Merge branch 'error-trace' into develop

clpipe/convert2bids.py

@@ -7,6 +7,7 @@
 import click
 import logging
 
+from .error_handler import exception_handler
 from .utils import get_logger
 from .status import needs_processing, write_record
 

clpipe/job_dependency_experiment.py

@@ -0,0 +1,48 @@
+import os
+import subprocess
+from typing import List, Optional
+
+class Job:
+    def __init__(self, job_name, job_string, parent_jobs = None):
+        self.job_name = job_name
+        self.job_string = job_string
+        self.parent_jobs: Optional[List[Job]] = parent_jobs
+        self.slurm_id = None
+
+# Kinda need to know how jobs are dependent in the first place to know how to submit
+# which imo defeats the purpose of using slurm dependencies? It just makes sure that
+# one job finishes running before the next one starts. 
+j1 = Job("j1", "sbatch --wrap='echo j1'")
+j2 = Job("j2", "sbatch --wrap='echo j2'", [j1])
+j3 = Job("j3", "sbatch --wrap='echo j3'", [j1])
+j4 = Job("j4", "sbatch --wrap='echo j4'", [j2, j3])
+j5 = Job("j5", "sbatch --wrap='echo j5'")
+j6 = Job("j6", "sbatch --wrap='echo j6'", [j4, j5])
+
+def run_job(job: Job) -> int:
+    """Take a job and returns the slurm id for the corresponding job"""
+    if job.parent_jobs:
+        dependency_string = " --dependency=afterany:"
+        for parent_job in job.parent_jobs:
+            dependency_string += str(parent_job.slurm_id)
+            dependency_string += ','
+        job.job_string += dependency_string[:-1]
+    result = subprocess.run(job.job_string, shell=True, capture_output=True, text=True)
+    job.slurm_id = int(result.stdout.split(" ")[-1])
+    return job.slurm_id
+
+run_job(j1)
+print(j1.slurm_id)
+print(j1.job_string)
+
+run_job(j2)
+print(j2.slurm_id)
+print(j2.job_string)
+
+run_job(j3)
+print(j3.slurm_id)
+print(j3.job_string)
+
+run_job(j4)
+print(j4.slurm_id)
+print(j4.job_string)

clpipe/utils.py

@@ -1,11 +1,11 @@
 import click
 import os
+import sys
 import logging
 from pathlib import Path
 
 from nipype.utils.filemanip import split_filename
 
-
 @click.command()
 @click.argument("subjects", nargs=-1, required=False, default=None)
 @click.option(
@@ -83,12 +83,16 @@ def resolve_fmriprep_dir(fmriprep_dir):
 
     return fmriprep_root
 
+def exception_handler(logger, exception_type, exception, traceback):
+    logger.error("%s: %s" % (exception_type.__name__, exception))
 
 def get_logger(name, debug=False, log_dir=None, f_name="clpipe.log"):
     logger = logging.getLogger("clpipe").getChild(name)
 
     if debug:
         logger.setLevel(logging.DEBUG)
+    else:
+        logger.setLevel(logging.INFO)
 
     if log_dir:
         add_file_handler(log_dir, f_name, logger=logger)
@@ -108,6 +112,10 @@ def get_logger(name, debug=False, log_dir=None, f_name="clpipe.log"):
     log_args = {"username": user_name}
 
     logger = logging.LoggerAdapter(logger, log_args)
+
+    if not debug:
+        sys.excepthook = lambda *exc_info: exception_handler(logger, *exc_info)
+
     return logger