Add stripping whitespace to linting (#194)

Motivated by #172

Author: cthoyt

src/biomappings/resources/__init__.py

@@ -204,7 +204,11 @@ def _load_table(path: str | Path, *, standardize: bool) -> list[SemanticMapping]
     with Path(path).expanduser().resolve().open() as file:
         return [
             SemanticMapping.from_row(
-                {k: v for k, v in record.items() if v and v.strip() and v.strip() != "."},
+                {
+                    key: value_stripped
+                    for key, value in record.items()
+                    if value and (value_stripped := value.strip()) and value_stripped != "."
+                },
                 reference_cls,
             )
             for record in csv.DictReader(file, delimiter="\t")

src/biomappings/resources/positive.sssom.tsv

@@ -6598,7 +6598,7 @@ mesh:D000076385	Diverticular Diseases	skos:exactMatch	efo:0009959	diverticular d
 mesh:D000077122	Sugammadex	skos:exactMatch	chebi:90953	sugammadex	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D000077123	Rocuronium	skos:exactMatch	chebi:8884	rocuronium	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D000077143	Docetaxel	skos:narrowMatch	chebi:4672	docetaxel anhydrous	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
-mesh:D000077143	Docetaxel	skos:narrowMatch	chebi:59809	docetaxel trihydrate 	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
+mesh:D000077143	Docetaxel	skos:narrowMatch	chebi:59809	docetaxel trihydrate	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D000077144	Clopidogrel	skos:exactMatch	chebi:37941	clopidogrel	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D000077145	Sulfanilamide	skos:exactMatch	chebi:45373	sulfanilamide	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D000077146	Irinotecan	skos:exactMatch	chebi:80630	irinotecan	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
@@ -7720,13 +7720,13 @@ mesh:D007169	Impetigo	skos:exactMatch	doid:8504	impetigo	semapv:ManualMappingCur
 mesh:D007172	Erectile Dysfunction	skos:exactMatch	doid:1875	impotence	semapv:ManualMappingCuration	orcid:0000-0003-1307-2508		
 mesh:D007213	Indomethacin	skos:exactMatch	chebi:49662	indometacin	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D007226	Infant Mortality	skos:exactMatch	ncit:C16729	Infant Mortality	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
-mesh:D007238	Infarction	skos:exactMatch	efo:0009463	infarction	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py
+mesh:D007238	Infarction	skos:exactMatch	efo:0009463	infarction	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py	
 mesh:D007249	Inflammation	skos:exactMatch	go:0006954	inflammatory response	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D007251	Influenza, Human	skos:exactMatch	doid:8469	influenza	semapv:ManualMappingCuration	orcid:0000-0003-1307-2508		
 mesh:D007305	Insecticide Resistance	skos:exactMatch	go:0017085	response to insecticide	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D007314	Insemination	skos:exactMatch	go:0007320	insemination	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
-mesh:D007340	Insulinoma	skos:exactMatch	efo:0000549	insulinoma	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py
-mesh:D007360	Intelligence	skos:exactMatch	efo:0004337	intelligence	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py
+mesh:D007340	Insulinoma	skos:exactMatch	efo:0000549	insulinoma	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py	
+mesh:D007360	Intelligence	skos:exactMatch	efo:0004337	intelligence	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370	https://github.com/biomappings/biomappings/blob/4324c1/scripts/import_gilda_mappings.py	
 mesh:D007378	Interleukins	skos:exactMatch	chebi:52998	interleukins	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D007382	Intermediate Filaments	skos:exactMatch	go:0005882	intermediate filament	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
 mesh:D007399	Interphase	skos:exactMatch	go:0051325	interphase	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346		
@@ -8294,7 +8294,7 @@ mesh:D016530	Orthopedic Nursing	skos:exactMatch	ncit:C20875	Orthopedic Nursing	s
 mesh:D016543	Central Nervous System Neoplasms	skos:exactMatch	efo:1000158	Central Nervous System Neoplasm	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D016553	Purpura, Thrombocytopenic, Idiopathic	skos:exactMatch	doid:1587	thrombocytopenia due to platelet alloimmunization	semapv:ManualMappingCuration	orcid:0000-0003-1307-2508		
 mesh:D016559	Tacrolimus	skos:narrowMatch	chebi:61049	tacrolimus (anhydrous)	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
-mesh:D016559	Tacrolimus	skos:narrowMatch	chebi:61057	tacrolimus hydrate 	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
+mesh:D016559	Tacrolimus	skos:narrowMatch	chebi:61057	tacrolimus hydrate	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D016595	Misoprostol	skos:exactMatch	chebi:63610	misoprostol	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D016606	Thyroid Nodule	skos:exactMatch	hp:0025388	Thyroid nodule	semapv:ManualMappingCuration	orcid:0000-0003-4423-4370		
 mesh:D016631	Lewy Bodies	skos:exactMatch	go:0097413	Lewy body	semapv:ManualMappingCuration	orcid:0000-0001-9439-5346