psi-complexes use local

psi-complexes/src/main/java/org/intermine/bio/dataconversion/PsiComplexesConverter.java

@@ -339,15 +339,17 @@ private String processProtein(Interactor participant)
             // if no SGD identifier, eg. for small molecules, accession and identifier are equal
             primaryIdentifier = accession;
         }
+        System.out.println("primary Identifier....."+ primaryIdentifier);
         String refId = interactors.get(primaryIdentifier);
         if (refId == null) {
             String typeTermIdentifier = participant.getInteractorType().getMIIdentifier();
             String interactorType = INTERACTOR_TYPES.get(typeTermIdentifier);
             if (interactorType == null) {
                 // see #1168
-                LOG.error("Unknown interactor type: " + typeTermIdentifier);
+                LOG.error("Unknown interactor type: " + interactorType);
                 interactorType = DEFAULT_INTERACTOR_TYPE;
             }
+            System.out.println("Interactor Type....."+ primaryIdentifier);
             Item protein = createItem(interactorType);
             protein.setAttribute("primaryIdentifier", primaryIdentifier);
             if (PROTEIN.equals(typeTermIdentifier)) {

psi-complexes/src/main/resources/psi-complexes_keys.properties

@@ -1,15 +1,19 @@
 DataSet.key_name=name
 DataSource.key_name=name
-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
-InteractionTerm.key_identifier=identifier
 Ontology.key_name=name
 OntologyTerm.key_identifier=identifier
 OntologyTerm.key_name_ontology=name, ontology
 Organism.key_taxonid=taxonId
 Publication.key_pubmed=pubMedId
+InteractionTerm.key_identifier=identifier
+InteractionTerm.key_name = name
+Protein.key_primaryidentifier=primaryIdentifier
 ProteinDomain.key_identifier=primaryIdentifier
-Protein.key_primaryidentifier=primaryIdentifier
+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
+
+
+

settings.gradle

@@ -22,7 +22,8 @@ include ':bio-source-cglabrata-homologs',
  ':bio-source-treefam', ':bio-source-homologene',
  ':bio-source-panther',
  ':bio-source-homologene',
- ':bio-source-ensembl-compara', ':bio-source-go-slim'
+ ':bio-source-ensembl-compara', ':bio-source-go-slim' 
+//':bio-source-psi-mi-ontology', ':bio-source-psi-complexes'
 
 
 
@@ -58,6 +59,8 @@ project(':bio-source-treefam').projectDir = new File(settingsDir, './treefam')
 project(':bio-source-panther').projectDir = new File(settingsDir, './panther')
 project(':bio-source-homologene').projectDir = new File(settingsDir, './homologene')
 project(':bio-source-ensembl-compara').projectDir = new File(settingsDir, './ensembl-compara')
+//project(':bio-source-psi-mi-ontology').projectDir = new File(settingsDir, './psi-mi-ontology')
+//project(':bio-source-psi-complexes').projectDir = new File(settingsDir, './psi-complexes')
 
 
 

sgd/src/main/resources/sgd_keys.properties

@@ -7,3 +7,13 @@ Gene.key_primaryidentifier=primaryIdentifier
 Chromosome.key_primaryidentifier=primaryIdentifier
 Protein.key_primaryidentifier=primaryIdentifier
 ProteinAbundance.key=abundance, treatment, assay
+
+SequenceFeature.key_primaryidentifier = primaryIdentifier
+Gene.key_secondaryidentifier = secondaryIdentifier, organism
+Gene.key_symbol_org = symbol, organism
+Protein.key_secondaryidentifier = secondaryIdentifier
+Protein.key_primaryacc = primaryAccession
+Protein.key_md5checksum_taxonid = md5checksum, organism
+# IntAct and BioGRID
+InteractionTerm.key_name = name
+InteractionTerm.key_identifier = identifier

treefam/src/main/java/org/intermine/bio/dataconversion/TreefamConverter.java

@@ -127,7 +127,6 @@ private void readConfig() {
             String[] configs = new String[2];
             configs[0] = col;
             configs[1] = value;
-
             config.put(taxonId, configs);
         }
     }