Fixed XrefRule and XrefUtil/Resolver issue - it couldn't detect db sp…

…elling variants and so misreported "unknown.db"

biopax-validator/src/main/java/org/biopax/validator/utils/OntologyUtils.java

@@ -215,7 +215,7 @@ public synchronized void init() {
       ontologyManager.loadOntologies(ontologyConfig);
       //Normalize ontology names
       for (String id : ontologyManager.getOntologyIDs()) {
-        Namespace ns = Resolver.getNamespace(id);
+        Namespace ns = Resolver.getNamespace(id, true);
         String officialName = id;
         if(ns != null) {
           officialName = ns.getName();
@@ -236,6 +236,7 @@ public synchronized void init() {
     // first, we prepare lists of db synonyms from
     //  - Bioregistry.io (get each entry's prefix, name, synonyms)
     //  - MI (OBO terms under the "database citation" root)
+    // but not adding the spelling variants from the Resolver.getSpellmap().
     for (Namespace ns : Resolver.getNamespaces().values()) {
       String name = dbName(ns.getName()); //trim,uppercase
       String prefix = dbName(ns.getPrefix());
@@ -289,7 +290,7 @@ public boolean match(Collection<String> a, Collection<String> b) {
         }
         //if possible, move the prefix and preferred name on top (the order is important)
         String topName = merged.get(0);
-        Namespace ns = Resolver.getNamespace(topName);
+        Namespace ns = Resolver.getNamespace(topName, true);
         if(ns != null) {
           merged.add(0, dbName(ns.getPrefix()));
           merged.add(1, dbName(ns.getName()));
@@ -321,9 +322,10 @@ public List<String> getSynonymsForDbName(String name) {
 
   @Override
   public String getPrimaryDbName(String name) {
-    List<String> names = getSynonymsForDbName(name);
+    List<String> names = getSynonymsForDbName(name); //these synonyms do not usually include all spelling variants
     if (names.isEmpty()) {
-      return null;
+      Namespace ns = Resolver.getNamespace(name, true); //also search in spelling variants
+      return ns != null ? ns.getName() : null;
     } else if (names.size() > 1) {
       return names.get(1);
     } else {
@@ -335,7 +337,8 @@ public String getPrimaryDbName(String name) {
   public String getPrefix(String name) {
     List<String> names = getSynonymsForDbName(name);
     if (names.isEmpty()) {
-      return null;
+      Namespace ns = Resolver.getNamespace(name, true); //also search in spelling variants
+      return ns != null ? ns.getPrefix() : null;
     } else {
       return names.get(0).toLowerCase();
     }
@@ -350,13 +353,13 @@ public boolean checkIdFormat(String db, String id) {
   @Override
   public boolean canCheckIdFormatIn(String name) {
     String db = getPrimaryDbName(name);
-    Namespace ns = Resolver.getNamespace(db);
+    Namespace ns = Resolver.getNamespace(db, true);
     return  ns != null && StringUtils.isNotBlank(ns.getPattern());
   }
 
   @Override
   public String getRegexpString(String db) {
-    Namespace ns = Resolver.getNamespace(getPrimaryDbName(db));
+    Namespace ns = Resolver.getNamespace(getPrimaryDbName(db), true); //TODO: why primary name?..
     return  (ns != null) ? ns.getPattern() : null;
   }
 

biopax-validator/src/main/resources/codes.properties

@@ -69,7 +69,7 @@ invalid.id.format.default=Xref 'id' value does not match the standard pattern fo
 invalid.id.format=db: {0} (recognized as: {1}), id: {2}, pattern: {3}
 invalid.id.format.category=recommendation
 
-unknown.db.default=Unknown database identifier. For Xref 'db' property and Provenance standard/display name properties, please use the official database names from MIRIAM. PSI-MI "database citation" and child terms are also allowed but they are deprecated. Please use MIRIAM when possible
+unknown.db.default=Unknown database identifier. For Xref 'db' property and Provenance standard/display name properties, please use the official database name/prefix or synonym. MI "database citation" and child terms are also allowed but deprecated. Please use Bioregistry.
 unknown.db=db name: {0}
 unknown.db.category=recommendation
 
@@ -81,7 +81,7 @@ cloned.utility.class.default=Two or more BioPAX objects are equivalent. Equivale
 cloned.utility.class=equivalent elements: {0} (utility class: {1})
 cloned.utility.class.category=recommendation
 
-shared.unification.xref.default=Two or more elements share the same unification xref. Please note that defining a UnificationXref to an external resource implies that this object and external resource are identical. Therefore elements that share the same unification xref must also be identical. Please consider merging these elements if they are identical, otherwise please consider converting this external reference to a RelationshipXref
+shared.unification.xref.default=Two or more elements share the same unification xref. Please note that defining a UnificationXref to an external resource implies that this object and external resource are identical. Therefore, elements that share the same unification xref must also be identical. Please consider merging these elements if they are identical, otherwise please consider converting this external reference to a RelationshipXref
 shared.unification.xref=is the xref of: {0}
 shared.unification.xref.category=recommendation