Merge pull request #27 from flywheel-apps/re-run-script

script to rerun fMRIPrep w/ previous output

notebooks/rerun-fmriprep.py

@@ -0,0 +1,112 @@
+#! /usr/bin/env python3
+"""Create a python script to re-run bids-fmriprep given the job ID for a gear
+that was run on Flywheel.
+
+Use the output of the previous job as input to the new job so it won't have
+to re-do as much.
+
+This was copied from 'copy-job.py'
+"""
+
+import argparse
+import os
+import sys
+from datetime import datetime
+
+import flywheel
+
+
+def main(job_id):
+
+    fw = flywheel.Client("")
+    print("Flywheel Instance", fw.get_config().site.api_url)
+
+    analysis = None
+    if args.analysis:
+        analysis = fw.get_analysis(job_id)
+        print(f"Getting job_id from analysis '{analysis.label}'")
+        job_id = analysis.job.id
+
+    print("Job ID", job_id)
+    job = fw.get_job(job_id)
+    oldgear = fw.get_gear(job.gear_id)
+    gear = fw.lookup("gears/bids-fmriprep")  # get current version in case gear inputs
+    gear_name = oldgear.gear.name
+    print(f"gear.gear.name is {gear_name}")
+    if gear_name != "bids-fmriprep":
+        print("Wat?  This script is to re-run fMRIPrep.  I quit.")
+        sys.exit(1)
+    destination_id = job.destination.id
+    destination_type = job.destination.type
+    print(f"job's destination_id is {destination_id} type {destination_type}")
+
+    if job.destination.type == "analysis":
+        analysis = fw.get_analysis(destination_id)
+        destination_id = analysis.parent.id
+        destination_type = analysis.parent.type
+        print(f"job's analysis's parent id is {destination_id} type {destination_type}")
+    else:
+        print(
+            "Wat?  This script is to re-run fMRIPrep.  The destination should be an analysis.  I quit."
+        )
+        sys.exit(1)
+
+    destination = fw.get(destination_id)
+    destination_label = destination.label
+    print(f"new job's destination is {destination_label} type {destination_type}")
+
+    inputs = dict()
+    for key, val in job.config.get("inputs").items():
+        if "hierarchy" in val:
+            input_container = fw.get(val["hierarchy"]["id"])
+            inputs[key] = input_container.get_file(val["location"]["name"])
+
+    # Add output of job as input to new job
+    file_name = "unknown"
+    for ff in analysis.files:
+        if ff.name.startswith("bids-fmriprep_") and not "_work_" in ff.name:
+            file_name = ff.name
+            inputs["previous-results"] = analysis.get_file(file_name)
+            break
+
+    if file_name == "unknown":
+        print("Could not find zipped output of original bids-fmriprep job")
+        sys.exit(1)
+
+    config = job["config"]["config"]
+
+    now = datetime.now()
+    analysis_label = (
+        f'{gear.gear.name} {now.strftime("%m-%d-%Y %H:%M:%S")} SDK re-launched'
+    )
+    print(f"analysis_label = {analysis_label}")
+
+    analysis_id = gear.run(
+        analysis_label=analysis_label,
+        config=config,
+        inputs=inputs,
+        destination=destination,
+    )
+    print(f"analysis_id = {analysis_id}")
+    return analysis_id
+
+
+if __name__ == "__main__":
+
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter
+    )
+    parser.add_argument("job_id", help="Flywheel job ID")
+    parser.add_argument(
+        "-a",
+        "--analysis",
+        action="store_true",
+        help="ID provided is for the analysis (job destination)",
+    )
+    parser.add_argument("-v", "--verbose", action="count", default=0)
+
+    args = parser.parse_args()
+
+    main(args.job_id)
+
+    os.sys.exit(0)