Update April 2024

static/files/omnicrobe.py

+#!/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)