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Added the following arguments: -settings-dir -destination-dir -forum-key-path 

Signed-off-by: Khalid Shakir <kshakir@broadinstitute.org>
This commit is contained in:
skashin 2014-02-13 21:55:14 -05:00 committed by Khalid Shakir
parent 7095a60c8e
commit 1b3ac95798
1 changed files with 29 additions and 12 deletions
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41
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/help/GATKDoclet.java
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@ -77,12 +77,15 @@ public class GATKDoclet {
*/ */
final protected static File DESTINATION_DIR = new File("gatkdocs"); 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 // 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 String buildTimestamp = null, absoluteVersion = null;
protected static boolean showHiddenFeatures = false; protected static boolean showHiddenFeatures = false;
@ -135,16 +138,27 @@ public class GATKDoclet {
// load arguments // load arguments
for (String[] options : rootDoc.options()) { 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")) if (options[0].equals("-build-timestamp"))
buildTimestamp = options[1]; buildTimestamp = options[1];
if (options[0].equals("-absolute-version")) if (options[0].equals("-absolute-version"))
absoluteVersion = options[1]; absoluteVersion = options[1];
if (options[0].equals("-include -hidden")) if (options[0].equals("-include-hidden"))
showHiddenFeatures = true; showHiddenFeatures = true;
if (options[0].equals("-test")) if (options[0].equals("-test"))
testOnly = true; 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 // process the docs
new GATKDoclet().processDocs(rootDoc); new GATKDoclet().processDocs(rootDoc);
@ -159,7 +173,10 @@ public class GATKDoclet {
* @return Number of potential parameters; 0 if not supported. * @return Number of potential parameters; 0 if not supported.
*/ */
public static int optionLength(String option) { 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("-absolute-version") ||
option.equals("-include-hidden")) { option.equals("-include-hidden")) {
return 2; return 2;
@ -187,19 +204,19 @@ public class GATKDoclet {
try { try {
// basic setup // basic setup
DESTINATION_DIR.mkdirs(); destinationDir.mkdirs();
FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.css"), new File(DESTINATION_DIR + "/bootstrap.min.css")); FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.css"), new File(destinationDir + "/bootstrap.min.css"));
FileUtils.copyFile(new File(SETTINGS_DIR + "/bootstrap.min.js"), new File(DESTINATION_DIR + "/bootstrap.min.js")); FileUtils.copyFile(new File(settingsDir + "/bootstrap.min.js"), new File(destinationDir + "/bootstrap.min.js"));
FileUtils.copyFile(new File(SETTINGS_DIR + "/jquery.min.js"), new File(DESTINATION_DIR + "/jquery.min.js")); FileUtils.copyFile(new File(settingsDir + "/jquery.min.js"), new File(destinationDir + "/jquery.min.js"));
// print the Version number // 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: */ /* You should do this ONLY ONCE in the whole application life-cycle: */
Configuration cfg = new Configuration(); Configuration cfg = new Configuration();
// Specify the data source where the template files come from. // 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... // Specify how templates will see the data-model. This is an advanced topic...
cfg.setObjectWrapper(new DefaultObjectWrapper()); cfg.setObjectWrapper(new DefaultObjectWrapper());
@ -222,7 +239,7 @@ public class GATKDoclet {
processIndex(cfg, new ArrayList<GATKDocWorkUnit>(myWorkUnits)); processIndex(cfg, new ArrayList<GATKDocWorkUnit>(myWorkUnits));
File forumKeyFile = new File(FORUM_KEY_FILE); File forumKeyFile = new File(forumKeyPath);
if (forumKeyFile.exists()) { if (forumKeyFile.exists()) {
String forumKey = null; String forumKey = null;
// Read in a one-line file so we can do a for loop // 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"); Template temp = cfg.getTemplate("generic.index.template.html");
/* Merge data-model with template */ /* 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 { try {
temp.process(groupIndexData(indexData), out); temp.process(groupIndexData(indexData), out);
out.flush(); out.flush();
@ -497,7 +514,7 @@ public class GATKDoclet {
Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc)); Template temp = cfg.getTemplate(unit.handler.getTemplateName(unit.classDoc));
// Merge data-model with template // Merge data-model with template
File outputPath = new File(DESTINATION_DIR + "/" + unit.filename); File outputPath = new File(destinationDir + "/" + unit.filename);
try { try {
Writer out = new OutputStreamWriter(new FileOutputStream(outputPath)); Writer out = new OutputStreamWriter(new FileOutputStream(outputPath));
temp.process(unit.forTemplate, out); temp.process(unit.forTemplate, out);