fixing brapi con replacement of argument in functions

R/ba_locations.R

@@ -26,7 +26,7 @@ ba_locations <- function(con = NULL,
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
   # fetch the url of the brapi implementation of the database
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # generate the brapi call specific url
   # locations_list <- paste0(brp, "locations/?") # TO BE CONSIDERED FOR VERSION 2
   locations_list <- paste0(brp, "locations?")

R/ba_markerprofiles_allelematrix_search.R

@@ -51,7 +51,7 @@ ba_markerprofiles_allelematrix_search <- function(con = NULL,
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
   # fetch the url of the brapi implementation of the database
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # generate the brapi call specific url
   pallelematrix_search <- paste0(brp, "allelematrix-search/?")
   pmarkerprofileDbId <- paste0("markerprofileDbId=", markerprofileDbId, "&") %>% paste(collapse = "")

R/ba_markerprofiles_details.R

@@ -39,7 +39,7 @@ ba_markerprofiles_details <- function(con = NULL,
   stopifnot(is.character(sepUnphased))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   markerprofiles_alleles <- paste0(brp, "markerprofiles/", markerprofilesDbId, "/?")
   expandHomozygotes <- ifelse(expandHomozygotes != "", paste0("expandHomozygotes=", expandHomozygotes, "&"), "")
   sepPhased <- ifelse(sepPhased != "", paste0("sepPhased=", sepPhased, "&"), "")

R/ba_markerprofiles_search.R

@@ -39,7 +39,7 @@ ba_markerprofiles_search <- function(con = NULL,
   stopifnot(is.character(methodDbId))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   pmarkerprofiles <- paste0(brp, "markerprofiles/?")
   pgermplasmDbId <- paste0("germplasm=", germplasmDbId, "&") %>% paste(collapse = "")
   pextractDbId <- paste0("extract=", extractDbId, "&") %>% paste(collapse = "")

R/ba_markers_details.R

@@ -23,7 +23,7 @@ ba_markers_details <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "markers/id")
   stopifnot(is.character(markerDbId))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   markers <- paste0(brp, "markers/", markerDbId)
   try({
     res <- brapiGET(url = markers, con = con)

R/ba_markers_search.R

@@ -37,7 +37,7 @@ ba_markers_search <- function(con = NULL,
   stopifnot(include == "synonyms")
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   marker_search <- paste0(brp, "markers/?")
   page <- ifelse(is.numeric(page), paste0("page=", page, "&"), "")
   pageSize <- ifelse(is.numeric(pageSize), paste0("pageSize=", pageSize, "&"), "")

R/ba_observationvariables.R

@@ -26,7 +26,7 @@ ba_observationvariables <- function(con = NULL,
   stopifnot(is.character(traitClass))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   brapi_variables <- paste0(brp, "variables/?")
   ptraitClass <- paste0("traitClass=", traitClass, "&")
   ppage <- paste0("page=", page, "")

R/ba_observationvariables_datatypes.R

@@ -17,7 +17,7 @@ ba_observationvariables_datatypes <- function(con = NULL,
                                               rclass = "tibble") {
   ba_check(con = con, verbose = FALSE, brapi_calls = "variables/datatypes")
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   variables_datatypes_list <- paste0(brp, "variables/datatypes/")
   try({
     res <- brapiGET(url = variables_datatypes_list, con = con)

R/ba_observationvariables_details.R

@@ -20,7 +20,7 @@ ba_observationvariables_details <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "variables/id")
   stopifnot(is.character(observationVariableDbId))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   brapi_variables_details <- paste0(brp, "variables/", observationVariableDbId)
   try({
     res <- brapiGET(url = brapi_variables_details, con = con)

R/ba_observationvariables_ontologies.R

@@ -21,7 +21,7 @@ ba_observationvariables_ontologies <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "ontologies")
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   variables_ontologies <- paste0(brp, "ontologies/?")
   ppage <- paste0("page=", page, "")
   ppageSize <- paste0("pageSize=", pageSize, "&")

R/ba_observationvariables_search.R

@@ -41,7 +41,7 @@ ba_observationvariables_search <- function(con = NULL,
     stopifnot(is.character(datatypes))
     stopifnot(is.character(traitClasses))
     check_rclass(rclass = rclass)
-    brp <- get_brapi(brapi = con)
+    brp <- get_brapi(con = con)
     pvariables <- paste0(brp, "variables-search/")
     try({
       res <- brapiPOST(pvariables, body, con = con)

R/ba_phenotypes_search.R

@@ -43,7 +43,7 @@ ba_phenotypes_search <- function(con = NULL,
   stopifnot(is.character(observationLevel))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   pvariables <- paste0(brp, "phenotypes-search/")
   try({
     body <- list(germplasmDbIds = germplasmDbIds,

R/ba_programs.R

@@ -29,7 +29,7 @@ ba_programs <- function(con = NULL,
   stopifnot(is.character(abbreviation))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # pprograms <- paste0(brp, "programs/?") # TO BE CONSIDERED v2
   pprograms <- paste0(brp, "programs?")
   pprogramName <- ifelse(programName != "any", paste0("programName=", gsub(" ", "%20", programName), "&"), "")

R/ba_programs_search.R

@@ -33,7 +33,7 @@ ba_programs_search <- function(con = NULL,
   stopifnot(is.character(leadPerson))
   check_rclass(rclass)
   # fetch url of the brapi implementation of the database
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # generate specific brapi call url
   pprograms <- paste0(brp, "programs-search/")
   try({

R/ba_samples.R

@@ -20,7 +20,7 @@ ba_samples <- function(con = NULL,
   stopifnot(is.character(sampleId))
   stopifnot(sampleId != "")
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   call_samples <- paste0(brp, "samples/", sampleId)
   tryCatch({
     res <- brapiGET(url = call_samples, con = con)

R/ba_samples_save.R

@@ -16,7 +16,7 @@ ba_samples_save <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "samples")
   stopifnot(is.list(sampleData))
   stopifnot(all(c("plotId", "plantId", "takenBy", "sampleDate", "sampleType", "tissueType", "notes") %in% names(sampleData)))
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   call_samples <- paste0(brp, "samples/")
   try({
     res <- brapiPUT(url = call_samples, body = sampleData, con = con)

R/ba_studies_details.R

@@ -20,7 +20,7 @@ ba_studies_details <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "studies/id")
   stopifnot(is.character(studiesDbId))
   check_rclass(rclass = rclass)
-  studies <- paste0(get_brapi(brapi = con), "studies/", studiesDbId, "/")
+  studies <- paste0(get_brapi(con = con), "studies/", studiesDbId, "/")
   try({
     res <- brapiGET(url = studies, con = con)
     out <- NULL

R/ba_studies_layout.R

@@ -20,7 +20,7 @@ ba_studies_layout <- function(con = NULL,
   ba_check(con = con, verbose =  FALSE, brapi_calls = "studies/id/layout")
   stopifnot(is.character(studyDbId))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   studies_layout_list <- paste0(brp, "studies/", studyDbId, "/layout/")
   try({
     res <- brapiGET(url = studies_layout_list, con = con)

R/ba_studies_observationVariables.R

@@ -20,7 +20,7 @@ ba_studies_observationvariables <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "studies/id/observationVariables")
   stopifnot(is.character(studyDbId))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   studies_observationVariables_list <- paste0(brp, "studies/", studyDbId, "/observationVariables/?")
   try({
     res <- brapiGET(url = studies_observationVariables_list, con = con)

R/ba_studies_observationlevels.R

@@ -19,7 +19,7 @@ ba_studies_observationlevels <- function(con = NULL,
                                          rclass = "vector") {
   ba_check(con = con, verbose = FALSE, brapi_calls = "observationLevels")
   check_rclass(rclass = rclass)
-  observationLevels_List <- paste0(get_brapi(brapi = con), "observationLevels")
+  observationLevels_List <- paste0(get_brapi(con = con), "observationLevels")
   try({
     res <- brapiGET(url = observationLevels_List, con = con)
     res <- httr::content(x = res, as = "text", encoding = "UTF-8")

R/ba_studies_observations.R

@@ -28,7 +28,7 @@ ba_studies_observations <- function(con = NULL,
   stopifnot(is.character(observationVariableDbId))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   studies_observations_list <- paste0(brp, "studies/", studyDbId, "/observations/?")
   observationVariableDbId <- paste0("observationVariableDbIds=", paste(observationVariableDbId, collapse = ","), "&")
   page <- ifelse(is.numeric(page), paste0("page=", page), "")

R/ba_studies_observationunits.R

@@ -23,7 +23,7 @@ ba_studies_observationunits <- function(con = NULL,
   stopifnot(is.character(studyDbId))
   stopifnot(observationLevel %in% c("plot", "plant"))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   studies_observationunits_list <- paste0(brp, "studies/", studyDbId, "/observationunits/?")
   observationLevel <- ifelse(observationLevel == "plant", "observationLevel=plant", "observationLevel=plot")
   studies_observationunits_list <- paste0(studies_observationunits_list, observationLevel)

R/ba_studies_observationunits_save.R

@@ -55,7 +55,7 @@ ba_studies_observationunits_save <- function(con = NULL,
               result = list(transactionDbId = transactionDbId,
                             commit = tolower(as.character(commit)),
                             data = obs))
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   call_samples <- paste0(brp, "studies/", studyDbId, "/observationunits?observationLevel=", observationLevel)
   try({
     brapiPOST(url = call_samples, body = dat, con = con)

R/ba_studies_search.R

@@ -37,7 +37,7 @@ ba_studies_search <- function(con = NULL,
                               pageSize = 1000,
                               rclass = "tibble") {
   ba_check(con = con, verbose = FALSE, brapi_calls = "studies-search")
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   stopifnot(is.character(studyType))
   stopifnot(is.character(programDbId))
   stopifnot(is.character(locationDbId))

R/ba_studies_seasons.R

@@ -21,7 +21,7 @@ ba_studies_seasons <- function(con = NULL,
                                pageSize = 1000,
                                rclass = "tibble") {
   ba_check(con = con, verbose = FALSE, brapi_calls = "seasons")
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   stopifnot(is.numeric(year))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)

R/ba_studies_studytypes.R

@@ -22,7 +22,7 @@ ba_studies_studytypes <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "studyTypes")
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   pstudyTypes <- paste0(brp, "studyTypes/?")
   page <- ifelse(is.numeric(page), paste0("page=", page, "&"), "")
   pageSize <- ifelse(is.numeric(pageSize), paste0("pageSize=", pageSize, "&"), "")

R/ba_studies_table.R

@@ -25,7 +25,7 @@ ba_studies_table <- function(con = NULL,
   stopifnot(is.character(studyDbId))
   stopifnot(format %in% c("json", "tsv", "csv"))
   check_rclass(rclass =  rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # studies_table <- paste0(brp, "studies/", studyDbId, "/table/?") # TO BE CONSIDERED FOR VERSION 2
   studies_table <- paste0(brp, "studies/", studyDbId, "/table?")
   if (rclass %in% c("data.frame", "tibble") & format == "json") {

R/ba_studies_table_save.R

@@ -20,7 +20,7 @@ ba_studies_table_save <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "studies/id/table")
   stopifnot(is.character(studyDbId))
   stopifnot(is.data.frame(study_table))
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   studies_table <- paste0(brp, "studies/", studyDbId, "/table/")
   try({
     metadata <- list(pagination = list(pageSize = 0, currentPage = 0, totalCount = 0, totalPages = 0),

R/ba_traits.R

@@ -21,7 +21,7 @@ ba_traits <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "traits")
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   traits <- paste0(brp, "traits/?")
   ppage <- paste0("page=", page, "")
   ppageSize <- paste0("pageSize=", pageSize, "&")

R/ba_traits_details.R

@@ -19,7 +19,7 @@ ba_traits_details <- function(con = NULL,
   ba_check(con = con, verbose = FALSE, brapi_calls = "traits")
   stopifnot(is.character(traitDbId))
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   traits <- paste0(brp, "traits/", traitDbId)
   try({
     res <- brapiGET(url = traits, con = con)

R/ba_trials.R

@@ -37,7 +37,7 @@ ba_trials <- function(con = NULL,
   stopifnot(is.character(sortOrder))
   check_paging(pageSize = pageSize, page = page)
   check_rclass(rclass = rclass)
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   # ptrials <- paste0(brp, "trials/?") # TO BE CONSIDERED FOR VERSION 2
   ptrials <- paste0(brp, "trials?")
   pprogramDbId <- ifelse(programDbId != "any", paste0("programDbId=", programDbId, "&"), "")

R/ba_trials_details.R

@@ -18,7 +18,7 @@ ba_trials_details <- function(con = NULL,
                               trialDbId = "any",
                               rclass = "tibble") {
   ba_check(con = con, verbose = FALSE, brapi_calls = "trials/id")
-  brp <- get_brapi(brapi = con)
+  brp <- get_brapi(con = con)
   stopifnot(is.character(trialDbId))
   check_rclass(rclass = rclass)
   ptrials <- paste0(brp, "trials/", trialDbId)

R/zzz.R

@@ -1,9 +1,9 @@
 .onAttach <- function(libname, pkgname) {
-  library(magrittr)
-  paste("This is the development version of the 'brapi' package!\nYou are using version ",
-        utils::packageVersion("brapi"), "\n\n") %>%
-    paste("Please register any issues at: https://github.com/c5sire/brapi/issues\n") %>%
-  packageStartupMessage()
+
+  txt <- paste("This is the development version of the 'brapi' package!\nYou are using version ",
+        utils::packageVersion("brapi"), "\n\n")
+  txt <- paste(txt, "Please register any issues at: https://github.com/c5sire/brapi/issues\n")
+  packageStartupMessage(txt)
 }
 
 .onLoad <- function(libname, pkgname) {

vignettes/tutorial.R

@@ -1,5 +1,5 @@
 ## ---- message=TRUE, warning=TRUE-----------------------------------------
-#library(DT)
+
 library(brapi)
 
 white_list <- ba_db()