class TestWetRun:
def test_wet_run(self, gtk_context):
acq = gtk_context.get_input_path('acquisition_table')
ses = gtk_context.get_input_path('session_table')
sub = gtk_context.get_input_path('subject_table')
if acq and ses and sub:
# All inputs provided, there should be no outputs
run.main(gtk_context)
outdir = Path(gtk_context.output_dir)
assert len(os.listdir(outdir)) == 0
elif not (acq or ses or sub):
# No inputs provided, there should be three outputs
run.main(gtk_context)
outdir = Path(gtk_context.output_dir)
outfiles = os.listdir(outdir)
assert len(outfiles) == 3
else:
# Raise system exit when not all three or none are provided
with pytest.raises(SystemExit):
run.main(gtk_context)
assert True
# if gtk_context.config:
if __name__ == '__main__':
gtk_context = flywheel_gear_toolkit.GearToolkitContext()
gtk_context.init_logging()
gtk_context.log_config()
run.main(gtk_context)
df = ld.load_text_dataframe(csv_file, first_row, delimiter)
mapping_column = ld.validate_df(df, mapping_column, subject_column)
df = id.import_data(
fw,
df,
project_id,
mapping_column,
subject_column,
object_type,
attached_files,
metadata_destination,
overwrite,
dry_run,
)
report_output = context.output_dir
id.save_df_to_csv(df, report_output)
except Exception as e:
log.exception(e)
return 1
return 0
if __name__ == "__main__":
result = main(gt.GearToolkitContext())
sys.exit(result)
def test_dry_run_works(tmp_path, caplog, install_gear, search_caplog_contains,
search_caplog):
caplog.set_level(logging.DEBUG)
user_json = Path(Path.home() / ".config/flywheel/user.json")
if not user_json.exists():
TestCase.skipTest("", f"No API key available in {str(user_json)}")
with open(user_json) as json_file:
data = json.load(json_file)
if "ga" not in data["key"]:
TestCase.skipTest("", "Not logged in to ga.")
FWV0 = Path.cwd()
install_gear("dry_run.zip")
with flywheel_gear_toolkit.GearToolkitContext(
input_args=[]) as gtk_context:
status = run.main(gtk_context)
assert status == 0
assert (FWV0 / "work/bids/.bidsignore").exists()
assert (FWV0 / "freesurfer/subjects/sub-42/label/empty").exists()
assert search_caplog_contains(
caplog,
"command is",
"--bids-filter-file=input/bids-filter-file/PyBIDS_filter.json",
)
assert search_caplog_contains(
caplog, "--work-dir",
"flywheel/v0/output/61608fc7dbf5f9487f231006")
# Since the "work-dir" option was used, the gear created the old data's /tmp/ path and
# ran in it, and a symbolic link was created from the current /tmp/ path to the old one.
# The "current" path was created just before these tests started (in conftest.py). E.g.:
# % ls /tmp
# gear-temp-dir-2cde80oy -> /tmp/gear-temp-dir-yhv7hq29
# gear-temp-dir-yhv7hq29
# where "yhv7hq29" is the old random part found in the provided "work-dir" data and
# "2cde80oy" is the new random part of the /tmp/ path created to run these tests.
# The new part is generated randomly so it will change but the old one is in the gear test
# data provided as an input to the gear.
old_tmp_path = Path(*(list(Path.cwd().parts)[:3]))
assert "yhv7hq29" in list(old_tmp_path.parts)[2]
current_tmp_path = Path(*(list(FWV0.parts)[:3]))
assert current_tmp_path.is_symlink()
# now change back to the original /tmp/ path so that following tests will not be affected
current_tmp_path.unlink()
old_tmp_path.replace(current_tmp_path)
assert search_caplog_contains(caplog, "command is", "participant")
assert search_caplog_contains(caplog, "command is", "'arg1', 'arg2'")
assert search_caplog(caplog, "No BIDS errors detected.")
assert search_caplog(caplog, "including sub-TOME3024/figures")
assert search_caplog(caplog, "Zipping work directory")
assert search_caplog(caplog,
"Zipping work/bids/dataset_description.json")
assert search_caplog(
caplog, "Zipping work/bids/sub-TOME3024/ses-Session2/anat")
assert search_caplog(
caplog, "Looked for anatsub-TOME3024_desc-about_T1w.html")
assert search_caplog(caplog, "Warning: gear-dry-run is set")
# Make sure platform-viewable archive includes figures
html_zip_files = list(FWV0.glob("output/sub-TOME3024_*.html.zip"))
html_zip_file = html_zip_files[0]
assert html_zip_file.exists()
unzip_archive(html_zip_file, tmp_path)
assert Path(tmp_path / "index.html").exists()
assert Path(
tmp_path /
"sub-TOME3024/figures/sub-TOME3024_ses-Session2_acq-MPRHA_dseg.svg"
).exists()
report_generator.upload_report(gear_args['api_key'], session_id,
gear_args.get('parent_acq'))
# Log number of DICOM files transmitted and exit accordingly
if DICOMS_SENT == 0:
log.error("No DICOM files were transmitted. Exiting.")
os.sys.exit(1)
elif DICOMS_SENT < DICOMS_PRESENT:
log.error(
"Not all DICOMS were successfully transmitted. Please check report."
)
os.sys.exit(1)
else:
log.info(
f"!!! TOTAL -- There were {DICOMS_SENT} DICOM files transmitted.")
exit_status = 0
return exit_status
if __name__ == "__main__":
with flywheel_gear_toolkit.GearToolkitContext() as gear_context:
gear_context.init_logging()
log = gear_context.log
exit_status = main(gear_context)
log.info(
f"Successful dicom-send gear execution with exit status {exit_status}."
)
