genTB website

Basic django site to facilitate the contribution and analysis of fastQ and VCF files.

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Authentication

Currently users the basic Django auth.

Pages

Homepage

A basic view/template combination

• View: "view_homepage" gentb_website/tb_website/apps/basic_pages/views.py
• Template: gentb_website/tb_website/templates/homepage.html

Predict

This pages requires the user to be logged in.

Share

A basic view/template combination. The template includes embedded Dataverse Widgets in the form of javascript snippets

• View: "view_share_page" gentb_website/tb_website/apps/basic_pages/views.py
• Template: gentb_website/tb_website/templates/share.html

Map

A basic view/template combination. The maps are actually hosted by a Shiny application and embedded in an iframe. The url to the iframe is written directly into the template.

• View: "view_map_page" gentb_website/tb_website/apps/maps/views.py
• Template: gentb_website/tb_website/templates/maps/basic_map.html

• Note: The Shiny app url is currently https://hmdc.shinyapps.io/genTB and part of the IQSS Shinyapps.io service

Explore (TwoRavens)

TwoRavens is a system of interlocking statistical tools for data exploration, analysis, and meta-analysis. This page uses TwoRavens via an iframe to analyze the genTB master data file.

TwoRavens needs two values which are supplied via the genTB database:

1. codebook_file_url - This url links directly to PDF file on Dataverse and identified by file id number - Example ```codebook_file_url``: https://dataverse.harvard.edu/api/access/datafile/2694344
2. two_ravens_url - This url contains the TwoRavens link and is used within an iframe.
   - The url contains both a Dataverse file id number and an API key
   • This API key within the url is bad practice and will probably be changed on the Dataverse side - Example two_ravens_url: https://rserve.dataverse.harvard.edu/dataexplore/gui.html?dfId=2693726&key=c54f07b7-5098-461c-adf3-a976c0d62f6e

These values may be supplied via the Django admin:

- Models.py file for the values above:
    - [gentb_website/tb_website/apps/explore/models.py](gentb_website/tb_website/apps/explore/models.py)

The view/template files may be found here:

• View: "view_explore_page" gentb_website/tb_website/apps/basic_pages/views.py
• Template: gentb_website/tb_website/templates/explore.html

About Page

A basic view/template combination

• View: "view_about_page" gentb_website/tb_website/apps/basic_pages/views.py
• Template: gentb_website/tb_website/templates/about.html