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Commit a69c15c6 authored by felmer's avatar felmer
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LMS-966 transaction handling for feeding result database, better log messaging 

SVN: 11697
parent a73c5258
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rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java
+ 39
− 246
View file @ a69c15c6
...@@ -22,49 +22,33 @@ import java.sql.SQLException; ...@@ -22,49 +22,33 @@ import java.sql.SQLException;
import java.util.List; import java.util.List;
import java.util.Properties; import java.util.Properties;
import javax.sql.DataSource;
import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBContext;
import javax.xml.bind.JAXBException; import javax.xml.bind.JAXBException;
import javax.xml.bind.Unmarshaller; import javax.xml.bind.Unmarshaller;
import net.lemnik.eodsql.QueryTool; import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel; import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException; import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException; import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.utilities.ExtendedProperties; import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.PropertyUtils; import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext; import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
import ch.systemsx.cisd.etlserver.IDataSetHandler; import ch.systemsx.cisd.etlserver.IDataSetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService; import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation; import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Peptide;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.PeptideModification;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Protein;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinAnnotation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinGroup;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary; import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/** /**
* *
* *
* @author Franz-Josef Elmer * @author Franz-Josef Elmer
*/ */
public class ResultDataSetHandler extends AbstractHandler implements IDataSetHandler public class ResultDataSetHandler implements IDataSetHandler
{ {
private static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
private static final String DATABASE_ENGINE = "database.engine"; private static final String DATABASE_ENGINE = "database.engine";
private static final String DATABASE_URL_HOST_PART = "database.url-host-part"; private static final String DATABASE_URL_HOST_PART = "database.url-host-part";
private static final String DATABASE_BASIC_NAME = "database.basic-name"; private static final String DATABASE_BASIC_NAME = "database.basic-name";
...@@ -72,56 +56,10 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan ...@@ -72,56 +56,10 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan
private static final String DATABASE_OWNER = "database.owner"; private static final String DATABASE_OWNER = "database.owner";
private static final String DATABASE_PASSWORD = "database.password"; private static final String DATABASE_PASSWORD = "database.password";
private static final class ProteinDescription private static final Logger operationLog =
{ LogFactory.getLogger(LogCategory.OPERATION, ResultDataSetHandler.class);
private final String uniprotID;
private final String description;
private final String sequence;
public ProteinDescription(String proteinDescription)
{
String[] items = proteinDescription.split("\\\\");
uniprotID = tryToGetUniprotID(items);
description = tryToGetValue(items, "DE");
sequence = tryToGetValue(items, "SEQ");
}
public final String getUniprotID()
{
return uniprotID;
}
public final String getDescription()
{
return description;
}
public final String getSequence()
{
return sequence;
}
private String tryToGetUniprotID(String[] items)
{
return items == null || items.length == 0 ? null : items[0].trim();
}
private String tryToGetValue(String[] items, String key)
{
for (String item : items)
{
int indexOfEqualSign = item.indexOf('=');
if (indexOfEqualSign > 0
&& item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
{
return item.substring(indexOfEqualSign + 1).trim();
}
}
return null;
}
}
private static Connection createDatabaseConnection(Properties properties) private static DataSource createDataSource(Properties properties)
{ {
DatabaseConfigurationContext context = new DatabaseConfigurationContext(); DatabaseConfigurationContext context = new DatabaseConfigurationContext();
context.setDatabaseEngineCode(properties.getProperty(DATABASE_ENGINE, "postgresql")); context.setDatabaseEngineCode(properties.getProperty(DATABASE_ENGINE, "postgresql"));
...@@ -130,25 +68,20 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan ...@@ -130,25 +68,20 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan
context.setDatabaseKind(PropertyUtils.getMandatoryProperty(properties, DATABASE_KIND)); context.setDatabaseKind(PropertyUtils.getMandatoryProperty(properties, DATABASE_KIND));
context.setOwner(properties.getProperty(DATABASE_OWNER, "")); context.setOwner(properties.getProperty(DATABASE_OWNER, ""));
context.setPassword(properties.getProperty(DATABASE_PASSWORD, "")); context.setPassword(properties.getProperty(DATABASE_PASSWORD, ""));
try return context.getDataSource();
{
Connection connection = context.getDataSource().getConnection();
return connection;
} catch (SQLException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
} }
private final IDataSetHandler delegator; private final IDataSetHandler delegator;
private final Unmarshaller unmarshaller; private final Unmarshaller unmarshaller;
private final IEncapsulatedOpenBISService openbisService; private final IEncapsulatedOpenBISService openbisService;
private final DataSource dataSource;
public ResultDataSetHandler(Properties properties, IDataSetHandler delegator, public ResultDataSetHandler(Properties properties, IDataSetHandler delegator,
IEncapsulatedOpenBISService openbisService) IEncapsulatedOpenBISService openbisService)
{ {
super(QueryTool.getQuery(createDatabaseConnection(ExtendedProperties.getSubset(properties, dataSource =
IDataSetHandler.DATASET_HANDLER_KEY + '.', true)), IProtDAO.class)); createDataSource(ExtendedProperties.getSubset(properties,
IDataSetHandler.DATASET_HANDLER_KEY + '.', true));
this.delegator = delegator; this.delegator = delegator;
this.openbisService = openbisService; this.openbisService = openbisService;
try try
...@@ -164,7 +97,15 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan ...@@ -164,7 +97,15 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan
public List<DataSetInformation> handleDataSet(File dataSet) public List<DataSetInformation> handleDataSet(File dataSet)
{ {
long time = System.currentTimeMillis();
ProteinSummary summary = readProtXML(dataSet); ProteinSummary summary = readProtXML(dataSet);
if (operationLog.isInfoEnabled())
{
operationLog.info(summary.getProteinGroups().size()
+ " protein groups are successfully read from '" + dataSet + "' in "
+ (System.currentTimeMillis() - time) + " msec");
}
time = System.currentTimeMillis();
List<DataSetInformation> dataSets = delegator.handleDataSet(dataSet); List<DataSetInformation> dataSets = delegator.handleDataSet(dataSet);
if (dataSets.isEmpty()) if (dataSets.isEmpty())
{ {
...@@ -178,68 +119,32 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan ...@@ -178,68 +119,32 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan
"Only data set handlers (like the primary one) " + "Only data set handlers (like the primary one) " +
"registering exactly one data set are allowed."); "registering exactly one data set are allowed.");
} }
DataSetInformation dataSetInfo = dataSets.get(0); DataSetInformation dataSetInformation = dataSets.get(0);
Experiment experiment = getOrCreateExperiment(dataSetInfo.getExperiment().getPermId()); if (operationLog.isInfoEnabled())
Sample sample = getOrCreateSample(experiment, dataSetInfo.getSample().getPermId());
String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
Database database = getOrGreateDatabase(referenceDatabase);
DataSet ds = getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
addToDatabase(ds, experiment, dataSetInfo.getSample().getGroup(), summary);
return dataSets;
}
private Database getOrGreateDatabase(String databaseNameAndVersion)
{
int indexOfLastSlash = databaseNameAndVersion.lastIndexOf('/');
String nameOrVersion;
if (indexOfLastSlash < 0)
{
nameOrVersion = databaseNameAndVersion;
} else
{ {
nameOrVersion = databaseNameAndVersion.substring(indexOfLastSlash + 1); operationLog.info("Registration at openBIS took "
+ (System.currentTimeMillis() - time) + " msec: " + dataSetInformation);
} }
Database database = dao.tryToGetDatabaseByName(nameOrVersion); time = System.currentTimeMillis();
if (database == null) Connection connection;
try
{ {
database = new Database(); connection = dataSource.getConnection();
database.setNameAndVersion(nameOrVersion); connection.setAutoCommit(false);
database.setId(dao.createDatabase(database.getNameAndVersion())); } catch (SQLException ex)
}
return database;
}
private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database,
String dataSetPermID)
{
DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
if (dataSet == null)
{ {
dataSet = new DataSet(); throw CheckedExceptionTunnel.wrapIfNecessary(ex);
dataSet.setPermID(dataSetPermID);
long experimentID = experiment.getId();
dataSet.setExperimentID(experimentID);
long sampleID = sample.getId();
dataSet.setSampleID(sampleID);
long databaseID = database.getId();
dataSet.setDatabaseID(databaseID);
dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID));
} }
return dataSet; ResultDataSetUploader upLoader = new ResultDataSetUploader(connection, openbisService);
} upLoader.upload(dataSetInformation, summary);
if (operationLog.isInfoEnabled())
private Experiment getOrCreateExperiment(String experimentPermID)
{
Experiment experiment = dao.tryToGetExperimentByPermID(experimentPermID);
if (experiment == null)
{ {
experiment = new Experiment(); operationLog.info("Feeding result database took "
experiment.setPermID(experimentPermID); + (System.currentTimeMillis() - time) + " msec.");
experiment.setId(dao.createExperiment(experimentPermID));
} }
return experiment; return dataSets;
} }
private ProteinSummary readProtXML(File dataSet) private ProteinSummary readProtXML(File dataSet)
{ {
try try
...@@ -257,116 +162,4 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan ...@@ -257,116 +162,4 @@ public class ResultDataSetHandler extends AbstractHandler implements IDataSetHan
} }
} }
private void addToDatabase(DataSet dataSet, Experiment experiment, GroupPE group,
ProteinSummary summary)
{
long dataSetID = dataSet.getId();
Long databaseID = dataSet.getDatabaseID();
GroupIdentifier groupIdentifier =
new GroupIdentifier(group.getDatabaseInstance().getCode(), group.getCode());
AbundanceHandler abundanceHandler =
new AbundanceHandler(openbisService, dao, groupIdentifier, experiment);
ModificationHandler modificationHandler = new ModificationHandler(dao);
createProbabilityToFDRMapping(dataSetID, summary);
List<ProteinGroup> proteinGroups = summary.getProteinGroups();
for (ProteinGroup proteinGroup : proteinGroups)
{
double probability = proteinGroup.getProbability();
List<Protein> proteins = proteinGroup.getProteins();
if (proteins.isEmpty() == false)
{
// Only the first protein of a ProteinGroup is valid
addProtein(proteins.get(0), probability, dataSetID, databaseID, abundanceHandler,
modificationHandler);
}
}
}
private void addProtein(Protein protein, double probability, long dataSetID, Long databaseID,
AbundanceHandler abundanceHandler, ModificationHandler modificationHandler)
{
long proteinID = dao.createProtein(dataSetID, probability);
for (Parameter parameter : protein.getParameters())
{
if (PARAMETER_TYPE_ABUNDANCE.equals(parameter.getType()))
{
abundanceHandler.addAbundancesToDatabase(parameter, proteinID, protein.getName());
}
}
createIdentifiedProtein(proteinID, databaseID, protein.getAnnotation());
for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins())
{
createIdentifiedProtein(proteinID, databaseID, annotatedProtein.getAnnotation());
}
List<Peptide> peptides = protein.getPeptides();
for (Peptide peptide : peptides)
{
String peptideSequence = peptide.getSequence();
int charge = peptide.getCharge();
long peptideID = dao.createPeptide(proteinID, peptideSequence, charge);
List<PeptideModification> modifications = peptide.getModifications();
for (PeptideModification modification : modifications)
{
List<AminoAcidMass> aminoAcidMasses = modification.getAminoAcidMasses();
for (AminoAcidMass aminoAcidMass : aminoAcidMasses)
{
modificationHandler.createModification(peptideID, peptideSequence, aminoAcidMass);
}
}
}
}
private void createIdentifiedProtein(long proteinID, Long databaseID,
ProteinAnnotation annotation)
{
ProteinDescription protDesc = new ProteinDescription(annotation.getDescription());
String uniprotID = protDesc.getUniprotID();
String description = protDesc.getDescription();
ProteinReference proteinReference = dao.tryToGetProteinReference(uniprotID);
if (proteinReference == null)
{
proteinReference = new ProteinReference();
proteinReference.setUniprotID(uniprotID);
proteinReference.setDescription(description);
proteinReference.setId(dao.createProteinReference(uniprotID, description));
} else if (description.equals(proteinReference.getDescription()) == false)
{
dao.updateProteinReferenceDescription(proteinReference.getId(), description);
}
Sequence sequence =
dao.tryToGetSequenceByReferenceAndDatabase(proteinReference.getId(), databaseID);
if (sequence == null || protDesc.getSequence().equals(sequence.getSequence()) == false)
{
sequence = new Sequence(protDesc.getSequence());
sequence.setDatabaseID(databaseID);
sequence.setProteinReferenceID(proteinReference.getId());
sequence.setId(dao.createSequence(sequence));
}
dao.createIdentifiedProtein(proteinID, sequence.getId());
}
private void createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
{
Object[] s = summary.getSummaryHeader().getProgramDetails().getSummary();
if (s != null)
{
for (Object object : s)
{
if (object instanceof ProteinProphetDetails)
{
ProteinProphetDetails details = (ProteinProphetDetails) object;
List<ProteinSummaryDataFilter> filters = details.getDataFilters();
for (ProteinSummaryDataFilter proteinSummaryDataFilter : filters)
{
double probability = proteinSummaryDataFilter.getMinProbability();
double fdr = proteinSummaryDataFilter.getFalsePositiveErrorRate();
dao.createProbabilityToFDRMapping(dataSetID, probability, fdr);
}
return;
}
}
}
throw new UserFailureException("Missing Protein Prophet details.");
}
} }
rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java 0 → 100644
+ 307
− 0
View file @ a69c15c6
/*
* Copyright 2009 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.etlserver.phosphonetx;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.List;
import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AnnotatedProtein;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.DataSet;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Database;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Peptide;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.PeptideModification;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Protein;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinAnnotation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinGroup;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinProphetDetails;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinReference;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
*
*
* @author Franz-Josef Elmer
*/
class ResultDataSetUploader extends AbstractHandler
{
private static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
private static final class ProteinDescription
{
private final String uniprotID;
private final String description;
private final String sequence;
public ProteinDescription(String proteinDescription)
{
String[] items = proteinDescription.split("\\\\");
uniprotID = tryToGetUniprotID(items);
description = tryToGetValue(items, "DE");
sequence = tryToGetValue(items, "SEQ");
}
public final String getUniprotID()
{
return uniprotID;
}
public final String getDescription()
{
return description;
}
public final String getSequence()
{
return sequence;
}
private String tryToGetUniprotID(String[] items)
{
return items == null || items.length == 0 ? null : items[0].trim();
}
private String tryToGetValue(String[] items, String key)
{
for (String item : items)
{
int indexOfEqualSign = item.indexOf('=');
if (indexOfEqualSign > 0
&& item.substring(0, indexOfEqualSign).trim().equalsIgnoreCase(key))
{
return item.substring(indexOfEqualSign + 1).trim();
}
}
return null;
}
}
private final Connection connection;
private final IEncapsulatedOpenBISService openbisService;
ResultDataSetUploader(Connection connection, IEncapsulatedOpenBISService openbisService)
{
super(QueryTool.getQuery(connection, IProtDAO.class));
this.connection = connection;
this.openbisService = openbisService;
}
void upload(DataSetInformation dataSetInfo, ProteinSummary summary)
{
try
{
Experiment experiment = getOrCreateExperiment(dataSetInfo.getExperiment().getPermId());
Sample sample = getOrCreateSample(experiment, dataSetInfo.getSample().getPermId());
String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
Database database = getOrGreateDatabase(referenceDatabase);
DataSet ds = getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
addToDatabase(ds, experiment, dataSetInfo.getSample().getGroup(), summary);
connection.commit();
} catch (Throwable throwable)
{
try
{
connection.rollback();
throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
} catch (SQLException ex)
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
}
}
private Database getOrGreateDatabase(String databaseNameAndVersion)
{
int indexOfLastSlash = databaseNameAndVersion.lastIndexOf('/');
String nameOrVersion;
if (indexOfLastSlash < 0)
{
nameOrVersion = databaseNameAndVersion;
} else
{
nameOrVersion = databaseNameAndVersion.substring(indexOfLastSlash + 1);
}
Database database = dao.tryToGetDatabaseByName(nameOrVersion);
if (database == null)
{
database = new Database();
database.setNameAndVersion(nameOrVersion);
database.setId(dao.createDatabase(database.getNameAndVersion()));
}
return database;
}
private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database,
String dataSetPermID)
{
DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
if (dataSet == null)
{
dataSet = new DataSet();
dataSet.setPermID(dataSetPermID);
long experimentID = experiment.getId();
dataSet.setExperimentID(experimentID);
long sampleID = sample.getId();
dataSet.setSampleID(sampleID);
long databaseID = database.getId();
dataSet.setDatabaseID(databaseID);
dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID));
}
return dataSet;
}
private Experiment getOrCreateExperiment(String experimentPermID)
{
Experiment experiment = dao.tryToGetExperimentByPermID(experimentPermID);
if (experiment == null)
{
experiment = new Experiment();
experiment.setPermID(experimentPermID);
experiment.setId(dao.createExperiment(experimentPermID));
}
return experiment;
}
private void addToDatabase(DataSet dataSet, Experiment experiment, GroupPE group,
ProteinSummary summary)
{
long dataSetID = dataSet.getId();
Long databaseID = dataSet.getDatabaseID();
GroupIdentifier groupIdentifier =
new GroupIdentifier(group.getDatabaseInstance().getCode(), group.getCode());
AbundanceHandler abundanceHandler =
new AbundanceHandler(openbisService, dao, groupIdentifier, experiment);
ModificationHandler modificationHandler = new ModificationHandler(dao);
createProbabilityToFDRMapping(dataSetID, summary);
List<ProteinGroup> proteinGroups = summary.getProteinGroups();
for (ProteinGroup proteinGroup : proteinGroups)
{
double probability = proteinGroup.getProbability();
List<Protein> proteins = proteinGroup.getProteins();
if (proteins.isEmpty() == false)
{
// Only the first protein of a ProteinGroup is valid
addProtein(proteins.get(0), probability, dataSetID, databaseID, abundanceHandler,
modificationHandler);
}
}
}
private void addProtein(Protein protein, double probability, long dataSetID, Long databaseID,
AbundanceHandler abundanceHandler, ModificationHandler modificationHandler)
{
long proteinID = dao.createProtein(dataSetID, probability);
for (Parameter parameter : protein.getParameters())
{
if (PARAMETER_TYPE_ABUNDANCE.equals(parameter.getType()))
{
abundanceHandler.addAbundancesToDatabase(parameter, proteinID, protein.getName());
}
}
createIdentifiedProtein(proteinID, databaseID, protein.getAnnotation());
for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins())
{
createIdentifiedProtein(proteinID, databaseID, annotatedProtein.getAnnotation());
}
List<Peptide> peptides = protein.getPeptides();
for (Peptide peptide : peptides)
{
String peptideSequence = peptide.getSequence();
int charge = peptide.getCharge();
long peptideID = dao.createPeptide(proteinID, peptideSequence, charge);
List<PeptideModification> modifications = peptide.getModifications();
for (PeptideModification modification : modifications)
{
List<AminoAcidMass> aminoAcidMasses = modification.getAminoAcidMasses();
for (AminoAcidMass aminoAcidMass : aminoAcidMasses)
{
modificationHandler.createModification(peptideID, peptideSequence, aminoAcidMass);
}
}
}
}
private void createIdentifiedProtein(long proteinID, Long databaseID,
ProteinAnnotation annotation)
{
ProteinDescription protDesc = new ProteinDescription(annotation.getDescription());
String uniprotID = protDesc.getUniprotID();
String description = protDesc.getDescription();
ProteinReference proteinReference = dao.tryToGetProteinReference(uniprotID);
if (proteinReference == null)
{
proteinReference = new ProteinReference();
proteinReference.setUniprotID(uniprotID);
proteinReference.setDescription(description);
proteinReference.setId(dao.createProteinReference(uniprotID, description));
} else if (description.equals(proteinReference.getDescription()) == false)
{
dao.updateProteinReferenceDescription(proteinReference.getId(), description);
}
Sequence sequence =
dao.tryToGetSequenceByReferenceAndDatabase(proteinReference.getId(), databaseID);
if (sequence == null || protDesc.getSequence().equals(sequence.getSequence()) == false)
{
sequence = new Sequence(protDesc.getSequence());
sequence.setDatabaseID(databaseID);
sequence.setProteinReferenceID(proteinReference.getId());
sequence.setId(dao.createSequence(sequence));
}
dao.createIdentifiedProtein(proteinID, sequence.getId());
}
private void createProbabilityToFDRMapping(long dataSetID, ProteinSummary summary)
{
Object[] s = summary.getSummaryHeader().getProgramDetails().getSummary();
if (s != null)
{
for (Object object : s)
{
if (object instanceof ProteinProphetDetails)
{
ProteinProphetDetails details = (ProteinProphetDetails) object;
List<ProteinSummaryDataFilter> filters = details.getDataFilters();
for (ProteinSummaryDataFilter proteinSummaryDataFilter : filters)
{
double probability = proteinSummaryDataFilter.getMinProbability();
double fdr = proteinSummaryDataFilter.getFalsePositiveErrorRate();
dao.createProbabilityToFDRMapping(dataSetID, probability, fdr);
}
return;
}
}
}
throw new UserFailureException("Missing Protein Prophet details.");
}
}
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