Merge remote-tracking branch 'origin/develop' into fb_databaseidentifier

Author: labkey-adam

genotyping/src/org/labkey/genotyping/ConcatenatedHaplotypesDisplayColumn.java

@@ -23,7 +23,7 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.TableInfo;
 import org.labkey.api.query.FieldKey;
-import org.labkey.api.util.Link;
+import org.labkey.api.util.LinkBuilder;
 import org.labkey.api.view.ActionURL;
 import org.labkey.api.writer.HtmlWriter;
 
@@ -101,8 +101,7 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out)
                     filter.addCondition(FieldKey.fromParts("Species"), speciesValue);
                 }
                 filter.applyToURL(url, "query");
-                String evaluatedURL = url.getURIString();
-                out.write(new Link.LinkBuilder(haplotype).href(evaluatedURL).target("_blank").clearClasses());
+                out.write(LinkBuilder.simpleLink(haplotype, url).target("_blank"));
             }
         }
     }

genotyping/src/org/labkey/genotyping/view/configure.jsp

@@ -124,31 +124,31 @@
             <td>External source of DNA reference sequences&nbsp;&nbsp;</td>
             <td><div id="sequencesQueryDiv"></div></td>
             <td>
-                <%=link("configure").href("#").onClick("chooseView('Choose DNA reference sequences query', 'Select a query that represents an external source of DNA reference sequences. This query will be used periodically to replace the reference sequences that link to results.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateSequencesQuery(query);}, queries['sequencesQuery'], includeSchema);return false;")%>
+                <%=link("configure", "#").onClick("chooseView('Choose DNA reference sequences query', 'Select a query that represents an external source of DNA reference sequences. This query will be used periodically to replace the reference sequences that link to results.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateSequencesQuery(query);}, queries['sequencesQuery'], includeSchema);return false;")%>
                 <input type="hidden" name="sequencesQuery" id="sequencesQuery">
             </td>
         </tr>
         <tr>
             <td>Runs</td>
             <td><div id="runsQueryDiv"></div></td>
             <td>
-                <%=link("configure").href("#").onClick("chooseView('Choose runs query', 'Select a query where runs are stored.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateRunsQuery(query);}, queries['runsQuery'], includeSchema);return false;")%>
+                <%=link("configure", "#").onClick("chooseView('Choose runs query', 'Select a query where runs are stored.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateRunsQuery(query);}, queries['runsQuery'], includeSchema);return false;")%>
                 <input type="hidden" name="runsQuery" id="runsQuery">
             </td>
         </tr>
         <tr>
             <td>Samples</td>
             <td><div id="samplesQueryDiv"></div></td>
             <td>
-                <%=link("configure").href("#").onClick("chooseView('Choose samples query', 'Select a query that provides a list of samples. This query is filtered by the library number specified in the run to produce the sample.txt file.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateSamplesQuery(query);}, queries['samplesQuery'], includeSchema);return false;")%>
+                <%=link("configure", "#").onClick("chooseView('Choose samples query', 'Select a query that provides a list of samples. This query is filtered by the library number specified in the run to produce the sample.txt file.', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateSamplesQuery(query);}, queries['samplesQuery'], includeSchema);return false;")%>
                 <input type="hidden" name="samplesQuery" id="samplesQuery">
             </td>
         </tr>
         <tr>
             <td>Haplotype Definitions</td>
             <td><div id="haplotypesQueryDiv"></div></td>
             <td>
-                <%=link("configure").href("#").onClick("chooseView('Choose haplotype definition query', 'Select a query that provides a list of haplotype definitions. ', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateHaplotypesQuery(query);}, queries['haplotypesQuery'], includeSchema);return false;")%>
+                <%=link("configure", "#").onClick("chooseView('Choose haplotype definition query', 'Select a query that provides a list of haplotype definitions. ', '" + GenotypingFolderSettings.SEPARATOR + "', function(query){updateHaplotypesQuery(query);}, queries['haplotypesQuery'], includeSchema);return false;")%>
                 <input type="hidden" name="haplotypesQuery" id="haplotypesQuery">
             </td>
         </tr>