t5-data

BilboMD

BilboMD is an example of storing an analysis output in JAMO. This is accomplished using JAT, a JAMO feature for grouping files together. To use JAT, a schema (a.k.a. template) is needed for defining what a collection of files and their associated metadata should look like. Currently, there is a single template that defines bilbomd results: bilbomd/bilbomd_classic_results.yaml. This template is used by specifying it in the JAMO config files.

The script bilbomd/bilbomd_release.py can be used to put BilboMD data into JAMO using the JAT. This script takes two arguments: the Jira BilboMD issue and the directory containing the BilboMD outputs. This script will use the Jira issue to retrieve necessary metadata for saving analysis results in JAMO. After saving the analysis results in JAMO, this script will create a Jira asset for the BilboMD results and close out the Jira issue.

To run this script, the following environment variables must be set:

• JIRA_HOST - the hostname for Jira
• JIRA_USER - the Jira user to use for authenticating with Jira
• JIRA_TOKEN - the Jira PAT to use for authenticating with Jira
• JAMO_HOST - the hostname for JAMO
• BILBOMD_JAMO_TOKEN - the BilboMD application token for JAMO