obo-svn-commit — sends mail for all commits to svn repository

[Obo-svn-commit] SF.net SVN: obo: [76] phenote/trunk/src/java/phenote/config/Config.java

[<mg...@us...>]

Revision: 76
Author:   mgibson
Date:     2006-07-28 09:19:53 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=76&view=rev

Log Message:
-----------
in looking for configuration file from jar try prepending "/".
this works for jboss - but not for webstart? or at least webstart
doesnt require it
this is consisten with how the ontology data adapter searches the jar

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 15:39:39 UTC (rev 75)
+++ phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 16:19:53 UTC (rev 76)
@@ -188,7 +188,7 @@
     if (document == null) { // try jar file
       URL url = Config.class.getResource(filename);
       if (url == null)
-        System.out.println("failed to get file from jar");
+        System.out.println("failed to get file from jar without '/' prepend");
       else
         document = tryFile(builder,url.toString());
     }


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[Obo-svn-commit] SF.net SVN: obo: [73] phenote/trunk/build.xml

[<mg...@us...>]

Revision: 73
Author:   mgibson
Date:     2006-07-28 08:09:13 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=73&view=rev

Log Message:
-----------
war-clean option for deleting previous war file

Modified Paths:
--------------
    phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-07-28 15:07:22 UTC (rev 72)
+++ phenote/trunk/build.xml	2006-07-28 15:09:13 UTC (rev 73)
@@ -217,6 +217,10 @@
     </war>
   </target>
 
+  <target name="war-clean">
+    <delete file="war-deployment-link/phenote.war"/>
+  </target>
+
   <target name="war-no-jar-depend">
     <delete file="war-deployment-link/phenote.war"/>
     <war destfile="war-deployment-link/phenote.war" webxml="src/web/web.xml">


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[Obo-svn-commit] SF.net SVN: obo: [78] phenote/trunk/src/java/phenote/util

[<mg...@us...>]

Revision: 78
Author:   mgibson
Date:     2006-07-28 11:31:33 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=78&view=rev

Log Message:
-----------
made term info terms clickable on web with sohels onClick example - 
done differently in standalone so html util is told of context
maybe html tuli should be an object rather static class?

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
    phenote/trunk/src/java/phenote/util/HtmlUtil.java
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-28 16:21:27 UTC (rev 77)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-28 18:31:33 UTC (rev 78)
@@ -30,6 +30,8 @@
   public void init() throws ServletException {
     initDate = new Date();
     super.init();
+    // makes links for term info - put this method in Phenote?
+    HtmlUtil.setStandAlone(false);
     phenote = Phenote.getPhenote();
     // cheesy - revisit
     String[] args = {"-c","initial-zfin.cfg"};
@@ -112,7 +114,7 @@
         return;
       }
       System.out.println("term info "+HtmlUtil.termInfo(oboClass));
-      out.println(HtmlUtil.termInfo(oboClass));
+      out.println(HtmlUtil.termInfo(oboClass,ontologyName));
     }
   }
 

Modified: phenote/trunk/src/java/phenote/util/HtmlUtil.java
===================================================================
--- phenote/trunk/src/java/phenote/util/HtmlUtil.java	2006-07-28 16:21:27 UTC (rev 77)
+++ phenote/trunk/src/java/phenote/util/HtmlUtil.java	2006-07-28 18:31:33 UTC (rev 78)
@@ -15,6 +15,16 @@
   public static final boolean DO_HTML = true; // take out
   static final String PHENOTE_LINK_PREFIX = "Phenote?id=";
 
+//   /** hmmmm - this is state - should probably do an object? 
+//    should this be somewhere else? gui.Phenote? */
+  private static boolean isStandAlone = true;
+  private static String ontologyName;
+
+  /** Stand alone and web app do different things for term links */
+  public static void setStandAlone(boolean standAlone) {
+    isStandAlone = standAlone;
+  }
+
   public static String termInfo(OBOClass oboClass) {
     if (oboClass == null) {
       System.out.println("null obo class for HtmlUtil.termInfo");
@@ -42,6 +52,20 @@
     return sb.toString();
   }
 
+  public static String termInfo(OBOClass oboClass, String ontology) {
+    // funny - revisit for sure - either should pass through all methods
+    // or util should actually be an object - singleton? i think maybe its
+    // an object???
+    setOntologyName(ontology);
+    return termInfo(oboClass);
+  }
+
+  private static void setOntologyName(String ont) {
+    ontologyName = ont;
+  }
+
+  private static String getOntologyName() { return ontologyName; }
+
   /** Only works in html mode - do with string buffers? */
   private static String bold(String text) {
     if (!DO_HTML) return text;
@@ -117,9 +141,23 @@
   }
 
   private static String termLink(LinkedObject term) {
-    return "<a href='"+makePhenoIdLink(term.getID())+"'>"+term.getName()+"</a>";
+    String clickString = getClickString(term.getID());
+    return "<a "+clickString+">"+term.getName()+"</a>";
   }
 
+  private static String getClickString(String id) {
+    if (isStandAlone)
+      return "href='"+makePhenoIdLink(id)+"'";
+    else
+      return "href=# "+onClickJavaScript(id);
+  }
+
+  //<A href='#' onClick='getTermInfo(".$_->term_id.")'>
+  private static String onClickJavaScript(String id) {
+    // need ontology name????
+    return " onClick='getTermInfo(\""+id+"\",\""+getOntologyName()+"\")' ";
+  }
+
   /** used internally & by TestPhenote */
   public static String makePhenoIdLink(String id) {
     return PHENOTE_LINK_PREFIX + id;


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[Obo-svn-commit] SF.net SVN: obo: [71] phenote/trunk/src/web/html/ncbo.html

[<mg...@us...>]

Revision: 71
Author:   mgibson
Date:     2006-07-28 08:02:25 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=71&view=rev

Log Message:
-----------
servlet/Phenote -> phenote/Phenote for war

Modified Paths:
--------------
    phenote/trunk/src/web/html/ncbo.html
Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-28 14:47:43 UTC (rev 70)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-28 15:02:25 UTC (rev 71)
@@ -96,7 +96,7 @@
    <!--   'ontologyname_auto_complete', '/phenote-ontology.cgi',{  }) -->
    <!-- new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/PhenoteStub',{  }) -->
    <!--  new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/phenote.servlet.PhenoteServlet',{  }) -->
-      var complete = new Ajax.Autocompleter( 'patoInput', 'pato_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=pato'   })
+      var complete = new Ajax.Autocompleter( 'patoInput', 'pato_auto_complete', '/phenote/Phenote',{parameters:'ontologyName=pato'   })
       <!-- complete.options.defaultParams = "ontology=pato"; -->
       <!--   complete.options.parameters = "ontology=pato"; -->
       <!-- more params? 'ontology=pato&x=y&...' -->


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[Obo-svn-commit] SF.net SVN: obo: [75] phenote/trunk/src/java/phenote/config/Config.java

[<mg...@us...>]

Revision: 75
Author:   mgibson
Date:     2006-07-28 08:39:39 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=75&view=rev

Log Message:
-----------
in looking for configuration file from jar try prepending "/". 
this works for jboss - but not for webstart? or at least webstart
doesnt require it
this is consisten with how the ontology data adapter searches the jar

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 15:19:25 UTC (rev 74)
+++ phenote/trunk/src/java/phenote/config/Config.java	2006-07-28 15:39:39 UTC (rev 75)
@@ -192,7 +192,19 @@
       else
         document = tryFile(builder,url.toString());
     }
+    // hmmmm - so ontology data adapter prepends "/" for jar file but above
+    // doesnt (which seems to work for web start but not jboss) try with 
+    // prepended slash as well - what the heck
+    // its true this works for jboss - above for webstart - very strange
     if (document == null) {
+      URL url = Config.class.getResource("/"+filename);
+      if (url == null)
+        System.out.println("failed to get file from jar with '/' prepend");
+      else
+        document = tryFile(builder,url.toString());
+    }
+
+    if (document == null) {
       System.out.println("Failed to find config file "+filename);
       throw new FileNotFoundException(filename);
     }


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[Obo-svn-commit] SF.net SVN: obo: [74] phenote/trunk/src/web/javascript

[<mg...@us...>]

Revision: 74
Author:   mgibson
Date:     2006-07-28 08:19:25 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=74&view=rev

Log Message:
-----------
/servlet/Phenote -> /phenote/Phenote for jboss war file

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
    phenote/trunk/src/web/javascript/ncbo-term-info.js
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-28 15:09:13 UTC (rev 73)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-28 15:19:25 UTC (rev 74)
@@ -160,7 +160,7 @@
   private String makeCompListHtmlItem(OBOClass term,String ontol) {
     String id = "'"+term.getID()+"'";
     return "<li onmouseover=\"getTermInfo("+id+",'"+ontol+"')\" id="+id+" "+
-      "onclick=\"set_ontology("+id+")\">"+term.getName()+"</li>\n";
+      "onclick=\"getTermInfo("+id+")\">"+term.getName()+"</li>\n";
   }
 
   /** for now search params hard wired - eventually from buttons on web page */

Modified: phenote/trunk/src/web/javascript/ncbo-term-info.js
===================================================================
--- phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-28 15:09:13 UTC (rev 73)
+++ phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-28 15:19:25 UTC (rev 74)
@@ -6,7 +6,8 @@
 // term info not yet implemented in PhenoteServlet - todo...
 // this should be a relative link - need to get servlets code in/close with scripts?
 //var url = '/servlet/PhenoteStub'; 
-var url = '/servlet/Phenote';
+//var url = '/servlet/Phenote'; // tomcat - not jboss
+var url = '/phenote/Phenote'; // jboss
       
 
 // getTermInfo should be called by the above url (at least for dichty it does)


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[Obo-svn-commit] SF.net SVN: obo: [70] phenote/trunk/src/web/html/ncbo.html

[<mg...@us...>]

Revision: 70
Author:   mgibson
Date:     2006-07-28 07:47:43 -0700 (Fri, 28 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=70&view=rev

Log Message:
-----------
servlet/Phenote -> phenote/Phenote to fit with phenote.war file -
otherwise war file would have to be called servlet.war which is vague

Modified Paths:
--------------
    phenote/trunk/src/web/html/ncbo.html
Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-27 20:26:00 UTC (rev 69)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-28 14:47:43 UTC (rev 70)
@@ -103,7 +103,7 @@
    </script>
 
    <script type="text/javascript">
-     new Ajax.Autocompleter( 'entityInput', 'entity_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=anatomy'})
+     new Ajax.Autocompleter( 'entityInput', 'entity_auto_complete', '/phenote/Phenote',{parameters:'ontologyName=anatomy'})
    </script>
 
 


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[Obo-svn-commit] SF.net SVN: obo: [66] phenote/trunk/src/web/css

[<mg...@us...>]

Revision: 66
Author:   mgibson
Date:     2006-07-25 15:01:06 -0700 (Tue, 25 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=66&view=rev

Log Message:
-----------
i got hip to css and html layout - needed to do layout with new fields
need to merge files with dichty - things are driftoing - but at the
moment im in a rush to get something up for zfin meeting

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
    phenote/trunk/src/web/css/control.css
    phenote/trunk/src/web/html/ncbo.html
    phenote/trunk/src/web/javascript/ncbo-term-info.js
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-25 19:07:46 UTC (rev 65)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-25 22:01:06 UTC (rev 66)
@@ -31,7 +31,9 @@
     initDate = new Date();
     super.init();
     phenote = Phenote.getPhenote();
-    phenote.initConfig(null); // no args for now, use default config file
+    // cheesy - revisit
+    String[] args = {"-c","initial-zfin.cfg"};
+    phenote.initConfig(args); // hardwire for now to zfin
     phenote.initOntologies();
   }
 
@@ -73,7 +75,10 @@
 
   /** this should be renamed from unintuitive "ontologyname" */
   private String getTermCompletionParam(HttpServletRequest req) {
-    return req.getParameter("patoInput");
+    String par = req.getParameter("patoInput"); // for now
+    if (par == null)
+      par = req.getParameter("entityInput");
+    return par;
   }
 
   private String getOntologyParamString(HttpServletRequest req) {

Modified: phenote/trunk/src/web/css/control.css
===================================================================
--- phenote/trunk/src/web/css/control.css	2006-07-25 19:07:46 UTC (rev 65)
+++ phenote/trunk/src/web/css/control.css	2006-07-25 22:01:06 UTC (rev 66)
@@ -6,7 +6,8 @@
       border: 1px solid gray;
       padding: 2px 2px 2px 2px;
       float: left;
-      width: 630;
+      width: 300;
+      margin: 5px;
    }
 
    div#ontologyinfo {
@@ -16,7 +17,7 @@
      float: left;
    }
 
-   /* div returned from ajax record retreival */
+   /* div returned from ajax record retreival ---> termInfo delete*/
    div#ontologyinfo table {
      border: 1px solid blue;
      width: 100%;
@@ -24,6 +25,28 @@
      background-color: lightgoldenrodyellow;
      height: 100%;
    }
+
+   div#termInfo {
+     float: left;
+     width: 375;
+     height: 180;
+     float: left;
+     border: 1px solid gray;
+     padding: 2px 2px 2px 2px;
+     margin: 5px;
+   }
+
+   /* div returned from ajax record retreival */
+   div#termInfo table {
+     border: 1px solid blue;
+     width: 100%;
+     font-size: 14px;
+     background-color: lightgoldenrodyellow;
+     height: 100%;
+   }
+
+   
+
    div#ontologyinfo td.label {
      font-weight: bold;
    }
@@ -45,7 +68,7 @@
       font-weight:bold;
    }
    fieldset.search {
-      width: 250;
+      width: 150;
    }
 
 

Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-25 19:07:46 UTC (rev 65)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-25 22:01:06 UTC (rev 66)
@@ -25,18 +25,51 @@
 </HEAD>
 <BODY>
 
-<table>
-<tr height="20%"><td>
+<!-- table width="50%" -->
 
-<form>
-   <div id="ontology">
-      <div style="float: left;">
+<!-- tr height="20%" -->
 
+<!-- td width="20%" -->
+
+<form width="20%">
+   <div id="ontology" width="20%">
+
+     <!-- table width="20%" -->
+     <!-- tr -->
+     <!-- td -->
+
+      <!-- ENTITY -->
+
+      <!-- div style="float: left;" -->
+      <div  style="float: left;" width="20%">
+
          <fieldset class="search">
-            Search terms in PATO ontology<br/><br/><br/>
-            <label>Name:</label>
+            <br/><br/><br/>
+            <label>Entity: </label>
 
             <!-- input autocomplete="off" id="ontologyname" name="ontologyname" size="20" type="text" value="" / -->
+            <input autocomplete="off" id="entityInput" name="entityInput" size="20" type="text" value="" />
+            </br>
+            <div class="auto_complete" id="entity_auto_complete"></div>
+         </fieldset>
+
+      </div>
+
+      <!-- /td -->
+      <!-- /tr -->
+      <!-- tr -- -->
+      <!-- td -->
+
+      <!-- PATO -->
+
+      <div style="clear: left;">
+      <!-- div width="20%" -->
+
+         <fieldset class="search">
+            <br/><br/><br/>
+            <label>PATO: </label>
+
+            <!-- input autocomplete="off" id="ontologyname" name="ontologyname" size="20" type="text" value="" / -->
             <input autocomplete="off" id="patoInput" name="patoInput" size="20" type="text" value="" />
             </br>
             <div class="auto_complete" id="pato_auto_complete"></div>
@@ -44,42 +77,54 @@
 
       </div>
 
-      <div id="ontologyinfo"></div>
+      <!-- /td -->
+      <!-- /tr -->
+      <!-- /table -->
+
+
    </div>
 
 
+
    <script type="text/javascript">
-   <!-- this is the crucial javascript bit here, ontologyname is the -->
-   <!-- input field, i think ontologyname_auto_complete is the div where-->
+   <!-- this is the crucial javascript bit here, patoInput is the -->
+   <!-- input field, i pato_auto_complete is the div where-->
    <!--the auto completion will pop up, and the last param is the-->
    <!--    script that will does the fetching of terms -->
    <!-- Autocomp is in js/prototype/controls.js -->
-
    <!--   new Ajax.Autocompleter( 'ontologyname', -->
    <!--   'ontologyname_auto_complete', '/phenote-ontology.cgi',{  }) -->
    <!-- new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/PhenoteStub',{  }) -->
    <!--  new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/phenote.servlet.PhenoteServlet',{  }) -->
-        var complete = new Ajax.Autocompleter( 'patoInput', 'pato_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=pato&aa=bb'   })
-        
-        <!-- complete.options.defaultParams = "ontology=pato"; -->
-        <!--   complete.options.parameters = "ontology=pato"; -->
+      var complete = new Ajax.Autocompleter( 'patoInput', 'pato_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=pato'   })
+      <!-- complete.options.defaultParams = "ontology=pato"; -->
+      <!--   complete.options.parameters = "ontology=pato"; -->
+      <!-- more params? 'ontology=pato&x=y&...' -->
+   </script>
 
-        <!-- more params? 'ontology=pato&x=y&...' -->
-
+   <script type="text/javascript">
+     new Ajax.Autocompleter( 'entityInput', 'entity_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=anatomy'})
    </script>
 
-   <!-- this is set by ncbo-term-info.js but its unclear what its for -->
+
+
+   <!-- this is set by ncbo-term-info.js but its unclear what its for is this the datamodel???? -->
    <input type="hidden" name="ontologyid">
 </form>
  
+<!-- /td -->
 
+<!-- td width="80%" -->
+      <div id="termInfo"></div>
+<!-- /td -->
 
 
-</td>
-</tr>
-<tr height="80%"><td>&nbsp;</td></tr>
-</table>
 
+<!-- /td -->
+<!-- /tr -->
+<!-- tr height="80%" --><!-- td -->&nbsp;<!-- /td --></tr -->
+<!-- /table -->
+
 </body>
 </html>
 

Modified: phenote/trunk/src/web/javascript/ncbo-term-info.js
===================================================================
--- phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-25 19:07:46 UTC (rev 65)
+++ phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-25 22:01:06 UTC (rev 66)
@@ -32,7 +32,7 @@
 
             // ontologyinfo is the div where the table goes for term info
             // note: this is a "get" not a post! (term comp is post)
-            var myAjax = new Ajax.Updater('ontologyinfo', url, {method: 'get', parameters: pars, onComplete: document.forms[0].patoInput.value = '' } );
+            var myAjax = new Ajax.Updater('termInfo', url, {method: 'get', parameters: pars, onComplete: document.forms[0].patoInput.value = '' } );
            // have to have [1] next to form item because the edit subform and
            // the main form both have donorid elements
             if ( document.forms[0].ontologyid.length > 1 ) {


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[Obo-svn-commit] SF.net SVN: obo: [69] phenote/trunk/build.xml

[<mg...@us...>]

Revision: 69
Author:   mgibson
Date:     2006-07-27 13:26:00 -0700 (Thu, 27 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=69&view=rev

Log Message:
-----------
added a war-no-jar-depend ant target - that doesnt have a dependency
to creating a phenote jar and compiling - which isnt needed if you
already have an up to date jar

Modified Paths:
--------------
    phenote/trunk/build.xml
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-07-27 18:46:08 UTC (rev 68)
+++ phenote/trunk/build.xml	2006-07-27 20:26:00 UTC (rev 69)
@@ -217,6 +217,17 @@
     </war>
   </target>
 
+  <target name="war-no-jar-depend">
+    <war destfile="war-deployment-link/phenote.war" webxml="src/web/web.xml">
+      <fileset dir="src/web"/>
+      <lib dir="${lib}"/>
+      <classes dir="${classfiles}" />
+      <zipfileset dir="${obo}"/>  <!-- prefix="obo-files"/ ??? -->
+      <zipfileset dir="${conf}"/>
+    </war>
+  </target>
+  
+
 </project>
 
 


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[Obo-svn-commit] SF.net SVN: obo: [68] phenote/trunk

[<mg...@us...>]

Revision: 68
Author:   mgibson
Date:     2006-07-27 11:46:08 -0700 (Thu, 27 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=68&view=rev

Log Message:
-----------
ant war file creation task to ant for war files for jboss
also fixed compile so it doesnt compile test (whether it needs it or not)

Modified Paths:
--------------
    phenote/trunk/build.xml
    phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxCharList.java
Modified: phenote/trunk/build.xml
===================================================================
--- phenote/trunk/build.xml	2006-07-27 16:21:55 UTC (rev 67)
+++ phenote/trunk/build.xml	2006-07-27 18:46:08 UTC (rev 68)
@@ -52,7 +52,7 @@
   <!-- The compile target runs javac on all the java files, and saves
         them into  the classfiles directory. -->
   <target name="compile" depends="init">
-    <javac srcdir="${src}" destdir="${classfiles}" debug="yes">
+    <javac srcdir="${src}" destdir="${classfiles}" debug="yes" excludes="test/**">
       <classpath refid="project.classpath3"/>
     </javac>
   </target>
@@ -143,13 +143,15 @@
             <exclude name="${dist}/**"/>
             <exclude name="svn-phenote/**"/>
             <exclude name="tars/**"/>
-            <exclude name="source/obo-files/**"/>
             <exclude name="src/obo-files/**"/>
             <exclude name="*.tar"/>
             <exclude name="*.jar"/>
             <exclude name="garbage/**"/>
             <exclude name="oldjars/**"/>
-            <exclude name="source/**"/>
+            <exclude name="src/java/**"/>
+            <exclude name="web-classfiles/**"/>
+            <exclude name="web-interface/**"/>
+            <exclude name="web-deployment/**"/>
       </tarfileset>
     </tar>
     <gzip zipfile="tars/${dist}/phenote-${dist}.tar.gz" src="tars/${dist}/phenote-${dist}.tar"/>
@@ -162,7 +164,6 @@
             <exclude name="${dist}/**"/>
             <exclude name="svn-phenote/**"/>
             <exclude name="tars/**"/>
-            <exclude name="source/obo-files/**"/>
             <exclude name="src/obo-files/**"/>
             <!-- for now take out go as its 8.5M & not being used yet -->
             <exclude name="obo-files/gene_ontology.obo"/>
@@ -170,10 +171,12 @@
             <exclude name="*.jar"/>
             <exclude name="garbage/**"/>
             <exclude name="oldjars/**"/>
-            <exclude name="jars/phenote.jar"/>
-            <exclude name="source/**"/>
+            <!-- exclude name="jars/phenote.jar"/ -->
             <exclude name="doc/**"/>
             <exclude name="classfiles/**"/>
+            <exclude name="web-classfiles/**"/>
+            <exclude name="web-interface/**"/>
+            <exclude name="web-deployment/**"/>
       </tarfileset>
     </tar>
     <gzip zipfile="tars/${dist}/phenote-${dist}-src.tar.gz" src="tars/${dist}/phenote-${dist}-src.tar"/>
@@ -204,6 +207,16 @@
      </copy>
   </target> 
 
+  <target name="war" depends="jar">
+    <war destfile="war-deployment-link/phenote.war" webxml="src/web/web.xml">
+      <fileset dir="src/web"/>
+      <lib dir="${lib}"/>
+      <classes dir="${classfiles}" />
+      <zipfileset dir="${obo}"/>  <!-- prefix="obo-files"/ ??? -->
+      <zipfileset dir="${conf}"/>
+    </war>
+  </target>
+
 </project>
 
 

Modified: phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxCharList.java
===================================================================
--- phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxCharList.java	2006-07-27 16:21:55 UTC (rev 67)
+++ phenote/trunk/src/java/phenote/dataadapter/phenosyntax/PhenoSyntaxCharList.java	2006-07-27 18:46:08 UTC (rev 68)
@@ -3,3 +3,4 @@
 
 /** not sure if this is needed as separate class. a lit of PhenoSyntaxChar objects
     that wrap CharacterIs */
+class PhenoSyntaxCharList {}


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[Obo-svn-commit] SF.net SVN: obo: [67] phenote/trunk/src/web

[<mg...@us...>]

Revision: 67
Author:   mgibson
Date:     2006-07-27 09:21:55 -0700 (Thu, 27 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=67&view=rev

Log Message:
-----------
added web.xml for war file for jboss server

Modified Paths:
--------------
    phenote/trunk/src/web/html/ncbo.html

Added Paths:
-----------
    phenote/trunk/src/web/web.xml
Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-25 22:01:06 UTC (rev 66)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-27 16:21:55 UTC (rev 67)
@@ -2,7 +2,7 @@
 <HTML>
 <HEAD>
 
-<TITLE> Phenote Ajax Control (from sohel) </TITLE>
+<TITLE> Phenote </TITLE>
 
 <!-- we need some way of parameterizing the root of the web files??? --> 
 <!-- set in some file somewhere? -->

Added: phenote/trunk/src/web/web.xml
===================================================================
--- phenote/trunk/src/web/web.xml	                        (rev 0)
+++ phenote/trunk/src/web/web.xml	2006-07-27 16:21:55 UTC (rev 67)
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<!DOCTYPE web-app
+    PUBLIC "-//Sun Microsystems, Inc.//DTD Web Application 2.2//EN"
+    "http://java.sun.com/j2ee/dtds/web-app_2_2.dtd">
+
+<web-app>
+  <servlet>
+    <servlet-name>Phenote</servlet-name>
+    <servlet-class>phenote.servlet.PhenoteServlet</servlet-class>
+    <load-on-startup>1</load-on-startup>
+  </servlet>
+
+  <servlet-mapping>
+     <servlet-name>Phenote</servlet-name>
+     <url-pattern>/Phenote</url-pattern>
+  </servlet-mapping>
+</web-app>


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[Obo-svn-commit] SF.net SVN: obo: [65] phenote/trunk/src/web/css/control.css

[<mg...@us...>]

Revision: 65
Author:   mgibson
Date:     2006-07-25 12:07:46 -0700 (Tue, 25 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=65&view=rev

Log Message:
-----------
took out ctrl-M window new lines

Modified Paths:
--------------
    phenote/trunk/src/web/css/control.css
Modified: phenote/trunk/src/web/css/control.css
===================================================================
--- phenote/trunk/src/web/css/control.css	2006-07-24 22:41:19 UTC (rev 64)
+++ phenote/trunk/src/web/css/control.css	2006-07-25 19:07:46 UTC (rev 65)
@@ -1,76 +1,77 @@
-/*
-// dynamically populated div on this page that holds
-//  ontology info and  form
-*/
-   div#ontology{
-      border: 1px solid gray;
-      padding: 2px 2px 2px 2px;
-      float: left;
-      width: 630;
-   }
-
-   div#ontologyinfo {
-     float: left;
-     width: 375;
-     height: 100%;
-     float: left;
-   }
-
-   /* div returned from ajax record retreival */
-   div#ontologyinfo table {
-     border: 1px solid blue;
-     width: 100%;
-     font-size: 14px;
-     background-color: lightgoldenrodyellow;
-     height: 100%;
-   }
-   div#ontologyinfo td.label {
-     font-weight: bold;
-   }
-   div#ontologyinfo td.data {
-     width: 60%;    
-   }
-
-   fieldset {
-      border: none;
-      padding: 0;
-      font:80%/1 sans-serif;
-   }
-
-   label {
-      float:left;
-      width:25%;
-      margin-right:0.5em;
-      text-align:right;
-      font-weight:bold;
-   }
-   fieldset.search {
-      width: 250;
-   }
-
-
-
-/* generated by HTML::Prototype library */
-div.auto_complete {
-    width: 350px;
-    background: #fff;
-}
-div.auto_complete ul {
-    border:1px solid #888;
-    margin:0;
-    padding:0;
-    width:100%;
-    list-style-type:none;
-}
-div.auto_complete ul li {
-    margin:0;
-    padding:3px;
-}
-div.auto_complete ul li.selected {
-    background-color: #ffb;
-}
-div.auto_complete ul strong.highlight {
-    color: #800;
-    margin:0;
-    padding:0;
-}
+/*
+// dynamically populated div on this page that holds
+//  ontology info and  form
+*/
+   div#ontology{
+      border: 1px solid gray;
+      padding: 2px 2px 2px 2px;
+      float: left;
+      width: 630;
+   }
+
+   div#ontologyinfo {
+     float: left;
+     width: 375;
+     height: 100%;
+     float: left;
+   }
+
+   /* div returned from ajax record retreival */
+   div#ontologyinfo table {
+     border: 1px solid blue;
+     width: 100%;
+     font-size: 14px;
+     background-color: lightgoldenrodyellow;
+     height: 100%;
+   }
+   div#ontologyinfo td.label {
+     font-weight: bold;
+   }
+   div#ontologyinfo td.data {
+     width: 60%;    
+   }
+
+   fieldset {
+      border: none;
+      padding: 0;
+      font:80%/1 sans-serif;
+   }
+
+   label {
+      float:left;
+      width:25%;
+      margin-right:0.5em;
+      text-align:right;
+      font-weight:bold;
+   }
+   fieldset.search {
+      width: 250;
+   }
+
+
+
+/* generated by HTML::Prototype library */
+div.auto_complete {
+    width: 350px;
+    background: #fff;
+}
+div.auto_complete ul {
+    border:1px solid #888;
+    margin:0;
+    padding:0;
+    width:100%;
+    list-style-type:none;
+}
+div.auto_complete ul li {
+    margin:0;
+    padding:3px;
+}
+div.auto_complete ul li.selected {
+    background-color: #ffb;
+}
+div.auto_complete ul strong.highlight {
+    color: #800;
+    margin:0;
+    padding:0;
+}
+


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[Obo-svn-commit] SF.net SVN: obo: [64] phenote/trunk/src/web/html

[<mg...@us...>]

Revision: 64
Author:   mgibson
Date:     2006-07-24 15:41:19 -0700 (Mon, 24 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=64&view=rev

Log Message:
-----------
now passing ontology name with term id for what ontology to actually
query - this will allow for multiple ontologies, multiple fields

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/config/Config.java
    phenote/trunk/src/java/phenote/datamodel/CharField.java
    phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
    phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
    phenote/trunk/src/web/html/ncbo.html
    phenote/trunk/src/web/javascript/ncbo-term-info.js
Modified: phenote/trunk/src/java/phenote/config/Config.java
===================================================================
--- phenote/trunk/src/java/phenote/config/Config.java	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/java/phenote/config/Config.java	2006-07-24 22:41:19 UTC (rev 64)
@@ -276,8 +276,6 @@
 
     String file = getFileAttribute(node);
 
-    // see if theres mutliple ontologies specified as ontology elements
-    //if (file == null) 
     OntologyConfig oc = new OntologyConfig(name,file);
     return oc;
   }

Modified: phenote/trunk/src/java/phenote/datamodel/CharField.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/CharField.java	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/java/phenote/datamodel/CharField.java	2006-07-24 22:41:19 UTC (rev 64)
@@ -51,7 +51,17 @@
     public String toString() { return name; }
     public abstract void setValue(CharacterI c, CharFieldValue v);
     public abstract CharFieldValue getValue(CharacterI c);
-    // is this getting silly? abstract?
+
+    // uncler if we need this???
+//     public CharFieldEnum getCharFieldEnum(String fieldString) {
+//       for ( CharFieldEnum cfe : CharFieldEnum.values()) {
+//         if (cfe.name.equalsIgnoreCase(fieldString))
+//           return cfe;
+//       }
+//       System.out.println("ERROR: No Char Field found for string "+fieldString);
+//       return null;
+//     }
+    // is this getting silly? abstract? --> char field value i think
     //public void setOboClass(CharacterI c, OBOClass o) {}
     //public OBOClass getOBOClass(CharacterI c) { return null; }
   };
@@ -113,6 +123,19 @@
     if (!hasOntologies()) return 0;
     return ontologyList.size();
   }
+
+  public boolean hasOntology(String ontologyName) {
+    return getOntologyForName(ontologyName) != null;
+  }
+
+  /** Returns Ontology with name ontologyName, null if dont have it */
+  public Ontology getOntologyForName(String ontologyName) {
+    for (Ontology o : getOntologyList()) {
+      if (o.getName().equalsIgnoreCase(ontologyName))
+        return o;
+    }
+    return null;
+  }
 }
 
 

Modified: phenote/trunk/src/java/phenote/datamodel/OntologyManager.java
===================================================================
--- phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/java/phenote/datamodel/OntologyManager.java	2006-07-24 22:41:19 UTC (rev 64)
@@ -27,6 +27,8 @@
   private List<Ontology> allOntologyList = new ArrayList<Ontology>();
   private Ontology geneticContextOntology;
   //private Map<CharFieldEnum,List<Ontology>> fieldToOntologyList;
+  /** CharFields generically hold one or more ontologies - i think above 
+   hardwired fields are pase - or at least should be */
   private List<CharField> charFieldList = new ArrayList<CharField>(6);
 
 
@@ -129,6 +131,16 @@
       has one or more ontologies (entity char field often has more than ontology)*/
   public List<CharField> getCharFieldList() { return charFieldList; }
 
+  /** Returns ontology with name, null if not found */
+  public static Ontology getOntologyForName(String ontologyName) { // static?
+    for (CharField cf : inst().getCharFieldList()) {
+      if (cf.hasOntology(ontologyName))
+        return cf.getOntologyForName(ontologyName);
+    }
+    System.out.println("ERROR: no ontology found for name "+ontologyName);
+    return null;
+  }
+
   // for now i know that only genetic context is in char field list...
   public CharField getGeneticContextCharField() {
     if (charFieldList == null || charFieldList.isEmpty())

Modified: phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-24 22:41:19 UTC (rev 64)
@@ -50,7 +50,7 @@
 
     if (isTermCompletionRequest(request)) {
       String userInput = getTermCompletionParam(request);
-      System.out.println("ontology? "+getOntologyParamString(request));
+      System.out.println("ontology? "+getOntologyParamString(request)+" param aa? "+request.getParameter("aa"));
 //ResourceBundle r=ResourceBundle.getBundle("LocalStrings",request.getLocale());
       //Content-Type: text/html; charset=ISO-8859-1
       response.setContentType("text/html");
@@ -59,8 +59,9 @@
 //         "onclick=\"set_ontology()\">"+userInput+"</li>\n"+
 //         "<li onmouseover=\"set_ontology()\" id=\"termId\" onclick=\"set_ontology()\">"+
 //         "test</li>\n<li onmouseover=\"set_ontology()\" id=\"termId\" onclick=\"set_ontology()\">dude</li></ul>";
-      String list = getCompletionList(userInput);
-      System.out.println("printing to response writer: "+list.substring(0,45)+"...");
+      String ontol = getOntologyParamString(request);
+      String list = getCompletionList(userInput,ontol);
+      System.out.println("printing to response writer: "+list.substring(0,85)+"...");
       out.println(list);
     }
         
@@ -72,11 +73,11 @@
 
   /** this should be renamed from unintuitive "ontologyname" */
   private String getTermCompletionParam(HttpServletRequest req) {
-    return req.getParameter("ontologyname");
+    return req.getParameter("patoInput");
   }
 
   private String getOntologyParamString(HttpServletRequest req) {
-    return req.getParameter("ontology");
+    return req.getParameter("ontologyName");
   }
 
   
@@ -88,13 +89,19 @@
     if (true || isTermInfoRequest(request)) {
       PrintWriter out = response.getWriter();
       String termId = getTermIdFromTermInfoRequest(request);
-      System.out.println("doGet term info param: "+termId);
+      String ontologyName = getOntologyParamString(request);
+      System.out.println("doGet term info param: "+termId+" ont "+ontologyName);
 //       out.println("<table><tr><td class=\"label\">Ontology</td> "+
 //                   "<td class=\"data\">"+initDate+"</td></tr>\n"+
 //                   "<tr><td class=\"label\">Term name...</td><td class=\"data\">"
 //                   +userInput+"</td></tr></table>");
       // for now hard wire to pato
-      OBOClass oboClass = getOntology(null).getOboClass(termId);
+      Ontology ont = getOntology(ontologyName);
+      if (ont == null) {
+        System.out.println("ERROR: Failed to get ontology for "+ontologyName);
+        return;
+      }
+      OBOClass oboClass = getOntology(ontologyName).getOboClass(termId);
       if (oboClass == null) {
         System.out.println("term info: no obo class found for "+termId);
         return;
@@ -109,29 +116,31 @@
   }
 
   private String getTermIdFromTermInfoRequest(HttpServletRequest req) {
-    return req.getParameter("ontologyid");
+    return req.getParameter("termId");
   }
 
 
   // List<String>? String[]? or String htmlLiString?
   // for now just return html ul-li list w onmouseover
-  private String getCompletionList(String userInput) {
+  private String getCompletionList(String userInput,String ontol) {
     StringBuffer sb = new StringBuffer("<ul>");
     // for now just grab the pato ontology - eventuall redo for multiple/config
-    Ontology ontology = getOntology(null);
+    Ontology ontology = getOntology(ontol);
     if (ontology == null) {
       System.out.println("failed to get pato from ontology manager");
       return "ontology retrieval failed";
     }
     Vector<OBOClass> v = ontology.getSearchTerms(userInput,getSearchParams());
     for (OBOClass oc : v)
-      sb.append(makeCompListHtmlItem(oc));
+      sb.append(makeCompListHtmlItem(oc,ontol));
     sb.append("</ul>");
     return sb.toString();
   }
 
-  private Ontology getOntology(String termId) { // termid?? or ontology name?
-    return getPatoOntology();
+  /** returns null if ontolName not found */
+  private Ontology getOntology(String ontolName) { // termid?? or ontology name?
+    //return getPatoOntology();
+    return OntologyManager.getOntologyForName(ontolName);
   }
   
   // for now...
@@ -143,9 +152,9 @@
     return null;
   }
 
-  private String makeCompListHtmlItem(OBOClass term) {
+  private String makeCompListHtmlItem(OBOClass term,String ontol) {
     String id = "'"+term.getID()+"'";
-    return "<li onmouseover=\"set_ontology("+id+")\" id="+id+" "+
+    return "<li onmouseover=\"getTermInfo("+id+",'"+ontol+"')\" id="+id+" "+
       "onclick=\"set_ontology("+id+")\">"+term.getName()+"</li>\n";
   }
 

Modified: phenote/trunk/src/web/html/ncbo.html
===================================================================
--- phenote/trunk/src/web/html/ncbo.html	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/web/html/ncbo.html	2006-07-24 22:41:19 UTC (rev 64)
@@ -36,9 +36,10 @@
             Search terms in PATO ontology<br/><br/><br/>
             <label>Name:</label>
 
-            <input autocomplete="off" id="ontologyname" name="ontologyname" size="20" type="text" value="" />
+            <!-- input autocomplete="off" id="ontologyname" name="ontologyname" size="20" type="text" value="" / -->
+            <input autocomplete="off" id="patoInput" name="patoInput" size="20" type="text" value="" />
             </br>
-            <div class="auto_complete" id="ontologyname_auto_complete"></div>
+            <div class="auto_complete" id="pato_auto_complete"></div>
          </fieldset>
 
       </div>
@@ -58,12 +59,16 @@
    <!--   'ontologyname_auto_complete', '/phenote-ontology.cgi',{  }) -->
    <!-- new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/PhenoteStub',{  }) -->
    <!--  new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/phenote.servlet.PhenoteServlet',{  }) -->
-        new Ajax.Autocompleter( 'ontologyname', 'ontologyname_auto_complete', '/servlet/Phenote',{  })
+        var complete = new Ajax.Autocompleter( 'patoInput', 'pato_auto_complete', '/servlet/Phenote',{parameters:'ontologyName=pato&aa=bb'   })
         
+        <!-- complete.options.defaultParams = "ontology=pato"; -->
+        <!--   complete.options.parameters = "ontology=pato"; -->
 
+        <!-- more params? 'ontology=pato&x=y&...' -->
+
    </script>
 
-
+   <!-- this is set by ncbo-term-info.js but its unclear what its for -->
    <input type="hidden" name="ontologyid">
 </form>
  

Modified: phenote/trunk/src/web/javascript/ncbo-term-info.js
===================================================================
--- phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-21 17:07:09 UTC (rev 63)
+++ phenote/trunk/src/web/javascript/ncbo-term-info.js	2006-07-24 22:41:19 UTC (rev 64)
@@ -8,19 +8,23 @@
 //var url = '/servlet/PhenoteStub'; 
 var url = '/servlet/Phenote';
       
-// set_ontology should be called by the above url (at least for dichty it does)
 
-      function set_ontology(ontologyid){
+// getTermInfo should be called by the above url (at least for dichty it does)
+// renaming this getTermInfo... from set_ontology,
+// ontologyid -> termId
 
+// ontologyName is the name of the ontology (not a term name!)
+      function getTermInfo(termId,ontologyName) {
+
         // for some reason 0 doesnt work
-        //ontologyid = 123;
+        //termId = 123;
 
-        //alert("phenote-control.js set_ontology called ontId isNan:"+isNaN(ontologyid)+" ontId: "+ontologyid);
+        //alert("phenote-control.js set_ontology called ontId isNan:"+isNaN(termId)+" ontId: "+termId);
 
         // isNan is "is Not a Number", ontology id has to be a number
-        // this aint gonna fly - ontology ids are string PATO:1234
-         //if ( !isNaN( ontologyid ) ) {      
-            var pars = 'ontologyid=' + ontologyid;
+         //if ( !isNaN( termId ) ) {      
+//            var pars = 'ontologyid=' + ontologyid;
+            var pars = 'termId=' + termId +'&ontologyName=' + ontologyName;
 
             
             //alert("phenote-control.js calling Ajax.Updater with "+pars);
@@ -28,15 +32,18 @@
 
             // ontologyinfo is the div where the table goes for term info
             // note: this is a "get" not a post! (term comp is post)
-            var myAjax = new Ajax.Updater('ontologyinfo', url, {method: 'get', parameters: pars, onComplete: document.forms[0].ontologyname.value = '' } );
+            var myAjax = new Ajax.Updater('ontologyinfo', url, {method: 'get', parameters: pars, onComplete: document.forms[0].patoInput.value = '' } );
            // have to have [1] next to form item because the edit subform and
            // the main form both have donorid elements
             if ( document.forms[0].ontologyid.length > 1 ) {
-               document.forms[0].ontologyid[1].value = ontologyid;
-               document.forms[0].ontologyid[2].value = ontologyid;
+               document.forms[0].ontologyid[1].value = termId;
+               document.forms[0].ontologyid[2].value = termId;
             }
             else {
-               document.forms[0].ontologyid.value = ontologyid;
+               document.forms[0].ontologyid.value = termId;
             }
          //}
       }
+
+
+


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[Obo-svn-commit] SF.net SVN: obo: [62] phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java

[<mg...@us...>]

Revision: 62
Author:   mgibson
Date:     2006-07-20 11:46:00 -0700 (Thu, 20 Jul 2006)
ViewCVS:  http://svn.sourceforge.net/obo/?rev=62&view=rev

Log Message:
-----------
testing email commit

Modified Paths:
--------------
    phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
Modified: phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java
===================================================================
--- phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-19 16:35:11 UTC (rev 61)
+++ phenote/trunk/src/java/phenote/servlet/PhenoteServlet.java	2006-07-20 18:46:00 UTC (rev 62)
@@ -27,7 +27,6 @@
   /** if <load-on-startup>1</load-on-startup> is in web.xml then init will
       happen when web server started (or if code recompiled) - so this is where
       the ontology reading & caching goes */
-
   public void init() throws ServletException {
     initDate = new Date();
     super.init();
@@ -37,7 +36,8 @@
   }
 
 
-  /** this should be done in java server faces/pages(?) */
+  /** this should be done in java server faces/pages(?), post comes from ajax
+      autocompleter on typing in stuff */
   public void doPost(HttpServletRequest request, HttpServletResponse response)
     throws IOException, ServletException  {
       
@@ -50,7 +50,8 @@
 
     if (isTermCompletionRequest(request)) {
       String userInput = getTermCompletionParam(request);
-      //ResourceBundle r=ResourceBundle.getBundle("LocalStrings",request.getLocale());
+      System.out.println("ontology? "+getOntologyParamString(request));
+//ResourceBundle r=ResourceBundle.getBundle("LocalStrings",request.getLocale());
       //Content-Type: text/html; charset=ISO-8859-1
       response.setContentType("text/html");
       //out.println("Content-Type: text/html; charset=ISO-8859-1"); // this messes things up
@@ -74,14 +75,10 @@
     return req.getParameter("ontologyname");
   }
 
-  private boolean isTermInfoRequest(HttpServletRequest req) {
-    return getTermIdFromTermInfoRequest(req) != null;
+  private String getOntologyParamString(HttpServletRequest req) {
+    return req.getParameter("ontology");
   }
 
-  private String getTermIdFromTermInfoRequest(HttpServletRequest req) {
-    return req.getParameter("ontologyid");
-  }
-
   
 
   /** i cant tell ya why but term info is done with a get and term completion
@@ -107,6 +104,15 @@
     }
   }
 
+  private boolean isTermInfoRequest(HttpServletRequest req) {
+    return getTermIdFromTermInfoRequest(req) != null;
+  }
+
+  private String getTermIdFromTermInfoRequest(HttpServletRequest req) {
+    return req.getParameter("ontologyid");
+  }
+
+
   // List<String>? String[]? or String htmlLiString?
   // for now just return html ul-li list w onmouseover
   private String getCompletionList(String userInput) {


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[Obo-svn-commit] test

[Mark G. <mg...@fr...>]

test