diff --git a/ivy.xml b/ivy.xml index a96567889..b197d0714 100644 --- a/ivy.xml +++ b/ivy.xml @@ -23,89 +23,90 @@ --> - - - - - - - - - - - + + + + + + + + + + + - - + + - - - - - - + + + + + + - - + + - - + + - - + + - - - - - - - - - - + + - - + + + + + + + - - + + - - + + - - + + - - - + + - - - - + + + - - - + + + + - - - + + + - - + + + - - + + - - + + - - - - - + + + + + + + + + diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java index b4e07716c..4ec2ac6d7 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java @@ -28,7 +28,7 @@ public class GATKDocUtils { /** * The URL root for RELEASED GATKDOC units */ - public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/"; + public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gatk/gatkdocs/"; /** * The URL root for STABLE GATKDOC units */ diff --git a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java index f40675a43..28bf2e158 100644 --- a/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java +++ b/public/java/src/org/broadinstitute/sting/utils/help/GATKDoclet.java @@ -41,12 +41,16 @@ import org.broadinstitute.sting.gatk.CommandLineGATK; import org.broadinstitute.sting.gatk.walkers.qc.DocumentationTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; +import org.broadinstitute.sting.utils.text.XReadLines; import java.io.*; import java.lang.annotation.Annotation; +<<<<<<< HEAD import java.net.HttpURLConnection; import java.net.MalformedURLException; import java.net.URL; +======= +>>>>>>> Added the ability to update the Forum import java.util.*; /** @@ -82,6 +86,7 @@ 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"; // ---------------------------------------------------------------------- // // Global variables that are set on the command line by javadoc @@ -142,7 +147,7 @@ public class GATKDoclet { 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; @@ -151,6 +156,7 @@ public class GATKDoclet { // process the docs new GATKDoclet().processDocs(rootDoc); + return true; } @@ -216,6 +222,15 @@ public class GATKDoclet { } processIndex(cfg, new ArrayList(myWorkUnits)); + + File forumKeyFile = new File(FORUM_KEY_FILE); + if (forumKeyFile.exists()) { + String forumKey = null; + // Read ing a one-line file so we can do a for loop + for (String line : new XReadLines(forumKeyFile)) + forumKey = line; + updateForum(myWorkUnits, forumKey); + } } catch (FileNotFoundException e) { throw new RuntimeException(e); } catch (IOException e) { @@ -223,6 +238,31 @@ public class GATKDoclet { } } + private void updateForum(Set docWorkUnits, String forumKey) { + //first get list of posts that need to be added + List old = ForumAPIUtils.getPostedTools(forumKey); + + for (String s : old) + System.out.println(s); + + System.out.printf("Forum has %d items%n", old.size()); + System.out.printf("Docs have %d items%n", docWorkUnits.size()); + + List toAdd = new ArrayList(); + for (GATKDocWorkUnit tool : docWorkUnits) { + if (!old.contains(tool.name)) { + System.out.println("WILL POST: " + tool.name + " TO FORUM"); + toAdd.add(tool); + } + } + + //update using list + for (GATKDocWorkUnit tool : toAdd) { + //if ( tool.name.equals("ApplyRecalibration") ) + ForumAPIUtils.postToForum(tool, forumKey); + } + } + private void processCategories(Map>> getCategories, Set classes) throws IOException { List categories = new LinkedList(); for (Category cat : getCategories.keySet()) { @@ -248,7 +288,6 @@ public class GATKDoclet { posts.add(properties); } - writeJson(DESTINATION_DIR + "/posts.json", posts); } private void writeJson(String filename, Object source) throws IOException { @@ -261,40 +300,6 @@ public class GATKDoclet { } - public static void postRestJson(String URL, String json) { - try { - URL url = new URL(URL); - HttpURLConnection conn = (HttpURLConnection) url.openConnection(); - conn.setDoOutput(true); - conn.setRequestMethod("POST"); - conn.setRequestProperty("Content-Type", "application/json"); - - OutputStream os = conn.getOutputStream(); - os.write(json.getBytes()); - os.flush(); - - if (conn.getResponseCode() != HttpURLConnection.HTTP_CREATED) { - throw new RuntimeException("Failed : HTTP error code : " - + conn.getResponseCode()); - } - - BufferedReader br = new BufferedReader(new InputStreamReader( - (conn.getInputStream()))); - - String output; - System.out.println("Output from Server .... \n"); - while ((output = br.readLine()) != null) { - System.out.println(output); - } - - conn.disconnect(); - } catch (MalformedURLException e) { - e.printStackTrace(); - } catch (IOException e) { - e.printStackTrace(); - } - } - /** * Returns the set of all GATKDocWorkUnits that we are going to generate docs for. * diff --git a/settings/helpTemplates/bootstrap.min.css b/settings/helpTemplates/bootstrap.min.css index a4b669001..34d1df853 100755 --- a/settings/helpTemplates/bootstrap.min.css +++ b/settings/helpTemplates/bootstrap.min.css @@ -724,4 +724,4 @@ button.close{padding:0;cursor:pointer;background:transparent;border:0;-webkit-ap .visible-phone{display:none !important;} .visible-tablet{display:none !important;} .hidden-desktop{display:none !important;} -@media 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.offset12{margin-left:1230px;} .offset11{margin-left:1130px;} .offset10{margin-left:1030px;} .offset9{margin-left:930px;} .offset8{margin-left:830px;} .offset7{margin-left:730px;} .offset6{margin-left:630px;} .offset5{margin-left:530px;} .offset4{margin-left:430px;} .offset3{margin-left:330px;} .offset2{margin-left:230px;} .offset1{margin-left:130px;} .row-fluid{width:100%;*zoom:1;}.row-fluid:before,.row-fluid:after{display:table;content:"";} .row-fluid:after{clear:both;} .row-fluid [class*="span"]{display:block;width:100%;min-height:28px;-webkit-box-sizing:border-box;-moz-box-sizing:border-box;-ms-box-sizing:border-box;box-sizing:border-box;float:left;margin-left:2.564102564%;*margin-left:2.510911074638298%;} .row-fluid [class*="span"]:first-child{margin-left:0;} .row-fluid .span12{width:100%;*width:99.94680851063829%;} .row-fluid .span11{width:91.45299145300001%;*width:91.3997999636383%;} .row-fluid .span10{width:82.905982906%;*width:82.8527914166383%;} .row-fluid 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.nav{float:none;margin:0 0 9px;} .nav-collapse .nav>li{float:none;} .nav-collapse .nav>li>a{margin-bottom:2px;} .nav-collapse .nav>.divider-vertical{display:none;} .nav-collapse .nav .nav-header{color:#999999;text-shadow:none;} .nav-collapse .nav>li>a,.nav-collapse .dropdown-menu a{padding:6px 15px;font-weight:bold;color:#999999;-webkit-border-radius:3px;-moz-border-radius:3px;border-radius:3px;} .nav-collapse .btn{padding:4px 10px 4px;font-weight:normal;-webkit-border-radius:4px;-moz-border-radius:4px;border-radius:4px;} .nav-collapse .dropdown-menu li+li a{margin-bottom:2px;} .nav-collapse .nav>li>a:hover,.nav-collapse .dropdown-menu a:hover{background-color:#222222;} .nav-collapse.in .btn-group{margin-top:5px;padding:0;} .nav-collapse .dropdown-menu{position:static;top:auto;left:auto;float:none;display:block;max-width:none;margin:0 15px;padding:0;background-color:transparent;border:none;-webkit-border-radius:0;-moz-border-radius:0;border-radius:0;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;} .nav-collapse .dropdown-menu:before,.nav-collapse .dropdown-menu:after{display:none;} .nav-collapse .dropdown-menu .divider{display:none;} .nav-collapse .navbar-form,.nav-collapse .navbar-search{float:none;padding:9px 15px;margin:9px 0;border-top:1px solid #222222;border-bottom:1px solid #222222;-webkit-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1);-moz-box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1);box-shadow:inset 0 1px 0 rgba(255,255,255,.1), 0 1px 0 rgba(255,255,255,.1);} .navbar .nav-collapse .nav.pull-right{float:none;margin-left:0;} .nav-collapse,.nav-collapse.collapse{overflow:hidden;height:0;} .navbar .btn-navbar{display:block;} .navbar-static .navbar-inner{padding-left:10px;padding-right:10px;}}@media (min-width:980px){.nav-collapse.collapse{height:auto !important;overflow:visible !important;}} \ No newline at end of file diff --git a/settings/helpTemplates/common.html b/settings/helpTemplates/common.html index a753b9ded..4561f6576 100644 --- a/settings/helpTemplates/common.html +++ b/settings/helpTemplates/common.html @@ -71,17 +71,8 @@
<#if isIndex> -
- -
-
+ +
diff --git a/settings/helpTemplates/generic.index.template.html b/settings/helpTemplates/generic.index.template.html index d092ec5a0..887a3908a 100644 --- a/settings/helpTemplates/generic.index.template.html +++ b/settings/helpTemplates/generic.index.template.html @@ -1,3 +1,27 @@ + + <#include "common.html"/> <#macro emitGroup group> @@ -40,7 +64,8 @@ <@makeHeader title="GATK documentation index" isIndex=true />

GATK documentation index -${version}

+ ${version} +
<#list groups?sort_by("name") as group> <@emitGroup group=group/> diff --git a/settings/helpTemplates/generic.template.html b/settings/helpTemplates/generic.template.html index 7d02fa865..b9be9e344 100644 --- a/settings/helpTemplates/generic.template.html +++ b/settings/helpTemplates/generic.template.html @@ -1,3 +1,27 @@ + + <#include "common.html"/> <#macro argumentlist name myargs> @@ -13,8 +37,7 @@ ${arg.summary} <#-- - < - td>${arg.required} + ${arg.required} -->