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Check added for MetaMap file existence and executable access for the user #38

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merged 1 commit into from
Jul 9, 2019
Merged

Check added for MetaMap file existence and executable access for the user #38

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7 changes: 6 additions & 1 deletion pymetamap/MetaMap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@
# limitations under the License.

import abc
from os.path import isabs
from os import access, X_OK
from os.path import isabs, isfile

DEFAULT_METAMAP_VERSION = '2012'

Expand All @@ -28,6 +29,8 @@ class MetaMap:

def __init__(self, metamap_filename, version=None):
self.metamap_filename = str(metamap_filename)
assert isfile(self.metamap_filename), "metamap_filename: {0} :: Please provide metamap executable file path".format(self.metamap_filename)
assert access(self.metamap_filename, X_OK), "User doesn't have executable access to metamap_filename: {0}".format(self.metamap_filename)
assert isabs(self.metamap_filename), "metamap_filename: {0} should be an absolute path".format(self.metamap_filename)
if version is None:
version = DEFAULT_METAMAP_VERSION
Expand All @@ -42,6 +45,8 @@ def extract_concepts(self, sentences=None, ids=None,
def get_instance(metamap_filename, version=None, backend='subprocess',
**extra_args):
extra_args.update(metamap_filename=metamap_filename, version=version)
assert isfile(metamap_filename), "metamap_filename: {0} :: Please provide metamap executable file path".format(metamap_filename)
assert access(metamap_filename, X_OK), "User doesn't have executable access to metamap_filename: {0}".format(metamap_filename)
assert isabs(metamap_filename), "metamap_filename: {0} should be an absolute path".format(metamap_filename)

if backend == 'subprocess':
Expand Down