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fix: process file upload before submitting isa-json to ena #65

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merged 1 commit into from
Nov 7, 2024
Merged

fix: process file upload before submitting isa-json to ena #65

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6 changes: 0 additions & 6 deletions mars-cli/mars_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -188,12 +188,6 @@ def cli(ctx, development):
multiple=True,
help="Path of files to upload",
)
# @click.option(
# "--data-submit-to-ena",
# type=click.BOOL,
# default=False,
# help="Submit data files to ENA.",
# )
@click.option(
"--submit-to-metabolights",
type=click.BOOL,
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22 changes: 10 additions & 12 deletions mars-cli/mars_lib/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,18 +59,16 @@ def submission(
f"ISA JSON with investigation '{isa_json.investigation.title}' is valid."
)

if (
TargetRepository.ENA in target_repositories
and data_file_paths
and file_transfer
):
upload_to_ena(
file_paths=data_file_paths,
user_credentials=user_credentials,
submission_url=urls["ENA"]["DATA-SUBMISSION"],
file_transfer=file_transfer,
)
elif TargetRepository.ENA in target_repositories:
if TargetRepository.ENA in target_repositories:
# Step 1 : upload data if file paths are provided
if data_file_paths and file_transfer:
upload_to_ena(
file_paths=data_file_paths,
user_credentials=user_credentials,
submission_url=urls["ENA"]["DATA-SUBMISSION"],
file_transfer=file_transfer,
)
# Step 2 : submit isa-json to ena
# TODO: Filter out other assays
ena_result = submit_to_ena(
isa_json=isa_json,
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