From 45c73ff0e59da0ddef03c4b7b500ebd037995c04 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Wed, 20 Jul 2011 17:16:33 -0400
Subject: [PATCH] Runs and emits an HTML document

---
 ivy.xml                                       |  3 +
 .../sting/utils/help/GATKDoclet.java          | 94 +++++++++++++++++++
 .../help/ResourceBundleExtractorDoclet.java   |  2 -
 3 files changed, 97 insertions(+), 2 deletions(-)
 create mode 100644 public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java

diff --git a/ivy.xml b/ivy.xml
index 3f3d1c97f..a394aa6d7 100644
--- a/ivy.xml
+++ b/ivy.xml
@@ -30,6 +30,9 @@
 
     <!-- Dependencies for the graph aligner -->  
     <dependency org="org.jgrapht" name="jgrapht-jdk1.5" rev="0.7.3"/>
+
+    <!-- Dependencies for the html walker documention -->  
+    <dependency org="org.freemarker" name="freemarker" rev="2.3.18"/>
      
     <!-- Commons Dependencies -->  
     <dependency org="org.apache.commons" name="commons-email" rev="1.2"/>
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
new file mode 100644
index 000000000..d73c3d6fc
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java
@@ -0,0 +1,94 @@
+/*
+ * Copyright (c) 2011, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.help;
+
+import com.sun.javadoc.*;
+import freemarker.template.Configuration;
+import freemarker.template.DefaultObjectWrapper;
+import freemarker.template.Template;
+import freemarker.template.TemplateException;
+import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+
+import java.io.*;
+import java.util.*;
+
+/**
+ *
+ */
+public class GATKDoclet {
+    /**
+     * Extracts the contents of certain types of javadoc and adds them to an XML file.
+     * @param rootDoc The documentation root.
+     * @return Whether the JavaDoc run succeeded.
+     * @throws java.io.IOException if output can't be written.
+     */
+    public static boolean start(RootDoc rootDoc) throws IOException {
+        /* ------------------------------------------------------------------- */
+        /* 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.
+        // Here I set a file directory for it:
+        cfg.setDirectoryForTemplateLoading(new File("settings/helpTemplates/"));
+        // Specify how templates will see the data-model. This is an advanced topic...
+        // but just use this:
+        cfg.setObjectWrapper(new DefaultObjectWrapper());
+
+
+        /* ------------------------------------------------------------------- */
+        /* You usually do these for many times in the application life-cycle:  */
+
+        /* Create a data-model */
+        // Create the root hash
+        Map root = new HashMap();
+        // Put string ``user'' into the root
+        root.put("user", "Mark DePristo");
+
+        /* Get or create a template */
+        Template temp = cfg.getTemplate("test.html");
+
+        /* Merge data-model with template */
+        Writer out = new OutputStreamWriter(System.out);
+        try {
+            temp.process(root, out);
+            out.flush();
+        } catch ( TemplateException e ) {
+            throw new ReviewedStingException("Failed to create GATK documentation", e);
+        }
+        return true;
+    }
+
+    /**
+     * Validate the given options against options supported by this doclet.
+     * @param option Option to validate.
+     * @return Number of potential parameters; 0 if not supported.
+     */
+    public static int optionLength(String option) {
+        return 0;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index 6ee12d42e..c0afcc338 100644
--- a/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/public/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -186,8 +186,6 @@ public class ResourceBundleExtractorDoclet {
      * @return True if the JavaDoc is missing.  False otherwise.
      */
     private static boolean isRequiredJavadocMissing(ClassDoc classDoc) {
-        if(classDoc.containingPackage().name().contains("oneoffprojects"))
-            return false;
         return classDoc.commentText().length() == 0 || classDoc.commentText().contains("Created by IntelliJ");
     }