tutorial.Rmd| This package is under development. It has not yet been exhaustively tested for all calls neither. Usage may also still change. If you have suggestions please use the issue tracker. |
Here we use as an example the sweetpotatobase.org database since it has currently one of the most complete implementations. Also, data are public and no login credentials are needed. It is part of the white list of the internal databases, too. So no further knowledge of configuration details are needed.
The package comes with a list of known databases (white list). Both the white list and the handle can be printed in summary form to the console. The $ sign can be used to access individual slots and overwrite values. This can also be used as a template to configure a handle to another brapi compliant database.
## Please note that current supports 44/44 BrAPI calls of version 1.1.
##
## Please note that current support is partially complete for BrAPI version 1.2
## - the additional calls in version 1.2 are not yet supported.
##
## Also, checks on response objects and fields are only loosely implemented to accomodate differences
## between BrAPI versions.
## If you find issues please
##
## - turn on comments with ba_show_info()
## .
## - You can double check against the database by copy/paste of the reported BrAPI URL
##
## at: http://webapps.ipk-gatersleben.de/brapivalidator!
##
## 0.9.4
##
## Please register any further issues at:
## https://github.com/CIP-RIU/brapi/issues## apiary
## bms_test
## cassavabase
## cropontology
## eu_sol
## germinate_test
## icrisat_prod
## mgis
## musabase
## ricebase
## snpseek
## sweetpotatobase
## t3s
## testserver
## tto
## ttw
## yambase## Crop = sweetpotato
##
## Addres:Port = sweetpotatobase.org:80
## User =This is interesting if you have multicrop databases. In the case of sweetpotatobase there is only one crop on that server.
## # A tibble: 1 x 1
## crops
## <chr>
## 1 sweetpotatoIn many cases when exploring a new database it will be useful to get any feedback from the server. The package provides a switch that allows to turn on or off such log information.
The brapi community and standard allows currently a large degree of freedom on implementation of individual parts of the standard (or calls). One call lists the functionality supported by the server.
## URL call was: https://sweetpotatobase.org/brapi/v1/calls/?## Waiting for response from server: ...## Server status: ok!## Status details from Server:##
## Infos:## BrAPI base call found with page=0, pageSize=10
## Loading CXGN::BrAPI::v1::Calls##
## Successes:## Calls result constructed##
## Errors:## ## No encoding supplied: defaulting to UTF-8.## Returning page 0 (max. 0) with max. 1000 items (out of a total of 48).## # A tibble: 48 x 4
## versions methods datatypes call
## * <list> <chr> <chr> <chr>
## 1 <chr [1]> POST; DELETE json token
## 2 <chr [1]> GET json calls
## 3 <chr [1]> GET json observationlevels
## 4 <chr [1]> GET; POST json germplasm-search
## 5 <chr [1]> GET json germplasm/{germplasmDbId}
## 6 <chr [2]> GET json germplasm/{germplasmDbId}/pedigree
## 7 <chr [2]> GET json germplasm/{germplasmDbId}/progeny
## 8 <chr [1]> GET json germplasm/{germplasmDbId}/markerprofi~
## 9 <chr [1]> GET json germplasm/{germplasmDbId}/attributes
## 10 <chr [1]> GET json attributes
## # ... with 38 more rowsAs you notice, the table is presented as a tibble. This has the advantage that it fits on the screen always even though there are big tables. But sometimes it may be useful to just print out the whole table. How to do that is the topic of the next section.
All functions always have two parameters: the first is always the database handle or connection details (‘con’), the last is always the R class of the returned object. Most parameters should be of class ‘character’. Exceptions are: the con parameter is always a list; the parameters ‘page’ and ‘pageSize’ if applicable are integers. For details see individual functions.
This is by default a tibble. However, there are several others supported. An alternative is the ‘data.frame’. In addition and mainly for debugging purposes you can set the value to ‘json’ which will return the full response json object; or you can set it to ‘list’ which will return a list equivalent.
So, let’s just print out the whole data.frame.
## No encoding supplied: defaulting to UTF-8.## versions methods datatypes
## 1 1.0 POST; DELETE json
## 2 1.0 GET json
## 3 1.0 GET json
## 4 1.0 GET; POST json
## 5 1.0 GET json
## 6 1.0, 1.2 GET json
## 7 1.0, 1.2 GET json
## 8 1.0 GET json
## 9 1.0 GET json
## 10 1.0 GET json
## 11 1.0 GET json
## 12 1.0 GET json
## 13 1.0 GET json
## 14 1.0 GET json
## 15 1.0 GET; POST json; tsv; csv; xls
## 16 1.0 GET; POST json; tsv; csv; xls
## 17 1.0 GET; POST json
## 18 1.0 GET json
## 19 1.0 GET; POST json
## 20 1.0 GET; POST json
## 21 1.0 GET; POST json
## 22 1.0 GET json
## 23 1.0 GET; POST json
## 24 1.0 GET json
## 25 1.0 GET json
## 26 1.0 GET json
## 27 1.0 GET json
## 28 1.0 GET json; csv; xls; tsv
## 29 1.0 GET json
## 30 1.0 GET json
## 31 1.0 GET; POST json
## 32 1.0 GET; POST json
## 33 1.0 GET; POST json
## 34 1.0 GET; POST json
## 35 1.0 GET json
## 36 1.0 GET json
## 37 1.0 GET json
## 38 1.0 GET json
## 39 1.0 GET json
## 40 1.0 GET json
## 41 1.0 GET json
## 42 1.0 GET json
## 43 1.0 GET json
## 44 1.0 GET json
## 45 1.0 GET json
## 46 1.0 GET; POST json
## 47 1.0 GET; POST json
## 48 1.0 GET json
## call
## 1 token
## 2 calls
## 3 observationlevels
## 4 germplasm-search
## 5 germplasm/{germplasmDbId}
## 6 germplasm/{germplasmDbId}/pedigree
## 7 germplasm/{germplasmDbId}/progeny
## 8 germplasm/{germplasmDbId}/markerprofiles
## 9 germplasm/{germplasmDbId}/attributes
## 10 attributes
## 11 attributes/categories
## 12 markerprofiles
## 13 markerprofiles/{markerprofileDbId}
## 14 markerprofiles/methods
## 15 allelematrix-search
## 16 allelematrices-search
## 17 programs
## 18 crops
## 19 seasons
## 20 studytypes
## 21 trials
## 22 trials/{trialDbId}
## 23 studies-search
## 24 studies/{studyDbId}
## 25 studies/{studyDbId}/germplasm
## 26 studies/{studyDbId}/observationvariables
## 27 studies/{studyDbId}/observationunits
## 28 studies/{studyDbId}/table
## 29 studies/{studyDbId}/layout
## 30 studies/{studyDbId}/observations
## 31 phenotypes-search
## 32 phenotypes-search/table
## 33 phenotypes-search/tsv
## 34 phenotypes-search/csv
## 35 traits
## 36 traits/{traitDbId}
## 37 maps
## 38 maps/{mapDbId}
## 39 maps/{mapDbId}/positions
## 40 maps/{mapDbId}/positions/id
## 41 locations
## 42 variables/datatypes
## 43 ontologies
## 44 variables
## 45 variables/{observationVariableDbId}
## 46 variables-search
## 47 samples-search
## 48 samples/{sampleDbId}The brapi models trial data in a three layer hierarchy: a) breeding program which has b) trials that c) may consist of one or more studies at one or more locations. A study at one location is also often referred to as a fieldbook.
## No encoding supplied: defaulting to UTF-8.## commonCropName leadPerson name programDbId abbreviation
## 1 SweetPotato Mozambique 135
## 2 SweetPotato Uganda 137
## 3 SweetPotato Ghana 140
## 4 SweetPotato NCSU 132
## 5 SweetPotato Lima 167
## 6 SweetPotato GT4SP-CIP 293
## 7 SweetPotato Kenya 1264
## 8 SweetPotato RAB 1282
## 9 SweetPotato INERA 1286
## 10 SweetPotato AARC 1288
## objective
## 1 Mozambique
## 2 Uganda
## 3 Ghana
## 4 NCSU Sweetpotato Breeding Program
## 5 Sweetpotato Breeding program CIP
## 6 Genomics Tools for Sweetpotato
## 7 Demo Breeding Program
## 8 Rubona
## 9 Ouagadougou
## 10 Hawassa## Using GET## No encoding supplied: defaulting to UTF-8.## # A tibble: 210 x 15
## seasons active programName name locationDbId trialDbId endDate
## * <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 2015 "" Ghana 15FOD07Tono 18 230 2015-Ju~
## 2 2015 "" Ghana 15FOD07Wa 26 230 2015-Ju~
## 3 2015 "" Ghana 15HST03Ny 28 230 2015-Ju~
## 4 2015 "" Ghana 15HST04Wa 26 230 <NA>
## 5 2015 "" Ghana 15ayt7SP_Im~ 16 230 <NA>
## 6 2016 "" Ghana 16CIP-Ghana~ 16 232 2016-Au~
## 7 2016 "" Ghana 16CIP-Ghana~ 22 232 2016-Ma~
## 8 2010 "" Ghana 2010ASPGH_A~ 38 284 2010-Ma~
## 9 2010 "" Ghana 2010ASPGH_A~ 16 284 2010-Ap~
## 10 2010 "" Ghana 2010ASPGH_A~ 39 284 2010-Ju~
## # ... with 200 more rows, and 8 more variables: trialName <chr>,
## # locationName <chr>, programDbId <chr>, startDate <chr>,
## # studyDbId <chr>, studyType <chr>, additionalInfo.design <chr>,
## # additionalInfo.description <chr>