Bigsdb

Potential fix for https://github.com/kjolley/BIGSdb/issues/970.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.47.2...v_1.47.3

This version adds hooks to PluginManager.pm, Plugin.pm and Offline::RunJobs.pm to run plugin tools written entirely in Python using the [BIGSdb Python Toolkit](https://github.com/kjolley/BIGSdb_Python_Toolkit).

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.47.1...v_1.47.2

This version adds an option to isolate field configurations to enable a different hyperlink to be set depending on the regular expression of the field value. The is the `web_regex` attribute, demonstrated below:


<field type="text" required="genome_expected" length="20" maindisplay="no" web_regex="^SAM|https://www.ebi.ac.uk/ena/browser/view/[?]?dataType=BIOSAMPLE;^[EDS]RS|https://www.ebi.ac.uk/ena/browser/view/[?]?dataType=SAMPLE" web="https://www.ebi.ac.uk/ena/browser/view/[?]" comments="ENA/SRA biosample accession number" multiple="yes" group="Tracking">biosample_accession</field>


If the value of the biosample_accession field above starts with 'SAM' then the hyperlinked URL will be 'https://www.ebi.ac.uk/ena/browser/view/[?]?dataType=BIOSAMPLE' (where [?] is the field value), whereas if the field value starts with ERS, EDS, or SRS then the hyperlinked URL will be 'https://www.ebi.ac.uk/ena/browser/view/[?]?dataType=SAMPLE'. If none of the regex defined are matched then the value set for the `web` attribute will be used, e.g. https://www.ebi.ac.uk/ena/browser/view/[?] in the above.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.47.0...v_1.47.1

ISOLATE EMBARGOES
Set to enable isolate embargoes and limit the time allowed. These can be
overridden in individual isolate database config files.
Values are in months.
embargo_enabled=1
default_embargo=12
max_initial_embargo=24
max_embargo=48


These values can also all be overridden in the `config.xml` file for a specific database, e.g. `embargo_enabled="yes"`.

If enabled, submitters will now see an option to request an embargo when they submit. They can choose an embargo length up to the value set by max_initial_embargo (default 24 months).


Users will be able to see embargoed isolates when they are logged in and they behave like any other private data in that they can be shared with others by adding them to a shared user project. Curators will also be able to see them, whereas normal private isolates cannot be seen by curators.


It is also possible to search for embargoed isolates and by embargo date and users will see a hyperlinked reminder when they are logged in of how many embargoed isolates they have and the date at which the first of these will become public.


Curators with the appropriate permission set are able to modify embargo dates for both currently public isolates (making them private if they were submitted publicly by mistake) or for currently embargoed isolates.



Finally, you should run the [check_embargoes.pl](https://github.com/kjolley/BIGSdb/blob/develop/scripts/maintenance/check_embargoes.pl) script once a day to automatically publish any isolate that reaches its embargo date.

In addition, quotas for projects has now been introduced. Previously only users could have quotas and projects could be set to be quota-free.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.46.2...v_1.47.0

BingMaps has been removed as an option for mapping as Microsoft will be retiring this service in June 2025. It has been replaced with options to use MapTiler (satellite) and ArcGIS streetmap/satellite imagery, alongside the existing option of OpenStreetMap for street level mapping.

OpenStreetMap

MapTiler

Esri/ArcGIS streetmap

Esri/ArcGIS satellite

You can select the appropriate options in bigsdb.conf (these can all also be overridden in individual database config.xml files if you wish to use different options or API keys):


MAPPING
Set the option for displaying location maps.
Note for Esri/ArcGIS services you must register
[https://developers.arcgis.com/en/sign-up/]
and abide by terms of service [https://developers.arcgis.com/en/terms/].
For MapTiler you need to register and get an API key [https://www.maptiler.com/].

0: OpenStreetMaps only
1: OpenStreetMaps + MapTiler satellite imagery
2: OpenStreetMaps + Esri/ArcGIS World Imagery (satellite)
3: Esri/ArcGIS World Street Map + Esri/ArcGIS World Imagery (satellite)

mapping_option=0
;maptiler_api_key=xxxxxxxxxx


Note that use of MapTiler requires an [API key](https://www.maptiler.com/) - the free tier allows up to 100,000 map tile requests per month. You must also [register for an Esri account](https://developers.arcgis.com/en/sign-up/) to use Esri/ArcGIS services (you will need a paid account if using this commercially).

See the [database setup documentation](https://bigsdb.readthedocs.io/en/latest/dbase_setup.html#creating-databases) if you wish to enable mapping - either using a location field that contains GPS coordinates, or a geographic field such as 'town_or_city' which can be linked to a lookup table of GPS coordinates. The latter lookup table can be automatically populated to find the coordinates of towns and cities using the [gp_town_lookups.pl](https://github.com/kjolley/BIGSdb/blob/develop/scripts/maintenance/gp_town_lookups.pl) script.

**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.46.1...v_1.46.2

Version 1.46.1 introduces a new SNPsites plugin.

The SNPsites plugin aligns sequences for specified loci for an isolate dataset. The alignment is then passed to [snp-sites](https://github.com/sanger-pathogens/snp-sites) to identify SNP positions. Output consists of a summary table including the number of alleles and polymorphic sites found for each locus, an interactive D3 chart that displays the summary, and ZIP files containing alignment FASTAs and VCF files for each locus.


Note that snp-sites needs to be installed and its path set in bigsdb.conf, e.g.


snp-sites
snp_sites_path=/usr/bin/snp-sites


**Full Changelog**: https://github.com/kjolley/BIGSdb/compare/v_1.46.0...v_1.46.1