Clinical-Genomics-Lund / bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen
https://bonsai-wgs.readthedocs.io/en/latest/
GNU General Public License v3.0
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Upload script complains about "Agrument list too long" from curl #144

Closed samuell closed 9 months ago

samuell commented 9 months ago

Describe the bug A clear and concise description of what the bug is.

To Reproduce Steps to reproduce the behavior:

  1. Checkout commit b10acfd8371ee227a00679ae996cbdda334db2e4
  2. Set up a user admin/admin
  3. Create a group named default
  4. Submit a .json file that is more than around 9000-10000 rows long (e.g. the result of running this data via Jasen), like so:
./scripts/upload_sample.sh \
  --api localhost:8011 \
  --group default \
  -u admin \
  -p admin \
  --input SRR12149876_result.json

Expected behavior Would expect the upload to succeed.

Actual behaviour I got this error message:

$ ./scripts/upload_sample.sh \
  --api localhost:8011 \
  --group default \
  -u admin \
  -p admin \
  --input SRR12149876_result.json
login
upload sample json
WARNING: tempfile is deprecated; consider using mktemp instead.
./scripts/upload_sample.sh: line 90: /home/shl/opt/mc3/bin/curl: Argument list too long