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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| check_bioc_version <- function(bioc){ | ||
|
|
||
| opts <- bioc_r_versions(return_opts = TRUE) | ||
| bioc <- tolower(as.character(bioc)) | ||
| if(bioc %in% c("release_*", | ||
| "release*", | ||
| "release")){ | ||
| bioc <- "release" | ||
| } else { | ||
| bioc <- gsub("_",".",gsub("RELEASE_","",bioc, ignore.case = TRUE)) | ||
| } | ||
| if(!bioc %in% opts){ | ||
| stopper(paste0("bioc=",shQuote(bioc)), | ||
| "bioc version must be one of:", | ||
| paste("\n -",shQuote(opts),collapse = "")) | ||
| } else { | ||
| return(bioc) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,44 @@ | ||
| #' Check containers exist | ||
| #' | ||
| #' Check that a list of containers are valid. | ||
| #' @inheritParams construct_runners | ||
| #' @param domain Container repository API domain. | ||
| #' @returns NUll | ||
| #' | ||
| #' @keywords internal | ||
| check_cont <- function(cont, | ||
| domain = "https://hub.docker.com/v2/repositories/", | ||
| verbose = TRUE){ | ||
|
|
||
| requireNamespace("jsonlite") | ||
| for(co in cont){ | ||
| if(is.null(co)) next() | ||
| if(isFALSE(grepl("/",co))){ | ||
| stopper("Container must be specificied in the following format:", | ||
| "'owner/repo:tag'") | ||
| } | ||
| splt <- strsplit(co,":")[[1]] | ||
| URL <- paste(domain, splt[1], | ||
| "tags?page_size=1000",sep="/" | ||
| ) | ||
| #### Check repo exists #### | ||
| messager("Checking public container repository exists:",shQuote(splt[1]), | ||
| v=verbose) | ||
| js <- tryCatch({ | ||
| jsonlite::read_json(URL) | ||
| }, error=function(e){ | ||
| stopper("Unable to find public container:",co) | ||
| } | ||
| ) | ||
| #### Check tag exists #### | ||
| if(length(splt)==2){ | ||
| messager("Checking tag exists:",shQuote(splt[2]), | ||
| v=verbose) | ||
| tags <- sapply(js$results ,function(x){x$name}) | ||
| if(!splt[2] %in% tags){ | ||
| stopper("The tag", shQuote(splt[2]), | ||
| "does not exist in the repo",shQuote(splt[1])) | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,67 @@ | ||
| #' Construct containers list | ||
| #' | ||
| #' @param run_check_cont Check whether the requested container repo | ||
| #' (and the tag, if specified) exist using \link[rworkflows]{check_cont}. | ||
| #' @param default_cont The DockerHub container to default to. | ||
| #' Used when it's detected that only the tag has been given in one or more | ||
| #' \code{cont} entry. | ||
| #' @param default_tag The DockerHub container tag to default to. | ||
| #' @inheritParams construct_runners | ||
| #' @returns Named list of containers | ||
| #' | ||
| #' @export | ||
| #' @importFrom stats setNames | ||
| #' @examples | ||
| #' cont <- construct_cont() | ||
| construct_cont <- function(default_cont = "bioconductor/bioconductor_docker", | ||
| default_tag = "devel", | ||
| cont = list( | ||
| paste(default_cont,default_tag,sep=":"), | ||
| NULL, | ||
| NULL), | ||
| versions_explicit = FALSE, | ||
| run_check_cont = FALSE, | ||
| verbose = TRUE){ | ||
| # devoptera::args2vars(construct_cont) | ||
|
|
||
| #### Remove any trailing : (e.g. when default_tag=NULL) #### | ||
| cont <- lapply(cont, function(x){ | ||
| if(is.null(x)) NULL else trimws(x,whitespace = ":") | ||
| }) | ||
| #### Run QC #### | ||
| cont2 <- lapply(cont,function(co){ | ||
| if(is.null(co)){ | ||
| return(NULL) | ||
| } else if(!grepl("/",co) && | ||
| !is.null(default_cont)){ | ||
| messager("Only tag name supplied to 'cont'.", | ||
| "Assuming default=",shQuote(default_cont),v=verbose) | ||
| co <- paste(default_cont,co,sep=":") | ||
| } else if(!grepl(":",co) | | ||
| !grepl(default_cont,co)) { | ||
| return(co) | ||
| } | ||
| splt <- strsplit(co,":")[[1]] | ||
| bioc_version <- rev(splt)[1] | ||
| if(isTRUE(versions_explicit)){ | ||
| if(grepl(":",co)){ | ||
| info <- bioc_r_versions(bioc_version = bioc_version) | ||
| return( | ||
| paste0(splt[[1]],":RELEASE_",gsub("[.]","_",info$bioc)) | ||
| ) | ||
| } else { | ||
| return(co) | ||
| } | ||
| } else if(tolower(bioc_version)=="release"){ | ||
| co <- gsub(":release",":latest",co, ignore.case = TRUE) | ||
| } | ||
| return(co) | ||
| }) | ||
| #### Check that the Dockerhub repo exists #### | ||
| if(isTRUE(run_check_cont)){ | ||
| check_cont(cont = cont, | ||
| verbose = verbose) | ||
| } | ||
| #### Return #### | ||
| return(cont2) | ||
| } |
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