Handle unknown external ID in interpro2ipr files.

Since we're not in control of the external datasources that are used by
datasource providers, validating all external IDs makes our code
brittle.  Since we don't use sources that we don't know about, we can
simply gloss over the external IDs that we don't recognise.

Doing so yields triples of the form:

<http://kabob.ucdenver.edu/iao/interpro/F_InterProProtein2IprDatFileData_externalReference_J7eGDFPyhBVMdgpi5AN9XzD1tu8> <http://purl.obolibrary.org/obo/IAO_0000219> <http://kabob.ucdenver.edu/iao/kabob/R_NonNormalizedIdentifierRecord_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> .
<http://kabob.ucdenver.edu/iao/kabob/R_NonNormalizedIdentifierRecord_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://kabob.ucdenver.edu/iao/kabob/NonNormalizedIdentifierRecord> .
<http://kabob.ucdenver.edu/iao/kabob/R_NonNormalizedIdentifierRecord_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://kabob.ucdenver.edu/iao/hasTemplate> <http://kabob.ucdenver.edu/iao/kabob/NonNormalizedIdentifierRecordSchema1> .
<http://kabob.ucdenver.edu/iao/kabob/R_NonNormalizedIdentifierRecord_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://purl.obolibrary.org/obo/BFO_0000051> <http://kabob.ucdenver.edu/iao/kabob/F_NonNormalizedIdentifierRecord_identifier_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> .
<http://kabob.ucdenver.edu/iao/kabob/F_NonNormalizedIdentifierRecord_identifier_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://kabob.ucdenver.edu/iao/hasTemplate> <http://kabob.ucdenver.edu/iao/kabob/NonNormalizedIdentifierRecord_identifierDataField1> .
<http://kabob.ucdenver.edu/iao/kabob/F_NonNormalizedIdentifierRecord_identifier_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://kabob.ucdenver.edu/iao/FieldValue> .
<http://kabob.ucdenver.edu/iao/kabob/F_NonNormalizedIdentifierRecord_identifier_fM4tG2mEQK7AzC4Z0DKJDbkbNGU> <http://purl.obolibrary.org/obo/IAO_0000219> "cd01991"@en .

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());