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Fixing Issue 1354 (random pipeline failures) #1355

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merged 2 commits into from
Oct 19, 2023
Merged

Fixing Issue 1354 (random pipeline failures) #1355

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fd7c838
Adding more logging
york-stsci Sep 11, 2023
c588e38
Merge branch 'develop' into issue-1354
mfixstsci Oct 19, 2023
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12 changes: 12 additions & 0 deletions jwql/shared_tasks/run_pipeline.py
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Original file line number Diff line number Diff line change
Expand Up @@ -52,18 +52,27 @@ def run_pipe(input_file, short_name, work_directory, instrument, outputs, max_co
status_f.write("\t start_dir is {} ({})\n".format(start_dir, type(start_dir)))
status_f.write("\t uncal_file is {} ({})\n".format(uncal_file, type(uncal_file)))
status_f.write(f"\t outputs is {outputs}\n")
sys.stderr.write("Running run_pipe\n")
sys.stderr.write("\t input_file_basename is {} ({})\n".format(input_file_basename, type(input_file_basename)))
sys.stderr.write("\t start_dir is {} ({})\n".format(start_dir, type(start_dir)))
sys.stderr.write("\t uncal_file is {} ({})\n".format(uncal_file, type(uncal_file)))
sys.stderr.write(f"\t outputs is {outputs}\n")

try:
sys.stderr.write("Copying file {} to working directory.\n".format(input_file))
copy_files([input_file], work_directory)
sys.stderr.write("Setting permissions on {}\n".format(uncal_file))
set_permissions(uncal_file)

steps = get_pipeline_steps(instrument)
sys.stderr.write("Pipeline steps initialized to {}\n".format(steps))

# If the input file is a file other than uncal.fits, then we may only need to run a
# subset of steps. Check the completed steps in the input file. Find the latest step
# that has been completed, and skip that plus all prior steps
if 'uncal' not in input_file:
completed_steps = completed_pipeline_steps(input_file)
sys.stderr.write("Steps {} already completed.\n".format(completed_steps))

# Reverse the boolean value, so that now steps answers the question: "Do we need
# to run this step?""
Expand All @@ -81,18 +90,21 @@ def run_pipe(input_file, short_name, work_directory, instrument, outputs, max_co

for step in steps:
if not steps[step]:
sys.stderr.write("Setting last_run to {}.\n".format(step))
last_run = deepcopy(step)

for step in steps:
if step == last_run:
break
if step != last_run:
sys.stderr.write("Setting {} to skip while looking for last_run.\n".format(step))
steps[step] = False

# Set any steps the user specifically asks to skip
for step, step_dict in step_args.items():
if 'skip' in step_dict:
if step_dict['skip']:
sys.stderr.write("Setting step {} to skip by user request.\n".format(step))
steps[step] = False

# Run each specified step
Expand Down