From aa0597f4a9c25c8d177fea46538a591a86ff9d83 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 10 May 2010 13:02:38 +0000
Subject: [PATCH] LMS-1529 separate generic exp/sample/dataset DTOs in yeastx
SVN: 15871
---
.../cisd/yeastx/db/AbstractDatasetLoader.java | 5 +-
.../ch/systemsx/cisd/yeastx/db/DBUtils.java | 77 --------------
.../cisd/yeastx/db/IDatasetLoader.java | 2 +
.../yeastx/db/{ => generic}/DMDataSetDTO.java | 8 +-
.../db/{ => generic}/DMExperimentDTO.java | 5 +-
.../yeastx/db/{ => generic}/DMSampleDTO.java | 5 +-
.../cisd/yeastx/db/generic/GenericUtils.java | 100 ++++++++++++++++++
.../yeastx/db/{ => generic}/IGenericDAO.java | 3 +-
.../cisd/yeastx/eicml/EICML2Database.java | 2 +-
.../cisd/yeastx/eicml/IEICMSRunDAO.java | 2 +-
.../cisd/yeastx/etl/ML2DatabaseUploader.java | 2 +-
.../cisd/yeastx/etl/MLArchiverTask.java | 2 +-
.../cisd/yeastx/fiaml/FIAML2Database.java | 2 +-
.../cisd/yeastx/fiaml/IFIAMSRunDAO.java | 2 +-
.../systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java | 4 +-
.../cisd/yeastx/mzxml/MzXml2Database.java | 2 +-
.../cisd/yeastx/quant/IQuantMSDAO.java | 2 +-
.../cisd/yeastx/quant/QuantML2Database.java | 2 +-
.../systemsx/cisd/yeastx/eicml/EICMLTest.java | 2 +-
.../systemsx/cisd/yeastx/fiaml/FIAMLTest.java | 7 +-
.../cisd/yeastx/mzxml/MzXml2DatabaseTest.java | 2 +-
.../cisd/yeastx/mzxml/MzXmlDAOTest.java | 2 +-
.../cisd/yeastx/quant/QuantMSDAOTest.java | 2 +-
23 files changed, 136 insertions(+), 106 deletions(-)
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/{ => generic}/DMDataSetDTO.java (95%)
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/{ => generic}/DMExperimentDTO.java (92%)
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/{ => generic}/DMSampleDTO.java (94%)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/{ => generic}/IGenericDAO.java (98%)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
index da604dc960e..ce76f575497 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/AbstractDatasetLoader.java
@@ -21,6 +21,9 @@ import javax.sql.DataSource;
import org.springframework.dao.DataAccessException;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.GenericUtils;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
/**
* Abstract class for dataset loaders. Provides commit and rollback functionality and creation of
@@ -73,7 +76,7 @@ abstract public class AbstractDatasetLoader<T extends IGenericDAO> implements ID
throw new IllegalStateException(
"The previous transaction of uploading a dataset has been neither commited nor rollbacked.");
}
- DBUtils.createDataSet(getDao(), dataSet);
+ GenericUtils.createDataSet(getDao(), dataSet);
isTransactionCompleted = false;
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
index 1c7b4a06d4e..598bc408135 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
@@ -71,81 +71,4 @@ public class DBUtils
}
}
- /**
- * 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.<br>
- * Sets sample, experiment and dataset id fields of the specified dataset.
- * <p>
- * NOTE: Code responsible for trying to get sample and experiment from the DB and creating them
- * if they don't exist is in synchronized block and uses currently opened transaction. Then the
- * transaction is closed and data set is added to the DB in second transaction. If second
- * transaction will be rolled back sample and experiment created in first transaction will stay
- * in the DB.
- */
- public static void createDataSet(IGenericDAO dao, DMDataSetDTO dataSet)
- {
- synchronized (IGenericDAO.class)
- {
- DMExperimentDTO experiment = getOrCreateExperiment(dao, dataSet);
- dataSet.setExperimentId(experiment.getId()); // make sure all the ids are set correctly.
-
- if (dataSet.getSample() != null)
- {
- String permId = dataSet.getSample().getPermId();
- DMSampleDTO sample;
- // it may have happened that the sample has been created by another thread after
- // we checked that it does not exist
-
- sample = dao.getSampleByPermId(permId);
- if (sample == null)
- {
- sample = dataSet.getSample();
- sample.setExperiment(experiment);
- sample = createSample(dao, sample, permId);
- }
-
- sample.setExperiment(experiment);
- dataSet.setSample(sample); // make sure all the ids are set correctly.
- }
- dao.close(true);
- }
-
- long dataSetId = dao.addDataSet(dataSet);
- dataSet.setId(dataSetId);
- }
-
- private static DMSampleDTO createSample(IGenericDAO dao, DMSampleDTO sample, String samplePermId)
- {
- final long sampleId = dao.addSample(sample);
- sample.setId(sampleId);
- return sample;
- }
-
- private static DMExperimentDTO getOrCreateExperiment(IGenericDAO dao, DMDataSetDTO dataSet)
- {
- String permId = dataSet.getExperiment().getPermId();
- // it may have happened that the experiment has been created by another thread after
- // we checked that it does not exist
- synchronized (IGenericDAO.class)
- {
- DMExperimentDTO experiment = dao.getExperimentByPermId(permId);
- if (experiment == null)
- {
- experiment = createExperiment(dao, dataSet, permId);
- }
- return experiment;
- }
- }
-
- private static DMExperimentDTO createExperiment(IGenericDAO dao, DMDataSetDTO dataSet,
- String permId)
- {
- DMExperimentDTO experiment;
- experiment = dataSet.getExperiment();
- long experimentId = dao.addExperiment(experiment);
- experiment.setId(experimentId);
- return experiment;
- }
-
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IDatasetLoader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IDatasetLoader.java
index 1e1fd4d9edf..799c49eae91 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IDatasetLoader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IDatasetLoader.java
@@ -19,6 +19,8 @@ package ch.systemsx.cisd.yeastx.db;
import java.io.File;
import java.sql.SQLException;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
+
/**
* @author Tomasz Pylak
*/
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
similarity index 95%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
index dfb88d75743..777097b59c2 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMDataSetDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.yeastx.db;
+package ch.systemsx.cisd.yeastx.db.generic;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
@@ -53,11 +53,13 @@ public class DMDataSetDTO
String expePermId, String expeName)
{
this.permId = dsPermId;
- final DMExperimentDTO experiment = new DMExperimentDTO(expePermId, expeName);
+ final DMExperimentDTO experiment = new DMExperimentDTO(expePermId);
+ experiment.setName(expeName);
if (sampPermIdOrNull != null)
{
assert sampNameOrNull != null : "sample name must be given when sample permId is given";
- this.sampleOrNull = new DMSampleDTO(sampPermIdOrNull, sampNameOrNull);
+ this.sampleOrNull = new DMSampleDTO(sampPermIdOrNull);
+ sampleOrNull.setName(sampNameOrNull);
sampleOrNull.setExperiment(experiment);
} else
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMExperimentDTO.java
similarity index 92%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMExperimentDTO.java
index 3df4cd07c45..340c4206540 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMExperimentDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMExperimentDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.yeastx.db;
+package ch.systemsx.cisd.yeastx.db.generic;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
@@ -39,10 +39,9 @@ public class DMExperimentDTO
// Bean compatibility.
}
- public DMExperimentDTO(String permId, String name)
+ public DMExperimentDTO(String permId)
{
this.permId = permId;
- this.name = name;
}
public long getId()
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMSampleDTO.java
similarity index 94%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMSampleDTO.java
index e44efaa844d..25894dc005e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DMSampleDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMSampleDTO.java
@@ -14,7 +14,7 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.yeastx.db;
+package ch.systemsx.cisd.yeastx.db.generic;
import net.lemnik.eodsql.AutoGeneratedKeys;
import net.lemnik.eodsql.ResultColumn;
@@ -45,10 +45,9 @@ public class DMSampleDTO
// Bean compatibility.
}
- public DMSampleDTO(String permId, String name)
+ public DMSampleDTO(String permId)
{
this.permId = permId;
- this.name = name;
}
public long getId()
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java
new file mode 100644
index 00000000000..0ead41406fc
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java
@@ -0,0 +1,100 @@
+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.yeastx.db.generic;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class GenericUtils
+{
+ /**
+ * 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.<br>
+ * Sets sample, experiment and dataset id fields of the specified dataset.
+ * <p>
+ * NOTE: Code responsible for trying to get sample and experiment from the DB and creating them
+ * if they don't exist is in synchronized block and uses currently opened transaction. Then the
+ * transaction is closed and data set is added to the DB in second transaction. If second
+ * transaction will be rolled back sample and experiment created in first transaction will stay
+ * in the DB.
+ */
+ public static void createDataSet(IGenericDAO dao, DMDataSetDTO dataSet)
+ {
+ synchronized (IGenericDAO.class)
+ {
+ DMExperimentDTO experiment = getOrCreateExperiment(dao, dataSet);
+ dataSet.setExperimentId(experiment.getId()); // make sure all the ids are set correctly.
+
+ if (dataSet.getSample() != null)
+ {
+ String permId = dataSet.getSample().getPermId();
+ DMSampleDTO sample;
+ // it may have happened that the sample has been created by another thread after
+ // we checked that it does not exist
+
+ sample = dao.getSampleByPermId(permId);
+ if (sample == null)
+ {
+ sample = dataSet.getSample();
+ sample.setExperiment(experiment);
+ sample = createSample(dao, sample, permId);
+ }
+
+ sample.setExperiment(experiment);
+ dataSet.setSample(sample); // make sure all the ids are set correctly.
+ }
+ dao.close(true);
+ }
+
+ long dataSetId = dao.addDataSet(dataSet);
+ dataSet.setId(dataSetId);
+ }
+
+ private static DMSampleDTO createSample(IGenericDAO dao, DMSampleDTO sample, String samplePermId)
+ {
+ final long sampleId = dao.addSample(sample);
+ sample.setId(sampleId);
+ return sample;
+ }
+
+ private static DMExperimentDTO getOrCreateExperiment(IGenericDAO dao, DMDataSetDTO dataSet)
+ {
+ String permId = dataSet.getExperiment().getPermId();
+ // it may have happened that the experiment has been created by another thread after
+ // we checked that it does not exist
+ synchronized (IGenericDAO.class)
+ {
+ DMExperimentDTO experiment = dao.getExperimentByPermId(permId);
+ if (experiment == null)
+ {
+ experiment = createExperiment(dao, dataSet, permId);
+ }
+ return experiment;
+ }
+ }
+
+ private static DMExperimentDTO createExperiment(IGenericDAO dao, DMDataSetDTO dataSet,
+ String permId)
+ {
+ DMExperimentDTO experiment;
+ experiment = dataSet.getExperiment();
+ long experimentId = dao.addExperiment(experiment);
+ experiment.setId(experimentId);
+ return experiment;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java
similarity index 98%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java
index 8e03104e266..63528310ea9 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/IGenericDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java
@@ -14,10 +14,11 @@
* limitations under the License.
*/
-package ch.systemsx.cisd.yeastx.db;
+package ch.systemsx.cisd.yeastx.db.generic;
import java.util.List;
+
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.TransactionQuery;
import net.lemnik.eodsql.Update;
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 86441c7123f..8d6eb6166de 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
@@ -23,7 +23,7 @@ import java.util.List;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IChromatogramObserver;
import ch.systemsx.cisd.yeastx.eicml.EICMLParser.IMSRunObserver;
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 7374352a384..d20462cee5d 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
@@ -20,7 +20,7 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
/**
* Interface for querying / updating the metabol database.
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 f3debfcbac1..45216aa01a2 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
@@ -32,8 +32,8 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.db.IDatasetLoader;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICML2Database;
import ch.systemsx.cisd.yeastx.fiaml.FIAML2Database;
import ch.systemsx.cisd.yeastx.mzxml.MzXml2Database;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
index 7a0e3a8c3f4..fded06e24dd 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/MLArchiverTask.java
@@ -32,7 +32,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.yeastx.db.DBUtils;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
/**
* Archiver that removes/adds data related to given data set from/to metabol database.
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 79246af8086..a98aa196162 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
@@ -23,7 +23,7 @@ import java.util.Iterator;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.fiaml.FIAMLParser.IMSRunObserver;
/**
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 26c302eea00..93831612b50 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
@@ -20,7 +20,7 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
/**
* Interface for querying / updating the metabol database.
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
index 74809ffcc21..8d8e2e8ebac 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
@@ -19,8 +19,8 @@ package ch.systemsx.cisd.yeastx.mzxml;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzInstrumentDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPrecursorDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzScanDTO;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
index 773f3870a3f..9af38d4413e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
@@ -27,7 +27,7 @@ import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPrecursorDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzRunDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzScanDTO;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
index e03ddcf1fe0..522a5e2305c 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.yeastx.quant;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
index fda48a38ce4..ac6b783778b 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
@@ -23,7 +23,7 @@ import java.util.List;
import javax.sql.DataSource;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.quant.dto.ConcentrationCompounds;
import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
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 3e6af129b79..fbae0e68946 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
@@ -32,7 +32,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
import ch.systemsx.cisd.yeastx.db.DBUtils;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
/**
* A test for thhe eicML tables.
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 559d1231625..7f53610483a 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
@@ -31,7 +31,8 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
import ch.systemsx.cisd.yeastx.db.DBUtils;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.GenericUtils;
/**
* A test for the fiaML tables.
@@ -114,10 +115,10 @@ public class FIAMLTest extends AbstractDBTest
{
try
{
- DBUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ GenericUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
"sample perm id4", "sample name", "experiment perm id", "experiment name"));
// This will fail with a DataIntegrityViolationException.
- DBUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ GenericUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
"sample perm id4", "sample name", "experiment perm id", "experiment name"));
// There is transaction commit inside createDataSet method before DS is added to DB.
// DS created in first invocation will be be commited in second invocation.
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
index 6837a6cf9c7..6b6f24028c9 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
@@ -30,7 +30,7 @@ import org.testng.annotations.Test;
import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.base.convert.NativeData;
import ch.systemsx.cisd.base.convert.NativeData.ByteOrder;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzInstrumentDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPeaksDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPrecursorDTO;
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXmlDAOTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXmlDAOTest.java
index d3f6c0b3cd1..1a6ce0bad34 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXmlDAOTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXmlDAOTest.java
@@ -25,7 +25,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
import ch.systemsx.cisd.yeastx.db.DBUtils;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
/**
* @author Tomasz Pylak
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
index 7ef67e5b061..469b1ff9d89 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
@@ -25,7 +25,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
import ch.systemsx.cisd.yeastx.db.DBUtils;
-import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
/**
* @author Tomasz Pylak
--
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