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microbiomedata / metadata-for-user-facility-template-transformations

CLI tool to convert metadata submissions from the NMDC submission portal to user facility Excel templates
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Metadata for User facility Template Transformations (MUTTs)

Introduction

The programs bundled in this repository intend to solve the problem of automatically retrieving Biosample metadata records for a given study submitted to NMDC through the NMDC Submission Portal, and converting the metadata into Excel spreadsheets that are accepted by DOE user facilities.

There are two components (of MUTTs) to keep in mind when trying to use this application -

  1. JSON header (sometimes also called mapper) configuration file

    • The headers that go into the user facility spreadsheet outputs is controlled by JSON files
    • The keys at the top level are used to indicate the main headers in the output. These values have mappings in the mapping configuration files described in the next point
    • You can use numbered keys to add more header information to clarify what a particular column contains
    • The header keyword is reserved in case you want to use some other column names as the main header
    • The sub_port_mapping keyword can be used to specify mappings between columns in the Submission Portal template and columns in the user facility spreadsheet outputs
    • Follow the examples that have already been specified in input-files. There are two user facility header customizations that have already been created as examples for the NMDC. They are:
    • EMSL header configuration: emsl_header.json
    • JGI MG and MT header configuration

  2. etl.py The command line application that can facilitate the conversion of metadata from the Submission Portal into user facility formats by consuming the above two files as inputs.

Software Requirements

  1. poetry
  2. Python > 3.9

Setup

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

  1. You need to obtain your NMDC Data and Submission Portal API Access Token and copy it over into your .env file, and associate it with the DATA_PORTAL_REFRESH_TOKEN environment variable.

    1. You can retrieve your Access Token by following this link: https://data.microbiomedata.org/user
    2. Go over to the .env file and copy the Refresh Token like DATA_PORTAL_REFRESH_TOKEN={refresh_token_value}

  2. Run etl.py with options as follows:

metadata-for-user-facility-template-transformations git:(main) ✗ poetry run python etl.py --help
Usage: etl.py [OPTIONS]

  Command-line interface for creating a spreadsheet based on metadata records.

  :param submission: The ID of the metadata submission. 
  :param user_facility: The user facility to retrieve data from. 
  :param header: True if the headers should be included, False otherwise. 
  :param mapper: Path to the JSON mapper specifying column mappings.
  :param unique_field: Unique field to identify the metadata records. 
  :param output: Path to the output XLSX file.

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