From 0ca782e172ece181e460dd8ae6883f852411ec5d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 5 Apr 2011 09:41:19 +0000
Subject: [PATCH] LMS-2174 feeding database with modification fractions
SVN: 20652
---
.../phosphonetx/AbstractHandler.java | 16 +--
.../phosphonetx/AbstractSampleHandler.java | 129 ++++++++++++++++++
.../phosphonetx/AbundanceHandler.java | 108 +++------------
.../etlserver/phosphonetx/IProtDAO.java | 7 +-
.../phosphonetx/ModificationFraction.java | 85 ++++++++++++
.../ModificationFractionHandler.java | 69 ++++++++++
.../phosphonetx/ResultDataSetUploader.java | 91 +++++++++++-
.../phosphonetx/dto/AminoAcidMass.java | 21 +++
.../etlserver/phosphonetx/dto/Peptide.java | 12 ++
9 files changed, 428 insertions(+), 110 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractSampleHandler.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFraction.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFractionHandler.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractHandler.java
index 8b342e98995..040907ec50e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractHandler.java
@@ -16,11 +16,9 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
-import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
-import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
/**
- *
+ * Abstract super class of classes using {@link IProtDAO}.
*
* @author Franz-Josef Elmer
*/
@@ -32,17 +30,5 @@ abstract class AbstractHandler
{
this.dao = dao;
}
-
- protected Sample getOrCreateSample(Experiment experiment, String samplePermID)
- {
- Sample sample = dao.tryToGetSampleByPermID(samplePermID);
- if (sample == null)
- {
- sample = new Sample();
- sample.setPermID(samplePermID);
- sample.setId(dao.createSample(experiment.getId(), samplePermID));
- }
- return sample;
- }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractSampleHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractSampleHandler.java
new file mode 100644
index 00000000000..9a771c3a5e1
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbstractSampleHandler.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright 2011 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.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
+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.openbis.plugin.phosphonetx.shared.basic.CommonConstants;
+
+/**
+ * Abstract super class of classes getting or creating {@link Sample} instances.
+ *
+ * @author Franz-Josef Elmer
+ */
+abstract class AbstractSampleHandler extends AbstractHandler
+{
+ @Private
+ static final String MZXML_FILENAME = "MZXML_FILENAME";
+
+ protected static final class SampleOrError
+ {
+ Sample sample;
+
+ String error;
+ }
+
+ protected final IEncapsulatedOpenBISService openbisService;
+
+ protected final ExperimentIdentifier experimentIdentifier;
+
+ private final SpaceIdentifier space;
+
+ private final Experiment experiment;
+
+ private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
+
+ AbstractSampleHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
+ ExperimentIdentifier experimentIdentifier, Experiment experiment)
+ {
+ super(dao);
+ this.openbisService = openbisService;
+ this.experimentIdentifier = experimentIdentifier;
+ this.experiment = experiment;
+ String databaseInstanceCode = experimentIdentifier.getDatabaseInstanceCode();
+ space = new SpaceIdentifier(databaseInstanceCode, CommonConstants.MS_DATA_SPACE);
+ }
+
+ protected SampleOrError getOrCreateSampleOrError(String sampleName)
+ {
+ SampleOrError sampleOrError = samplesOrErrors.get(sampleName);
+ if (sampleOrError == null)
+ {
+ // first we look for a sample in space MS_DATA
+ SampleIdentifier sampleIdentifier = new SampleIdentifier(space, sampleName);
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+ openbisService.tryGetSampleWithExperiment(sampleIdentifier);
+ sampleOrError = new SampleOrError();
+ if (sample != null)
+ {
+ sampleOrError.sample = getOrCreateSample(sample.getPermId());
+ } else
+ {
+ // second we look for a sample in same space as search experiment with
+ // a property specified by 'sampleName'
+ String spaceCode = experimentIdentifier.getSpaceCode();
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> list =
+ openbisService.listSamplesByCriteria(new ListSamplesByPropertyCriteria(
+ MZXML_FILENAME, sampleName, spaceCode, null));
+ if (list == null || list.size() == 0)
+ {
+ sampleOrError.error = "an unidentified sample: " + sampleName;
+ } else if (list.size() > 1)
+ {
+ sampleOrError.error =
+ "a not uniquely specified sample (" + list.size()
+ + " samples are found): " + sampleName;
+ } else
+ {
+ sample = list.get(0);
+ sampleOrError.sample = getOrCreateSample(sample.getPermId());
+ }
+ }
+ if (sample != null)
+ {
+ handleSample(sampleName, sample);
+ }
+ samplesOrErrors.put(sampleName, sampleOrError);
+ }
+ return sampleOrError;
+ }
+
+ private Sample getOrCreateSample(String samplePermID)
+ {
+ Sample sample = dao.tryToGetSampleByPermID(samplePermID);
+ if (sample == null)
+ {
+ sample = new Sample();
+ sample.setPermID(samplePermID);
+ sample.setId(dao.createSample(experiment.getId(), samplePermID));
+ }
+ return sample;
+ }
+
+ protected abstract void handleSample(String parameterName,
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample);
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
index 4235d564efc..754120f59a0 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
@@ -16,11 +16,6 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
@@ -28,51 +23,23 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
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.openbis.plugin.phosphonetx.shared.basic.CommonConstants;
/**
* Handler of {@link Parameter} objects of type 'abundance'.
*
* @author Franz-Josef Elmer
*/
-class AbundanceHandler extends AbstractHandler
+class AbundanceHandler extends AbstractSampleHandler
{
- @Private
- static final String MZXML_FILENAME = "MZXML_FILENAME";
-
- private static final class SampleOrError
- {
- Sample sample;
-
- String error;
- }
-
- private final IEncapsulatedOpenBISService openbisService;
-
- private final ExperimentIdentifier experimentIdentifier;
-
- private final SpaceIdentifier msData;
-
- private final Experiment experiment;
-
- private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
-
private final SampleType sampleType;
AbundanceHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
ExperimentIdentifier experimentIdentifier, Experiment experiment)
{
- super(dao);
- this.openbisService = openbisService;
- this.experimentIdentifier = experimentIdentifier;
- this.experiment = experiment;
- msData =
- new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
- CommonConstants.MS_DATA_SPACE);
+ super(openbisService, dao, experimentIdentifier, experiment);
sampleType = new SampleType();
sampleType.setCode(Constants.SEARCH_SAMPLE_TYPE);
}
@@ -91,59 +58,9 @@ class AbundanceHandler extends AbstractHandler
}
}
- @SuppressWarnings("deprecation")
private Sample getOrCreateSample(String parameterName, String proteinName)
{
- SampleOrError sampleOrError = samplesOrErrors.get(parameterName);
- if (sampleOrError == null)
- {
- // first we look for a sample in space MS_DATA
- SampleIdentifier sampleIdentifier = new SampleIdentifier(msData, parameterName);
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- openbisService.tryGetSampleWithExperiment(sampleIdentifier);
- sampleOrError = new SampleOrError();
- if (sample != null)
- {
- sampleOrError.sample = getOrCreateSample(experiment, sample.getPermId());
- } else
- {
- // second we look for a sample in same space as search experiment with
- // a property specified by 'parameterName'
- String spaceCode = experimentIdentifier.getSpaceCode();
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> list =
- openbisService.listSamplesByCriteria(new ListSamplesByPropertyCriteria(
- MZXML_FILENAME, parameterName, spaceCode, null));
- if (list == null || list.size() == 0)
- {
- sampleOrError.error = "an unidentified sample: " + parameterName;
- } else if (list.size() > 1)
- {
- sampleOrError.error =
- "a not uniquely specified sample (" + list.size()
- + " samples are found): " + parameterName;
- } else
- {
- sample = list.get(0);
- sampleOrError.sample = getOrCreateSample(experiment, sample.getPermId());
- }
- }
- if (sample != null)
- {
- NewSample searchSample = new NewSample();
- searchSample.setSampleType(sampleType);
- SpaceIdentifier spaceIdentifier =
- new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
- experimentIdentifier.getSpaceCode());
- SampleIdentifier identifier =
- new SampleIdentifier(spaceIdentifier, parameterName + "_"
- + experimentIdentifier.getExperimentCode());
- searchSample.setIdentifier(identifier.toString());
- searchSample.setExperimentIdentifier(experimentIdentifier.toString());
- searchSample.setParentIdentifier(sample.getIdentifier());
- openbisService.registerSample(searchSample, null);
- }
- samplesOrErrors.put(parameterName, sampleOrError);
- }
+ SampleOrError sampleOrError = getOrCreateSampleOrError(parameterName);
if (sampleOrError.error != null)
{
throw new UserFailureException("Protein '" + proteinName
@@ -151,4 +68,23 @@ class AbundanceHandler extends AbstractHandler
}
return sampleOrError.sample;
}
+
+ @Override
+ @SuppressWarnings("deprecation")
+ protected void handleSample(String parameterName,
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
+ {
+ NewSample searchSample = new NewSample();
+ searchSample.setSampleType(sampleType);
+ SpaceIdentifier spaceIdentifier =
+ new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
+ experimentIdentifier.getSpaceCode());
+ SampleIdentifier identifier =
+ new SampleIdentifier(spaceIdentifier, parameterName + "_"
+ + experimentIdentifier.getExperimentCode());
+ searchSample.setIdentifier(identifier.toString());
+ searchSample.setExperimentIdentifier(experimentIdentifier.toString());
+ searchSample.setParentIdentifier(sample.getIdentifier());
+ openbisService.registerSample(searchSample, null);
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
index 058bc2417a1..25acfc4a438 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
@@ -73,8 +73,8 @@ public interface IProtDAO extends BaseQuery
@Select("insert into modified_peptides (pept_id, nterm_mass, cterm_mass) values (?{1}, ?{2}, ?{3}) returning id")
public long createModifiedPeptide(long peptideID, double nTermMass, double cTermMass);
- @Update("insert into modifications (mope_id, pos, mass) values (?{1}, ?{2}, ?{3})")
- public void createModification(long modPeptideID, int position, double mass);
+ @Select("insert into modifications (mope_id, pos, mass) values (?{1}, ?{2}, ?{3}) returning id")
+ public long createModification(long modPeptideID, int position, double mass);
@Select("select * from protein_references where accession_number = ?{1}")
public ProteinReference tryToGetProteinReference(String accessionNumber);
@@ -99,4 +99,7 @@ public interface IProtDAO extends BaseQuery
@Update("insert into abundances (prot_id, samp_id, value) values (?{1}, ?{2}, ?{3})")
public void createAbundance(long proteinID, long sampleID, double value);
+ @Update("insert into modification_fractions (modi_id, samp_id, fraction) values (?{1}, ?{2}, ?{3})")
+ public void createModificationFraction(long modID, long sampleID, double fraction);
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFraction.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFraction.java
new file mode 100644
index 00000000000..b640ea27206
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFraction.java
@@ -0,0 +1,85 @@
+/*
+ * Copyright 2011 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 ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.AminoAcidMass;
+
+/**
+ * Data class keeping data extracted from a peptide <parameter> element of type 'modification'.
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+final class ModificationFraction
+{
+ private final String sample;
+ private final double fraction;
+ private final AminoAcidMass aminoAcidMass;
+
+ ModificationFraction(String sample, String value)
+ {
+ this.sample = sample;
+ String[] parts = value.split(":");
+ if (parts.length != 3)
+ {
+ throw exception(value, "Three parts separated by ':' expected.");
+ }
+ aminoAcidMass = new AminoAcidMass();
+ try
+ {
+ aminoAcidMass.setPosition(Integer.parseInt(parts[0]));
+ } catch (NumberFormatException ex)
+ {
+ throw exception(value, "Position part isn't an integer number: " + parts[0]);
+ }
+ try
+ {
+ aminoAcidMass.setMass(Double.parseDouble(parts[1]));
+ } catch (NumberFormatException ex)
+ {
+ throw exception(value, "Mass part isn't a floating-point number: " + parts[1]);
+ }
+ try
+ {
+ fraction = Double.parseDouble(parts[2]);
+ } catch (NumberFormatException ex)
+ {
+ throw exception(value, "Fraction part isn't a floating-point number: " + parts[2]);
+ }
+ }
+
+ private IllegalArgumentException exception(String value, String message)
+ {
+ return new IllegalArgumentException("Peptide parameter value [" + value
+ + "] for sample '" + sample + "' is invalid: " + message);
+ }
+
+ public String getSample()
+ {
+ return sample;
+ }
+
+ public AminoAcidMass getAminoAcidMass()
+ {
+ return aminoAcidMass;
+ }
+
+ public double getFraction()
+ {
+ return fraction;
+ }
+}
\ No newline at end of file
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFractionHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFractionHandler.java
new file mode 100644
index 00000000000..961f7bbac4e
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ModificationFractionHandler.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2011 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.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * Handler of modification fractions.
+ *
+ * @author Franz-Josef Elmer
+ */
+class ModificationFractionHandler extends AbstractSampleHandler
+{
+ public ModificationFractionHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
+ ExperimentIdentifier experimentIdentifier, Experiment experiment)
+ {
+ super(openbisService, dao, experimentIdentifier, experiment);
+ }
+
+ @Override
+ protected void handleSample(String parameterName,
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
+ {
+ // Do nothing
+ }
+
+ public void addModificationFractions(String peptideSequence, long modID,
+ List<ModificationFraction> modificationFractions)
+ {
+ for (ModificationFraction modificationFraction : modificationFractions)
+ {
+ Sample sample = getOrCreateSample(modificationFraction.getSample(), peptideSequence);
+ double fraction = modificationFraction.getFraction();
+ dao.createModificationFraction(modID, sample.getId(), fraction);
+ }
+ }
+
+ private Sample getOrCreateSample(String sampleName, String peptideSequence)
+ {
+ SampleOrError sampleOrError = getOrCreateSampleOrError(sampleName);
+ if (sampleOrError.error != null)
+ {
+ throw new UserFailureException("Protein '" + peptideSequence
+ + "' has an abundance value for " + sampleOrError.error);
+ }
+ return sampleOrError.sample;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index 4e8344d7b90..f6ad0840c1c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -18,8 +18,12 @@ package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.sql.Connection;
import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import net.lemnik.eodsql.QueryTool;
@@ -45,6 +49,7 @@ 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.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ProbabilityToFDRCalculator;
@@ -59,6 +64,8 @@ class ResultDataSetUploader extends AbstractHandler
private static final double MAX_FALSE_DISCOVERY_RATE = 0.1;
static final String PARAMETER_TYPE_ABUNDANCE = "abundance";
+
+ static final String PARAMETER_TYPE_MODIFICATION = "modification";
private final Connection connection;
@@ -198,6 +205,9 @@ class ResultDataSetUploader extends AbstractHandler
Long databaseID = dataSet.getDatabaseID();
AbundanceHandler abundanceHandler =
new AbundanceHandler(openbisService, dao, experimentIdentifier, experiment);
+ ModificationFractionHandler modificationFractionHandler =
+ new ModificationFractionHandler(openbisService, dao, experimentIdentifier,
+ experiment);
ProbabilityToFDRCalculator calculator = createProbabilityToFDRMapping(dataSetID, summary);
List<ProteinGroup> proteinGroups = summary.getProteinGroups();
for (ProteinGroup proteinGroup : proteinGroups)
@@ -211,7 +221,8 @@ class ResultDataSetUploader extends AbstractHandler
{
if (calculator.calculateFDR(protein.getProbability()) <= MAX_FALSE_DISCOVERY_RATE)
{
- addProtein(protein, dataSetID, databaseID, abundanceHandler);
+ addProtein(protein, dataSetID, databaseID, abundanceHandler,
+ modificationFractionHandler);
}
} catch (Exception e)
{
@@ -236,7 +247,8 @@ class ResultDataSetUploader extends AbstractHandler
}
private void addProtein(Protein protein, long dataSetID, Long databaseID,
- AbundanceHandler abundanceHandler)
+ AbundanceHandler abundanceHandler,
+ ModificationFractionHandler modificationFractionHandler)
{
long proteinID = dao.createProtein(dataSetID, protein.getProbability());
for (Parameter parameter : protein.getParameters())
@@ -252,7 +264,7 @@ class ResultDataSetUploader extends AbstractHandler
{
try
{
- addPeptide(proteinID, peptide);
+ addPeptide(proteinID, peptide, modificationFractionHandler);
peptideSequences.add(peptide.getSequence());
} catch (Exception e)
{
@@ -266,7 +278,8 @@ class ResultDataSetUploader extends AbstractHandler
}
}
- private void addPeptide(long proteinID, Peptide peptide)
+ private void addPeptide(long proteinID, Peptide peptide,
+ ModificationFractionHandler modificationFractionHandler)
{
String peptideSequence = peptide.getSequence();
int charge = peptide.getCharge();
@@ -282,6 +295,54 @@ class ResultDataSetUploader extends AbstractHandler
logException(e, "modification", modification.toString());
}
}
+ List<ModificationFraction> modificationFractions = extractModificationFractions(peptide);
+ if (modificationFractions.isEmpty())
+ {
+ return;
+ }
+ long modPeptideID = dao.createModifiedPeptide(peptideID, 0, 0);
+ Map<AminoAcidMass, List<ModificationFraction>> map =
+ groupByPositionAndMass(modificationFractions);
+ Set<Entry<AminoAcidMass, List<ModificationFraction>>> entrySet = map.entrySet();
+ for (Entry<AminoAcidMass, List<ModificationFraction>> entry : entrySet)
+ {
+ AminoAcidMass positionAndMass = entry.getKey();
+ long modID = createModification(modPeptideID, positionAndMass);
+ List<ModificationFraction> list = entry.getValue();
+ modificationFractionHandler.addModificationFractions(peptideSequence, modID, list);
+ }
+ }
+
+ private Map<AminoAcidMass, List<ModificationFraction>> groupByPositionAndMass(
+ List<ModificationFraction> modificationFractions)
+ {
+ Map<AminoAcidMass, List<ModificationFraction>> result =
+ new HashMap<AminoAcidMass, List<ModificationFraction>>();
+ for (ModificationFraction modificationFraction : modificationFractions)
+ {
+ AminoAcidMass positionAndMass = modificationFraction.getAminoAcidMass();
+ List<ModificationFraction> list = result.get(positionAndMass);
+ if (list == null)
+ {
+ list = new ArrayList<ModificationFraction>();
+ result.put(positionAndMass, list);
+ }
+ list.add(modificationFraction);
+ }
+ return result;
+ }
+
+ private List<ModificationFraction> extractModificationFractions(Peptide peptide)
+ {
+ List<ModificationFraction> result = new ArrayList<ModificationFraction>();
+ for (Parameter parameter : peptide.getParameters())
+ {
+ if (PARAMETER_TYPE_MODIFICATION.equals(parameter.getType()))
+ {
+ result.add(new ModificationFraction(parameter.getName(), parameter.getValue()));
+ }
+ }
+ return result;
}
private void addPeptideModification(long peptideID, PeptideModification modification)
@@ -292,12 +353,16 @@ class ResultDataSetUploader extends AbstractHandler
List<AminoAcidMass> aminoAcidMasses = modification.getAminoAcidMasses();
for (AminoAcidMass aminoAcidMass : aminoAcidMasses)
{
- double mass = aminoAcidMass.getMass();
- int position = aminoAcidMass.getPosition();
- dao.createModification(modPeptideID, position, mass);
+ createModification(modPeptideID, aminoAcidMass);
}
}
+ private long createModification(long modPeptideID, AminoAcidMass aminoAcidMass)
+ {
+ return dao.createModification(modPeptideID, aminoAcidMass.getPosition(),
+ aminoAcidMass.getMass());
+ }
+
private void createIdentifiedProtein(long proteinID, Set<String> peptideSequences,
Long databaseID, ProteinAnnotation annotation, boolean primary)
{
@@ -380,4 +445,16 @@ class ResultDataSetUploader extends AbstractHandler
}
throw new UserFailureException("Missing Protein Prophet details.");
}
+
+ protected Sample getOrCreateSample(Experiment experiment, String samplePermID)
+ {
+ Sample sample = dao.tryToGetSampleByPermID(samplePermID);
+ if (sample == null)
+ {
+ sample = new Sample();
+ sample.setPermID(samplePermID);
+ sample.setId(dao.createSample(experiment.getId(), samplePermID));
+ }
+ return sample;
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/AminoAcidMass.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/AminoAcidMass.java
index 91801aa5624..2e948ec5330 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/AminoAcidMass.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/AminoAcidMass.java
@@ -48,6 +48,27 @@ public class AminoAcidMass
this.mass = mass;
}
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (obj == this)
+ {
+ return true;
+ }
+ if (obj instanceof AminoAcidMass == false)
+ {
+ return false;
+ }
+ AminoAcidMass that = (AminoAcidMass) obj;
+ return this.position == that.position && this.mass == that.mass;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return (int) (37 * position + mass);
+ }
+
@Override
public String toString()
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Peptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Peptide.java
index 2d7da97a5a7..26020f39c3d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Peptide.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/Peptide.java
@@ -38,6 +38,7 @@ public class Peptide
private int charge;
private double initialProbability;
private double weight;
+ private List<Parameter> parameters = new ArrayList<Parameter>();
private List<PeptideModification> modifications = new ArrayList<PeptideModification>();
@XmlAttribute(name = "peptide_sequence", required = true)
@@ -95,6 +96,17 @@ public class Peptide
this.modifications = modifications;
}
+ @XmlElement(name = "parameter", namespace = Constants.NAMESPACE)
+ public final List<Parameter> getParameters()
+ {
+ return parameters;
+ }
+
+ public final void setParameters(List<Parameter> parameters)
+ {
+ this.parameters = parameters;
+ }
+
@Override
public String toString()
{
--
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