Bigsdb

- An option has been added to filter alleles, profiles, and isolates for non-logged in users to records added before a specified date. This requires users to log in if they wish to access more recent data and has been introduced to provide licensing options. This can be activated globally in bigsdb.conf or within individual database config.xml files by setting the login_to_show_after_date attribute.

In bigsdb.conf:

login_to_show_after_date=2024-01-01


In config.xml:

login_to_show_after_date="2024-01-01"


- Fix for missing foreign key on the query_interface_fields table and missing primary key on scheme completion cache tables.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.45.0...v_1.46.0

- An option has been added to highlight private data in the Excel file generated for isolate exports. If a user has access to private data (which may belong to others and been shared with them) there will be a section on the form that allows the user to select how these records are shaded within the output.


- An option has been added for an admin to create customized isolate query forms with pre-selected fields shown. New options will appear in the admin interface (with the Misc toggle selected):


Clicking the Add Query Interface link will allow a user to define new link text that will appear within the Search list on the contents page. Once this has been done, the Query Interface Fields links will become visible and this allows the admin to select any number of provenance, scheme, or LINcode fields to be pre-selected when the link is clicked.



- Finally, separate options have been added to force users to be logged in to download alleles or profiles when using the web interface. This is to encourage users to script downloads using the API. There are global settings in the bigsdb.conf file:


DOWNLOADS
Require users to be logged in to download records via web interface
Note that this is likely to prevent automated downloads (which generally
should be done via API). These values can be overridden in the database
config.xml file.

allele_downloads_require_login=1
profile_downloads_require_login=1

These can also be overridden on a per-database basis in the database config.xml file, e.g.

allele_downloads_require_login="yes"
profile_downloads_require_login="no"


**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.44.1...v_1.45.0

- An option has been added to show if assembly checks have passed in the isolate results table. This can be enabled by default by setting `display_assembly_checks="yes"` in the database config.xml file. It can also be set by end users in the user customization panels (https://bigsdb.readthedocs.io/en/latest/data_query/0100_options.html#main-results-table).


- An option has been added to scannew.pl to only scan records that have passed assembly checks.
- An option has also been added to not scan private records.

See https://bigsdb.readthedocs.io/en/latest/offline_tools.html#automated-offline-allele-definition for all scannew.pl options.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.44.0...v_1.44.1

- New database indexes have been added to improve performance (thanks braffes).
- Some rarely or never used indexes have been dropped.
- The option to set an allele designation with a status of 'ignore' has been removed. This was not really used but added an unnecessary filtering contraint on multiple queries.
- The number of isolates that match the current isolate at different LIN code thresholds are now displayed on an isolate record page (if LIN code has been assigned). The number is hyperlinked and takes you to a query that returns the matching isolates.


An administrator can also decide whether or not to include classification scheme or LIN code scheme matches on the isolate information page. These are enabled by default, if defined, but can be disabled with the following options in config.xml:


show_lincode_matches="no"
show_classification_schemes="no"


In addition, the number of LIN code thresholds to display can be set with the following option (replace the number with the required number of thresholds):


show_lincode_thresholds="5"

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.43.3...v_1.44.0

- An optional message can be added on the allele and profile download pages to indicate that users should use the API for scripted data downloads. It is much easier to rate-limit the API than the web interface and it generally uses less resources to serve data. This message can be enabled by setting the URL for the API in bigsdb.conf, e.g. `rest_url=https://rest.pubmlst.org`


- The [JQuery.UI.multiselect widget](https://github.com/ehynds/jquery-ui-multiselect-widget) is now used for dropdown boxes with large numbers of options, e.g. locus lists on the isolate query page, or where multiple options can be selected, such as the the 'includes' field list on various plugins. Where appropriate, the list is also searchable to make finding and selecting values quicker and easier.


- Javascript performance has been improved for background loading of isolate query form elements.
- Limits can now be set for the number of offline jobs that any single user can run for individual plugins. See the updated format of the [job_limits.conf](https://github.com/kjolley/BIGSdb/blob/develop/conf/job_limits.conf) file found in the conf directory. If the limit is reached then further jobs for that particular plugin and user will be queued.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.43.2...v_1.43.3

- Additional logging information added. This includes the particular locus or scheme selected in data downloads, or the isolate record being shown.
- The cgST with fewest missing loci is now highlighted on the isolate info page when the isolate has multiple cgSTs.
- The query dashboard is now shown for bookmarked and publication queries.
- There is now an option to force users to log-in if they want to run offline jobs (see `jobs_require_login=1` in bigsdb.conf).
- There is now an option to automatically check the box to tag incomplete loci at specified identity thresholds (rather than just at 100% identity)
- 'Ambiguous read' flags are now automatically set on tags if sequence contains non-A,G,T,C characters.
- [JQuery.UI.multiselect](https://github.com/ehynds/jquery-ui-multiselect-widget) is now used for the flag dropdown box on the tag scan page. Previously we used an unformatted scrolling list box where an allele already had a flag but this was 4-5 lines long and made the table ugly and multiple flags difficult to select. For new tags there was a standard dropdown box which meant only one flag could be selected. As scan tables can be many thousands of rows long, the dropbox is only rendered when it is first visible in the current viewport.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.43.1...v_1.43.2