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issue_tracker_github

This is server-side software for managing new package issues submitted to the 'Contribution' Bioconductor github repository.

Setup

The software runs on an Amazon nano-instance at issues.bioconductor.org, accessible via ssh.

Setup is via a chef recipe. Update the recipe by commiting to the github repository, then berks install. On the issues.bioconductor.org

sudo su - www-data
chef-client

Work flow

The software notifies the single package builder of the repository to retrieve the package from, and the package is build across Linux, Mac, and Windows.

Debugging

  • issues.bioconductor.org
  • checkip.amazonaws.com
  • EC2 Management Console
    • NETWORK & SECURITY
    • ssh; edit inbound rules
  • ssh ubuntu@issues.bioconductor.org sudo su - www-data

The software is running under apache. Error and access logs are at /var/log/apache2 as ubuntu.

Use pry for interactive ruby. Ensure that the approporiate pry is available (via rbenv)

$ which pry
/var/www/.rbenv/shims/rpy

start pry (from the home directory of www-data) and require the core application

$ pry
[1] pry(main)> require_relative './app/core'
=> true
[2] pry(main)>

Updating

Make changes in personal clone of git repository, push to github.com/Bioconductor/issue_tracker_github.

On ubuntu@issues.bioconductor.org

sudo chef-client

Updating data bags

There are authentication credentials encoded by chef data bags. See git credentials for keys to authorize changes. To show contains of a data bag:

 knife data bag show IssueTrackerConfig IssueTrackerConfig --secret-file /home/lori/Documents/databag.key

To edit the contents of the data bag:

knife data bag edit IssueTrackerConfig IssueTrackerConfig --secret-file /home/lori/Documents/databag.key

The data bag should remain encrypted but to test run the show command without including --secret-file and it should show encrypted contents.

You can list all managed data bags by doing

knife data bag list

The aws keys correspond to the sdk-email user security credentials.