File: CHANGES.txt

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biomaj3 3.1.8-1
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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