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Using new parameters via skashin to run gatkdocs in the maven conventional subdirectory. 

Updated path for output gatkdocs in nightly build script.
Removed patch in plugin manager that contained a workaround for gatkdocs running in the top level directory.
This commit is contained in:
Khalid Shakir 2014-02-14 15:57:21 +08:00
parent 1b3ac95798
commit 225ee4880b
2 changed files with 1 additions and 24 deletions
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14
pom.xml
View File

@ -754,19 +754,7 @@
<useStandardDocletOptions>false</useStandardDocletOptions>
<quiet>true</quiet>
<show>private</show>
<!--
TODO: Stop GATKDoclet from hardcoding paths and start using parameters.
For now... just run from the base directory, target/site/../..
-->
<destDir>../..</destDir>
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden}</additionalparam>
<!--
TODO: Leaving this true applies a patch to the git commited file
TODO: private/resources/clover/api/index.html
TODO: Determine if this file was generated and shoudldn't be touched,
TODO: or patch the file and commit a new version.
-->
<applyJavadocSecurityFix>false</applyJavadocSecurityFix>
<additionalparam>-build-timestamp "${maven.build.timestamp}" -absolute-version ${build.version} ${gatkdocs.include.hidden} -settings-dir ${sting.basedir}/settings/helpTemplates -destination-dir ${project.build.directory}/gatkdocs</additionalparam>
</configuration>
</reportSet>
</reportSets>

11
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/classloader/PluginManager.java
View File

@ -154,17 +154,6 @@ public class PluginManager<PluginType> {
@SuppressWarnings("unchecked")
Set<Class<? extends PluginType>> allTypes = reflections.getSubTypesOf(pluginType);
for( Class<? extends PluginType> type: allTypes ) {
// Depending on the root directories/URLs fed to org.reflections, the scanner may pick up classes that are
// NOT actually in the classpath. When this happens, Class.forName() returns null, and the allTypes ends up
// containing null elements.
// This happens for example when the gatkdocs generator is invoked from the root of the source tree.
// In this case, ignore the null types, as they were most likely NOT supposed to be scanned, and continue.
// TODO: Fix location that the GATKDocs scans, since it currently runs from the source code root, due to
// TODO: hardcoded paths!
if (type == null)
continue;
// The plugin manager does not support anonymous classes; to be a plugin, a class must have a name.
if(JVMUtils.isAnonymous(type))
continue;