complex goannot

yeastgenome · Oct 6, 2020 · 8c2f028 · 8c2f028
1 parent c1666c3
commit 8c2f028
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Showing 3 changed files with 29 additions and 15 deletions.
diff --git a/go-annotation-db/src/main/java/org/intermine/bio/dataconversion/GoAnnotationDbConverter.java b/go-annotation-db/src/main/java/org/intermine/bio/dataconversion/GoAnnotationDbConverter.java
@@ -206,7 +206,6 @@ public void processGOAnnotations(Connection connection) throws SQLException, Obj
 					String goTermIdentifier = newGoTerm(goId, dataSource, dataSourceCode);
 					Evidence evidence = new Evidence(newStrEvidence, pubRefId, withText, organism,
 							dataSource, dataSourceCode);
-					System.out.print("evidence");
 					allEvidenceForAnnotation = new LinkedHashSet<Evidence>();
 					allEvidenceForAnnotation.add(evidence);
 					goTermGeneToEvidence.put(key, allEvidenceForAnnotation);
@@ -490,8 +489,7 @@ private void storeEvidenceCode(String code, String annotType, String withText) t
 			if(!annotType.isEmpty()) {item.setAttribute("annotType", annotType); }
 			if(withText != null && !withText.isEmpty()) { item.setAttribute("withText", withText); } 
 			store(item);
-			evidenceCodes.put(combinationcode, item.getIdentifier()); 
-			System.out.println("Code is :  "+ combinationcode);
+			evidenceCodes.put(combinationcode, item.getIdentifier());
 		}
 	}
 
@@ -768,7 +766,6 @@ public boolean equals(Object o) {
 							&& pub.equals(go.pub)
 							&& pubxref.equals(go.pubxref);
 				}else{
-					System.out.println("in GoTermToGene...." + annotationExtension);
 					return productId.equals(go.productId)
 							&& goId.equals(go.goId)
 							&& qualifier.equals(go.qualifier)

diff --git a/sgd-complexes/src/main/java/org/intermine/bio/dataconversion/SgdComplexesConverter.java b/sgd-complexes/src/main/java/org/intermine/bio/dataconversion/SgdComplexesConverter.java
@@ -49,6 +49,7 @@ public class SgdComplexesConverter extends BioDBConverter
     private Map<String, Item> publications = new HashMap();
     private Map<String, String> terms = new HashMap<String, String>();
     private Map<String, Item> complexes = new HashMap();
+    //private Map<String, Item> complexnames = new HashMap();
     private final Map<String, Item> genes = new HashMap<String, Item>();
     private static final String TAXON_ID = "4932";
     private Item yorganism;
@@ -60,10 +61,11 @@ public class SgdComplexesConverter extends BioDBConverter
      * @param model the Model used by the object store we will write to with the ItemWriter
      * @param writer an ItemWriter used to handle Items created
      */
-    public SgdComplexesConverter(Database database, Model model, ItemWriter writer) {
+    public SgdComplexesConverter(Database database, Model model, ItemWriter writer) throws ObjectStoreException{
         super(database, model, writer, DATA_SOURCE_NAME, DATASET_TITLE);
         yorganism = createItem("Organism");
         yorganism.setAttribute("taxonId", TAXON_ID);
+        store(yorganism);
     }
 
 
@@ -73,7 +75,8 @@ public SgdComplexesConverter(Database database, Model model, ItemWriter writer)
     public void process() throws Exception {
         Connection connection = getDatabase().getConnection();
         processComplexes(connection);
-        //processComplexInteractions(connection);
+        processComplexInteractions(connection);
+        storeGenes();
         storeComplexes();
     }
 
@@ -194,9 +197,7 @@ private Item getGoAnnot(String goId) throws ObjectStoreException {
             } catch (ObjectStoreException e) {
                 throw new ObjectStoreException(e);
             }
-
             return goAnnotation;
-
     }
 
     /**
@@ -245,7 +246,6 @@ private String getEvidence(String value) throws ObjectStoreException{
             evidence.setReference("ontologyTerm", eco.getIdentifier());
         }
 
-
         try {
             store(evidence);
         } catch (ObjectStoreException e) {
@@ -316,8 +316,9 @@ private void processComplexInteractions(Connection connection) throws ObjectStor
 
             Item gene1 = getGeneItem(dbentity1);
             Item gene2 = null;
-            if(dbentity2 != null) {  gene2 = getGeneItem(dbentity2); }
-
+            if(dbentity2 != null) {
+                gene2 = getGeneItem(dbentity2);
+            }
             processInteractions(complex_accession, gene1, gene2, range_start, range_end,
                     stochiometry, role, type);
         }
@@ -338,6 +339,7 @@ private void processComplexInteractions(Connection connection) throws ObjectStor
     private void processInteractions(String complexacc, Item ref, Item binderRef, String range_start, String range_end,
                 String stochiometry, String role, String type) throws ObjectStoreException {
 
+                Item complex = complexes.get(complexacc);
                 Item interactor = createItem("Interactor");
                 //interactor.setAttribute("annotations", annotations.toString());
                 if (StringUtils.isNotEmpty(role)) { interactor.setAttribute("biologicalRole", role);}
@@ -350,7 +352,7 @@ private void processInteractions(String complexacc, Item ref, Item binderRef, St
                 if (binderRef != null) {
                     interaction.setReference("participant2", binderRef);
                 }
-                interaction.setReference("complex", complexacc);
+                interaction.setReference("complex", complex);
                 store(interaction);
                 interactor.addToCollection("interactions", interaction);
 
@@ -372,7 +374,6 @@ private void processInteractions(String complexacc, Item ref, Item binderRef, St
                 store(interactor);
                 //detail.addInteractor(interactor.getIdentifier());
 
-                Item complex = complexes.get(complexacc);
                 if (complex != null) {
                     complex.addToCollection("allInteractors", interactor);
                 }
@@ -434,6 +435,20 @@ private void storeComplexes() throws ObjectStoreException {
         }
     }
 
+    /**
+     *
+     * @throws ObjectStoreException
+     */
+
+    private void storeGenes() throws ObjectStoreException {
+        for (Item gene : genes.values()) {
+            try {
+                store(gene);
+            } catch (ObjectStoreException e) {
+                throw new ObjectStoreException(e);
+            }
+        }
+    }
     /**
      *
      * @param geneId
@@ -446,7 +461,7 @@ private Item getGeneItem(String geneId)
         Item gene = genes.get(geneId);
 
         if (gene == null) {
-            gene = createItem("Gene");
+            gene = createItem("Protein");
             genes.put(geneId, gene);
             gene.setAttribute("primaryIdentifier", geneId);
             gene.setReference("organism", yorganism);

diff --git a/sgd-complexes/src/main/resources/sgd-complexes_keys.properties b/sgd-complexes/src/main/resources/sgd-complexes_keys.properties
@@ -14,4 +14,6 @@ Gene.key_primaryidentifier=primaryIdentifier
 Gene.key_secondaryidentifier=secondaryIdentifier
 Gene.key_symbol_org=symbol, organism
 #yes merge - kk;  no merging, I think.
-#Interaction.key_interaction=participant1, participant2
+#Interaction.key_interaction=participant1, participant2
+Protein.key_primaryacc=primaryAccession
+GOEvidenceCode.key_code=code