tanu/funpdbe-validator
1
0
Fork 0
Code Issues Pull requests Projects Releases Packages Wiki Activity

Fixes

Browse source
This commit is contained in:
Mihaly Varadi 2019-11-01 13:52:48 +00:00
parent 7a60569631
commit a99fd6fd4e
2 changed files with 11 additions and 4 deletions
Download patch file Download diff file Expand all files Collapse all files

7
validator/residue_index.py
View file

@ -69,8 +69,15 @@ class ResidueIndexes(object):
""" """
chain_id = chain_data["chain_label"] chain_id = chain_data["chain_label"]
url = "%s%s/chain/%s" % (self.api_url, self.pdb_id, chain_id) url = "%s%s/chain/%s" % (self.api_url, self.pdb_id, chain_id)
try:
response = requests.get(url) response = requests.get(url)
except:
return False
try:
residue_numbering = json.loads(response.text) residue_numbering = json.loads(response.text)
except:
print("Failed to load residues from PDBe API")
return False
if not residue_numbering.keys(): if not residue_numbering.keys():
self.mismatches.append("No residues in PDB for this entry - probably obsoleted entry") self.mismatches.append("No residues in PDB for this entry - probably obsoleted entry")
return False return False

4
validator/validator.py
View file

@ -87,8 +87,8 @@ class Validator(object):
with open(path, "r") as json_file: with open(path, "r") as json_file:
try: try:
return json.load(json_file) return json.load(json_file)
except json.decoder.JSONDecodeError as err: except:
self.error_log = "JSON error: %s" % err self.error_log = "JSON error: %s" % path
return None return None
except IOError as ioerr: except IOError as ioerr:
self.error_log = "File error: %s" % ioerr self.error_log = "File error: %s" % ioerr