From 21c55f26ccdb191f290333f6b7ecbf21c42e8ee0 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 10 May 2010 13:08:20 +0000
Subject: [PATCH] LMS-1529 coherent naming for data mart infrastructure
SVN: 15874
---
.../cisd/yeastx/db/AbstractDatasetLoader.java | 8 ++++----
.../cisd/yeastx/db/generic/DMDataSetDTO.java | 4 ++--
.../{GenericUtils.java => DMGenericUtils.java} | 16 +++++++++-------
.../{IGenericDAO.java => IDMGenericDAO.java} | 4 ++--
.../systemsx/cisd/yeastx/eicml/IEICMSRunDAO.java | 4 ++--
.../systemsx/cisd/yeastx/etl/MLArchiverTask.java | 4 ++--
.../systemsx/cisd/yeastx/fiaml/IFIAMSRunDAO.java | 4 ++--
.../ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java | 4 ++--
.../systemsx/cisd/yeastx/quant/IQuantMSDAO.java | 4 ++--
.../ch/systemsx/cisd/yeastx/fiaml/FIAMLTest.java | 6 +++---
10 files changed, 30 insertions(+), 28 deletions(-)
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/{GenericUtils.java => DMGenericUtils.java} (86%)
rename rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/{IGenericDAO.java => IDMGenericDAO.java} (94%)
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 ce76f575497..941ae9ff9cd 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
@@ -22,8 +22,8 @@ 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;
+import ch.systemsx.cisd.yeastx.db.generic.DMGenericUtils;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
/**
* Abstract class for dataset loaders. Provides commit and rollback functionality and creation of
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
*
* @author Tomasz Pylak
*/
-abstract public class AbstractDatasetLoader<T extends IGenericDAO> implements IDatasetLoader
+abstract public class AbstractDatasetLoader<T extends IDMGenericDAO> implements IDatasetLoader
{
// if false transaction has to be commited or rollbacked before the next dataset will be created
protected boolean isTransactionCompleted = true;
@@ -76,7 +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.");
}
- GenericUtils.createDataSet(getDao(), dataSet);
+ DMGenericUtils.createDataSet(getDao(), dataSet);
isTransactionCompleted = false;
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
index 777097b59c2..07a645712f5 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMDataSetDTO.java
@@ -50,11 +50,11 @@ public class DMDataSetDTO
}
public DMDataSetDTO(String dsPermId, String sampPermIdOrNull, String sampNameOrNull,
- String expePermId, String expeName)
+ String expePermId, String experimentName)
{
this.permId = dsPermId;
final DMExperimentDTO experiment = new DMExperimentDTO(expePermId);
- experiment.setName(expeName);
+ experiment.setName(experimentName);
if (sampPermIdOrNull != null)
{
assert sampNameOrNull != null : "sample name must be given when sample permId is given";
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/DMGenericUtils.java
similarity index 86%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMGenericUtils.java
index 0ead41406fc..70776f4cb9e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/DMGenericUtils.java
@@ -17,9 +17,11 @@
package ch.systemsx.cisd.yeastx.db.generic;
/**
+ * Utilities to perform operations on the Data Mart.
+ *
* @author Tomasz Pylak
*/
-public class GenericUtils
+public class DMGenericUtils
{
/**
* Creates the data set based on the information given in <var>dataSet</var>. The sample and
@@ -33,9 +35,9 @@ public class GenericUtils
* 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)
+ public static void createDataSet(IDMGenericDAO dao, DMDataSetDTO dataSet)
{
- synchronized (IGenericDAO.class)
+ synchronized (IDMGenericDAO.class)
{
DMExperimentDTO experiment = getOrCreateExperiment(dao, dataSet);
dataSet.setExperimentId(experiment.getId()); // make sure all the ids are set correctly.
@@ -65,19 +67,19 @@ public class GenericUtils
dataSet.setId(dataSetId);
}
- private static DMSampleDTO createSample(IGenericDAO dao, DMSampleDTO sample, String samplePermId)
+ private static DMSampleDTO createSample(IDMGenericDAO dao, DMSampleDTO sample, String samplePermId)
{
final long sampleId = dao.addSample(sample);
sample.setId(sampleId);
return sample;
}
- private static DMExperimentDTO getOrCreateExperiment(IGenericDAO dao, DMDataSetDTO dataSet)
+ private static DMExperimentDTO getOrCreateExperiment(IDMGenericDAO 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)
+ synchronized (IDMGenericDAO.class)
{
DMExperimentDTO experiment = dao.getExperimentByPermId(permId);
if (experiment == null)
@@ -88,7 +90,7 @@ public class GenericUtils
}
}
- private static DMExperimentDTO createExperiment(IGenericDAO dao, DMDataSetDTO dataSet,
+ private static DMExperimentDTO createExperiment(IDMGenericDAO dao, DMDataSetDTO dataSet,
String permId)
{
DMExperimentDTO experiment;
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IDMGenericDAO.java
similarity index 94%
rename from rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java
rename to rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IDMGenericDAO.java
index 63528310ea9..7f49208cae0 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IDMGenericDAO.java
@@ -24,11 +24,11 @@ import net.lemnik.eodsql.TransactionQuery;
import net.lemnik.eodsql.Update;
/**
- * Interface for the "generic" methods (i.e. experiment, sample and data set).
+ * Interface for the "generic" methods on the Data Mart (i.e. experiment, sample and data set).
*
* @author Bernd Rinn
*/
-public interface IGenericDAO extends TransactionQuery
+public interface IDMGenericDAO extends TransactionQuery
{
@Select("select * from EXPERIMENTS where PERM_ID = ?{1}")
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 d20462cee5d..913988e6bef 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
@@ -20,14 +20,14 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
/**
* Interface for querying / updating the metabol database.
*
* @author Bernd Rinn
*/
-public interface IEICMSRunDAO extends IGenericDAO
+public interface IEICMSRunDAO extends IDMGenericDAO
{
final String ALL_EIC_MSRUN_COLUMNS =
"EIC_MS_RUNS.ID, EIC_MS_RUNS.EXPE_ID, EIC_MS_RUNS.SAMP_ID, EIC_MS_RUNS.DS_ID, "
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 fded06e24dd..7606271da6c 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.generic.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
/**
* Archiver that removes/adds data related to given data set from/to metabol database.
@@ -62,7 +62,7 @@ public class MLArchiverTask extends AbstractArchiverProcessingPlugin
{
DataSource dataSource = getDataSource(dataSourceName);
- final IGenericDAO dao = DBUtils.getQuery(dataSource, IGenericDAO.class);
+ final IDMGenericDAO dao = DBUtils.getQuery(dataSource, IDMGenericDAO.class);
try
{
dao.deleteDataSet(dataset.getDatasetCode());
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 93831612b50..e0ecaa79c62 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
@@ -20,14 +20,14 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
-import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
/**
* Interface for querying / updating the metabol database.
*
* @author Bernd Rinn
*/
-public interface IFIAMSRunDAO extends IGenericDAO
+public interface IFIAMSRunDAO extends IDMGenericDAO
{
final String ALL_FIA_MSRUN_COLUMNS =
"FIA_MS_RUNS.ID, FIA_MS_RUNS.EXPE_ID, "
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 8d8e2e8ebac..ab62445fa22 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
@@ -20,7 +20,7 @@ import net.lemnik.eodsql.Select;
import net.lemnik.eodsql.Update;
import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.generic.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzInstrumentDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzPrecursorDTO;
import ch.systemsx.cisd.yeastx.mzxml.dto.MzScanDTO;
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.yeastx.mzxml.dto.MzScanDTO;
*
* @author Tomasz Pylak
*/
-public interface IMzXmlDAO extends IGenericDAO
+public interface IMzXmlDAO extends IDMGenericDAO
{
@Select(sql = "insert into MZ_MS_RUNS "
+ " ( EXPE_ID, SAMP_ID, DS_ID, INSTRUMENT_TYPE, INSTRUMENT_MANUFACTURER, "
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 522a5e2305c..2760bae9f43 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.generic.IGenericDAO;
+import ch.systemsx.cisd.yeastx.db.generic.IDMGenericDAO;
import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
*
* @author Tomasz Pylak
*/
-public interface IQuantMSDAO extends IGenericDAO
+public interface IQuantMSDAO extends IDMGenericDAO
{
@Select(sql = "insert into MS_QUANTIFICATIONS "
+ "( EXPE_ID, DS_ID, SOURCE, VALID, COMMENT, REGISTRATOR, REGISTRATION_DATE ) "
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 7f53610483a..23d396582ea 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
@@ -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.generic.DMDataSetDTO;
-import ch.systemsx.cisd.yeastx.db.generic.GenericUtils;
+import ch.systemsx.cisd.yeastx.db.generic.DMGenericUtils;
/**
* A test for the fiaML tables.
@@ -115,10 +115,10 @@ public class FIAMLTest extends AbstractDBTest
{
try
{
- GenericUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ DMGenericUtils.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.
- GenericUtils.createDataSet(fiamsDAO, new DMDataSetDTO("data set perm id 4",
+ DMGenericUtils.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.
--
GitLab