From 6da1b74265ff65919ea4cd7211d53c014773fa57 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 12 Jan 2011 12:52:35 +0000
Subject: [PATCH] LMS-1957 rename ProteinTableReport to APMSReport. Columns
'num unique peptides' and 'spec count' in agreement with Lars. APMSReportTest
written.
SVN: 19389
---
rtd_phosphonetx/etc/service.properties | 12 +-
...roteinTableReport.java => APMSReport.java} | 56 ++--
.../server/plugins/APMSReportTest.java | 289 ++++++++++++++++++
.../plugins/ProteinTableReportTest.java | 74 -----
4 files changed, 333 insertions(+), 98 deletions(-)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/{ProteinTableReport.java => APMSReport.java} (89%)
create mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReportTest.java
delete mode 100644 rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReportTest.java
diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
index c7349c5bf02..447eb4f760c 100644
--- a/rtd_phosphonetx/etc/service.properties
+++ b/rtd_phosphonetx/etc/service.properties
@@ -109,7 +109,7 @@ data-set-file-name-entity-separator = _
# Note that this can increase the server load.
# reprocess-faulty-datasets = false
-reporting-plugins = demo-reporter
+reporting-plugins = demo-reporter, protein-table-report
# Label of the plugin which will be shown for the users.
demo-reporter.label = Show Dataset Size
@@ -120,8 +120,12 @@ demo-reporter.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.demo.D
# The property file. Its content will be passed as a parameter to the plugin.
demo-reporter.properties-file =
+protein-table-report.label = APMS Report
+protein-table-report.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.APMSReport
+protein-table-report.dataset-types = PROT_RESULT
+
# Comma separated names of processing plugins. Each plugin should have configuration properties prefixed with its name.
-processing-plugins = copy-data-sets, ms-inj-copy
+processing-plugins = copy-data-sets, ms-inj-copy, protein-table-report-creation
# The configuration of the processing plugin is the same as the reporting plugins configuration.
copy-data-sets.label = Data Set Copier to User Location
@@ -139,6 +143,10 @@ ms-inj-copy.send-detailed-email = true
#ms-inj-copy.destination = /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/
ms-inj-copy.destination = vesuvio:tmp
+protein-table-report-creation.label = Send me the APMS Report
+protein-table-report-creation.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.APMSReport
+protein-table-report-creation.dataset-types = PROT_RESULT
+
data-set-validators = val1
val1.data-set-type = HCS_IMAGE_ANALYSIS_DATA
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReport.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReport.java
similarity index 89%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReport.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReport.java
index 724bfdc6246..ed24ec4c88d 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReport.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReport.java
@@ -48,6 +48,7 @@ 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.mail.EMailAddress;
+import ch.systemsx.cisd.common.utilities.Template;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractTableModelReportingPlugin;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ProcessingStatus;
@@ -59,7 +60,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
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.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -72,11 +72,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
- * Creates a report from proteins.csv
+ * Creates an APMS report from proteins.csv
*
* @author Franz-Josef Elmer
*/
-public class ProteinTableReport extends AbstractTableModelReportingPlugin implements IProcessingPluginTask
+public class APMSReport extends AbstractTableModelReportingPlugin implements IProcessingPluginTask
{
private static final class Header
{
@@ -189,16 +189,21 @@ public class ProteinTableReport extends AbstractTableModelReportingPlugin implem
@Private static final String PROTEIN_FILE_NAME = "proteins.csv";
private static final String PROTEIN_PROPERTY_CODE_KEY = "protein-property-code";
- private static final String DEFAULT_PROTEIN_PROPERTY_CODE = "PROTEIN";
+ @Private static final String DEFAULT_PROTEIN_PROPERTY_CODE = "PROTEIN";
+
+ private
+ static final Template E_MAIL_CONTENT_TEMPLATE = new Template("Dear User\n\n"
+ + "Enclosed you will find the Protein APMS report file for experiment ${experiment-identifier}.\n"
+ + "Data Set: ${data-set}");
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
- ProteinTableReport.class);
+ APMSReport.class);
private final String proteinPropertyCode;
private IEncapsulatedOpenBISService service;
- public ProteinTableReport(Properties properties, File storeRoot)
+ public APMSReport(Properties properties, File storeRoot)
{
super(properties, storeRoot);
proteinPropertyCode = properties.getProperty(PROTEIN_PROPERTY_CODE_KEY, DEFAULT_PROTEIN_PROPERTY_CODE);
@@ -258,11 +263,17 @@ public class ProteinTableReport extends AbstractTableModelReportingPlugin implem
}
csvWriter.writeRecord(stringArray);
}
+ String experimentIdentifier =
+ datasetDescription.getSpaceCode() + '/' + datasetDescription.getProjectCode()
+ + '/' + datasetDescription.getExperimentCode();
+ Template template = E_MAIL_CONTENT_TEMPLATE.createFreshCopy();
+ template.bind("experiment-identifier", experimentIdentifier);
+ template.bind("data-set", datasetDescription.getDatasetCode());
ByteArrayDataSource dataSource =
new ByteArrayDataSource(writer.toString(), "text/plain");
context.getMailClient().sendEmailMessageWithAttachment("Protein APMS Report",
- "Here is your report",
- datasetDescription.getExperimentCode() + "-protein-report.txt",
+ template.createText(),
+ datasetDescription.getExperimentCode() + "-APMS-report.txt",
new DataHandler(dataSource), null, null,
new EMailAddress(context.getUserEmailOrNull()));
@@ -281,8 +292,6 @@ public class ProteinTableReport extends AbstractTableModelReportingPlugin implem
builder.addHeader("Sample ID");
builder.addHeader("Bait");
builder.addHeader("Prey");
- builder.addHeader("num unique peptides");
- builder.addHeader("spec count");
builder.addHeader("freq of obs");
builder.addHeader("avg MS1 intensities (normalized for the bait)");
builder.addHeader("STDV MS1 intensity");
@@ -340,12 +349,12 @@ public class ProteinTableReport extends AbstractTableModelReportingPlugin implem
for (Entry<String, List<Header>> group : groups)
{
String biologicalSample = group.getKey();
- List<Header> hs = group.getValue();
+ List<Header> headers = group.getValue();
String protein = null;
double countNonZeroAbundances = 0;
double sum = 0;
double sum2 = 0;
- for (Header header : hs)
+ for (Header header : headers)
{
if (biologicalSample != null && protein == null)
{
@@ -367,17 +376,20 @@ public class ProteinTableReport extends AbstractTableModelReportingPlugin implem
+ value + ") for column " + header.getHeader() + ": " + row);
}
}
- double averagedAbundance = sum / hs.size();
+ double averagedAbundance = sum / headers.size();
double abundanceStandardDeviation =
- Math.sqrt(averagedAbundance * averagedAbundance - sum2 / hs.size());
- double frequencyOfObservation = countNonZeroAbundances / hs.size();
- builder.addRow(Arrays.<ISerializableComparable> asList(new StringTableCell(
- biologicalSample), new StringTableCell(protein), new StringTableCell(
- identifiedProtein),
- new IntegerTableCell(Long.parseLong(row.getValue("n_peptides"))),
- new StringTableCell(""), new DoubleTableCell(frequencyOfObservation),
- new DoubleTableCell(averagedAbundance), new DoubleTableCell(
- abundanceStandardDeviation)));
+ Math.sqrt(Math.max(0, sum2 / headers.size() - averagedAbundance
+ * averagedAbundance));
+ double frequencyOfObservation = countNonZeroAbundances / headers.size();
+ StringTableCell biologicalSampleCell = StringTableCell.wrap(biologicalSample);
+ StringTableCell proteinCell = StringTableCell.wrap(protein);
+ StringTableCell identifiedProteinCell = new StringTableCell(identifiedProtein);
+ DoubleTableCell freqOfObsvCell = new DoubleTableCell(frequencyOfObservation);
+ DoubleTableCell abundanceCell = new DoubleTableCell(averagedAbundance);
+ DoubleTableCell abundanceStdvCell = new DoubleTableCell(abundanceStandardDeviation);
+ builder.addRow(Arrays.<ISerializableComparable> asList(biologicalSampleCell,
+ proteinCell, identifiedProteinCell, freqOfObsvCell, abundanceCell,
+ abundanceStdvCell));
}
}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReportTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReportTest.java
new file mode 100644
index 00000000000..b13269dffca
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/APMSReportTest.java
@@ -0,0 +1,289 @@
+/*
+ * Copyright 2011 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.openbis.dss.phosphonetx.server.plugins;
+
+import static ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.APMSReport.DEFAULT_PROTEIN_PROPERTY_CODE;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.List;
+import java.util.Properties;
+import java.util.Set;
+
+import javax.activation.DataHandler;
+
+import org.apache.commons.io.IOUtils;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.hamcrest.core.IsNull;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+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.mail.EMailAddress;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ProcessingStatus;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+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;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses = APMSReport.class)
+public class APMSReportTest extends AbstractFileSystemTestCase
+{
+ private static final String EXAMPLE_PROTEINS =
+ "# Protein abundances computed from file 'result.consensusXML'\n"
+ + "# Parameters (relevant only): top=3, average=median, include_all, consensus:normalize\n"
+ + "# Files/samples associated with abundance values below:"
+ + " 0: '/cluster/s1.featureXML',"
+ + " 1: '/cluster/s2.featureXML',"
+ + " 2: '/cluster/s3.featureXML'\n"
+ + "\"protein\",\"n_proteins\",\"protein_score\",\"n_peptides\",\"abundance_0\",\"abundance_1\",\"abundance_2\"\n"
+ + "\"P1\",1,1,5,1.5,2.5,3.5\n"
+ + "\"P2\",1,1,6,11.5,0,13.5\n"
+ + "\"P3\",1,1,14,21.5,22.5,0\n";
+
+ private Mockery context;
+
+ private APMSReport report;
+
+ private IEncapsulatedOpenBISService service;
+
+ private IMailClient mailClient;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ File dataSetFolder = createDataSet("1");
+ FileUtilities.writeToFile(new File(dataSetFolder, APMSReport.PROTEIN_FILE_NAME),
+ EXAMPLE_PROTEINS);
+ createDataSet("2");
+
+ context = new Mockery();
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ mailClient = context.mock(IMailClient.class);
+ report = new APMSReport(new Properties(), workingDirectory);
+ report.setService(service);
+ }
+
+ private File createDataSet(String location)
+ {
+ File originalFolder = new File(new File(workingDirectory, location), "original");
+ originalFolder.mkdirs();
+ File dataSetFolder = new File(originalFolder, "data-set-folder");
+ dataSetFolder.mkdirs();
+ return dataSetFolder;
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testProcess() throws IOException
+ {
+ Sample b2 = new SampleBuilder("/S/B2").id(12).getSample();
+ prepareGetSample(new SampleBuilder("/MS_DATA/S1").id(1).childOf(b2).getSample());
+ prepareGetSample(new SampleBuilder("/MS_DATA/S2").id(2).childOf(b2).getSample());
+ prepareGetSample(new SampleBuilder("/MS_DATA/S3").id(3).childOf(b2).getSample());
+ DatasetDescriptionBuilder ds1 =
+ new DatasetDescriptionBuilder("ds1").location("1").space("s").project("p")
+ .experiment("e");
+ DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location("2");
+ List<DatasetDescription> dataSets =
+ Arrays.asList(ds1.getDatasetDescription(), ds2.getDatasetDescription());
+ DataSetProcessingContext processingContext =
+ new DataSetProcessingContext(Collections.<String, String> emptyMap(), mailClient,
+ "a@bc.de");
+ final RecordingMatcher<String> subjectMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<String> contentMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<String> fileNameMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ context.checking(new Expectations()
+ {
+ {
+ one(mailClient).sendEmailMessageWithAttachment(with(subjectMatcher),
+ with(contentMatcher), with(fileNameMatcher), with(attachmentMatcher),
+ with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
+ with(addressesMatcher));
+ }
+ });
+
+ ProcessingStatus status = report.process(dataSets, processingContext);
+ assertEquals("Protein APMS Report", subjectMatcher.recordedObject());
+ assertEquals("Dear User\n\n"
+ + "Enclosed you will find the Protein APMS report file for experiment s/p/e.\n"
+ + "Data Set: ds1", contentMatcher.recordedObject());
+ @SuppressWarnings("unchecked")
+ List<String> fileLines =
+ IOUtils.readLines(attachmentMatcher.recordedObject().getInputStream());
+ assertEquals("Sample ID,Bait,Prey,freq of obs,"
+ + "avg MS1 intensities (normalized for the bait),STDV MS1 intensity",
+ fileLines.get(0));
+ assertEquals(4, fileLines.size());
+ assertEquals("[ERROR: \"Exception occured: "
+ + "ch.systemsx.cisd.common.exceptions.UserFailureException: File "
+ + APMSReport.PROTEIN_FILE_NAME + " missing.\"]", status.getErrorStatuses()
+ .toString());
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCreateReport()
+ {
+ Sample master =
+ new SampleBuilder("/master").property(DEFAULT_PROTEIN_PROPERTY_CODE, "Q1")
+ .getSample();
+ Sample b1 = new SampleBuilder("/S/B1").id(11).childOf(master).getSample();
+ Sample b2 = new SampleBuilder("/S/B2").id(12).getSample();
+ prepareGetSample(new SampleBuilder("/MS_DATA/S1").id(1).childOf(b1).getSample());
+ prepareGetSample(new SampleBuilder("/MS_DATA/S2").id(2).childOf(b1).getSample());
+ prepareGetSample(new SampleBuilder("/MS_DATA/S3").id(3).childOf(b2).getSample());
+ DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
+ List<DatasetDescription> dataSets = Arrays.asList(ds1.getDatasetDescription());
+
+ TableModel table = report.createReport(dataSets);
+
+ List<TableModelColumnHeader> headers = table.getHeader();
+ assertEquals("[Sample ID, Bait, Prey, freq of obs, "
+ + "avg MS1 intensities (normalized for the bait), STDV MS1 intensity]",
+ headers.toString());
+ List<TableModelRow> rows = table.getRows();
+ assertEquals("[B1, Q1, P1, 1.0, 2.0, 0.5]", rows.get(0).getValues().toString());
+ assertEquals("[B2, , P1, 1.0, 3.5, 0.0]", rows.get(1).getValues().toString());
+ assertEquals("[B1, Q1, P2, 0.5, 5.75, 5.75]", rows.get(2).getValues().toString());
+ assertEquals("[B2, , P2, 1.0, 13.5, 0.0]", rows.get(3).getValues().toString());
+ assertEquals("[B1, Q1, P3, 1.0, 22.0, 0.5]", rows.get(4).getValues().toString());
+ assertEquals("[B2, , P3, 0.0, 0.0, 0.0]", rows.get(5).getValues().toString());
+ assertEquals(3 * 2, rows.size());
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCreateReportForMissingProteinsFile()
+ {
+ DatasetDescriptionBuilder ds = new DatasetDescriptionBuilder("ds2").location("2");
+ try
+ {
+ report.createReport(Arrays.asList(ds.getDatasetDescription()));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("File " + APMSReport.PROTEIN_FILE_NAME + " missing.", ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testCreateReportForTwoDataSets()
+ {
+ DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
+ DatasetDescriptionBuilder ds2 = new DatasetDescriptionBuilder("ds2").location("2");
+ try
+ {
+ report.createReport(Arrays.asList(ds1.getDatasetDescription(),
+ ds2.getDatasetDescription()));
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Chosen plugin works with exactly one data set. 2 data sets selected.",
+ ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ private void prepareGetSample(final Sample sample)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(
+ SampleIdentifierFactory.parse(sample.getIdentifier()));
+ will(returnValue(sample));
+ }
+ });
+ prepareGetAncestors(sample);
+ }
+
+ protected void prepareGetAncestors(final Sample sample)
+ {
+ List<IEntityProperty> properties = sample.getProperties();
+ for (IEntityProperty property : properties)
+ {
+ if (property.getPropertyType().getCode().equals(DEFAULT_PROTEIN_PROPERTY_CODE))
+ {
+ return;
+ }
+ }
+ final Set<Sample> parents = sample.getParents();
+ context.checking(new Expectations()
+ {
+ {
+ one(service).listSamples(with(new BaseMatcher<ListSampleCriteria>()
+ {
+ public boolean matches(Object item)
+ {
+ return sample.getId() == ((ListSampleCriteria) item)
+ .getChildSampleId().getId();
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendText("parents of " + sample.getIdentifier());
+ }
+ }));
+ will(returnValue(new ArrayList<Sample>(parents)));
+ }
+ });
+ for (Sample parent : parents)
+ {
+ prepareGetAncestors(parent);
+ }
+ }
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReportTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReportTest.java
deleted file mode 100644
index b35c6727b27..00000000000
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/ProteinTableReportTest.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2011 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.openbis.dss.phosphonetx.server.plugins;
-
-import java.io.File;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-import java.util.Properties;
-
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
-import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.openbis.generic.shared.dto.builders.DatasetDescriptionBuilder;
-
-
-/**
- *
- *
- * @author Franz-Josef Elmer
- */
-@Friend(toClasses=ProteinTableReport.class)
-public class ProteinTableReportTest extends AbstractFileSystemTestCase
-{
- private static final String EXAMPLE_PROTEINS =
- "# Protein abundances computed from file 'result.consensusXML'\n"
- + "# Parameters (relevant only): top=3, average=median, include_all, consensus:normalize\n"
- + "# Files/samples associated with abundance values below:"
- + " 0: '/cluster/weisserh_B1012_053.featureXML',"
- + " 1: '/cluster/weisserh_B1012_057.featureXML'\n"
- + "\"protein\",\"n_proteins\",\"protein_score\",\"n_peptides\",\"abundance_0\",\"abundance_1\"\n"
- + "\"13621327\",1,1,5,7846763.86498425,8159570.13467505\n"
- + "\"13621329\",1,1,6,2976845.93289974,3670078.89677526\n"
- + "\"13621337\",1,1,14,18114384.6420854,14119249.6148974\n";
-
- @BeforeMethod
- public void beforeMethod()
- {
- File originalFolder = new File(new File(workingDirectory, "1"), "original");
- originalFolder.mkdirs();
- File dataSetFolder = new File(originalFolder, "data-set-folder");
- dataSetFolder.mkdirs();
- FileUtilities.writeToFile(new File(dataSetFolder, ProteinTableReport.PROTEIN_FILE_NAME), EXAMPLE_PROTEINS);
- }
-
- @Test
- public void test()
- {
- ProteinTableReport report = new ProteinTableReport(new Properties(), workingDirectory);
- DataSetProcessingContext context = new DataSetProcessingContext(Collections.<String, String>emptyMap(), null, "a@bc.de");
- DatasetDescriptionBuilder ds1 = new DatasetDescriptionBuilder("ds1").location("1");
- List<DatasetDescription> dataSets = Arrays.asList(ds1.getDatasetDescription());
- report.process(dataSets, context);
- }
-}
--
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