Add missing test

biopragmatics · Nov 2, 2023 · 3a899bd · 3a899bd
1 parent 200f4e4
commit 3a899bd
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Showing 7 changed files with 20 additions and 15 deletions.
diff --git a/exports/contexts/obo.context.jsonld b/exports/contexts/obo.context.jsonld
@@ -254,7 +254,7 @@
         "PLANA": "http://purl.obolibrary.org/obo/PLANA_",
         "PLANP": "http://purl.obolibrary.org/obo/PLANP_",
         "PLO": "http://purl.obolibrary.org/obo/PLO_",
-        "PMID": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "PMID": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "PO": "http://purl.obolibrary.org/obo/PO_",
         "PORO": "http://purl.obolibrary.org/obo/PORO_",
         "PPO": "http://purl.obolibrary.org/obo/PPO_",

diff --git a/exports/contexts/obo.context.ttl b/exports/contexts/obo.context.ttl
@@ -257,7 +257,7 @@
     [ sh:prefix "PLANA" ; sh:namespace "http://purl.obolibrary.org/obo/PLANA_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],
     [ sh:prefix "PLANP" ; sh:namespace "http://purl.obolibrary.org/obo/PLANP_"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PLO" ; sh:namespace "http://purl.obolibrary.org/obo/PLO_"^^xsd:anyURI  ],
-    [ sh:prefix "PMID" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "PMID" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PO" ; sh:namespace "http://purl.obolibrary.org/obo/PO_"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PORO" ; sh:namespace "http://purl.obolibrary.org/obo/PORO_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],
     [ sh:prefix "PPO" ; sh:namespace "http://purl.obolibrary.org/obo/PPO_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],

diff --git a/exports/contexts/obo.epm.json b/exports/contexts/obo.epm.json
@@ -4366,7 +4366,7 @@
             "pmid",
             "pubmed"
         ],
-        "uri_prefix": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "uri_prefix": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "uri_prefix_synonyms": [
             "http://bio2rdf.org/pubmed:",
             "http://bioregistry.io/MEDLINE:",
@@ -4382,6 +4382,7 @@
             "http://pubmed.ncbi.nlm.nih.gov/",
             "http://purl.uniprot.org/citations/",
             "http://purl.uniprot.org/pubmed/",
+            "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
             "http://scholia.toolforge.org/pubmed/",
             "http://www.hubmed.org/display.cgi?uids=",
             "http://www.ncbi.nlm.nih.gov/pubmed/",
@@ -4401,8 +4402,7 @@
             "https://purl.uniprot.org/pubmed/",
             "https://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
             "https://scholia.toolforge.org/pubmed/",
-            "https://www.hubmed.org/display.cgi?uids=",
-            "https://www.ncbi.nlm.nih.gov/pubmed/"
+            "https://www.hubmed.org/display.cgi?uids="
         ]
     },
     {

diff --git a/exports/contexts/obo_synonyms.context.jsonld b/exports/contexts/obo_synonyms.context.jsonld
@@ -297,7 +297,7 @@
         "MC": "http://purl.obolibrary.org/obo/MC_",
         "MCO": "http://purl.obolibrary.org/obo/MCO_",
         "MCRO": "http://purl.obolibrary.org/obo/MCRO_",
-        "MEDLINE": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "MEDLINE": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "MEDRA": "http://purl.bioontology.org/ontology/MDRFRE/",
         "MESH": "http://id.nlm.nih.gov/mesh/",
         "MESHA": "http://id.nlm.nih.gov/mesh/",
@@ -437,7 +437,7 @@
         "PLO": "http://purl.obolibrary.org/obo/PLO_",
         "PMC": "http://europepmc.org/articles/",
         "PMCID": "http://europepmc.org/articles/",
-        "PMID": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "PMID": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "PO": "http://purl.obolibrary.org/obo/PO_",
         "PORO": "http://purl.obolibrary.org/obo/PORO_",
         "PPO": "http://purl.obolibrary.org/obo/PPO_",
@@ -459,7 +459,7 @@
         "Progenetix": "https://progenetix.org/services/ids/",
         "PuRO": "http://purl.org/spar/pro/",
         "PubChem_Compound_CID": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID",
-        "PubMed": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "PubMed": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "Pubchem": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID",
         "RBO": "http://purl.obolibrary.org/obo/RBO_",
         "RCSB_PDB": "https://rdf.wwpdb.org/pdb/",
@@ -1657,7 +1657,7 @@
         "pmap.substratedb": "https://identifiers.org/pmap.substratedb:",
         "pmc": "http://europepmc.org/articles/",
         "pmdb": "https://bioinformatics.cineca.it/PMDB/user//search.php?idsearch=",
-        "pmid": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "pmid": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "pmp": "http://purl.uniprot.org/uniprot/",
         "pmr": "https://models.physiomeproject.org/exposure/",
         "pmr.workspace": "https://models.physiomeproject.org/workspace/",
@@ -1697,7 +1697,7 @@
         "pubchem_id": "http://rdf.ncbi.nlm.nih.gov/pubchem/compound/CID",
         "publons.publication": "https://publons.com/publon/",
         "publons.researcher": "https://publons.com/researcher/",
-        "pubmed": "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/",
+        "pubmed": "https://www.ncbi.nlm.nih.gov/pubmed/",
         "px": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=",
         "pypi": "https://pypi.org/project/",
         "qb": "http://purl.org/linked-data/cube#",

diff --git a/exports/contexts/obo_synonyms.context.ttl b/exports/contexts/obo_synonyms.context.ttl
@@ -338,11 +338,11 @@
     [ sh:prefix "PLANA" ; sh:namespace "http://purl.obolibrary.org/obo/PLANA_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],
     [ sh:prefix "PLANP" ; sh:namespace "http://purl.obolibrary.org/obo/PLANP_"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PLO" ; sh:namespace "http://purl.obolibrary.org/obo/PLO_"^^xsd:anyURI  ],
-    [ sh:prefix "PMID" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
-    [ sh:prefix "MEDLINE" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
-    [ sh:prefix "PubMed" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
-    [ sh:prefix "pmid" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
-    [ sh:prefix "pubmed" ; sh:namespace "http://rdf.ncbi.nlm.nih.gov/pubchem/reference/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "PMID" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "MEDLINE" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "PubMed" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "pmid" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
+    [ sh:prefix "pubmed" ; sh:namespace "https://www.ncbi.nlm.nih.gov/pubmed/"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PO" ; sh:namespace "http://purl.obolibrary.org/obo/PO_"^^xsd:anyURI ; sh:pattern "^\\d+$" ],
     [ sh:prefix "PORO" ; sh:namespace "http://purl.obolibrary.org/obo/PORO_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],
     [ sh:prefix "PPO" ; sh:namespace "http://purl.obolibrary.org/obo/PPO_"^^xsd:anyURI ; sh:pattern "^\\d{7}$" ],

diff --git a/src/bioregistry/resource_manager.py b/src/bioregistry/resource_manager.py
@@ -730,6 +730,7 @@ def get_prefix_map(
         prefix_priority: Optional[Sequence[str]] = None,
         include_synonyms: bool = False,
         remapping: Optional[Mapping[str, str]] = None,
+        rewiring: Optional[Mapping[str, str]] = None,
         blacklist: Optional[typing.Collection[str]] = None,
     ) -> Mapping[str, str]:
         """Get a mapping from Bioregistry prefixes to their URI prefixes .
@@ -743,13 +744,15 @@ def get_prefix_map(
         :param include_synonyms: Should synonyms of each prefix also be included as additional prefixes, but with
             the same URI prefix?
         :param remapping: A mapping from Bioregistry prefixes to preferred prefixes.
+        :param rewiring: A mapping from Bioregistry prefixes to URI prefixes.
         :param blacklist: Prefixes to skip
         :return: A mapping from prefixes to URI prefixes.
         """
         converter = self.get_converter(
             prefix_priority=prefix_priority,
             uri_prefix_priority=uri_prefix_priority,
             remapping=remapping,
+            rewiring=rewiring,
             blacklist=blacklist,
         )
         rv = {}
@@ -1610,6 +1613,7 @@ def get_context_artifacts(
             prefix_priority=context.prefix_priority,
             include_synonyms=include_synonyms,
             blacklist=context.blacklist,
+            rewiring=context.custom_prefix_map,
         )
         prescriptive_pattern_map = self.get_pattern_map(
             remapping=context.prefix_remapping,

diff --git a/tests/test_contexts.py b/tests/test_contexts.py
@@ -65,6 +65,7 @@ def test_obo_converter(self):
         self.assertEqual("Orphanet", converter.standardize_prefix("ordo"))
         self.assertEqual("GO", converter.standardize_prefix("GO"))
         self.assertEqual("GO", converter.standardize_prefix("gomf"))
+        self.assertEqual("https://www.ncbi.nlm.nih.gov/pubmed/", converter.bimap["PMID"])
         # FIXME later, handle adding canonical bioregistry prefix
         #  as synonym when non-default prefix priority ordering is given
         # self.assertEqual("GO", converter.standardize_prefix("go"))