Pull createPipelineConfig task out of gradle plugin (#4)

Author: labkey-tchad

SequenceAnalysis/build.gradle

@@ -1,4 +1,11 @@
-import org.labkey.gradle.util.BuildUtils;
+import org.labkey.gradle.plugin.TeamCity
+import org.labkey.gradle.plugin.extension.ServerDeployExtension
+import org.labkey.gradle.plugin.extension.TeamCityExtension
+import org.labkey.gradle.util.BuildUtils
+import org.labkey.gradle.util.GroupNames
+import org.labkey.gradle.util.PropertiesUtils
+
+import java.util.regex.Matcher
 
 repositories {
    jcenter()
@@ -22,4 +29,34 @@ dependencies {
    external("com.github.broadinstitute:picard:2.18.4") {
       exclude group: "javax.servlet", module: "servlet-api"
    }
+}
+
+if (project.findProject(BuildUtils.getTestProjectPath(project.gradle)) != null && project.hasProperty("teamcity"))
+{
+   def testProject = project.findProject(BuildUtils.getTestProjectPath(project.gradle))
+   def createPipelineConfigTask = project.tasks.register("createPipelineConfig", Copy) {
+      Copy task ->
+         task.group = GroupNames.TEST_SERVER
+         task.description = "Create pipeline configs for running tests on the test server"
+         task.from project.file("test/configs")
+         task.include "pipelineConfig.xml"
+         task.filter({ String line ->
+            Matcher matcher = PropertiesUtils.PROPERTY_PATTERN.matcher(line)
+            def extension = testProject.extensions.findByType(TeamCityExtension.class)
+            String newLine = line
+            while (matcher.find())
+            {
+               if (matcher.group(1).equals("SEQUENCEANALYSIS_CODELOCATION") || matcher.group(1).equals("SEQUENCEANALYSIS_TOOLS"))
+                  newLine = newLine.replace(matcher.group(), extension.getTeamCityProperty("additional.pipeline.tools"))
+               else if (matcher.group(1).equals("SEQUENCEANALYSIS_EXTERNALDIR"))
+                  newLine = newLine.replace(matcher.group(), project.file("pipeline_code/external").getAbsolutePath())
+            }
+            return newLine
+
+         })
+         task.destinationDir = new File("${ServerDeployExtension.getServerDeployDirectory(project)}/config")
+   }
+   testProject.tasks.named("startTomcat").configure {
+      dependsOn(createPipelineConfigTask)
+   }
 }

SequenceAnalysis/test/configs/pipelineConfig.xml

@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<beans xmlns="http://www.springframework.org/schema/beans"
+       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+       xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans-2.0.xsd">
+
+    <bean id="pipelineJobService" class="org.labkey.pipeline.api.PipelineJobServiceImpl">
+        <property name="configProperties">
+            <bean class="org.labkey.pipeline.api.properties.ConfigPropertiesImpl">
+                <property name="softwarePackages">
+                    <map>
+                        <!--This is the path to the checked out copy of the SequenceAnalysis perl code.
+                            sequence_tools_install.sh would have placed this in the path below-->
+                        <entry key="SEQUENCEANALYSIS_CODELOCATION" value="@@SEQUENCEANALYSIS_CODELOCATION@@"/>
+                        <!--This is the path where the /external directory from the SequenceAnalysis module is checked out.
+                            This contains several JARs.  sequence_tools_install.sh would have placed these in the path below-->
+                        <entry key="SEQUENCEANALYSIS_EXTERNALDIR" value="@@SEQUENCEANALYSIS_EXTERNALDIR@@"/>
+                        <!--If the sequence tools are not in the standard pipeline tools dir, this is required.
+                            These are the external binaries installed by sequence_tools_install.sh-->
+                        <entry key="SEQUENCEANALYSIS_TOOLS" value="@@SEQUENCEANALYSIS_TOOLS@@"/>
+                    </map>
+                </property>
+            </bean>
+        </property>
+    </bean>	
+</beans>