Updates DOB (but is off by TimeZone) and Age

Dockerfile

@@ -4,7 +4,7 @@ FROM python:3.10-alpine
 RUN apk update && apk add bash
 
 RUN pip install --no-cache-dir --upgrade pip
-RUN pip install --no-cache-dir --extra-index-url https://package_access_token:5pBy3bmcwmL-_Mwa4_T6@git.biohpc.swmed.edu/api/v4/projects/1606/packages/pypi/simple flywheel-gear-toolkit[sdk] fiffreader
+RUN pip install --no-cache-dir --extra-index-url https://package_access_token:5pBy3bmcwmL-_Mwa4_T6@git.biohpc.swmed.edu/api/v4/projects/1606/packages/pypi/simple flywheel-gear-toolkit[sdk] fiffreader pytz
 
 ENV FLYWHEEL=/flywheel/v0
 RUN mkdir -p ${FLYWHEEL}

manifest.json

@@ -16,7 +16,7 @@
         },
         "gear-builder": {
             "category": "utility",
-            "image": "ansir/meg-metadata-importer:0.0.013"
+            "image": "ansir/meg-metadata-importer:0.0.028"
         }
     },
     "description": "Import file metadata into Flywheel. Metadata is stored under file.info.header. May also update blank fields in acquisition, session, and subject. Supports FIFF files.",
@@ -28,7 +28,7 @@
         "input-file": {
             "base": "file",
             "description": "Input file.",
-            "optional": false,
+            "optional": true,
             "type": {
                 "enum": [
                     "fiff"
@@ -42,5 +42,5 @@
     "name": "meg-metadata-importer",
     "source": "https://git.biohpc.swmed.edu/ben.wagner/meg-metadata-importer",
     "url": "https://git.biohpc.swmed.edu/ben.wagner/meg-metadata-importer",
-    "version": "0.0.013"
+    "version": "0.0.028"
 }
\ No newline at end of file

run.py

@@ -4,6 +4,7 @@ import logging
 import math
 import os
 import pprint
+import pytz
 import sys
 
 from flywheel_gear_toolkit import GearToolkitContext
@@ -117,19 +118,23 @@ def main(context):
 
     if session_id:
         session = context.client.get(session_id)
-        if not session.age and meas_date and dob:
+        if (not session.age or session.age == 0) and meas_date and dob:
             age_delta = datetime.datetime.strptime(
                 meas_date, "%Y-%m-%d %H:%M:%S"
             ) - datetime.datetime.strptime(dob, "%Y-%m-%d")
-            age = math.floor(age_delta.days / 365.2425)
-            print(f"Setting age to {age}")
-            session.update(age=age)
+            age_years = math.floor(age_delta.days / 365.2425)
+            age_seconds = int(age_delta.total_seconds())
+            print(f"Setting age to {age_years} ({age_seconds} seconds)")
+            session.update(age=age_seconds)
         if not session.weight and weight:
             print(f"Setting weight to {weight}")
             session.update(weight=weight)
         if not session.operator and experimenter:
             print(f"Setting operator to {experimenter}")
-            session.update(operator=experimenter)
+            if isinstance(experimenter, str):
+                session.update(operator=experimenter)
+            else:
+                session.update(operator=set(experimenter))
 
     if subject_id:
         subject = context.client.get(subject_id)
@@ -139,15 +144,19 @@ def main(context):
         if not subject.lastname and subj_last_name:
             print(f"Setting lastname to {subj_last_name}")
             subject.update(lastname=subj_last_name)
-        if not subject.sex and sex:
+        if (not subject.sex or subject.sex == "unknown") and sex:
             mfu = "unknown"
-            # not sure if 0 is male/female or something else...same for 1
-            if sex == 0:
-                mfu = "male"
             if sex == 1:
+                mfu = "male"
+            if sex == 2:
                 mfu = "female"
             print(f"Setting sex to {mfu}")
             subject.update(sex=mfu)
+        if (not subject.date_of_birth) and dob:
+            dt_dob = datetime.datetime.strptime(dob, "%Y-%m-%d")
+            dt_dob = dt_dob.replace(tzinfo=pytz.UTC)
+            print(f"Setting DOB to {dt_dob} from {dob}")
+            subject.update(date_of_birth=dt_dob)
 
     # return sucessful exit code
     return 0