/standalone_scripts

Repository to store standalone scripts that do not belong to any bigger package or repository

Primary LanguagePythonMIT LicenseMIT

Standalone scripts

Repository to store standalone scripts that do not belong to any bigger package or repository.

backup_zendesk_tickets.py

Used to automatically back up tickets from zendesk

Usage

Example: backup_zendesk_tickets.py --config-file ~/config_files/backup_zendesk_tickets.yaml --days 30

Usage: backup_zendesk_tickets.py [OPTIONS]

Options:
  --config-file PATH  Path to the config file  [required]
  --days INTEGER      Since how many days ago to backup tickets
  --help              Show this message and exit.

Dependencies

  • zendesk
  • click
  • yaml

Configuration

Requires a config file:

url: https://ngisweden.zendesk.com
username: mattias.ormestad@scilifelab.se
token: <ask Mattias to get token>
output_path: /Users/kate/Dropbox/dropbox_work/zendesk/output

backup_github.py

Performs a backup of all the repositories in user's GitHub account.

Dependencies
  • logbook
  • pygithub3

data_to_ftp.py

Used to transfer data to user's ftp server maintaing the directory tree structure. Main intention is to get the data to user outside Sweden.

db_sync.sh

Script used to mirror (completely) Clarity LIMS database from production to staging server

quota_log.py

DO NOT USE THIS SCRIPT!

Use taca server_status uppmax instead!

Returns a summary of quota usage in Uppmax

Dependencies
  • couchdb
  • pprint

couchdb_replication.py

handles the replication of the couchdb instance

Dependencies

  • couchdb
  • logbook
  • pycrypto
  • yaml

ZenDesk Attachments Backup

Takes a ZenDesk XML dump backup file and searches for attachment URLs that match specified filename patterns. These are then downloaded to a local directory.

This script should be run manually on tools when the manual ZenDesk backup zip files are saved.

Usage

Run with a typical ZenDesk backup zip file (will look for tickets.xml inside the zip file):

zendesk_attachment_backup.py -i xml-export-yyyy-mm-dd-tttt-xml.zip

Alternatively, run directly on tickets.xml:

zendesk_attachment_backup.py -i ngisweden-yyyymmdd/tickets.xml
Usage

If you're using this on tools for the first time, you'll need to set up conda. tools only has v2.6 of Python installed by default, which is old and not compatible with this script

These instructions get a copy of Python 2.7 for you. You only need to do this once:

  1. Download & install Miniconda
wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
  1. Tell the installer to prepend itself to your .bashrc file
  2. Log out and log in again, check that conda is in your path
  3. Create an environment for Python 2.7
conda create --name tools_py2.7 python pip
  1. Add it to your .bashrc file so it always loads
echo source activate tools_py2.7 >> .bashrc

Now Python 2.7 is installed, the zendesk attachment backup script should work. You can run it by going to the Zendesk backup directory and running it on any new downloads:

zendesk_attachment_backup.py <latest_backup>.zip
Dependencies
  • argparse
  • os
  • urllib2
  • re
  • sys
  • zipfile

repooler.py

Calculates a decent way to re-pool samples in the case that the amount of clusters from each sample doesn't reach the required threshold due to mismeasurements in concentration.

Dependencies
  • couchdb
  • click
  • Genologics: lims, config, entities

set_bioinforesponsible.py

Calls up the genologics LIMS directly in order to more quickly set a bioinformatics responsible.

Dependencies

  • Genologics: lims, config