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jordeujordeu
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CSV/TSV importer first version
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‎.gitignore‎

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@@ -12,7 +12,7 @@
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# Maven files
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target/
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site/
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# Operating System annoyances
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*.DS_Store

‎org.gitools.analysis/pom.xml‎

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<modelVersion>4.0.0</modelVersion>
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<artifactId>org.gitools.analysis</artifactId>
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<name>org.gitools.analysis</name>
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<dependencies>
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</dependencies>
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<distributionManagement>
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<site>
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<id>site</id>
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<name>Gitools Github ghpages checkout</name>
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<url>file://${basedir}/../site/${project.version}/${project.artifactId}</url>
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</site>
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</distributionManagement>
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</project>

‎org.gitools.analysis/src/main/java/org/gitools/analysis/groupcomparison/GroupComparisonAnalysis.java‎

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@@ -53,7 +53,6 @@ public class GroupComparisonAnalysis extends Analysis implements Serializable {
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private DimensionGroupEnum columnGrouping = null;
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protected String dataFile = "";
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@XmlTransient
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private String mtc;
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private ResourceReference<IMatrix> data;
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private ResourceReference<? extends IMatrix> data;
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private ResourceReference<IMatrix> results;
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private ResourceReference<? extends IMatrix> results;
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private Double nullConversion;
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@@ -166,7 +165,7 @@ public void addGroups(List<DimensionGroup> groups) {
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}
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}
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public ResourceReference<IMatrix> getData() {
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public ResourceReference<? extends IMatrix> getData() {
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return data;
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}
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this.data = data;
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}
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public ResourceReference<IMatrix> getResults() {
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public ResourceReference<? extends IMatrix> getResults() {
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return results;
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}
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public void setResults(ResourceReference<IMatrix> results) {
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public void setResults(ResourceReference<? extends IMatrix> results) {
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this.results = results;
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}
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‎org.gitools.analysis/src/main/java/org/gitools/analysis/htest/enrichment/EnrichmentProcessor.java‎

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import java.util.Date;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.concurrent.CancellationException;
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public class EnrichmentProcessor implements AnalysisProcessor {
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@@ -56,7 +57,7 @@ public EnrichmentProcessor(EnrichmentAnalysis analysis) {
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}
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@Override
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public void run(IProgressMonitor monitor) throws AnalysisException {
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public void run(final IProgressMonitor monitor) throws AnalysisException {
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Date startTime = new Date();
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IMatrix data = analysis.getData().get();
@@ -92,6 +93,10 @@ public Map<String, CommonResult> apply(Double value, IMatrixPosition position) {
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Map<String, CommonResult> results = new HashMap<>();
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for (String module : moduleMap.getModules()) {
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if (monitor.isCancelled()) {
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throw new CancellationException();
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}
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Iterable<Double> moduleValues = position.iterate(layer, items).filter(moduleMap.getMappingItems(module));
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CommonResult result = test.processTest(moduleValues);

‎org.gitools.analysis/src/test/java/org/gitools/analysis/enrichment/ZScoreEnrichmentProcessorTest.java‎

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super(EnrichmentAnalysis.class, "/enrichment/test02.enrichment");
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}
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@Test
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public void testResourceFormat() {
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assertEquals("test", getAnalysis().getTitle());
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}
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@Test
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public void testAnalysisProcessor() throws IOException {
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‎org.gitools.analysis/src/test/java/org/gitools/analysis/groupcomparison/GroupComparisonProcessorTest.java‎

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import org.gitools.analysis.AbstractProcessorTest;
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import org.gitools.analysis.AssertMatrix;
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import org.gitools.analysis.groupcomparison.DimensionGroups.DimensionGroupEnum;
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import org.gitools.api.matrix.IMatrix;
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import org.junit.Test;
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@Test
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public void testResourceFormat() {
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assertEquals(getAnalysis().getTitle(), "tp53-signalling CIS-effect");
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assertEquals(getAnalysis().getDescription(), "GBM: CNA effect in expression in TP53 signalling pathway. This test assesses the effecto of copy umber alteration on the expression status of the gene. Read under the following link on how to perform the test: http://help.gitools.org/xwiki/bin/view/Tutorials/Tutorial63");
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assertEquals(getAnalysis().getLayerName(), 0);
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assertEquals(getAnalysis().getColumnGrouping(), "Group by value");
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assertEquals("tp53-signalling CIS-effect", getAnalysis().getTitle());
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assertEquals("GBM: CNA effect in expression in TP53 signalling pathway. This test assesses the effecto of copy umber alteration on the expression status of the gene. Read under the following link on how to perform the test: http://help.gitools.org/xwiki/bin/view/Tutorials/Tutorial63", getAnalysis().getDescription());
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}
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}

‎org.gitools.api/pom.xml‎

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<modelVersion>4.0.0</modelVersion>
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<artifactId>org.gitools.api</artifactId>
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<name>org.gitools.api</name>
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<dependencies>
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</dependencies>
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<distributionManagement>
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<site>
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<id>site</id>
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<name>Gitools Github ghpages checkout</name>
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<url>file://${basedir}/../site/${project.version}/${project.artifactId}</url>
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</site>
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</distributionManagement>
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</project>

‎org.gitools.cli/pom.xml‎

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<modelVersion>4.0.0</modelVersion>
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<artifactId>org.gitools.cli</artifactId>
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<name>org.gitools.cli</name>
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<description>gitools command line interface</description>
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<properties>
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<mainClass>org.gitools.cli.Main</mainClass>
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</plugin>
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</plugins>
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</build>
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<distributionManagement>
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<site>
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<id>site</id>
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<name>Gitools Github ghpages checkout</name>
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<url>file://${basedir}/../site/${project.version}/${project.artifactId}</url>
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</site>
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</distributionManagement>
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</project>

‎org.gitools.datasources/pom.xml‎

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<modelVersion>4.0.0</modelVersion>
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<artifactId>org.gitools.datasources</artifactId>
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<name>org.gitools.datasources</name>
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<dependencies>
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</plugins>
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</build>
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<distributionManagement>
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<site>
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<id>site</id>
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<name>Gitools Github ghpages checkout</name>
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<url>file://${basedir}/../site/${project.version}/${project.artifactId}</url>
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</site>
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</distributionManagement>
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</project>

‎org.gitools.heatmap/pom.xml‎

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<modelVersion>4.0.0</modelVersion>
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<artifactId>org.gitools.heatmap</artifactId>
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<name>org.gitools.heatmap</name>
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<dependencies>
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</dependencies>
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<distributionManagement>
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<site>
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<id>site</id>
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<name>Gitools Github ghpages checkout</name>
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<url>file://${basedir}/../site/${project.version}/${project.artifactId}</url>
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</site>
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</distributionManagement>
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</project>

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