Changeset 22698

Timestamp:

03/09/10 13:00:45 (17 months ago)

Author:

julie

Message:

update to new model

Location:

trunk

Files:

• bio/tools/test/src/org/intermine/bio/web/export/GFF3UtilTest.java (modified) (1 diff)
• modmine/webapp/project.properties (modified) (1 diff)
• modmine/webapp/resources/default-template-queries.xml (modified) (1 diff)
• modmine/webapp/resources/web.properties (modified) (2 diffs)

trunk/bio/tools/test/src/org/intermine/bio/web/export/GFF3UtilTest.java

@@ -66 +66 @@
         Map<String, String> soClassNameMap = getSoClassNameMap();
 
-        GFF3Record gff3Gene = GFF3Util.makeGFF3Record(gene, soClassNameMap, "FlyMine", extraAttributes);
+        GFF3Record gff3Gene = org.intermine.bio.web.export.GFF3Util.makeGFF3Record(gene, soClassNameMap, "FlyMine", extraAttributes);
 
-        GFF3Record gff3Exon = GFF3Util.makeGFF3Record(exon, soClassNameMap, "FlyMine",
+        GFF3Record gff3Exon = org.intermine.bio.web.export.GFF3Util.makeGFF3Record(exon, soClassNameMap, "FlyMine",
                                                       new HashMap<String, List<String>>());
 

trunk/modmine/webapp/project.properties

@@ -6 +6 @@
                        bio/core/main,\
                        bio/webapp
-                       
+
 # The products and their immediate library dependencies of these projects
 # will be included in the webapp

trunk/modmine/webapp/resources/default-template-queries.xml

@@ -2 +2 @@
 
   <template-queries>
-    <template name="A_IdentifierSynonym_Object" title="primaryIdentifier or synonym --&gt; Database object." longDescription="Find an entry in the database using any primaryIdentifier or synonym." comment="This is the template that the quick search runs.  If the name is changed it also has to be changed for the quick search configuration - Rachel. Removed tags so no longer displayed - just used for quick search now.  Rachel.">
-      <query name="A_IdentifierSynonym_Object" model="genomic" view="Synonym.subject.primaryIdentifier Synonym.value Synonym.subject.organism.name" sortOrder="Synonym.subject.primaryIdentifier asc">
-        <node path="Synonym" type="Synonym">
-        </node>
-        <node path="Synonym.value" type="String">
-          <constraint op="=" value="timeout" description="" identifier="" editable="true" code="A">
-          </constraint>
-        </node>
-      </query>
-    </template>
     <template name="All_Genes_In_Organism_To_Publications" title="All genes in organism -&gt; Publications." longDescription="Show the publications for each gene in an organism. Data currently available for D.melanogaster." comment="">
       <query name="All_Genes_In_Organism_To_Publications" model="genomic" view="Gene.primaryIdentifier Gene.symbol Gene.publications.pubMedId Gene.publications.firstAuthor Gene.publications.journal Gene.publications.year Gene.organism.name" sortOrder="Gene.primaryIdentifier asc">

trunk/modmine/webapp/resources/web.properties

@@ -159 +159 @@
 # home page
 begin.query.classes=Gene,Protein,Submission,TranscriptionRegion,TFBindingsite,HistoneBindingSite
-begin.browse.template=A_IdentifierSynonym_Object
 
 # portal
@@ -175 +174 @@
 # quicksearch examples
 quickSearch.identifiers = e.g zen, Q9V4E1
-quickSearch.templates = e.g. gene orthologue
-quickSearch.lists = e.g. transcription factors
 
 #list of pages with fixed width layout