metaspace2020 / metaspace

Cloud engine and platform for metabolite annotation for imaging mass spectrometry
https://metaspace2020.eu/
Apache License 2.0
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Downloading imzML/ibd files from IBM Cloud #1407

Closed sergii-mamedov closed 1 year ago

sergii-mamedov commented 1 year ago

This PR is a part of Backup imzML/ibd files task.

This is a temporary script that is required for a one-time download of imzML/ibd from IBM Cloud. Credentials are read from a shell file because it's easier in this case.

How to run

  1. Create shell file (ibm_cos.sh) with credentials:
    export COS_ENDPOINT='https://s3.eu-de.cloud-object-storage.appdomain.cloud'
    export COS_API_KEY_ID=<API_KEY>
    export COS_INSTANCE_CRN=<INSTANCE_CRN>
  2. Run shell file:
    source ibm_cos.sh
  3. Put dataset list on TSV file:
    2021-07-21_21h41m21s    s3a://sm-engine-upload/01234567-0123-0123-0123-67a48593911e
  4. Run script:
    python download_imzml_ibd_from_ibm.py --datasets datasets.tsv

Postscript

Made cosmetic changes and renamed the script for AWS cloud.