From 7d2e214ed90900c5e00b1fb96ab17213b2b665c9 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 15 Apr 2010 08:41:33 +0000
Subject: [PATCH] LMS-1485 more unit tests
SVN: 15474
---
.../dss/LcaMicDataSetPropertiesExtractor.java | 4 +-
.../cisd/dss/LcaMicDataSetUploader.java | 2 +-
.../LcaMicDataSetPropertiesExtractorTest.java | 79 ++++++++++
.../cisd/dss/LcaMicDataSetUploaderTest.java | 143 ++++++++++++++++++
4 files changed, 226 insertions(+), 2 deletions(-)
create mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
create mode 100644 eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
index 9cbf08b8f42..c1161d8474d 100644
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
+++ b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractor.java
@@ -34,6 +34,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
class LcaMicDataSetPropertiesExtractor extends TimeSeriesDataSetPropertiesExtractor
{
+ static final String GROWTH_RATE = "GROWTH_RATE";
+
LcaMicDataSetPropertiesExtractor(Properties properties)
{
super(properties);
@@ -49,7 +51,7 @@ class LcaMicDataSetPropertiesExtractor extends TimeSeriesDataSetPropertiesExtrac
throw new UserFailureException("Empty file: " + file);
}
String[] items = StringUtils.split(lines.get(0), " \t");
- NewProperty growthRate = new NewProperty("GROWTH_RATE", items[items.length - 1]);
+ NewProperty growthRate = new NewProperty(GROWTH_RATE, items[items.length - 1]);
List<NewProperty> properties =
HeaderUtils.extractHeaderProperties(incomingDataSetPath, ignoreEmptyLines, true, true);
properties.add(growthRate);
diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
index 8398f03ad7a..fa7d89a06de 100644
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
+++ b/eu_basysbio/source/java/eu/basysbio/cisd/dss/LcaMicDataSetUploader.java
@@ -66,7 +66,7 @@ class LcaMicDataSetUploader extends AbstractDataSetUploader
super(dataSource, service, parameters);
}
- public LcaMicDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
+ LcaMicDataSetUploader(ITimeSeriesDAO dao, IEncapsulatedOpenBISService service,
TimeSeriesDataSetUploaderParameters parameters)
{
super(dao, service, parameters);
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
new file mode 100644
index 00000000000..4fca45bcd3e
--- /dev/null
+++ b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetPropertiesExtractorTest.java
@@ -0,0 +1,79 @@
+/*
+ * 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 eu.basysbio.cisd.dss;
+
+import static eu.basysbio.cisd.dss.HeaderUtils.TIME_SERIES_HEADER_PROPERTIES;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class LcaMicDataSetPropertiesExtractorTest extends AbstractFileSystemTestCase
+{
+ static final String EXAMPLE =
+ "# Ma::MS::B1::NT::EX::T1::NC::GrowthRate::Value[h^(-1)]::LIN::BBA9001#A_S20090325-2::NC\t0.68\n"
+ + "Time (s)\t"
+ + "Ma::MS::B1::NT::EX::T1::NC::LcaMicCfd::Value[um]::LIN::BBA9001#A_S20090325-2::NC\t"
+ + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::BBA9001#A_S20090325-2::NC\t"
+ + "Ma::MS::B1::NT::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::BBA9001#A_S20090325-2::NC\n";
+
+ @Test
+ public void test() throws IOException
+ {
+ File ds = new File(workingDirectory, "ds");
+ ds.mkdirs();
+ File file = new File(ds, "t.txt");
+ FileUtilities.writeToFile(file, EXAMPLE);
+ IDataSetPropertiesExtractor extractor =
+ new LcaMicDataSetPropertiesExtractor(new Properties());
+ List<NewProperty> props = extractor.extractDataSetProperties(ds);
+ assertEquals(TIME_SERIES_HEADER_PROPERTIES.length + 1, props.size());
+ Map<String, String> map = new HashMap<String, String>();
+ for (NewProperty property : props)
+ {
+ map.put(property.getPropertyCode(), property.getValue());
+ }
+ assertEquals("BBA9001#A_S20090325-2", map.get(TimeSeriesPropertyType.BI_ID.toString()));
+ assertEquals("B1", map.get(TimeSeriesPropertyType.BIOLOGICAL_REPLICATE_CODE.toString()));
+ assertEquals("NC", map.get(TimeSeriesPropertyType.CEL_LOC.toString()));
+ assertEquals("NC", map.get(TimeSeriesPropertyType.CG_LIST.toString()));
+ assertEquals("MS", map.get(TimeSeriesPropertyType.CULTIVATION_METHOD_EXPERIMENT_CODE.toString()));
+ assertEquals("Ma", map.get(TimeSeriesPropertyType.EXPERIMENT_CODE.toString()));
+ assertEquals("LIN", map.get(TimeSeriesPropertyType.SCALE_LIST.toString()));
+ assertEquals("T1", map.get(TimeSeriesPropertyType.TECHNICAL_REPLICATE_CODE_LIST.toString()));
+ assertEquals("0", map.get(TimeSeriesPropertyType.TIME_POINT_LIST.toString()));
+ assertEquals("LcaMicAbsFl, LcaMicCfd", map.get(TimeSeriesPropertyType.TIME_SERIES_DATA_SET_TYPE.toString()));
+ assertEquals(null, map.get(TimeSeriesPropertyType.UPLOADER_EMAIL.toString()));
+ assertEquals("Mean[Au], Std[Au], Value[um]", map.get(TimeSeriesPropertyType.VALUE_TYPE_LIST.toString()));
+ assertEquals("0.68", map.get(LcaMicDataSetPropertiesExtractor.GROWTH_RATE));
+ }
+
+}
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
new file mode 100644
index 00000000000..65495e07958
--- /dev/null
+++ b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/LcaMicDataSetUploaderTest.java
@@ -0,0 +1,143 @@
+/*
+ * 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 eu.basysbio.cisd.dss;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.util.List;
+import java.util.Properties;
+
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.etlserver.cifex.CifexExtractorHelper;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class LcaMicDataSetUploaderTest extends AbstractFileSystemTestCase
+{
+ private static FilenameFilter TXT_FILTER = new FilenameFilter()
+ {
+ public boolean accept(File dir, String name)
+ {
+ return name.endsWith(".txt");
+ }
+ };
+
+ private static FilenameFilter PROPERTIES_FILTER = new FilenameFilter()
+ {
+ public boolean accept(File dir, String name)
+ {
+ return name.equals(CifexExtractorHelper.REQUEST_PROPERTIES_FILE);
+ }
+ };
+
+ private Mockery context;
+ private ITimeSeriesDAO dao;
+ private IEncapsulatedOpenBISService service;
+ private LcaMicDataSetUploader uploader;
+ private IDropBoxFeeder feeder;
+ private File dropBox;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ dao = context.mock(ITimeSeriesDAO.class);
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ feeder = context.mock(IDropBoxFeeder.class);
+ dropBox = new File(workingDirectory, "drop-box");
+ dropBox.mkdirs();
+ Properties properties = new Properties();
+ properties.setProperty(
+ TimeSeriesDataSetUploaderParameters.TIME_SERIES_DATA_SET_DROP_BOX_PATH, dropBox
+ .toString());
+ uploader =
+ new LcaMicDataSetUploader(dao, service, new TimeSeriesDataSetUploaderParameters(
+ properties, true));
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one does not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void test()
+ {
+ File tsvFile = new File(workingDirectory, "data.tsv");
+ FileUtilities.writeToFile(tsvFile, LcaMicDataSetPropertiesExtractorTest.EXAMPLE
+ + "12\t2.5\t5.5\tN/A\n42\t42.5\t45.5\t3.25\n");
+
+ DataSetInformation dataSetInformation = new DataSetInformation();
+ dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier("p1", "e1"));
+ dataSetInformation.setDataSetCode("abc-1");
+ dataSetInformation.setUploadingUserEmail("ab@c.de");
+ uploader.handleTSVFile(tsvFile, dataSetInformation, feeder);
+
+ List<String> data = getData(1);
+ assertEquals("BBA ID\t" +
+ "Ma::MS::B1::12::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC\t" +
+ "Ma::MS::B1::42::EX::T1::NC::LcaMicCfd::Value[um]::LIN::NB::NC", data.get(0));
+ assertEquals("BBA9001#A_S20090325-2\t2.5\t42.5", data.get(1));
+ checkProperties(1);
+ data = getData(2);
+ assertEquals("BBA ID\t" +
+ "Ma::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC\t" +
+ "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Mean[Au]::LIN::NB::NC", data.get(0));
+ assertEquals("BBA9001#A_S20090325-2\t5.5\t45.5", data.get(1));
+ checkProperties(2);
+ data = getData(3);
+ assertEquals("BBA ID\t" +
+ "Ma::MS::B1::12::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC\t" +
+ "Ma::MS::B1::42::EX::T1::NC::LcaMicAbsFl::Std[Au]::LIN::NB::NC", data.get(0));
+ assertEquals("BBA9001#A_S20090325-2\tN/A\t3.25", data.get(1));
+ checkProperties(3);
+ context.assertIsSatisfied();
+ }
+
+ private List<String> getData(int number)
+ {
+ File ds = new File(dropBox, DataSetHandler.LCA_MIC_TIME_SERIES + number);
+ List<String> data = FileUtilities.loadToStringList(ds.listFiles(TXT_FILTER)[0]);
+ assertEquals(2, data.size());
+ return data;
+ }
+
+ private void checkProperties(int number)
+ {
+ File ds = new File(dropBox, DataSetHandler.LCA_MIC_TIME_SERIES + number);
+ List<String> data = FileUtilities.loadToStringList(ds.listFiles(PROPERTIES_FILTER)[0]);
+ assertEquals(2, data.size());
+ assertEquals("comment=null,p1/e1,abc-1,LCA_MIC_TIME_SERIES,PROPRIETARY", data.get(0));
+ assertEquals("user-email=ab@c.de", data.get(1));
+ }
+
+}
--
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