From 977b2e2203e125e91f4283ca201a6de1be145d3d Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 28 Oct 2013 09:45:00 +0000
Subject: [PATCH] SP-982, CCS-62: Threshold introduce to prevent feeding
protein database for prot.xml files which are too large. In this case search
experiment property NOT_PROCESSED is set to give a reason visible for the
user on the experiment details view.
SVN: 30031
---
.../drop-boxes/ms-search/plugin.properties | 1 +
...DataSetInfoExtractorForProteinResults.java | 36 +++++++-
.../etlserver/proteomics/ProtXMLUploader.java | 39 ++++-----
.../openbis/etlserver/proteomics/Util.java | 22 +++++
...SetInfoExtractorForProteinResultsTest.java | 85 +++++++++++++++----
.../proteomics/ProtXMLUploaderTest.java | 23 ++---
6 files changed, 153 insertions(+), 53 deletions(-)
diff --git a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
index fc80280936e..619875ae92e 100644
--- a/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
+++ b/rtd_phosphonetx/source/core-plugins/proteomics/1/dss/drop-boxes/ms-search/plugin.properties
@@ -13,6 +13,7 @@ incoming-data-completeness-condition = auto-detection
data-set-info-extractor = ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults
data-set-info-extractor.separator = +
+data-set-info-extractor.prot-xml-size-threshold-in-MB = 1
type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
type-extractor.file-format-type = XML
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
index 199e9398f7e..601fbc3d3c2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResults.java
@@ -21,20 +21,26 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
+import org.apache.commons.io.FileUtils;
import org.apache.commons.lang.StringUtils;
+import org.apache.log4j.Logger;
import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.io.PropertyIOUtils;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.properties.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ParentDataSetCodes;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -45,6 +51,16 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
*/
public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoExtractorWithService
{
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DataSetInfoExtractorForProteinResults.class);
+
+ static final String NOT_PROCESSED_PROPERTY = "NOT_PROCESSED";
+
+ @Private
+ static final String PROT_XML_SIZE_THRESHOLD = "prot-xml-size-threshold-in-MB";
+
+ private static final int DEFAULT_PROT_XML_SIZE_THRESHOLD = 256;
+
@Private
static final String EXPERIMENT_TYPE_CODE_KEY = "experiment-type-code";
@@ -76,6 +92,8 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
private final String experimentTypeCode;
+ private final long protXmlSizeThreshold;
+
public DataSetInfoExtractorForProteinResults(Properties properties)
{
this(properties, ServiceProvider.getOpenBISService());
@@ -90,6 +108,8 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME);
experimentTypeCode =
properties.getProperty(EXPERIMENT_TYPE_CODE_KEY, DEFAULT_EXPERIMENT_TYPE_CODE);
+ protXmlSizeThreshold = PropertyUtils.getInt(properties, PROT_XML_SIZE_THRESHOLD,
+ DEFAULT_PROT_XML_SIZE_THRESHOLD) * FileUtils.ONE_MB;
}
@Override
@@ -118,6 +138,20 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
NewExperiment experiment =
new NewExperiment(experimentIdentifier.toString(), experimentTypeCode);
ExperimentType experimentType = service.getExperimentType(experimentTypeCode);
+ File protXMLFile = Util.tryGetProtXMLFile(incomingDataSetPath);
+ if (protXMLFile == null)
+ {
+ throw new UserFailureException("No *prot.xml file found in data set '" + incomingDataSetPath + "'.");
+ }
+ long fileSize = protXMLFile.length();
+ if (fileSize > protXmlSizeThreshold)
+ {
+ String reason = "Size of prot.xml file " + protXMLFile.getName() + " is with "
+ + FileUtilities.byteCountToDisplaySize(fileSize) + " too large. Maximum size is "
+ + FileUtilities.byteCountToDisplaySize(protXmlSizeThreshold);
+ operationLog.warn(reason);
+ properties.setProperty(NOT_PROCESSED_PROPERTY, reason);
+ }
experiment.setProperties(Util.getAndCheckProperties(properties, experimentType));
DataSetInformation info = new DataSetInformation();
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
index 6c9b459f480..4783867a474 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.etlserver.proteomics;
import java.io.File;
import java.sql.Connection;
import java.sql.SQLException;
+import java.util.List;
import java.util.Properties;
import javax.sql.DataSource;
@@ -26,7 +27,6 @@ import javax.sql.DataSource;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.properties.PropertyUtils;
@@ -35,6 +35,8 @@ import ch.systemsx.cisd.etlserver.IDataSetUploader;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
/**
* @author Franz-Josef Elmer
@@ -103,8 +105,20 @@ public class ProtXMLUploader implements IDataSetUploader
@Override
public void upload(File dataSet, DataSetInformation dataSetInformation)
{
+ Experiment experiment = dataSetInformation.tryToGetExperiment();
+ if (experiment != null)
+ {
+ List<IEntityProperty> properties = experiment.getProperties();
+ for (IEntityProperty property : properties)
+ {
+ if (property.getPropertyType().getCode().equals(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY))
+ {
+ return;
+ }
+ }
+ }
long time = System.currentTimeMillis();
- File protXMLFile = getProtXMLFile(dataSet);
+ File protXMLFile = Util.tryGetProtXMLFile(dataSet);
ProteinSummary summary = loader.readProtXML(protXMLFile);
if (operationLog.isInfoEnabled())
{
@@ -132,7 +146,10 @@ public class ProtXMLUploader implements IDataSetUploader
{
try
{
- currentResultDataSetUploader.commit();
+ if (currentResultDataSetUploader != null)
+ {
+ currentResultDataSetUploader.commit();
+ }
} finally
{
currentResultDataSetUploader = null;
@@ -169,20 +186,4 @@ public class ProtXMLUploader implements IDataSetUploader
msInjectionSampleDelimiter, restrictedSampleResolving);
}
- private File getProtXMLFile(File dataSet)
- {
- if (dataSet.isDirectory() == false)
- {
- return dataSet;
- }
- File[] files = dataSet.listFiles();
- for (File file : files)
- {
- if (file.getName().endsWith("prot.xml"))
- {
- return file;
- }
- }
- throw new UserFailureException("No *prot.xml file found in data set '" + dataSet + "'.");
- }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java
index 85bd6a5709d..44cb45261ee 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/Util.java
@@ -39,6 +39,28 @@ class Util
private Util()
{
}
+
+ /**
+ * Tries to return the prot.xml file in the specified data set.
+ *
+ * @return <code>null</code> if non found.
+ */
+ static File tryGetProtXMLFile(File dataSet)
+ {
+ if (dataSet.isDirectory() == false)
+ {
+ return dataSet;
+ }
+ File[] files = dataSet.listFiles();
+ for (File file : files)
+ {
+ if (file.getName().endsWith("prot.xml"))
+ {
+ return file;
+ }
+ }
+ return null;
+ }
/**
* Returns an array of all entity properties defined by the specified entity type for which
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
index 376b995fa47..15b9ceb78cb 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/DataSetInfoExtractorForProteinResultsTest.java
@@ -25,6 +25,8 @@ import static ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractor
import java.io.File;
import java.util.Arrays;
import java.util.Collections;
+import java.util.HashMap;
+import java.util.Map;
import java.util.Properties;
import org.hamcrest.BaseMatcher;
@@ -39,15 +41,15 @@ import ch.rinn.restrictions.Friend;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.DataSetInfoExtractorForProteinResults;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentTypePropertyType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
@@ -71,6 +73,8 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
private File dataSet;
+ private File protXmlFile;
+
@BeforeMethod
public void beforeMethod()
{
@@ -78,6 +82,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
service = context.mock(IEncapsulatedOpenBISService.class);
dataSet = new File(workingDirectory, "space1&project1");
dataSet.mkdirs();
+ protXmlFile = new File(dataSet, "prot.xml");
}
@AfterMethod
@@ -91,6 +96,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testWithNonDefaultExperimentTypeAndPropertiesFileName()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP_TO_BE_IGNORED\n"
@@ -123,6 +129,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testWithProvidedExperimentCode()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ DataSetInfoExtractorForProteinResults.EXPERIMENT_CODE_KEY + "= MY_EXP1\n");
@@ -132,11 +139,11 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
prepare(experimentType, false);
context.checking(new Expectations()
- {
{
- one(service).registerExperiment(with(any(NewExperiment.class)));
- }
- });
+ {
+ one(service).registerExperiment(with(any(NewExperiment.class)));
+ }
+ });
IDataSetInfoExtractor extractor = createExtractor(properties);
@@ -149,6 +156,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testRegistrationWithOneMandatoryProperty()
{
+ FileUtilities.writeToFile(protXmlFile, "");
FileUtilities.writeToFile(new File(dataSet,
DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME),
"answer=42\nblabla=blub\n" + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
@@ -198,7 +206,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
@Test
- public void testRegistrationWithMissingMandatoryProperty()
+ public void testRegistrationWithMissingProtXmlFile()
{
prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
@@ -209,15 +217,35 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
- assertEquals("The following mandatory properties are missed: [answer]", ex.getMessage());
+ assertEquals("No *prot.xml file found in data set '" + dataSet + "'.", ex.getMessage());
}
context.assertIsSatisfied();
}
-
+
+ @Test
+ public void testRegistrationWithMissingMandatoryProperty()
+ {
+ FileUtilities.writeToFile(protXmlFile, "");
+ prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
+
+ IDataSetInfoExtractor extractor = createExtractor(new Properties());
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("The following mandatory properties are missed: [answer]", ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
@Test
- public void testWithParentDataSetsDefinedByBaseExperiment()
+ public void testWithParentDataSetsDefinedByBaseExperimentAndProtXmlFileTooLarge()
{
+ FileUtilities.writeToFile(protXmlFile, "abc");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n");
@@ -225,7 +253,9 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
String experimentType = "MY_EXPERIMENT";
properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
+ properties.setProperty(DataSetInfoExtractorForProteinResults.PROT_XML_SIZE_THRESHOLD, "0");
prepare(experimentType);
+ final RecordingMatcher<NewExperiment> experimentMatcher = new RecordingMatcher<NewExperiment>();
context.checking(new Expectations()
{
{
@@ -240,7 +270,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
AbstractExternalData ds2 = new DataSetBuilder().code("ds2").getDataSet();
will(returnValue(Arrays.asList(ds1, ds2)));
- one(service).registerExperiment(with(any(NewExperiment.class)));
+ one(service).registerExperiment(with(experimentMatcher));
}
});
@@ -250,12 +280,16 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
assertEquals("/SPACE1/PROJECT1/E4711", info.getExperimentIdentifier().toString());
assertEquals("[ds1, ds2]", info.getParentDataSetCodes().toString());
+ IEntityProperty[] expProps = experimentMatcher.recordedObject().getProperties();
+ assertEquals("Size of prot.xml file prot.xml is with 3 bytes too large. Maximum size is 0 bytes",
+ asMap(expProps).get(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY).getValue());
context.assertIsSatisfied();
}
@Test
public void testWithUnkownBaseExperiment()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n");
@@ -291,6 +325,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testWithUnkownParentDataSets()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n" + PARENT_DATA_SET_CODES_KEY
@@ -320,6 +355,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testWithParentDataSetsSeparatedBySpaces()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n" + PARENT_DATA_SET_CODES_KEY
@@ -350,6 +386,7 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
@Test
public void testWithParentDataSetsSeparatedByComma()
{
+ FileUtilities.writeToFile(protXmlFile, "");
String propertiesFile = "my.properties";
FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ PARENT_DATA_SET_CODES_KEY + " = ds1,ds2");
@@ -394,12 +431,16 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
one(service).getExperimentType(experimentType);
ExperimentType type = new ExperimentType();
- ExperimentTypePropertyType etpt = new ExperimentTypePropertyType();
- PropertyType propertyType = new PropertyType();
- propertyType.setCode("answer");
- etpt.setPropertyType(propertyType);
- etpt.setMandatory(true);
- type.setExperimentTypePropertyTypes(Arrays.asList(etpt));
+ ExperimentTypePropertyType etpt1 = new ExperimentTypePropertyType();
+ PropertyType propertyType1 = new PropertyType();
+ propertyType1.setCode("answer");
+ etpt1.setPropertyType(propertyType1);
+ etpt1.setMandatory(true);
+ ExperimentTypePropertyType etpt2 = new ExperimentTypePropertyType();
+ PropertyType propertyType2 = new PropertyType();
+ propertyType2.setCode(DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY);
+ etpt2.setPropertyType(propertyType2);
+ type.setExperimentTypePropertyTypes(Arrays.asList(etpt1, etpt2));
will(returnValue(type));
}
});
@@ -420,6 +461,16 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
}
});
}
+
+ private Map<String, IEntityProperty> asMap(IEntityProperty[] properties)
+ {
+ Map<String, IEntityProperty> result = new HashMap<String, IEntityProperty>();
+ for (IEntityProperty property : properties)
+ {
+ result.put(property.getPropertyType().getCode(), property);
+ }
+ return result;
+ }
private IDataSetInfoExtractor createExtractor(Properties properties)
{
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
index 5c4912e98d1..cfcfd3bacb2 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
@@ -24,14 +24,12 @@ import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.ProtXMLUploader;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.ResultDataSetUploader;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.ProteinSummaryHeader;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
/**
*
@@ -137,25 +135,18 @@ public class ProtXMLUploaderTest extends ProtXMLTestCase
}
@Test
- public void testDataSetIsFolderWithoutProtXMLFile()
+ public void testDataSetIsFolderWithProtXMLFileToBeTooLarge()
{
File dataSet = new File(workingDirectory, "data-set");
dataSet.mkdir();
- FileUtilities.writeToFile(new File(dataSet, "pep.xml"), "peptides");
+ FileUtilities.writeToFile(new File(dataSet, "test-prot.xml"), EXAMPLE);
DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setExperiment(new ExperimentBuilder().property(
+ DataSetInfoExtractorForProteinResults.NOT_PROCESSED_PROPERTY, "too large").getExperiment());
- try
- {
- uploader.upload(dataSet, dataSetInformation);
- fail("UserFailureException expected");
- } catch (UserFailureException ex)
- {
- assertEquals(
- "No *prot.xml file found in data set "
- + "'targets/unit-test-wd/ch.systemsx.cisd.openbis.etlserver.proteomics.ProtXMLUploaderTest/data-set'.",
- ex.getMessage());
- }
+ uploader.upload(dataSet, dataSetInformation);
+ assertEquals(null, uploader.getDataSetInformation());
context.assertIsSatisfied();
}
}
--
GitLab