From 95e1402d21154ec6894dee909a50a61fb50d095c Mon Sep 17 00:00:00 2001
From: David Roazen <droazen@broadinstitute.org>
Date: Tue, 11 Feb 2014 14:03:26 -0500
Subject: [PATCH] Add ability to run *KnowledgeBaseTests to maven

Run with: mvn verify -Dsting.knowledgebasetests.skipped=false
---
 ant-bridge.sh                    |  3 +++
 pom.xml                          | 21 +++++++++++++++++++++
 protected/gatk-protected/pom.xml |  3 +++
 public/gatk-framework/pom.xml    |  3 +++
 public/gatk-package/pom.xml      |  9 +++++++++
 public/package-tests/pom.xml     | 11 +++++++++++
 public/queue-framework/pom.xml   |  3 +++
 public/queue-package/pom.xml     |  9 +++++++++
 public/sting-root/pom.xml        | 15 +++++++++++++++
 9 files changed, 77 insertions(+)

diff --git a/ant-bridge.sh b/ant-bridge.sh
index 860b3ecc5..9f4713d7c 100755
--- a/ant-bridge.sh
+++ b/ant-bridge.sh
@@ -127,6 +127,9 @@ for arg in "${@}" ; do
         elif [[ "${arg}" == "largescaletest" ]] ; then
             mvn_args="verify -Dsting.largescaletests.skipped=false"
 
+        elif [[ "${arg}" == "knowledgebasetest" ]] ; then
+            mvn_args="verify -Dsting.knowledgebasetests.skipped=false"
+
         elif [[ "${arg}" == "pipelinetest" ]] ; then
             mvn_args="verify -Dsting.pipelinetests.skipped=false"
 
diff --git a/pom.xml b/pom.xml
index aef2baab3..5a7bb2f97 100644
--- a/pom.xml
+++ b/pom.xml
@@ -50,6 +50,7 @@
         <sting.packageintegrationtests.skipped>${sting.packagecommittests.skipped}</sting.packageintegrationtests.skipped>
         <sting.packagepipelinetests.skipped>${sting.packagecommittests.skipped}</sting.packagepipelinetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+        <sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
 
         <!--
         Serial tests use the test jars to run tests, such that all tests are run from a single TestNG invocation.
@@ -63,6 +64,7 @@
         <sting.serialintegrationtests.skipped>${sting.serialcommittests.skipped}</sting.serialintegrationtests.skipped>
         <sting.serialpipelinetests.skipped>${sting.serialcommittests.skipped}</sting.serialpipelinetests.skipped>
         <sting.seriallargescaletests.skipped>true</sting.seriallargescaletests.skipped>
+        <sting.serialknowledgebasetests.skipped>true</sting.serialknowledgebasetests.skipped>
     </properties>
 
     <dependencies>
@@ -641,6 +643,25 @@
                                 </properties>
                             </configuration>
                         </execution>
+                        <execution>
+                            <id>package-knowledgebasetests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <configuration>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <reportsDirectory>${project.build.directory}/invoker-reports/knowledgebase/${it.test}</reportsDirectory>
+                                <skipInvocation>${sting.packageknowledgebasetests.skipped}</skipInvocation>
+                                <properties>
+                                    <integrationtests.profile.enabled>true</integrationtests.profile.enabled>
+                                    <sting.packageknowledgebasetests.skipped>${sting.packageknowledgebasetests.skipped}</sting.packageknowledgebasetests.skipped>
+                                    <failsafe.summaryFile>${project.build.directory}/failsafe-reports/knowledgebase/failsafe-summary-${it.test}.xml</failsafe.summaryFile>
+                                </properties>
+                            </configuration>
+                        </execution>
                     </executions>
                 </plugin>
                 <plugin>
diff --git a/protected/gatk-protected/pom.xml b/protected/gatk-protected/pom.xml
index 9fcd6f6cf..3a7d89f4c 100644
--- a/protected/gatk-protected/pom.xml
+++ b/protected/gatk-protected/pom.xml
@@ -95,6 +95,9 @@
                     <execution>
                         <id>package-largescaletests</id>
                     </execution>
+                    <execution>
+                        <id>package-knowledgebasetests</id>
+                    </execution>
                     <execution>
                         <id>package-pipelinetests</id>
                     </execution>
diff --git a/public/gatk-framework/pom.xml b/public/gatk-framework/pom.xml
index 956cf693a..6b82c8618 100644
--- a/public/gatk-framework/pom.xml
+++ b/public/gatk-framework/pom.xml
@@ -82,6 +82,9 @@
                     <execution>
                         <id>package-largescaletests</id>
                     </execution>
+                    <execution>
+                        <id>package-knowledgebasetests</id>
+                    </execution>
                     <execution>
                         <id>package-pipelinetests</id>
                     </execution>
diff --git a/public/gatk-package/pom.xml b/public/gatk-package/pom.xml
index b9400cbb6..1e9bb5bc9 100644
--- a/public/gatk-package/pom.xml
+++ b/public/gatk-package/pom.xml
@@ -121,6 +121,15 @@
                             </dependenciesToScan>
                         </configuration>
                     </execution>
+                    <execution>
+                        <id>knowledge-base-tests</id>
+                        <configuration>
+                            <skip>${sting.serialknowledgebasetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
                 </executions>
             </plugin>
 
diff --git a/public/package-tests/pom.xml b/public/package-tests/pom.xml
index 8b7c4e7f7..3bd10e478 100644
--- a/public/package-tests/pom.xml
+++ b/public/package-tests/pom.xml
@@ -23,6 +23,7 @@
         <sting.packageintegrationtests.skipped>true</sting.packageintegrationtests.skipped>
         <sting.packagepipelinetests.skipped>true</sting.packagepipelinetests.skipped>
         <sting.packagelargescaletests.skipped>true</sting.packagelargescaletests.skipped>
+        <sting.packageknowledgebasetests.skipped>true</sting.packageknowledgebasetests.skipped>
         <failsafe.summaryFile>${project.build.directory}/failsafe-reports/failsafe-summary.xml</failsafe.summaryFile>
     </properties>
 
@@ -181,6 +182,16 @@
                                     <skip>${sting.packagelargescaletests.skipped}</skip>
                                 </configuration>
                             </execution>
+                            <execution>
+                                <id>knowledge-base-tests</id>
+                                <goals>
+                                    <goal>verify</goal>
+                                </goals>
+                                <!-- run knowledge base tests -->
+                                <configuration>
+                                    <skip>${sting.packageknowledgebasetests.skipped}</skip>
+                                </configuration>
+                            </execution>
                         </executions>
                     </plugin>
                 </plugins>
diff --git a/public/queue-framework/pom.xml b/public/queue-framework/pom.xml
index 7a292ffe4..2f3f7b59a 100644
--- a/public/queue-framework/pom.xml
+++ b/public/queue-framework/pom.xml
@@ -183,6 +183,9 @@
                     <execution>
                         <id>package-largescaletests</id>
                     </execution>
+                    <execution>
+                        <id>package-knowledgebasetests</id>
+                    </execution>
                     <execution>
                         <id>package-pipelinetests</id>
                     </execution>
diff --git a/public/queue-package/pom.xml b/public/queue-package/pom.xml
index 087ffb6e7..790eeac72 100644
--- a/public/queue-package/pom.xml
+++ b/public/queue-package/pom.xml
@@ -159,6 +159,15 @@
                             </dependenciesToScan>
                         </configuration>
                     </execution>
+                    <execution>
+                        <id>knowledge-base-tests</id>
+                        <configuration>
+                            <skip>${sting.serialknowledgebasetests.skipped}</skip>
+                            <dependenciesToScan>
+                                <scan>org.broadinstitute.sting:.*</scan>
+                            </dependenciesToScan>
+                        </configuration>
+                    </execution>
                 </executions>
             </plugin>
 
diff --git a/public/sting-root/pom.xml b/public/sting-root/pom.xml
index 9297c6569..66f4c5ff1 100644
--- a/public/sting-root/pom.xml
+++ b/public/sting-root/pom.xml
@@ -33,6 +33,7 @@
         <sting.integrationtests.skipped>${sting.committests.skipped}</sting.integrationtests.skipped>
         <sting.pipelinetests.skipped>${sting.committests.skipped}</sting.pipelinetests.skipped>
         <sting.largescaletests.skipped>true</sting.largescaletests.skipped>
+        <sting.knowledgebasetests.skipped>true</sting.knowledgebasetests.skipped>
         <sting.pipelinetests.run>false</sting.pipelinetests.run>
         <scala.maxmemory>1g</scala.maxmemory>
         <test.maxmemory>4g</test.maxmemory>
@@ -456,6 +457,20 @@
                                 </includes>
                             </configuration>
                         </execution>
+                        <execution>
+                            <id>knowledge-base-tests</id>
+                            <goals>
+                                <goal>integration-test</goal>
+                                <goal>verify</goal>
+                            </goals>
+                            <!-- run knowledge base tests -->
+                            <configuration>
+                                <skip>${sting.knowledgebasetests.skipped}</skip>
+                                <includes>
+                                    <include>**/*KnowledgeBaseTest.class</include>
+                                </includes>
+                            </configuration>
+                        </execution>
                     </executions>
                 </plugin>