Merge pull request #605 from opencobra/fix-json

Fix json output error reporting

HISTORY.rst

@@ -3,6 +3,8 @@ History
 
 Next Release
 ------------
+* Improve logging output when there is a problem with serializing a result to
+  JSON.
 * Fix some test cases that got broken by cobrapy's new boundary identification.
 
 0.9.2 (2019-01-28)

memote/suite/tests/test_thermodynamics.py

@@ -84,7 +84,9 @@ def test_find_candidate_irreversible_reactions(model):
     rev_index, incomplete, problematic, unbalanced = \
         thermo.find_thermodynamic_reversibility_index(met_rxns)
     ann["data"] = (
-        [(r.id, i) for r, i in rev_index],
+        # The reversibility index can be infinite so we convert it to a JSON
+        # compatible string.
+        [(r.id, str(i)) for r, i in rev_index],
         get_ids(incomplete),
         get_ids(problematic),
         get_ids(unbalanced)

memote/utils.py

@@ -25,6 +25,7 @@
 from textwrap import TextWrapper
 
 from future.utils import raise_with_traceback
+from numpy import isfinite
 from numpydoc.docscrape import NumpyDocString
 from six import string_types
 from depinfo import print_dependencies
@@ -186,13 +187,15 @@ def log_json_incompatible_types(obj):
     while len(keys_to_explore) > 0:
         key = keys_to_explore.pop()
         if not isinstance(key, str):
-            LOGGER.debug(type(key))
+            LOGGER.info(type(key))
         value = obj[key]
         if isinstance(value, dict):
-            LOGGER.debug("%s:", key)
+            LOGGER.info("%s:", key)
             log_json_incompatible_types(value)
         elif not isinstance(value, JSON_TYPES):
-            LOGGER.debug("%s: %s", key, type(value))
+            LOGGER.info("%s: %s", key, type(value))
+        elif isinstance(value, (int, float)) and not isfinite(value):
+            LOGGER.info("%s: %f", key, value)
 
 
 def extended_summary(func):
@@ -240,7 +243,10 @@ def jsonify(obj, pretty=False):
                       separators=(",", ":"), ensure_ascii=False)
     try:
         return json.dumps(obj, **params)
-    except TypeError as error:
+    except (TypeError, ValueError) as error:
+        LOGGER.critical(
+            "The memote result structure is incompatible with the JSON "
+            "standard.")
         log_json_incompatible_types(obj)
         raise_with_traceback(error)