Refresh data: fix gx prefix mapping (Gaia-X)

src/prefixmaps/data/go.csv

@@ -1,5 +1,4 @@
 context,prefix,namespace,status
-go,AspGD_LOCUS,http://identifiers.org/aspgd.locus/,canonical
 go,BFO,http://purl.obolibrary.org/obo/BFO_,canonical
 go,BTO,http://purl.obolibrary.org/obo/BTO_,canonical
 go,CARO,http://purl.obolibrary.org/obo/CARO_,canonical
@@ -10,6 +9,7 @@ go,CL,http://purl.obolibrary.org/obo/CL_,canonical
 go,dbSNP,http://identifiers.org/dbsnp/,canonical
 go,DDANAT,http://purl.obolibrary.org/obo/DDANAT_,canonical
 go,dictyBase,http://identifiers.org/dictybase.gene/,canonical
+go,EC,http://purl.uniprot.org/enzyme/,canonical
 go,ECO,http://purl.obolibrary.org/obo/ECO_,canonical
 go,EMAPA,http://purl.obolibrary.org/obo/EMAPA_,canonical
 go,ENSEMBL,http://identifiers.org/ensembl/,canonical
@@ -31,6 +31,7 @@ go,IntAct,http://identifiers.org/intact/,canonical
 go,InterPro,http://identifiers.org/interpro/,canonical
 go,KEGG_ENZYME,http://identifiers.org/kegg.enzyme/,canonical
 go,KEGG_PATHWAY,http://identifiers.org/kegg.pathway/,canonical
+go,KEGG_REACTION,http://www.kegg.jp/entry/,canonical
 go,MA,http://purl.obolibrary.org/obo/MA_,canonical
 go,MaizeGDB_Locus,http://identifiers.org/maizegdb.locus/,canonical
 go,MetaCyc,http://identifiers.org/metacyc.reaction/,canonical
@@ -46,18 +47,23 @@ go,PomBase,http://identifiers.org/pombase/,canonical
 go,PR,http://purl.obolibrary.org/obo/PR_,canonical
 go,Reactome,http://identifiers.org/reactome/,canonical
 go,RGD,http://identifiers.org/rgd/,canonical
+go,RHEA,http://rdf.rhea-db.org/,canonical
 go,RO,http://purl.obolibrary.org/obo/RO_,canonical
 go,SGD,http://identifiers.org/sgd/,canonical
-go,SGN,http://identifiers.org/sgn/,canonical
 go,SO,http://purl.obolibrary.org/obo/SO_,canonical
-go,TAIR,http://identifiers.org/tair.locus/,canonical
+go,TAIR,https://registry.identifiers.org/registry/tair.name/,canonical
+go,TCDB,http://identifiers.org/tcdb/,canonical
 go,TGD,http://identifiers.org/tgd/,canonical
 go,TreeGrafter,http://identifiers.org/panther.family/,namespace_alias
 go,TriTrypDB,http://identifiers.org/tritrypdb/,canonical
 go,UBERON,http://purl.obolibrary.org/obo/UBERON_,canonical
+go,UM-BBD_pathwayID,http://identifiers.org/umbbd.pathway/,canonical
+go,UM-BBD_reactionID,http://identifiers.org/umbbd.reaction/,canonical
 go,UniProtKB,http://identifiers.org/uniprot/,canonical
+go,VZ,https://viralzone.expasy.org/,canonical
 go,WB,http://identifiers.org/wormbase/,canonical
 go,WBls,http://purl.obolibrary.org/obo/WBls_,canonical
 go,WBPhenotype,http://purl.obolibrary.org/obo/WBPhenotype_,canonical
 go,Xenbase,http://identifiers.org/xenbase/,canonical
+go,ZFA,http://purl.obolibrary.org/obo/ZFA_,canonical
 go,ZFIN,http://identifiers.org/zfin/,canonical

src/prefixmaps/data/obo.csv

@@ -186,6 +186,7 @@ obo,ORNASEQ,http://purl.obolibrary.org/obo/ORNASEQ_,canonical
 obo,OVAE,http://purl.obolibrary.org/obo/OVAE_,canonical
 obo,PAO,http://purl.obolibrary.org/obo/PAO_,canonical
 obo,PATO,http://purl.obolibrary.org/obo/PATO_,canonical
+obo,PBPKO,http://purl.obolibrary.org/obo/PBPKO_,canonical
 obo,PCL,http://purl.obolibrary.org/obo/PCL_,canonical
 obo,PCO,http://purl.obolibrary.org/obo/PCO_,canonical
 obo,PD_ST,http://purl.obolibrary.org/obo/PD_ST_,canonical
@@ -201,6 +202,7 @@ obo,PO,http://purl.obolibrary.org/obo/PO_,canonical
 obo,PORO,http://purl.obolibrary.org/obo/PORO_,canonical
 obo,PPO,http://purl.obolibrary.org/obo/PPO_,canonical
 obo,PR,http://purl.obolibrary.org/obo/PR_,canonical
+obo,PREFER,http://purl.obolibrary.org/obo/PREFER_,canonical
 obo,PROCO,http://purl.obolibrary.org/obo/PROCO_,canonical
 obo,PROPREO,http://purl.obolibrary.org/obo/PROPREO_,canonical
 obo,PSDO,http://purl.obolibrary.org/obo/PSDO_,canonical

src/prefixmaps/datamodel/context.py

@@ -107,10 +107,8 @@ def validate(self) -> List[str]:
         if not PREFIX_RE.match(self.prefix):
             messages.append(f"prefix {self.prefix} does not match {PREFIX_RE}")
         if not NAMESPACE_RE.match(self.namespace):
-            messages.append(
-                f"namespace {self.namespace} does not match {NAMESPACE_RE}\
-                (prefix: {self.prefix})"
-            )
+            messages.append(f"namespace {self.namespace} does not match {NAMESPACE_RE}\
+                (prefix: {self.prefix})")
         return messages
 
 

tests/test_core/test_prefixmaps.py

@@ -199,8 +199,9 @@ def test_w3c_semweb_prefixes_in_dyn_merged(self):
                 self.assertIn(pfx, pm, f"prefix {pfx!r} missing from dynamic merged context")
                 self.assertEqual(pm[pfx], exp)
                 self.assertEqual(
-                    pmi[exp], pfx,
-                    f"expected canonical prefix {pfx!r} for {exp}, got {pmi.get(exp)!r}"
+                    pmi[exp],
+                    pfx,
+                    f"expected canonical prefix {pfx!r} for {exp}, got {pmi.get(exp)!r}",
                 )
 
     def test_prefixcc(self):