Automated Archiving

python v3.8.17

Summary

This script automates archiving projects and directories on DNAnexus platform - runs on the 1st and 15th of each month. It finds 002 / 003 projects, directories in 001_stagingarea52 and directories in precision brain projects which fit the pre-determined criteria for archiving, send notification to Slack and perform archiving in the next run.

What does the script do

Check for 002 003 projects, directories in staging52, folders in "precision" projects which are not modified in the last X months (inactive) and send Slack notification to notify. Archiving happens on the next run (for example, if project A is notified for archiving on Slack on the 1st, it will be archived on the 15th when the script runs again)

Tag never-archive in projects.setting to skip archiving permanently. Tag never-archive in a file in directories in staging-52 to skip archiving for that directory.

Typical use case

Check for archivable projects or directories or folders in "precision" projects on DNANexus, send Slack notification and archive them.

Archive Pickle

The script generates a pickle file at location specified at AUTOMATED_ARCHIVE_PICKLE_PATH.

Member

The script requires members.ini with section [members]. See example in repo. Mount the members.ini to read the file

-v /<path>/<to>/members.ini:/members.ini:ro

Workflow

1. If 1st or 15th, check memory (pickle) for archivable projects, directories, precision folders
   • if yes, run archiving.
2. Find archivable projects
3. Send Slack notification on those projects

Example Notification

003 Slack Notification

tar.gz Slack Notification

Environment Variables Required

dnanexus

• DNANEXUS_TOKEN : DNANexus API Token
• PROJECT_52 : staging52 project-id

general envs

• AUTOMATED_MONTH_002 : period (in months) before being marked for archiving (e.g. 3) for 002 projects
• AUTOMATED_MONTH_003 : period (in months) before being marked for archiving (e.g. 1) for 003 projects
• AUTOMATED_CEN_WES_MONTH: period (in months) before being marked for archiving (e.g. 6) for CEN/WES projects
• AUTOMATED_ARCHIVE_PICKLE_PATH : pickle file (memory) directory pathway
• ARCHIVING_LOGGING_PATH: path for logging
• TAR_MONTH: period (in months) for tar.gz being inactive to be considered 'old enough'
• ARCHIVE_MODIFIED_MONTH: period (in months) to determine whether to skip archiving if project or file is modified within this month (e.g. 1)
• ARCHIVE_DEBUG: env to comment out actionable codes (e.g. tag file, remove file tag, archive)
• AUTOMATED_REGEX_EXCLUDE: comma-separated regex word e.g. megaqc.json,some-filename..*,^megapc.csv
• PRECISION_ARCHIVING: comma separated project-id that need specific archiving (folder by folder archiving)

slack

• SLACK_TOKEN : Slack Bot API Token

Logging

The main logging script is helper.py

The script will generate a log file automated-archiving.log in ARCHIVING_LOGGING_PATH

Tags

There are 2 tags recognized by the script:

• never-archive
• archive

#never-archive

Projects tagged will bypass archiving indefintely, same goes to any directory within staging52.

#archive

Tagged project will be listed for archiving, regardless of modified date

Docker

Dockerfile is included for rebuilding docker image

To rebuild image: docker build -t <image name> .

Current docker command (server):

docker run --env-file <path to environment file> -v <path>/members.ini:/members.ini:ro -v <path to logging directory>:/monitoring archive --datetime 20240131

• optional argument datetime to override script datetime

Automation

A cron job can be set up to run the script on 1st and 15th of each month