Add execution report (#17)

fnirsapp_qr.json

@@ -2,11 +2,11 @@
     "name": "fNIRS Apps: Quality Reports",
     "description": "Generate quality reports for fNIRS data",
     "author": "Robert Luke",
-    "tool-version": "v0.3.1",
+    "tool-version": "v0.3.2",
     "schema-version": "0.5",
     "command-line": "/run.py [InputDataset] [OutputLocation] [SubjectLabel] [SessionLabel] [TaskLabel] [SCIThreshold] [PeakPowerThreshold]",
     "container-image": {
-        "image": "ghcr.io/rob-luke/fnirs-apps-quality-reports/app:v0.3.1",
+        "image": "ghcr.io/rob-luke/fnirs-apps-quality-reports/app:v0.3.2",
         "index": "ghcr.io",
         "type": "docker",
         "entrypoint": true

fnirsapp_qr.py

@@ -15,10 +15,15 @@
 import os
 import subprocess
 from mne.utils import logger
+from pathlib import Path
+from datetime import datetime
+import json
+import hashlib
+from pprint import pprint
 
 matplotlib.use('agg')
 
-__version__ = "v0.3.1"
+__version__ = "v0.3.2"
 
 
 def fnirsapp_qr(command, env={}):
@@ -74,6 +79,19 @@ def fnirsapp_qr(command, env={}):
                     f'{__version__}')
 args = parser.parse_args()
 
+def create_report(app_name=None, pargs=None):
+
+    exec_rep = dict()
+    exec_rep["ExecutionStart"] = datetime.now().isoformat()
+    exec_rep["ApplicationName"] = app_name
+    exec_rep["ApplicationVersion"] = __version__
+    exec_rep["Arguments"] = vars(pargs)
+
+    return exec_rep
+
+exec_files = dict()
+exec_rep =create_report(app_name="fNIRS-Apps: Quality Reports", pargs=args)
+
 mne.set_log_level("INFO")
 logger.info("\n")
 
@@ -263,11 +281,16 @@ def run_report(path, path_out):
         for ses in sess:
 
             logger.info(f"Processing: sub-{sub}/ses-{ses}/task-{task}")
+            exec_files[f"sub-{sub}_ses-{ses}_task-{task}"] = dict()
+
             in_path = BIDSPath(subject=sub, task=task, session=ses,
                                root=f"{args.input_datasets}",
                                datatype="nirs", suffix="nirs",
                                extension=".snirf")
 
+            exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileName"] = str(in_path.fpath)
+            exec_files[f"sub-{sub}_ses-{ses}_task-{task}"]["FileHash"] = hashlib.md5(open(in_path.fpath, 'rb').read()).hexdigest()
+
             out_path = BIDSPath(subject=sub, task=task, session=ses,
                                 root=f"{args.output_location}",
                                 datatype="nirs", suffix="qualityReport",
@@ -279,3 +302,13 @@ def run_report(path, path_out):
                 run_report(in_path, out_path)
             else:
                 logger.info(f"    No file exists: {in_path}")
+
+exec_rep["Files"] = exec_files
+exec_path = f"{args.input_datasets}/execution"
+exec_rep["ExecutionEnd"] = datetime.now().isoformat()
+
+Path(exec_path).mkdir(parents=True, exist_ok=True)
+with open(f"{exec_path}/{exec_rep['ExecutionStart'].replace(':', '-')}-quality_reports.json", "w") as fp:
+    json.dump(exec_rep, fp)
+
+pprint(exec_rep)