Changeset 16233

Timestamp:

15/07/08 16:37:49 (1 month ago)

Author:

julie

Message:

create synonyms for go terms. Refs #1709

Files:

• trunk/bio/sources/go-annotation/main/src/org/intermine/bio/dataconversion/GoConverter.java (modified) (9 diffs)

trunk/bio/sources/go-annotation/main/src/org/intermine/bio/dataconversion/GoConverter.java

@@ -71 +71 @@
-    private static final Logger LOG = Logger.getLogger(GoConverter.class);
-    protected IdResolverFactory resolverFactory;
-
+
-    // TODO: datasources Map to contains ids not items? - need the dataset later on
-    // TODO: store product after each one finished? - 'with' field may be a problem
@@ -90 +90 @@
-        synonymTypes.put("gene", "identifier");
-        synonymTypes.put("Gene", "identifier");
-
+
-        // only construct factory here so can be replaced by mock factory in tests
-        resolverFactory = new FlyBaseIdResolverFactory();
-
+
-        readConfig();
-    }
@@ -248 +248 @@
-                Item newDatasource = newDatasource(ds);
-                String newPublicationId = newPublication(array[5]);
-
+, newDatasource
-                ReferenceList newGoEvidenceColl =
-                    new ReferenceList("goEvidenceCodes", new ArrayList());
@@ -262 +262 @@
-                // temporary object while we are rattling through the file
-                // needed because we may have extra publications
-
+
-                // check for null productWrapper - where idResolver could not find a current id
-                if (newProductWrapper != null) {
- 
- 
+
+
-                                        newGoEvidenceColl, newProductWrapper, newGoTerm,
-                                        array[7], newOrganism);
@@ -421 +421 @@
-
-        for (String parentTermGoId : parentTermIdsSet) {
-
+, placeHolder.getDatasource()
-
-            Item parentItem = null;
@@ -603 +603 @@
-            }
-
-    
+
-            if (taxonId.equals("7227")) {
-                IdResolver resolver = resolverFactory.getIdResolver();
@@ -637 +637 @@
-
-        // if a Dmel gene we need to use FlyBaseIdResolver to find a current id
-
+
-        Item product = createItem(clsName);
-        if (organism != null && createOrganism) {
@@ -675 +675 @@
-    }
-
-
+, Item dataSource
-        Item item = goTerms.get(identifier);
-        if (item == null) {
@@ -682 +682 @@
-            goTerms.put(identifier, item);
-            store(item);
+
+            Item synonym = newSynonym(
+                                      item.getIdentifier(),
+                                      "identifier",
+                                      identifier,
+                                      dataSource);
+            store(synonym);
+
-        }
-        return item;