Bigsdb

This version fixes an issue with exporting LINcode fields with isolate records.

This version includes the following:
- Search isolates by SAVs or SNPs defined in typing database.
- Use caching for dashboard AJAX calls where possible.
- Add option to batch download full allele records via API - see https://bigsdb.readthedocs.io/en/latest/rest.html#db-loci-locus-alleles.
- Fix for export of LINcode field values.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.42.1...v_1.42.2

This introduces the following changes:

• Update to FontAwesome 6.
• Provenance completeness metrics – these work like scheme annotation metrics, but you can define specific fields in config.xml as important for completeness (set annotation_metric=”yes” in the field definition). Note the new update_provenance_metrics.pl script if you want to cache the metrics table (although it calculates on-the-fly and is pretty quick if not used). The score is simply a percentage of selected fields with a value (null values are excluded – see https://github.com/kjolley/BIGSdb/blob/develop/lib/BIGSdb/Constants.pm#LL296C1-L298C4 for definitions of these).
• Isolates can now be searched by allele extended attributes defined in the typing database (https://bigsdb.readthedocs.io/en/latest/administration.html#defining-locus-extended-attributes).

This version adds the option to define schemes that can include locus presence in profile definitions. This can be enabled by setting the 'allow_presence' flag in a scheme definition and then using the value 'P' for 'present' within a profile. Locus absence can be assigned with a '0'. Note that scheme caching must be enabled in isolate databases to make use of these gene presence schemes.

There is also a new single amino acid variant (SAAV) and single nucleotide polymorphism (SNP) detection tool. SAAVs and SNPs can be defined for a locus, and then alleles can be annotated by running the new `scan_mutations.pl` script. SAAV and SNPs will be displayed within allele records, and can be searched in locus-specific queries in the typing database.

Finally, security of cookies has been improved with -secure and -httponly attributes set. Note that to prevent breaking installations running over HTTP, to enable -secure you need to set `secure_cookies=1` in bigsdb.conf.

* MLST sequence type
* species (e.g. K. pneumoniae, K. quasipneumoniae, K. variicola, etc.)
* ICEKp associated virulence loci: yersiniabactin (ybt), colibactin (clb), salmochelin (iro), hypermucoidy (rmpA)
* virulence plasmid associated loci: salmochelin (iro), aerobactin (iuc), hypermucoidy (rmpA, rmpA2)
* antimicrobial resistance determinants: acquired genes, SNPs, gene truncations and intrinsic β-lactamases
* K (capsule) and O antigen (LPS) serotype prediction, via wzi alleles and [Kaptive](https://github.com/katholt/Kaptive)


The output is a table in HTML, tab-delimited text, and Excel formats.


In addition, if the analysis is run with the --all option then the results are stored as an arbitrary analysis within the isolate database linked to the isolate record (this is the same way that we store the rMLST species identification in the screenshot below). A formatted display of these results is available in the isolate information page.


The analysis can also be run using a standalone script - `update_kleborate.pl` - found in the scripts/maintenance directory. This will run the analysis against all isolates in a database and populate the arbitrary analysis table for display.

Arbitrary analysis results are stored within the isolate database as a JSON object and can be displayed within isolate information pages using a template file stored in /etc/bigsdb/templates. Currently, this information is not searchable within the BIGSdb search interface, but the plan is to develop this so that specific fields can be registered for searching.

Kleborate needs to be installed on the system and the path to the executable file specifed in the BIGSdb global configuration file (/etc/bigsdb/bigsdb.conf), e.g.

`kleborate_path=/usr/local/bin/kleborate`

The plugin is not enabled by default, even on databases with all_plugins="yes" set in the config.xml file, as it is only appropriate for use against _Klebsiella_ assemblies. To enable the plugin, set the following attribute within the config.xml `<system>` section for the database.

`Kleborate="yes"`

This version adds a choice of colour palettes to front-end and query dashboards.