Merge pull request #1337 from nipreps/fix/handle-nan-iqms

ENH: Use ``orjson`` to serialize JSON, addressing Numpy serialization issues

Author: oesteban

mriqc/interfaces/bids.py

@@ -23,7 +23,7 @@
 import re
 from pathlib import Path
 
-import simplejson as json
+import orjson as json
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
     DynamicTraitedSpec,
@@ -187,16 +187,17 @@ def _run_interface(self, runtime):
             self._out_dict['provenance'] = {}
         self._out_dict['provenance'].update(prov_dict)
 
-        with open(out_file, 'w') as f:
-            f.write(
-                json.dumps(
-                    self._out_dict,
-                    sort_keys=True,
-                    indent=2,
-                    ensure_ascii=False,
-                )
+        Path(out_file).write_bytes(
+            json.dumps(
+                self._out_dict,
+                option=(
+                    json.OPT_SORT_KEYS
+                    | json.OPT_INDENT_2
+                    | json.OPT_APPEND_NEWLINE
+                    | json.OPT_SERIALIZE_NUMPY
+                ),
             )
-
+        )
         return runtime
 
 

mriqc/interfaces/webapi.py

@@ -20,8 +20,9 @@
 #
 #     https://www.nipreps.org/community/licensing/
 #
-import json
+from pathlib import Path
 
+import orjson
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
     Bunch,
@@ -127,6 +128,7 @@ class UploadIQMsInputSpec(BaseInterfaceInputSpec):
 
 class UploadIQMsOutputSpec(TraitedSpec):
     api_id = traits.Either(None, traits.Str, desc='Id for report returned by the web api')
+    payload_file = File(desc='Submitted payload (only for debugging)')
 
 
 class UploadIQMs(SimpleInterface):
@@ -153,6 +155,18 @@ def _run_interface(self, runtime):
             modality=self.inputs.modality,
         )
 
+        payload_str = orjson.dumps(
+            payload,
+            option=(
+                orjson.OPT_SORT_KEYS
+                | orjson.OPT_INDENT_2
+                | orjson.OPT_APPEND_NEWLINE
+                | orjson.OPT_SERIALIZE_NUMPY
+            ),
+        )
+        Path('payload.json').write_bytes(payload_str)
+        self._results['payload_file'] = str(Path('payload.json').absolute())
+
         try:
             self._results['api_id'] = response.json()['_id']
         except (AttributeError, KeyError, ValueError):
@@ -161,7 +175,7 @@ def _run_interface(self, runtime):
                 'QC metrics upload failed to create an ID for the record '
                 f'uploaded. Response from server follows: {response.text}'
                 '\n\nPayload:\n'
-                f'{json.dumps(payload, indent=2)}'
+                f'{payload_str}'
             )
             config.loggers.interface.warning(errmsg)
 
@@ -177,7 +191,7 @@ def _run_interface(self, runtime):
                 '',
                 '',
                 'Payload:',
-                json.dumps(payload, indent=2),
+                payload_str,
             ]
         )
         config.loggers.interface.warning(errmsg)
@@ -209,8 +223,6 @@ def upload_qc_metrics(
 
     """
     from copy import deepcopy
-    from json import dumps, loads
-    from pathlib import Path
 
     import requests
 
@@ -219,7 +231,7 @@ def upload_qc_metrics(
         errmsg = 'Unknown API endpoint' if not endpoint else 'Authentication failed.'
         return Bunch(status_code=1, text=errmsg)
 
-    in_data = loads(Path(in_iqms).read_text())
+    in_data = orjson.loads(Path(in_iqms).read_bytes())
 
     # Extract metadata and provenance
     meta = in_data.pop('bids_meta')
@@ -267,20 +279,23 @@ def upload_qc_metrics(
 
     start_message = messages.QC_UPLOAD_START.format(url=endpoint)
     config.loggers.interface.info(start_message)
+
+    errmsg = None
     try:
         # if the modality is bold, call "bold" endpoint
         response = requests.post(
             f'{endpoint}/{modality}',
             headers=headers,
-            data=dumps(data),
+            data=orjson.dumps(data, option=orjson.OPT_SERIALIZE_NUMPY),
             timeout=15,
         )
     except requests.ConnectionError as err:
-        errmsg = f'Error uploading IQMs -- Connection error:\n{err}'
-        return Bunch(status_code=1, text=errmsg)
+        errmsg = (f'Error uploading IQMs: Connection error:', f'{err}')
     except requests.exceptions.ReadTimeout as err:
-        errmsg = f'Error uploading IQMs -- {endpoint} seems down:\n{err}'
-        return Bunch(status_code=1, text=errmsg)
+        errmsg = (f'Error uploading IQMs: Server {endpoint} is down.', f'{err}')
+
+    if errmsg is not None:
+        response = Bunch(status_code=1, text='\n'.join(errmsg))
 
     return response, data
 

pyproject.toml

@@ -30,6 +30,7 @@ dependencies = [
   "nitransforms ~= 24.0",
   "niworkflows ~=1.10.1",
   "numpy ~=1.20",
+  "orjson",
   "pandas",
   "pybids >= 0.15.6",
   "PyYAML",