From 3b5e9c58d26fb42447cf1846b086648634c420e2 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 25 May 2009 13:05:17 +0000
Subject: [PATCH] LMS-910 index.tsv file parser + tests
SVN: 11135
---
rtd_yeastx/.classpath | 6 +-
.../yeastx/etl/DataSetInformationParser.java | 105 ++++++++++++++++++
.../yeastx/etl/PlainDataSetInformation.java | 95 ++++++++++++++++
.../etl/DataSetInformationParserTest.java | 81 ++++++++++++++
rtd_yeastx/sourceTest/java/tests.xml | 12 ++
5 files changed, 298 insertions(+), 1 deletion(-)
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParser.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/PlainDataSetInformation.java
create mode 100644 rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
create mode 100644 rtd_yeastx/sourceTest/java/tests.xml
diff --git a/rtd_yeastx/.classpath b/rtd_yeastx/.classpath
index eb162b4b474..879ad6ffbbb 100644
--- a/rtd_yeastx/.classpath
+++ b/rtd_yeastx/.classpath
@@ -9,7 +9,11 @@
<classpathentry kind="lib" path="/libraries/postgresql/postgresql.jar" sourcepath="/libraries/postgresql/postgresql-src.zip"/>
<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
- <classpathentry combineaccessrules="false" kind="src" path="/dbmigration"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/openbis"/>
<classpathentry combineaccessrules="false" kind="src" path="/common"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/dbmigration"/>
+ <classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/base"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParser.java
new file mode 100644
index 00000000000..43535be058f
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParser.java
@@ -0,0 +1,105 @@
+/*
+ * Copyright 2008 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.etl;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.parser.AbstractParserObjectFactory;
+import ch.systemsx.cisd.common.parser.IParserObjectFactory;
+import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
+import ch.systemsx.cisd.common.parser.IPropertyMapper;
+import ch.systemsx.cisd.common.parser.IPropertyModel;
+import ch.systemsx.cisd.common.parser.ParserException;
+import ch.systemsx.cisd.common.parser.TabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ * A {@link AbstractParserObjectFactory} extension for creating {@link NewProperty}.
+ *
+ * @author Tomasz Pylak
+ */
+final class DataSetInformationParser
+{
+ public static List<PlainDataSetInformation> parse(File indexFile)
+ {
+ TabFileLoader<PlainDataSetInformation> tabFileLoader =
+ new TabFileLoader<PlainDataSetInformation>(
+ new IParserObjectFactoryFactory<PlainDataSetInformation>()
+ {
+
+ public IParserObjectFactory<PlainDataSetInformation> createFactory(
+ IPropertyMapper propertyMapper) throws ParserException
+ {
+ return new NewPropertyParserObjectFactory(propertyMapper);
+ }
+ });
+ // TODO 2009-05-25, Tomasz Pylak: consider handling exception similar to BisTabFileLoader
+ return tabFileLoader.load(indexFile);
+ }
+
+ private static final class NewPropertyParserObjectFactory extends
+ AbstractParserObjectFactory<PlainDataSetInformation>
+ {
+
+ private NewPropertyParserObjectFactory(final IPropertyMapper propertyMapper)
+ {
+ super(PlainDataSetInformation.class, propertyMapper);
+ }
+
+ private final void setProperties(final PlainDataSetInformation dataset,
+ final String[] lineTokens)
+ {
+ final List<NewProperty> properties = new ArrayList<NewProperty>();
+ for (final String unmatchedProperty : getUnmatchedProperties())
+ {
+ final IPropertyModel propertyModel = tryGetPropertyModel(unmatchedProperty);
+ final String propertyValue = getPropertyValue(lineTokens, propertyModel);
+ if (StringUtils.isEmpty(propertyValue) == false)
+ {
+ final NewProperty property = new NewProperty();
+ property.setPropertyCode(propertyModel.getCode());
+ property.setValue(propertyValue);
+ properties.add(property);
+ }
+ }
+ dataset.setProperties(properties);
+ }
+
+ //
+ // AbstractParserObjectFactory
+ //
+
+ @Override
+ protected final boolean ignoreUnmatchedProperties()
+ {
+ return true;
+ }
+
+ @Override
+ public final PlainDataSetInformation createObject(final String[] lineTokens)
+ throws ParserException
+ {
+ final PlainDataSetInformation dataset = super.createObject(lineTokens);
+ setProperties(dataset, lineTokens);
+ return dataset;
+ }
+ }
+}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/PlainDataSetInformation.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/PlainDataSetInformation.java
new file mode 100644
index 00000000000..9904932890c
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/PlainDataSetInformation.java
@@ -0,0 +1,95 @@
+/*
+ * Copyright 2009 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.etl;
+
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.annotation.BeanProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class PlainDataSetInformation
+{
+ private String fileName;
+
+ private String sampleCodeOrLabel;
+
+ private String experimentCode;
+
+ private String conversion;
+
+ private List<NewProperty> properties;
+
+ public String getFileName()
+ {
+ return fileName;
+ }
+
+ @BeanProperty(label = "file_name")
+ public void setFileName(String fileName)
+ {
+ this.fileName = fileName;
+ }
+
+ public String getSampleCodeOrLabel()
+ {
+ return sampleCodeOrLabel;
+ }
+
+ @BeanProperty(label = "sample")
+ public void setSampleCodeOrLabel(String sampleCodeOrLabel)
+ {
+ this.sampleCodeOrLabel = StringUtils.trimToNull(sampleCodeOrLabel);
+ }
+
+ public String getExperimentCode()
+ {
+ return experimentCode;
+ }
+
+ @BeanProperty(label = "experiment", optional = true)
+ public void setExperimentCode(String experimentCode)
+ {
+ this.experimentCode = experimentCode;
+ }
+
+ public String getConversion()
+ {
+ return conversion;
+ }
+
+ @BeanProperty(label = "conversion", optional = true)
+ public void setConversion(String conversion)
+ {
+ this.conversion = conversion;
+ }
+
+ public List<NewProperty> getProperties()
+ {
+ return properties;
+ }
+
+ public void setProperties(List<NewProperty> dataSetProperties)
+ {
+ this.properties = dataSetProperties;
+ }
+
+}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
new file mode 100644
index 00000000000..8dde97baed4
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/etl/DataSetInformationParserTest.java
@@ -0,0 +1,81 @@
+/*
+ * Copyright 2009 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.etl;
+
+import java.io.File;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.parser.MandatoryPropertyMissingException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class DataSetInformationParserTest extends AbstractFileSystemTestCase
+{
+ private static final String HEADER =
+ "file_name sample experiment conversion dataset_property_1 dataset_property_2\n";
+
+ private static final String TAB = "\t";
+
+ @Test
+ public void testLoadIndexFile()
+ {
+ File indexFile = writeFile(HEADER + "data.txt sample1 experiment1 conversion1 v1 v2");
+ List<PlainDataSetInformation> list = DataSetInformationParser.parse(indexFile);
+ AssertJUnit.assertEquals(1, list.size());
+ PlainDataSetInformation elem = list.get(0);
+ AssertJUnit.assertEquals("data.txt", elem.getFileName());
+ AssertJUnit.assertEquals(2, elem.getProperties().size());
+ NewProperty prop1 = elem.getProperties().get(0);
+ AssertJUnit.assertEquals("v1", prop1.getValue());
+ AssertJUnit.assertEquals("dataset_property_1", prop1.getPropertyCode());
+ }
+
+ // TODO 2009-05-25, Tomasz Pylak: remove from broken after LMS-914 is fixed
+ @Test(expectedExceptions = MandatoryPropertyMissingException.class, groups = "broken")
+ public void testLoadIndexFileWithMissingFieldValueFails()
+ {
+ File indexFile = writeFile(HEADER + TAB + TAB + TAB + TAB + TAB);
+ DataSetInformationParser.parse(indexFile);
+ }
+
+ @Test(expectedExceptions = MandatoryPropertyMissingException.class)
+ public void testLoadIndexFileWithMissingFieldHeaderFails()
+ {
+ File indexFile = writeFile("xxx");
+ DataSetInformationParser.parse(indexFile);
+ }
+
+ private File writeFile(String content)
+ {
+ String contentWithTabs = spacesToTabs(content);
+ File indexFile = new File(workingDirectory, "index.tsv");
+ FileUtilities.writeToFile(indexFile, contentWithTabs);
+ return indexFile;
+ }
+
+ private static String spacesToTabs(String text)
+ {
+ return text.replaceAll(" ", TAB);
+ }
+}
diff --git a/rtd_yeastx/sourceTest/java/tests.xml b/rtd_yeastx/sourceTest/java/tests.xml
new file mode 100644
index 00000000000..f186f91b1ea
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/tests.xml
@@ -0,0 +1,12 @@
+<suite name="All" verbose="2" >
+ <test name="All" annotations="JDK">
+ <groups>
+ <run>
+ <exclude name="broken" />
+ </run>
+ </groups>
+ <packages>
+ <package name="ch.systemsx.cisd.yeastx.*" />
+ </packages>
+ </test>
+</suite>
--
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