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Dgenies 1.5.0

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@pbordron pbordron released this 04 May 15:20
· 6 commits to master since this release
v1.5.0
83af6bd

Changes

If you run dgenies in webserver mode, database schema has changed.

The column batch_type was changed to runner_type in job table.
You can update the database with following sql command:

ALTER TABLE job RENAME COLUMN batch_type TO runner_type;

and if you use analytics

ALTER TABLE analytics RENAME COLUMN batch_type TO runner_type;

This change was also reflected for cluster configuration in application.properties, where batch_system_type was renamed to runner_type.

For users:

  • Update batch mode:
    • Local files upload
    • Batch content checked in web interface
    • Single upload per file
    • Batch file format has changed, in particular, option keys have been change to be more comprehensible. Please read the doc.
  • Dotplot:
    • Files generated through "Query Fasta" and "Query assembled as reference" are updated if new sorting and contig reversal are done.
    • Files linked in email are stable until the job is cleanned. They dont change if sort and contig reversal are updated.
    • You can reset the sort (usefull when playing with manual contig reversal)
    • "Query assembled as reference" file is now compressed in webserver mode.
  • Job logs are now available to download and are included in backup file.
  • Update user interface to bootstrap 4.6

For sysadmin:

  • Tools config file format (tools.yaml) has changed. Please update it if you use a custom one.
  • Basic app logging.
  • Configuration files:
    • In application.properties, batch_system_type was renamed to runner_type in order to avoid confusion with batch jobs intoduced with dgenies 1.4.
    • Cluster walltime can be set in the config file.
    • In database, the column batch_type was changed to runner_type in job table.
    • It is possible to set config files directly when running dgenies with --config and --tools-config options. Please be careful to use the correct config files when managing a running instance of dgenies.
    • It is now possible to use a the option --flask-config in order to set some flask options. You can use it to set some email server parameters.
    • For server mode, the number of download sessions in parallel can be now set with max_download_sessions (default is alway 5). Session delays can also be modified now.
    • Reinforce tar file checking
    • Drop Flask<2

Bugfix

  • When sorted, "Association table", "Query Fasta" and "Query assembled as reference" files match dotplot. Before, only the last reversed contig on dotplot was token in account.
  • Fix some bugs with Flask>=2
    • Add compatibility with Flask 2.2
    • Some gzipped files were uncompressed by browser when downloaded.
    • Backup file name was incomplete.
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