Bigsdb

This version provides support for LINcodes based on cgMLST schemes. See https://doi.org/10.1101/2021.07.26.453808 for more information about LINcodes.

Documentation for using setting up LINcodes within BIGSdb can be found at https://bigsdb.readthedocs.io/en/latest/administration.html#setting-up-lincode-definitions-for-cgmlst-schemes.

This adds data drill-down functionality linked to the front-end dashboards on isolate databases.

This version updates the Microreact plugin to support breaking changes introduced on the Microreact website. API uploads to Microreact now require an account token - this needs to be set in the bigsdb.conf file.

In addition, it is no longer a requirement for databases to have fields named 'country' and 'year' in order for the plugin to be enabled. Fields with different names can be used and set within the config.xml file using the microreact_country_field and microreact_year_field attributes in the system tag. Note that countries should use the standardised list of names as defined in BIGSdb since these are mapped internally to ISO 3166-2 2 letter country codes used by Microreact. The easiest way to use these is to define a country field in the config.xml as below:


<field type="text" required="yes" maindisplay="yes" comments="country where strain was isolated" optlist="yes" values="COUNTRIES" sort="no">country
<optlist>
<option>Unknown</option>
</optlist>
</field>


If either a country or year field is not used, data are still uploaded to Microreact but either the map or timeline is not shown.

This version adds optional front-end dashboards to isolate databases.

Dashboards are fully customisable by end users so you can select the fields and visualisations that you want to see. Modify the layout by dragging elements or change their size. Any changes made are remembered between sessions. A default dashboard can be set for all databases on the system, and overridden for individual database configurations. See https://bigsdb.readthedocs.io/en/latest/dbase_setup.html#setting-up-front-end-dashboards for details on setting up.

In addition, alternative start codons, e.g. CTG, ATT, can now be set on a per-database or a per-locus basis.

Includes classification scheme information in profile results returned by the RESTful API.

This version changes the way that classification schemes are made available via the API. This is now more consistent with the rest of the interface.