validate: Clarify output messages

augur/export_v2.py

@@ -400,12 +400,13 @@ def set_filters(data_json, config):
 def validate_data_json(filename):
     print("Validating produced JSON")
     try:
-        validate_v2(json_v2=filename)
+        validate_v2(main_json=filename)
     except ValidateError as e:
         print(e)
         print("\n------------------------")
         print("Validation of {} failed. Please check this in a local instance of `auspice`, as it is not expected to display correctly. ".format(filename))
         print("------------------------")
+        sys.exit(2)
 
 
 def set_panels(data_json, config, cmd_line_panels):
@@ -813,7 +814,7 @@ def get_config(args):
     config = read_config(args.auspice_config)
     try:
         print("Validating config file {} against the JSON schema".format(args.auspice_config))
-        validate_auspice_config_v2(config_json=config)
+        validate_auspice_config_v2(args.auspice_config)
     except ValidateError:
         print("Validation of {} failed. Please check the formatting of this file & refer to the augur documentation for further help. ".format(args.auspice_config))
         sys.exit(2)

augur/utils.py

@@ -201,7 +201,7 @@ def read_node_data(fnames, tree=None):
                 tmp_data = json.load(jfile)
             if tmp_data.get("annotations"):
                 try:
-                    validate(tmp_data.get("annotations"), load_json_schema("schema-annotations.json"))
+                    validate(tmp_data.get("annotations"), load_json_schema("schema-annotations.json"), fname)
                 except ValidateError as err:
                     print("{} contains an `annotations` block of an invalid JSON format. "
                         "Was it produced by different version of augur the one you are currently using ({})? "

augur/validate.py

@@ -57,7 +57,8 @@ def load_json(path):
             raise ValidateError("Supplied JSON to validate ({}) is not a valid JSON".format(path))
     return jsonToValidate
 
-def validate(jsonToValidate, schema):
+def validate(jsonToValidate, schema, filename):
+    print("Validating schema of {!r}...".format(filename))
     try:
         schema.validate(jsonToValidate) # https://python-jsonschema.readthedocs.io/en/latest/validate/
     except jsonschema.exceptions.ValidationError:
@@ -67,45 +68,57 @@ def validate(jsonToValidate, schema):
                 trace = ["..."] + trace[-5:]
             trace = [str(x) for x in trace]
             print("\tERROR: {}. Trace: {}".format(error.message, " - ".join(trace)), file=sys.stderr)
-        raise ValidateError("Validation failed.")
-    else:
-        print("Validation succeeded")
+        raise ValidateError("Validation of {!r} failed.".format(filename))
 
 def auspice_config_v2(config_json, **kwargs):
     schema = load_json_schema("schema-auspice-config-v2.json")
-    jsonToValidate = load_json(config_json) if isinstance(config_json, str) else config_json
-    validate(jsonToValidate, schema)
+    config = load_json(config_json)
+    validate(config, schema, config_json)
 
-def export_v2(json_v2, **kwargs):
+def export_v2(main_json, **kwargs):
     # validationWarnings = ValidationWarnings()
     # validationErrors = ValidationErrors()
-    schema = load_json_schema("schema-export-v2.json")
-    if json_v2.endswith("frequencies.json") or json_v2.endswith("entropy.json") or json_v2.endswith("sequences.json"):
+    main_schema = load_json_schema("schema-export-v2.json")
+
+    if main_json.endswith("frequencies.json") or main_json.endswith("entropy.json") or main_json.endswith("sequences.json"):
         raise ValidateError("This validation subfunction is for the main `augur export v2` JSON only.")
-    jsonToValidate = load_json(json_v2)
-    validate(jsonToValidate, schema)
-    verifyMainJSONIsInternallyConsistent(jsonToValidate, ValidateError)
+
+    main = load_json(main_json)
+    validate(main, main_schema, main_json)
+
+    if verifyMainJSONIsInternallyConsistent(main, ValidateError):
+        print("Validation of {!r} succeeded.".format(main_json))
+    else:
+        print("Validation of {!r} succeeded, but there were warnings you may want to resolve.".format(main_json))
 
 
 def export_v1(meta_json, tree_json, **kwargs):
-    schema_meta = load_json_schema("schema-export-v1-meta.json")
-    schema_tree = load_json_schema("schema-export-v1-tree.json")
+    meta_schema = load_json_schema("schema-export-v1-meta.json")
+    tree_schema = load_json_schema("schema-export-v1-tree.json")
+
     if not meta_json.endswith("_meta.json"):
         raise ValidateError("The metadata JSON pathname {} must end with '_meta.json'.".format(meta_json))
+
     if not tree_json.endswith("_tree.json"):
         raise ValidateError("The metadata JSON pathname {} must end with '_tree.json'.".format(tree_json))
-    meta_json = load_json(meta_json)
-    tree_json = load_json(tree_json)
-    validate(meta_json, schema_meta)
-    validate(tree_json, schema_tree)
-    verifyMetaAndOrTreeJSONsAreInternallyConsistent(meta_json, tree_json, ValidateError)
+
+    meta = load_json(meta_json)
+    tree = load_json(tree_json)
+
+    validate(meta, meta_schema, meta_json)
+    validate(tree, tree_schema, tree_json)
+
+    if verifyMetaAndOrTreeJSONsAreInternallyConsistent(meta, tree, ValidateError):
+        print("Validation of {!r} and {!r} succeeded.".format(meta_json, tree_json))
+    else:
+        print("Validation of {!r} and {!r} succeeded, but there were warnings you may want to resolve.".format(meta_json, tree_json))
 
 
 def register_arguments(parser):
     subparsers = parser.add_subparsers(dest="subcommand", help="Which file(s) do you want to validate?")
 
     subparsers.add_parser("export-v2", help="validate JSON intended for auspice v2") \
-        .add_argument('json_v2', metavar='JSON', help="exported (main) v2 auspice JSON")
+        .add_argument('main_json', metavar='JSON', help="exported (main) v2 auspice JSON")
 
     export_v1 = subparsers.add_parser("export-v1", help="validate tree+meta JSONs intended for auspice v1")
     export_v1.add_argument('meta_json', metavar='META-JSON', help="exported (v1) meta JSON")

augur/validate_export.py

@@ -72,7 +72,7 @@ def warn(msg):
         warnings = True
         print("\tWARNING: ", msg, file=sys.stderr)
 
-    print("Validating that the JSON is internally consistent")
+    print("Validating that the JSON is internally consistent...")
 
     if "entropy" in data["meta"]["panels"] and "genome_annotations" not in data["meta"]:
         warn("The entropy panel has been specified but annotations don't exist.")
@@ -144,10 +144,7 @@ def warn(msg):
                 if gene not in data["meta"]["genome_annotations"]:
                     warn("The tree defined mutations on gene {} which doesn't appear in the metadata annotations object.".format(gene))
 
-    if not warnings:
-        print("Validation succeeded")
-    else:
-        print("Validation failed")
+    return not warnings
 
 
 def collectTreeAttrsV1(root):
@@ -199,11 +196,14 @@ def verifyMetaAndOrTreeJSONsAreInternallyConsistent(meta_json, tree_json, Valida
     Check all possible sources of conflict internally & between the metadata & tree JSONs
     This is only that which cannot be checked by the schemas
     """
+    warnings = False
     def warn(msg):
+        nonlocal warnings
+        warnings = True
         print("\tWARNING: ", msg, file=sys.stderr)
 
 
-    print("Validating that meta + tree JSONs are internally consistent... ")
+    print("Validating that meta + tree JSONs are internally consistent...")
     mj = meta_json
 
     if "panels" in mj and "entropy" in mj["panels"] and "annotations" not in mj:
@@ -260,3 +260,5 @@ def warn(msg):
             for gene in genes_with_aa_muts:
                 if gene not in mj["annotations"]:
                     warn("The tree defined AA mutations on gene {} which doesn't appear in the metadata annotations object.".format(gene))
+
+    return not warnings