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Update April 2024

Merged Sandra Derozier requested to merge dev into master
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#!/usr/bin/env python3.6
# Copyright 2022 Robert Bossy (INRAE)
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -12,7 +15,6 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#!/usr/bin/env python3.6
'''Wrapper objects and functions for the Omnicrobe REST API. See: http://omnicrobe.migale.inrae.fr/api.
@@ -27,7 +29,9 @@ Variables:
import requests
BASE_URL = 'http://omnicrobe.migale.inrae.fr/api'
BASE_URL = 'https://omnicrobe.migale.inrae.fr/api'
class OmnicrobeError(Exception):
def __init__(self, *args, **kwargs):
@@ -200,6 +204,7 @@ class OBTType(object):
return obt_type.name
return str(obt_type)
HABITAT = OBTType('habitat')
PHENOTYPE = OBTType('phenotype')
USE = OBTType('use')
@@ -330,42 +335,41 @@ class Relation:
)
if __name__ == '__main__':
print ('Version')
print (version())
print ('\n')
print('Version')
print(version())
print('\n')
print ('taxon info by id')
print('taxon info by id')
bs = Taxon('ncbi:1423')
print (bs)
print(bs)
print('\n')
print ('obt info by id')
print('obt info by id')
soil = OBT('OBT:000427')
print (soil)
print(soil)
print('\n')
print ('search taxon descendants')
print('search taxon descendants')
for t in Taxon.search(root=bs):
print (t.identifier)
print(t.identifier)
print('\n')
print ('search taxon name')
print('search taxon name')
for t in Taxon.search('propionibacterium'):
print (t.identifier)
print(t.identifier)
print('\n')
print ('search obt descendants')
print('search obt descendants')
for o in OBT.search(root=soil):
print (o.identifier)
print ('\n')
print(o.identifier)
print('\n')
print ('search obt name')
print('search obt name')
for o in OBT.search('food'):
print (o.identifier)
print ('\n')
print(o.identifier)
print('\n')
print ('search relations')
print('search relations')
for r in Relation.search(taxon=bs, obt=soil, qps=True, sources='GenBank'):
print (r)
print(r)
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