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Merge pull request #518 from broadinstitute/ks_skashin_gatkdocs_arguments 

Ks skashin gatkdocs arguments
This commit is contained in:
droazen 2014-02-14 13:57:19 -05:00
parent f6022a944b c64131e9fd
commit 1e82f117ad
3 changed files with 30 additions and 36 deletions
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14
pom.xml
View File

@ -769,19 +769,7 @@
<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;

41
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java
View File

@ -77,12 +77,15 @@ public class GATKDoclet {
*/
final protected static File DESTINATION_DIR = new File("gatkdocs");
final private static String FORUM_KEY_FILE = "/local/gsa-engineering/gatkdocs_publisher/forum.key";
final private static String FORUM_KEY_PATH = "/local/gsa-engineering/gatkdocs_publisher/forum.key";
// ----------------------------------------------------------------------
//
// Global variables that are set on the command line by javadoc
//
// ----------------------------------------------------------------------
protected static File settingsDir = SETTINGS_DIR;
protected static File destinationDir = DESTINATION_DIR;
protected static String forumKeyPath = FORUM_KEY_PATH;
protected static String buildTimestamp = null, absoluteVersion = null;
protected static boolean showHiddenFeatures = false;
@ -135,16 +138,27 @@ public class GATKDoclet {
// load arguments
for (String[] options : rootDoc.options()) {
if (options[0].equals("-settings-dir"))
settingsDir = new File(options[1]);
if (options[0].equals("-destination-dir"))
destinationDir = new File(options[1]);
if (options[0].equals("-forum-key-path"))
forumKeyPath = options[1];
if (options[0].equals("-build-timestamp"))
buildTimestamp = options[1];
if (options[0].equals("-absolute-version"))
absoluteVersion = options[1];
if (options[0].equals("-include -hidden"))
if (options[0].equals("-include-hidden"))
showHiddenFeatures = true;
if (options[0].equals("-test"))
testOnly = true;
}
if (!settingsDir.exists())
throw new RuntimeException("-settings-dir " + settingsDir.getPath() + " does not exist");
else if (!settingsDir.isDirectory())
throw new RuntimeException("-settings-dir " + settingsDir.getPath() + " is not a directory");
// process the docs
new GATKDoclet().processDocs(rootDoc);
@ -159,7 +173,10 @@ public class GATKDoclet {
* @return Number of potential parameters; 0 if not supported.
*/
public static int optionLength(String option) {
if (option.equals("-build-timestamp") ||
if (option.equals("-settings-dir") ||
option.equals("-destination-dir") ||
option.equals("-forum-key-path") ||
option.equals("-build-timestamp") ||
option.equals("-absolute-version") ||
option.equals("-include-hidden")) {
return 2;
@ -187,19 +204,19 @@ public class GATKDoclet {
try {
// basic setup
DESTINATION_DIR.mkdirs();
FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.css"), new File(DESTINATION_DIR + "/bootstrap.min.css"));
FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.js"), new File(DESTINATION_DIR + "/bootstrap.min.js"));
FileUtils.copyFile(new File(SETTINGS_DIR + "/jquery.min.js"), new File(DESTINATION_DIR + "/jquery.min.js"));
destinationDir.mkdirs();
FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.css"), new File(destinationDir + "/bootstrap.min.css"));
FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.js"), new File(destinationDir + "/bootstrap.min.js"));
FileUtils.copyFile(new File(settingsDir + "/jquery.min.js"), new File(destinationDir + "/jquery.min.js"));
// print the Version number
FileUtils.writeByteArrayToFile(new File(DESTINATION_DIR + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes());
FileUtils.writeByteArrayToFile(new File(destinationDir + "/current.version.txt"), getSimpleVersion(absoluteVersion).getBytes());
/* ------------------------------------------------------------------- */
/* You should do this ONLY ONCE in the whole application life-cycle: */
Configuration cfg = new Configuration();
// Specify the data source where the template files come from.
cfg.setDirectoryForTemplateLoading(SETTINGS_DIR);
cfg.setDirectoryForTemplateLoading(settingsDir);
// Specify how templates will see the data-model. This is an advanced topic...
cfg.setObjectWrapper(new DefaultObjectWrapper());
@ -222,7 +239,7 @@ public class GATKDoclet {
processIndex(cfg, new ArrayList<GATKDocWorkUnit>(myWorkUnits));
File forumKeyFile = new File(FORUM_KEY_FILE);
File forumKeyFile = new File(forumKeyPath);
if (forumKeyFile.exists()) {
String forumKey = null;
// Read in a one-line file so we can do a for loop
@ -377,7 +394,7 @@ public class GATKDoclet {
Template temp = cfg.getTemplate("generic.index.template.html");
/* Merge data-model with template */
Writer out = new OutputStreamWriter(new FileOutputStream(new File(DESTINATION_DIR + "/index.html")));
Writer out = new OutputStreamWriter(new FileOutputStream(new File(destinationDir + "/index.html")));
try {
temp.process(groupIndexData(indexData), out);
out.flush();
@ -497,7 +514,7 @@ public class GATKDoclet {
Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc));
// Merge data-model with template
File outputPath = new File(DESTINATION_DIR + "/" + unit.filename);
File outputPath = new File(destinationDir + "/" + unit.filename);
try {
Writer out = new OutputStreamWriter(new FileOutputStream(outputPath));
temp.process(unit.forTemplate, out);