ADMINISTRATORS.md

Introduction

This guide details how to use the custom manage.py shell commands. All commands can be invoked using the shell command format:

python manage.py <command name> --settings=settings.<your settings module>

You can omit the settings argument to use the default settings module (the module imported in mavedb/settings.py).

Django-reversion

Django-reversion has been integrated with the site. This is a well maintained model versioning application that keeps a history of each instance in the database for models that have been registered. There are two key commands to run when deploying:

python manage.py createinitialrevisions

To delete the recorded history for a particular model:

python manage.py deleterevisions <appname.modelname> --keep=[int] --days=[int]

This will keep anything from last n days or keep at least n history items.

Custom Commands

createlicences

This command expects the file data/main/licenes.json and folder data/main/licence_legal_code containing the licence text for your licences. The licences.json file should follow the format below:

{
  "licences": [
    {
      "short_name": "CC0",
      "long_name": "CC0 (Public domain)",
      "legal_code": {
        "file": true,
        "value": "CC0.txt"
      },
      "logo": "cc-zero.svg",
      "link": "https://creativecommons.org/publicdomain/zero/1.0/",
      "version": "1.0"
    },
    {
      "short_name": "Other - See Data Usage Guidelines",
      "long_name": "Other - See Data Usage Guidelines",
      "legal_code": {
        "file": false,
        "value": "See Data Usage Guidelines"
      },
      "logo": "",
      "link": "",
      "version": "1.0"
    }
  ]
}

This file specifies a list of licences to create/update. This command has no arguments. Existing licences matching short_name in the json file will be updated.

createreferences

This command expects the file data/genome/reference_genomes.json The reference_genomes.json file should follow the format below:

[
    {
        "assembly_identifier": {
            "dbname": "GenomeAssembly",
            "dbversion": null,
            "identifier": "GCF_000001405.10",
            "url": "http://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.10"
        },
        "short_name": "hg16",
        "organism_name": "Homo sapiens"
    },
    {
        "assembly_identifier": null,
        "short_name": "Synthetic",
        "organism_name": "Synthetic sequence"
    }
]

This file specifies a list of reference genomes to create/update. This command has no arguments. Only entries with a short_name that does not exist will be created. Existing instances will not be updated since other models rely on the ReferenceGenome table.

savereferences

This command will serialize the ReferenceGenome models into data/genome/reference_genomes.json. It will overwrite any existing file. This command accepts no arguments.

updatesiteinfo

Invoke this command to updat the SiteInformation singleton row. It expects the file data/main/site_info.json to exist with the following format:

{
    "branch": "",
    "md_about": "about.md",
    "md_citation": "",
    "md_documentation": "userdocs.md",
    "md_privacy": "",
    "md_terms": "",
    "md_usage_guide": "",
    "version": "1.6.3-beta"
}

You can specify markdown files on fields with the md_ prefix (must be saved in the same directory as the JSON file) to set as the field text. This command accepts no arguments.

savesiteinfo

This command will serialize the SiteInformation singleton into data/main/site_info.json. It will overwrite any existing file. This command accepts no arguments.

geterror

This command displays a detailed celery error for a given task_id and username. The username specifies the submitting user's ORCID. This command must be invoked as:

python manage.py geterror --task_id=<task-uuid> --username=<ORCID>

renamegroups

This command renames the contributor groups for all ScoreSets, ExperimentSets and Experiments. It was used to correct a naming bug in production so it should not be necessary to run this again. This command accepts no arguments.

renumber

This command renumbers the Variants in a ScoreSet starting from 1. It was used to correct a numbering bug in production so it should not be necessary to run this again. This command must be invoked as:

python manage.py renumber --urns=<space separated urns> --all

Specify a list of space-separated urns to correct, or alternatively set the boolean flag --all to correct all ScoreSets.

savesitestats

Export a gzipped tarball containing site page view statistics. Specify an absolute save path with the --path argument.

setprivate

Set a ScoreSet, Experiment or ExperimentSet as private. It is recommended that it is used only on ScoreSet models. Settings parent models as private will not alter child models. This could create strange behaviour such as not being able to view the parent of a public child. Invoke the command as:

python manage.py setprivate --urn=<model-urn>

setstate

Set a the celery state of a ScoreSet. Invoke the command as:

python manage.py setprivate --urn=<model-urn> --state=<state text>

The state argument will accept the values processing, failed or success.

createnews

Create a news item for the landing page. Invoke the command as:

python manage.py createnews --message=<string message> --level=<string level>

The message argument can specify a string message or a markdown file. The level argument can take the values Critical, Important, Information, Happy holidays or April fools.

createtestentries

For development purposes to seed the database with test entries. Also creates test users with the password 1234qwer and username user-<number> where number ranges from 1 to 40.

createdefaultsecrets

Creates a default secrets json file. Used by settings module to create a secrets file if one does not exist. This should not be called directly.

cleanusers

Deletes accounts with malicious looking usernames. Pass --commit to commit changes, otherwise it is run in dry mode and will only list accounts that will be deleted. Pass a list of comma separated usernames via --exclude to ignore these associated accounts.