This is an implementation of the Breeding API (http://docs.brapi.apiary.io/) for Drupal with Tripal installed.
The Breeding API specifies a standard interface for plant phenotype/genotype databases to serve their data to crop breeding applications. It is a shared, open API, to be used by all data providers and data consumers who wish to participate. Initiated in May 2014, it is currently in an actively developing state, so now is the time for potential participants to help shape the specifications to ensure their needs are addressed. The listserve for discussions and announcements is at Cornell University. Additional documentation is in the Github wiki. The latest up-to-date specifications and discussions can be found on the git repository 3 and the issue queue 4.
This module requires the following modules:
- Drupal 7.x
- Tripal 7.x-2.x (3.x not tested yet) (http://www.drupal.org/project/tripal)
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Install as you would normally install a contributed Drupal module. See: https://drupal.org/documentation/install/modules-themes/modules-7 for further information.
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Enable the module in "Admin menu > Site building > Modules" (path /admin/modules).
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In case you have an obsolete version of the MCPD vocabulary, you may need to update it using the button "Reload Chado MCPD CV" in the MCPD Settings section of admin/tripal/extension/brapi/configuration page.
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Adjust the CV settings according to your Chado database instance and the way you store your biological data. You may also setup germplasm attribute settings, add some external BrAPI site references and setup call aggregation if needed.
You can query the BrAPI service through the URL http(s):///brapi/v1/?
Ex.: https://www.crop-diversity.org/mgis/brapi/v1/calls
It will return a JSON structure that can be processed by BrAPI-compliant applications.
Testing: To test your instance, you can either use the RestClient plugin for your favorite web browser client from http://restclient.net/ or use the provided BrAPI query interface (path brapi/query). Note that when you use this interface as admin, you will have an additional checkbox which can enable debug mode.
Javascript & dynamic HTML: If you want to add BrAPI fields on your pages that should be automatically and dynamically populated using external BrAPI site, you can use the following HTML snippet:
where "BRAPI_SERVER" is the BrAPI server name, "SERVICE?PARAMETERS..." is the BrAPI service to query with its optional parameters and values and "URL_ENCODED_HTML_STRING" is the URL-encoded HTML code to use to replace the form. In this string, not encoded place-holder string will be replaced by properties of the (first) JSON object returned. A place-holder is a the property name as described in the BrAPI specs inside square-brackets. For instance "[germplasmName]" (for the "germplasm-search" call) will be replace by the germplasm name of the first germplasm returned by the call. Note: array or object properties can not be used here. The form can contain additional call parameters using hidden input or select fields wrapped by an HTML element having the CSS class "brapi-query-filter-post"
There is extensive documentation for this module hosted on ReadtheDocs at https://brapi.readthedocs.io/en/latest/. This includes documentation for installing, using and extending this module.
Current maintainers:
- Valentin Guignon (vguignon) - https://www.drupal.org/user/423148
The Breeding API Drupal implementation has been sponsored by Bioversity International, a CGIAR Research Centre. The Breeding API project has been sponsored by the Bill and Melinda Gates Foundation which funded the breeding API hackathon in June 2015 in Seattle and in July 2016 in Ithaca.
Partners of the Breeding API project are: Bioversity International http://www.bioversityinternational.org/ BMS http://www.integratedbreeding.net/breeding-management-system/ BTI (Cassavabase, Musabase) http://bti.cornell.edu/ CIMMYT http://www.cimmyt.org/ CIP http://cipotato.org/ CIRAD http://www.cirad.fr/ GOBII Porject http://gobiiproject.org/ IRRI http://irri.org/ The James Hutton Institute http://www.hutton.ac.uk/ WUR http://www.wur.nl/