tanu/funpdbe-validator
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This commit is contained in:
Mihaly Varadi 2019-10-07 14:49:35 +01:00
parent 7a60569631
commit 410ba6c4af
4 changed files with 15 additions and 5 deletions
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3
.gitignore vendored
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@ -2,3 +2,6 @@
.cache* .cache*
*vcs.xml *vcs.xml
sample_data/* sample_data/*
local-test.py
.DS_Store
*.pyc

0
__init__.py Normal file
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11
validator/residue_index.py
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@ -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)
response = requests.get(url) try:
residue_numbering = json.loads(response.text) response = requests.get(url)
except:
return False
try:
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
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@ -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