LMS-1529 coherent naming for data mart infrastructure

SVN: 15874

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;
     }
 

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";

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/GenericUtils.java → 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;

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/generic/IGenericDAO.java → 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}")

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, "

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());

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, "

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, "

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 ) "

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.