From 2e80016e5cf7ef81fdc8b52b5fba6ec2d9c2accb Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 2 May 2011 19:26:19 +0000
Subject: [PATCH] remove: deprecated class BDSStorageProcessor and test
SVN: 21099
---
.../cisd/etlserver/BDSStorageProcessor.java | 660 ------------------
.../etlserver/BDSStorageProcessorTest.java | 615 ----------------
2 files changed, 1275 deletions(-)
delete mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
delete mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
deleted file mode 100644
index 2a0236e64f6..00000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/BDSStorageProcessor.java
+++ /dev/null
@@ -1,660 +0,0 @@
-/*
- * Copyright 2007 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;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.commons.lang.time.DurationFormatUtils;
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.bds.Constants;
-import ch.systemsx.cisd.bds.DataSet;
-import ch.systemsx.cisd.bds.DataStructureFactory;
-import ch.systemsx.cisd.bds.DataStructureLoader;
-import ch.systemsx.cisd.bds.ExperimentRegistrationTimestamp;
-import ch.systemsx.cisd.bds.ExperimentRegistrator;
-import ch.systemsx.cisd.bds.Format;
-import ch.systemsx.cisd.bds.FormatParameter;
-import ch.systemsx.cisd.bds.IDataStructure.Mode;
-import ch.systemsx.cisd.bds.IFormatParameterFactory;
-import ch.systemsx.cisd.bds.IFormattedData;
-import ch.systemsx.cisd.bds.Reference;
-import ch.systemsx.cisd.bds.ReferenceType;
-import ch.systemsx.cisd.bds.Sample;
-import ch.systemsx.cisd.bds.UnknownFormatV1_0;
-import ch.systemsx.cisd.bds.Version;
-import ch.systemsx.cisd.bds.hcs.Geometry;
-import ch.systemsx.cisd.bds.hcs.HCSImageAnnotations;
-import ch.systemsx.cisd.bds.hcs.IHCSImageFormattedData;
-import ch.systemsx.cisd.bds.hcs.IHCSImageFormattedData.NodePath;
-import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.bds.hcs.PlateGeometry;
-import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.bds.storage.IFile;
-import ch.systemsx.cisd.bds.storage.ILink;
-import ch.systemsx.cisd.bds.storage.INode;
-import ch.systemsx.cisd.bds.storage.filesystem.FileStorage;
-import ch.systemsx.cisd.bds.storage.filesystem.NodeFactory;
-import ch.systemsx.cisd.bds.v1_1.ExperimentIdentifierWithUUID;
-import ch.systemsx.cisd.bds.v1_1.IDataStructureV1_1;
-import ch.systemsx.cisd.bds.v1_1.SampleWithOwner;
-import ch.systemsx.cisd.common.collections.CollectionUtils;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.filesystem.IFileOperations;
-import ch.systemsx.cisd.common.logging.LogCategory;
-import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.utilities.ClassUtils;
-import ch.systemsx.cisd.etlserver.HCSImageCheckList.FullLocation;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-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.Person;
-import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
-
-/**
- * The <code>AbstractStorageAdapter</code> extension for <i>BDS</i> (Biological Data Standards).
- * <p>
- * When declared in <code>service.properties</code> file, it must specify a property called
- * <code>storage-adapter.version</code>. Otherwise instantiation will fail.
- * </p>
- *
- * @author Christian Ribeaud
- */
-// TODO 2010-07-28, Tomasz Pylak: remove this class
-@Deprecated
-public final class BDSStorageProcessor extends AbstractStorageProcessor
-{
-
- private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- BDSStorageProcessor.class);
-
- private static final Logger notificationLog = LogFactory.getLogger(LogCategory.OPERATION,
- BDSStorageProcessor.class);
-
- private static final String PROPERTY_PREFIX = "Property '%s': ";
-
- private static final String NO_FORMAT_FORMAT = PROPERTY_PREFIX
- + "no valid and known format could be extracted from text '%s'.";
-
- static final String VERSION_KEY = "version";
-
- static final String SAMPLE_TYPE_DESCRIPTION_KEY = "sampleTypeDescription";
-
- static final String SAMPLE_TYPE_CODE_KEY = "sampleTypeCode";
-
- static final String FORMAT_KEY = "format";
-
- static final String FILE_EXTRACTOR_KEY = "file-extractor";
-
- static final String NO_VERSION_FORMAT = PROPERTY_PREFIX
- + "no version could be extracted from text '%s'.";
-
- private final Format format;
-
- private final String sampleTypeCode;
-
- private final String sampleTypeDescription;
-
- private final IHCSImageFileExtractor imageFileExtractor;
-
- private final Version version;
-
- private final List<FormatParameter> formatParameters;
-
- // candidates
- private IDataStructureV1_1 dataStructure;
-
- private IHCSImageFormattedData imageFormattedData;
-
- public BDSStorageProcessor(final Properties properties)
- {
- super(properties);
- version = parseVersion(getMandatoryProperty(VERSION_KEY));
- if (version.equals(new Version(1, 1)) == false)
- {
- throw new ConfigurationFailureException("Invalid version: " + version);
- }
- format = parseFormat(getMandatoryProperty(FORMAT_KEY));
- formatParameters = createFormatParameters();
- sampleTypeDescription = getMandatoryProperty(SAMPLE_TYPE_DESCRIPTION_KEY);
- if (needsImageFileExtractor())
- {
- final String property = getMandatoryProperty(FILE_EXTRACTOR_KEY);
- imageFileExtractor =
- ClassUtils.create(IHCSImageFileExtractor.class, property, properties);
- } else
- {
- imageFileExtractor = null;
- }
- try
- {
- sampleTypeCode = getMandatoryProperty(SAMPLE_TYPE_CODE_KEY);
- } catch (final IllegalArgumentException ex)
- {
- throw new ConfigurationFailureException(ex.getMessage());
- }
- }
-
- private List<FormatParameter> createFormatParameters()
- {
- final IFormatParameterFactory formatParameterFactory = format.getFormatParameterFactory();
- List<FormatParameter> result = new ArrayList<FormatParameter>();
- for (final String parameterName : format.getMandatoryParameterNames())
- {
- final String value = properties.getProperty(parameterName);
- if (value == null)
- {
- throw ConfigurationFailureException.fromTemplate(
- "No value has been defined for parameter '%s'", parameterName);
- }
- FormatParameter parameter =
- createFormatParameter(formatParameterFactory, parameterName, value);
- result.add(parameter);
- }
- for (final String parameterName : format.getOptionalParameterNames())
- {
- final String value = properties.getProperty(parameterName);
- if (value != null)
- {
- FormatParameter parameter =
- createFormatParameter(formatParameterFactory, parameterName, value);
- result.add(parameter);
- }
- }
- return result;
- }
-
- private FormatParameter createFormatParameter(
- final IFormatParameterFactory formatParameterFactory, final String parameterName,
- final String value)
- {
- final FormatParameter formatParameter =
- formatParameterFactory.createFormatParameter(parameterName, value);
- if (formatParameter == null)
- {
- throw ConfigurationFailureException.fromTemplate(
- "Given value '%s' is not understandable for parameter '%s'", value,
- parameterName);
- }
- return formatParameter;
- }
-
- final static Version parseVersion(final String versionString)
- {
- final Version version = Version.createVersionFromString(versionString);
- if (version == null)
- {
- throw ConfigurationFailureException.fromTemplate(NO_VERSION_FORMAT, VERSION_KEY,
- versionString);
- }
- return version;
- }
-
- final static Format parseFormat(final String formatString)
- {
- final Format format = Format.tryToCreateFormatFromString(formatString);
- if (format == null)
- {
- throw ConfigurationFailureException.fromTemplate(NO_FORMAT_FORMAT, FORMAT_KEY,
- formatString);
- }
- return format;
- }
-
- private final ExperimentIdentifierWithUUID createExperimentIdentifier(
- final DataSetInformation dataSetInformation)
- {
- final ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier experimentIdentifier =
- dataSetInformation.getExperimentIdentifier();
- final String projectCode = experimentIdentifier.getProjectCode();
- final String experimentCode = experimentIdentifier.getExperimentCode();
- final String spaceCode = experimentIdentifier.getSpaceCode();
- final String instanceCode = dataSetInformation.getInstanceCode();
- return new ExperimentIdentifierWithUUID(instanceCode, dataSetInformation.getInstanceUUID(),
- spaceCode, projectCode, experimentCode);
- }
-
- private final static void checkDataSetInformation(final DataSetInformation dataSetInformation)
- {
- assert dataSetInformation != null : "Unspecified data set information";
- assert dataSetInformation.getSampleIdentifier() != null : "Unspecified sample identifier";
- final ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier experimentIdentifier =
- dataSetInformation.getExperimentIdentifier();
- assert experimentIdentifier != null : "Unspecified experiment identifier";
- checkExperimentIdentifier(experimentIdentifier);
- }
-
- private final static void checkExperimentIdentifier(
- final ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier experimentIdentifier)
- {
- assert experimentIdentifier.getSpaceCode() != null : "Space code is null";
- assert experimentIdentifier.getExperimentCode() != null : "Experiment code is null";
- assert experimentIdentifier.getProjectCode() != null : "Project code is null";
- }
-
- private final IDataStructureV1_1 createDataStructure(final Experiment experiment,
- final DataSetInformation dataSetInformation, final ITypeExtractor typeExtractor,
- final File incomingDataSetPath, final File rootDir)
- {
- final FileStorage storage = new FileStorage(rootDir);
- final IDataStructureV1_1 structure =
- (IDataStructureV1_1) DataStructureFactory.createDataStructure(storage, version);
-
- List<FormatParameter> parameters = new ArrayList<FormatParameter>(formatParameters);
- final Geometry plateGeometry = getPlateGeometry(dataSetInformation);
- parameters.add(new FormatParameter(PlateGeometry.PLATE_GEOMETRY, plateGeometry));
-
- structure.create(parameters);
- structure.setFormat(format);
- structure.setExperimentIdentifier(createExperimentIdentifier(dataSetInformation));
- structure.setExperimentRegistrationTimestamp(new ExperimentRegistrationTimestamp(experiment
- .getRegistrationDate()));
- final Person registrator = experiment.getRegistrator();
- final String firstName = registrator.getFirstName();
- final String lastName = registrator.getLastName();
- final String email = registrator.getEmail();
- structure.setExperimentRegistrator(new ExperimentRegistrator(firstName, lastName, email));
- structure.setSample(createSample(dataSetInformation));
- structure.setDataSet(createDataSet(dataSetInformation, typeExtractor, incomingDataSetPath));
-
- return structure;
- }
-
- private Geometry getPlateGeometry(final DataSetInformation dataSetInformation)
- {
- final IEntityProperty[] sampleProperties = dataSetInformation.getProperties();
- final PlateDimension plateDimension =
- PlateDimensionParser.tryToGetPlateDimension(sampleProperties);
- if (plateDimension == null)
- {
- throw new EnvironmentFailureException(
- "Missing plate geometry for the plate registered for sample identifier '"
- + dataSetInformation.getSampleIdentifier() + "'.");
- }
- final Geometry plateGeometry =
- new PlateGeometry(plateDimension.getRowsNum(), plateDimension.getColsNum());
- return plateGeometry;
- }
-
- private final Sample createSample(final DataSetInformation dataSetInformation)
- {
- final String spaceCode = StringUtils.defaultString(dataSetInformation.getSpaceCode());
- final String instanceCode = dataSetInformation.getInstanceCode();
- final String instanceUUID = dataSetInformation.getInstanceUUID();
- assert instanceCode != null : "Unspecified database instance code";
- assert instanceUUID != null : "Unspecified database instance UUID";
- // TODO 2009-09-15, Tomasz Pylak: deal with the case when sample is null
- return new SampleWithOwner(dataSetInformation.getSampleCode(), sampleTypeCode,
- sampleTypeDescription, instanceUUID, instanceCode, spaceCode);
- }
-
- private final static DataSet createDataSet(final DataSetInformation dataSetInformation,
- final ITypeExtractor typeExtractor, final File incomingDataSetPath)
- {
- final String dataSetCode = dataSetInformation.getDataSetCode();
- final List<String> parentCodes =
- new ArrayList<String>(dataSetInformation.getParentDataSetCodes());
- final boolean isMeasured = typeExtractor.isMeasuredData(incomingDataSetPath);
- final DataSetType dataSetType = typeExtractor.getDataSetType(incomingDataSetPath);
- final DataSet dataSet =
- new DataSet(dataSetCode, dataSetType.getCode(),
- ch.systemsx.cisd.bds.Utilities.Boolean.fromBoolean(isMeasured),
- dataSetInformation.getProductionDate(),
- dataSetInformation.getProducerCode(), parentCodes);
- return dataSet;
- }
-
- private final static String getPathOf(final INode node)
- {
- final StringBuilder builder = new StringBuilder(node.getName());
- IDirectory parent = node.tryGetParent();
- while (parent != null)
- {
- builder.insert(0, '/');
- builder.insert(0, parent.getName());
- parent = parent.tryGetParent();
- }
- return builder.toString();
- }
-
- private final boolean needsImageFileExtractor()
- {
- return format.getCode().equals(UnknownFormatV1_0.UNKNOWN_1_0.getCode()) == false;
- }
-
- //
- // AbstractStorageProcessor
- //
- public IStorageProcessorTransaction createTransaction()
- {
- return new BDSStorageProcessorTransaction();
- }
-
- @Override
- public final StorageFormat getStorageFormat()
- {
- return StorageFormat.BDS_DIRECTORY;
- }
-
- private final class BDSStorageProcessorTransaction extends AbstractStorageProcessorTransaction
- implements IHCSImageFileAccepter
- {
- private File imageFileRootDirectory;
-
- private File dataStructureDir;
-
- private HCSImageCheckList imageCheckList;
-
- @Override
- protected File storeData(DataSetInformation dataSetInformation,
- ITypeExtractor typeExtractor, IMailClient mailClient)
- {
- checkDataSetInformation(dataSetInformation);
- assert rootDirectory != null : "Root directory can not be null.";
- assert incomingDataSetDirectory != null : "Incoming data set directory can not be null.";
- assert typeExtractor != null : "Unspecified IProcedureAndDataTypeExtractor implementation.";
-
- dataStructureDir = rootDirectory;
- dataStructureDir.mkdirs();
- Experiment experiment = dataSetInformation.tryToGetExperiment();
- if (experiment == null)
- {
- throw new UserFailureException("Experiment unknown for data set "
- + dataSetInformation);
- }
- dataStructure =
- createDataStructure(experiment, dataSetInformation, typeExtractor,
- incomingDataSetDirectory, dataStructureDir);
- final IFormattedData formattedData = dataStructure.getFormattedData();
- if (formattedData instanceof IHCSImageFormattedData)
- {
- imageFormattedData = (IHCSImageFormattedData) formattedData;
- final int channels = imageFormattedData.getChannelCount();
- final Geometry plateGeometry = imageFormattedData.getPlateGeometry();
- final Geometry wellGeometry = imageFormattedData.getWellGeometry();
- imageCheckList = new HCSImageCheckList(channels, plateGeometry, wellGeometry);
- }
- if (needsImageFileExtractor())
- {
- imageFileRootDirectory = incomingDataSetDirectory;
- final HCSImageFileExtractionResult result =
- imageFileExtractor.process(
- NodeFactory.createDirectoryNode(incomingDataSetDirectory),
- dataSetInformation, this);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("Extraction of %d files took %s.",
- result.getTotalFiles(),
- DurationFormatUtils.formatDurationHMS(result.getDuration())));
- }
- if (result.getInvalidFiles().size() > 0)
- {
- throw UserFailureException.fromTemplate(
- "Following invalid files %s have been found.",
- CollectionUtils.abbreviate(result.getInvalidFiles(), 10));
- }
- if (result.getTotalFiles() == 0)
- {
- throw UserFailureException.fromTemplate(
- "No extractable files were found inside a dataset '%s'."
- + " Have you changed your naming convention?",
- incomingDataSetDirectory.getAbsolutePath());
- }
- dataStructure.setAnnotations(new HCSImageAnnotations(result.getChannels()));
- checkCompleteness(dataSetInformation, incomingDataSetDirectory.getName(),
- mailClient);
- } else
- {
- if (imageFormattedData != null && imageFormattedData.isIncomingSymbolicLink())
- {
- ILink symbolicLink =
- NodeFactory.createSymbolicLinkNode(incomingDataSetDirectory);
- dataStructure.getOriginalData().tryAddLink(symbolicLink.getName(),
- symbolicLink.getReference());
-
- } else
- {
- dataStructure.getOriginalData().addFile(incomingDataSetDirectory, null, true);
- }
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format("File '%s' added to original data.",
- incomingDataSetDirectory));
- }
- }
- dataStructure.close();
- return dataStructureDir;
- }
-
- @Override
- protected UnstoreDataAction executeRollback(Throwable ex)
- {
- unstoreData();
- return getDefaultUnstoreDataAction(ex);
- }
-
- @Override
- protected void executeCommit()
- {
- // no commit logic
- }
-
- // Although this check should be performed in the BDS library when closing is
- // performed, we set
- // the complete flag here as we want to inform the registrator about the
- // incompleteness.
- private void checkCompleteness(final DataSetInformation dataSetInformation,
- final String dataSetFileName, final IMailClient mailClientOrNull)
- {
- final List<FullLocation> fullLocations = imageCheckList.getCheckedOnFullLocations();
- final boolean complete = fullLocations.size() == 0;
- final IDataStructureV1_1 thisStructure = getDataStructure(dataStructureDir);
- final DataSet dataSet = thisStructure.getDataSet();
- dataSet.setComplete(complete);
- thisStructure.setDataSet(dataSet);
- dataSetInformation.setComplete(complete);
- if (complete == false)
- {
- final String message =
- String.format("Incomplete data set '%s': %d image file(s) "
- + "are missing (locations: %s)", dataSetFileName,
- fullLocations.size(), CollectionUtils.abbreviate(fullLocations, 10));
- operationLog.warn(message);
- if (mailClientOrNull != null)
- {
- final ExperimentRegistrator registrator =
- thisStructure.getExperimentRegistrator();
- final String email = registrator.getEmail();
- if (StringUtils.isBlank(email) == false)
- {
- try
- {
- mailClientOrNull.sendMessage("Incomplete data set '" + dataSetFileName
- + "'", message, null, null, email);
- } catch (final EnvironmentFailureException e)
- {
- notificationLog.error("Couldn't send the following e-mail to '" + email
- + "': " + message, e);
- }
- } else
- {
- notificationLog
- .error("Unspecified e-mail address of experiment registrator "
- + registrator);
- }
- }
- }
- }
-
- private final void unstoreData()
- {
- checkParameters(incomingDataSetDirectory, dataStructureDir);
-
- if (dataStructure == null)
- {
- // Nothing to do here.
- return;
- }
- final IDirectory originalData = getDataStructure(dataStructureDir).getOriginalData();
- final INode node = originalData.tryGetNode(incomingDataSetDirectory.getName());
- // If the 'incoming' data have been moved to 'original' directory. This only
- // happens if
- // 'containsOriginalData' returns 'true'.
- if (node != null)
- {
- final File incomingDirectory = incomingDataSetDirectory.getParentFile();
- try
- {
- node.moveTo(incomingDirectory);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info(String.format(
- "Node '%s' has moved to incoming directory '%s'.", node,
- incomingDirectory.getAbsolutePath()));
- }
- } catch (final EnvironmentFailureException ex)
- {
- notificationLog.error(String.format(
- "Could not move '%s' to incoming directory '%s'.", node,
- incomingDirectory.getAbsolutePath()), ex);
- return;
- }
- }
- final IFileOperations fileOps = FileOperations.getMonitoredInstanceForCurrentThread();
- if (fileOps.exists(incomingDataSetDirectory))
- {
- if (dataStructureDir != null
- && fileOps.removeRecursivelyQueueing(dataStructureDir) == false)
- {
- operationLog.error("Cannot delete '" + dataStructureDir.getAbsolutePath()
- + "'.");
- }
- } else
- {
- notificationLog.error(String.format("Incoming data set directory '%s' does not "
- + "exist, keeping store directory '%s'.", incomingDataSetDirectory,
- storedDataDirectory));
- }
- }
-
- public final void accept(final int channel, final Location wellLocation,
- final Location tileLocation, final IFile imageFile)
- {
- assert imageFileRootDirectory != null : "Incoming data set directory has not been set.";
- final String imageRelativePath =
- FileUtilities.getRelativeFile(imageFileRootDirectory,
- new File(imageFile.getPath()));
- assert imageRelativePath != null : "Image relative path should not be null.";
- final NodePath nodePath =
- imageFormattedData.addStandardNode(imageFileRootDirectory, imageRelativePath,
- channel, wellLocation, tileLocation);
- imageCheckList.checkOff(channel, wellLocation, tileLocation);
- if (nodePath.getNode() instanceof ILink)
- {
- // We made a link in the 'standard' directory to the 'original' directory
- // image file
- // name. The image file did not change during the operation.
- final Reference reference =
- new Reference(nodePath.getPath(), imageFileRootDirectory.getName()
- + Constants.PATH_SEPARATOR + imageRelativePath,
- ReferenceType.IDENTICAL);
- getDataStructure(dataStructureDir).addReference(reference);
- }
- }
-
- /**
- * For given <var>directory</var> returns the {@link IDataStructureV1_1}.
- * <p>
- * In ideal case returns internally saved <code>dataStructureDir</code> but when given
- * <var>storedDataDirectory</var> changed (meaning no longer equal to storage root), then we
- * have to reload the data structure.
- * </p>
- */
- private final IDataStructureV1_1 getDataStructure(File directory)
- {
- final IDataStructureV1_1 thisStructure;
- if (directory.equals(dataStructureDir) == false)
- {
- final DataStructureLoader dataStructureLoader =
- new DataStructureLoader(directory.getParentFile());
- thisStructure =
- (IDataStructureV1_1) dataStructureLoader.load(directory.getName(), true);
- } else
- {
- thisStructure = dataStructure;
- if (thisStructure.isOpenOrCreated() == false)
- {
- thisStructure.open(Mode.READ_ONLY);
- }
- }
- return thisStructure;
- }
-
- public final File tryGetProprietaryData()
- {
- assert storedDataDirectory != null : "Unspecified stored data directory.";
- if (dataStructure == null)
- {
- operationLog.error("No data structure defined.");
- return null;
- }
- if (imageFormattedData != null)
- {
- if (imageFormattedData.containsOriginalData() == false)
- {
- operationLog.warn("Original data are not available.");
- return null;
- }
- }
- final IDataStructureV1_1 thisStructure = getDataStructure(storedDataDirectory);
- final IDirectory originalData = thisStructure.getOriginalData();
- final Iterator<INode> iterator = originalData.iterator();
- if (iterator.hasNext() == false)
- {
- return null;
- }
- final INode node = iterator.next();
- final String path = getPathOf(node);
- final File originalDataFile = new File(path);
- if (originalDataFile.exists() == false)
- {
- operationLog.error("Original data set file '" + originalDataFile.getAbsolutePath()
- + "' does not exist.");
- return null;
- }
- return originalDataFile;
- }
-
- }
-
- @Override
- public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
- {
- return UnstoreDataAction.MOVE_TO_ERROR;
- }
-}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
deleted file mode 100644
index 3c2b6d54041..00000000000
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/BDSStorageProcessorTest.java
+++ /dev/null
@@ -1,615 +0,0 @@
-/*
- * Copyright 2007 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;
-
-import java.io.File;
-import java.io.IOException;
-import java.sql.Date;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.log4j.Level;
-import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.testng.annotations.AfterMethod;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.DataProvider;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.bds.DataSet;
-import ch.systemsx.cisd.bds.DataStructureLoader;
-import ch.systemsx.cisd.bds.ExperimentRegistrator;
-import ch.systemsx.cisd.bds.Format;
-import ch.systemsx.cisd.bds.IDataStructure;
-import ch.systemsx.cisd.bds.Sample;
-import ch.systemsx.cisd.bds.UnknownFormatV1_0;
-import ch.systemsx.cisd.bds.Utilities;
-import ch.systemsx.cisd.bds.Utilities.Boolean;
-import ch.systemsx.cisd.bds.Version;
-import ch.systemsx.cisd.bds.hcs.Channel;
-import ch.systemsx.cisd.bds.hcs.HCSImageFormatV1_0;
-import ch.systemsx.cisd.bds.hcs.Location;
-import ch.systemsx.cisd.bds.hcs.WellGeometry;
-import ch.systemsx.cisd.bds.storage.IDirectory;
-import ch.systemsx.cisd.bds.storage.IFile;
-import ch.systemsx.cisd.bds.v1_1.IDataStructureV1_1;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
-import ch.systemsx.cisd.common.filesystem.SoftLinkMaker;
-import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.types.BooleanOrUnknown;
-import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional.IStorageProcessorTransaction;
-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.generic.shared.basic.dto.DataType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
-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.Person;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-
-/**
- * Test cases for corresponding {@link BDSStorageProcessor} class.
- *
- * @author Christian Ribeaud
- */
-// TODO 2010-07-28, Tomasz Pylak: remove this class
-@Deprecated
-@Friend(toClasses = DssPropertyParametersUtil.class)
-public final class BDSStorageProcessorTest extends AbstractFileSystemTestCase
-{
- private static final String EXAMPLE_EMAIL = "j@d";
-
- private static final String DATA_SET_CODE = "D";
-
- private static final String INCOMING_DATA_SET_DIR = "NEMO.EXP1==CP001A-3AB";
-
- private static final String EXAMPLE_TYPE_DESCRIPTION = "Screening Plate";
-
- private static final Date REGISTRATION_DATE = new Date(47110000);
-
- private static final String EXAMPLE_INSTANCE = "I";
-
- private static final String EXAMPLE_INSTANCE_GLOBAL = "222-333";
-
- private static final String EXAMPLE_SPACE = "G";
-
- private static final String DATA_STRUCTURE_NAME = "originalData";
-
- private static final String EXAMPLE_DATA = "hello world!";
-
- private static final String ORIGINAL_DATA_TXT = DATA_STRUCTURE_NAME + ".txt";
-
- private static final String VERSION_PROPERTY_KEY = BDSStorageProcessor.VERSION_KEY;
-
- private static final String FORMAT_KEY = BDSStorageProcessor.FORMAT_KEY;
-
- private static final String SAMPLE_TYPE_DESCRIPTION_KEY =
- BDSStorageProcessor.SAMPLE_TYPE_DESCRIPTION_KEY;
-
- private static final String SAMPLE_TYPE_CODE_KEY =
-
- BDSStorageProcessor.SAMPLE_TYPE_CODE_KEY;
-
- private static final String CHANNEL_COUNT_KEY = HCSImageFormatV1_0.NUMBER_OF_CHANNELS;
-
- private static final String CONTAINS_ORIGINAL_DATA_KEY =
- HCSImageFormatV1_0.CONTAINS_ORIGINAL_DATA;
-
- private static final String WELL_GEOMETRY_KEY = WellGeometry.WELL_GEOMETRY;
-
- private static final String FILE_EXTRACTOR_KEY = IHCSImageFileExtractor.FILE_EXTRACTOR;
-
- private final static ITypeExtractor TYPE_EXTRACTOR =
- new DefaultStorageProcessorTest.TestProcedureAndDataTypeExtractor();
-
- private final static String STORE_ROOT_DIR = "store";
-
- private BufferedAppender logRecorder;
-
- private Mockery context;
-
- private IMailClient mailClient;
-
- private final static Properties createProperties(final Format format)
- {
- final Properties props = createPropertiesWithVersion();
- props.setProperty(DssPropertyParametersUtil.STOREROOT_DIR_KEY, "store");
- props.setProperty(SAMPLE_TYPE_DESCRIPTION_KEY, EXAMPLE_TYPE_DESCRIPTION);
- props.setProperty(SAMPLE_TYPE_CODE_KEY, "CELL_PLATE");
- props.setProperty(FORMAT_KEY, format.getCode() + " " + format.getVersion());
- props.setProperty(CHANNEL_COUNT_KEY, "1");
- props.setProperty(CONTAINS_ORIGINAL_DATA_KEY, Utilities.Boolean.TRUE.toString());
- props.setProperty(WELL_GEOMETRY_KEY, "3x3");
- props.setProperty(FILE_EXTRACTOR_KEY, TestImageFileExtractor.class.getName());
- return props;
- }
-
- final static DataSetInformation createDataSetInformation()
- {
- final DataSetInformation dataSetInformation = new DataSetInformation();
- dataSetInformation.setInstanceCode(EXAMPLE_INSTANCE);
- dataSetInformation.setInstanceUUID(EXAMPLE_INSTANCE_GLOBAL);
- final ExperimentIdentifier experimentIdentifier = new ExperimentIdentifier();
- experimentIdentifier.setExperimentCode("E");
- experimentIdentifier.setProjectCode("P");
- experimentIdentifier.setSpaceCode(EXAMPLE_SPACE);
- dataSetInformation.setExperimentIdentifier(experimentIdentifier);
- dataSetInformation.setSampleCode("S");
- dataSetInformation.setDataSetCode(DATA_SET_CODE);
- final IEntityProperty plateGeometry =
- createSampleProperty(PlateDimensionParser.PLATE_GEOMETRY_PROPERTY_NAME,
- DataTypeCode.VARCHAR, "_16X24");
- dataSetInformation.setProperties(new IEntityProperty[]
- { plateGeometry });
- return dataSetInformation;
- }
-
- private final static IEntityProperty createSampleProperty(final String code,
- final DataTypeCode dataType, final String value)
- {
- final IEntityProperty property = new EntityProperty();
- final SampleTypePropertyType entityTypePropertyType = new SampleTypePropertyType();
- final PropertyType propertyType = new PropertyType();
- propertyType.setCode(code);
- propertyType.setLabel(code);
- final DataType type = new DataType();
- type.setCode(dataType);
- propertyType.setDataType(type);
- entityTypePropertyType.setPropertyType(propertyType);
- property.setPropertyType(propertyType);
- property.setValue(value);
- return property;
- }
-
- private final File createOriginalDataInDir() throws IOException
- {
- final File dir = createDirInIncoming(INCOMING_DATA_SET_DIR);
- final File originalData = new File(dir, ORIGINAL_DATA_TXT);
- FileUtilities.writeToFile(originalData, EXAMPLE_DATA);
- return dir;
- }
-
- private File createDirInIncoming(String incomingItemName)
- {
- final File incoming = getIncomingDir();
- final File dir = new File(incoming, incomingItemName);
- dir.mkdir();
- return dir;
- }
-
- private File getIncomingDir()
- {
- final File incoming = new File(workingDirectory, "incoming");
- incoming.mkdir();
- return incoming;
- }
-
- static final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample createSample()
- {
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
- sample.setExperiment(createExperiment());
- return sample;
- }
-
- static final Experiment createExperiment()
- {
- final Experiment baseExperiment = new Experiment();
- baseExperiment.setRegistrationDate(REGISTRATION_DATE);
- final Person person = new Person();
- person.setFirstName("Joe");
- person.setLastName("Doe");
- person.setEmail(EXAMPLE_EMAIL);
- final Space space = new Space();
- space.setCode(EXAMPLE_SPACE);
- final Project project = new Project();
- project.setSpace(space);
- baseExperiment.setProject(project);
- baseExperiment.setRegistrator(person);
- return baseExperiment;
- }
-
- private final static Properties createPropertiesWithVersion()
- {
- final Properties props = new Properties();
- props.setProperty(VERSION_PROPERTY_KEY, "1.1");
- return props;
- }
-
- @BeforeClass
- public void startQueueingPathRemover()
- {
- if (QueueingPathRemoverService.isRunning() == false)
- {
- QueueingPathRemoverService.start();
- }
- }
-
- @Override
- @BeforeMethod
- public void setUp() throws IOException
- {
- try
- {
- super.setUp();
- } catch (AssertionError e)
- {
- super.setUp();
- }
- logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.INFO);
- context = new Mockery();
- mailClient = context.mock(IMailClient.class);
- }
-
- @AfterMethod
- public void tearDown()
- {
- logRecorder.reset();
- // The following line of code should also be called at the end of each test method.
- // Otherwise one do not known which test failed.
- context.assertIsSatisfied();
- }
-
- @Test
- public final void testConstructorWithUnspecifiedArgument()
- {
- boolean fail = true;
- try
- {
- new BDSStorageProcessor(null);
- } catch (final AssertionError ex)
- {
- fail = false;
- }
- assertFalse(fail);
- }
-
- @Test
- public final void testCheckVersionInProperties()
- {
- final Properties props = new Properties();
- props.setProperty(DssPropertyParametersUtil.STOREROOT_DIR_KEY, "store");
- final String version = "ae";
- props.setProperty(VERSION_PROPERTY_KEY, version);
- try
- {
- new BDSStorageProcessor(props);
- fail("No '.' in given version.");
- } catch (final ConfigurationFailureException ex)
- {
- assertEquals(String.format(BDSStorageProcessor.NO_VERSION_FORMAT,
- BDSStorageProcessor.VERSION_KEY, version), ex.getMessage());
- }
- }
-
- @Test
- public final void testCheckVersionCompatible()
- {
- final Properties props = new Properties();
- props.setProperty(DssPropertyParametersUtil.STOREROOT_DIR_KEY, "store");
- props.setProperty(VERSION_PROPERTY_KEY, "1.2");
- try
- {
- new BDSStorageProcessor(props);
- fail("ConfigurationFailureException expected");
- } catch (final ConfigurationFailureException e)
- {
- assertEquals("Invalid version: V1.2", e.getMessage());
- }
- }
-
- @Test
- public final void testMissingFormat() throws Exception
- {
- final Properties props = createPropertiesWithVersion();
- try
- {
- new BDSStorageProcessor(props);
- fail("ConfigurationFailureException expected");
- } catch (final ConfigurationFailureException e)
- {
- assertEquals("Given key 'format' not found in properties '[version]'", e.getMessage());
- }
- }
-
- @Test
- public final void testMissingSampleTypeDescription() throws Exception
- {
- final Properties props = createPropertiesWithVersion();
- final Format format = UnknownFormatV1_0.UNKNOWN_1_0;
- props.setProperty(FORMAT_KEY, format.getCode() + " " + format.getVersion());
- try
- {
- new BDSStorageProcessor(props);
- fail("ConfigurationFailureException expected");
- } catch (final ConfigurationFailureException e)
- {
- assertEquals("Given key 'sampleTypeDescription' not found in properties "
- + "'[version, format]'", e.getMessage());
- }
- }
-
- @Test
- // we check the mode where the incoming folder has just a link to the real data. The original
- // data folder in the store should point to this data (and not to the data in incoming folder)
- public final void testStoreDataWithSymbolicLink() throws Exception
- {
- final Properties properties = createProperties(UnknownFormatV1_0.UNKNOWN_1_0);
- properties.setProperty(HCSImageFormatV1_0.IS_INCOMING_SYMBOLIC_LINK, "true");
- final IStorageProcessorTransaction storageProcessor = createTransaction(properties);
-
- final File orgData = new File(workingDirectory, "org-data.txt");
- FileUtilities.writeToFile(orgData, "hello!");
-
- final File incoming = getIncomingDir();
- SoftLinkMaker.createSymbolicLink(orgData, incoming);
-
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample baseSample = createSample();
- final DataSetInformation dataSetInformation = createDataSetInformation();
- dataSetInformation.setSample(baseSample);
-
- storeData(storageProcessor, new File(incoming, orgData.getName()), dataSetInformation);
- File datasetOriginalDir = new File(getStoreDir(), "data/original/" + orgData.getName());
- assertTrue("link to original file has not been created", datasetOriginalDir.isFile());
- String orgDataAbsPath = orgData.getAbsolutePath();
- String datasetOriginalDirReference = datasetOriginalDir.getCanonicalPath();
- assertEquals("link to original file does not point to the original data " + orgDataAbsPath
- + ", but to " + datasetOriginalDirReference, datasetOriginalDirReference,
- orgDataAbsPath);
- }
-
- @DataProvider(name = "formatProvider")
- public Object[][] getFormats()
- {
- return new Object[][]
- {
- { UnknownFormatV1_0.UNKNOWN_1_0 },
- { HCSImageFormatV1_0.HCS_IMAGE_1_0 } };
- }
-
- @Test(dataProvider = "formatProvider")
- public final void testStoreData(final Format format) throws Exception
- {
- final Properties properties = createProperties(format);
- final IStorageProcessorTransaction storageProcessor = createTransaction(properties);
- assertEquals(0, workingDirectory.list().length);
- final File incomingDataSetDirectory = createOriginalDataInDir();
- assertEquals(true, incomingDataSetDirectory.exists());
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample baseSample = createSample();
- final DataSetInformation dataSetInformation = createDataSetInformation();
- dataSetInformation.setSample(baseSample);
- prepareMailClient(format);
- final File dataFile =
- storeData(storageProcessor, incomingDataSetDirectory, dataSetInformation);
- assertEquals(getStoreDir().getAbsolutePath(), dataFile.getAbsolutePath());
- final IDataStructure dataStructure =
- new DataStructureLoader(workingDirectory).load(STORE_ROOT_DIR, true);
- assertEquals(true, dataStructure instanceof IDataStructureV1_1);
- final IDataStructureV1_1 ds = (IDataStructureV1_1) dataStructure;
- assertEquals(new Version(1, 1), ds.getVersion());
- final ch.systemsx.cisd.bds.ExperimentIdentifier eid = ds.getExperimentIdentifier();
- assertEquals(EXAMPLE_INSTANCE, eid.getInstanceCode());
- assertEquals(EXAMPLE_SPACE, eid.getSpaceCode());
- assertEquals(dataSetInformation.getExperimentIdentifier().getProjectCode(), eid
- .getProjectCode());
- assertEquals(dataSetInformation.getExperimentIdentifier().getExperimentCode(), eid
- .getExperimentCode());
- final ExperimentRegistrator registrator = ds.getExperimentRegistrator();
- final Experiment baseExperiment = baseSample.getExperiment();
- assertEquals(baseExperiment.getRegistrator().getFirstName(), registrator.getFirstName());
- assertEquals(baseExperiment.getRegistrator().getLastName(), registrator.getLastName());
- assertEquals(baseExperiment.getRegistrator().getEmail(), registrator.getEmail());
- assertEquals(REGISTRATION_DATE, ds.getExperimentRegistratorTimestamp().getDate());
- final Sample sample = ds.getSample();
- assertEquals(EXAMPLE_TYPE_DESCRIPTION, sample.getTypeDescription());
- assertEquals(dataSetInformation.getSampleIdentifier().getSampleCode(), sample.getCode());
- final Format f = ds.getFormattedData().getFormat();
- assertEquals(format, f);
- final IDirectory directory =
- (IDirectory) ds.getOriginalData().tryGetNode(INCOMING_DATA_SET_DIR);
- assertEquals(EXAMPLE_DATA, Utilities.getTrimmedString(directory, ORIGINAL_DATA_TXT));
- assertEquals(false, incomingDataSetDirectory.exists());
- // DataSet
- final DataSet dataSet = ds.getDataSet();
- assertEquals(DATA_SET_CODE, dataSet.getCode());
- assertEquals(TYPE_EXTRACTOR.getDataSetType(null).getCode(), dataSet.getDataSetTypeCode());
- assertEquals(0, dataSet.getParentCodes().size());
- assertNull(dataSet.getProducerCode());
- assertNull(dataSet.getProductionTimestamp());
- assertEquals(Boolean.TRUE, dataSet.isMeasured());
-
- context.assertIsSatisfied();
- }
-
- private File storeData(final IStorageProcessorTransaction transaction,
- final File incomingDataSetDirectory, final DataSetInformation dataSetInformation)
- {
- transaction.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
- incomingDataSetDirectory, getStoreDir());
- return transaction.getStoredDataDirectory();
- }
-
- private File getStoreDir()
- {
- return new File(workingDirectory, STORE_ROOT_DIR);
- }
-
- @Test(dataProvider = "formatProvider")
- public final void testUnstoreData(final Format format) throws Exception
- {
- final Properties properties = createProperties(format);
- final IStorageProcessorTransaction transaction = createTransaction(properties);
-
- assertEquals(0, workingDirectory.list().length);
- final File incomingDirectoryData = createOriginalDataInDir();
- // incoming/NEMO.EXP1==CP001A-3AB in 'workingDirectory'
- assert incomingDirectoryData.exists();
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample baseSample = createSample();
- final DataSetInformation dataSetInformation = createDataSetInformation();
- dataSetInformation.setSample(baseSample);
- // NEMO.EXP1==CP001A-3AB in 'workingDirectory'
- prepareMailClient(format);
- final File storeRootDir = getStoreDir();
- transaction.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
- incomingDirectoryData, storeRootDir);
- File dataStore = transaction.getStoredDataDirectory();
- assertEquals(true, dataStore.isDirectory());
- assertEquals(false, incomingDirectoryData.exists());
- transaction.rollback(null);
- assertEquals(false, dataStore.exists());
- assertEquals(true, incomingDirectoryData.isDirectory());
-
- context.assertIsSatisfied();
- }
-
- private IStorageProcessorTransaction createTransaction(final Properties properties)
- {
- return new BDSStorageProcessor(properties).createTransaction();
- }
-
- @Test(dataProvider = "formatProvider")
- public void testTryToGetOriginalData(final Format format) throws Exception
- {
- final Properties properties = createProperties(format);
- final IStorageProcessorTransaction transaction = createTransaction(properties);
- final File incomingDirectoryData = createOriginalDataInDir();
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample baseSample = createSample();
- final DataSetInformation dataSetInformation = createDataSetInformation();
- dataSetInformation.setSample(baseSample);
- prepareMailClient(format);
- transaction.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
- incomingDirectoryData, workingDirectory);
- final File originalDataSet = transaction.tryGetProprietaryData();
- assertNotNull(originalDataSet);
- assertEquals(INCOMING_DATA_SET_DIR, originalDataSet.getName());
- assertEquals(true, originalDataSet.isDirectory());
- assertEquals(format == UnknownFormatV1_0.UNKNOWN_1_0 ? BooleanOrUnknown.U
- : BooleanOrUnknown.F, dataSetInformation.getIsCompleteFlag());
- final File[] files = originalDataSet.listFiles();
- assertEquals(1, files.length);
- final File file = files[0];
- assertEquals(true, file.exists());
- assertEquals(false, file.isDirectory());
- assertEquals(ORIGINAL_DATA_TXT, file.getName());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testTryToGetOriginalDataWhichAreNotAvailable() throws Exception
- {
- final Properties properties = createProperties(HCSImageFormatV1_0.HCS_IMAGE_1_0);
- properties.setProperty(CONTAINS_ORIGINAL_DATA_KEY, Utilities.Boolean.FALSE.toString());
- final IStorageProcessorTransaction transaction = createTransaction(properties);
- final File incomingDirectoryData = createOriginalDataInDir();
- final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample baseSample = createSample();
- final DataSetInformation dataSetInformation = createDataSetInformation();
- dataSetInformation.setSample(baseSample);
- prepareMailClient(HCSImageFormatV1_0.HCS_IMAGE_1_0);
- transaction.storeData(dataSetInformation, TYPE_EXTRACTOR, mailClient,
- incomingDirectoryData, workingDirectory);
- logRecorder.resetLogContent();
- final File originalDataSet = transaction.tryGetProprietaryData();
- assertEquals(null, originalDataSet);
- assertEquals("WARN OPERATION.BDSStorageProcessor - " + "Original data are not available.",
- logRecorder.getLogContent());
-
- context.assertIsSatisfied();
- }
-
- @Test
- public void testConstructorWithInvalidFormat() throws Exception
- {
- final Properties properties = createProperties(new Format("bla", new Version(1, 2), "v"));
- try
- {
- new BDSStorageProcessor(properties);
- fail("ConfigurationFailureException expected");
- } catch (final ConfigurationFailureException e)
- {
- assertEquals("Property 'format': no valid and known format could be extracted "
- + "from text 'bla V1.2'.", e.getMessage());
- }
- }
-
- private void prepareMailClient(final Format format)
- {
- if (format != UnknownFormatV1_0.UNKNOWN_1_0)
- {
- context.checking(new Expectations()
- {
- {
- one(mailClient)
- .sendMessage(
- "Incomplete data set 'NEMO.EXP1==CP001A-3AB'",
- "Incomplete data set 'NEMO.EXP1==CP001A-3AB': "
- + "3455 image file(s) are missing (locations: "
- + "[[well=[x=16,y=1],tile=[x=3,y=3]], [well=[x=16,y=2],tile=[x=2,y=3]], "
- + "[well=[x=16,y=3],tile=[x=1,y=3]], [well=[x=24,y=10],tile=[x=1,y=3]], "
- + "[well=[x=24,y=9],tile=[x=2,y=3]], [well=[x=24,y=8],tile=[x=3,y=3]], "
- + "[well=[x=7,y=6],tile=[x=1,y=2]], [well=[x=7,y=5],tile=[x=2,y=2]], "
- + "[well=[x=7,y=4],tile=[x=3,y=2]], [well=[x=14,y=6],tile=[x=3,y=1]], "
- + "... (3445 left)])", null, null, EXAMPLE_EMAIL);
- }
- });
- }
- }
-
- //
- // Helper classes
- //
-
- public final static class TestImageFileExtractor implements IHCSImageFileExtractor
- {
-
- public TestImageFileExtractor(final Properties properties)
- {
- }
-
- //
- // IHCSImageFileExtractor
- //
-
- public final HCSImageFileExtractionResult process(
- final IDirectory incomingDataSetDirectory,
- final DataSetInformation dataSetInformation, final IHCSImageFileAccepter accepter)
- {
- assertEquals(INCOMING_DATA_SET_DIR, incomingDataSetDirectory.getName());
- final List<IFile> listFiles = incomingDataSetDirectory.listFiles(null, true);
- assertEquals(1, listFiles.size());
- final IFile file = listFiles.get(0);
- assertEquals(ORIGINAL_DATA_TXT, file.getName());
- accepter.accept(1, new Location(1, 1), new Location(1, 1), file);
- return new HCSImageFileExtractionResult(0, listFiles.size(), new ArrayList<IFile>(),
- Collections.singleton(new Channel(1, 123)));
- }
- }
-
-}
--
GitLab