feat: example on how to integrate some tests from Memote #3

runner.py

@@ -3,6 +3,7 @@
 from os import environ
 import tests.cobra
 import tests.yaml
+import tests.memote
 
 API_ENDPOINT = 'https://api.github.com/graphql'
 API_TOKEN = environ['GH_TOKEN']
@@ -91,9 +92,10 @@ def validate(nameWithOwner):
                 test_results.update(tests.yaml.validate(model))
                 test_results.update(tests.cobra.load(model))
                 test_results.update(tests.cobra.validateSBML(model))
+                test_results.update(tests.memote.get_consistency(model))
             else:
                 print('is not following standard')
             release_data = { 'standard-GEM' : [ { standard_version : gem_is_standard }, { 'test_results' : test_results} ] }
         data[nameWithOwner].append({ model_release: release_data })
     with open('results/{}_{}.json'.format(owner, model), 'w') as output:
-        output.write(json.dumps(data, indent=2, sort_keys=True))
+        output.write(json.dumps(data, indent=2, sort_keys=True))

tests/memote.py

@@ -0,0 +1,17 @@
+import memote
+import cobra
+import json
+from memote.support import consistency
+# needed by memote.support.consitency
+from memote.support import consistency_helpers as con_helpers
+
+def get_consistency(model_filename):
+    try:
+        model = cobra.io.read_sbml_model(model_filename + '.xml')
+    except Exception as e:
+        errors = json.dumps(str(e))
+        print(e)
+
+    is_consistent = consistency.check_stoichiometric_consistency(model)
+
+    return {'memote-tests': { memote.__version__ : is_consistent, 'errors': errors } }