Merge pull request #44 from linkml/update_bioregistry

update dependencies and registry contents to resolve teh prefix 'action' in the merge file not having a canonical expansion
linkml · Oct 12, 2023 · 932cbda · 932cbda
2 parents 589ded6 + 52f647a
commit 932cbda
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diff --git a/.github/workflows/main.yaml b/.github/workflows/main.yaml
@@ -32,7 +32,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [ "3.11", "3.7" ]
+        python-version: [ "3.11", "3.8" ]
 
     steps:
 

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "prefixmaps"
-version = "0.1.4"
+version = "0.1.6"
 description = "A python library for retrieving semantic prefix maps"
 readme = "README.md"
 authors = ["cmungall <[email protected]>"]
@@ -23,7 +23,7 @@ homepage = "https://github.com/linkml/prefixmaps"
 
 
 [tool.poetry.dependencies]
-python = "^3.7.6"
+python = "^3.8.0"
 pyyaml = ">=5.3.1"
 sphinx-rtd-theme = {version = "^1.0.0", extras = ["docs"]}
 Sphinx = {version = "^5.3.0", extras = ["docs"]}
@@ -32,9 +32,13 @@ sphinx-click = {version = "^4.3.0", extras = ["docs"]}
 myst-parser = {version = "^0.18.1", extras = ["docs"]}
 click = ">=8.1.3"
 requests = {version = "^2.28.1", extras = ["refresh"]}
-bioregistry = {version = "^0.8.0", extras = ["refresh"]}
+bioregistry = {version = "^0.10.0", extras = ["refresh"]}
 rdflib = {version = "^6.2.0", extras = ["refresh"]}
 curies = ">=0.5.3"
+tox = "^4.11.3"
+# this forces tox to use pydantic ^1 instead of installing pydantic 2 as part of its "refresh" environment.
+# bioregistry is still at pydantic 1.0, so this is necessary to avoid refresh failure.
+pydantic = "^1.8.2"
 
 [tool.poetry.dev-dependencies]
 pytest = ">=6.2"

diff --git a/src/prefixmaps/data/bioregistry.csv b/src/prefixmaps/data/bioregistry.csv
diff --git a/src/prefixmaps/data/bioregistry.upper.csv b/src/prefixmaps/data/bioregistry.upper.csv
diff --git a/src/prefixmaps/data/merged.csv b/src/prefixmaps/data/merged.csv
diff --git a/src/prefixmaps/data/merged.oak.csv b/src/prefixmaps/data/merged.oak.csv
diff --git a/src/prefixmaps/data/obo.csv b/src/prefixmaps/data/obo.csv
@@ -118,6 +118,7 @@ obo,MAO,http://purl.obolibrary.org/obo/MAO_,canonical
 obo,MAT,http://purl.obolibrary.org/obo/MAT_,canonical
 obo,MAXO,http://purl.obolibrary.org/obo/MAXO_,canonical
 obo,MCO,http://purl.obolibrary.org/obo/MCO_,canonical
+obo,MCRO,http://purl.obolibrary.org/obo/MCRO_,canonical
 obo,MF,http://purl.obolibrary.org/obo/MF_,canonical
 obo,MFMO,http://purl.obolibrary.org/obo/MFMO_,canonical
 obo,MFO,http://purl.obolibrary.org/obo/MFO_,canonical

diff --git a/src/prefixmaps/data/prefixcc.csv b/src/prefixmaps/data/prefixcc.csv
diff --git a/src/prefixmaps/data/w3id.csv b/src/prefixmaps/data/w3id.csv
diff --git a/src/prefixmaps/datamodel/context.py b/src/prefixmaps/datamodel/context.py
@@ -1,6 +1,7 @@
 """Classes for managing individual Contexts."""
 
 import re
+import warnings
 from collections import defaultdict
 from dataclasses import dataclass, field
 from enum import Enum
@@ -294,8 +295,18 @@ def as_extended_prefix_map(self) -> List[curies.Record]:
 
         prefix_synonyms = defaultdict(set)
         for expansion in self.prefix_expansions:
-            if expansion.status == StatusType.namespace_alias:
+            if (
+                expansion.status == StatusType.namespace_alias
+                and expansion.namespace in reverse_prefix_map
+            ):
                 prefix_synonyms[reverse_prefix_map[expansion.namespace]].add(expansion.prefix)
+            elif (
+                expansion.status == StatusType.namespace_alias
+                and expansion.namespace not in reverse_prefix_map
+            ):
+                warnings.warn(
+                    f"Namespace {expansion.namespace} has no canonical prefix", stacklevel=2
+                )
 
         return [
             curies.Record(