with '"
- + migrator.getDescription() + "'.");
- } else
- {
- operationLog.error("Migration with '" + migrator.getDescription()
- + "' failed for the following " + failedDataSets.size() + " data sets: "
- + failedDataSets);
- }
- return failedDataSets.isEmpty();
- }
-
-}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/IMigrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/IMigrator.java
deleted file mode 100644
index 4d0f177e8895765479ff2590266d653482dd5584..0000000000000000000000000000000000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/IMigrator.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * 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.systemsx.cisd.etlserver.plugins;
-
-import java.io.File;
-import java.util.Properties;
-
-/**
- * Interface of classes which are able to migrate a single data set. Classes implementing this
- * interface should have a public constructor with a single argument of type {@link Properties}.
- *
- * @author Tomasz Pylak
- * @author Franz-Josef Elmer
- */
-public interface IMigrator
-{
- /**
- * Migrates specified dataset.
- *
- * @return <code>true</code> if migration was successful.
- */
- boolean migrate(File dataset);
-
- /** user-friendly description of the migrator */
- String getDescription();
-
- /**
- * Free any held resources. Called once when migration is finished.
- */
- void close();
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
deleted file mode 100644
index 466577d6179dcf898840e3173fdecf285a0bcebc..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/AbstractFeatureVectorMigrator.java
+++ /dev/null
@@ -1,274 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * 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.systemsx.cisd.openbis.dss.etl.featurevector;
-
-import java.io.File;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.QueryTool;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.etlserver.plugins.IMigrator;
-import ch.systemsx.cisd.openbis.dss.etl.HCSContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-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;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
-
-/**
- * Imports individual data sets into the imaging db.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public abstract class AbstractFeatureVectorMigrator implements IMigrator
-{
- protected final IImagingQueryDAO dao;
-
- protected final IEncapsulatedOpenBISService openBisService;
-
- protected final List<SimpleDataSetInformationDTO> knownDataSets;
-
- protected final HashMap<String, SimpleDataSetInformationDTO> knownDataSetsByCode;
-
- public AbstractFeatureVectorMigrator(Properties properties)
- {
- DataSource dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
- dao = QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
- openBisService = ServiceProvider.getOpenBISService();
- knownDataSets = openBisService.listDataSets();
- knownDataSetsByCode =
- new HashMap<String, SimpleDataSetInformationDTO>(knownDataSets.size());
-
- initializeDataSetsByCode();
- }
-
- /**
- * Create a map of associations from code to data set info. Assumes knownDataSets and been
- * initialized.
- */
- private void initializeDataSetsByCode()
- {
- for (SimpleDataSetInformationDTO dataSetInfo : knownDataSets)
- {
- knownDataSetsByCode.put(dataSetInfo.getDataSetCode(), dataSetInfo);
- }
- }
-
- public String getDescription()
- {
- return "uploading feature vectors to the imaging database";
- }
-
- public boolean migrate(File dataset)
- {
- AbstractMigrationDecision decision = createMigrationDecision(dataset);
- decision.process();
- if (false == decision.shouldMigrate)
- {
- // Vacuously true
- return true;
- }
-
- ImgDatasetDTO imgDataset = dao.tryGetDatasetByPermId(decision.dataSetInfo.getDataSetCode());
- if (null != imgDataset)
- {
- // Has already been imported into the db
- return true;
- }
-
- AbstractImageDbImporter importer;
- importer =
- createImporter(createScreeningDatasetInfo(decision.getDataSetInfo()),
- decision.fileToMigrate);
-
- importer.doImport();
-
- return importer.isSuccessful;
- }
-
- protected abstract AbstractMigrationDecision createMigrationDecision(File dataset);
-
- protected abstract AbstractImageDbImporter createImporter(HCSContainerDatasetInfo dataSetInfo,
- File fileToMigrate);
-
- private HCSContainerDatasetInfo createScreeningDatasetInfo(
- SimpleDataSetInformationDTO dataSetInfo)
- {
- Sample sample = findSampleCodeForDataSet(dataSetInfo);
- assert sample != null : "no sample connected to a dataset";
-
- Experiment experiment = sample.getExperiment();
- HCSContainerDatasetInfo info = new HCSContainerDatasetInfo();
- info.setExperimentPermId(experiment.getPermId());
- info.setContainerPermId(sample.getPermId());
- info.setDatasetPermId(dataSetInfo.getDataSetCode());
-
- return info;
- }
-
- private Sample findSampleCodeForDataSet(SimpleDataSetInformationDTO dataSetInfo)
- {
- String sampleCodeOrNull = dataSetInfo.getSampleCode();
- SampleIdentifier sampleId = null;
- if (null == sampleCodeOrNull)
- {
- // check the parent data sets for a sample
- Collection<String> parentDataSetCodes = dataSetInfo.getParentDataSetCodes();
- for (String dataSetCode : parentDataSetCodes)
- {
- ExternalData externalData = openBisService.tryGetDataSetForServer(dataSetCode);
- if (externalData == null)
- {
- throw new EnvironmentFailureException(
- "Cannot find a parent dataset in openBIS: " + dataSetCode);
- }
- if (externalData.getSample() != null)
- {
- sampleId = SampleIdentifierFactory.parse(externalData.getSampleIdentifier());
- break;
- }
- }
- } else
- {
- sampleId =
- new SampleIdentifier(new SpaceIdentifier(dataSetInfo.getDatabaseInstanceCode(),
- dataSetInfo.getGroupCode()), dataSetInfo.getSampleCode());
- }
-
- return openBisService.tryGetSampleWithExperiment(sampleId);
- }
-
- public void close()
- {
- // close the dao
- dao.close();
- }
-
- /**
- * Helper class for figuring out what to do with files
- *
- * @author Chandrasekhar Ramakrishnan
- */
- protected abstract static class AbstractMigrationDecision
- {
- protected final File dataset;
-
- private final HashMap<String, SimpleDataSetInformationDTO> knownDataSetsByCode;
-
- private SimpleDataSetInformationDTO dataSetInfo;
-
- private boolean shouldMigrate = false;
-
- private File fileToMigrate = null;
-
- public AbstractMigrationDecision(File dataset,
- HashMap<String, SimpleDataSetInformationDTO> knownDataSetsByCode)
- {
- this.dataset = dataset;
- this.knownDataSetsByCode = knownDataSetsByCode;
- }
-
- protected void setDataSetInfo(SimpleDataSetInformationDTO dataSetInfo)
- {
- this.dataSetInfo = dataSetInfo;
- }
-
- public SimpleDataSetInformationDTO getDataSetInfo()
- {
- return dataSetInfo;
- }
-
- // Figure out what to do with this file
- public void process()
- {
- setDataSetInfo(tryDataSetInformation());
- if (null == getDataSetInfo())
- {
- shouldMigrate = false;
- return;
- }
-
- // Only import this data set if it is of an analysis type
- if (false == getDataSetInfo().getDataSetType().matches(
- ScreeningConstants.HCS_IMAGE_ANALYSIS_DATASET_TYPE_PATTERN))
- {
- shouldMigrate = false;
- return;
- }
-
- // Figure out which file we need to migrate
- fileToMigrate = tryFileToMigrate();
-
- if (null == fileToMigrate)
- {
- shouldMigrate = false;
- return;
- }
-
- shouldMigrate = true;
- return;
- }
-
- protected abstract File tryFileToMigrate();
-
- private SimpleDataSetInformationDTO tryDataSetInformation()
- {
- String dataSetCode = dataset.getName();
- SimpleDataSetInformationDTO dsInfo = knownDataSetsByCode.get(dataSetCode);
- return dsInfo;
- }
- }
-
- /**
- * Helper class for importing data into the image db.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- protected abstract static class AbstractImageDbImporter
- {
- protected final IImagingQueryDAO dao;
-
- protected final HCSContainerDatasetInfo screeningDataSetInfo;
-
- protected final File fileToMigrate;
-
- protected boolean isSuccessful = false;
-
- protected AbstractImageDbImporter(IImagingQueryDAO dao,
- HCSContainerDatasetInfo screeningDataSetInfo, File fileToMigrate)
- {
- this.dao = dao;
- this.screeningDataSetInfo = screeningDataSetInfo;
- this.fileToMigrate = fileToMigrate;
- }
-
- public abstract void doImport();
- }
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
deleted file mode 100644
index b2497efa30d9829c6cd8e22c235aa4f789a84e8b..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/featurevector/CsvFeatureVectorMigrator.java
+++ /dev/null
@@ -1,165 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * 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.systemsx.cisd.openbis.dss.etl.featurevector;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
-import ch.systemsx.cisd.openbis.dss.etl.HCSContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser.CsvFeatureVectorParserConfiguration;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CsvFileReaderHelper;
-import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetFileLines;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-public class CsvFeatureVectorMigrator extends AbstractFeatureVectorMigrator
-{
- protected final FeatureVectorStorageProcessorConfiguration configuration;
-
- protected final CsvFeatureVectorParserConfiguration convertorConfig;
-
- /**
- * @param properties
- */
- public CsvFeatureVectorMigrator(Properties properties)
- {
- super(properties);
-
- this.configuration = new FeatureVectorStorageProcessorConfiguration(properties);
- convertorConfig = new CsvFeatureVectorParserConfiguration(configuration);
- }
-
- @Override
- protected AbstractImageDbImporter createImporter(HCSContainerDatasetInfo dataSetInfo,
- File fileToMigrate)
- {
- AbstractImageDbImporter importer;
-
- importer = new ImporterCsv(dao, dataSetInfo, fileToMigrate, configuration, convertorConfig);
-
- return importer;
- }
-
- @Override
- protected AbstractMigrationDecision createMigrationDecision(File dataset)
- {
- AbstractMigrationDecision decision = new MigrationDecision(dataset, knownDataSetsByCode);
- return decision;
- }
-
- /**
- * Helper class for deciding if a file needs to be migrated.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static class MigrationDecision extends AbstractMigrationDecision
- {
-
- /**
- * @param dataset
- * @param knownDataSetsByCode
- */
- public MigrationDecision(File dataset,
- HashMap<String, SimpleDataSetInformationDTO> knownDataSetsByCode)
- {
- super(dataset, knownDataSetsByCode);
- }
-
- @Override
- protected File tryFileToMigrate()
- {
- File originalDataset = DefaultStorageProcessor.getOriginalDirectory(dataset);
- File[] files = originalDataset.listFiles();
-
- if (files.length == 1)
- {
- File file = files[0];
- if (file.isDirectory())
- {
- return null;
- }
- return file;
- }
- return null;
- }
-
- }
-
- /**
- * Helper class for importing CSV feature vector files
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static class ImporterCsv extends AbstractImageDbImporter
- {
- private final FeatureVectorStorageProcessorConfiguration configuration;
-
- private final CsvFeatureVectorParserConfiguration convertorConfig;
-
- protected ImporterCsv(IImagingQueryDAO dao, HCSContainerDatasetInfo screeningDataSetInfo,
- File fileToMigrate, FeatureVectorStorageProcessorConfiguration configuration,
- CsvFeatureVectorParserConfiguration convertorConfig)
- {
- super(dao, screeningDataSetInfo, fileToMigrate);
- this.configuration = configuration;
- this.convertorConfig = convertorConfig;
- }
-
- @Override
- public void doImport()
- {
- DatasetFileLines fileLines;
- try
- {
- fileLines = getDatasetFileLines(fileToMigrate);
- CsvToCanonicalFeatureVector convertor =
- new CsvToCanonicalFeatureVector(fileLines, convertorConfig,
- screeningDataSetInfo.getContainerRows(),
- screeningDataSetInfo.getContainerColumns());
- List<CanonicalFeatureVector> fvecs = convertor.convert();
-
- FeatureVectorUploader uploader =
- new FeatureVectorUploader(dao, screeningDataSetInfo);
- uploader.uploadFeatureVectors(fvecs);
- dao.commit();
- isSuccessful = true;
- } catch (IOException ex)
- {
- throw new IOExceptionUnchecked(ex);
- }
-
- }
-
- /**
- * Return the tabular data as a DatasetFileLines.
- */
- private DatasetFileLines getDatasetFileLines(File file) throws IOException
- {
- return CsvFileReaderHelper.getDatasetFileLines(file, configuration);
- }
-
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java
deleted file mode 100644
index 4aa15db2ba049bc2848029dbcd7fb77abbd8aaaa..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/genedata/GenedataFeatureVectorMigrator.java
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * 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.systemsx.cisd.openbis.dss.etl.genedata;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
-import ch.systemsx.cisd.openbis.dss.etl.HCSContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.AbstractFeatureVectorMigrator;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.CanonicalFeatureVector;
-import ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorUploader;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SimpleDataSetInformationDTO;
-
-/**
- * Imports Genedata feature vectors into the database.
- *
- * @author Chandrasekhar Ramakrishnan
- */
-public class GenedataFeatureVectorMigrator extends AbstractFeatureVectorMigrator
-{
-
- private static final String GENEDATA_FEATURES_EXTENSION = ".stat";
-
- /**
- * @param properties
- */
- public GenedataFeatureVectorMigrator(Properties properties)
- {
- super(properties);
- }
-
- @Override
- protected AbstractImageDbImporter createImporter(HCSContainerDatasetInfo dataSetInfo,
- File fileToMigrate)
- {
- AbstractImageDbImporter importer;
- importer = new ImporterGenedata(dao, dataSetInfo, fileToMigrate);
-
- return importer;
- }
-
- @Override
- protected AbstractMigrationDecision createMigrationDecision(File dataset)
- {
- AbstractMigrationDecision decision = new MigrationDecision(dataset, knownDataSetsByCode);
- return decision;
- }
-
- /**
- * Helper class for deciding if a file needs to be migrated.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static class MigrationDecision extends AbstractMigrationDecision
- {
- /**
- * @param dataset
- * @param knownDataSetsByCode
- */
- public MigrationDecision(File dataset,
- HashMap<String, SimpleDataSetInformationDTO> knownDataSetsByCode)
- {
- super(dataset, knownDataSetsByCode);
- }
-
- @Override
- protected File tryFileToMigrate()
- {
- File originalDataset = DefaultStorageProcessor.getOriginalDirectory(dataset);
- File[] files = originalDataset.listFiles();
-
- for (File file : files)
- {
- if (file.getName().endsWith(GENEDATA_FEATURES_EXTENSION))
- {
- return file;
- }
- }
-
- return null;
- }
- }
-
- /**
- * Helper class for importing genedata feature vecotr files.
- *
- * @author Chandrasekhar Ramakrishnan
- */
- private static class ImporterGenedata extends AbstractImageDbImporter
- {
-
- /**
- * @param fileToMigrate
- */
- private ImporterGenedata(IImagingQueryDAO dao,
- HCSContainerDatasetInfo screeningDataSetInfo, File fileToMigrate)
- {
- super(dao, screeningDataSetInfo, fileToMigrate);
- }
-
- @Override
- public void doImport()
- {
- List<String> lines = FileUtilities.loadToStringList(fileToMigrate);
- GenedataFormatToCanonicalFeatureVector convertor =
- new GenedataFormatToCanonicalFeatureVector(lines,
- FeatureStorageProcessor.LAYER_PREFIX);
- ArrayList<CanonicalFeatureVector> fvecs = convertor.convert();
-
- FeatureVectorUploader uploader = new FeatureVectorUploader(dao, screeningDataSetInfo);
- uploader.uploadFeatureVectors(fvecs);
- dao.commit();
- isSuccessful = true;
- }
- }
-
-}