<commit_before><%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
<%@ taglib uri="/WEB-INF/struts-html.tld" prefix="html" %>
<%@ taglib uri="/WEB-INF/struts-tiles.tld" prefix="tiles" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
<%@ taglib tagdir="/WEB-INF/tags" prefix="im"%>

<!-- begin.jsp -->
<html:xhtml/>

<div class="body">
        
<!-- First column -->
     <div id="aspectsFront" class="actionArea">
     <h1><html:link action="/dataCategories.do">Data</html:link></h1>
     <em><p><fmt:message key="begin.data"/></p></em>
     <c:set var="numPerCol" value="${fn:length(ASPECTS)/2}"/>
          <table cellpadding="0" cellspacing="0" border="0"><tr>
	       <c:forEach var="entry" items="${ASPECTS}" varStatus="status">
	         <c:set var="set" value="${entry.value}"/>
	         <c:if test="${status.count%2 == '1'}"></tr><tr></c:if>
                   <td style="height:80px;padding:10px">
                     <html:link action="/aspect?name=${set.name}">
                       <img src="<html:rewrite page="/${set.iconImage}"/>" class="aspectIcon" width="40px" height="40px" />
                     </html:link>
                     <p>
                       <html:link action="/aspect?name=${set.name}">
                         ${set.name}
                       </html:link><br/>
                     </p>
                  </td>
             </c:forEach>
          </tr></table>
     </div>
	

<!-- Second column - elastic -->
<div id="rightColumn">

  <div>
    <div style="float:right"><tiles:insert name="tipWrapper.tile"/></div>
    <div style="width:400px;margin-left:20px">
 	  <span style="font-size:+2em;"><a href="${WEB_PROPERTIES['project.sitePrefix']}/what.shtml">What is FlyMine?</a></span><br>
 	  <span style="font-size:+1.4em"><a href="${WEB_PROPERTIES['project.sitePrefix']}/tour/start.html" target="_help"  onclick="javascript:window.open('${WEB_PROPERTIES['project.sitePrefix']}/tour/start.html','_help','toolbar=0,scrollbars=1,location=1,statusbar=1,menubar=0,resizable=1,width=800,height=600');return false">Take a tour!</a></span>
      <p class="errors">This is release 8.0 of FlyMine.  See the <a href="${WEB_PROPERTIES['project.sitePrefix']}/release-notes.shtml">release notes</a> to find out what's new.</p>
    </div>
  </div>	

      <im:roundbox title="Templates" titleLink="/templates.do" stylename="frontBox">
        <em><p><fmt:message key="begin.templates"/></p></em>
        <br/>
        <div>
          Example templates (<html:link action="/templates.do">${templateCount} total</html:link>):
        </div>
        <div id="templatesList" class="frontBoxList">
          <tiles:insert name="webSearchableList.tile">
            <!-- optional -->
            <tiles:put name="limit" value="3"/>
            <!-- bag or template? -->
            <tiles:put name="type" value="template"/>
            <!-- user or global -->
            <tiles:put name="wsListId" value="global_template"/>
            <tiles:put name="scope" value="global"/>
            <tiles:put name="tags" value="im:frontpage"/>
            <tiles:put name="showDescriptions" value="false"/>
            <tiles:put name="showSearchBox" value="false"/>
          </tiles:insert>
        </div>
        <im:useTransparentImage src="/images/search_with_templates.png" id="search_with_templates" link="templates" height="22px" width="153px" floatValue="right" breakFloat="true" />
      </im:roundbox>
     
      <im:roundbox title="Lists" titleLink="/bag.do" stylename="frontBox">
        <p><em><fmt:message key="begin.bags"/></em></p>
        <br/>
        <div>
          Example lists (<html:link action="/bag.do?subtab=view">${bagCount} total</html:link>):
        </div>
        <div id="bagsList" class="frontBoxList">
        <tiles:insert name="webSearchableList.tile">
          <tiles:put name="limit" value="2"/>
          <tiles:put name="wsListId" value="global_bag"/>
          <%-- bag or template? --%>
          <tiles:put name="type" value="bag"/>
          <%-- user or global --%>
          <tiles:put name="scope" value="global"/>
          <tiles:put name="tags" value="im:frontpage"/>
          <tiles:put name="showSearchBox" value="false"/>
          <%--<tiles:put name="height" value="100"/>--%>
        </tiles:insert>
        </div>
        <im:useTransparentImage src="/images/view_lists.png" id="view_lists" link="
bag.do?subtab=view" height="32px" width="115px" floatValue="right" breakFloat="true"/>
        <im:useTransparentImage src="/images/create_lists.png" id="create_lists" link="bag.do?subtab=upload" height="22px" width="120px" floatValue="right" breakFloat="true"/>
      </im:roundbox>

      <im:roundbox title="Query Builder" titleLink="/customQuery.do" stylename="frontBox">
        <p><em><fmt:message key="begin.querybuilder"/></em></p>
        <br/>
        <div>
          <div id="qbStartQuery">
            Start a query from:
            <html:link action="/queryClassSelect.do?action=Select&className=org.flymine.model.genomic.Gene">
              Gene 
            </html:link>,
            <html:link action="/queryClassSelect.do?action=Select&className=org.flymine.model.genomic.Protein">
              Protein
            </html:link>
          </div>
        </div>
        <div id="qbImport">
          <html:link action="/importQueries.do?query_builder=yes">
            <fmt:message key="begin.importQuery"/>
          </html:link>
        </div>
        <im:useTransparentImage src="/images/build_a_query.png" id="build_a_query" link="query" height="22px" width="120px" floatValue="right" breakFloat="true"/>
      </im:roundbox>
</div>

</div>

<!-- /begin.jsp --><commit_msg>Fixed broken 'Start query' link<commit_after><%@ taglib uri="http://java.sun.com/jsp/jstl/core" prefix="c" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/fmt" prefix="fmt" %>
<%@ taglib uri="/WEB-INF/struts-html.tld" prefix="html" %>
<%@ taglib uri="/WEB-INF/struts-tiles.tld" prefix="tiles" %>
<%@ taglib uri="http://java.sun.com/jsp/jstl/functions" prefix="fn" %>
<%@ taglib tagdir="/WEB-INF/tags" prefix="im"%>

<!-- begin.jsp -->
<html:xhtml/>

<div class="body">
        
<!-- First column -->
     <div id="aspectsFront" class="actionArea">
     <h1><html:link action="/dataCategories.do">Data</html:link></h1>
     <em><p><fmt:message key="begin.data"/></p></em>
     <c:set var="numPerCol" value="${fn:length(ASPECTS)/2}"/>
          <table cellpadding="0" cellspacing="0" border="0"><tr>
	       <c:forEach var="entry" items="${ASPECTS}" varStatus="status">
	         <c:set var="set" value="${entry.value}"/>
	         <c:if test="${status.count%2 == '1'}"></tr><tr></c:if>
                   <td style="height:80px;padding:10px">
                     <html:link action="/aspect?name=${set.name}">
                       <img src="<html:rewrite page="/${set.iconImage}"/>" class="aspectIcon" width="40px" height="40px" />
                     </html:link>
                     <p>
                       <html:link action="/aspect?name=${set.name}">
                         ${set.name}
                       </html:link><br/>
                     </p>
                  </td>
             </c:forEach>
          </tr></table>
     </div>
	

<!-- Second column - elastic -->
<div id="rightColumn">

  <div>
    <div style="float:right"><tiles:insert name="tipWrapper.tile"/></div>
    <div style="width:400px;margin-left:20px">
 	  <span style="font-size:+2em;"><a href="${WEB_PROPERTIES['project.sitePrefix']}/what.shtml">What is FlyMine?</a></span><br>
 	  <span style="font-size:+1.4em"><a href="${WEB_PROPERTIES['project.sitePrefix']}/tour/start.html" target="_help"  onclick="javascript:window.open('${WEB_PROPERTIES['project.sitePrefix']}/tour/start.html','_help','toolbar=0,scrollbars=1,location=1,statusbar=1,menubar=0,resizable=1,width=800,height=600');return false">Take a tour!</a></span>
      <p class="errors">This is release 8.0 of FlyMine.  See the <a href="${WEB_PROPERTIES['project.sitePrefix']}/release-notes.shtml">release notes</a> to find out what's new.</p>
    </div>
  </div>	

      <im:roundbox title="Templates" titleLink="/templates.do" stylename="frontBox">
        <em><p><fmt:message key="begin.templates"/></p></em>
        <br/>
        <div>
          Example templates (<html:link action="/templates.do">${templateCount} total</html:link>):
        </div>
        <div id="templatesList" class="frontBoxList">
          <tiles:insert name="webSearchableList.tile">
            <!-- optional -->
            <tiles:put name="limit" value="3"/>
            <!-- bag or template? -->
            <tiles:put name="type" value="template"/>
            <!-- user or global -->
            <tiles:put name="wsListId" value="global_template"/>
            <tiles:put name="scope" value="global"/>
            <tiles:put name="tags" value="im:frontpage"/>
            <tiles:put name="showDescriptions" value="false"/>
            <tiles:put name="showSearchBox" value="false"/>
          </tiles:insert>
        </div>
        <im:useTransparentImage src="/images/search_with_templates.png" id="search_with_templates" link="templates" height="22px" width="153px" floatValue="right" breakFloat="true" />
      </im:roundbox>
     
      <im:roundbox title="Lists" titleLink="/bag.do" stylename="frontBox">
        <p><em><fmt:message key="begin.bags"/></em></p>
        <br/>
        <div>
          Example lists (<html:link action="/bag.do?subtab=view">${bagCount} total</html:link>):
        </div>
        <div id="bagsList" class="frontBoxList">
        <tiles:insert name="webSearchableList.tile">
          <tiles:put name="limit" value="2"/>
          <tiles:put name="wsListId" value="global_bag"/>
          <%-- bag or template? --%>
          <tiles:put name="type" value="bag"/>
          <%-- user or global --%>
          <tiles:put name="scope" value="global"/>
          <tiles:put name="tags" value="im:frontpage"/>
          <tiles:put name="showSearchBox" value="false"/>
          <%--<tiles:put name="height" value="100"/>--%>
        </tiles:insert>
        </div>
        <im:useTransparentImage src="/images/view_lists.png" id="view_lists" link="
bag.do?subtab=view" height="32px" width="115px" floatValue="right" breakFloat="true"/>
        <im:useTransparentImage src="/images/create_lists.png" id="create_lists" link="bag.do?subtab=upload" height="22px" width="120px" floatValue="right" breakFloat="true"/>
      </im:roundbox>

      <im:roundbox title="Query Builder" titleLink="/customQuery.do" stylename="frontBox">
        <p><em><fmt:message key="begin.querybuilder"/></em></p>
        <br/>
        <div>
          <div id="qbStartQuery">
            Start a query from:
            <html:link action="/queryClassSelect.do?action=Select&className=org.flymine.model.genomic.Gene">
              Gene 
            </html:link>,
            <html:link action="/queryClassSelect.do?action=Select&className=org.flymine.model.genomic.Protein">
              Protein
            </html:link>
          </div>
        </div>
        <div id="qbImport">
          <html:link action="/importQueries.do?query_builder=yes">
            <fmt:message key="begin.importQuery"/>
          </html:link>
        </div>
        <im:useTransparentImage src="/images/build_a_query.png" id="build_a_query" link="customQuery" height="22px" width="120px" floatValue="right" breakFloat="true"/>
      </im:roundbox>
</div>

</div>

<!-- /begin.jsp -->
{'fraction_non_alphanumeric': 0.20006910850034554, 'fraction_numerical': 0.010884588804422944, 'mean_word_length': 2.7746984023475707, 'pattern_counts': {'":': 0, '<': 295, '<?xml version=': 0, '>': 295, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6953217', 'n_tokens_mistral': 3860, 'n_tokens_neox': 3699, 'n_words': 568}