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microbiomedata / metadata-template-transformation

ETL between NMDC submission portal study records and user facility templates
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suggested updates to the documentation #31

Open mslarae13 opened 3 months ago

mslarae13 commented 3 months ago

Learning how to run MUTTs with @sujaypatil96 I have some suggestions for the readme page for this repo.

Software Requirements

  1. poetry ## I found this site to be more helpful https://python-poetry.org/docs/#installing-with-the-official-installer
  2. Python 3.9 ## add link

Setup

  1. Clone this repo
git clone https://github.com/microbiomedata/metadata-template-transformation.git
  1. Install dependencies with poetry
poetry install

  1. Cookie access to the submission portal is required and can be provided by editing the .env file. Requires you be an individual with appropriate access to the submission you're transforming.

      1. When in the NMDC data portal or submission portal, right click & select 'Inspect'
      1. In the 'Application' menu, select 'Local Storage', specifically, the storage for the NMDC portal
      1. For the 'Storage Refresh Token' copy the 'Value'
      1. Edit your .env file and add this value to the file. This should read 
        DATA_PORTAL_COOKIE = {value}

  2. Run etl.py with options as follows:

➜  metadata-template-transformation git:(main) ✗ poetry run python etl.py --help                                          
Usage: etl.py [OPTIONS]

Options:
  -o, --output TEXT           Path to result output XLSX file.  [required]
  -m, --mapper PATH           Path to user facility specific JSON file.
                              [required]
  -h, --header / --no-header  [default: no-header]
  -u, --user-facility TEXT    User facility to send data to.  [required]
  -s, --submission TEXT       Metadata submission id.  [required]
  --help                      Show this message and exit.