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Feature/fix variable #39

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Feature/fix variable #39

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39bf33d
renamed log_file_writer
ellendejong Jan 17, 2024
4fd6894
fix flake8
ellendejong Jan 17, 2024
d58452b
rename branches in github workflows
ellendejong Jan 17, 2024
da4cbbc
split line date and run_folder
ellendejong Jan 17, 2024
855b0ec
Merge remote-tracking branch 'origin/development' into feature/fix_va…
ellendejong Feb 20, 2024
65c013c
flake8: > 127 chrs
ellendejong Feb 20, 2024
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8 changes: 4 additions & 4 deletions rsync_to_rdisc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -217,7 +217,7 @@ def rsync_server_remote(hpc_server, client, to_be_transferred, mount_path, run_f
for run in to_be_transferred:
with open(settings.log_path, 'a', newline='\n') as log_file:
log_file_writer = writer(log_file, delimiter='\t')
log_file_writer.writerows([["#########"], [f"Date: {date}", f"Run_folder: {run}"]])
log_file_writer.writerows([["#########"], [f"Date: {date}"], [f"Run_folder: {run}"]])

transfer_settings = to_be_transferred[run]
# settings per folder data type, such as remote input dir and local output dir, etc.
Expand Down Expand Up @@ -272,9 +272,9 @@ def rsync_server_remote(hpc_server, client, to_be_transferred, mount_path, run_f
upload_result_exomedepth=upload_result_exomedepth
)
# Do not include run in transferred_runs.txt if temp error file is not empty.
with open(f"{settings.wkdir}/transferred_runs.txt", 'a', newline='\n') as log_file:
log_file_writer = writer(log_file, delimiter='\t')
log_file_writer.writerow([f"{run}_{transfer_settings['name']}", email_state])
with open(f"{settings.wkdir}/transferred_runs.txt", 'a', newline='\n') as transferred_file:
file_writer = writer(transferred_file, delimiter='\t')
file_writer.writerow([f"{run}_{transfer_settings['name']}", email_state])

return rsync_succes

Expand Down
16 changes: 11 additions & 5 deletions test_rsync_to_rdisc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -45,8 +45,8 @@ def set_up_test(tmp_path_factory):
run = "230920_A01131_0356_AHKM7VDRX3"
analysis = f"{run}_1" # run ok + exomedepth
analysis_transfer_settings = rsync_to_rdisc.settings.transfer_settings['bgarray']['transfers'][0]
Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").write_text(analysis) # Other analysis will be added as part of the tests.

# Other analysis will be added as part of the tests.
Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").write_text(analysis)

# Processed folder
for project in range(1, 6):
Expand Down Expand Up @@ -327,7 +327,9 @@ def test_rsync_ok(self, set_up_test, mocker, mock_send_mail_transfer_state):
mock_check_rsync.assert_called_once()
mock_send_mail_transfer_state.assert_called_once()
mock_send_mail_transfer_state.reset_mock()
assert f"{set_up_test['run']}_3_TRANSFER\tok" in Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").read_text()
assert (
f"{set_up_test['run']}_3_TRANSFER\tok" in Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").read_text()
)

def test_rsync_error(self, set_up_test, mocker, mock_send_mail_transfer_state):
mocker.patch("rsync_to_rdisc.check_if_file_missing", return_value=[])
Expand All @@ -338,7 +340,9 @@ def test_rsync_error(self, set_up_test, mocker, mock_send_mail_transfer_state):
{f"{set_up_test['run']}_3": rsync_to_rdisc.settings.transfer_settings['bgarray']['transfers'][0]},
set_up_test['tmp_path'], f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt",
)
assert f"{set_up_test['run']}_3_Exomes" not in Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").read_text()
assert (
f"{set_up_test['run']}_3_Exomes" not in Path(f"{rsync_to_rdisc.settings.wkdir}/transferred_runs.txt").read_text()
)

# parametrize GATK / ExomeDepth error and no errors.
@pytest.mark.parametrize("project,gatk_succes,ed_succes,state", [
Expand All @@ -351,7 +355,9 @@ def test_rsync_error(self, set_up_test, mocker, mock_send_mail_transfer_state):
("5", "warning", "error", "vcf_upload_error"),
("6", "error", "warning", "vcf_upload_error"),
])
def test_vcf_upload_error(self, project, gatk_succes, ed_succes, state, set_up_test, mocker, mock_send_mail_transfer_state):
def test_vcf_upload_error(
self, project, gatk_succes, ed_succes, state, set_up_test, mocker, mock_send_mail_transfer_state
):
analysis = f"{set_up_test['run']}_{project}"
mocker.patch("rsync_to_rdisc.check_if_file_missing", return_value=[])
mocker.patch("rsync_to_rdisc.os.system")
Expand Down
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