README.md

GDC Open Source code

======= GDC is Open Source, Github Repositories containing source code of GDC Applications can be found on GDC GitHub Organization page.

• GDC Data Portal: https://github.com/NCI-GDC/portal-ui
• GDC Legacy Archive: https://github.com/NCI-GDC/portal-ui-legacy
• GDC Data Transfer Tool: https://github.com/NCI-GDC/gdc-client
• GDC Data Dictionary: https://github.com/NCI-GDC/gdcdictionary
• GDC Data Model: https://github.com/NCI-GDC/gdcdatamodel
• GDC Psqlgraph: https://github.com/NCI-GDC/psqlgraph

Support

Please direct technical questions to GDC Support.

GDC Documentation Site

Technology

• Python 2.6, 2.7, 3.3, 3.4 and 3.5.
• mkdocs
• BSCodeTabs for mkdocs

Install & Run

(Optional) Set up virtualenv:

• Install virtualenv
• python -m virtualenv venv
• source venv/bin/activate
• Run the installation commands below
• To leave the virtual environment: deactivate

Install GDC-docs:

• pip install -r requirements.txt
• mkdocs serve (optionally set port --dev-addr=0.0.0.0:<PORT>)

Build

• mkdocs build --clean

Repository Conventions

• All Shared content in the "Commons" directory
• One Directory per GDC product (API, Data_Portal, Data_Submission_Portal, Data_Transfer_Tool)
• Each GDC product have a Users_Guide and Release_Notes directory

Linking

To another documentation page

[Authentication and Authorization](../../Commons/Authentication.md)

Inside another documentation page

[Authentication and Authorization](../../Commons/Authentication.md#internal-section)

Adding icons and PDFs

The convention for this, when updating mkdocs.yml is the following:

• <url ending in .pdf>: 'index.md' example:
• fa-file-pdf-o Download PDF /API/PDF/API_UG.pdf: 'index.md'

Documentation Conventions

A detailed list of all conventions is available on GDC Website

Build PDF

Install mkdocs2pandoc, following instructions available here:

https://github.com/jgrassler/mkdocs-pandoc

Prepare a yml file dedicated to your Userguide, using Data_Portal_UG.yml as an example.

Run the following commands to:

• Convert the User Guide to Pandoc:
• Tweak the pandoc file
• Build a PDF

mkdocs2pandoc -f Data_Portal_UG.yml -o docs/Data_Portal/PDF/Data_portal_UG.pd
sed -i -e 's/# / /g' docs/Data_Portal/PDF/Data_portal_UG.pd
sed -i -e 's/### /## /g' docs/Data_Portal/PDF/Data_portal_UG.pd
sed -i -e 's/\/site\//\/docs\//g' docs/Data_Portal/PDF/Data_portal_UG.pd
pandoc --toc -V documentclass=report -V geometry:"top=2cm, bottom=1.5cm, left=1cm, right=1cm" -f markdown+grid_tables+table_captions -o docs/Data_Portal/PDF/Data_portal_UG.pdf docs/Data_Portal/PDF/Data_portal_UG.pd