Merge pull request #246 from cokelaer/fix_uniprot_failedids

Fix regression in uniprot module
cokelaer · Jan 2, 2023 · 4b05921 · 4b05921
2 parents 07577b6 + 8f96aff
commit 4b05921
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Showing 7 changed files with 13 additions and 4 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -4,4 +4,5 @@ recursive-exclude doc *
 recursive-exclude * __pycache__
 recursive-exclude * *pyc
 recursive-exclude .github *
+recursive-exclude src/bioservices/attic *
 
diff --git a/README.rst b/README.rst
@@ -189,6 +189,8 @@ Changelog
 ========= ====================================================================
 Version Description
 ========= ====================================================================
+1.11.1 * Fix regression i uniprot.mapping 
+ (https://github.com/cokelaer/bioservices/issues/245)
 1.11.0 * Fix uniprot limitation of 25 results only (
  * For developers: all services are now refactorised to use services
  as an attribute rather than a parent class.

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 _MAJOR = 1
 _MINOR = 11
-_MICRO = 0
+_MICRO = 1
 version = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release = '%d.%d' % (_MAJOR, _MINOR)
 

diff --git a/src/bioservices/intact.py b/src/bioservices/intact.py
@@ -141,7 +141,7 @@ def search(self, query, frmt="json", facets=None, first=None, number=None, filte
 
 
  """
- self.devtools.check_param_in_list(frmt, ["pandas", "json"])
+ self.services.devtools.check_param_in_list(frmt, ["pandas", "json"])
 
  # note that code format to be json, which is the only option so
  # we can use pandas as a frmt without addition code.

diff --git a/src/bioservices/uniprot.py b/src/bioservices/uniprot.py
@@ -479,14 +479,14 @@ def mapping(
  if results != 500 and "results" in results:
  total = int(self.services.last_response.headers["X-Total-Results"])
  batches = results["results"]
- fails = results["failedIds"]
+ fails = results.get("failedIds", [])
 
  size = 25
  for x in tqdm.tqdm(range(size, total, size), disable=not progress):
  link = self._get_next_link(self.services.last_response.headers)
  batch = self.services.http_get(link, frmt="json")
  batches += batch["results"]
- fails += results["failedIds"]
+ fails += results.get("failedIds", [])
  return {"results": batches, "failedIds": fails}
 
  else: # pragma: no cover

diff --git a/test/webservices/test_panther.py b/test/webservices/test_panther.py
@@ -1,3 +1,4 @@
+import pytest
 from bioservices.panther import Panther
 
 

diff --git a/test/webservices/test_uniprot.py b/test/webservices/test_uniprot.py
@@ -106,3 +106,8 @@ def test_get_df(uniprot):
 
 def test_fasta(uniprot):
  "Q9Y617" in uniprot.get_fasta(["Q9Y617-1"])
+
+
+#https://github.com/cokelaer/bioservices/issues/245
+def test_mapping_regression(uniprot):
+ uniprot.mapping("UniProtKB_AC-ID", "KEGG", "P43403,P123456")