From c58ffd2efd5f10bdb8cc5a3a1feaa153359d5328 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 23 Nov 2010 15:15:53 +0000
Subject: [PATCH] SE-316 renaming data set info extractor class make properties
file name and experiment type configurable
SVN: 18886
---
...ataSetInfoExtractorForProteinResults.java} | 28 +++++++++++++------
...etInfoExtractorForProteinResultsTest.java} | 16 +++++------
2 files changed, 27 insertions(+), 17 deletions(-)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/{DataSetInfoExtractorForSearchExperiment.java => DataSetInfoExtractorForProteinResults.java} (74%)
rename rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/{DataSetInfoExtractorForSearchExperimentTest.java => DataSetInfoExtractorForProteinResultsTest.java} (90%)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperiment.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
similarity index 74%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperiment.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
index ace0a08d0a9..fce6e06e84b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperiment.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
@@ -39,25 +39,33 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
*
* @author Franz-Josef Elmer
*/
-public class DataSetInfoExtractorForSearchExperiment extends AbstractDataSetInfoExtractorWithService
+public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoExtractorWithService
{
- @Private static final String EXPERIMENT_TYPE_CODE = "MS_SEARCH";
+ @Private static final String EXPERIMENT_TYPE_CODE_KEY = "experiment-type-code";
+ @Private static final String EXPERIMENT_PROPERTIES_FILE_NAME_KEY = "experiment-properties-file-name";
+ @Private static final String DEFAULT_EXPERIMENT_TYPE_CODE = "MS_SEARCH";
@Private static final String SEPARATOR_KEY = "separator";
@Private static final String DEFAULT_SEPARATOR = "&";
- @Private static final String SEARCH_PROPERTIES = "search.properties";
+ @Private static final String DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME = "search.properties";
@Private static final String PARENT_DATA_SET_CODES = "parent-data-set-codes";
private final String separator;
+ private final String experimentPropertiesFileName;
+ private final String experimentTypeCode;
- public DataSetInfoExtractorForSearchExperiment(Properties properties)
+ public DataSetInfoExtractorForProteinResults(Properties properties)
{
this(properties, ServiceProvider.getOpenBISService());
}
- DataSetInfoExtractorForSearchExperiment(Properties properties, IEncapsulatedOpenBISService service)
+ DataSetInfoExtractorForProteinResults(Properties properties, IEncapsulatedOpenBISService service)
{
super(service);
separator = properties.getProperty(SEPARATOR_KEY, DEFAULT_SEPARATOR);
+ experimentPropertiesFileName =
+ properties.getProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY,
+ DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME);
+ experimentTypeCode = properties.getProperty(EXPERIMENT_TYPE_CODE_KEY, DEFAULT_EXPERIMENT_TYPE_CODE);
}
public DataSetInformation getDataSetInformation(File incomingDataSetPath,
@@ -75,10 +83,12 @@ public class DataSetInfoExtractorForSearchExperiment extends AbstractDataSetInfo
ProjectIdentifier projectIdentifier = new ProjectIdentifier(items[0], items[1]);
ExperimentIdentifier experimentIdentifier =
new ExperimentIdentifier(projectIdentifier, "E" + service.drawANewUniqueID());
- NewExperiment experiment = new NewExperiment(experimentIdentifier.toString(),
- EXPERIMENT_TYPE_CODE);
- ExperimentType experimentType = service.getExperimentType(EXPERIMENT_TYPE_CODE);
- Properties properties = loadSearchProperties(new File(incomingDataSetPath, SEARCH_PROPERTIES));
+ NewExperiment experiment =
+ new NewExperiment(experimentIdentifier.toString(), experimentTypeCode);
+ ExperimentType experimentType = service.getExperimentType(experimentTypeCode);
+
+ Properties properties =
+ loadSearchProperties(new File(incomingDataSetPath, experimentPropertiesFileName));
experiment.setProperties(Util.getAndCheckProperties(properties, experimentType));
service.registerExperiment(experiment);
DataSetInformation info = new DataSetInformation();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperimentTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
similarity index 90%
rename from rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperimentTest.java
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
index 40725380a43..e6d416959fb 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForSearchExperimentTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
@@ -16,8 +16,8 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
-import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForSearchExperiment.EXPERIMENT_TYPE_CODE;
-import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForSearchExperiment.PARENT_DATA_SET_CODES;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_TYPE_CODE;
+import static ch.systemsx.cisd.openbis.etlserver.phosphonetx.DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES;
import java.io.File;
import java.util.Arrays;
@@ -49,8 +49,8 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
*
* @author Franz-Josef Elmer
*/
-@Friend(toClasses=DataSetInfoExtractorForSearchExperiment.class)
-public class DataSetInfoExtractorForSearchExperimentTest extends AbstractFileSystemTestCase
+@Friend(toClasses=DataSetInfoExtractorForProteinResults.class)
+public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSystemTestCase
{
private Mockery context;
private IEncapsulatedOpenBISService service;
@@ -77,7 +77,7 @@ public class DataSetInfoExtractorForSearchExperimentTest extends AbstractFileSys
public void testRegistrationWithOneMandatoryProperty()
{
FileUtilities.writeToFile(new File(dataSet,
- DataSetInfoExtractorForSearchExperiment.SEARCH_PROPERTIES),
+ DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME),
"answer=42\nblabla=blub\n" + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
prepare();
@@ -91,7 +91,7 @@ public class DataSetInfoExtractorForSearchExperimentTest extends AbstractFileSys
if (item instanceof NewExperiment)
{
NewExperiment experiment = (NewExperiment) item;
- assertEquals(EXPERIMENT_TYPE_CODE, experiment
+ assertEquals(DEFAULT_EXPERIMENT_TYPE_CODE, experiment
.getExperimentTypeCode());
IEntityProperty[] properties = experiment.getProperties();
assertEquals(1, properties.length);
@@ -144,7 +144,7 @@ public class DataSetInfoExtractorForSearchExperimentTest extends AbstractFileSys
one(service).drawANewUniqueID();
will(returnValue(4711L));
- one(service).getExperimentType(EXPERIMENT_TYPE_CODE);
+ one(service).getExperimentType(DEFAULT_EXPERIMENT_TYPE_CODE);
ExperimentType type = new ExperimentType();
ExperimentTypePropertyType etpt = new ExperimentTypePropertyType();
PropertyType propertyType = new PropertyType();
@@ -159,6 +159,6 @@ public class DataSetInfoExtractorForSearchExperimentTest extends AbstractFileSys
private IDataSetInfoExtractor createExtractor(Properties properties)
{
- return new DataSetInfoExtractorForSearchExperiment(properties, service);
+ return new DataSetInfoExtractorForProteinResults(properties, service);
}
}
--
GitLab