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Add constants for resource file paths #12

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merged 1 commit into from Mar 17, 2020
Merged

Add constants for resource file paths #12

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6 changes: 2 additions & 4 deletions gilda/generate_terms.py
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Expand Up @@ -14,12 +14,10 @@
go_client, mesh_client
from .term import Term
from .process import normalize
from .resources import resource_dir


indra_module_path = indra.__path__[0]
indra_resources = os.path.join(indra_module_path, 'resources')
gilda_resources = os.path.join(os.path.dirname(__file__), 'resources')

logger = logging.getLogger('gilda.generate_terms')

Expand Down Expand Up @@ -139,7 +137,7 @@ def generate_chebi_terms():

def generate_mesh_terms(ignore_mappings=False):
# Load MeSH ID/label mappings
mesh_mappings_file = os.path.join(gilda_resources, 'mesh_mappings.tsv')
from .resources import MESH_MAPPINGS_PATH as mesh_mappings_file
mesh_mappings = {}
for row in read_csv(mesh_mappings_file, delimiter='\t'):
mesh_mappings[row[1]] = (row[3], row[4])
Expand Down Expand Up @@ -367,6 +365,6 @@ def get_all_terms():

if __name__ == '__main__':
terms = get_all_terms()
fname = os.path.join(resource_dir, 'grounding_terms.tsv')
from .resources import GROUNDING_TERMS_PATH as fname
logger.info('Dumping into %s' % fname)
write_unicode_csv(fname, [t.to_list() for t in terms], delimiter='\t')
10 changes: 8 additions & 2 deletions gilda/resources/__init__.py
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Expand Up @@ -6,6 +6,9 @@

logger = logging.getLogger(__name__)

HERE = os.path.abspath(os.path.dirname(__file__))
MESH_MAPPINGS_PATH = os.path.join(HERE, 'mesh_mappings.tsv')

home_dir = os.path.expanduser('~')
resource_dir = os.path.join(home_dir, '.gilda', __version__)

Expand All @@ -16,6 +19,9 @@
except Exception:
logger.warning('%s already exists' % resource_dir)

GROUNDING_TERMS_BASE_NAME = 'grounding_terms.tsv'
GROUNDING_TERMS_PATH = os.path.join(resource_dir, GROUNDING_TERMS_BASE_NAME)


def _download_from_s3(path, base_name):
config = botocore.client.Config(signature_version=botocore.UNSIGNED)
Expand All @@ -28,8 +34,8 @@ def _download_from_s3(path, base_name):


def get_grounding_terms():
base_name = 'grounding_terms.tsv'
full_path = os.path.join(resource_dir, base_name)
base_name = GROUNDING_TERMS_BASE_NAME
full_path = GROUNDING_TERMS_PATH
if not os.path.exists(full_path):
logger.info('Downloading grounding terms from S3.')
out_file = _download_from_s3(resource_dir, base_name)
Expand Down