Changeset 22838

Timestamp:

09/09/10 11:22:21 (17 months ago)

Author:

julie

Message:

add test, keys to example source

Location:

trunk/bio/sources/example-sources

Files:

• kegg-example/.classpath (modified) (2 diffs)
• kegg-example/kegg-example_additions.xml (modified) (1 diff)
• kegg-example/main/src/org/intermine/bio/dataconversion/KeggExampleConverter.java (modified) (3 diffs)
• kegg-example/resources/kegg-example_keys.properties (modified) (1 diff)
• kegg-example/test (added)
• kegg-example/test/build.xml (added)
• kegg-example/test/lib (added)
• kegg-example/test/project.properties (added)
• kegg-example/test/resources (added)
• kegg-example/test/resources/KeggConverterTest_tgt.xml (added)
• kegg-example/test/resources/pfa_gene_map.tab (added)
• kegg-example/test/src (added)
• kegg-example/test/src/org (added)
• kegg-example/test/src/org/intermine (added)
• kegg-example/test/src/org/intermine/bio (added)
• kegg-example/test/src/org/intermine/bio/dataconversion (added)
• kegg-example/test/src/org/intermine/bio/dataconversion/KeggExampleConverterTest.java (added)
• kegg-identifiers/resources/kegg-identifiers_keys.properties (modified) (1 diff)

trunk/bio/sources/example-sources/kegg-example/.classpath

@@ -2 +2 @@
 <classpath>
     <classpathentry kind="src" path="main/src"/>
+    <classpathentry kind="src" path="test/src"/>
     <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
     <classpathentry combineaccessrules="false" kind="src" path="/bio-core-main"/>
@@ -10 +11 @@
     <classpathentry combineaccessrules="false" kind="src" path="/intermine-objectstore-main"/>
     <classpathentry combineaccessrules="false" kind="src" path="/intermine-objectstore-test"/>
+    <classpathentry kind="lib" path="test/resources"/>
     <classpathentry kind="output" path="bin"/>
 </classpath>

trunk/bio/sources/example-sources/kegg-example/kegg-example_additions.xml

@@ -3 +3 @@
 <class name="Pathway" is-interface="true" >
   <attribute name="identifier" type="java.lang.String"/>
-  <attribute name="name" type="java.lang.String"/>
   <collection name="genes" referenced-type="Gene" reverse-reference="pathways"/>
 </class>

trunk/bio/sources/example-sources/kegg-example/main/src/org/intermine/bio/dataconversion/KeggExampleConverter.java

@@ -80 +80 @@
 
         Iterator lineIter = FormattedTextParser.parseTabDelimitedReader(reader);
-
         while (lineIter.hasNext()) {
             // line is a string array with the one element for each tab separated value
             // on the next line of the file
             String[] line = (String[]) lineIter.next();
-
             String geneId = line[0];
 
@@ -113 +111 @@
      * @param pathwayId the id of a KEGG pathway to look up
      * @return an Item representing the pathway
+     * @throws ObjectStoreException
      */
-    private Item getPathway(String pathwayId) {
+    private Item getPathway(String pathwayId)
+        throws ObjectStoreException {
         Item pathway = pathwayMap.get(pathwayId);
         if (pathway == null) {
@@ -120 +120 @@
             pathway.setAttribute("identifier", pathwayId);
             pathwayMap.put(pathwayId, pathway);
+            store(pathway);
         }
         return pathway;

trunk/bio/sources/example-sources/kegg-example/resources/kegg-example_keys.properties

@@ -1 @@
-Organism=key_taxonid
-DataSource=key_name
-Gene=key_primaryidentifier
-DataSet=key_title
-OntologyTerm=key_name_ontology
-Ontology=key_title
+Organism.key_taxonid=taxonId
+Gene.key_primaryidentifier=primaryIdentifier
+Pathway.key_identifier=identifier

trunk/bio/sources/example-sources/kegg-identifiers/resources/kegg-identifiers_keys.properties

@@ -1 +1 @@
 DataSet=key_title
 DataSource=key_name
-Synonym=key_synonym
-SequenceOntologyTerm=key_name