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Version 1.53.2

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@kjolley kjolley released this 14 May 13:23
· 20 commits to develop since this release
v_1.53.2
a13d9c2

What's new?

  • New LINvis functionality
    • Support for labelling list of specific LIN prefixes.
    • Label resizing controls.
    • Search visualisation for isolate by id or name.
    • Fit to visible vertical height.
  • New auto-registration script to register existing users to all available databases.
  • Added setting to require log-in for sequence queries.

New LINvis functionality

Labelling of specific LIN prefixes:

A popup listbox will appear when you click 'Show specific labels' (this can be undocked and repositioned if it's in the way, and closed once list has been entered).
image
Enter a list of any LIN code prefixes and these will be annotated on the display (if they are present):
image

Label resizing:

Increase or decrease the size of labels using the new controls.
image

Search visualisation for isolate by id or name:

You can search by id or isolate name. If present, all encompassing circles representing different LIN code thresholds will be highlighted by a dotted red border and the inner node containing the specific record will be shown with a solid red border. Note that as isolate names are not guaranteed to be unique, if there are multiple matches then they will all be shown.
image

Fit to visible height

You can now fit the visualisation to the available visible height (only fit to width was previously available).
image

New auto-registration script

Since the last update introduced automatic registration of available databases for new site-wide accounts, what was missing was a way to register existing accounts similarly. This can now be done with the new auto_reg.pl script. By default, only active accounts are registered - this is defined as accounts that logged in up to 30 days ago where the last login date is later than the creation date. This time period can be adjusted or you can choose to override completely and register all accounts.

For a user database called pubmlst_bigsdb_users, run with:
auto_reg.pl --user_database pubmlst_bigsdb_users

Available options are shown below:

auto_reg.pl --help                                                                
NAME
    auto_reg.pl - Automatically register site-wide user accounts with all
    databases that allow self-registration.

SYNOPSIS
    auto_reg.pl --user_database NAME [options]

OPTIONS

--dry_run
    Use for testing - just displays what would be done, without actually 
    registering users.

--help
    This help page.
    
--include_inactive
    Include all registered users, even those that have not logged in recently.
    If this option is set then --last_rel_login is ignored.
    
--last_rel_login DAYS
    Only target active users by only including those that have logged in within
    this many days. Default is 30.

--quiet
    Only display error messages.

--user_database NAME
    Database name (actual postgres name - user databases don't have config 
    names).

Added setting to require log-in for sequence queries.

I have recently noticed a lot of anonymous scripted sequence queries targeting the web interface rather than the API that is available for this purpose. These were causing a significant load on the web server. There is now a new setting that can be set in bigsdb.conf to require authentication to perform sequence queries (even when the database is otherwise accessible without log in):

seq_queries_require_login=1

This complements the existing settings to require authentication for downloads via the web interface:

allele_downloads_require_login=1
profile_downloads_require_login=1
seqbin_downloads_require_login=1

Full Changelog: v_1.53.1...v_1.53.2

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