Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update monitor_duplicate_accessions.py #434

Closed
wants to merge 1 commit into from
Closed

Update monitor_duplicate_accessions.py #434

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion eva-accession-pipeline/src/main/resources/monitoring/monitor_duplicate_accessions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ def get_mongo_uri(mongo_connection_properties):
def export_mongo_accessions(mongo_connection_properties, collection_name, export_output_filename):
export_command = 'mongoexport --uri {0} ' \
'--collection {1} --type=csv --fields accession ' \
"--query '{{remappedFrom: {{$exists: false}}}}' " \
"--query '{{\"remappedFrom\": {{\"$exists\": false}}}}' " \
'-o "{2}" 2>&1' \
.format(get_mongo_uri(mongo_connection_properties), collection_name, export_output_filename)
run_command_with_output("Exporting accessions in the {0} collection in the {1} database at {2}..."
Expand Down
Loading