Merge pull request #225 from AllenInstitute/axon_parent_validation_fix

Axon parent validation fix

neuron_morphology/validation/report.py

@@ -51,7 +51,8 @@ def add_swc_stats(self, swc_file, stats):
         self.file_record[swc_file] = record
 
     def to_json(self):
-        return json.dumps(self.file_record.values(), indent=4, separators=(',', ': '))
+        record_list = list(self.file_record.values())
+        return json.dumps(record_list, indent=4, separators=(',', ': '))
 
     def has_results(self):
 

neuron_morphology/validation/type_validation.py

@@ -81,7 +81,7 @@ def validate_node_parent(morphology):
 
     for node in axon_nodes_with_invalid_parents:
         result.append(ve("Type 2 can only have a parent of the following types: %s" % valid_axon_parents, node['id'],
-                         "Error"))
+                         "Warning"))
 
     basal_dendrite_nodes = morphology.get_node_by_types([BASAL_DENDRITE])
 

neuron_morphology/validation/validate_reconstruction.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import json
 import logging
 import neuron_morphology.swc_io as swc
 import neuron_morphology.validation as validation
@@ -21,6 +22,7 @@ def parse_arguments(args):
     parser.add_argument('--dir', type=str, nargs='+', help="SWC and Marker files")
     parser.add_argument('--swc', type=str, help="SWC file")
     parser.add_argument('--marker', type=str, help="Marker file")
+    parser.add_argument('--report_json', type=str, help="Report output json file")
     return parser.parse_args(args)
 
 
@@ -89,8 +91,12 @@ def main():
             except InvalidMarkerFile as imf:
                 report.add_marker_results(marker_file, imf.validation_errors)
 
-    print(report.to_json())
+    report_output = report.to_json()
+    print(report_output)
     if report.has_results():
+        if args['report_json']:
+            with open(args['report_json'],'w') as f:
+                json.dump(report_output, f)
         sys.exit(1)