Changeset 22684


Ignore:
Timestamp:
03/09/10 11:45:30 (17 months ago)
Author:
fhu
Message:

Submission List tracks to GBrowse

Location:
trunk
Files:
9 added
6 edited

Legend:

Unmodified
Added
Removed

  • trunk/intermine/webapp/main/resources/webapp/bagDetails.jsp

    r21764 r22684  
    166166<c:choose> 
    167167    <c:when test="${myBag == 'true'}"> 
    168       <div id="bagDescriptionDiv" onclick="jQuery('#bagDescriptionDiv').toggle();jQuery('#bagDescriptionTextarea').toggle();jQuery('#textarea').focus()"> 
     168      <div id="bagDescriptionDiv" style="height:65px;" onclick="jQuery('#bagDescriptionDiv').toggle();jQuery('#bagDescriptionTextarea').toggle();jQuery('#textarea').focus()"> 
    169169        <h3><img src="images/icons/description.png" title="Description of your list"/>&nbsp;Description</h3> 
    170170        <c:choose> 
    … …  
    195195</div> 
    196196 
     197<%-- BagDisplayers--%> 
     198    <tiles:insert page="/bagDisplayers.jsp"> 
     199       <tiles:put name="bag" beanName="bag"/> 
     200       <tiles:put name="showOnLeft" value="true"/> 
     201    </tiles:insert> 
     202 
    197203</TD> 
    198204 
    … …  
    214220</p> 
    215221 
    216 <tiles:insert page="/bagDisplayers.jsp"> 
    217    <tiles:put name="bag" beanName="bag"/> 
    218 </tiles:insert> 
     222<%-- BagDisplayers used to be inserted here --%> 
    219223 
    220224</div> 

  • trunk/modmine/webapp/resources/struts-config-model.xml

    r22316 r22684  
    1 <!-- this comment is here to prevent ant from setting model.struts.config to null --> 
     1subListGBrowseTrackDisplayer<!-- this comment is here to prevent ant from setting model.struts.config to null --> 
    22 
    33<action path="/sequenceExporter" 
    … …  
    2424  type="org.intermine.bio.web.AttributeLinkDisplayerController" /> 
    2525 
    26 <action path="/initTracksDisplayer" 
    27   type="org.modmine.web.TrackDisplayerController" /> 
     26<action path="/initSubListGBrowseTrackDisplayer" 
     27  type="org.modmine.web.SubListGBrowseTrackController" /> 
    2828 
    2929<action path="/initProjectList" 

  • trunk/modmine/webapp/resources/tiles-defs-model.xml

    r22501 r22684  
    1818<definition name="tracksDisplayer.tile" path="/model/tracksDisplayer.jsp" 
    1919          controllerUrl="/initTracksDisplayer.do"/> 
     20 
     21<definition name="subListGBrowseTrackDisplayer.tile" path="/model/subListGBrowseTrackDisplayer.jsp" 
     22          controllerUrl="/initSubListGBrowseTrackDisplayer.do"/> 
    2023 
    2124<definition name="projects.tile" path="/model/projects.jsp" 

  • trunk/modmine/webapp/resources/webapp/WEB-INF/tags/singleTrack.tag

    r21894 r22684  
    55 
    66<% 
    7 org.modmine.web.GBrowseParser.GBrowseTrack track = ((org.modmine.web.GBrowseParser.GBrowseTrack) jspContext.getAttribute("track"));  
     7org.modmine.web.GBrowseParser.GBrowseTrack track = ((org.modmine.web.GBrowseParser.GBrowseTrack) jspContext.getAttribute("track")); 
    88%> 
    99 
    1010<c:set var="track" value="<%=track%>"/> 
    1111<html:link 
    12   href="${WEB_PROPERTIES['gbrowse.prefix']}/${track.organism}/?label=${track.track}/${track.subTrack}" title="View ${track.subTrack} in GBrowse" target="_blank"><c:out value="${track.subTrack}"/> 
     12  href="${WEB_PROPERTIES['gbrowse.prefix']}/${track.organism}/?label=${track.track}/${track.subTrack}" title="View ${track.subTrack} in GBrowse" target="_blank"><c:out value="${track.track}/${track.subTrack}"/> 
    1313</html:link> 

  • trunk/modmine/webapp/resources/webapp/WEB-INF/webconfig-model.xml

    r22653 r22684  
    130130      <displayer src="submissionProtocolsDisplayer.tile" showOnLeft="true"/> 
    131131    </longdisplayers> 
     132    <bagdisplayers> 
     133      <displayer src="subListGBrowseTrackDisplayer.tile" showOnLeft="true"/> 
     134    </bagdisplayers> 
    132135  </class> 
    133136 

  • trunk/modmine/webapp/src/org/modmine/web/GBrowseParser.java

    r21962 r22684  
    1 /** 
     1package org.modmine.web; 
     2 
     3/* 
     4 * Copyright (C) 2002-2010 FlyMine 
     5 * 
     6 * This code may be freely distributed and modified under the 
     7 * terms of the GNU Lesser General Public Licence.  This should 
     8 * be distributed with the code.  See the LICENSE file for more 
     9 * information or http://www.gnu.org/copyleft/lesser.html. 
    210 * 
    311 */ 
    4 package org.modmine.web; 
    512 
    613import java.io.BufferedReader; 
    … …  
    2128 * 
    2229 */ 
    23 public class GBrowseParser { 
    24  
    25     private static final Logger LOG = Logger.getLogger(MetadataCache.class); 
     30public class GBrowseParser 
     31{ 
     32    private static final Logger LOG = Logger.getLogger(GBrowseParser.class); 
    2633 
    2734    private static final String GBROWSE_BASE_URL = getGBrowsePrefix(); 
    … …  
    4350        private String track;    // e.g. Snyder_PHA4_GFP_COMB 
    4451        private String subTrack; // e.g. PHA4_L2_GFP 
     52        private Integer DCCid; 
    4553 
    4654        /** 
    … …  
    6270         * @param track        e.g. Snyder_PHA4_GFP_COMB 
    6371         * @param subTrack     e.g. PHA4_L2_GFP 
    64          */ 
    65         public GBrowseTrack(String organism, String track, String subTrack) { 
     72         * @param DCCid 
     73         */ 
     74        public GBrowseTrack(String organism, String track, String subTrack, Integer DCCid) { 
    6675            this.organism  = organism; 
    6776            this.track = track; 
    6877            this.subTrack = subTrack; 
     78            this.DCCid = DCCid; 
    6979        } 
    7080 
    … …  
    8898        public String getSubTrack() { 
    8999            return subTrack; 
     100        } 
     101 
     102        /** 
     103         * @return the DCCid 
     104         */ 
     105        public Integer getDCCid() { 
     106            return DCCid; 
    90107        } 
    91108    } 
    … …  
    154171                            toAppend.setLength(0); // empty buffer 
    155172                            GBrowseTrack newTrack = 
    156                                 new GBrowseTrack(organism, trackName.toString(), subTrack); 
     173                                new GBrowseTrack(organism, trackName.toString(), subTrack, dccId); 
    157174                            addToGBMap(submissionsToTracks, dccId, newTrack); 
    158175                        } 
    … …  
    194211     * @return the base URL 
    195212     */ 
    196     private static String getGBrowsePrefix() { 
     213    public static String getGBrowsePrefix() { 
    197214        Properties props = PropertiesUtil.getProperties(); 
    198215        String gbURL = props.getProperty("gbrowse.prefix") + "/"; 
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