Merge pull request UCDenver-ccp#7 from sinistral/develop.interpro-unk…

…nown-source

Handle unknown external ID in interpro2ipr files.

datasource-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/ebi/interpro/InterProExternalReferenceFactory.java

@@ -34,6 +34,7 @@
  */
 
 import edu.ucdenver.ccp.datasource.identifiers.DataSourceIdentifier;
+import edu.ucdenver.ccp.datasource.identifiers.UnknownDataSourceIdentifier;
 import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.Gene3dID;
 import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.HamapAnnotationRuleID;
 import edu.ucdenver.ccp.datasource.identifiers.ebi.interpro.PantherID;
@@ -63,7 +64,9 @@ public class InterProExternalReferenceFactory {
 	private static final String PRODOM_PREFIX = "PD";
 
 
-	public static DataSourceIdentifier<String> parseExternalReference(String databaseReferenceID) {
+    public static DataSourceIdentifier<String> parseExternalReference(
+			String databaseReferenceID)
+    {
 		if (databaseReferenceID.startsWith(PFAM_PREFIX))
 			return new PfamID(databaseReferenceID);
 		if (databaseReferenceID.startsWith(TIGRFAMS_PREFIX))
@@ -87,9 +90,9 @@ public static DataSourceIdentifier<String> parseExternalReference(String databas
 		if (databaseReferenceID.startsWith(HAMAP_PREFIX))
 			return new HamapAnnotationRuleID(databaseReferenceID);
 		if (databaseReferenceID.startsWith(PRODOM_PREFIX))
-			return new ProDomID(databaseReferenceID);
-		throw new IllegalArgumentException(String.format("Unknown external database ID type for ID: %s",
-				databaseReferenceID));
+            return new ProDomID(databaseReferenceID);
+
+        return new UnknownDataSourceIdentifier(databaseReferenceID);
 	}
 
 }

datasource-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/hgnc/HgncDownloadFileParser.java

@@ -558,7 +558,7 @@ private DataSourceIdentifier<?> resolveSpecialistId(String idStr, String link) {
 			return new SlcId(idStr);
 		}
 
-		return new UnknownDataSourceIdentifier(idStr, null);
+		return new UnknownDataSourceIdentifier(idStr);
 	}
 
 	/**

datasource-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/irefweb/IRefWebPsiMitab2_6FileParser.java

@@ -334,7 +334,7 @@ private Set<DataSourceIdentifier<?>> resolveInteractionDbIds(String interactionI
 				} else if (id.startsWith("HPRD")) {
 					ids.add(new HprdID(StringUtil.removePrefix(id, "HPRD:")));
 				} else {
-					ids.add(new UnknownDataSourceIdentifier(id, null));
+					ids.add(new UnknownDataSourceIdentifier(id));
 				}
 			} catch (IllegalArgumentException e) {
 				ids.add(new ProbableErrorDataSourceIdentifier(id, null, e.getMessage()));
@@ -360,10 +360,10 @@ private DataSourceIdentifier<?> resolveInteractorId(String idStr) {
 			return null;
 		}
 		if (idStr.startsWith("xx:")) {
-			return new UnknownDataSourceIdentifier(idStr, null);
+			return new UnknownDataSourceIdentifier(idStr);
 		}
 		if (idStr.startsWith("other:")) {
-			return new UnknownDataSourceIdentifier(idStr, null);
+			return new UnknownDataSourceIdentifier(idStr);
 		}
 		if (idStr.equals("null")) {
 			return null;
@@ -486,7 +486,7 @@ private DataSourceIdentifier<?> resolveInteractorId(String idStr) {
 			return new ProbableErrorDataSourceIdentifier(idStr, null, e.getMessage());
 		}
 
-		return new UnknownDataSourceIdentifier(idStr, null);
+		return new UnknownDataSourceIdentifier(idStr);
 	}
 
 	/**
@@ -683,7 +683,7 @@ private DataSourceIdentifier<?> resolveAliasId(String aliasStr) {
 		} else if (aliasStr.startsWith("hgnc:")) {
 			return new HgncGeneSymbolID(StringUtil.removePrefix(aliasStr, "hgnc:"));
 		}
-		return new UnknownDataSourceIdentifier(aliasStr, null);
+		return new UnknownDataSourceIdentifier(aliasStr);
 	}
 
 }

datasource-fileparsers/src/main/java/edu/ucdenver/ccp/datasource/fileparsers/pharmgkb/PharmGkbGeneFileParser.java

@@ -274,7 +274,7 @@ private DataSourceIdentifier<?> resolveCrossRefId(String refStr) {
 			} else if (refStr.startsWith(URL_PREFIX)) {
 				return new CrossReferenceUrl(StringUtil.removePrefix(refStr, URL_PREFIX));
 			} else {
-				return new UnknownDataSourceIdentifier(refStr, null);
+				return new UnknownDataSourceIdentifier(refStr);
 			}
 		} catch (IllegalArgumentException e) {
 			return new ProbableErrorDataSourceIdentifier(refStr, null, e.getMessage());