MAN biomaj

SYNOPSIS

biomaj-cli.py [options]

Description

BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated
to data synchronization and processing. The Software automates
the update cycle and the supervision of the locally mirrored
databank repository. The user must have root rights to run BioMAJ.

--config: global.properties file path

--proxy: BioMAJ daemon url (http://x.y.z) [micro services only]

--trace: Trace workflow in Zipkin server

--api-key: User API key to authenticate against proxy [micro services only]

--whatsup: Get info on what BioMAJ is doing [micro services only]

--about-me: Get my info [micro services only]
    [MANDATORY]
    --proxy http://x.y.z
    --user-login XX
    --user-password XX

--update-status: get status of an update [micro services only]
    [MANDATORY]
    --bank xx: name of the bank to check
    --proxy http://x.y.z

--update-cancel: cancel current update [micro services only]
    [MANDATORY]
    --bank xx: name of the bank to cancel
    --proxy http://x.y.z


--check: Checks bank configuration
     [MANDATORY]
     --bank xx: bank name to check

--status: list of banks with published release
    [OPTIONAL]
    --bank xx / bank: Get status details of bank

--status-ko: list of banks in error status (last run)
  ( >= 3.0.14)

--log DEBUG|INFO|WARN|ERR  [OPTIONAL]: set log level in logs for this run, default is set in global.properties file

--update: Update bank
    [MANDATORY]
    --bank xx: name of the bank to update
    [OPTIONAL]
    --publish: after update set as *current* version
    --from-scratch: force a new update cycle, even if release is identical, release will be incremented like (myrel_1)
    --stop-before xx: stop update cycle before the start of step xx
    --stop-after xx: stop update cycle after step xx has completed
    --from-task xx --release yy: Force an re-update cycle for bank release *yy* or from current cycle (in production directories), skipping steps up to *xx*
    --process xx: linked to from-task, optionally specify a block, meta or process name to start from
    --release xx: release to update

--publish : Publish bank as current release to use
    [MANDATORY]
    --bank xx: name of the bank to update
    --release xx: release of the bank to publish

--unpublish: Unpublish bank (remove current)
    [MANDATORY]
    --bank xx: name of the bank to update

--remove-all: Remove all bank releases and database records
    Remove processes are not executed, this deletes directly database and files content.
    [MANDATORY]
    --bank xx: name of the bank to update
    [OPTIONAL]
    --force: remove freezed releases

--remove-pending: Remove pending releases (BioMAJ >= 3.0.6)
    [MANDATORY]
    --bank xx: name of the bank to update

--remove: Remove bank release (files and database release)
    [MANDATORY]
    --bank xx: name of the bank to update
    --release xx: release of the bank to remove

    Release must not be the *current* version. If this is the case, publish a new release before.

--freeze: Freeze bank release (cannot be removed)
    [MANDATORY]
    --bank xx: name of the bank to update
    --release xx: release of the bank to remove

--unfreeze: Unfreeze bank release (can be removed)
    [MANDATORY]
    --bank xx: name of the bank to update
    --release xx: release of the bank to remove

--search: basic search in bank production releases, return list of banks
   --formats xx,yy : list of comma separated format
  AND/OR
   --types xx,yy : list of comma separated type
  OR
   --query "sometext or chr:chr1" : Lucene query syntax to query index
--show: Show bank files per format
  [MANDATORY]
  --bank xx: name of the bank to show
  [OPTIONAL]
  --release xx: release of the bank to show

--owner yy: Change owner fo the bank (user id), BioMAJ >= 3.0.1
    [MANDATORY]
    --bank xx: name of the bank

--change-dbname yy: Change name of the bank to this new name, BioMAJ >= 3.0.1
    [MANDATORY]
    --bank xx: current name of the bank

--move-production-directories yy: Change bank production directories location to this new path, path must exists, BioMAJ >= 3.0.1
    [MANDATORY]
    --bank xx: current name of the bank

--visibility public|private: change visibility public/private of a bank
    [MANDATORY]
    --bank xx: name of the bank

--maintenance on/off/status: (un)set BioMAJ in maintenance mode to prevent updates/removal

--data-list: List availablebank templates
    [MANDATORY]
    biomaj-data package

--data-import: Import a bank template
    [MANDATORY]
    biomaj-data package
    --bank xx: template name

Examples

General example:

The global.properties file is mandatory. If not specified, ‘global.properties’ will be searched in the current directory or at BIOMAJ_CONF environment variable path (export BIOMAJ_CONF=/xx/yy/global.properties)

biomaj-cli.py --config </path/to/>global.properties [options]

 Monolithic usage:

biomaj-cli.py --config </path/to/>global.properties --update --bank alu

Update in microservices:

biomaj-cli.py --proxy http://biomaj-publix-proxy:5000 --api-key XYZ --update --bank alu

Remove a bank in microservices:

biomaj-cli.py --proxy http://biomaj-publix-proxy:5000 --api-key XYZ --remove --bank alu

An error occured:
Bank is locked due to an other action

rm lock/alu.lock

Example for whatsup (microservices only):

biomaj-cli.py --proxy http://biomaj-publix-proxy:5000 --api-key XYZ --whatsup

#daemon        bank    action
#------------  ------  --------
#queue         0       waiting
#e13b7b6b308e  hg38    update

Whatsup is an option that gives a list of what Biomaj is doing, and more precisely the status of the update queue.
To delete banks waiting for update, it is possible to make a –update-cancel (when the bank is processed, it will take into account the cancel and stop the update).
It is possible to have identifiers without associated bank names that correspond to redis (and thus allow its backup), they are rated « pending ». A new identifier is created each time BioMAJ is restarted, this identifier corresponds to that of the daemon-message container. They will be deleted when nothing else happens (i.e. no more updates).

Restarting workflow partially

The update option propose a –from-task option to restart workflow only from a workflow step (to run a modified post-process for example). Available steps are:

• ‘init’
• ‘check’
• ‘depends’
• ‘preprocess’
• ‘release’
• ‘download’
• ‘postprocess’
• ‘removeprocess’
• ‘publish’
• ‘over’

For post-process you can also specify from which process step (block/meta or process name) the worflow should start from (skipping all previous steps).

API Documentation: Here.