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NOAA-Omics / noaa-omics-templates

Documentation for study data templates developed by NOAA Omics
https://noaa-omics-templates.readthedocs.io
GNU Affero General Public License v3.0
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NOAA Omics Study Data Templates

This project is actively under development. Reach out to bayden.willms@noaa.gov for questions.

Overview of Scripts

Creating new data templates and updating the data dictionary accordingly have now been automated, in addition to the term markdown file generation in generate_term_docs.py. The new script, generate_template.py, will perform the following tasks:

  1. Get Latest MIMARKS Terms: Retrieve the latest terms and their comments from the latest MIMARKS package (Excel file).
  2. Get up-to-date AOML and Darwin Core Terms: Obtain up-to-date AOML and Darwin Core terms from the data dictionary (Google Sheet).
  3. Compare and Create New Data Template: Compare terms from those files and an existing data template to create a new data template (Google Sheet) for a new environment.
  4. Update Data Dictionary: Update the data dictionary (study-data-template-dict Google Sheet) with new terms and update existing terms appropriately.

Additionally, there is a script to verify the Google Sheets API connection called test_auth.py.

Setup

Administrator Setup

An AOML Omics Google Drive admin must grant permission for the Google Sheets and Drive API.

  1. Go to the Google Cloud Console.
  2. Log in with AOML Omics account.
  3. The project name is data-templates.

Creating a Service Account

  1. Go to API & Services > Credentials.
  2. Click on "Create Credentials" and select "Service Account".
  3. Fill in the service account details (name, ID, description) and click "Create".

Assign Roles

  1. In the next step, assign the "Editor" role to the service account to grant access to modify Google Sheets.
  2. Click "Continue".

Create Key

  1. Under the service account you created, click "Add Key" and select "JSON".
  2. This will download a JSON file with the credentials to your computer.
  3. Share this JSON file securely with the user who needs to set up the environment.

Grant Access to Service Account

  1. The service account has an email address (e.g., service-account-name@data-templates.iam.gserviceaccount.com).
  2. Share the Google Sheets with this email address to grant access.

User Setup

This project works on both macOS and Windows. Ensure you have Git and Anaconda installed on your computer:

Setup Project Locally

  1. Clone the GitHub project to your local machine:

    git clone https://github.com/NOAA-Omics/noaa-omics-templates.git
cd noaa-omics-templates

  2. Configure Anaconda environment using provided environment.yml 

    conda env create -f environment.yml 
conda activate data-templates-env

Setup Google API Authentication

  1. The admin will provide you with your credentials.json file.
  2. Place the credentials.json in your 'script-dependencies' folder.
  3. You can use the test_auth.py script to test API connection.

Run

Preparing Input Files

  1. Create a Copy of an Existing Data Template:

    • Go to the AOML Omics Google Drive.
    • Create a copy of an existing data template.
    • Rename the copy according to your new environment name.
    • Rename the sheet name, for example, from water_sample_data to sediment_sample_data.

  2. Download MIMARKS File:

    • Download the latest MIMARKS package from NCBI Biosample Templates.
    • Move the downloaded Excel file to the script-dependencies folder in the project.
    • Copy and paste the filename into the generate_template.py script at the line: 
      mimarks_filename = 'MIMARKS.survey.sediment.6.0.xlsx' # EDIT ME

  3. Configure Credentials:

    • Copy your credentials.json filename and paste it into the generate_template.py script at the line: 
      credentials_filename = 'data-templates-c7159dc891a7.json' # EDIT ME

  4. Set Up Google Sheet IDs:

    • The Google Sheet ID is available in the URL of the Google Sheet, between /d/ and /edit. For example, in the URL https://docs.google.com/spreadsheets/d/abc123XYZ456/edit, the Google Sheet ID is abc123XYZ456.
    • You will need two Google Sheet IDs:
      1. One for study-data-template-dict.
      2. One for your newly created data template (the one that is a copy of an existing template).
    • Then, copy and paste those IDs into the generate_template.py script at the line: 
      
study_template_dict_sheet_id = "abc123XYZ456" #EDIT ME
new_template_id = "abc123XYZ456" #EDIT ME

Running the Script

  1. Navigate to the Scripts Folder: 
    
cd scripts
python generate_template.py