diff --git a/rtd_yeastx/etc/log.xml b/rtd_yeastx/etc/log.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5cee0a68436a19a6c4ec4b14b580e6d9f75bf84f
--- /dev/null
+++ b/rtd_yeastx/etc/log.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j='http://jakarta.apache.org/log4j/'>
+
+ <appender name="STDOUT" class="org.apache.log4j.ConsoleAppender">
+ <layout class="org.apache.log4j.PatternLayout">
+ <param name="ConversionPattern" value="%d %-5p [%t] %c - %m%n"/>
+ </layout>
+ </appender>
+
+ <appender name="NULL" class="org.apache.log4j.varia.NullAppender" />
+
+ <root>
+ <priority value ="info" />
+ <appender-ref ref="STDOUT" />
+ </root>
+
+</log4j:configuration>
diff --git a/rtd_yeastx/etc/service.properties b/rtd_yeastx/etc/service.properties
new file mode 100644
index 0000000000000000000000000000000000000000..07d265ca3bd11707815ff4641f340faea5a530bc
--- /dev/null
+++ b/rtd_yeastx/etc/service.properties
@@ -0,0 +1,308 @@
+# Unique code of this Data Store Server. Not more than 40 characters.
+data-store-server-code = DSS1
+
+root = targets/yeastx
+
+# The root directory of the data store
+storeroot-dir = ${root}/store
+
+# The directory where the command queue file is located; defaults to storeroot-dir
+commandqueue-dir = ${root}
+
+# Port
+port = 8444
+
+# Session timeout in minutes
+session-timeout = 30
+
+# Path to the keystore
+keystore.path = dist/etc/openBIS.keystore
+
+use-ssl = false
+
+# Password of the keystore
+keystore.password = changeit
+
+# Key password of the keystore
+keystore.key-password = changeit
+
+# The check interval (in seconds)
+check-interval = 2
+
+# The time-out for clean up work in the shutdown sequence (in seconds).
+# Note that that the maximal time for the shutdown sequence to complete can be as large
+# as twice this time.
+shutdown-timeout = 2
+
+#�If free disk space goes below value defined here, a notification email will be sent.
+# Value must be specified in kilobytes (1048576 = 1024 * 1024 = 1GB). If no high water mark is
+# specified or if value is negative, the system will not be watching.
+highwater-mark = 1048576
+
+# The URL of the openBIS server
+server-url = http://localhost:8888/openbis
+
+# The username to use when contacting the openBIS server
+username = etlserver_yeastx
+
+# The password to use when contacting the openBIS server
+password = doesnotmatter
+
+# The base URL for Web client access.
+download-url = http://localhost:8444
+
+# SMTP properties (must start with 'mail' to be considered).
+mail.smtp.host = file://${root}
+mail.from = datastore_server@localhost
+mail.smtp.user =
+mail.smtp.password =
+
+yeastx-databaseEngineCode = postgresql
+yeastx-basicDatabaseName = metabol
+yeastx-databaseKind = dev
+yeastx-readOnlyGroup = metabol_readonly
+yeastx-readWriteGroup = metabol_readwrite
+yeastx-scriptFolder = sql
+
+# ---------------------------------------------------------------------------
+
+#maintenance-plugins=ds-remover
+
+ds-remover.class = ch.systemsx.cisd.yeastx.etl.MetabolDatabaseUpdater
+ds-remover.interval = 10
+ds-remover.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+ds-remover.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+ds-remover.database.databaseKind = ${yeastx-databaseKind}
+
+# ---------------------------------------------------------------------------
+
+# list of additional web servlets which will be exposed
+plugin-services = chromatogram-image-download-servlet
+# class of the web servlet
+chromatogram-image-download-servlet.class = ch.systemsx.cisd.openbis.dss.yeastx.server.EICMLChromatogramGeneratorServlet
+# URL which will be mapped to this servlet
+chromatogram-image-download-servlet.path = /datastore_server/chromatogram
+chromatogram-image-download-servlet.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+chromatogram-image-download-servlet.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+chromatogram-image-download-servlet.database.databaseKind = ${yeastx-databaseKind}
+
+
+# ------------------------
+
+# Comma separated names of reporting plugins. Each plugin should have configuration properties prefixed with its name.
+reporting-plugins = eicml-chromatograms-reporter, eicml-runs-reporter, eicml-chromatogram-images-reporter
+
+# Label of the plugin which will be shown for the users.
+eicml-chromatograms-reporter.label = Show eicML chromatograms
+# Comma separated list of dataset type codes which can be handled by this plugin.
+eicml-chromatograms-reporter.dataset-types = EICML
+# Plugin class specification (together with the list of packages this class belongs to).
+eicml-chromatograms-reporter.class = ch.systemsx.cisd.yeastx.eicml.EICMLChromatogramsReporter
+# The property file. Its content will be passed as a parameter to the plugin.
+eicml-chromatograms-reporter.properties-file =
+eicml-chromatograms-reporter.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+eicml-chromatograms-reporter.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+eicml-chromatograms-reporter.database.databaseKind = ${yeastx-databaseKind}
+eicml-chromatograms-reporter.database.readOnlyGroup = ${yeastx-readOnlyGroup}
+eicml-chromatograms-reporter.database.readWriteGroup = ${yeastx-readWriteGroup}
+eicml-chromatograms-reporter.database.scriptFolder = ${yeastx-scriptFolder}
+
+# Label of the plugin which will be shown for the users.
+eicml-runs-reporter.label = Show eicML runs
+# Comma separated list of dataset type codes which can be handled by this plugin.
+eicml-runs-reporter.dataset-types = EICML
+# Plugin class specification (together with the list of packages this class belongs to).
+eicml-runs-reporter.class = ch.systemsx.cisd.yeastx.eicml.EICMLRunsReporter
+# The property file. Its content will be passed as a parameter to the plugin.
+eicml-runs-reporter.properties-file =
+eicml-runs-reporter.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+eicml-runs-reporter.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+eicml-runs-reporter.database.databaseKind = ${yeastx-databaseKind}
+
+# Label of the plugin which will be shown for the users.
+eicml-chromatogram-images-reporter.label = Show eicML chromatogram images
+# Comma separated list of dataset type codes which can be handled by this plugin.
+eicml-chromatogram-images-reporter.dataset-types = EICML
+# Plugin class specification (together with the list of packages this class belongs to).
+eicml-chromatogram-images-reporter.class = ch.systemsx.cisd.yeastx.eicml.EICMLChromatogramImagesReporter
+# The property file. Its content will be passed as a parameter to the plugin.
+eicml-chromatogram-images-reporter.properties-file =
+eicml-chromatogram-images-reporter.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+eicml-chromatogram-images-reporter.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+eicml-chromatogram-images-reporter.database.databaseKind = ${yeastx-databaseKind}
+eicml-chromatogram-images-reporter.database.readOnlyGroup = ${yeastx-readOnlyGroup}
+eicml-chromatogram-images-reporter.database.readWriteGroup = ${yeastx-readWriteGroup}
+eicml-chromatogram-images-reporter.database.scriptFolder = ${yeastx-scriptFolder}
+
+# ------------------------
+
+# The period of no write access that needs to pass before an incoming data item is considered
+# complete and ready to be processed (in seconds) [default: 300].
+# Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
+quiet-period = 3
+
+# ------------------------
+
+inputs=main-thread, eicml-uploader, fiaml-uploader, quantml-uploader
+
+# Globally used separator character which separates entities in a data set file name
+data-set-file-name-entity-separator = .
+
+# ---------------------------------------------------------------------------
+# 'main-thread' thread configuration
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+main-thread.incoming-dir = ${root}/incoming
+
+# Determines when the incoming data should be considered complete and ready to be processed.
+# Allowed values:
+# - auto-detection - when no write access will be detected for a specified 'quite-period'
+# - marker-file - when an appropriate marker file for the data exists.
+# The default value is 'marker-file'.
+main-thread.incoming-data-completeness-condition = auto-detection
+main-thread.incoming-dir.format =
+main-thread.reprocess-faulty-datasets = true
+
+sample-name-property-code = samplename
+experiment-name-property-code = name
+file-name-property-code = file_name
+
+gain-write-access-script = ../datastore_server_yeastx/takeCifsOwnershipRecursive.sh
+
+main-thread.dataset-handler = ch.systemsx.cisd.yeastx.etl.BatchDataSetHandler
+main-thread.dataset-handler.preprocessing-script = ${gain-write-access-script}
+main-thread.dataset-handler.preprocessing-script-max-retries = 4
+main-thread.dataset-handler.preprocessing-script-failure-interval = 3
+main-thread.dataset-handler.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.dataset-handler.unique-experiment-name-property-code = ${experiment-name-property-code}
+
+# The extractor class to use for code extraction
+main-thread.data-set-info-extractor = ch.systemsx.cisd.yeastx.etl.BatchDataSetInfoExtractor
+main-thread.data-set-info-extractor.file-name-property-code = ${file-name-property-code}
+main-thread.data-set-info-extractor.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.data-set-info-extractor.unique-experiment-name-property-code = ${experiment-name-property-code}
+
+# The extractor class to use for type extraction
+main-thread.type-extractor = ch.systemsx.cisd.yeastx.etl.TypeExtractorYeastX
+# comma separated list of pairs: file-extension file-type
+# It is assumed that for each file extension a dataset type with the same name is defined in openBIS.
+# The corresponding file types have to be defined in openBIS as well.
+# Files with unspecified extensions will have the file type and dataset type UNKNOWN in openBIS.
+main-thread.type-extractor.file-types = pdf pdf, mat matlab, zip archive, eicml xml, fiaml xml, mzxml xml
+
+# The storage processor (IStorageProcessor implementation)
+main-thread.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithDropboxes
+main-thread.storage-processor.eicml-dropbox-dir = ${root}/dropbox-eicml
+main-thread.storage-processor.fiaml-dropbox-dir = ${root}/dropbox-fiaml
+main-thread.storage-processor.entity-separator = .
+main-thread.storage-processor.processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+main-thread.storage-processor.processor.unique-sample-name-property-code = ${sample-name-property-code}
+main-thread.storage-processor.processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+main-thread.storage-processor.processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+main-thread.storage-processor.processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+main-thread.storage-processor.processor.database.databaseKind = ${yeastx-databaseKind}
+main-thread.storage-processor.processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+# ---------------------------------------------------------------------------
+# plugin properties for the thread which uploads eicML files
+# ---------------------------------------------------------------------------
+
+# The directory to watch for incoming data.
+eicml-uploader.incoming-dir = ${root}/incoming-eicml
+eicml-uploader.incoming-data-completeness-condition = auto-detection
+eicml-uploader.incoming-dir.format =
+eicml-uploader.reprocess-faulty-datasets = false
+
+# The extractor class to use for code extraction
+eicml-uploader.data-set-info-extractor = ch.systemsx.cisd.yeastx.etl.DataSetInfoExtractorYeastX
+eicml-uploader.data-set-info-extractor.file-name-property-code = ${file-name-property-code}
+eicml-uploader.data-set-info-extractor.index-of-experiment-identifier = 0
+eicml-uploader.data-set-info-extractor.index-of-parent-data-set-codes = 1
+eicml-uploader.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+
+# The extractor class to use for type extraction
+eicml-uploader.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+eicml-uploader.type-extractor.file-format-type = XML
+eicml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+eicml-uploader.type-extractor.data-set-type = EICML
+eicml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+eicml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+eicml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+eicml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+eicml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+eicml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+eicml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+eicml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+# ---------------- plugin properties for the thread which uploads fiaML files
+
+# The directory to watch for incoming data.
+fiaml-uploader.incoming-dir = ${root}/incoming-fiaml
+fiaml-uploader.incoming-data-completeness-condition = auto-detection
+fiaml-uploader.incoming-dir.format =
+fiaml-uploader.reprocess-faulty-datasets = false
+
+# The extractor class to use for code extraction
+fiaml-uploader.data-set-info-extractor = ch.systemsx.cisd.yeastx.etl.DataSetInfoExtractorYeastX
+fiaml-uploader.data-set-info-extractor.file-name-property-code = ${file-name-property-code}
+fiaml-uploader.data-set-info-extractor.index-of-experiment-identifier = 0
+fiaml-uploader.data-set-info-extractor.index-of-parent-data-set-codes = 1
+fiaml-uploader.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
+
+# The extractor class to use for type extraction
+fiaml-uploader.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+fiaml-uploader.type-extractor.file-format-type = XML
+fiaml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+fiaml-uploader.type-extractor.data-set-type = FIAML
+fiaml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+fiaml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.StorageProcessorWithMLUploader
+fiaml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+fiaml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+fiaml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+fiaml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+fiaml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+fiaml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+# ---------------- plugin properties for the thread which uploads quantML files
+
+# The directory to watch for incoming data.
+quantml-uploader.incoming-dir = ${root}/incoming-quantml
+quantml-uploader.incoming-data-completeness-condition = auto-detection
+quantml-uploader.incoming-dir.format =
+quantml-uploader.reprocess-faulty-datasets = false
+
+# The extractor class to use for code extraction
+quantml-uploader.data-set-info-extractor = ch.systemsx.cisd.yeastx.etl.QuantMLDataSetInfoExtractor
+quantml-uploader.data-set-info-extractor.index-of-experiment-identifier = 0
+quantml-uploader.data-set-info-extractor.sub-entity-separator = &
+# unused but required to be different than sub-entity-separator
+quantml-uploader.data-set-info-extractor.entity-separator = .
+
+# The extractor class to use for type extraction
+quantml-uploader.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
+quantml-uploader.type-extractor.file-format-type = XML
+quantml-uploader.type-extractor.locator-type = RELATIVE_LOCATION
+quantml-uploader.type-extractor.data-set-type = UNKNOWN
+quantml-uploader.type-extractor.is-measured = false
+
+# The storage processor which uploads the content of the files to the additional database
+quantml-uploader.storage-processor = ch.systemsx.cisd.yeastx.etl.QuantMLStorageProcessor
+quantml-uploader.storage-processor.preprocessing-script = ${gain-write-access-script}
+quantml-uploader.storage-processor.unique-sample-name-property-code = ${sample-name-property-code}
+quantml-uploader.storage-processor.unique-experiment-name-property-code = ${experiment-name-property-code}
+quantml-uploader.storage-processor.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+quantml-uploader.storage-processor.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+quantml-uploader.storage-processor.database.databaseKind = ${yeastx-databaseKind}
+quantml-uploader.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
+
+archiver.class = ch.systemsx.cisd.yeastx.etl.MLArchiverTask
+archiver.database.databaseEngineCode = ${yeastx-databaseEngineCode}
+archiver.database.basicDatabaseName = ${yeastx-basicDatabaseName}
+archiver.database.databaseKind = ${yeastx-databaseKind}
+archiver.unique-sample-name-property-code = ${sample-name-property-code}
+archiver.unique-experiment-name-property-code = ${experiment-name-property-code}
diff --git a/rtd_yeastx/resource/eclipse/yeastx Data Store Server.launch b/rtd_yeastx/resource/eclipse/yeastx Data Store Server.launch
new file mode 100644
index 0000000000000000000000000000000000000000..e4c351b6f44411b59fb0f3860575bace59aa3d1a
--- /dev/null
+++ b/rtd_yeastx/resource/eclipse/yeastx Data Store Server.launch
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<launchConfiguration type="org.eclipse.jdt.launching.localJavaApplication">
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_PATHS">
+<listEntry value="/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/DataStoreServer.java"/>
+</listAttribute>
+<listAttribute key="org.eclipse.debug.core.MAPPED_RESOURCE_TYPES">
+<listEntry value="1"/>
+</listAttribute>
+<booleanAttribute key="org.eclipse.debug.core.appendEnvironmentVariables" value="true"/>
+<stringAttribute key="org.eclipse.jdt.launching.MAIN_TYPE" value="ch.systemsx.cisd.openbis.dss.generic.DataStoreServer"/>
+<stringAttribute key="org.eclipse.jdt.launching.PROJECT_ATTR" value="rtd_yeastx"/>
+<stringAttribute key="org.eclipse.jdt.launching.VM_ARGUMENTS" value="-ea"/>
+</launchConfiguration>
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
index a6258f0df9e89d63ccb4dc757ddcef3df499d18a..8e03104e266f530995c855217f7c98a7e08a54ad 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
@@ -62,4 +62,7 @@ public interface IGenericDAO extends TransactionQuery
@Update(sql = "delete from DATA_SETS where PERM_ID=?{1.permId}", batchUpdate = true)
public void deleteDataSets(List<DMDataSetDTO> dataSets);
+ @Update(sql = "delete from DATA_SETS where PERM_ID=?{1}")
+ public void deleteDataSet(String permId);
+
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
index ae61eb7f28249933b6fe0d4a495eda5910da1495..a5f81b33371c385c6bfb4c37f3dba6ae50487d8a 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
@@ -84,6 +84,21 @@ public class ML2DatabaseUploader implements IDataSetUploader
/** uploads files with recognized extensions to the additional database */
public void upload(File dataSet, DataSetInformation dataSetInformation)
throws EnvironmentFailureException
+ {
+ uploadData(dataSet, dataSetInformation.tryToGetSample(), dataSetInformation
+ .tryToGetExperiment(), dataSetInformation.getDataSetCode(), dataSetInformation);
+ }
+
+ /**
+ * Uploads files with recognized extensions to the additional database.
+ */
+ public void upload(File dataSet, Sample sampleOrNull, Experiment experiment, String dataSetCode)
+ {
+ uploadData(dataSet, sampleOrNull, experiment, dataSetCode, null);
+ }
+
+ private void uploadData(File dataSet, Sample sample, Experiment experiment, String dataSetCode,
+ DataSetInformation dataSetInformationOrNull)
{
try
{
@@ -92,10 +107,12 @@ public class ML2DatabaseUploader implements IDataSetUploader
throw new IllegalStateException(
"Current transaction has been neither commited nor rollbacked.");
}
- this.currentTransaction = tryGetDatasetUploader(dataSet, dataSetInformation);
+ this.currentTransaction =
+ tryGetDatasetUploader(dataSet, isMZXMLWithNoConversion(dataSet,
+ dataSetInformationOrNull));
if (currentTransaction != null)
{
- DMDataSetDTO openbisBacklink = createBacklink(dataSetInformation);
+ DMDataSetDTO openbisBacklink = createBacklink(dataSetCode, sample, experiment);
currentTransaction.upload(dataSet, openbisBacklink);
}
} catch (SQLException e)
@@ -104,12 +121,11 @@ public class ML2DatabaseUploader implements IDataSetUploader
.fromTemplate(
e,
"A database error occured while extracting additional information from '%s' file content for '%s' dataset.",
- dataSet.getPath(), dataSetInformation.getDataSetCode());
+ dataSet.getPath(), dataSetCode);
}
}
- private IDatasetLoader tryGetDatasetUploader(File dataSet, DataSetInformation dataSetInformation)
- throws SQLException
+ private IDatasetLoader tryGetDatasetUploader(File dataSet, boolean isMZXML) throws SQLException
{
String extension = getExtension(dataSet);
if (extension.equalsIgnoreCase(ConstantsYeastX.FIAML_EXT))
@@ -121,17 +137,23 @@ public class ML2DatabaseUploader implements IDataSetUploader
} else if (extension.equalsIgnoreCase(ConstantsYeastX.QUANTML_EXT))
{
return quantML2Database;
- } else if (extension.equalsIgnoreCase(ConstantsYeastX.MZXML_EXT))
+ } else if (isMZXML)
{
- DataSetInformationYeastX info = (DataSetInformationYeastX) dataSetInformation;
- if (info.getConversion() == MLConversionType.NONE)
- {
- return mzXml2Database;
- }
+ return mzXml2Database;
}
return null;
}
+ private static boolean isMZXMLWithNoConversion(File dataSet,
+ DataSetInformation dataSetInformationOrNull)
+ {
+ boolean isMZXMLExtension =
+ getExtension(dataSet).equalsIgnoreCase(ConstantsYeastX.MZXML_EXT);
+ boolean dataSetUndefined = dataSetInformationOrNull == null;
+ return (isMZXMLExtension && (dataSetUndefined || ((dataSetInformationOrNull instanceof DataSetInformationYeastX && ((DataSetInformationYeastX) dataSetInformationOrNull)
+ .getConversion() == MLConversionType.NONE))));
+ }
+
public void commit()
{
try
@@ -160,10 +182,8 @@ public class ML2DatabaseUploader implements IDataSetUploader
}
}
- private DMDataSetDTO createBacklink(DataSetInformation dataSetInformation)
+ private DMDataSetDTO createBacklink(String datasetPermId, Sample sample, Experiment experiment)
{
- String datasetPermId = dataSetInformation.getDataSetCode();
- Sample sample = dataSetInformation.tryToGetSample();
String sampleName = UNKNOWN_NAME;
String sampPermIdOrNull = null;
if (sample != null)
@@ -171,12 +191,10 @@ public class ML2DatabaseUploader implements IDataSetUploader
sampleName = findSampleName(sample.getProperties());
sampPermIdOrNull = sample.getPermId();
}
- Experiment experiment = dataSetInformation.tryToGetExperiment();
if (experiment == null)
{
throw new EnvironmentFailureException(
- "No information about the experiment connected to a dataset "
- + dataSetInformation);
+ "No information about the experiment connected to a dataset " + datasetPermId);
}
String experimentName = findExperimentName(experiment.getProperties());
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
new file mode 100644
index 0000000000000000000000000000000000000000..2489c04fde25c74514edf3733103c59ff3417860
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
@@ -0,0 +1,132 @@
+/*
+ * 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.yeastx.etl;
+
+import java.io.File;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractArchiverProcessingPlugin;
+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.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+
+/**
+ * Archiver that removes/adds data related to given data set from/to metabol database.
+ *
+ * @author Izabela Adamczyk
+ */
+public class MLArchiverTask extends AbstractArchiverProcessingPlugin
+{
+
+ private static final long serialVersionUID = 1L;
+
+ public MLArchiverTask(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot, null, null);
+ }
+
+ /**
+ * Deletes data related to given data set from metabol database.
+ */
+ @Override
+ protected void archive(DatasetDescription dataset) throws UserFailureException
+ {
+ final IGenericDAO dao = createQuery(properties);
+ try
+ {
+ dao.deleteDataSet(dataset.getDatasetCode());
+ dao.commit();
+ } catch (Exception ex)
+ {
+ dao.rollback();
+ throw new UserFailureException(ex.getMessage());
+ } finally
+ {
+ dao.close();
+ }
+ }
+
+ private static IGenericDAO createQuery(Properties properties)
+ {
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ DataSource dataSource = dbContext.getDataSource();
+ return QueryTool.getQuery(dataSource, IGenericDAO.class);
+ }
+
+ /**
+ * Adds data related to given data set to metabol database.
+ */
+ @Override
+ protected void unarchive(DatasetDescription dataset) throws UserFailureException
+ {
+ try
+ {
+ Sample sample = null;
+ if (dataset.getSampleCode() != null)
+ {
+ SampleIdentifier sampleIdentifier =
+ new SampleIdentifier(new SpaceIdentifier(dataset.getDatabaseInstanceCode(),
+ dataset.getGroupCode()), dataset.getSampleCode());
+ sample =
+ ServiceProvider.getOpenBISService().tryGetSampleWithExperiment(
+ sampleIdentifier);
+ }
+ ExperimentIdentifier experimentIdentifier =
+ new ExperimentIdentifier(dataset.getDatabaseInstanceCode(), dataset
+ .getGroupCode(), dataset.getProjectCode(), dataset.getExperimentCode());
+ Experiment experiment =
+ ServiceProvider.getOpenBISService().tryToGetExperiment(experimentIdentifier);
+ ML2DatabaseUploader databaseUploader = new ML2DatabaseUploader(properties);
+ databaseUploader.upload(getDataFile(dataset), sample, experiment, dataset
+ .getDatasetCode());
+ databaseUploader.commit();
+ } catch (Exception ex)
+ {
+ throw new UserFailureException(ex.getMessage());
+ }
+ }
+
+ private File getDataFile(DatasetDescription dataset)
+ {
+ File datasetDir = getDataSubDir(dataset);
+ File[] files = datasetDir.listFiles();
+ if (files.length < 1)
+ {
+ throw new UserFailureException(
+ "Data set directory contains no files (exactly one expected)");
+ } else if (files.length > 1)
+ {
+ throw new UserFailureException(
+ "Data set directory contains more than one file (exactly one expected)");
+ } else
+ {
+ return files[0];
+ }
+ }
+}