Merge pull request #99 from indralab/uniprot_legacy

Use legacy UniProt service to generate terms
gyorilab · Jul 19, 2022 · 962218e · 962218e
2 parents 0bd65d7 + 3be0c44
commit 962218e
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Showing 3 changed files with 4 additions and 2 deletions.
diff --git a/gilda/__init__.py b/gilda/__init__.py
@@ -1,4 +1,4 @@
-__version__ = '0.10.1'
+__version__ = '0.10.2'
 
 import logging
 

diff --git a/gilda/generate_terms.py b/gilda/generate_terms.py
@@ -339,7 +339,7 @@ def generate_uniprot_terms(download=False, organisms=None):
     path = os.path.join(resource_dir, 'up_synonyms.tsv')
     org_filter_str = ' OR '.join(organisms)
     if not os.path.exists(path) or download:
-        url = (f'https://www.uniprot.org/uniprot/?format=tab&columns=id,'
+        url = (f'https://legacy.uniprot.org/uniprot/?format=tab&columns=id,'
                f'genes(PREFERRED),genes(ALTERNATIVE),protein%20names,organism-id&sort=score&'
                f'query=reviewed:yes&fil=organism:{org_filter_str}')
         logger.info('Downloading UniProt resource file')

diff --git a/gilda/grounder.py b/gilda/grounder.py
@@ -311,6 +311,8 @@ def get_models(self):
             The list of entity texts for which a disambiguation model is
             available.
         """
+        if self.gilda_disambiguators is None:
+            self.gilda_disambiguators = load_gilda_models()
         return sorted(list(self.gilda_disambiguators.keys()))
 
     def get_names(self, db, id, status=None, source=None):