From 25cef4b0e52e3572f233713c83fdbedc3a4aa96b Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 19 Aug 2010 12:08:09 +0000
Subject: [PATCH] LMS-1707 refactoring: replace 'name' in places where label
and code is used, FeatureTableBuilderTest added
SVN: 17531
---
.../generic/server/FeatureTableBuilder.java | 13 +-
.../server/TabularDataGraphServlet.java | 2 +-
...mageAnalysisMergedRowsReportingPlugin.java | 6 +-
.../server/DssServiceRpcScreening.java | 2 +-
.../server/FeatureTableBuilderTest.java | 204 ++++++++++++++++++
5 files changed, 216 insertions(+), 11 deletions(-)
create mode 100644 screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
index 90f1f322c33..bdc5d700342 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilder.java
@@ -154,16 +154,11 @@ public class FeatureTableBuilder
return bundle;
}
- private CodeAndTitle getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
- {
- return new CodeAndTitle(featureDefinition.getCode(), featureDefinition.getLabel());
- }
-
/**
* Returns all feature codes/labels found. If the feature code list in the constructor is not empty the
* result will a list where the codes are a subset of this list.
*/
- public List<CodeAndTitle> getFeatureCodes()
+ public List<CodeAndTitle> getCodesAndLabels()
{
return new ArrayList<CodeAndTitle>(featureCodeLabelToIndexMap.keySet());
}
@@ -238,4 +233,10 @@ public class FeatureTableBuilder
row.setFeatureValues(valueArray);
return row;
}
+
+ private CodeAndTitle getCodeAndLabel(final ImgFeatureDefDTO featureDefinition)
+ {
+ return new CodeAndTitle(featureDefinition.getCode(), featureDefinition.getLabel());
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
index 1cec3fbd9c1..041b34216ef 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/TabularDataGraphServlet.java
@@ -84,7 +84,7 @@ public class TabularDataGraphServlet extends AbstractTabularDataGraphServlet
final FeatureTableBuilder tableBuilder = new FeatureTableBuilder(dao, service);
tableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
- List<CodeAndTitle> featureNames = tableBuilder.getFeatureCodes();
+ List<CodeAndTitle> featureNames = tableBuilder.getCodesAndLabels();
int headerTokensLength = featureNames.size() + 3;
headerTokens = new String[headerTokensLength];
headerTokens[0] = WELL_NAME_COLUMN;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
index b97f743f8e8..2129aa7eaad 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.java
@@ -85,16 +85,16 @@ public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDatastorePlu
String dataSetCode = datasetDescription.getDatasetCode();
featureTableBuilder.addFeatureVectorsOfDataSet(dataSetCode);
}
- List<CodeAndTitle> featureNames = featureTableBuilder.getFeatureCodes();
+ List<CodeAndTitle> codeAndLabels = featureTableBuilder.getCodesAndLabels();
List<FeatureTableRow> rows = featureTableBuilder.createFeatureTableRows();
SimpleTableModelBuilder builder = new SimpleTableModelBuilder(true);
builder.addHeader(DATA_SET_CODE_TITLE);
builder.addHeader(PLATE_IDENTIFIER_TITLE);
builder.addHeader(ROW_TITLE);
builder.addHeader(COLUMN_TITLE);
- for (CodeAndTitle featureName : featureNames)
+ for (CodeAndTitle codeAndLabel : codeAndLabels)
{
- builder.addHeader(featureName.getTitle(), featureName.getCode());
+ builder.addHeader(codeAndLabel.getTitle(), codeAndLabel.getCode());
}
for (FeatureTableRow row : rows)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index f21722530b8..5168ceb069e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -250,7 +250,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private List<String> getCodes(FeatureTableBuilder builder)
{
- List<CodeAndTitle> featureCodesAndLabels = builder.getFeatureCodes();
+ List<CodeAndTitle> featureCodesAndLabels = builder.getCodesAndLabels();
List<String> codes = new ArrayList<String>();
for (CodeAndTitle codeAndTitle : featureCodesAndLabels)
{
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
new file mode 100644
index 00000000000..6f742a637c0
--- /dev/null
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/FeatureTableBuilderTest.java
@@ -0,0 +1,204 @@
+/*
+ * 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 ch.systemsx.cisd.openbis.dss.generic.server;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.CodeAndTitle;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.PlateUtils;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.dto.PlateFeatureValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureDefDTO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgFeatureValuesDTO;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FeatureTableBuilderTest extends AssertJUnit
+{
+ private static final int EXPERIMENT_ID = 42;
+ private static final String DATA_SET_CODE1 = "ds1";
+ private static final String DATA_SET_CODE2 = "ds2";
+ private static final String DATA_SET_CODE3 = "ds3";
+
+ private Mockery context;
+
+ private IEncapsulatedOpenBISService service;
+
+ private IImagingQueryDAO dao;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ dao = context.mock(IImagingQueryDAO.class);
+ }
+
+ @AfterMethod
+ public final void tearDown()
+ {
+ // The 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 testNoFiltering()
+ {
+ prepareAddFeatureVectors(1, null, "<A>a", "<B>b");
+ prepareAddFeatureVectors(2, null, "<B>beta", "c");
+ prepareAddFeatureVectors(3, null, "<B>b");
+
+ FeatureTableBuilder builder = createBuilder();
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE1);
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE2);
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE3);
+ List<CodeAndTitle> codesAndLabels = builder.getCodesAndLabels();
+ List<FeatureTableRow> rows = builder.createFeatureTableRows();
+
+ assertEquals("[<A> a, <B> b, <B> beta, <C> c]", codesAndLabels.toString());
+ assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "1.5, 11.5, NaN, NaN", rows.get(0));
+ assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "0.5, 10.5, NaN, NaN", rows.get(1));
+ assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, NaN, 2.5, 12.5", rows.get(2));
+ assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, NaN, 1.5, 11.5", rows.get(3));
+ assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "NaN, 3.5, NaN, NaN", rows.get(4));
+ assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "NaN, 2.5, NaN, NaN", rows.get(5));
+ assertEquals(6, rows.size());
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testFiltering()
+ {
+ prepareAddFeatureVectors(1, "B", "<A>a", "b");
+ prepareAddFeatureVectors(2, "B", "<B>beta", "c");
+ prepareAddFeatureVectors(3, "B", "b");
+
+ FeatureTableBuilder builder = createBuilder("B");
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE1);
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE2);
+ builder.addFeatureVectorsOfDataSet(DATA_SET_CODE3);
+ List<CodeAndTitle> codesAndLabels = builder.getCodesAndLabels();
+ List<FeatureTableRow> rows = builder.createFeatureTableRows();
+
+ assertEquals("[<B> b, <B> beta]", codesAndLabels.toString());
+ assertFeatureTableRow(DATA_SET_CODE1, "A1", "db:/s/S1", "11.5, NaN", rows.get(0));
+ assertFeatureTableRow(DATA_SET_CODE1, "A2", "db:/s/S1", "10.5, NaN", rows.get(1));
+ assertFeatureTableRow(DATA_SET_CODE2, "A1", "db:/s/S2", "NaN, 2.5", rows.get(2));
+ assertFeatureTableRow(DATA_SET_CODE2, "A2", "db:/s/S2", "NaN, 1.5", rows.get(3));
+ assertFeatureTableRow(DATA_SET_CODE3, "A1", "db:/s/S3", "3.5, NaN", rows.get(4));
+ assertFeatureTableRow(DATA_SET_CODE3, "A2", "db:/s/S3", "2.5, NaN", rows.get(5));
+ assertEquals(6, rows.size());
+ context.assertIsSatisfied();
+ }
+
+ private void prepareAddFeatureVectors(final int dataSetID, final String filteredCodeOrNull,
+ final String... featureCodesAndLabels)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ String dataSetCode = "ds" + dataSetID;
+ one(dao).tryGetDatasetByPermId(dataSetCode);
+ int containerId = dataSetID + 100;
+ ImgDatasetDTO dataSet = new ImgDatasetDTO(dataSetCode, null, null, containerId, false);
+ dataSet.setId(dataSetID);
+ will(returnValue(dataSet));
+
+ List<ImgFeatureDefDTO> defs = new ArrayList<ImgFeatureDefDTO>();
+ Geometry geometry = Geometry.createFromCartesianDimensions(2, 1);
+ for (int i = 0; i < featureCodesAndLabels.length; i++)
+ {
+ String codeAndLabels = featureCodesAndLabels[i];
+ CodeAndTitle codeAndTitle = new CodeAndTitle(codeAndLabels);
+ String title = codeAndTitle.getTitle();
+ String code = codeAndTitle.getCode();
+ if (filteredCodeOrNull == null || filteredCodeOrNull.equals(code))
+ {
+ ImgFeatureDefDTO def = new ImgFeatureDefDTO(title, code, title, dataSetID);
+ def.setId(2 * dataSetID);
+ defs.add(def);
+ one(dao).getFeatureValues(def);
+ PlateFeatureValues values = new PlateFeatureValues(geometry);
+ values.setForWellLocation(dataSetID + 10 * i + 0.5f, 1, 1);
+ values.setForWellLocation(dataSetID + 10 * i - 0.5f, 1, 2);
+ will(returnValue(Arrays.asList(new ImgFeatureValuesDTO(0.0, 0.0, values, def.getId()))));
+ }
+ }
+ one(dao).listFeatureDefsByDataSetId(dataSetID);
+ will(returnValue(defs));
+
+ one(dao).getContainerById(containerId);
+ String samplePermID = "s" + containerId;
+ will(returnValue(new ImgContainerDTO(samplePermID, geometry.getNumberOfRows(),
+ geometry.getNumberOfColumns(), EXPERIMENT_ID)));
+
+ one(service).tryToGetSampleIdentifier(samplePermID);
+ will(returnValue(new SampleIdentifier(new SpaceIdentifier("db", "s"), "S" + dataSetID)));
+ }
+ });
+ }
+
+ private void assertFeatureTableRow(String expectedDataSetCode, String expectedWell,
+ String expectedPlate, String expectedValues, FeatureTableRow row)
+ {
+ assertEquals(expectedDataSetCode, row.getDataSetCode());
+ String rowLetter =
+ PlateUtils.translateRowNumberIntoLetterCode(row.getWellPosition().getWellRow());
+ assertEquals(expectedWell, rowLetter + row.getWellPosition().getWellColumn());
+ assertEquals(expectedPlate, row.getPlateIdentifier().toString());
+ assertEquals(expectedValues, render(row.getFeatureValuesAsDouble()));
+ }
+
+ private String render(double[] values)
+ {
+ StringBuilder builder = new StringBuilder();
+ for (double value : values)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(", ");
+ }
+ builder.append(value);
+ }
+ return builder.toString();
+ }
+
+ private FeatureTableBuilder createBuilder(String... featureCodes)
+ {
+ return new FeatureTableBuilder(Arrays.asList(featureCodes), dao, service);
+ }
+
+}
--
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