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Loading data

load_data.Rmd

All ShinyBrAPPs use the same module to load data.

Use the application with any endpoint

Connection parameters

In this section, the user is expected to provide the parameters to establish the connection with a BrAPI endpoint (server)

  • BrAPI endpoint: the web services URL (e.g. https://test-server.brapi.org/)
  • Token: a valid token to be used for authentication
  • cropDB: the crop name (for multicrop systems)

Data Import

In the Data import section, the user will provide details to query the BrAPI endpoint and extract the dataset he’s interested in.

  • Observation unit levels: either PLOT or MEANS, or both. NB that depending on the application, the observation unit level may be filtered (e.g. STABrAPP only uses PLOT observation level)
  • Study: select a study among the list of available studies (NB: study follows here BMS terminology. It corresponds to trial in the BrAPI terminology)
  • Available environments: once one or more study is selected the list of environments (studies in the BrAPI terminology) appears, and the user is expected to select one or several of them and click on Load Selected to retrieve the corresponding dataset. Alternatively the user can click on Load All to load the data corresponding to all environments of the selected study.
The load data module as displayed in STABrAPP.
The load data module as displayed in STABrAPP.

Integration with a BrAPI compliant system

ShinyBrAPPs can be launched from a BrAPI compliant system, providing connection and data import parameters using the following URL parameters. In this case the connection and data import UI components are not displayed.

Parameter Description Used in Example
apiURL base URL for the BrAPI server that the BrAPP needs to connect to All ?apiURL=https://test-server.brapi.org/
cropDb crop database name All ?cropDb=Maize
token a valid token All ?token=user:avalidtoken
studyDbIds a comma separated list of studyDbIds that the BrAPP needs to retrieve data from STABrAPP, BrAVISE ?studyDbIds=121,122,123
obs_unit_level a comma separated list of observation unit levels to filter on STABrAPP, BrAVISE ?obs_unit_level=PLOT,MEANS