From 6dfbd4f9a75a30afd2c7374c617cb2bc243a6abd Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 13 Jan 2010 08:43:00 +0000
Subject: [PATCH] SE-179 YeastX: DSS reporting plugins
SVN: 14267
---
.../tasks/SimpleTableModelBuilder.java | 27 ++-
.../ch/systemsx/cisd/yeastx/db/DBUtils.java | 12 ++
.../eicml/EICMLChromatogramsReporter.java | 163 ++++++++++++++++++
.../cisd/yeastx/eicml/EICMLRunsReporter.java | 114 ++++++++++++
.../cisd/yeastx/eicml/IEICMSRunDAO.java | 22 +--
.../cisd/yeastx/etl/ML2DatabaseUploader.java | 8 +-
.../systemsx/cisd/yeastx/eicml/EICMLTest.java | 38 ++--
...eeningPlateImageParamsReportingPlugin.java | 15 +-
8 files changed, 349 insertions(+), 50 deletions(-)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
index 0610c5d3671..6be09a3cec2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
@@ -17,9 +17,14 @@
package ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks;
import java.util.ArrayList;
+import java.util.Date;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DateTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelColumnHeader;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
@@ -50,7 +55,7 @@ public class SimpleTableModelBuilder
{
addHeader(title, false);
}
-
+
public void addRow(List<ISerializableComparable> values)
{
assert values.size() == header.size() : "header has different number of columns than a row";
@@ -61,4 +66,24 @@ public class SimpleTableModelBuilder
{
return new TableModel(header, rows);
}
+
+ public static ISerializableComparable asText(String text)
+ {
+ return new StringTableCell(text);
+ }
+
+ public static ISerializableComparable asNum(int num)
+ {
+ return new IntegerTableCell(num);
+ }
+
+ public static ISerializableComparable asNum(double num)
+ {
+ return new DoubleTableCell(num);
+ }
+
+ public static ISerializableComparable asDate(Date date)
+ {
+ return new DateTableCell(date);
+ }
}
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 12269f43956..42d437ed91d 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
@@ -23,6 +23,7 @@ import net.lemnik.eodsql.TransactionQuery;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.utilities.BeanUtils;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
@@ -37,11 +38,22 @@ public class DBUtils
/** Current version of the database. */
public static final String DATABASE_VERSION = "004";
+ private static final String DATABASE_PROPERTIES_PREFIX = "database.";
+
static
{
QueryTool.getTypeMap().put(float[].class, new FloatArrayMapper());
}
+ public static DatabaseConfigurationContext createAndInitDBContext(Properties properties)
+ {
+ final Properties dbProps =
+ ExtendedProperties.getSubset(properties, DATABASE_PROPERTIES_PREFIX, true);
+ final DatabaseConfigurationContext dbContext = DBUtils.createDBContext(dbProps);
+ DBUtils.init(dbContext);
+ return dbContext;
+ }
+
public static DatabaseConfigurationContext createDBContext(Properties dbProps)
{
DatabaseConfigurationContext context =
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
new file mode 100644
index 00000000000..65abf1ad749
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
@@ -0,0 +1,163 @@
+/*
+ * 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.eicml;
+
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asNum;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asText;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+
+/**
+ * Reporting plugin which shows all the chromatograms details for the chosen datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public class EICMLChromatogramsReporter extends AbstractDatastorePlugin implements
+ IReportingPluginTask
+{
+ private final IEICMSRunDAO query;
+
+ public EICMLChromatogramsReporter(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ this.query = createQuery(properties);
+ }
+
+ private static IEICMSRunDAO createQuery(Properties properties)
+ {
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ DataSource dataSource = dbContext.getDataSource();
+ return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
+ }
+
+ private static final long serialVersionUID = 1L;
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+ addReportHeaders(builder);
+ List<EICMSRunDTO> runs = fetchRuns(datasets);
+ for (EICMSRunDTO run : runs)
+ {
+ DataIterator<ChromatogramDTO> chromatograms = query.getChromatogramsForRun(run);
+ addRun(builder, run, chromatograms);
+ }
+ return builder.getTableModel();
+ }
+
+ private List<EICMSRunDTO> fetchRuns(List<DatasetDescription> datasets)
+ {
+ List<EICMSRunDTO> runs = new ArrayList<EICMSRunDTO>();
+ for (DatasetDescription dataset : datasets)
+ {
+ EICMSRunDTO run = query.getMSRunByDatasetPermId(dataset.getDatasetCode());
+ if (run != null)
+ {
+ runs.add(run);
+ }
+ }
+ return runs;
+ }
+
+ private static void addRun(SimpleTableModelBuilder builder, EICMSRunDTO run,
+ DataIterator<ChromatogramDTO> chromatograms)
+ {
+ for (ChromatogramDTO chromatogram : chromatograms)
+ {
+ builder.addRow(createRow(builder, run, chromatogram));
+ }
+ }
+
+ private static List<ISerializableComparable> createRow(SimpleTableModelBuilder builder,
+ EICMSRunDTO run, ChromatogramDTO chromatogram)
+ {
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+
+ row.add(asText(chromatogram.getLabel()));
+ row.add(asNum(calcMin(chromatogram.getRunTimes())));
+ row.add(asNum(calcMax(chromatogram.getRunTimes())));
+ row.add(asNum(calcMax(chromatogram.getIntensities())));
+ row.add(asNum(chromatogram.getQ1Mz()));
+ row.add(asNum(chromatogram.getQ3LowMz()));
+ row.add(asNum(chromatogram.getQ3HighMz()));
+ row.add(asText("" + chromatogram.getPolarity()));
+ return row;
+ }
+
+ private static float calcMax(float[] values)
+ {
+ if (values.length == 0)
+ {
+ return -1;
+ }
+ float max = values[0];
+ for (int i = 1; i < values.length; i++)
+ {
+ if (values[i] > max)
+ {
+ max = values[i];
+ }
+ }
+ return max;
+ }
+
+ private static float calcMin(float[] values)
+ {
+ if (values.length == 0)
+ {
+ return -1;
+ }
+ float min = values[0];
+ for (int i = 1; i < values.length; i++)
+ {
+ if (values[i] < min)
+ {
+ min = values[i];
+ }
+ }
+ return min;
+ }
+
+ private static void addReportHeaders(SimpleTableModelBuilder builder)
+ {
+ builder.addHeader("Label");
+ builder.addHeader("RT Start");
+ builder.addHeader("RT End");
+ builder.addHeader("Max. Intensity");
+ builder.addHeader("Q1 Mz", true);
+ builder.addHeader("Q3Low Mz", true);
+ builder.addHeader("Q3High Mz", true);
+ builder.addHeader("Polarity");
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
new file mode 100644
index 00000000000..efbecba4b7c
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
@@ -0,0 +1,114 @@
+/*
+ * 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.eicml;
+
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asDate;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asNum;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asText;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+
+/**
+ * Reporting plugin which shows all the run details for the chosen datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public class EICMLRunsReporter extends AbstractDatastorePlugin implements IReportingPluginTask
+{
+ private final IEICMSRunDAO query;
+
+ public EICMLRunsReporter(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ this.query = createQuery(properties);
+ }
+
+ private static IEICMSRunDAO createQuery(Properties properties)
+ {
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ DataSource dataSource = dbContext.getDataSource();
+ return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
+ }
+
+ private static final long serialVersionUID = 1L;
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+ addReportHeaders(builder);
+ for (DatasetDescription dataset : datasets)
+ {
+ EICMSRunDTO run = query.getMSRunByDatasetPermId(dataset.getDatasetCode());
+ if (run != null)
+ {
+ builder.addRow(createRow(run, dataset));
+ }
+ }
+ return builder.getTableModel();
+ }
+
+ private static List<ISerializableComparable> createRow(EICMSRunDTO run,
+ DatasetDescription dataset)
+ {
+ List<ISerializableComparable> row = new ArrayList<ISerializableComparable>();
+ row.add(asText(dataset.getDatasetCode()));
+ row.add(asText(run.getRawDataFilePath()));
+ row.add(asText(run.getRawDataFileName()));
+ row.add(asText(run.getInstrumentType()));
+ row.add(asText(run.getInstrumentManufacturer()));
+ row.add(asText(run.getInstrumentModel()));
+ row.add(asText(run.getMethodIonisation()));
+ row.add(asText(run.getMethodSeparation()));
+ row.add(asDate(run.getAcquisitionDate()));
+ row.add(asNum(run.getStartTime()));
+ row.add(asNum(run.getEndTime()));
+ row.add(asText(run.getOperator()));
+ return row;
+ }
+
+ private static void addReportHeaders(SimpleTableModelBuilder builder)
+ {
+ builder.addHeader("Dataset");
+ builder.addHeader("Raw data file path");
+ builder.addHeader("Raw data file name");
+ builder.addHeader("Instrument type");
+ builder.addHeader("Instrument manufacturer");
+ builder.addHeader("Instrument model");
+ builder.addHeader("Method ionisation");
+ builder.addHeader("Method separation");
+ builder.addHeader("Acquisition date");
+ builder.addHeader("Start time");
+ builder.addHeader("End time");
+ builder.addHeader("Operator");
+ }
+}
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 3aadd5a8bdc..562634c1377 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
@@ -61,25 +61,9 @@ public interface IEICMSRunDAO extends IGenericDAO
@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 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 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(ID) "
- + "where EIC_CHROMATOGRAMS.ID = ?{1.id}")
- public EICMSRunDTO getMSRunForChromatogram(ChromatogramDTO chromatogram);
-
- @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(sql = "select EIC_MS_RUNS.* from EIC_MS_RUNS left join DATA_SETS on DATA_SETS.id = EIC_MS_RUNS.ds_id "
+ + "where DATA_SETS.perm_id = ?{1} group by " + ALL_EIC_MSRUN_COLUMNS)
+ public EICMSRunDTO getMSRunByDatasetPermId(String datasetPermId);
@Select("select * FROM EIC_CHROMATOGRAMS where EIC_MS_RUN_ID=?{1.id}")
public DataIterator<ChromatogramDTO> getChromatogramsForRun(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 d546f5df15d..ae61eb7f282 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
@@ -26,7 +26,6 @@ import javax.sql.DataSource;
import org.apache.commons.io.FilenameUtils;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
-import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
import ch.systemsx.cisd.etlserver.IDataSetUploader;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -51,8 +50,6 @@ public class ML2DatabaseUploader implements IDataSetUploader
{
private static final String UNKNOWN_NAME = "unknown";
- private static final String DATABASE_PROPERTIES_PREFIX = "database.";
-
private final IDatasetLoader eicML2Database;
private final IDatasetLoader fiaML2Database;
@@ -71,10 +68,7 @@ public class ML2DatabaseUploader implements IDataSetUploader
public ML2DatabaseUploader(Properties properties)
{
- final Properties dbProps =
- ExtendedProperties.getSubset(properties, DATABASE_PROPERTIES_PREFIX, true);
- final DatabaseConfigurationContext dbContext = DBUtils.createDBContext(dbProps);
- DBUtils.init(dbContext);
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
DataSource dataSource = dbContext.getDataSource();
this.eicML2Database = new EICML2Database(dataSource);
this.fiaML2Database = new FIAML2Database(dataSource);
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 6616901c685..8b2f6543106 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
@@ -27,6 +27,7 @@ import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.QueryTool;
import org.apache.commons.lang.ArrayUtils;
+import org.testng.AssertJUnit;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -41,6 +42,8 @@ import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
public class EICMLTest extends AbstractDBTest
{
+ private static final String DATA_SET_PERM_ID = "data set perm id eicml";
+
private IEICMSRunDAO eicmlDAO;
@BeforeMethod(alwaysRun = true)
@@ -60,8 +63,16 @@ public class EICMLTest extends AbstractDBTest
private DMDataSetDTO createDataset()
{
- return new DMDataSetDTO("data set perm id eicml", "sample perm id eicml",
- "sample name eicml", "experiment perm id eicml", "experiment name eicml");
+ return new DMDataSetDTO(DATA_SET_PERM_ID, "sample perm id eicml", "sample name eicml",
+ "experiment perm id eicml", "experiment name eicml");
+ }
+
+ @Test(dependsOnMethods = "testUploadEicML")
+ public void testGetMSRunByDatasetPermId() throws ParseException
+ {
+ EICMSRunDTO run = eicmlDAO.getMSRunByDatasetPermId(DATA_SET_PERM_ID);
+ AssertJUnit.assertNotNull(run);
+ assertRunCorrect(run);
}
private void checkChromatograms(int count, ChromatogramDTO chrom)
@@ -132,6 +143,20 @@ public class EICMLTest extends AbstractDBTest
final EICMSRunDTO run = runs.next();
assertFalse(runs.hasNext());
assertEquals(4, run.getChromCount());
+ assertRunCorrect(run);
+ final DataIterator<ChromatogramDTO> chromatograms = eicmlDAO.getChromatogramsForRun(run);
+ int count = 0;
+ while (chromatograms.hasNext())
+ {
+ final ChromatogramDTO chrom = chromatograms.next();
+ checkChromatograms(count, chrom);
+ ++count;
+ }
+ assertEquals(run.getChromCount(), count);
+ }
+
+ private void assertRunCorrect(final EICMSRunDTO run) throws ParseException
+ {
assertEquals(EICMLParser.getDateFormat().parse("16-Jun-2009 11:58:14"), run
.getAcquisitionDate());
assertEquals(370.109f, run.getStartTime());
@@ -146,14 +171,5 @@ public class EICMLTest extends AbstractDBTest
assertEquals(17L, run.getMsRunId().longValue());
assertEquals(32L, run.getSetId().longValue());
assertEquals("???", run.getOperator());
- final DataIterator<ChromatogramDTO> chromatograms = eicmlDAO.getChromatogramsForRun(run);
- int count = 0;
- while (chromatograms.hasNext())
- {
- final ChromatogramDTO chrom = chromatograms.next();
- checkChromatograms(count, chrom);
- ++count;
- }
- assertEquals(run.getChromCount(), count);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
index a66f64f85dd..36047326534 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ScreeningPlateImageParamsReportingPlugin.java
@@ -16,6 +16,9 @@
package ch.systemsx.cisd.openbis.dss.generic.server.plugins;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asNum;
+import static ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder.asText;
+
import java.io.File;
import java.util.Arrays;
import java.util.List;
@@ -30,8 +33,6 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractData
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.StringTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
@@ -106,16 +107,6 @@ public class ScreeningPlateImageParamsReportingPlugin extends AbstractDatastoreP
builder.addRow(row);
}
- private static ISerializableComparable asText(String text)
- {
- return new StringTableCell(text);
- }
-
- private static ISerializableComparable asNum(int num)
- {
- return new IntegerTableCell(num);
- }
-
private IHCSImageFormattedData getImageAccessor(IDataStructureV1_0 structure)
{
return (IHCSImageFormattedData) structure.getFormattedData();
--
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