diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/AbstractBDSMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/AbstractBDSMigrator.java
deleted file mode 100644
index 663751aed99ea3f2f7d138df6d0b09f3e6a2fd51..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/AbstractBDSMigrator.java
+++ /dev/null
@@ -1,69 +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.bdsmigration;
-
-import java.io.File;
-
-import ch.systemsx.cisd.etlserver.plugins.IMigrator;
-
-/**
- * @author Franz-Josef Elmer
- */
-abstract class AbstractBDSMigrator implements IMigrator
-{
- public boolean migrate(File dataset)
- {
- if (isBDS(dataset))
- {
- return doMigration(dataset);
- }
- return true;
- }
-
- protected abstract boolean doMigration(File dataset);
-
- private static boolean isBDS(File dataset)
- {
- File[] files = dataset.listFiles();
- return containsDir(files, BDSMigrationUtils.VERSION_DIR)
- && containsDir(files, BDSMigrationUtils.DATA_DIR)
- && containsDir(files, BDSMigrationUtils.METADATA_DIR)
- && containsDir(files, BDSMigrationUtils.ANNOTATIONS_DIR);
- }
-
- private static boolean containsDir(File[] files, String dirName)
- {
- if (files != null)
- {
- for (File file : files)
- {
- if (file.getName().equalsIgnoreCase(dirName))
- {
- return true;
- }
- }
- }
- return false;
- }
-
- public void close()
- {
- // do nothing
-
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSDataRemoverMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSDataRemoverMigrator.java
deleted file mode 100644
index e1b05bc1630bc45dbb5e0bab67bd3f8edc8f8658..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSDataRemoverMigrator.java
+++ /dev/null
@@ -1,78 +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.bdsmigration;
-
-import java.io.File;
-import java.util.Properties;
-
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-
-/**
- * Removes unnecessary BDS data as a part of the migration.
- *
- * @author Tomasz Pylak
- */
-public class BDSDataRemoverMigrator extends AbstractBDSMigrator
-{
- public BDSDataRemoverMigrator()
- {
- }
-
- // Every IMigrator needs the following constructor.
- public BDSDataRemoverMigrator(Properties properties)
- {
- }
-
- public String getDescription()
- {
- return "removing unnecessary BDS data";
- }
-
- @Override
- protected boolean doMigration(File dataset)
- {
- if (BDSMigrationUtils.tryGetOriginalDir(dataset) != null)
- {
- BDSMigrationUtils.logError(dataset, "original data has not been moved");
- return false;
- }
- try
- {
- removeDir(dataset, BDSMigrationUtils.METADATA_DIR);
- removeDir(dataset, BDSMigrationUtils.VERSION_DIR);
- removeDir(dataset, BDSMigrationUtils.ANNOTATIONS_DIR);
- removeDir(dataset, BDSMigrationUtils.DATA_DIR);
- } catch (EnvironmentFailureException ex)
- {
- return false;
- }
- return true;
- }
-
- private void removeDir(File dataset, String relativeDirPath) throws EnvironmentFailureException
- {
- File dir = new File(dataset, relativeDirPath);
- boolean ok = FileUtilities.deleteRecursively(dir);
- if (ok == false)
- {
- String errorMsg = "Cannot delete the directory: " + dir.getAbsolutePath();
- BDSMigrationUtils.operationLog.error(errorMsg);
- throw new EnvironmentFailureException(errorMsg);
- }
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java
deleted file mode 100644
index 586fc4bd91ae28cac29a44f5854bfbb1f8caf472..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDatabaseMigrator.java
+++ /dev/null
@@ -1,125 +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.bdsmigration;
-
-import java.io.File;
-import java.util.List;
-import java.util.Properties;
-
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.QueryTool;
-
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.utilities.PropertyUtils;
-import ch.systemsx.cisd.openbis.dss.etl.AbstractHCSImageFileExtractor;
-import ch.systemsx.cisd.openbis.dss.etl.PlateStorageProcessor;
-import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
-
-/**
- * @author Franz-Josef Elmer
- */
-public class BDSImagingDatabaseMigrator extends AbstractBDSMigrator
-{
- private final List<String> channelNames;
-
- private final List<ColorComponent> channelColorComponentsOrNull;
-
- private final DataSource dataSource;
-
- private static File tryGetOriginalDir(File dataset)
- {
- File orgDir =
- new File(dataset, BDSMigrationUtils.DATA_DIR + BDSMigrationUtils.DIR_SEP
- + BDSMigrationUtils.ORIGINAL_DIR);
- if (orgDir.isDirectory() == false)
- {
- return null;
- }
- return orgDir;
- }
-
- private static String tryGetOriginalDatasetDirName(File dataset)
- {
- File originalDir = tryGetOriginalDir(dataset);
- if (originalDir == null)
- {
- BDSMigrationUtils.logError(dataset, "Original directory does not exist.");
- return null;
- }
- File[] files = originalDir.listFiles();
- if (files.length != 1)
- {
- BDSMigrationUtils.logError(dataset, "Original directory '" + originalDir
- + "' should contain exactly one file, but contains " + files.length + ": "
- + files);
- return null;
- }
- return files[0].getName();
- }
-
- public BDSImagingDatabaseMigrator(Properties properties)
- {
- this.dataSource = ServiceProvider.getDataSourceProvider().getDataSource(properties);
- this.channelNames =
- PropertyUtils.getMandatoryList(properties, PlateStorageProcessor.CHANNEL_NAMES);
- this.channelColorComponentsOrNull =
- AbstractHCSImageFileExtractor.tryGetChannelComponents(properties);
- if (channelColorComponentsOrNull != null
- && channelColorComponentsOrNull.size() != channelNames.size())
- {
- throw new ConfigurationFailureException(
- "There should be exactly one color component for each channel name."
- + " Correct the list of values for the components property.");
- }
- }
-
- public String getDescription()
- {
- return "uploading data to the imaging database";
- }
-
- @Override
- protected boolean doMigration(File dataset)
- {
- String originalDatasetDirName = tryGetOriginalDatasetDirName(dataset);
- if (originalDatasetDirName == null)
- {
- return false;
- }
- IImagingQueryDAO dao = createQuery();
- boolean ok =
- new BDSImagingDbUploader(dataset, dao, originalDatasetDirName, channelNames,
- channelColorComponentsOrNull).migrate();
- dao = null;
- return ok;
- }
-
- private IImagingQueryDAO createQuery()
- {
- return QueryTool.getQuery(dataSource, IImagingQueryDAO.class);
- }
-
- @Override
- public void close()
- {
- // do nothing
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
deleted file mode 100644
index 62002ba11310bd76f6e99f8e4b35c935c302256e..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSImagingDbUploader.java
+++ /dev/null
@@ -1,327 +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.bdsmigration;
-
-import static ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSMigrationUtils.DIR_SEP;
-import static ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSMigrationUtils.METADATA_DIR;
-import static ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSMigrationUtils.ORIGINAL_DIR;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.openbis.dss.etl.AcquiredPlateImage;
-import ch.systemsx.cisd.openbis.dss.etl.HCSDatasetUploader;
-import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult;
-import ch.systemsx.cisd.openbis.dss.etl.RelativeImageReference;
-import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-import ch.systemsx.cisd.openbis.dss.etl.HCSImageFileExtractionResult.Channel;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ColorComponent;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
-
-/**
- * Uploads data to the imaging database.
- *
- * @author Tomasz Pylak
- */
-class BDSImagingDbUploader
-{
- private final File dataset;
-
- private final String originalDatasetDirName;
-
- private final List<String> channelNames;
-
- private final List<ColorComponent> channelColorComponentsOrNull;
-
- private final IImagingQueryDAO dao;
-
- public BDSImagingDbUploader(File dataset, IImagingQueryDAO dao, String originalDatasetDirName,
- List<String> channelNames, List<ColorComponent> channelColorComponentsOrNull)
- {
- this.dao = dao;
- this.dataset = dataset;
- this.originalDatasetDirName = originalDatasetDirName;
- this.channelNames = channelNames;
- this.channelColorComponentsOrNull = channelColorComponentsOrNull;
-
- }
-
- public boolean migrate()
- {
- List<AcquiredPlateImage> images = tryExtractMappings();
- if (images == null)
- {
- return false;
- }
-
- String relativeImagesDirectory = getRelativeImagesDirectory();
- for (AcquiredPlateImage acquiredPlateImage : images)
- {
- acquiredPlateImage.getImageReference().setRelativeImageFolder(relativeImagesDirectory);
- }
-
- ScreeningContainerDatasetInfo info = ScreeningDatasetInfoExtractor.tryCreateInfo(dataset);
- if (info == null)
- {
- return false;
- }
-
- Set<HCSImageFileExtractionResult.Channel> channels = extractChannels();
-
- return storeInDatabase(images, info, channels);
- }
-
- private Set<Channel> extractChannels()
- {
- Set<Channel> channels = new HashSet<Channel>();
- for (String channelName : channelNames)
- {
- channels.add(new Channel(channelName, null, null));
- }
- return channels;
- }
-
- private boolean storeInDatabase(List<AcquiredPlateImage> images,
- ScreeningContainerDatasetInfo info, Set<HCSImageFileExtractionResult.Channel> channels)
- {
- try
- {
- HCSDatasetUploader.upload(dao, info, images, channels);
- dao.commit();
- return true;
- } catch (Exception ex)
- {
- ex.printStackTrace();
- logError("Uploading to the imaging db failed: " + ex.getMessage());
- dao.rollback();
- return false;
- } finally
- {
- dao.close();
- }
- }
-
- private String getRelativeImagesDirectory()
- {
- return ORIGINAL_DIR + DIR_SEP + originalDatasetDirName;
- }
-
- private List<AcquiredPlateImage> tryExtractMappings()
- {
- File mappingFile = new File(dataset, METADATA_DIR + DIR_SEP + "standard_original_mapping");
- if (mappingFile.isFile() == false)
- {
- logError("File '" + mappingFile + "' does not exist.");
- return null;
- }
-
- try
- {
- List<String> lines = readLines(mappingFile);
- return tryParseMappings(lines);
- } catch (IOException ex)
- {
- logError("Error when reading mapping file '" + mappingFile + "': " + ex.getMessage());
- return null;
- }
- }
-
- @SuppressWarnings("unchecked")
- private static List<String> readLines(File mappingFile) throws IOException,
- FileNotFoundException
- {
- FileInputStream stream = new FileInputStream(mappingFile);
- try
- {
- return IOUtils.readLines(stream);
- } finally
- {
- stream.close();
- }
- }
-
- private List<AcquiredPlateImage> tryParseMappings(List<String> lines)
- {
- List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
- for (String line : lines)
- {
- List<AcquiredPlateImage> mapping = tryParseMapping(line);
- if (mapping != null)
- {
- images.addAll(mapping);
- } else
- {
- return null;
- }
- }
- return images;
- }
-
- private List<AcquiredPlateImage> tryParseMapping(String line)
- {
- String[] tokens = StringUtils.split(line);
- if (tokens.length != 3)
- {
- logError("Wrong number of tokens in the mapping line: " + line);
- return null;
- } else
- {
- try
- {
- return tryParseMappingLine(tokens[0], tokens[2]);
- } catch (NumberFormatException ex)
- {
- logError("Incorrect format of mapping line: " + line + ". Cannot parse a number: "
- + ex.getMessage());
- return null;
- }
- }
- }
-
- // Example of standardPath: channel2/row1/column4/row2_column2.tiff
- private List<AcquiredPlateImage> tryParseMappingLine(String standardPath, String originalPath)
- throws NumberFormatException
- {
- String[] pathTokens = standardPath.split("/");
- if (pathTokens.length != 4)
- {
- logError("Wrong number of tokens in standard path: " + standardPath);
- return null;
- }
- int channelNum = asNum(pathTokens[0], "channel");
- int row = asNum(pathTokens[1], "row");
- int col = asNum(pathTokens[2], "column");
- Location wellLocation = new Location(col, row);
-
- String[] tileTokens = tryParseTileToken(pathTokens[3]);
- if (tileTokens == null)
- {
- return null;
- }
- int tileRow = asNum(tileTokens[0], "row");
- int tileCol = asNum(tileTokens[1], "column");
- Location tileLocation = new Location(tileCol, tileRow);
-
- String relativeImagePath = tryGetRelativeImagePath(originalPath);
- if (relativeImagePath == null)
- {
- return null;
- }
- String channelName = tryGetChannelName(channelNum, standardPath);
- if (channelName == null)
- {
- return null;
- }
-
- return createImages(wellLocation, tileLocation, relativeImagePath, channelName);
- }
-
- private static int asNum(String standardPathToken, String prefix) throws NumberFormatException
- {
- String number = standardPathToken.substring(prefix.length());
- return Integer.parseInt(number);
- }
-
- private List<AcquiredPlateImage> createImages(Location wellLocation, Location tileLocation,
- String relativeImagePath, String channelName)
- {
- List<AcquiredPlateImage> images = new ArrayList<AcquiredPlateImage>();
- if (channelColorComponentsOrNull != null)
- {
- for (int i = 0; i < channelColorComponentsOrNull.size(); i++)
- {
- ColorComponent colorComponent = channelColorComponentsOrNull.get(i);
- String channel = channelNames.get(i);
- images.add(createImage(wellLocation, tileLocation, relativeImagePath, channel,
- colorComponent));
- }
- } else
- {
- images
- .add(createImage(wellLocation, tileLocation, relativeImagePath, channelName,
- null));
- }
- return images;
- }
-
- private static AcquiredPlateImage createImage(Location plateLocation, Location wellLocation,
- String imageRelativePath, String channelName, ColorComponent colorComponent)
- {
- return new AcquiredPlateImage(plateLocation, wellLocation, channelName, null, null,
- new RelativeImageReference(imageRelativePath, null, colorComponent));
- }
-
- // channelId - starts with 1
- private String tryGetChannelName(int channelId, String standardPath)
- {
- if (channelNames.size() < channelId)
- {
- logError("Name of the channel with the id " + channelId
- + " has not been configured but is referenced in the path: " + standardPath
- + ".");
- return null;
- }
- return channelNames.get(channelId - 1);
- }
-
- private String tryGetRelativeImagePath(String originalPath)
- {
- String prefixPath = originalDatasetDirName + "/";
- if (originalPath.startsWith(prefixPath) == false)
- {
- logError("Original path " + originalPath + " should start with " + prefixPath);
- return null;
- }
- return originalPath.substring(prefixPath.length());
- }
-
- // tileFile - e.g. row2_column2.tiff
- private String[] tryParseTileToken(String tileFile)
- {
- String tileDesc;
- int dotIndex = tileFile.indexOf(".");
- if (dotIndex != -1)
- {
- tileDesc = tileFile.substring(0, dotIndex);
- } else
- {
- tileDesc = tileFile;
- }
- String[] tileTokens = tileDesc.split("_");
- if (tileTokens.length != 2)
- {
- logError("Wrong number of tokens in tile file name: " + tileDesc);
- return null;
- }
- return tileTokens;
- }
-
- private void logError(String reason)
- {
- BDSMigrationUtils.logError(dataset, reason);
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSMigrationUtils.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSMigrationUtils.java
deleted file mode 100644
index 503d0c73f371a5ae3a657cd079da62adb843a577..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSMigrationUtils.java
+++ /dev/null
@@ -1,64 +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.bdsmigration;
-
-import java.io.File;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
-
-/**
- * Constants and utility methods usful to migrate BDS datasets.
- *
- * @author Tomasz Pylak
- */
-public class BDSMigrationUtils
-{
- static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, BDSMigrationUtils.class);
-
- static final String ANNOTATIONS_DIR = "annotations";
-
- static final String METADATA_DIR = "metadata";
-
- static final String DATA_DIR = "data";
-
- static final String VERSION_DIR = "version";
-
- static final String ORIGINAL_DIR = ScreeningConstants.ORIGINAL_DATA_DIR;
-
- static final String DIR_SEP = "/";
-
- static File tryGetOriginalDir(File dataset)
- {
- File orgDir = new File(dataset, DATA_DIR + DIR_SEP + ORIGINAL_DIR);
- if (orgDir.isDirectory() == false)
- {
- return null;
- }
- return orgDir;
- }
-
- static void logError(File dataset, String reason)
- {
- operationLog.error("Cannot migrate dataset '" + dataset.getName() + "'. " + reason);
- }
-
-}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSOriginalDataRelocatorMigrator.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSOriginalDataRelocatorMigrator.java
deleted file mode 100644
index 25ebccc12cc582e4e24d2d6f4560bb5075454e93..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/BDSOriginalDataRelocatorMigrator.java
+++ /dev/null
@@ -1,65 +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.bdsmigration;
-
-import java.io.File;
-import java.util.Properties;
-
-/**
- * Second step of BDS migration, moves data from data/original to original.
- *
- * @author Tomasz Pylak
- */
-public class BDSOriginalDataRelocatorMigrator extends AbstractBDSMigrator
-{
-
- BDSOriginalDataRelocatorMigrator()
- {
- }
-
- // Every IMigrator needs the following constructor.
- public BDSOriginalDataRelocatorMigrator(Properties properties)
- {
- }
-
- public String getDescription()
- {
- return "moving data from data/original to original/";
- }
-
- @Override
- protected boolean doMigration(File dataset)
- {
- File originalDir = BDSMigrationUtils.tryGetOriginalDir(dataset);
- if (originalDir == null)
- {
- BDSMigrationUtils.operationLog.warn("No original data directory in dataset " + dataset);
- return false;
- }
- File destinationDir = new File(dataset, BDSMigrationUtils.ORIGINAL_DIR);
- boolean ok = originalDir.renameTo(destinationDir);
- if (ok == false)
- {
- BDSMigrationUtils.operationLog.error("Cannot move " + originalDir + " to "
- + destinationDir);
- return false;
- } else
- {
- return true;
- }
- }
-}
\ No newline at end of file
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/ScreeningDatasetInfoExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/ScreeningDatasetInfoExtractor.java
deleted file mode 100644
index 5b4b3c0cb960814851879fff73915c497552985a..0000000000000000000000000000000000000000
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/bdsmigration/ScreeningDatasetInfoExtractor.java
+++ /dev/null
@@ -1,124 +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.bdsmigration;
-
-import static ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSMigrationUtils.DIR_SEP;
-import static ch.systemsx.cisd.openbis.dss.etl.bdsmigration.BDSMigrationUtils.METADATA_DIR;
-
-import java.io.File;
-
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.openbis.dss.etl.ScreeningContainerDatasetInfo;
-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.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
-
-/**
- * Extract the dataset metadata from BDS and by asking openBIS. Used to migrate BDS to imaging db.
- *
- * @author Tomasz Pylak
- */
-class ScreeningDatasetInfoExtractor
-{
- public static ScreeningContainerDatasetInfo tryCreateInfo(File dataset)
- {
- Sample sample = tryGetSampleWithExperiment(dataset);
- if (sample == null)
- {
- return null;
- }
- try
- {
- return createInfo(dataset, sample);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- BDSMigrationUtils.logError(dataset, "Unexpected exception: " + ex.getMessage());
- return null;
- }
- }
-
- private static Sample tryGetSampleWithExperiment(File dataset)
- {
- IEncapsulatedOpenBISService openBISService = ServiceProvider.getOpenBISService();
- SampleIdentifier sampleIdentifier = createSampleIdentifier(dataset);
- Sample sample = openBISService.tryGetSampleWithExperiment(sampleIdentifier);
- if (sample == null)
- {
- BDSMigrationUtils.logError(dataset, "Sample '" + sampleIdentifier
- + "' cannot be found in openBIS");
- }
- return sample;
- }
-
- private static SampleIdentifier createSampleIdentifier(File dataset)
- {
- File sampleDir = new File(dataset, METADATA_DIR + DIR_SEP + "sample");
- String databaseInstanceCode = contentAsString(new File(sampleDir, "instance_code"));
- String spaceCode = contentAsString(new File(sampleDir, "space_code"));
- String sampleCode = contentAsString(new File(sampleDir, "code"));
-
- SpaceIdentifier spaceIdentifier = new SpaceIdentifier(databaseInstanceCode, spaceCode);
- return new SampleIdentifier(spaceIdentifier, sampleCode);
- }
-
- private static ScreeningContainerDatasetInfo createInfo(File dataset, Sample sample)
- {
- int rows = extractGeometryDim(dataset, "plate_geometry", "rows");
- int columns = extractGeometryDim(dataset, "plate_geometry", "columns");
- int tileRows = extractGeometryDim(dataset, "well_geometry", "rows");
- int tileColumns = extractGeometryDim(dataset, "well_geometry", "columns");
-
- ScreeningContainerDatasetInfo info = new ScreeningContainerDatasetInfo();
- info.setContainerRows(rows);
- info.setContainerColumns(columns);
- info.setTileRows(tileRows);
- info.setTileColumns(tileColumns);
- info.setDatasetPermId(extractDatasetPermId(dataset));
- info.setContainerPermId(sample.getPermId());
- info.setExperimentPermId(sample.getExperiment().getPermId());
-
- return info;
- }
-
- private static int extractGeometryDim(File dataset, String geometryName, String fieldName)
- {
- File parentDir =
- new File(dataset, METADATA_DIR + DIR_SEP + "parameters" + DIR_SEP + geometryName);
- return contentAsNumber(new File(parentDir, fieldName));
- }
-
- private static String extractDatasetPermId(File dataset)
- {
- File file =
- new File(dataset, BDSMigrationUtils.METADATA_DIR + DIR_SEP + "data_set" + DIR_SEP
- + "code");
- return contentAsString(file);
- }
-
- private static int contentAsNumber(File file)
- {
- return Integer.parseInt(contentAsString(file));
- }
-
- private static String contentAsString(File file)
- {
- return FileOperations.getInstance().getContentAsString(file).trim();
- }
-}
\ No newline at end of file