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 ce76f5754973c47b1e1867965657ca7c0e211964..941ae9ff9cd676426f85d8299963fdbb374e6b56 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 777097b59c28dec2b953d7f7cce04443d9e3de3c..07a645712f56fde675da46a6884dad89dd962f75 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 0ead41406fc61e1df01b67d84fff03f17d55fa82..70776f4cb9e0b2828baa33d693e091eb127308fb 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 63528310ea9377fe9151e367f3cfabdd3819b4e4..7f49208cae0cb3f2d420b9ece9f786a5fcd893f3 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 d20462cee5de1180173a52f57f3a12ba4091448b..913988e6bef75f345c7784cb9dcc87013030cdd9 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 fded06e24ddb480990d68d95807bdfcaad690a1d..7606271da6cc0488708f489992e7a59a6cf1eabe 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 93831612b50856b2bae5dcfb561b02aa315e6837..e0ecaa79c62347046a142fe36b194a5055f39296 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 8d8e2e8ebac36fb16d8d710d94b3af16c88a5e5a..ab62445fa22ffc2515dd90c266b9cba6ca359ddb 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 522a5e2305cc3a72146c632d2177f369226bf036..2760bae9f43a8e59f7cdf5783f63248e262b479b 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 7f53610483af0610205c83d8616107fcb437b399..23d396582ea89d85fba6f00456027a9cb5752aa9 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.