diff --git a/DESCRIPTION b/DESCRIPTION index 41b3dd9..ff044be 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: brapi Title: Client to Access Breeding Databases Using BrAPI -Version: 0.9.3 +Version: 0.9.4 Authors@R: c( person("Reinhard", "Simon", email = "rsimon64@gmail.com", role = c("aut", "cre")), person("Maikel", "Verouden", role = c("aut", "ctb") , email = "Maikel.Verouden@wur.nl"), diff --git a/NAMESPACE b/NAMESPACE index 6530ffa..04c0d8b 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -13,6 +13,7 @@ export(ba_genomemaps) export(ba_genomemaps_data) export(ba_genomemaps_data_range) export(ba_genomemaps_details) +export(ba_germplasm_attributes) export(ba_germplasm_details) export(ba_germplasm_details_study) export(ba_germplasm_markerprofiles) diff --git a/R/ba_germplasm_attributes.R b/R/ba_germplasm_attributes.R new file mode 100644 index 0000000..d2c5ff0 --- /dev/null +++ b/R/ba_germplasm_attributes.R @@ -0,0 +1,80 @@ +#' ba_germplasm_attributes +#' +#' germplasm_attibutes call. +#' +#' @param con brapi connection object +#' @param rclass character; default: tibble; or else: json, list, data.frame. +#' @param germplasmDbId character; default: ''. +#' @param attributeList character vector; default: ''. +#' @param page integer; default: 0. +#' @param pageSize integer; default: 10. +#' +#' @return rclass as set by parameter. +#' @example inst/examples/ex-ba_germplasmattributes_details.R +#' @import httr +#' @author Reinhard Simon +#' @references \href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md}{github} +#' @family germplasmattributes +#' @family genotyping +#' @export +ba_germplasm_attributes <- function(con = NULL, + germplasmDbId = "", + attributeList = "", + page = 0, + pageSize = 10, + rclass = "tibble") { + ba_check(con = con, verbose = FALSE) + stopifnot(is.character(germplasmDbId)) + stopifnot(germplasmDbId != "") + stopifnot(is.character(attributeList)) + check_paging(pageSize = pageSize, page = page) + check_rclass(rclass = rclass) + # fetch the url of the brapi implementation of the database + brp <- get_brapi(con = con) + # generate the specific brapi call url + pattributeList <- ifelse(attributeList != "", paste("attributeList=", attributeList, collapse = ",", sep=""), "") + germplasm_attributes_list <- paste0(brp, + "germplasm/", + germplasmDbId, + "/attributes/?", + pattributeList, + + "&page=", + page, + "&pageSize=", + pageSize) + try({ + res <- brapiGET(url = germplasm_attributes_list, con = con) + res2 <- httr::content(x = res, as = "text", encoding = "UTF-8") + ms2tbl <- function(res) { + lst <- tryCatch( + jsonlite::fromJSON(txt = res) + ) + + assertthat::assert_that("data" %in% names(lst$result), + msg = "The json return object lacks a data element.") + dat <- jsonlite::toJSON(x = lst$result$data) + germplasmDbId <- lst$result$germplasmDbId + + df <- jsonlite::fromJSON(txt = dat, simplifyDataFrame = TRUE, + flatten = TRUE) + df <- cbind(germplasmDbId, df) + # assertthat::validate_that(nrow(df) > 0, + # msg = "The json return object lacks a data element.") + + return(df) + } + if (rclass %in% c("json", "list")) { + out <- dat2tbl(res = res2, rclass = rclass) + } + if (rclass == "data.frame") { + out <- ms2tbl(res = res2)%>% tibble::as_tibble() %>% as.data.frame() + } + if (rclass == "tibble") { + out <- ms2tbl(res = res2) %>% tibble::as_tibble() + } + class(out) <- c(class(out), "ba_germplasmattributes_details") + show_metadata(res) + return(out) + }) +} diff --git a/R/ba_germplasm_markerprofiles.R b/R/ba_germplasm_markerprofiles.R index 2989569..cd8dc7d 100644 --- a/R/ba_germplasm_markerprofiles.R +++ b/R/ba_germplasm_markerprofiles.R @@ -29,7 +29,7 @@ ba_germplasm_markerprofiles <- function(con = NULL, out <- NULL ms2tbl <- function(res) { lst <- tryCatch( - jsonlite::fromJSON(txt = res2) + jsonlite::fromJSON(txt = res) ) assertthat::assert_that("result" %in% names(lst), @@ -37,18 +37,22 @@ ba_germplasm_markerprofiles <- function(con = NULL, dat <- jsonlite::toJSON(x = lst$result) df <- jsonlite::fromJSON(txt = dat, simplifyDataFrame = TRUE, flatten = TRUE) + if(length(df$markerprofileDbIds) == 0) { + df$markerprofileDbIds <- '' + } - assertthat::assert_that(all(c("germplasmDbId", - "markerprofileDbIds") %in% - names(df)), - msg = "The json return object lacks germplasmDbId and - markerprofileDbIds.") - assertthat::assert_that((length(df$markerprofileDbIds) >= 1), - msg = "No markerprofileDbIdas") - res3 <- as.data.frame(cbind(germplasmDbId = rep(df$germplasmDbId, - length(df$markerprofileDbIds)), - markerProfiles = df$markerprofileDbIds), - stringsAsFactors = FALSE) + res3 <- tibble::as.tibble(df) + # assertthat::assert_that(all(c("germplasmDbId", + # "markerprofileDbIds") %in% + # names(df)), + # msg = "The json return object lacks germplasmDbId and + # markerprofileDbIds.") + # # assertthat::assert_that((length(df$markerprofileDbIds) >= 1), + # # msg = "No markerprofileDbIdas") + # res3 <- as.data.frame(cbind(germplasmDbId = rep(df$germplasmDbId, + # length(df$markerprofileDbIds)), + # markerProfiles = df$markerprofileDbIds), + # stringsAsFactors = FALSE) return(res3) } if (rclass %in% c("json", "list")) { diff --git a/R/ba_germplasm_pedigree.R b/R/ba_germplasm_pedigree.R index 7a36679..d848ebb 100644 --- a/R/ba_germplasm_pedigree.R +++ b/R/ba_germplasm_pedigree.R @@ -37,10 +37,21 @@ ba_germplasm_pedigree <- function(con = NULL, lst <- jsonlite::fromJSON(txt = res) dat <- jsonlite::toJSON(x = lst$result) res3 <- jsonlite::fromJSON(txt = dat, simplifyDataFrame = TRUE) + for (i in 1:length(res3)) { + if (length(res3[[i]]) == 0) res[[i]] <- '' + } # Set null length list-type elements to '' for (i in 1:length(res3)) { if (length(res3[[i]]) == 0) res3[[i]] <- "" } + if (length(res3$siblings) > 1) { + siblings <- res3$siblings + names(siblings) <- paste0('siblings.', names(siblings)) + res3$siblings <- NULL + res3 <- tibble::as.tibble(res3) + res3 <- cbind(res3, siblings) + siblings <- NULL + } attr(res3, "metadata") <- lst$metadata return(res3) } diff --git a/R/ba_germplasmattributes.R b/R/ba_germplasmattributes.R index f7eb211..92b3fae 100644 --- a/R/ba_germplasmattributes.R +++ b/R/ba_germplasmattributes.R @@ -17,6 +17,7 @@ ba_germplasmattributes <- function(con = NULL, attributeCategoryDbId = "0", rclass = "tibble") { + ba_check(con = con, verbose = FALSE) stopifnot(is.character(attributeCategoryDbId)) check_rclass(rclass = rclass) diff --git a/R/ba_germplasmattributes_details.R b/R/ba_germplasmattributes_details.R index 4706bfa..60695c9 100644 --- a/R/ba_germplasmattributes_details.R +++ b/R/ba_germplasmattributes_details.R @@ -23,6 +23,7 @@ ba_germplasmattributes_details <- function(con = NULL, page = 0, pageSize = 10, rclass = "tibble") { + .Deprecated('ba_germplasm_attributes') ba_check(con = con, verbose = FALSE) stopifnot(is.character(germplasmDbId)) stopifnot(germplasmDbId != "") diff --git a/R/ba_studies_table.R b/R/ba_studies_table.R index 2ead3b4..177b8a0 100644 --- a/R/ba_studies_table.R +++ b/R/ba_studies_table.R @@ -11,7 +11,7 @@ #' @param rclass character; default: "tibble" possible other values: "json"/"list"/"data.frame" #' @param studyDbId character; default: '' #' @param con list; brapi connection object -#' @param format character; one of: json, csv, tsv. Default: json +#' @param format character; one of: json, csv, tsv. Default: csv #' #' @author Reinhard Simon, Maikel Verouden #' @references \href{https://github.com/plantbreeding/API/blob/master/Specification/Studies/StudyObservationUnitsAsTable.md}{github} @@ -25,7 +25,7 @@ #' @export ba_studies_table <- function(con = NULL, studyDbId = "", - format = "json", + format = "csv", rclass = "tibble") { ba_check(con = con, verbose = FALSE, brapi_calls = "studies/id/table") stopifnot(is.character(studyDbId)) @@ -46,6 +46,7 @@ ba_studies_table <- function(con = NULL, pformat)) try({ res <- brapiGET(url = studies_table, con = con) + }) res <- httr::content(x = res, as = "text", encoding = "UTF-8") out <- NULL if (rclass %in% c("json", "list")) { @@ -56,6 +57,8 @@ ba_studies_table <- function(con = NULL, res2 <- jsonlite::fromJSON(txt = res)$result out <- res2$data out <- tibble::as.tibble(out) + if(length(res2$headerRow) != length(colnames(out))) + stop('Header row length does not coincide with column count. Contact database provider.') colnames(out) <- res2$headerRow } if (format == "csv") { @@ -82,5 +85,5 @@ ba_studies_table <- function(con = NULL, } class(out) <- c(class(out), "ba_studies_table") return(out) - }) + } diff --git a/R/mpa2tbl.R b/R/mpa2tbl.R index 1275dca..7b63cbe 100644 --- a/R/mpa2tbl.R +++ b/R/mpa2tbl.R @@ -4,8 +4,11 @@ mpa2tbl <- function(res, rclass = "tibble") { dba <- jsonlite::fromJSON(txt = dat) udb <- unlist(dba) udb <- udb[!is.na(udb)] %>% as.data.frame(stringsAsFactors = FALSE) - udb <- as.data.frame(x = cbind(marker = rownames(udb), alleles = udb[, 1]), - stringsAsFactors = FALSE) + if (nrow(udb) > 0) { + udb <- as.data.frame(x = cbind(marker = rownames(udb), alleles = udb[, 1]), + stringsAsFactors = FALSE) + + } if (rclass == "tibble") { udb <- tibble::as_tibble(udb) } diff --git a/R/zzz.R b/R/zzz.R index ff74b14..338d854 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -5,7 +5,7 @@ You are using version ", utils::packageVersion("brapi"), "\n\n") txt <- paste( - "Please note that current support is complete for BrAPI version 1.1.\n + "Please note that current supports 44/44 BrAPI calls of version 1.1.\n Please note that current support is partially complete for BrAPI version 1.2 - the additional calls in version 1.2 are not yet supported.\n Also, checks on response objects and fields are only loosely implemented to accomodate differences diff --git a/README.Rmd b/README.Rmd index 747a10a..0b5c6d0 100644 --- a/README.Rmd +++ b/README.Rmd @@ -15,9 +15,11 @@ output: github_document [![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/brapi)](https://cran.r-project.org/package=brapi) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) -## This version is still under development. The implementation sometimes changes minor details. +This version is still under development. The implementation sometimes changes minor details. -## Current support is only for BrAPI version 1.1. +Current support is mainly for BrAPI version 1.1. + +Support for version 1.2 is underway. For independent checks against database you may use http://webapps.ipk-gatersleben.de/brapivalidator. @@ -34,6 +36,7 @@ knitr::opts_chunk$set( # README An R package to use the [Breeding API (BrAPI)](http://docs.brapi.apiary.io) for accessing plant breeding data. +See the [documentation](https://cip-riu.github.io/brapi/) for details. It can be installed using: diff --git a/README.md b/README.md index 93bdcd8..59f7b60 100644 --- a/README.md +++ b/README.md @@ -14,9 +14,12 @@ Status](https://img.shields.io/codecov/c/github/CIP-RIU/brapi/master.svg)](https [![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/brapi)](https://cran.r-project.org/package=brapi) [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing) -## This version is still under development. The implementation sometimes changes minor details. +This version is still under development. The implementation sometimes +changes minor details. -## Current support is only for BrAPI version 1.1. +Current support is mainly for BrAPI version 1.1. + +Support for version 1.2 is underway. For independent checks against database you may use . @@ -28,6 +31,7 @@ protocol changes. An R package to use the [Breeding API (BrAPI)](http://docs.brapi.apiary.io) for accessing plant breeding data. +See the [documentation](https://cip-riu.github.io/brapi/) for details. It can be installed using: diff --git a/docs/articles/index.html b/docs/articles/index.html index b25e1e0..0cc5e63 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -55,7 +55,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/articles/tutorial.html b/docs/articles/tutorial.html index 7c56c6d..0599132 100644 --- a/docs/articles/tutorial.html +++ b/docs/articles/tutorial.html @@ -29,7 +29,7 @@ brapi - 0.9.1 + 0.9.4 @@ -69,17 +69,13 @@ - - - - -
+

Basic Tutorial

Reinhard Simon

-

2018-06-01

+

2018-06-21

@@ -100,11 +96,24 @@

Get the database handle

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.

-
## This is the development version of the 'brapi' package!
+
## Please note that current supports 44/44 BrAPI calls of version 1.1.
 ## 
-##         You are using version  0.9.1 
+##      Please note that current support is partially complete for BrAPI version 1.2
+##       - the additional calls in version 1.2 are not yet supported.
 ## 
-##  Please register any issues at:
+##      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

 
library(magrittr)
 
@@ -166,23 +175,34 @@ 

 
## 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 47).

-
## # A tibble: 47 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/id               
-##  6 <chr [2]> GET          json      germplasm/id/pedigree      
-##  7 <chr [2]> GET          json      germplasm/id/progeny       
-##  8 <chr [1]> GET          json      germplasm/id/markerprofiles
-##  9 <chr [1]> GET          json      germplasm/id/attributes    
-## 10 <chr [1]> GET          json      attributes                 
-## # ... with 37 more rows

-
+
## 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 rows

+
 
As 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.

 

 

@@ -195,7 +215,7 @@ 

 Output formats

 
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.

-
ba_calls(con = sp_base, rclass = "data.frame")

+
ba_calls(con = sp_base, rclass = "data.frame")

 
## No encoding supplied: defaulting to UTF-8.

 
##    versions      methods           datatypes
 ## 1       1.0 POST; DELETE                json
@@ -213,25 +233,25 @@ 

 ## 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
-## 17      1.0          GET                json
-## 18      1.0    GET; POST                json
+## 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                json
-## 22      1.0    GET; POST                json
-## 23      1.0          GET                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; csv; xls; tsv
-## 28      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; POST                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                json
+## 34      1.0    GET; POST                json
 ## 35      1.0          GET                json
 ## 36      1.0          GET                json
 ## 37      1.0          GET                json
@@ -242,57 +262,59 @@ 

 ## 42      1.0          GET                json
 ## 43      1.0          GET                json
 ## 44      1.0          GET                json
-## 45      1.0    GET; POST                json
+## 45      1.0          GET                json
 ## 46      1.0    GET; POST                json
-## 47      1.0          GET                json
-##                               call
-## 1                            token
-## 2                            calls
-## 3                observationlevels
-## 4                 germplasm-search
-## 5                     germplasm/id
-## 6            germplasm/id/pedigree
-## 7             germplasm/id/progeny
-## 8      germplasm/id/markerprofiles
-## 9          germplasm/id/attributes
-## 10                      attributes
-## 11           attributes/categories
-## 12                  markerprofiles
-## 13               markerprofiles/id
-## 14          markerprofiles/methods
-## 15           allelematrices-search
-## 16                        programs
-## 17                           crops
-## 18                         seasons
-## 19                      studytypes
-## 20                          trials
-## 21                       trials/id
-## 22                  studies-search
-## 23                      studies/id
-## 24            studies/id/germplasm
-## 25 studies/id/observationvariables
-## 26     studies/id/observationunits
-## 27                studies/id/table
-## 28               studies/id/layout
-## 29         studies/id/observations
-## 30               phenotypes-search
-## 31         phenotypes-search/table
-## 32           phenotypes-search/tsv
-## 33           phenotypes-search/csv
-## 34                          traits
-## 35                       traits/id
-## 36                            maps
-## 37                         maps/id
-## 38               maps/id/positions
-## 39            maps/id/positions/id
-## 40                       locations
-## 41             variables/datatypes
-## 42                      ontologies
-## 43                       variables
-## 44                    variables/id
-## 45                variables-search
-## 46                  samples-search
-## 47                      samples/id

+## 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}

@@ -301,59 +323,61 @@

Which breeding programs are there?

-
ba_programs(sp_base, rclass = "data.frame")
+
ba_programs(sp_base, rclass = "data.frame")
## 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             
-##                           objective
-## 1                        Mozambique
-## 2                            Uganda
-## 3                             Ghana
-## 4 NCSU Sweetpotato Breeding Program
-## 5  Sweetpotato Breeding program CIP
-## 6    Genomics Tools for Sweetpotato
+
##    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

Which studies are there?

-
ba_studies_search(sp_base, programDbId = "140")
+
ba_studies_search(sp_base, programDbId = "140")
## Using GET
## No encoding supplied: defaulting to UTF-8.
-
## # A tibble: 204 x 15
-##    seasons active programName locationDbId trialDbId endDate  studyName   
-##  * <chr>   <chr>  <chr>       <chr>            <int> <chr>    <chr>       
-##  1 2015    ""     Ghana       18                 230 2015-Ju… 15FOD07Tono 
-##  2 2015    ""     Ghana       26                 230 2015-Ju… 15FOD07Wa   
-##  3 2015    ""     Ghana       28                 230 2015-Ju… 15HST03Ny   
-##  4 2015    ""     Ghana       26                 230 <NA>     15HST04Wa   
-##  5 2015    ""     Ghana       16                 230 <NA>     15ayt7SP_Im…
-##  6 2016    ""     Ghana       16                 232 2016-Au… 16CIP-Ghana…
-##  7 2016    ""     Ghana       22                 232 2016-Ma… 16CIP-Ghana…
-##  8 2010    ""     Ghana       38                 284 2010-Ma… 2010ASPGH_A…
-##  9 2010    ""     Ghana       16                 284 2010-Ap… 2010ASPGH_A…
-## 10 2010    ""     Ghana       39                 284 2010-Ju… 2010ASPGH_A…
-## # ... with 194 more rows, and 8 more variables: trialName <chr>,
+
## # 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 <int>, studyType <chr>, additionalInfo.design <chr>,
+## #   studyDbId <chr>, studyType <chr>, additionalInfo.design <chr>,
 ## #   additionalInfo.description <chr>

Get a study (or fieldbook)

- -<<<<<<< HEAD -
- -======= -
- ->>>>>>> be4bcf08cee72dd59344ef8835745957d8db09e2 +

diff --git a/docs/authors.html b/docs/authors.html index 94736c2..c44dd5a 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -55,7 +55,7 @@ brapi - 0.9.1 + 0.9.4
diff --git a/docs/index.html b/docs/index.html index 5bb393d..ed61be7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -30,7 +30,7 @@ brapi - 0.9.1 + 0.9.4
@@ -82,15 +82,16 @@ BrAPI R package -
-

-This version is still under development. The implementation sometimes changes minor details.

-
+

This version is still under development. The implementation sometimes changes minor details.

+

Current support is mainly for BrAPI version 1.1.

+

Support for version 1.2 is underway.

+

For independent checks against database you may use http://webapps.ipk-gatersleben.de/brapivalidator.

+

It seems several databases may not currently be fully accessible due to protocol changes.

README

-

An R package to use the Breeding API (BrAPI) for accessing plant breeding data.

+

An R package to use the Breeding API (BrAPI) for accessing plant breeding data. See the documentation for details.

It can be installed using:

diff --git a/docs/news/index.html b/docs/news/index.html index 84b211b..e1fae55 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -55,7 +55,7 @@ brapi - 0.9.1 + 0.9.4
diff --git a/docs/reference/as.ba_db.html b/docs/reference/as.ba_db.html index 6a56a37..3c72d01 100644 --- a/docs/reference/as.ba_db.html +++ b/docs/reference/as.ba_db.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_calls.html b/docs/reference/ba_calls.html index 355f364..f7fe92c 100644 --- a/docs/reference/ba_calls.html +++ b/docs/reference/ba_calls.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_can_internet.html b/docs/reference/ba_can_internet.html index 52722a6..15969f0 100644 --- a/docs/reference/ba_can_internet.html +++ b/docs/reference/ba_can_internet.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_check.html b/docs/reference/ba_check.html index 282cb0e..a81ee2a 100644 --- a/docs/reference/ba_check.html +++ b/docs/reference/ba_check.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_connect.html b/docs/reference/ba_connect.html index ea22d43..77bcce2 100644 --- a/docs/reference/ba_connect.html +++ b/docs/reference/ba_connect.html @@ -59,7 +59,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_crops.html b/docs/reference/ba_crops.html index 3d34460..ff9204b 100644 --- a/docs/reference/ba_crops.html +++ b/docs/reference/ba_crops.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_db.html b/docs/reference/ba_db.html index 2fb9cce..dbb9a74 100644 --- a/docs/reference/ba_db.html +++ b/docs/reference/ba_db.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_genomemaps.html b/docs/reference/ba_genomemaps.html index 3a3f1f0..dbc1016 100644 --- a/docs/reference/ba_genomemaps.html +++ b/docs/reference/ba_genomemaps.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -168,6 +168,7 @@

See a

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_data, ba_genomemaps_details, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_genomemaps_data.html b/docs/reference/ba_genomemaps_data.html index fb56dfc..ae797bf 100644 --- a/docs/reference/ba_genomemaps_data.html +++ b/docs/reference/ba_genomemaps_data.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -163,6 +163,7 @@

See a

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_genomemaps_data_range.html b/docs/reference/ba_genomemaps_data_range.html index 77b20d0..ff6795b 100644 --- a/docs/reference/ba_genomemaps_data_range.html +++ b/docs/reference/ba_genomemaps_data_range.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -116,8 +116,8 @@

ba_genomemaps_data_range

ba_genomemaps_data_range(con = NULL, mapDbId = "1",
-  linkageGroupName = "1", min = 1, max = 1000, page = 0,
-  pageSize = 30, rclass = "tibble")
+ linkageGroupName = "1", min = "", max = "", page = 0, pageSize = 30, + rclass = "tibble")

Arguments

@@ -136,11 +136,11 @@

Arg

- + - + @@ -176,6 +176,7 @@

See a

Other genotyping: ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_genomemaps_details.html b/docs/reference/ba_genomemaps_details.html index f6f674b..f486952 100644 --- a/docs/reference/ba_genomemaps_details.html +++ b/docs/reference/ba_genomemaps_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -150,6 +150,7 @@

See a

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_data, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_germplasm_attributes.html b/docs/reference/ba_germplasm_attributes.html new file mode 100644 index 0000000..c6561ac --- /dev/null +++ b/docs/reference/ba_germplasm_attributes.html @@ -0,0 +1,226 @@ + + + + + + + + +ba_germplasm_attributes — ba_germplasm_attributes • brapi + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+
+ + + +
+ +
+
+
+

ba_germplasm_attributes

+ + +
+ +
+ +

germplasm_attibutes call.

+ +
+ + 
ba_germplasm_attributes(con = NULL, germplasmDbId = "",
+  attributeList = "", page = 0, pageSize = 10, rclass = "tibble")
+ +

Arguments

+

min

integer; default 1

character; default ''
max

integer; default 1000

character; default ''
page
+ + + + + + + + + + + + + + + + + + + + + + + + + +
con

brapi connection object

germplasmDbId

character; default: ''.

attributeList

character vector; default: ''.

page

integer; default: 0.

pageSize

integer; default: 10.

rclass

character; default: tibble; or else: json, list, data.frame.

+ +

Value

+ +

rclass as set by parameter.

+ +

References

+ +

github

+ +

See also

+ +

Other germplasmattributes: ba_germplasmattributes_categories, + ba_germplasmattributes_details, + ba_germplasmattributes

+

Other genotyping: ba_genomemaps_data_range, + ba_genomemaps_data, + ba_genomemaps_details, + ba_genomemaps, + ba_germplasm_markerprofiles, + ba_germplasm_search, + ba_germplasmattributes_categories, + ba_germplasmattributes_details, + ba_germplasmattributes, + ba_markerprofiles_allelematrix_search, + ba_markerprofiles_details, + ba_markerprofiles_search, + ba_markers_details, + ba_markers_search

+ + +

Examples

+ 
if (interactive()) {
+  library(brapi)
+  # Need to connect to a database with genetic data
+
+  # con <- ba_db()$xxxxx
+
+  # ba_germplasmattributes_details(con = con, ...)
+}
+ + + + +
+
+

Developed by Reinhard Simon, Maikel Verouden.

+
+ +
+

Site built with pkgdown.

+
+ +
+ + + + + + + diff --git a/docs/reference/ba_germplasm_details.html b/docs/reference/ba_germplasm_details.html index 53a42aa..7836947 100644 --- a/docs/reference/ba_germplasm_details.html +++ b/docs/reference/ba_germplasm_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_germplasm_details_study.html b/docs/reference/ba_germplasm_details_study.html index 7e88baa..e8d510e 100644 --- a/docs/reference/ba_germplasm_details_study.html +++ b/docs/reference/ba_germplasm_details_study.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_germplasm_markerprofiles.html b/docs/reference/ba_germplasm_markerprofiles.html index 3fd947a..92b0eca 100644 --- a/docs/reference/ba_germplasm_markerprofiles.html +++ b/docs/reference/ba_germplasm_markerprofiles.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -153,6 +153,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_search, ba_germplasmattributes_categories, ba_germplasmattributes_details, diff --git a/docs/reference/ba_germplasm_pedigree.html b/docs/reference/ba_germplasm_pedigree.html index 0e7cc18..74cca8b 100644 --- a/docs/reference/ba_germplasm_pedigree.html +++ b/docs/reference/ba_germplasm_pedigree.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_germplasm_search.html b/docs/reference/ba_germplasm_search.html index 3b0f4b1..a439f57 100644 --- a/docs/reference/ba_germplasm_search.html +++ b/docs/reference/ba_germplasm_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -184,6 +184,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasmattributes_categories, ba_germplasmattributes_details, diff --git a/docs/reference/ba_germplasmattributes.html b/docs/reference/ba_germplasmattributes.html index 95451f7..71155cc 100644 --- a/docs/reference/ba_germplasmattributes.html +++ b/docs/reference/ba_germplasmattributes.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -145,12 +145,14 @@

R

See also

-

Other germplasmattributes: ba_germplasmattributes_categories, +

Other germplasmattributes: ba_germplasm_attributes, + ba_germplasmattributes_categories, ba_germplasmattributes_details

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_germplasmattributes_categories.html b/docs/reference/ba_germplasmattributes_categories.html index c2f7a39..6ab6035 100644 --- a/docs/reference/ba_germplasmattributes_categories.html +++ b/docs/reference/ba_germplasmattributes_categories.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4

@@ -149,12 +149,14 @@

R

See also

-

Other germplasmattributes: ba_germplasmattributes_details, +

Other germplasmattributes: ba_germplasm_attributes, + ba_germplasmattributes_details, ba_germplasmattributes

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_details, diff --git a/docs/reference/ba_germplasmattributes_details.html b/docs/reference/ba_germplasmattributes_details.html index 1db10b2..a5c0096 100644 --- a/docs/reference/ba_germplasmattributes_details.html +++ b/docs/reference/ba_germplasmattributes_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4

@@ -157,12 +157,14 @@

R

See also

-

Other germplasmattributes: ba_germplasmattributes_categories, +

Other germplasmattributes: ba_germplasm_attributes, + ba_germplasmattributes_categories, ba_germplasmattributes

Other genotyping: ba_genomemaps_data_range, ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_locations.html b/docs/reference/ba_locations.html index 8223902..c378581 100644 --- a/docs/reference/ba_locations.html +++ b/docs/reference/ba_locations.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4

diff --git a/docs/reference/ba_login.html b/docs/reference/ba_login.html index 03766e6..fe82cec 100644 --- a/docs/reference/ba_login.html +++ b/docs/reference/ba_login.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4
diff --git a/docs/reference/ba_logout.html b/docs/reference/ba_logout.html index 410cd07..2e67032 100644 --- a/docs/reference/ba_logout.html +++ b/docs/reference/ba_logout.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4
diff --git a/docs/reference/ba_markerprofiles_allelematrix_search.html b/docs/reference/ba_markerprofiles_allelematrix_search.html index 07b24ce..a7ff33f 100644 --- a/docs/reference/ba_markerprofiles_allelematrix_search.html +++ b/docs/reference/ba_markerprofiles_allelematrix_search.html @@ -60,7 +60,7 @@ brapi - 0.9.1 + 0.9.4
@@ -193,6 +193,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_markerprofiles_details.html b/docs/reference/ba_markerprofiles_details.html index 8be4301..5273778 100644 --- a/docs/reference/ba_markerprofiles_details.html +++ b/docs/reference/ba_markerprofiles_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -176,6 +176,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_markerprofiles_search.html b/docs/reference/ba_markerprofiles_search.html index afe7791..38ba1cc 100644 --- a/docs/reference/ba_markerprofiles_search.html +++ b/docs/reference/ba_markerprofiles_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -176,6 +176,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_markers_details.html b/docs/reference/ba_markers_details.html index 07dfe56..03a01c0 100644 --- a/docs/reference/ba_markers_details.html +++ b/docs/reference/ba_markers_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -149,6 +149,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_markers_search.html b/docs/reference/ba_markers_search.html index 747292b..f801373 100644 --- a/docs/reference/ba_markers_search.html +++ b/docs/reference/ba_markers_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -171,6 +171,7 @@

See a ba_genomemaps_data, ba_genomemaps_details, ba_genomemaps, + ba_germplasm_attributes, ba_germplasm_markerprofiles, ba_germplasm_search, ba_germplasmattributes_categories, diff --git a/docs/reference/ba_observationvariables.html b/docs/reference/ba_observationvariables.html index c14580b..93e57e5 100644 --- a/docs/reference/ba_observationvariables.html +++ b/docs/reference/ba_observationvariables.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_observationvariables_datatypes.html b/docs/reference/ba_observationvariables_datatypes.html index cc5725e..0c493df 100644 --- a/docs/reference/ba_observationvariables_datatypes.html +++ b/docs/reference/ba_observationvariables_datatypes.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_observationvariables_details.html b/docs/reference/ba_observationvariables_details.html index ac9932a..525ea63 100644 --- a/docs/reference/ba_observationvariables_details.html +++ b/docs/reference/ba_observationvariables_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_observationvariables_ontologies.html b/docs/reference/ba_observationvariables_ontologies.html index 32030d8..35a150b 100644 --- a/docs/reference/ba_observationvariables_ontologies.html +++ b/docs/reference/ba_observationvariables_ontologies.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_observationvariables_search.html b/docs/reference/ba_observationvariables_search.html index 9aa6ee0..18faa16 100644 --- a/docs/reference/ba_observationvariables_search.html +++ b/docs/reference/ba_observationvariables_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_phenotypes_search.html b/docs/reference/ba_phenotypes_search.html index 483aeed..021eb4b 100644 --- a/docs/reference/ba_phenotypes_search.html +++ b/docs/reference/ba_phenotypes_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_programs.html b/docs/reference/ba_programs.html index 952329d..1872eee 100644 --- a/docs/reference/ba_programs.html +++ b/docs/reference/ba_programs.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_programs_search.html b/docs/reference/ba_programs_search.html index f1656d8..f709a61 100644 --- a/docs/reference/ba_programs_search.html +++ b/docs/reference/ba_programs_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_samples.html b/docs/reference/ba_samples.html index 04869a8..e4fe008 100644 --- a/docs/reference/ba_samples.html +++ b/docs/reference/ba_samples.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_samples_save.html b/docs/reference/ba_samples_save.html index ae8c200..dad84b7 100644 --- a/docs/reference/ba_samples_save.html +++ b/docs/reference/ba_samples_save.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_show_expiration.html b/docs/reference/ba_show_expiration.html index aba0c60..e8ec7f3 100644 --- a/docs/reference/ba_show_expiration.html +++ b/docs/reference/ba_show_expiration.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_show_info.html b/docs/reference/ba_show_info.html index 385beb7..c045b3f 100644 --- a/docs/reference/ba_show_info.html +++ b/docs/reference/ba_show_info.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_details.html b/docs/reference/ba_studies_details.html index 0fc23f4..0e8154b 100644 --- a/docs/reference/ba_studies_details.html +++ b/docs/reference/ba_studies_details.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_layout.html b/docs/reference/ba_studies_layout.html index 7c62c40..c2133ce 100644 --- a/docs/reference/ba_studies_layout.html +++ b/docs/reference/ba_studies_layout.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_observationlevels.html b/docs/reference/ba_studies_observationlevels.html index f875a11..6a33ef8 100644 --- a/docs/reference/ba_studies_observationlevels.html +++ b/docs/reference/ba_studies_observationlevels.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_observations.html b/docs/reference/ba_studies_observations.html index 06ef23c..fbe3dce 100644 --- a/docs/reference/ba_studies_observations.html +++ b/docs/reference/ba_studies_observations.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_observationunits.html b/docs/reference/ba_studies_observationunits.html index d11fc60..a03b61d 100644 --- a/docs/reference/ba_studies_observationunits.html +++ b/docs/reference/ba_studies_observationunits.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_observationunits_save.html b/docs/reference/ba_studies_observationunits_save.html index bbaeaa2..2e11f64 100644 --- a/docs/reference/ba_studies_observationunits_save.html +++ b/docs/reference/ba_studies_observationunits_save.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_observationvariables.html b/docs/reference/ba_studies_observationvariables.html index 5cffd60..dfc2b4c 100644 --- a/docs/reference/ba_studies_observationvariables.html +++ b/docs/reference/ba_studies_observationvariables.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_search.html b/docs/reference/ba_studies_search.html index 03e56d2..81f38b2 100644 --- a/docs/reference/ba_studies_search.html +++ b/docs/reference/ba_studies_search.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_seasons.html b/docs/reference/ba_studies_seasons.html index 622d338..164aea2 100644 --- a/docs/reference/ba_studies_seasons.html +++ b/docs/reference/ba_studies_seasons.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_studytypes.html b/docs/reference/ba_studies_studytypes.html index fd674a9..ff63599 100644 --- a/docs/reference/ba_studies_studytypes.html +++ b/docs/reference/ba_studies_studytypes.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 diff --git a/docs/reference/ba_studies_table.html b/docs/reference/ba_studies_table.html index fa17f76..bde7cd2 100644 --- a/docs/reference/ba_studies_table.html +++ b/docs/reference/ba_studies_table.html @@ -58,7 +58,7 @@ brapi - 0.9.1 + 0.9.4 @@ -115,7 +115,7 @@

ba_studies_table

- 
ba_studies_table(con = NULL, studyDbId = "", format = "json",
+    
ba_studies_table(con = NULL, studyDbId = "", format = "csv",
   rclass = "tibble")

     
     
Arguments

@@ -131,7 +131,7 @@ 
Arg
     
     
       format
-      
character; one of: json, csv, tsv. Default: json

+      
character; one of: json, csv, tsv. Default: csv

     
     
       rclass
diff --git a/docs/reference/ba_studies_table_save.html b/docs/reference/ba_studies_table_save.html
index 7da26a4..da15a86 100644
--- a/docs/reference/ba_studies_table_save.html
+++ b/docs/reference/ba_studies_table_save.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/ba_traits.html b/docs/reference/ba_traits.html
index bbe7894..2666793 100644
--- a/docs/reference/ba_traits.html
+++ b/docs/reference/ba_traits.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/ba_traits_details.html b/docs/reference/ba_traits_details.html
index d560a92..53afa66 100644
--- a/docs/reference/ba_traits_details.html
+++ b/docs/reference/ba_traits_details.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/ba_trials.html b/docs/reference/ba_trials.html
index 9fe604d..1cca5d1 100644
--- a/docs/reference/ba_trials.html
+++ b/docs/reference/ba_trials.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/ba_trials_details.html b/docs/reference/ba_trials_details.html
index afcc0eb..848d61a 100644
--- a/docs/reference/ba_trials_details.html
+++ b/docs/reference/ba_trials_details.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/brapi.html b/docs/reference/brapi.html
index e98bfdf..18e6dff 100644
--- a/docs/reference/brapi.html
+++ b/docs/reference/brapi.html
@@ -61,7 +61,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 35b6e3d..7269bb5 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -55,7 +55,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
@@ -184,6 +184,12 @@ 
ba_genomemaps_details() 

         
         
ba_genomemaps_details

+      
+        
+        
+          
ba_germplasm_attributes() 

+        
+        
ba_germplasm_attributes

       
         
         
diff --git a/docs/reference/is.ba_con.html b/docs/reference/is.ba_con.html
index a86e8b3..e5d5729 100644
--- a/docs/reference/is.ba_con.html
+++ b/docs/reference/is.ba_con.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/print.ba_con.html b/docs/reference/print.ba_con.html
index 55d356b..181ab71 100644
--- a/docs/reference/print.ba_con.html
+++ b/docs/reference/print.ba_con.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/docs/reference/print.ba_db_list.html b/docs/reference/print.ba_db_list.html
index 7ef2f2d..a99cd5c 100644
--- a/docs/reference/print.ba_db_list.html
+++ b/docs/reference/print.ba_db_list.html
@@ -58,7 +58,7 @@
       
       
         brapi
-        0.9.1
+        0.9.4
       
     
 
diff --git a/man/ba_genomemaps.Rd b/man/ba_genomemaps.Rd
index 9a5c847..4f57ea2 100644
--- a/man/ba_genomemaps.Rd
+++ b/man/ba_genomemaps.Rd
@@ -52,6 +52,7 @@ Other genomemaps: \code{\link{ba_genomemaps_data_range}},
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_genomemaps_data.Rd b/man/ba_genomemaps_data.Rd
index 3882496..bcb96b7 100644
--- a/man/ba_genomemaps_data.Rd
+++ b/man/ba_genomemaps_data.Rd
@@ -49,6 +49,7 @@ Other genomemaps: \code{\link{ba_genomemaps_data_range}},
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_genomemaps_data_range.Rd b/man/ba_genomemaps_data_range.Rd
index 1bf2f13..429ee90 100644
--- a/man/ba_genomemaps_data_range.Rd
+++ b/man/ba_genomemaps_data_range.Rd
@@ -57,6 +57,7 @@ Other genomemaps: \code{\link{ba_genomemaps_data}},
 Other genotyping: \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_genomemaps_details.Rd b/man/ba_genomemaps_details.Rd
index d8c7976..e18123b 100644
--- a/man/ba_genomemaps_details.Rd
+++ b/man/ba_genomemaps_details.Rd
@@ -41,6 +41,7 @@ Other genomemaps: \code{\link{ba_genomemaps_data_range}},
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_germplasm_attributes.Rd b/man/ba_germplasm_attributes.Rd
new file mode 100644
index 0000000..60fd617
--- /dev/null
+++ b/man/ba_germplasm_attributes.Rd
@@ -0,0 +1,64 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/ba_germplasm_attributes.R
+\name{ba_germplasm_attributes}
+\alias{ba_germplasm_attributes}
+\title{ba_germplasm_attributes}
+\usage{
+ba_germplasm_attributes(con = NULL, germplasmDbId = "",
+  attributeList = "", page = 0, pageSize = 10, rclass = "tibble")
+}
+\arguments{
+\item{con}{brapi connection object}
+
+\item{germplasmDbId}{character; default: ''.}
+
+\item{attributeList}{character vector; default: ''.}
+
+\item{page}{integer; default: 0.}
+
+\item{pageSize}{integer; default: 10.}
+
+\item{rclass}{character; default: tibble; or else: json, list, data.frame.}
+}
+\value{
+rclass as set by parameter.
+}
+\description{
+germplasm_attibutes call.
+}
+\examples{
+if (interactive()) {
+  library(brapi)
+  # Need to connect to a database with genetic data
+
+  # con <- ba_db()$xxxxx
+
+  # ba_germplasmattributes_details(con = con, ...)
+}
+}
+\references{
+\href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md}{github}
+}
+\seealso{
+Other germplasmattributes: \code{\link{ba_germplasmattributes_categories}},
+  \code{\link{ba_germplasmattributes_details}},
+  \code{\link{ba_germplasmattributes}}
+
+Other genotyping: \code{\link{ba_genomemaps_data_range}},
+  \code{\link{ba_genomemaps_data}},
+  \code{\link{ba_genomemaps_details}},
+  \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_markerprofiles}},
+  \code{\link{ba_germplasm_search}},
+  \code{\link{ba_germplasmattributes_categories}},
+  \code{\link{ba_germplasmattributes_details}},
+  \code{\link{ba_germplasmattributes}},
+  \code{\link{ba_markerprofiles_allelematrix_search}},
+  \code{\link{ba_markerprofiles_details}},
+  \code{\link{ba_markerprofiles_search}},
+  \code{\link{ba_markers_details}},
+  \code{\link{ba_markers_search}}
+}
+\author{
+Reinhard Simon
+}
diff --git a/man/ba_germplasm_markerprofiles.Rd b/man/ba_germplasm_markerprofiles.Rd
index d68c4ad..e1da8aa 100644
--- a/man/ba_germplasm_markerprofiles.Rd
+++ b/man/ba_germplasm_markerprofiles.Rd
@@ -43,6 +43,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
   \code{\link{ba_germplasmattributes_details}},
diff --git a/man/ba_germplasm_search.Rd b/man/ba_germplasm_search.Rd
index a46f20a..71aa0fc 100644
--- a/man/ba_germplasm_search.Rd
+++ b/man/ba_germplasm_search.Rd
@@ -65,6 +65,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasmattributes_categories}},
   \code{\link{ba_germplasmattributes_details}},
diff --git a/man/ba_germplasmattributes.Rd b/man/ba_germplasmattributes.Rd
index cf3d9b5..da10fcd 100644
--- a/man/ba_germplasmattributes.Rd
+++ b/man/ba_germplasmattributes.Rd
@@ -34,13 +34,15 @@ if (interactive()) {
 \href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/ListAttributesByAttributeCategoryDbId.md}{github}
 }
 \seealso{
-Other germplasmattributes: \code{\link{ba_germplasmattributes_categories}},
+Other germplasmattributes: \code{\link{ba_germplasm_attributes}},
+  \code{\link{ba_germplasmattributes_categories}},
   \code{\link{ba_germplasmattributes_details}}
 
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_germplasmattributes_categories.Rd b/man/ba_germplasmattributes_categories.Rd
index 0e851ff..0f7a549 100644
--- a/man/ba_germplasmattributes_categories.Rd
+++ b/man/ba_germplasmattributes_categories.Rd
@@ -36,13 +36,15 @@ if (interactive()) {
 \href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/ListAttributeCategories.md}{github}
 }
 \seealso{
-Other germplasmattributes: \code{\link{ba_germplasmattributes_details}},
+Other germplasmattributes: \code{\link{ba_germplasm_attributes}},
+  \code{\link{ba_germplasmattributes_details}},
   \code{\link{ba_germplasmattributes}}
 
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_details}},
diff --git a/man/ba_germplasmattributes_details.Rd b/man/ba_germplasmattributes_details.Rd
index 5bb2f02..69b9ab4 100644
--- a/man/ba_germplasmattributes_details.Rd
+++ b/man/ba_germplasmattributes_details.Rd
@@ -40,13 +40,15 @@ if (interactive()) {
 \href{https://github.com/plantbreeding/API/blob/master/Specification/GermplasmAttributes/GermplasmAttributeValuesByGermplasmDbId.md}{github}
 }
 \seealso{
-Other germplasmattributes: \code{\link{ba_germplasmattributes_categories}},
+Other germplasmattributes: \code{\link{ba_germplasm_attributes}},
+  \code{\link{ba_germplasmattributes_categories}},
   \code{\link{ba_germplasmattributes}}
 
 Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_markerprofiles_allelematrix_search.Rd b/man/ba_markerprofiles_allelematrix_search.Rd
index 59b2972..264834d 100644
--- a/man/ba_markerprofiles_allelematrix_search.Rd
+++ b/man/ba_markerprofiles_allelematrix_search.Rd
@@ -65,6 +65,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_markerprofiles_details.Rd b/man/ba_markerprofiles_details.Rd
index 67776fe..1eeae8c 100644
--- a/man/ba_markerprofiles_details.Rd
+++ b/man/ba_markerprofiles_details.Rd
@@ -55,6 +55,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_markerprofiles_search.Rd b/man/ba_markerprofiles_search.Rd
index 6ccd04e..8e8c061 100644
--- a/man/ba_markerprofiles_search.Rd
+++ b/man/ba_markerprofiles_search.Rd
@@ -55,6 +55,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_markers_details.Rd b/man/ba_markers_details.Rd
index bb744cb..baab631 100644
--- a/man/ba_markers_details.Rd
+++ b/man/ba_markers_details.Rd
@@ -40,6 +40,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_markers_search.Rd b/man/ba_markers_search.Rd
index c9e1d8f..0ac1ccc 100644
--- a/man/ba_markers_search.Rd
+++ b/man/ba_markers_search.Rd
@@ -52,6 +52,7 @@ Other genotyping: \code{\link{ba_genomemaps_data_range}},
   \code{\link{ba_genomemaps_data}},
   \code{\link{ba_genomemaps_details}},
   \code{\link{ba_genomemaps}},
+  \code{\link{ba_germplasm_attributes}},
   \code{\link{ba_germplasm_markerprofiles}},
   \code{\link{ba_germplasm_search}},
   \code{\link{ba_germplasmattributes_categories}},
diff --git a/man/ba_studies_table.Rd b/man/ba_studies_table.Rd
index fe3214d..0aa4404 100644
--- a/man/ba_studies_table.Rd
+++ b/man/ba_studies_table.Rd
@@ -4,7 +4,7 @@
 \alias{ba_studies_table}
 \title{ba_studies_table}
 \usage{
-ba_studies_table(con = NULL, studyDbId = "", format = "json",
+ba_studies_table(con = NULL, studyDbId = "", format = "csv",
   rclass = "tibble")
 }
 \arguments{
@@ -12,7 +12,7 @@ ba_studies_table(con = NULL, studyDbId = "", format = "json",
 
 \item{studyDbId}{character; default: ''}
 
-\item{format}{character; one of: json, csv, tsv. Default: json}
+\item{format}{character; one of: json, csv, tsv. Default: csv}
 
 \item{rclass}{character; default: "tibble" possible other values: "json"/"list"/"data.frame"}
 }
diff --git a/tests/testthat/test_sp_germplasm_attributes.R b/tests/testthat/test_sp_germplasm_attributes.R
new file mode 100644
index 0000000..7b48c1d
--- /dev/null
+++ b/tests/testthat/test_sp_germplasm_attributes.R
@@ -0,0 +1,24 @@
+context("sp germplasm_attributes")
+
+con <- ba_db()$sweetpotatobase
+
+test_that(" are present", {
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "103412")
+  expect_that(nrow(res) >= 2, is_true())
+
+})
+
+test_that("  out formats work", {
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "103412", rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "103412", rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "103412", rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_germplasm_markerprofiles.R b/tests/testthat/test_sp_germplasm_markerprofiles.R
new file mode 100644
index 0000000..29626ff
--- /dev/null
+++ b/tests/testthat/test_sp_germplasm_markerprofiles.R
@@ -0,0 +1,27 @@
+context("sp germplasm_markerprofiles")
+
+con <- ba_db()$sweetpotatobase
+
+test_that(" are present", {
+
+
+    res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "103412")
+    expect_true(nrow(res) == 1)
+
+
+
+})
+
+test_that(" out formats work", {
+
+  res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "103412", rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "103412", rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "103412", rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_germplasm_pedigree.R b/tests/testthat/test_sp_germplasm_pedigree.R
new file mode 100644
index 0000000..289bd8b
--- /dev/null
+++ b/tests/testthat/test_sp_germplasm_pedigree.R
@@ -0,0 +1,25 @@
+context("sp germplasm_pedigree")
+
+con <- ba_db()$sweetpotatobase
+
+test_that("Germplasm_pedigree results are present", {
+
+  res <- ba_germplasm_pedigree(con = con, germplasmDbId = "103412")
+  expect_that(nrow(res) >= 1, is_true())
+  expect_that(ncol(res) >= 7, is_true())
+
+})
+
+test_that("out formats work", {
+
+  res <- ba_germplasm_pedigree(con = con, germplasmDbId = "103412", rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasm_pedigree(con = con, germplasmDbId = "103412", rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasm_pedigree(con = con, germplasmDbId = "103412", rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_germplasmattributes.R b/tests/testthat/test_sp_germplasmattributes.R
new file mode 100644
index 0000000..29a8a13
--- /dev/null
+++ b/tests/testthat/test_sp_germplasmattributes.R
@@ -0,0 +1,23 @@
+context("sp germplasmattributes")
+
+con <- ba_db()$sweetpotatobase
+
+test_that("  are present", {
+
+  res <- ba_germplasmattributes(con = con)
+  expect_that(nrow(res) >= 7, is_true())
+
+})
+
+test_that("  out formats work", {
+
+  res <- ba_germplasmattributes(con = con, rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasmattributes(con = con, rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasmattributes(con = con, rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
diff --git a/tests/testthat/test_sp_germplasmattributes_categories.R b/tests/testthat/test_sp_germplasmattributes_categories.R
new file mode 100644
index 0000000..01ae155
--- /dev/null
+++ b/tests/testthat/test_sp_germplasmattributes_categories.R
@@ -0,0 +1,11 @@
+context("sp germplasmattributes_categories")
+
+con <- ba_db()$sweetpotatobase
+
+test_that(" are present", {
+
+  res <- ba_germplasmattributes_categories(con = con)
+  expect_that(nrow(res) >= 1, is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_markerprofiles_details.R b/tests/testthat/test_sp_markerprofiles_details.R
new file mode 100644
index 0000000..1dce0cd
--- /dev/null
+++ b/tests/testthat/test_sp_markerprofiles_details.R
@@ -0,0 +1,12 @@
+context("sp markerprofiles_details")
+
+con <- ba_db()$sweetpotatobase
+
+test_that("  are present", {
+
+
+  res <- ba_markerprofiles_details(con = con, markerprofilesDbId = "1" )
+  expect_that(nrow(res) == 0, is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_markerprofiles_search.R b/tests/testthat/test_sp_markerprofiles_search.R
new file mode 100644
index 0000000..024d748
--- /dev/null
+++ b/tests/testthat/test_sp_markerprofiles_search.R
@@ -0,0 +1,11 @@
+context("ts markerprofiles_search")
+
+con <- ba_db()$sweetpotatobase
+
+test_that("Calls are present", {
+
+  res <- ba_markerprofiles_search(con = con)
+  expect_that(nrow(res) >= 0, is_true())
+
+})
+
diff --git a/tests/testthat/test_sp_studies_table.R b/tests/testthat/test_sp_studies_table.R
new file mode 100644
index 0000000..f0d3214
--- /dev/null
+++ b/tests/testthat/test_sp_studies_table.R
@@ -0,0 +1,41 @@
+context("sp studies_table")
+
+# Brapi test server does not return correct header row, so using sweetpotatobase for the moment!
+con <- ba_db()$sweetpotatobase
+
+test_that("Studies_table are present", {
+
+  res <- ba_studies_table(con = con, studyDbId = "148", format = 'csv')
+  expect_that(nrow(res) >= 8, is_true())
+
+})
+
+
+test_that("Studies_table are presented as json", {
+
+  res <- ba_studies_table(con = con, studyDbId = "148", format = 'csv', rclass = "json")
+  expect_that("json" %in%  class(res), is_true())
+
+})
+
+test_that("Studies_table are presented as data.frame", {
+
+  res <- ba_studies_table(con = con, studyDbId = "148", format = 'csv', rclass = "data.frame")
+  expect_that("data.frame" %in%  class(res), is_true())
+
+})
+
+
+test_that("Studies_table are requested as csv", {
+
+  res <- ba_studies_table(con = con, studyDbId = "148", format = "csv")
+  expect_that(nrow(res) >= 8, is_true())
+
+})
+
+test_that("Studies_table are requested as tsv", {
+
+  res <- ba_studies_table(con = con, studyDbId = "148", format = "tsv")
+  expect_that(nrow(res) >= 8, is_true())
+
+})
diff --git a/tests/testthat/test_ts_germplasm_attributes.R b/tests/testthat/test_ts_germplasm_attributes.R
new file mode 100644
index 0000000..e553782
--- /dev/null
+++ b/tests/testthat/test_ts_germplasm_attributes.R
@@ -0,0 +1,24 @@
+context("ts germplasm_attributes")
+
+con <- ba_db()$testserver
+
+test_that(" are present", {
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = '1')
+  expect_that(nrow(res) == 10, is_true())
+
+})
+
+test_that("  out formats work", {
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "1", rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "1", rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasm_attributes(con = con, germplasmDbId = "1", rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
+
diff --git a/tests/testthat/test_ts_germplasm_markerprofiles.R b/tests/testthat/test_ts_germplasm_markerprofiles.R
index cb00d56..667992e 100644
--- a/tests/testthat/test_ts_germplasm_markerprofiles.R
+++ b/tests/testthat/test_ts_germplasm_markerprofiles.R
@@ -20,8 +20,5 @@ test_that(" out formats work", {
   res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "1", rclass = "data.frame")
   expect_that("data.frame" %in% class(res), is_true())
 
-  res <- ba_germplasm_markerprofiles(con = con, germplasmDbId = "1", rclass = "vector")
-  expect_that("character" %in% class(res), is_true())
-
 })
 
diff --git a/tests/testthat/test_ts_germplasm_pedigree.R b/tests/testthat/test_ts_germplasm_pedigree.R
index 0655c98..b6dc81d 100644
--- a/tests/testthat/test_ts_germplasm_pedigree.R
+++ b/tests/testthat/test_ts_germplasm_pedigree.R
@@ -1,4 +1,4 @@
-context("germplasm_pedigree")
+context("ts germplasm_pedigree")
 
 con <- ba_db()$testserver
 
diff --git a/tests/testthat/test_ts_germplasm_search.R b/tests/testthat/test_ts_germplasm_search.R
index 5fb0a01..50e6d46 100644
--- a/tests/testthat/test_ts_germplasm_search.R
+++ b/tests/testthat/test_ts_germplasm_search.R
@@ -1,4 +1,4 @@
-context("germplasm_search")
+context("ts germplasm_search")
 
 con <- ba_db()$testserver
 
diff --git a/tests/testthat/test_ts_germplasmattributes.R b/tests/testthat/test_ts_germplasmattributes.R
index 0682753..3514f32 100644
--- a/tests/testthat/test_ts_germplasmattributes.R
+++ b/tests/testthat/test_ts_germplasmattributes.R
@@ -1,11 +1,23 @@
-context("germplasmattributes")
+context("ts germplasmattributes")
 
 con <- ba_db()$testserver
 
-test_that(" are present", {
+test_that("  are present", {
 
   res <- ba_germplasmattributes(con = con)
   expect_that(nrow(res) == 10, is_true())
 
 })
 
+test_that("  out formats work", {
+
+  res <- ba_germplasmattributes(con = con, rclass = "json")
+  expect_that("json" %in% class(res), is_true())
+
+  res <- ba_germplasmattributes(con = con, rclass = "list")
+  expect_that("list" %in% class(res), is_true())
+
+  res <- ba_germplasmattributes(con = con, rclass = "data.frame")
+  expect_that("data.frame" %in% class(res), is_true())
+
+})
diff --git a/tests/testthat/test_ts_germplasmattributes_categories.R b/tests/testthat/test_ts_germplasmattributes_categories.R
index f98723e..f3bb283 100644
--- a/tests/testthat/test_ts_germplasmattributes_categories.R
+++ b/tests/testthat/test_ts_germplasmattributes_categories.R
@@ -1,8 +1,8 @@
-context("germplasmattributes_categories")
+context("ts germplasmattributes_categories")
 
 con <- ba_db()$testserver
 
-test_that("Studies_details are present", {
+test_that(" are present", {
 
   res <- ba_germplasmattributes_categories(con = con)
   expect_that(nrow(res) == 4, is_true())
diff --git a/tests/testthat/test_ts_germplasmattributes_details.R b/tests/testthat/test_ts_germplasmattributes_details.R
deleted file mode 100644
index eba800c..0000000
--- a/tests/testthat/test_ts_germplasmattributes_details.R
+++ /dev/null
@@ -1,23 +0,0 @@
-context("germplasmattributes_details")
-
-con <- ba_db()$testserver
-
-test_that("  are present", {
-
-  res <- ba_germplasmattributes_details(con = con, germplasmDbId = "1" )
-  expect_that(nrow(res) == 10, is_true())
-
-})
-
-test_that("  out formats work", {
-
-  res <- ba_germplasmattributes_details(con = con, germplasmDbId = "1", rclass = "json")
-  expect_that("json" %in% class(res), is_true())
-
-  res <- ba_germplasmattributes_details(con = con, germplasmDbId = "1", rclass = "list")
-  expect_that("list" %in% class(res), is_true())
-
-  res <- ba_germplasmattributes_details(con = con, germplasmDbId = "1", rclass = "data.frame")
-  expect_that("data.frame" %in% class(res), is_true())
-
-})
diff --git a/tests/testthat/test_ts_markerprofiles_details.R b/tests/testthat/test_ts_markerprofiles_details.R
index eb22ee4..1956ce8 100644
--- a/tests/testthat/test_ts_markerprofiles_details.R
+++ b/tests/testthat/test_ts_markerprofiles_details.R
@@ -1,4 +1,4 @@
-context("markerprofiles_details")
+context("ts markerprofiles_details")
 
 con <- ba_db()$testserver
 
diff --git a/tests/testthat/test_ts_markerprofiles_search.R b/tests/testthat/test_ts_markerprofiles_search.R
index d39e42c..943199d 100644
--- a/tests/testthat/test_ts_markerprofiles_search.R
+++ b/tests/testthat/test_ts_markerprofiles_search.R
@@ -1,4 +1,4 @@
-context("markerprofiles_search")
+context("ts markerprofiles_search")
 
 con <- ba_db()$testserver
 
diff --git a/tests/testthat/test_ts_studies_seasons.R b/tests/testthat/test_ts_studies_seasons.R
index 7727d79..125bf86 100644
--- a/tests/testthat/test_ts_studies_seasons.R
+++ b/tests/testthat/test_ts_studies_seasons.R
@@ -1,4 +1,4 @@
-context("studies_seasons")
+context("ts studies_seasons")
 
 con <- ba_db()$testserver
 
diff --git a/tests/testthat/test_ts_studies_table.R b/tests/testthat/test_ts_studies_table.R
index 08391e7..9070522 100644
--- a/tests/testthat/test_ts_studies_table.R
+++ b/tests/testthat/test_ts_studies_table.R
@@ -1,41 +1,42 @@
-context("studies_table")
+context("ts studies_table")
 
 # Brapi test server does not return correct header row, so using sweetpotatobase for the moment!
-con <- ba_db()$sweetpotatobase
+con <- ba_db()$testserver
 
 test_that("Studies_table are present", {
 
-  res <- ba_studies_table(con = con, studyDbId = "148")
-  expect_that(nrow(res) >= 8, is_true())
+  expect_error({
+    res <- ba_studies_table(con = con, studyDbId = "1001")
+  })
 
 })
 
 
-test_that("Studies_table are presented as json", {
-
-  res <- ba_studies_table(con = con, studyDbId = "148", rclass = "json")
-  expect_that("json" %in%  class(res), is_true())
-
-})
-
-test_that("Studies_table are presented as data.frame", {
-
-  res <- ba_studies_table(con = con, studyDbId = "148", rclass = "data.frame")
-  expect_that("data.frame" %in%  class(res), is_true())
-
-})
-
-
-test_that("Studies_table are requested as csv", {
-
-  res <- ba_studies_table(con = con, studyDbId = "148", format = "csv")
-  expect_that(nrow(res) >= 8, is_true())
-
-})
-
-test_that("Studies_table are requested as tsv", {
-
-  res <- ba_studies_table(con = con, studyDbId = "148", format = "tsv")
-  expect_that(nrow(res) >= 8, is_true())
-
-})
+# test_that("Studies_table are presented as json", {
+#
+#   res <- ba_studies_table(con = con, studyDbId = "148", rclass = "json")
+#   expect_that("json" %in%  class(res), is_true())
+#
+# })
+#
+# test_that("Studies_table are presented as data.frame", {
+#
+#   res <- ba_studies_table(con = con, studyDbId = "148", rclass = "data.frame")
+#   expect_that("data.frame" %in%  class(res), is_true())
+#
+# })
+#
+#
+# test_that("Studies_table are requested as csv", {
+#
+#   res <- ba_studies_table(con = con, studyDbId = "148", format = "csv")
+#   expect_that(nrow(res) >= 8, is_true())
+#
+# })
+#
+# test_that("Studies_table are requested as tsv", {
+#
+#   res <- ba_studies_table(con = con, studyDbId = "148", format = "tsv")
+#   expect_that(nrow(res) >= 8, is_true())
+#
+# })