From 0df6a9da5cdf69437f819fc6e2579e82d2a2eecb Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 9 Sep 2009 15:01:40 +0000
Subject: [PATCH] -Seperating out normal (unit) tests and integration tests. 
 From now on if your test are more of an integration test (i.e. you're testing
 a walker and all the subunits it relies on) please name the test
 "______IntegrationTest.java" instead of "______Test.java".

-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.

-Also added a bunch of unit tests for VariantEval walker

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
---
 build.xml                                     |  23 +++
 ...SingleSampleGenotyperIntegrationTest.java} |  19 +--
 ...est.java => IntervalsIntegrationTest.java} |   2 +-
 ... RecalibrationWalkersIntegrationTest.java} |   2 +-
 .../VariantEvalWalkerIntegrationTest.java     | 148 ++++++++++++++++++
 .../varianteval/VariantEvalWalkerTest.java    |  43 -----
 6 files changed, 178 insertions(+), 59 deletions(-)
 rename java/test/org/broadinstitute/sting/gatk/walkers/genotyper/{SingleSampleGenotyperTest.java => SingleSampleGenotyperIntegrationTest.java} (92%)
 rename java/test/org/broadinstitute/sting/gatk/walkers/indels/{IntervalsTest.java => IntervalsIntegrationTest.java} (96%)
 rename java/test/org/broadinstitute/sting/gatk/walkers/recalibration/{RecalibrationWalkersTest.java => RecalibrationWalkersIntegrationTest.java} (97%)
 create mode 100644 java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
 delete mode 100644 java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerTest.java

diff --git a/build.xml b/build.xml
index 0d1474572..bb59a6dac 100644
--- a/build.xml
+++ b/build.xml
@@ -249,6 +249,29 @@
                 <fileset dir="${test.classes}">
                     <include name="**/${single}.class"/>
                     <exclude name="**/BaseTest.class"/>
+                    <exclude name="**/*IntegrationTest.class"/>
+                </fileset>
+            </batchtest>
+        </junit>
+        <fail message="test failed" if="test.failure" />
+    </target>
+    <!-- Our long tests, tests that are more software integration and test -->
+    <target name="integrationtest" depends="test.compile"
+            description="Run the long integration unit tests">
+        <mkdir dir="${report}"/>
+        <echo message="Sting: Running integration test cases!"/>
+        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes" failureProperty="test.failure">
+            <formatter type="${testOutput}" usefile="${usefile}" />
+            <classpath>
+                <path refid="runtime.dependencies"/>
+                <pathelement location="build"/>
+                <pathelement location="${test.classes}"/>
+                <pathelement location="lib/junit-4.4.jar"/>
+            </classpath>
+
+            <batchtest fork="yes" todir="${report}">
+                <fileset dir="${test.classes}">
+                  <include name="**/*IntegrationTest.class"/>
                 </fileset>
             </batchtest>
         </junit>
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java
similarity index 92%
rename from java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperTest.java
rename to java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java
index f5ca640c2..43c65354e 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/SingleSampleGenotyperIntegrationTest.java
@@ -1,23 +1,14 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.WalkerTest;
-import org.broadinstitute.sting.utils.genotype.Variant;
-import org.broadinstitute.sting.utils.genotype.GenotypeWriterFactory;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.junit.Test;
-import org.broadinstitute.sting.gatk.GATKArgumentCollection;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.executive.Accumulator;
 
-import java.io.*;
-import java.util.*;
-import java.security.MessageDigest;
-import java.math.BigInteger;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
-import junit.framework.Assert;
-
-public class SingleSampleGenotyperTest extends WalkerTest {
+public class SingleSampleGenotyperIntegrationTest extends WalkerTest {
     public static String baseTestString() {
         return "-T SingleSampleGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s";
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java
similarity index 96%
rename from java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java
rename to java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java
index 5283bd2e3..524357208 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java
@@ -5,7 +5,7 @@ import org.junit.Test;
 
 import java.util.Arrays;
 
-public class IntervalsTest extends WalkerTest {
+public class IntervalsIntegrationTest extends WalkerTest {
     @Test
     public void testIntervals() {
 
diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
similarity index 97%
rename from java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersTest.java
rename to java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
index 672c79b29..ea9d41393 100755
--- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
@@ -9,7 +9,7 @@ import java.util.Arrays;
 import java.util.List;
 import java.io.File;
 
-public class RecalibrationWalkersTest extends WalkerTest {
+public class RecalibrationWalkersIntegrationTest extends WalkerTest {
     static HashMap<String, String> paramsFiles = new HashMap<String, String>();
 
     @Test
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
new file mode 100644
index 000000000..ea0189104
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
@@ -0,0 +1,148 @@
+package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class VariantEvalWalkerTest
+ *         <p/>
+ *         test out the variant eval walker under different runtime conditions.
+ */
+public class VariantEvalWalkerIntegrationTest extends WalkerTest {
+
+    @Test
+    public void testEvalVariantROD() {
+        List<String> md5 = new ArrayList<String>();
+        md5.add("094c0adb8e4ae4de424f26482fd43152");
+
+        /**
+         * the above MD5 was calculated from running the following command:
+         *
+         * java -jar ./dist/GenomeAnalysisTK.jar \
+         * -R /broad/1KG/reference/human_b36_both.fasta \
+         * -T VariantEval \
+         * --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
+         * -L 1:10,000,000-11,000,000 \
+         * --outerr myVariantEval \
+         * --supressDateInformation \
+         * --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls
+         *
+         */
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /broad/1KG/reference/human_b36_both.fasta" +
+                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                        " -T VariantEval" +
+                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                        " -L 1:10,000,000-11,000,000" +
+                        " --outerr %s" +
+                        " --supressDateInformation",
+                1, // just one output file
+                md5);
+        List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
+    }
+
+    @Test
+    public void testEvalVariantRODConfSix() {
+        List<String> md5 = new ArrayList<String>();
+        md5.add("eb8716965fa1df93954c5a22b0aeda7c");
+
+        /**
+         * the above MD5 was calculated from running the following command:
+         *
+         * java -jar ./dist/GenomeAnalysisTK.jar \
+         * -R /broad/1KG/reference/human_b36_both.fasta \
+         * -T VariantEval \
+         * --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
+         * -L 1:10,000,000-11,000,000 \
+         * --outerr myVariantEval \
+         * --supressDateInformation \
+         * --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls \
+         * -minConfidenceScore 6
+         */
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /broad/1KG/reference/human_b36_both.fasta" +
+                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                        " -T VariantEval" +
+                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                        " -L 1:10,000,000-11,000,000" +
+                        " --outerr %s" +
+                        " --supressDateInformation" +
+                        " -minConfidenceScore 6",
+                1, // just one output file
+                md5);
+        List<File> result = executeTest("testEvalVariantRODConfSix", spec).getFirst();
+    }
+
+     @Test
+    public void testEvalVariantRODOutputViolations() {
+        List<String> md5 = new ArrayList<String>();
+        md5.add("9449cfb668f5175013161d2f287c30ff");
+
+        /**
+         * the above MD5 was calculated from running the following command:
+         *
+         * java -jar ./dist/GenomeAnalysisTK.jar \
+         * -R /broad/1KG/reference/human_b36_both.fasta \
+         * -T VariantEval \
+         * --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
+         * -L 1:10,000,000-11,000,000 \
+         * --outerr myVariantEval \
+         * --supressDateInformation \
+         * --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls \
+         * --includeViolations
+         */
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /broad/1KG/reference/human_b36_both.fasta" +
+                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
+                        " -T VariantEval" +
+                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                        " -L 1:10,000,000-11,000,000" +
+                        " --outerr %s" +
+                        " --supressDateInformation" +
+                        " --includeViolations",
+                1, // just one output file
+                md5);
+        List<File> result = executeTest("testEvalVariantRODOutputViolations", spec).getFirst();
+    }
+
+    @Test
+    public void testEvalGenotypeROD() {
+        List<String> md5 = new ArrayList<String>();
+        md5.add("ff2bf8987e288198b28201b5c3121c0e");
+        /**
+         * the above MD5 was calculated after running the following command:
+         *
+         * java -jar ./dist/GenomeAnalysisTK.jar \
+         * -R /broad/1KG/reference/human_b36_both.fasta \
+         * -T VariantEval \
+         * --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod \
+         * -L 1:10,000,000-11,000,000 \
+         * --outerr myVariantEval \
+         * --supressDateInformation \
+         * --evalContainsGenotypes \
+         * --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls \
+         * --rodBind hapmap-chip,GFF,/humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff
+         */
+
+        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
+                "-R /broad/1KG/reference/human_b36_both.fasta" +
+                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
+                        " -T VariantEval" +
+                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
+                        " -L 1:10,000,000-11,000,000" +
+                        " --outerr %s" +
+                        " --supressDateInformation" +
+                        " --evalContainsGenotypes" +
+                        " --rodBind hapmap-chip,GFF,/humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff",
+                1, // just one output file
+                md5);
+        List<File> result = executeTest("testEvalGenotypeROD", spec).getFirst();
+    }
+}
+
diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerTest.java
deleted file mode 100644
index 727a342b3..000000000
--- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerTest.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers.varianteval;
-
-import org.broadinstitute.sting.WalkerTest;
-import org.junit.Test;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * @author aaron
- *         <p/>
- *         Class VariantEvalWalkerTest
- *         <p/>
- *         test out the variant eval walker under a bunch of different runtime conditions.
- */
-public class VariantEvalWalkerTest extends WalkerTest {
-
-    @Test
-    public void emptyTest() {
-
-    }
-
-    @Test
-    public void testEvalVariantROD() {
-        List <String> md5 = new ArrayList<String>();
-        md5.add("094c0adb8e4ae4de424f26482fd43152");
-
-        WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
-                "-R /broad/1KG/reference/human_b36_both.fasta" +
-                        " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
-                        " -T VariantEval" +
-                        " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
-                        " -L 1:10,000,000-11,000,000" +
-                        " --outerr %s" +
-                        " --supressDateInformation",
-                1, // just one output file
-                md5);
-        List<File> result = executeTest("testEvalVariantROD", spec).getFirst();
-
-    }
-}
-