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change syn file format #113

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merged 12 commits into from
May 8, 2023
Merged

change syn file format #113

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a76cac4
change syn file format
cbizon Mar 10, 2023
5f101bd
fixed sort; names
cbizon Mar 13, 2023
aa32ec3
Added workaround for missing label on pref identifier.
gaurav Mar 23, 2023
45b6a85
Improved exception error message.
gaurav Mar 23, 2023
7849022
Increased Babel outputs because of significantly larger synonym files.
gaurav Apr 19, 2023
13a13dd
Remove relationships when writing out synonyms.
gaurav Apr 20, 2023
2b9d264
Added support for generating new-format synonym files for leftover_umls.
gaurav Apr 23, 2023
4a1bafa
Fixed bug in variable naming.
gaurav Apr 24, 2023
b02fc1f
Attempt to convert set() to list().
gaurav Apr 24, 2023
4e16fbb
Fixed bug in leftover synonym generation.
gaurav May 5, 2023
7603273
Updated NCBIGene synonym format to add relations.
gaurav May 5, 2023
f367b35
leftover_umls now sorts synonyms.
gaurav May 5, 2023
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11 changes: 7 additions & 4 deletions src/babel_utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,7 @@ def write_compendium(synonym_list,ofname,node_type,labels={},extra_prefixes=[]):
synonym_factory = SynonymFactory(make_local_name(''))
ic_factory = InformationContentFactory(f'{get_config()["input_directory"]}/icRDF.tsv')
node_test = node_factory.create_node(input_identifiers=[],node_type=node_type,labels={},extra_prefixes = extra_prefixes)
with jsonlines.open(os.path.join(cdir,'compendia',ofname),'w') as outf, open(os.path.join(cdir,'synonyms',ofname),'w') as sfile:
with jsonlines.open(os.path.join(cdir,'compendia',ofname),'w') as outf, jsonlines.open(os.path.join(cdir,'synonyms',ofname),'w') as sfile:
for slist in synonym_list:
node = node_factory.create_node(input_identifiers=slist, node_type=node_type,labels = labels, extra_prefixes = extra_prefixes)
if node is not None:
Expand All @@ -227,9 +227,12 @@ def write_compendium(synonym_list,ofname,node_type,labels={},extra_prefixes=[]):
nw['identifiers'] = [ {k[0]:v for k,v in nids.items()} for nids in node['identifiers']]
outf.write( nw )
synonyms = synonym_factory.get_synonyms(node)
if len(synonyms) > 0:
for p,o in synonyms:
sfile.write(f'{node["identifiers"][0]["identifier"]}\t{p}\t{o}\n')
synonyms.sort(key=lambda x:len(x))
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document = {"curie": node["identifiers"][0]["identifier"],
"preferred_name": node["identifiers"][0]["label"],
"name": synonyms,
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"types": [ t[8:] for t in node_factory.get_ancestors(node["type"])]} #remove biolink:
sfile.write( document )

def glom(conc_set, newgroups, unique_prefixes=['INCHIKEY'],pref='HP',close={}):
"""We want to construct sets containing equivalent identifiers.
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