biomaj 3.1.24
BioMAJ

BioMAJ3
=====

This project is a complete rewrite of BioMAJ and the documentation is available here : http://biomaj.genouest.org.

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.

Common usages are to download remote databanks (Genbank for example) and apply
some transformations (blast indexing, emboss indexing, etc.). Any script can be
applied on downloaded data. When all treatments are successfully applied, bank
is put in "production" on a dedicated release directory.
With cron tasks, update tasks can be executed at regular interval, data are
downloaded again only if a change is detected.

More documentation is available in wiki page.

BioMAJ is python 2 and 3 compatible until release 3.1.17.
After 3.1.17, only python 3 is supported.

Getting started
===============

Edit global.properties file to match your settings. Minimal conf are database connection and directories.

    biomaj-cli.py -h

    biomaj-cli.py --config global.properties --status

    biomaj-cli.py --config global.properties  --bank alu --update

Migration
=========

To migrate from previous BioMAJ 1.x, a script is available at:
https://github.com/genouest/biomaj-migrate. Script will import old database to
the new database, and update configuration files to the modified format. Data directory is the same.

Migration for 3.0 to 3.1:

Biomaj 3.1 provides an optional micro service architecture, allowing to separate and distributute/scale biomaj components on one or many hosts. This implementation is optional but recommended for server installations. Monolithic installation can be kept for local computer installation.
To upgrade an existing 3.0 installation, as biomaj code has been split into multiple components, it is necessary to install/update biomaj python package but also biomaj-cli and biomaj-daemon packages. Then database must be upgraded manually (see Upgrading in documentation).

To execute database migration:

    python biomaj_migrate_database.py

Application Features
====================

* Synchronisation:
  * Multiple remote protocols (ftp, ftps, http, local copy, etc.)
  * Data transfers integrity check
  * Release versioning using a incremental approach
  * Multi threading
  * Data extraction (gzip, tar, bzip)
  * Data tree directory normalisation
  * Plugins support for custom downloads

* Pre &Post processing :
  * Advanced workflow description (D.A.G)
  * Post-process indexation for various bioinformatics software (blast, srs, fastacmd, readseq, etc.)
  * Easy integration of personal scripts for bank post-processing automation

* Supervision:
  * Optional Administration web interface (biomaj-watcher)
  * CLI management
  * Mail alerts for the update cycle supervision
  * Prometheus and Influxdb optional integration
  * Optional consul supervision of processes


* Scalability:
  * Monolithic (local install) or microservice architecture (remote access to a BioMAJ server)
  * Microservice installation allows per process scalability and supervision (number of process in charge of download, execution, etc.)

* Remote access:
  * Optional FTP server providing authenticated or anonymous data access
  * HTTP access to bank files (/db endpoint, microservice setup only)

Dependencies
============

Packages:

* Debian: libcurl-dev, gcc
* CentOs: libcurl-devel, openldap-devel, gcc

 Linux tools: tar, unzip, gunzip, bunzip

Database:
 * mongodb (local or remote)

Indexing (optional):
 * elasticsearch (global property, use_elastic=1)

ElasticSearch indexing adds advanced search features to biomaj to find bank having files with specific format or type.
Configuration of ElasticSearch is not in the scope of BioMAJ documentation.
For a basic installation, one instance of ElasticSearch is enough (low volume of data), in such a case, the ElasticSearch configuration file should be modified accordingly:

    node.name: "biomaj" (or any other name)
    index.number_of_shards: 1
    index.number_of_replicas: 0

Installation
============

From source:

After dependencies installation, go in BioMAJ source directory:

    pip install .

From packages:

    pip install biomaj biomaj-cli biomaj-daemon

You should consider using a Python virtual environment (virtualenv) to install BioMAJ.

In tools/examples, copy the global.properties and update it to match your local
installation.

The tools/process contains example process files (python and shell).

Docker
======

You can use BioMAJ with Docker (osallou/biomaj-docker)

    docker pull osallou/biomaj-docker
    docker pull mongo
    docker run --name biomaj-mongodb -d mongo
    # Wait ~10 seconds for mongo to initialize
    # Create a local directory where databases will be permanently stored
    # *local_path*
    docker run --rm -v local_path:/var/lib/biomaj --link biomaj-mongodb:biomaj-mongodb osallou/biomaj-docker --help

Copy your bank properties in directory *local_path*/conf and post-processes (if any) in *local_path*/process

You can override global.properties in /etc/biomaj/global.properties (-v xx/global.properties:/etc/biomaj/global.properties)

No default bank property file or process are available in the container.

Examples are available at https://github.com/genouest/biomaj-data


Import bank templates
=====================

Once biomaj is installed, it is possible to import some bank examples with the biomaj client


    # List available templates
    biomaj-cli ... --data-list
    # Import a bank template
    biomaj-cli ... --data-import --bank alu
    # then edit bank template in config directory if needed and launch bank update
    biomaj-cli ... --update --bank alu

Plugins
=======

BioMAJ support python plugins to manage custom downloads where supported protocols
are not enough (http page with unformatted listing, access to protected pages, etc.).

Example of plugins and how to configure them are available on [biomaj-plugins](https://github.com/genouest/biomaj-plugins) repository.

Plugins can define a specific way to:

* retreive release
* list remote files to download
* download remote files

Plugin can define one or many of those features.

Basically, one defined in bank property file:

    # Location of plugins
    plugins_dir=/opt/biomaj-plugins
    # Use plugin to fetch release
    release.plugin=github
    # List of arguments of plugin function with key=value format, comma separated
    release.plugin_args=repo=osallou/goterra-cli

Plugins are used when related workflow step is used:

* release.plugin <= returns remote release
* remote.plugin <= returns list of files to download
* download.plugin <= download files from list of files

API documentation
=================

https://readthedocs.org/projects/biomaj/

Status
======

[![Build Status](https://travis-ci.org/genouest/biomaj.svg?branch=master)](https://travis-ci.org/genouest/biomaj)

[![Documentation Status](https://readthedocs.org/projects/biomaj/badge/?version=latest)](https://readthedocs.org/projects/biomaj/?badge=latest)

[![Code Health](https://landscape.io/github/genouest/biomaj/master/landscape.svg?style=flat)](https://landscape.io/github/genouest/biomaj/master)

Testing
=======

Execute unit tests

    python -m pytest -v tests/biomaj_tests.py

Execute unit tests but disable ones needing network access

    NETWORK=0 python -m pytest -v tests/biomaj_tests.py


Monitoring
==========

InfluxDB (optional) can be used to monitor biomaj. Following series are available:

* biomaj.banks.quantity (number of banks)
* biomaj.production.size.total (size of all production directories)
* biomaj.workflow.duration (workflow duration)
* biomaj.production.size.latest (size of latest update)
* biomaj.bank.update.downloaded_files (number of downloaded files)
* biomaj.bank.update.new (track updates)

*WARNING* Influxdb database must be created, biomaj does not create the database (see https://docs.influxdata.com/influxdb/v1.6/query_language/database_management/#create-database)

License
=======

A-GPL v3+

Remarks
=======

To delete elasticsearch index:

 curl -XDELETE '<http://localhost:9200/biomaj_test/'>

Credits
=======

Special thanks for tuco at Pasteur Institute for the intensive testing and new ideas.
Thanks to the old BioMAJ team for the work they have done.

BioMAJ is developped at IRISA research institute.


3.1.24
  Update documentation
  Fix tests
  Remove dependency on python3-future
3.1.23:
  Use pytest instead of nose
3.1.21:
  Freeze pymongo to 3.12.3 (4.x breaks)
  Change isAlive() which is deprecated in python 3.9 to is_alive

3.1.20:
  Follow-up of #127 to get last release in file (refactor and bug fix)
3.1.19:
  Add tgz archive support
  Add log file info to production info
  #126 Issue with getting last release in file
3.1.18:
  Python 3 support only
  If multiple files match release.file, take most recent one
  If mail template not found, log and use default
3.1.17:
  Fix regression when saving file with a differe,t structure such as xxx/(FASTA)/(file.txt) to save under FASTA/file.txt
  Send removal mail for --remove-all option
  #119 add support for custom notification emails with templates and log tail/attach options
    New optional fields in global.properties (or per bank properties):
      mail.body.tail=0
      mail.body.attach=9000000
      mail.template.subject=file_path_to_subject.jinja2
      mail.template.body=file_path_to_body.jinja2
    Available variables:
            'log_file': path to log file
            'log_tail': last lines of log file
            'bank': bank name
            'release': release related tooperation
            'status': operation status (true/false)
            'modified': did operation modified bank (true/false)
            'update': was operation an update
            'remove': was operation a removal
3.1.16:
  Fix status check of process for --from-task postprocess
  #118 Rename protocol options to options
  Add more debug logging
3.1.15:
  #117 Fix incorrect behavior with --post-process
3.1.14:
  Add repair option
3.1.13:
  Add process name and status in logs
  PR #116 update to use download 3.1.0
3.1.12:
  In case of multiple matches for release regexp, try to determine most recent one
  #115 Correctly use save_as for release file name
3.1.11:
  Increase one log level
  #110 Allow ftps and directftps protocols (needs biomaj-download 3.0.26 and biomaj-core 3.0.19)
  #111 locked bank after bad update command
  Ignore UTF-8 errors in release file
  Add plugin support via biomaj-plugins repo (https://github.com/genouest/biomaj-plugins) to get release and list of files to download from a plugin script.
  Add support for protocol options in global and bank properties (options.names=x,y   options.x=val options.y=val). Options may be ignored or used differently depending on used protocol.
3.1.10:
  Allow to use hardlinks when reusing files from previous releases
3.1.9:
  Fix remote.files recursion
3.1.8:
  Fix uncompress when saved files contains subdirectory
3.1.7:
  Fix utf/ascii encoding issue with python3
  In case of uncompress failure, put back all compressed files to avoid redownload
3.1.6:
  Fix #100 Catch error and log error if biomaj fails to connect to InfluxDB
  Add history to update/remove operations
  Add log in case of file deletion error during bank removal
  check lock file exists when removing it
  Update protobuf to work with biomaj.download 3.0.18

3.1.5:
  Fix #97 Wrong offline dir checks

3.1.4:
  Fix #88 Unset 'last_update_session' when found in pending sessions using --remove-pending
  Add formats in bank info request
  Add checks for some production fields before display
  Add irods download support

3.1.3:
  Remove post-install step for automatic upgrades, not supported by wheel package

3.1.2:
  Fix #86 remove special character from README.md
  Feature #85 SchemaVersion automatically add new property

3.1.1:
  Fix #80 Check process exists with `--from-task` and `--process`
  Manage old banks with no status

3.1.0:
  ## Needs database upgrade
  If using biomaj-watcher, must use version >= 3.1.0
  Feature #67,#66,#61 switch to micro service architecture. Still works in local monolithic install
  Fix some configuration parameter loading when not defined in config
  Fix HTTP parsing parameters loading
  Fix download_or_copy to copy files in last production release if available instead of downloading files again
  Manage user migration for micro services
  Feature #74 add influxdb statistics
  Feature #65 add a release info file at the root of the bank which can be used by other services to know the latest release available
  Feature #25 experimental support of rsync protocol
  Add rate limiting for download with micro services
  Limit email size to 2Mb, log file may be truncated

3.0.20:
  Fix #55: Added support for https and directhttps
  Add possibility to define files to download from a local file with remote.list parameter
  Fix visibility modification (bug deleted the bank properties field)
  Fix #65 Add release file in bank dir after update
  Add md5 or sha256 checksum checks if files are downloaded and available

3.0.19:
  Fix missing README.md in package
  Fix #53 avoid duplicates in pending databases

3.0.18:
  Add migration method to update schema when needed
  Manage HTTP month format to support text format (Jan, Feb, ...) and int format (01, 02, ...)
  New optional bank property http.parse.file.date.format to extract date in HTTP protocol following python date regexp format (http://www.tutorialspoint.com/python/time_strptime.htm)
      Example: %d-%b-%Y %H:%M

3.0.17:
  Fix #47: save_as error with directhttp protocol
  Fix #45: error with pending releases when release has dots in value
  typo/pylint fixes

3.0.16:
  Do not use config values, trust database values #39
  Fix #42: Add optional release.separator to name the bank directory bankname_release (underscore as default)

3.0.15:
  Fix #37: remote local files history from db and put it in cache.dir
  Feature #38: add optional keep.old.sessions parameter to keep all sessions in database, even for removed releases
  Feature #28: add optional release.format parameter to specify the date format of a release

3.0.14:
  Fix in method set_owner
  Force release to be a str
  Fix #32: fix --from-task issue when calling a meta process
  Fix #34: remove release from pending when doing cleanup of old sessions
  Remove logs on some operations
  Add --status-ko option to list bank in error state
  Fix #36 manage workflows over by error or unfinished

3.0.13:
  Fix #27: Thread lock issue during download
           New optional attribute in bank properties: timeout.download
  HTTP protocol fix (deepcopy error)

3.0.12:
  Fix index deletion on bank removal
  Fix lock errors on dir creation for multi-threads,
      pre-create directroy structure in offline directory
  Fix #26: save error when too many files in bank

3.0.11:
  Fix in session management with pre and rm processes
  Fix #23: Check workflow step name passed to
           --stop-after/--start-after/--from-task
  Fix #24: deprecated delete_by_query method in elasticsearch
  Add some controls on base directories


3.0.10:
  Change dir to process.dir to find processes in subdirs
  If all files found in offline dir, continue workflow with no download
  Remove extra log files for bank dependencies (computed banks)
  Fix computed bank update when sub banks are not updated
  Fix #15 when remote reverts to a previous release
  Feature #16: get possibility not to download files (for computed banks for
               example). Set protocol='none' in bank properties.
  Fix on --check with some protocols
  Fix #21 release.file not supported for directhttp protocol
  Feature #22: add localrelease and remoterelease bank properties to use the
               remote release as an expression in other properties
               => remote.dir = xx/yy/%(remoterelease)s/zz
  Feature #17,#20: detect remote modifications even if release is the same
               new parameter release.control (true, false) to force a check
               even if remote release (file controlled or date) is the same.
  Fix on 'multi' protocol
  Fix on "save_as" regexp when remote.files starts with a ^ character.

3.0.9:
  Fix thread synchro issue:
      during download some download threads could be alive while main thread continues worflow
      the fix prevents using Ctrl-C during download
  Workflow fix:
      if subtask of workflow fails, fail main task

3.0.8:
  do not test index if elasticsearch is not up
  minor fixes
  add http proxy support
  pylint fixes
  retry uncompress once in case of failure (#13)

3.0.7:
  Reindent code, pep8 fixes
  Various fixes on var names and OrderedDict suport for Python < 2.7
  Merge config files to be able to reference global.properties variables in bank
    property file in format %(xx)s
  Use ConfigParser instead of SafeConfigParser that will be deprecated

3.0.6:
  Add option --remove-pending to remove all pending sessions and directories
  Add process env variables logdir and logfile
  Fix Unicode issue with old versions of PyCurl.

3.0.5:
  Fix removal workflow during an update workflow, removedrelease was current
  release.
  Fix shebang of biomaj-cli, and python 2/3 compat issue

3.0.4:
  Update code to make it Python 3 compatible
  Use ldap3 library (pure Python and p2,3 compatible) instead of python-ldap
  get possiblity to save downloaded files for ftp and http without keeping full
  directory structure:
    remote.files can include groups to save file without directory structure,
     or partial directories only, examples:
     remote.files = genomes/fasta/.*\.gz => save files in offline directory, keeping remote structure offlinedir/genomes/fasta/
     remote.files = genomes/fasta/(.*\.gz) => save files in offline directory offlinedir/
     remote.files = genomes/(fasta)/(.*\.gz) => save files in offline directory offlinedir/fasta