From 4086791f716b6ea641fb64abff0e340adf91188c Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Wed, 17 Jun 2009 18:11:17 +0000
Subject: [PATCH] refactor: database to have the "standard" experiment, sample
and data_set dimensions
SVN: 11419
---
.../ch/systemsx/cisd/yeastx/db/DBFactory.java | 39 ++++++
.../systemsx/cisd/yeastx/db/DMDataSetDTO.java | 114 +++++++++++++++++
.../cisd/yeastx/db/DMExperimentDTO.java | 77 +++++++++++
.../systemsx/cisd/yeastx/db/DMSampleDTO.java | 105 +++++++++++++++
.../systemsx/cisd/yeastx/db/IGenericDAO.java | 59 +++++++++
.../cisd/yeastx/eicml/ChromatogramDTO.java | 10 +-
.../cisd/yeastx/eicml/EICML2Database.java | 17 ++-
.../cisd/yeastx/eicml/EICML2TabConverter.java | 6 +-
.../cisd/yeastx/eicml/EICMLParser.java | 8 +-
.../cisd/yeastx/eicml/EICMSRunDTO.java | 49 +++++--
.../cisd/yeastx/eicml/IEICMSRunDAO.java | 29 +++--
.../cisd/yeastx/etl/ML2DatabaseUploader.java | 7 +-
.../cisd/yeastx/fiaml/CentroidDTO.java | 13 +-
.../cisd/yeastx/fiaml/FIAML2Database.java | 12 +-
.../cisd/yeastx/fiaml/FIAMLParser.java | 6 +-
.../cisd/yeastx/fiaml/FIAMSRunDTO.java | 49 +++++--
.../cisd/yeastx/fiaml/FIAMSRunDataDTO.java | 16 ---
.../cisd/yeastx/fiaml/IFIAMSRunDAO.java | 19 +--
.../cisd/yeastx/fiaml/ProfileDTO.java | 11 +-
.../source/sql/postgresql/001/schema-001.sql | 121 +++++++++++++-----
.../systemsx/cisd/yeastx/eicml/EICMLTest.java | 10 +-
.../systemsx/cisd/yeastx/fiaml/FIAMLTest.java | 14 +-
22 files changed, 647 insertions(+), 144 deletions(-)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
index c49777bd2d3..b1e26701bab 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBFactory.java
@@ -70,4 +70,43 @@ public class DBFactory
return context;
}
+ /**
+ * Returns the data access object for the generic tables of the data mart.
+ */
+ public static IGenericDAO getDAO(Connection conn)
+ {
+ return QueryTool.getQuery(conn, IGenericDAO.class);
+ }
+
+ /**
+ * Creates the data set based on the information given in <var>dataSet</var>. The sample and
+ * experiment of the data set may already exist in the database. If they don't, they are created
+ * as well.
+ */
+ public static void createDataSet(IGenericDAO dao, DMDataSetDTO dataSet)
+ {
+ DMSampleDTO sample = dao.getSample(dataSet.getSample().getPermId());
+ if (sample == null)
+ {
+ DMExperimentDTO experiment = dao.getExperiment(dataSet.getExperiment().getPermId());
+ if (experiment == null)
+ {
+ experiment = dataSet.getExperiment();
+ final long experimentId = dao.addExperiment(experiment);
+ experiment.setId(experimentId);
+ }
+ sample = dataSet.getSample();
+ sample.setExperiment(experiment);
+ final long sampleId = dao.addSample(sample);
+ sample.setId(sampleId);
+ dataSet.setSample(sample); // make sure all the ids are set correctly.
+ } else
+ {
+ dataSet.setSample(sample);
+ sample.setExperiment(dao.getExperiment(sample.getExperimentId()));
+ }
+ long dataSetId = dao.addDataSet(dataSet);
+ dataSet.setId(dataSetId);
+ }
+
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java
new file mode 100644
index 00000000000..6d480c39103
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java
@@ -0,0 +1,114 @@
+/*
+ * 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.yeastx.db;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * The generic information about a data set for the data mart.
+ *
+ * @author Bernd Rinn
+ */
+public class DMDataSetDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ @ResultColumn("EXPE_ID")
+ private long experimentId;
+
+ @ResultColumn("SAMP_ID")
+ private long sampleId;
+
+ private DMSampleDTO sample;
+
+ public DMDataSetDTO()
+ {
+ // Bean compatibility.
+ }
+
+ public DMDataSetDTO(String dsPermId, String sampPermId, String sampName, String expePermId,
+ String expeName)
+ {
+ this.permId = dsPermId;
+ final DMExperimentDTO experiment = new DMExperimentDTO(expePermId, expeName);
+ this.sample = new DMSampleDTO(sampPermId, sampName);
+ sample.setExperiment(experiment);
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public long getExperimentId()
+ {
+ return experimentId;
+ }
+
+ public void setExperimentId(long experimentId)
+ {
+ this.experimentId = experimentId;
+ }
+
+ public long getSampleId()
+ {
+ return sampleId;
+ }
+
+ public void setSampleId(long sampleId)
+ {
+ this.sampleId = sampleId;
+ }
+
+ public DMSampleDTO getSample()
+ {
+ return sample;
+ }
+
+ public void setSample(DMSampleDTO sample)
+ {
+ this.sample = sample;
+ this.sampleId = sample.getId();
+ this.experimentId = sample.getExperimentId();
+ }
+
+ public DMExperimentDTO getExperiment()
+ {
+ return sample.getExperiment();
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java
new file mode 100644
index 00000000000..3df4cd07c45
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java
@@ -0,0 +1,77 @@
+/*
+ * 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.yeastx.db;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * The DTO for an experiment in the data mart.
+ *
+ * @author Bernd Rinn
+ */
+public class DMExperimentDTO
+{
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ private String name;
+
+ public DMExperimentDTO()
+ {
+ // Bean compatibility.
+ }
+
+ public DMExperimentDTO(String permId, String name)
+ {
+ this.permId = permId;
+ this.name = name;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java
new file mode 100644
index 00000000000..e44efaa844d
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java
@@ -0,0 +1,105 @@
+/*
+ * 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.yeastx.db;
+
+import net.lemnik.eodsql.AutoGeneratedKeys;
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * The DTO for a sample in the data mart.
+ *
+ * @author Bernd Rinn
+ */
+public class DMSampleDTO
+{
+
+ @AutoGeneratedKeys
+ private long id;
+
+ @ResultColumn("PERM_ID")
+ private String permId;
+
+ private String name;
+
+ @ResultColumn("EXPE_ID")
+ private long experimentId;
+
+ private DMExperimentDTO experiment;
+
+ public DMSampleDTO()
+ {
+ // Bean compatibility.
+ }
+
+ public DMSampleDTO(String permId, String name)
+ {
+ this.permId = permId;
+ this.name = name;
+ }
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getPermId()
+ {
+ return permId;
+ }
+
+ public void setPermId(String permId)
+ {
+ this.permId = permId;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public long getExperimentId()
+ {
+ return experimentId;
+ }
+
+ public void setExperimentId(long experimentId)
+ {
+ this.experimentId = experimentId;
+ }
+
+ public DMExperimentDTO getExperiment()
+ {
+ return experiment;
+ }
+
+ public void setExperiment(DMExperimentDTO experiment)
+ {
+ this.experiment = experiment;
+ this.experimentId = experiment.getId();
+ }
+
+}
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
new file mode 100644
index 00000000000..e972e23b7a0
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
@@ -0,0 +1,59 @@
+/*
+ * 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.yeastx.db;
+
+import net.lemnik.eodsql.BaseQuery;
+import net.lemnik.eodsql.Select;
+
+/**
+ * Interface for the "generic" methods (i.e. experiment, sample and data set).
+ *
+ * @author Bernd Rinn
+ */
+public interface IGenericDAO extends BaseQuery
+{
+
+ @Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
+ public DMExperimentDTO getExperiment(String experimentPermId);
+
+ @Select("select * from EXPERIMENTS where ID = ?{1}")
+ public DMExperimentDTO getExperiment(long id);
+
+ @Select("insert into EXPERIMENTS (PERM_ID, NAME) values (?{1.permId}, ?{1.name}) returning ID")
+ public long addExperiment(DMExperimentDTO experiment);
+
+ @Select("select * from SAMPLES where PERM_ID = ?{1}")
+ public DMSampleDTO getSample(String samplePermId);
+
+ @Select("select * from SAMPLES where ID = ?{1}")
+ public DMSampleDTO getSample(long id);
+
+ @Select("insert into SAMPLES (PERM_ID, NAME, EXPE_ID) values (?{1.permId}, ?{1.name}, ?{1.experiment.id}) "
+ + "returning ID")
+ public long addSample(DMSampleDTO sample);
+
+ @Select("select * from DATA_SETS where PERM_ID = ?{1}")
+ public DMDataSetDTO getDataSet(String dataSetPermId);
+
+ @Select("select * from DATA_SETS where ID = ?{1}")
+ public DMDataSetDTO getDataSet(long id);
+
+ @Select("insert into DATA_SETS (PERM_ID, EXPE_ID, SAMP_ID) values "
+ + "(?{1.permId}, ?{1.experiment.id}, ?{1.sample.id}) returning ID")
+ public long addDataSet(DMDataSetDTO dataSet);
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
index 6c80933a987..b8d32a4e23e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/ChromatogramDTO.java
@@ -27,7 +27,7 @@ import org.apache.commons.lang.builder.ToStringBuilder;
public class ChromatogramDTO
{
@AutoGeneratedKeys
- private long chromId;
+ private long id;
@ResultColumn("EIC_MS_RUN_ID")
private long eicMsRunId;
@@ -60,14 +60,14 @@ public class ChromatogramDTO
return eicMsRunId;
}
- public void setChromId(long chromId)
+ public void setId(long id)
{
- this.chromId = chromId;
+ this.id = id;
}
- public long getChromId()
+ public long getId()
{
- return chromId;
+ return id;
}
public void setQ1Mz(float q1Mz)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
index 495444f0268..e82fe396aaa 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2Database.java
@@ -31,6 +31,7 @@ import org.xml.sax.SAXException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IChromatogramObserver;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
@@ -63,21 +64,25 @@ public class EICML2Database
* Method for uploading an <var>eicMLFile</var> to the database.
*/
public static void uploadEicMLFile(final Connection conn, final File eicMLFile,
- String dataSetPermId)
- throws SQLException
+ final DMDataSetDTO dataSet) throws SQLException
{
final long[] eicMLId = new long[1];
final List<ChromatogramDTO> chromatograms =
new ArrayList<ChromatogramDTO>(CHROMATOGRAM_BATCH_SIZE);
try
{
+ DBFactory.createDataSet(DBFactory.getDAO(conn), dataSet);
final IEICMSRunDAO dao = getDAO(conn);
- new EICMLParser(eicMLFile.getPath(), dataSetPermId, new IMSRunObserver()
+ new EICMLParser(eicMLFile.getPath(), new IMSRunObserver()
{
public void observe(EICMSRunDTO run)
{
- // add chromatograms from the last run to the database before setting the new run id
+ // add chromatograms from the last run to the database before setting the
+ // new run id
addChromatograms(dao, eicMLId[0], chromatograms, 1);
+ run.setExperimentId(dataSet.getExperimentId());
+ run.setSampleId(dataSet.getSampleId());
+ run.setDataSetId(dataSet.getId());
eicMLId[0] = dao.addMSRun(run);
}
}, new IChromatogramObserver()
@@ -114,7 +119,9 @@ public class EICML2Database
int permId = 0;
for (String f : new File(dir).list(new EICMLFilenameFilter()))
{
- uploadEicMLFile(conn, new File(dir, f), Integer.toString(++permId));
+ uploadEicMLFile(conn, new File(dir, f), new DMDataSetDTO(
+ Integer.toString(++permId), "sample1", "the sample name", "experiment1",
+ "the experiment name"));
}
} finally
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
index eb79da2ffcb..a03cda70915 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICML2TabConverter.java
@@ -41,7 +41,7 @@ public class EICML2TabConverter
for (String f : new File(dir).list(new EICMLFilenameFilter()))
{
final String[] msRunName = new String[1];
- new EICMLParser(dir + "/" + f, null, new EICMLParser.IMSRunObserver()
+ new EICMLParser(dir + "/" + f, new EICMLParser.IMSRunObserver()
{
public void observe(EICMSRunDTO run)
{
@@ -104,9 +104,9 @@ public class EICML2TabConverter
{
out.println("endTime\t" + run.getEndTime());
}
- if (run.getEicMsRunId() >= 0)
+ if (run.getId() >= 0)
{
- out.println("msRunId\t" + run.getEicMsRunId());
+ out.println("msRunId\t" + run.getId());
}
out.close();
} catch (FileNotFoundException ex)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
index 81264d39b27..833a2df1db7 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLParser.java
@@ -70,8 +70,6 @@ public class EICMLParser extends DefaultHandler
private StringBuilder buffer = new StringBuilder();
- private String permIdOrNull;
-
private EICMSRunDTO msRun;
private ChromatogramDTO chromatogram;
@@ -84,13 +82,12 @@ public class EICMLParser extends DefaultHandler
private final IChromatogramObserver chromatogramObserverOrNull;
- public EICMLParser(String fileName, String permIdOrNull, IMSRunObserver msRunObserverOrNull,
+ public EICMLParser(String fileName, IMSRunObserver msRunObserverOrNull,
IChromatogramObserver chromatogramObserverOrNull) throws ParserConfigurationException,
SAXException, IOException
{
assert fileName != null;
- this.permIdOrNull = permIdOrNull;
this.msRunObserverOrNull = msRunObserverOrNull;
this.chromatogramObserverOrNull = chromatogramObserverOrNull;
parseDocument(fileName);
@@ -112,7 +109,6 @@ public class EICMLParser extends DefaultHandler
if (MS_RUN.equals(name))
{
msRun = new EICMSRunDTO();
- msRun.setDataSetPermId(permIdOrNull);
parsingMsRun = true;
} else if ("chromatogram".equals(name))
{
@@ -164,7 +160,7 @@ public class EICMLParser extends DefaultHandler
msRun.setChromCount(Integer.parseInt(value));
} else if ("msRunId".equals(name) && value.length() > 0)
{
- msRun.setEicMsRunId(Long.parseLong(value));
+ msRun.setId(Long.parseLong(value));
} else if ("startTime".equals(name) && value.length() > 0)
{
msRun.setStartTime(Float.parseFloat(value));
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMSRunDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMSRunDTO.java
index 017d901d513..0fafb092ae2 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMSRunDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMSRunDTO.java
@@ -29,11 +29,16 @@ import org.apache.commons.lang.builder.ToStringBuilder;
public class EICMSRunDTO
{
@AutoGeneratedKeys
- @ResultColumn("EIC_MS_RUN_ID")
- private long eicMsRunId;
+ private long id;
- @ResultColumn("DATA_SET_PERM_ID")
- private String dataSetPermId;
+ @ResultColumn("DS_ID")
+ private long dataSetId;
+
+ @ResultColumn("SAMP_ID")
+ private long sampleId;
+
+ @ResultColumn("EXPE_ID")
+ private long experimentId;
@ResultColumn("RAW_DATA_FILE_PATH")
private String rawDataFilePath;
@@ -72,24 +77,44 @@ public class EICMSRunDTO
@ResultColumn("END_TIME")
private float endTime = Float.NaN;
- public String getDataSetPermId()
+ public long getId()
+ {
+ return id;
+ }
+
+ public long getDataSetId()
+ {
+ return dataSetId;
+ }
+
+ public void setDataSetId(long dataSetId)
+ {
+ this.dataSetId = dataSetId;
+ }
+
+ public long getSampleId()
+ {
+ return sampleId;
+ }
+
+ public void setSampleId(long sampleId)
{
- return dataSetPermId;
+ this.sampleId = sampleId;
}
- public void setDataSetPermId(String permId)
+ public long getExperimentId()
{
- this.dataSetPermId = permId;
+ return experimentId;
}
- public long getEicMsRunId()
+ public void setExperimentId(long experimentId)
{
- return eicMsRunId;
+ this.experimentId = experimentId;
}
- public void setEicMsRunId(long eicMsRunId)
+ public void setId(long id)
{
- this.eicMsRunId = eicMsRunId;
+ this.id = id;
}
public String getRawDataFilePath()
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
index 5a4ef5883d6..9b751682628 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java
@@ -31,18 +31,21 @@ import net.lemnik.eodsql.Update;
public interface IEICMSRunDAO extends BaseQuery
{
final String ALL_EIC_MSRUN_COLUMNS =
- "EIC_MS_RUNS.EIC_MS_RUN_ID, EIC_MS_RUNS.DATA_SET_PERM_ID, EIC_MS_RUNS.RAW_DATA_FILE_NAME, EIC_MS_RUNS.RAW_DATA_FILE_PATH, "
+ "EIC_MS_RUNS.ID, EIC_MS_RUNS.EXPE_ID, EIC_MS_RUNS.SAMP_ID, EIC_MS_RUNS.DS_ID, "
+ + "EIC_MS_RUNS.RAW_DATA_FILE_NAME, EIC_MS_RUNS.RAW_DATA_FILE_PATH, "
+ "EIC_MS_RUNS.ACQUISITION_DATE, EIC_MS_RUNS.INSTRUMENT_TYPE, EIC_MS_RUNS.INSTRUMENT_MANUFACTURER, "
+ "EIC_MS_RUNS.INSTRUMENT_MODEL, EIC_MS_RUNS.METHOD_IONISATION, EIC_MS_RUNS.METHOD_SEPARATION, "
+ "EIC_MS_RUNS.SET_ID, EIC_MS_RUNS.OPERATOR, "
+ "EIC_MS_RUNS.START_TIME, EIC_MS_RUNS.END_TIME";
- @Select("insert into EIC_MS_RUNS (DATA_SET_PERM_ID, RAW_DATA_FILE_NAME, RAW_DATA_FILE_PATH, ACQUISITION_DATE, "
+ @Select("insert into EIC_MS_RUNS (EXPE_ID, SAMP_ID, DS_ID, "
+ + "RAW_DATA_FILE_NAME, RAW_DATA_FILE_PATH, ACQUISITION_DATE, "
+ "INSTRUMENT_TYPE, INSTRUMENT_MANUFACTURER, INSTRUMENT_MODEL, METHOD_IONISATION, "
- + "METHOD_SEPARATION, SET_ID, OPERATOR, START_TIME, END_TIME) values (?{1.dataSetPermId}, ?{1.rawDataFileName}, "
+ + "METHOD_SEPARATION, SET_ID, OPERATOR, START_TIME, END_TIME) values "
+ + "(?{1.experimentId}, ?{1.sampleId}, ?{1.dataSetId}, ?{1.rawDataFileName}, "
+ "?{1.rawDataFilePath}, ?{1.acquisitionDate}, ?{1.instrumentType}, "
+ "?{1.instrumentManufacturer}, ?{1.instrumentModel}, ?{1.methodIonisation}, "
- + "?{1.methodSeparation}, ?{1.setId}, ?{1.operator}, ?{1.startTime}, ?{1.endTime}) returning EIC_MS_RUN_ID")
+ + "?{1.methodSeparation}, ?{1.setId}, ?{1.operator}, ?{1.startTime}, ?{1.endTime}) returning ID")
public long addMSRun(EICMSRunDTO msRun);
@Update(sql = "insert into EIC_CHROMATOGRAMS (EIC_MS_RUN_ID, Q1_MZ, Q3_LOW_MZ, Q3_HIGH_MZ, LABEL, POLARITY, RUN_TIMES, "
@@ -52,37 +55,37 @@ public interface IEICMSRunDAO extends BaseQuery
public void addChromatograms(long EIC_MS_RUN_ID, List<ChromatogramDTO> chromatogram);
@Select(sql = "select EIC_MS_RUNS.*,count(EIC_CHROMATOGRAMS.*) as chromCount from EIC_MS_RUNS "
- + "left join EIC_CHROMATOGRAMS using(EIC_MS_RUN_ID) group by " + ALL_EIC_MSRUN_COLUMNS)
+ + "left join EIC_CHROMATOGRAMS on EIC_MS_RUN_ID = EIC_MS_RUNS.ID group by " + ALL_EIC_MSRUN_COLUMNS)
public DataIterator<EICMSRunDTO> getMsRuns();
@Select(sql = "select * from EIC_MS_RUNS where RAW_DATA_FILE_NAME=?{1}")
public DataIterator<EICMSRunDTO> getMsRunsForRawDataFile(String rawDataFileName);
@Select("select EIC_MS_RUNS.*, count(EIC_CHROMATOGRAMS.*) AS chromCount from EIC_MS_RUNS "
- + "left join EIC_CHROMATOGRAMS using(EIC_MS_RUN_ID) where EIC_MS_RUNS.EIC_MS_RUN_ID=?{1} group by "
+ + "left join EIC_CHROMATOGRAMS on EIC_MS_RUN_ID = EIC_MS_RUNS.ID where EIC_MS_RUNS.EIC_MS_RUN_ID=?{1} group by "
+ ALL_EIC_MSRUN_COLUMNS)
public EICMSRunDTO getMSRunById(long id);
@Select("select EIC_MS_RUNS.*, count(EIC_CHROMATOGRAMS.*) AS chromCount from EIC_MS_RUNS "
- + "left join EIC_CHROMATOGRAMS using(EIC_MS_RUN_ID) where EIC_MS_RUNS.DATA_SET_PERM_ID=?{1} group by "
+ + "left join EIC_CHROMATOGRAMS on EIC_MS_RUN_ID = eic_ms_run.id where EIC_MS_RUNS.DATA_SET_PERM_ID=?{1} group by "
+ ALL_EIC_MSRUN_COLUMNS)
public EICMSRunDTO getMSRunByPermId(String permId);
- @Select("select EIC_MS_RUNS.* FROM msrun LEFT JOIN EIC_CHROMATOGRAMS USING(EIC_MS_RUN_ID) "
- + "where EIC_CHROMATOGRAMS.CHROM_ID = ?{1.chromId}")
+ @Select("select EIC_MS_RUNS.* FROM msrun LEFT JOIN EIC_CHROMATOGRAMS USING(ID) "
+ + "where EIC_CHROMATOGRAMS.ID = ?{1.id}")
public EICMSRunDTO getMSRunForChromatogram(ChromatogramDTO chromatogram);
- @Select("select EIC_CHROMATOGRAMS.* FROM EIC_CHROMATOGRAMS where CHROM_ID=?{1}")
+ @Select("select EIC_CHROMATOGRAMS.* FROM EIC_CHROMATOGRAMS where ID=?{1}")
public ChromatogramDTO getChromatogramById(long id);
@Select("select EIC_CHROMATOGRAMS.* FROM EIC_CHROMATOGRAMS where LABEL=?{1}")
public ChromatogramDTO getChromatogramByLabel(String label);
- @Select("select * FROM EIC_CHROMATOGRAMS where EIC_MS_RUN_ID=?{1.eicMsRunId}")
+ @Select("select * FROM EIC_CHROMATOGRAMS where EIC_MS_RUN_ID=?{1.id}")
public DataIterator<ChromatogramDTO> getChromatogramsForRun(EICMSRunDTO msRun);
- @Select(sql = "select CHROM_ID, EIC_MS_RUN_ID, Q1_MZ, Q3_LOW_MZ, Q3_HIGH_MZ, LABEL, POLARITY FROM EIC_CHROMATOGRAMS "
- + "LEFT JOIN EIC_MS_RUNS USING(EIC_MS_RUN_ID) " + "where EIC_MS_RUN_ID=?{1.eicMsRunId}")
+ @Select(sql = "select ID, EIC_MS_RUN_ID, Q1_MZ, Q3_LOW_MZ, Q3_HIGH_MZ, LABEL, POLARITY FROM EIC_CHROMATOGRAMS "
+ + "LEFT JOIN EIC_MS_RUNS on EIC_MS_RUN_ID = EIC_MS_RUNS.ID where EIC_MS_RUN_ID=?{1.id}")
public DataIterator<ChromatogramDTO> getChromatogramsForRunNoData(EICMSRunDTO msRun);
}
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 de01a35f5f6..b3ffcad6722 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
@@ -25,6 +25,7 @@ import org.apache.commons.io.FilenameUtils;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICML2Database;
import ch.systemsx.cisd.yeastx.fiaml.FIAML2Database;
@@ -85,12 +86,14 @@ public class ML2DatabaseUploader
private void translateEIC(File dataSet, String datasetPermId) throws SQLException
{
- EICML2Database.uploadEicMLFile(connection, dataSet, datasetPermId);
+ EICML2Database.uploadEicMLFile(connection, dataSet, new DMDataSetDTO(datasetPermId,
+ "sample perm id", "sample name", "experiment perm id", "eperiment name"));
}
private void translateFIA(File dataSet, String datasetPermId) throws SQLException
{
- FIAML2Database.uploadFiaMLFile(connection, dataSet, datasetPermId);
+ FIAML2Database.uploadFiaMLFile(connection, dataSet, new DMDataSetDTO(datasetPermId,
+ "sample perm id", "sample name", "experiment perm id", "experiment name"));
}
private static String getExtension(final File incomingDataSetPath)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/CentroidDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/CentroidDTO.java
index f386e4a744c..1a2d5d6ef2f 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/CentroidDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/CentroidDTO.java
@@ -20,7 +20,7 @@ import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
/**
- *
+ * The data transfer object for FIA centroids.
*
* @author Bernd Rinn
*/
@@ -28,20 +28,19 @@ public class CentroidDTO
{
@AutoGeneratedKeys
- @ResultColumn("CENTROID_ID")
- private long centroidId;
+ private long id;
@ResultColumn("FIA_MS_RUN_ID")
private long fiaMsRunId;
- public long getCentroidId()
+ public long getId()
{
- return centroidId;
+ return id;
}
- public void setCentroidId(long centroidId)
+ public void setId(long id)
{
- this.centroidId = centroidId;
+ this.id = id;
}
public long getFiaMsRunId()
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
index f017266053b..2d0db836a53 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAML2Database.java
@@ -25,6 +25,7 @@ import net.lemnik.eodsql.QueryTool;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.yeastx.db.DBFactory;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.fiaml.FIAMLParser.IMSRunObserver;
/**
@@ -81,15 +82,19 @@ public class FIAML2Database
* Method for uploading an <var>fiaMLFile</var> to the database.
*/
public static void uploadFiaMLFile(final Connection conn, final File fiaMLFile,
- final String permId) throws SQLException
+ final DMDataSetDTO dataSet) throws SQLException
{
try
{
+ DBFactory.createDataSet(DBFactory.getDAO(conn), dataSet);
final IFIAMSRunDAO dao = getDAO(conn);
- new FIAMLParser(fiaMLFile.getPath(), permId, new IMSRunObserver()
+ new FIAMLParser(fiaMLFile.getPath(), new IMSRunObserver()
{
public void observe(FIAMSRunDTO run, FIAMSRunDataDTO runData)
{
+ run.setExperimentId(dataSet.getExperimentId());
+ run.setSampleId(dataSet.getSampleId());
+ run.setDataSetId(dataSet.getId());
final long fiaMsRunId = dao.addMSRun(run);
getDAO(conn).addProfiles(fiaMsRunId, profileChunk(runData));
getDAO(conn)
@@ -123,7 +128,8 @@ public class FIAML2Database
for (String f : new File(dir).list(new FIAMLFilenameFilter()))
{
System.out.println(f);
- uploadFiaMLFile(conn, new File(dir, f), Integer.toString(++permId));
+ uploadFiaMLFile(conn, new File(dir, f), new DMDataSetDTO(Integer.toString(++permId),
+ "sample perm id", "sample name", "experiment perm id", "experiment name"));
}
} finally
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
index 14e07299200..39687b086c5 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLParser.java
@@ -64,8 +64,6 @@ public class FIAMLParser extends DefaultHandler
private StringBuilder buffer = new StringBuilder();
- private String permIdOrNull;
-
private FIAMSRunDTO msRun;
private FIAMSRunDataDTO fiaRunData;
@@ -74,12 +72,11 @@ public class FIAMLParser extends DefaultHandler
private final IMSRunObserver msRunObserverOrNull;
- public FIAMLParser(String fileName, String permIdOrNull, IMSRunObserver msRunObserverOrNull)
+ public FIAMLParser(String fileName, IMSRunObserver msRunObserverOrNull)
throws ParserConfigurationException, SAXException, IOException
{
assert fileName != null;
- this.permIdOrNull = permIdOrNull;
this.msRunObserverOrNull = msRunObserverOrNull;
parseDocument(fileName);
}
@@ -101,7 +98,6 @@ public class FIAMLParser extends DefaultHandler
{
msRun = new FIAMSRunDTO();
fiaRunData = new FIAMSRunDataDTO();
- msRun.setDataSetPermId(permIdOrNull);
parsingMsRun = true;
}
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDTO.java
index 59cf08f9131..4f0238310ad 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDTO.java
@@ -29,11 +29,16 @@ import org.apache.commons.lang.builder.ToStringBuilder;
public class FIAMSRunDTO
{
@AutoGeneratedKeys
- @ResultColumn("FIA_MS_RUN_ID")
- private long fiaMsRunId;
+ private long id;
- @ResultColumn("DATA_SET_PERM_ID")
- private String dataSetPermId;
+ @ResultColumn("DS_ID")
+ private long dataSetId;
+
+ @ResultColumn("SAMP_ID")
+ private long sampleId;
+
+ @ResultColumn("EXPE_ID")
+ private long experimentId;
@ResultColumn("RAW_DATA_FILE_PATH")
private String rawDataFilePath;
@@ -85,24 +90,44 @@ public class FIAMSRunDTO
this.profileCount = profileCount;
}
- public String getDataSetPermId()
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long eicMsRunId)
+ {
+ this.id = eicMsRunId;
+ }
+
+ public long getDataSetId()
+ {
+ return dataSetId;
+ }
+
+ public void setDataSetId(long dataSetId)
+ {
+ this.dataSetId = dataSetId;
+ }
+
+ public long getSampleId()
{
- return dataSetPermId;
+ return sampleId;
}
- public void setDataSetPermId(String permId)
+ public void setSampleId(long sampleId)
{
- this.dataSetPermId = permId;
+ this.sampleId = sampleId;
}
- public long getFiaMsRunId()
+ public long getExperimentId()
{
- return fiaMsRunId;
+ return experimentId;
}
- public void setFiaMsRunId(long eicMsRunId)
+ public void setExperimentId(long experimentId)
{
- this.fiaMsRunId = eicMsRunId;
+ this.experimentId = experimentId;
}
public String getRawDataFilePath()
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDataDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDataDTO.java
index 2e6e38d64f3..98b4d14e8b0 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDataDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMSRunDataDTO.java
@@ -16,8 +16,6 @@
package ch.systemsx.cisd.yeastx.fiaml;
-import net.lemnik.eodsql.AutoGeneratedKeys;
-import net.lemnik.eodsql.ResultColumn;
/**
* A class that represents the data of a {@link FIAMSRunDTO}.
@@ -27,10 +25,6 @@ import net.lemnik.eodsql.ResultColumn;
public class FIAMSRunDataDTO
{
- @AutoGeneratedKeys
- @ResultColumn("FIA_MS_RUN_ID")
- private long fiaMsRunId;
-
private float[] profileMz;
private float[] profileIntensities;
@@ -41,16 +35,6 @@ public class FIAMSRunDataDTO
private float[] centroidCorrelations;
- public long getFiaMsRunId()
- {
- return fiaMsRunId;
- }
-
- public void setFiaMsRunId(long fiaMsRunId)
- {
- this.fiaMsRunId = fiaMsRunId;
- }
-
public float[] getProfileMz()
{
return profileMz;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
index f885106c10a..f8de0f12da5 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java
@@ -29,20 +29,22 @@ import net.lemnik.eodsql.Update;
public interface IFIAMSRunDAO extends BaseQuery
{
final String ALL_FIA_MSRUN_COLUMNS =
- "FIA_MS_RUNS.FIA_MS_RUN_ID, FIA_MS_RUNS.DATA_SET_PERM_ID, FIA_MS_RUNS.RAW_DATA_FILE_NAME, "
+ "FIA_MS_RUNS.ID, FIA_MS_RUNS.EXPE_ID, "
+ + "FIA_MS_RUNS.SAMP_ID, FIA_MS_RUNS.DS_ID, FIA_MS_RUNS.RAW_DATA_FILE_NAME, "
+ "FIA_MS_RUNS.RAW_DATA_FILE_PATH, FIA_MS_RUNS.ACQUISITION_DATE, "
+ "FIA_MS_RUNS.INSTRUMENT_TYPE, FIA_MS_RUNS.INSTRUMENT_MANUFACTURER, "
+ "FIA_MS_RUNS.INSTRUMENT_MODEL, FIA_MS_RUNS.METHOD_IONISATION, "
+ "FIA_MS_RUNS.METHOD_SEPARATION, FIA_MS_RUNS.POLARITY, FIA_MS_RUNS.LOW_MZ, "
+ "FIA_MS_RUNS.HIGH_MZ, FIA_MS_RUNS.INTERNAL_STANDARD, FIA_MS_RUNS.od, FIA_MS_RUNS.OPERATOR";
- @Select("insert into FIA_MS_RUNS (DATA_SET_PERM_ID, RAW_DATA_FILE_NAME, RAW_DATA_FILE_PATH, ACQUISITION_DATE, "
- + "INSTRUMENT_TYPE, INSTRUMENT_MANUFACTURER, INSTRUMENT_MODEL, METHOD_IONISATION, "
+ @Select("insert into FIA_MS_RUNS (EXPE_ID, SAMP_ID, DS_ID, RAW_DATA_FILE_NAME, RAW_DATA_FILE_PATH, "
+ + "ACQUISITION_DATE, INSTRUMENT_TYPE, INSTRUMENT_MANUFACTURER, INSTRUMENT_MODEL, METHOD_IONISATION, "
+ "METHOD_SEPARATION, POLARITY, LOW_MZ, HIGH_MZ, INTERNAL_STANDARD, od, OPERATOR) values "
- + "(?{1.dataSetPermId}, ?{1.rawDataFileName}, ?{1.rawDataFilePath}, ?{1.acquisitionDate}, "
+ + "(?{1.experimentId}, ?{1.sampleId}, ?{1.dataSetId}, ?{1.rawDataFileName}, "
+ + "?{1.rawDataFilePath}, ?{1.acquisitionDate}, "
+ "?{1.instrumentType}, ?{1.instrumentManufacturer}, ?{1.instrumentModel}, "
+ "?{1.methodIonisation}, ?{1.methodSeparation}, ?{1.polarity}, ?{1.lowMz}, ?{1.highMz}, "
- + "?{1.internalStandard}, ?{1.od}, ?{1.operator}) returning FIA_MS_RUN_ID")
+ + "?{1.internalStandard}, ?{1.od}, ?{1.operator}) returning ID")
public long addMSRun(FIAMSRunDTO msRun);
@Update(sql = "insert into FIA_CENTROIDS (FIA_MS_RUN_ID, MZ, INTENSITY, CORRELATION) "
@@ -55,13 +57,14 @@ public interface IFIAMSRunDAO extends BaseQuery
public void addProfiles(long fiaMsRunId, Iterable<ProfileDTO> profiles);
@Select(sql = "select FIA_MS_RUNS.*,count(FIA_PROFILES.*) as profileCount from FIA_MS_RUNS "
- + "left join FIA_PROFILES using(FIA_MS_RUN_ID) group by " + ALL_FIA_MSRUN_COLUMNS)
+ + "left join FIA_PROFILES on FIA_MS_RUN_ID = FIA_MS_RUNS.ID group by "
+ + ALL_FIA_MSRUN_COLUMNS)
public DataIterator<FIAMSRunDTO> getMsRuns();
- @Select("select * from FIA_PROFILES where FIA_MS_RUN_ID=?{1.fiaMsRunId}")
+ @Select("select * from FIA_PROFILES where FIA_MS_RUN_ID=?{1.id}")
public DataIterator<ProfileDTO> getProfilesForRun(FIAMSRunDTO msRun);
- @Select("select * from FIA_CENTROIDS where FIA_MS_RUN_ID=?{1.fiaMsRunId}")
+ @Select("select * from FIA_CENTROIDS where FIA_MS_RUN_ID=?{1.id}")
public DataIterator<CentroidDTO> getCentroidsForRun(FIAMSRunDTO msRun);
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
index 3ec3aa44b2f..9cf92bc078a 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/ProfileDTO.java
@@ -27,8 +27,7 @@ import net.lemnik.eodsql.ResultColumn;
public class ProfileDTO
{
@AutoGeneratedKeys
- @ResultColumn("PROFILE_ID")
- private long profileId;
+ private long id;
@ResultColumn("FIA_MS_RUN_ID")
private long fiaMsRunId;
@@ -55,14 +54,14 @@ public class ProfileDTO
return dto;
}
- public long getProfileId()
+ public long getId()
{
- return profileId;
+ return id;
}
- public void setProfileId(long profileId)
+ public void setId(long id)
{
- this.profileId = profileId;
+ this.id = id;
}
public long getFiaMsRunId()
diff --git a/rtd_yeastx/source/sql/postgresql/001/schema-001.sql b/rtd_yeastx/source/sql/postgresql/001/schema-001.sql
index dec8e9b3321..88321b4638e 100644
--- a/rtd_yeastx/source/sql/postgresql/001/schema-001.sql
+++ b/rtd_yeastx/source/sql/postgresql/001/schema-001.sql
@@ -4,6 +4,8 @@
-- Create domain types section -------------------------------------------------
+CREATE DOMAIN TECH_ID AS BIGINT;
+
CREATE DOMAIN CODE AS VARCHAR(40);
CREATE DOMAIN FILE_NAME as VARCHAR(255);
@@ -18,9 +20,48 @@ CREATE DOMAIN CHAR as VARCHAR(1);
-- Create tables section -------------------------------------------------
+-- Table EXPERIMENTS
+
+CREATE TABLE EXPERIMENTS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ NAME LONG_LABEL NOT NULL,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID)
+);
+
+-- Table SAMPLES
+
+CREATE TABLE SAMPLES (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ NAME LONG_LABEL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table DATA_SETS
+
+CREATE TABLE DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_DATA_SET_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_DATA_SET_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table EIC_MS_RUNS
+
CREATE TABLE EIC_MS_RUNS (
- EIC_MS_RUN_ID BIGSERIAL NOT NULL,
- DATA_SET_PERM_ID CODE NOT NULL,
+ ID BIGSERIAL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID NOT NULL,
+ DS_ID TECH_ID NOT NULL,
RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
@@ -30,16 +71,24 @@ CREATE TABLE EIC_MS_RUNS (
METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
METHOD_SEPARATION LONG_LABEL DEFAULT NULL,
OPERATOR SHORT_LABEL DEFAULT NULL,
- SET_ID BIGINT DEFAULT NULL,
+ SET_ID TECH_ID DEFAULT NULL,
START_TIME REAL NOT NULL,
END_TIME REAL NOT NULL,
- PRIMARY KEY (EIC_MS_RUN_ID),
- UNIQUE(DATA_SET_PERM_ID)
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_EIC_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIC_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIC_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
+CREATE INDEX EIC_MS_RUNS_FK_DS_ID_IDX ON EIC_MS_RUNS(DS_ID);
+CREATE INDEX EIC_MS_RUNS_FK_SAMP_ID_IDX ON EIC_MS_RUNS(SAMP_ID);
+CREATE INDEX EIC_MS_RUNS_FK_EXPE_ID_IDX ON EIC_MS_RUNS(EXPE_ID);
+
+-- Table EIC_CHROMATOGRAMS
+
CREATE TABLE EIC_CHROMATOGRAMS (
- CHROM_ID BIGSERIAL NOT NULL,
- EIC_MS_RUN_ID BIGINT NOT NULL,
+ ID BIGSERIAL NOT NULL,
+ EIC_MS_RUN_ID TECH_ID NOT NULL,
Q1_MZ REAL NOT NULL,
Q3_LOW_MZ REAL NOT NULL,
Q3_HIGH_MZ REAL NOT NULL,
@@ -47,15 +96,19 @@ CREATE TABLE EIC_CHROMATOGRAMS (
POLARITY CHAR DEFAULT NULL,
RUN_TIMES TEXT NOT NULL,
INTENSITIES TEXT NOT NULL,
- PRIMARY KEY (CHROM_ID),
- CONSTRAINT FK_CHROMATOGRAM_1 FOREIGN KEY (EIC_MS_RUN_ID) REFERENCES EIC_MS_RUNS (EIC_MS_RUN_ID) ON DELETE CASCADE ON UPDATE CASCADE
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_EIC_CHROMATOGRAM_1 FOREIGN KEY (EIC_MS_RUN_ID) REFERENCES EIC_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX EIC_CHROMATOGRAM_FK_IDX ON EIC_CHROMATOGRAMS(EIC_MS_RUN_ID);
+-- Table FIA_MS_RUNS
+
CREATE TABLE FIA_MS_RUNS (
- FIA_MS_RUN_ID BIGSERIAL NOT NULL,
- DATA_SET_PERM_ID CODE,
+ ID BIGSERIAL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID NOT NULL,
+ DS_ID TECH_ID NOT NULL,
RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
@@ -71,32 +124,38 @@ CREATE TABLE FIA_MS_RUNS (
-- Is this a good name?
OD REAL NOT NULL,
OPERATOR SHORT_LABEL DEFAULT NULL,
- PRIMARY KEY (FIA_MS_RUN_ID),
- UNIQUE(DATA_SET_PERM_ID)
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIA_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIA_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
+-- Table FIA_PROFILES
+
CREATE TABLE FIA_PROFILES (
- PROFILE_ID BIGSERIAL NOT NULL,
- FIA_MS_RUN_ID BIGINT NOT NULL,
+ ID BIGSERIAL NOT NULL,
+ FIA_MS_RUN_ID TECH_ID NOT NULL,
LOW_MZ REAL NOT NULL,
HIGH_MZ REAL NOT NULL,
MZ TEXT NOT NULL,
INTENSITIES TEXT NOT NULL,
- PRIMARY KEY (PROFILE_ID),
- CONSTRAINT FK_EIC_PROFILE_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (FIA_MS_RUN_ID) ON DELETE CASCADE ON UPDATE CASCADE
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_PROFILE_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX FIA_PROFILE_I_ID on FIA_PROFILES(FIA_MS_RUN_ID);
CREATE INDEX FIA_PROFILE_I_ID_MZ on FIA_PROFILES(FIA_MS_RUN_ID, LOW_MZ, HIGH_MZ);
+-- Table FIA_CENTROIDS
+
CREATE TABLE FIA_CENTROIDS (
- CENTROID_ID BIGSERIAL NOT NULL,
- FIA_MS_RUN_ID BIGINT NOT NULL,
+ ID BIGSERIAL NOT NULL,
+ FIA_MS_RUN_ID TECH_ID NOT NULL,
MZ REAL NOT NULL,
INTENSITY REAL NOT NULL,
CORRELATION REAL NOT NULL,
- PRIMARY KEY (CENTROID_ID),
- CONSTRAINT FK_EIC_CENTROID_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (FIA_MS_RUN_ID) ON DELETE CASCADE ON UPDATE CASCADE
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_CENTROID_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
);
CREATE INDEX FIA_CENTROID_I_ID on FIA_CENTROIDS(FIA_MS_RUN_ID);
@@ -107,19 +166,19 @@ GRANT SELECT ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readonly;
GRANT SELECT ON TABLE FIA_MS_RUNS TO GROUP metabol_readonly;
GRANT SELECT ON TABLE FIA_PROFILES TO GROUP metabol_readonly;
GRANT SELECT ON TABLE FIA_CENTROIDS TO GROUP metabol_readonly;
-GRANT SELECT ON SEQUENCE EIC_MS_RUNS_EIC_MS_RUN_ID_SEQ TO GROUP metabol_readonly;
-GRANT SELECT ON SEQUENCE EIC_CHROMATOGRAMS_CHROM_ID_SEQ TO GROUP metabol_readonly;
-GRANT SELECT ON SEQUENCE FIA_MS_RUNS_FIA_MS_RUN_ID_SEQ TO GROUP metabol_readonly;
-GRANT SELECT ON SEQUENCE FIA_PROFILES_PROFILE_ID_SEQ TO GROUP metabol_readonly;
-GRANT SELECT ON SEQUENCE FIA_CENTROIDS_CENTROID_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readonly;
GRANT ALL PRIVILEGES ON TABLE EIC_MS_RUNS TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON TABLE FIA_MS_RUNS TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON TABLE FIA_PROFILES TO GROUP metabol_readwrite;
GRANT ALL PRIVILEGES ON TABLE FIA_CENTROIDS TO GROUP metabol_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EIC_MS_RUNS_EIC_MS_RUN_ID_SEQ TO GROUP metabol_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE EIC_CHROMATOGRAMS_CHROM_ID_SEQ TO GROUP metabol_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE FIA_MS_RUNS_FIA_MS_RUN_ID_SEQ TO GROUP metabol_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE FIA_PROFILES_PROFILE_ID_SEQ TO GROUP metabol_readwrite;
-GRANT ALL PRIVILEGES ON SEQUENCE FIA_CENTROIDS_CENTROID_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readwrite;
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
index 2c9cb833495..c54dbab5eb7 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/eicml/EICMLTest.java
@@ -25,6 +25,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import static org.testng.AssertJUnit.*;
@@ -37,7 +38,7 @@ public class EICMLTest extends AbstractDBTest
{
private IEICMSRunDAO eicmlDAO;
-
+
@BeforeMethod(alwaysRun = true)
public void setDAO() throws SQLException
{
@@ -48,9 +49,10 @@ public class EICMLTest extends AbstractDBTest
public void testUploadEicML() throws SQLException
{
EICML2Database.uploadEicMLFile(conn, new File("resource/examples/example.eicML"),
- "some perm id");
+ new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
+ "experiment perm id", "experiment name"));
}
-
+
@Test(dependsOnMethods = "testUploadEicML")
public void testGetMsRuns()
{
@@ -67,6 +69,6 @@ public class EICMLTest extends AbstractDBTest
++count;
}
assertEquals(22, count);
- chromatograms.close(); // Shoudn't be necessary, just to be sure.
+ chromatograms.close(); // Shoudn't be necessary, just to be sure.
}
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
index 9ef20b6e781..3ec406e2976 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java
@@ -25,6 +25,7 @@ import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import static org.testng.AssertJUnit.*;
@@ -47,9 +48,10 @@ public class FIAMLTest extends AbstractDBTest
public void testUploadFiaML() throws SQLException
{
FIAML2Database.uploadFiaMLFile(conn, new File("resource/examples/example.fiaML"),
- "some perm id");
+ new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
+ "experiment perm id", "experiment name"));
}
-
+
@Test(dependsOnMethods = "testUploadFiaML")
public void testGetMsRuns()
{
@@ -63,8 +65,8 @@ public class FIAMLTest extends AbstractDBTest
while (profiles.hasNext())
{
final ProfileDTO prof = profiles.next();
- assertFalse(prof.getProfileId() == 0);
- assertEquals(run.getFiaMsRunId(), prof.getFiaMsRunId());
+ assertFalse(prof.getId() == 0);
+ assertEquals(run.getId(), prof.getFiaMsRunId());
++count;
}
assertEquals(686, count);
@@ -74,8 +76,8 @@ public class FIAMLTest extends AbstractDBTest
while (centroids.hasNext())
{
final CentroidDTO cent = centroids.next();
- assertFalse(cent.getCentroidId() == 0);
- assertEquals(run.getFiaMsRunId(), cent.getFiaMsRunId());
+ assertFalse(cent.getId() == 0);
+ assertEquals(run.getId(), cent.getFiaMsRunId());
++count;
}
assertEquals(556, count);
--
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