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Refactor dockerfile generation code #117
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@chainsawriot
chainsawriot committed Mar 20, 2023
1 parent de0f640 commit 0978db8
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Showing 2 changed files with 60 additions and 54 deletions.
59 changes: 59 additions & 0 deletions R/dockerfile.R
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Original file line number Diff line number Diff line change
@@ -0,0 +1,59 @@
## .insert_cache_dir <- function(dockerfile_content) {
## rang_line <- which(dockerfile_content == "RUN Rscript rang.R")
## c(dockerfile_content[1:(rang_line - 1)],
## "COPY cache ./cache",
## dockerfile_content[rang_line:length(dockerfile_content)])
## }

.insert_materials_dir <- function(dockerfile_content) {
dockerfile_content$COPY <- append(dockerfile_content$COPY, "COPY materials/ ./materials/")
dockerfile_content
}

.generate_debian_eol_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny") {
dockerfile_content <- list(
FROM = c(paste0("FROM debian/eol:", debian_version)),
chores = c("ENV TZ UTC",
"RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && apt-get update -qq && apt-get install wget locales build-essential r-base-dev -y"),
COPY = c("COPY rang.R ./rang.R", "COPY compile_r.sh ./compile_r.sh"),
RUN = c(paste("RUN", sysreqs_cmd)),
CMD = c("CMD [\"R\"]"))
if (!is.na(lib)) {
dockerfile_content$RUN <- append(dockerfile_content$RUN, paste0("RUN mkdir ", lib, " && bash compile_r.sh ", r_version))
} else {
dockerfile_content$RUN <- append(dockerfile_content$RUN, paste0("RUN bash compile_r.sh ", r_version))
}
if (isTRUE(cache)) {
dockerfile_content$COPY <- append(dockerfile_content$COPY,
c("COPY cache/rpkgs ./cache/rpkgs", "COPY cache/rsrc ./cache/rsrc"))
dockerfile_content$FROM <- c("FROM scratch", "ADD cache/debian/rootfs.tar.xz /")
}
return(dockerfile_content)
}

.generate_rocker_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, image) {
dockerfile_content <- list(
FROM = c(paste0("FROM rocker/", image, ":", r_version)),
chores = NULL,
COPY = c("COPY rang.R ./rang.R"),
RUN = c(paste("RUN", sysreqs_cmd)),
"CMD [\"R\"]")
if (!is.na(lib)) {
dockerfile_content$RUN <- append(dockerfile_content$RUN, paste0("RUN mkdir ", lib, " && Rscript rang.R"))
} else {
dockerfile_content$RUN <- append(dockerfile_content$RUN, "Rscript rang.R")
}
if (isTRUE(cache)) {
dockerfile_content$COPY <- append(dockerfile_content$COPY, "COPY cache ./cache")
}
if (image == "rstudio") {
dockerfile_content$RUN <- c("EXPOSE 8787", "CMD [\"/init\"]")
}
return(dockerfile_content)
}

.write_dockerfile <- function(dockerfile_content, path) {
content <- c(dockerfile_content$FROM, dockerfile_content$chores,
dockerfile_content$COPY, dockerfile_content$RUN)
writeLines(content, path)
}
55 changes: 1 addition & 54 deletions R/installation.R
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Original file line number Diff line number Diff line change
Expand Up @@ -114,59 +114,6 @@
utils::compareVersion(rang$r_version, r_version) == -1
}

.insert_cache_dir <- function(dockerfile_content) {
rang_line <- which(dockerfile_content == "RUN Rscript rang.R")
c(dockerfile_content[1:(rang_line - 1)],
"COPY cache ./cache",
dockerfile_content[rang_line:length(dockerfile_content)])
}

.insert_materials_dir <- function(dockerfile_content) {
rang_line <- which(dockerfile_content == "COPY rang.R ./rang.R")
c(dockerfile_content[1:rang_line],
"COPY materials/ ./materials/",
dockerfile_content[(rang_line + 1):length(dockerfile_content)])
}

.generate_debian_eol_dockerfile_content<- function(r_version, lib, sysreqs_cmd, cache, debian_version = "lenny") {
dockerfile_content <- c(
paste0("FROM debian/eol:", debian_version),
"ENV TZ UTC",
"RUN ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone && apt-get update -qq && apt-get install wget locales build-essential r-base-dev -y",
"COPY rang.R ./rang.R",
"COPY compile_r.sh ./compile_r.sh",
paste("RUN", sysreqs_cmd),
paste("RUN bash compile_r.sh", r_version),
"CMD [\"R\"]")
if (!is.na(lib)) {
dockerfile_content[7] <- paste0("RUN mkdir ", lib, " && bash compile_r.sh ", r_version)
}
if (isTRUE(cache)) {
dockerfile_content <- c(dockerfile_content[1:5], "COPY cache/rpkgs ./cache/rpkgs", dockerfile_content[6:8])
dockerfile_content <- append(dockerfile_content, "COPY cache/rsrc ./cache/rsrc", after = 6)
dockerfile_content[1] <- "ADD cache/debian/rootfs.tar.xz /"
dockerfile_content <- c("FROM scratch", dockerfile_content)
}
return(dockerfile_content)
}

.generate_rocker_dockerfile_content <- function(r_version, lib, sysreqs_cmd, cache, image) {
dockerfile_content <- c("", "", "COPY rang.R ./rang.R", "RUN Rscript rang.R", "CMD [\"R\"]")
if (!is.na(lib)) {
dockerfile_content[4] <- paste0("RUN mkdir ", lib, " && Rscript rang.R")
}
dockerfile_content[1] <- paste0("FROM rocker/", image, ":", r_version)
dockerfile_content[2] <- paste("RUN", sysreqs_cmd)
if (image == "rstudio") {
dockerfile_content[5] <- "EXPOSE 8787"
dockerfile_content[6] <- "CMD [\"/init\"]"
}
if (isTRUE(cache)) {
dockerfile_content <- .insert_cache_dir(dockerfile_content)
}
return(dockerfile_content)
}

.generate_docker_readme <- function(output_dir,image) {
file.create(file.path(output_dir,"README"))
con <- file(file.path(output_dir,"README"), open="w")
Expand Down Expand Up @@ -428,7 +375,7 @@ dockerize <- function(rang, output_dir, materials_dir = NULL, image = c("r-ver",
recursive = TRUE)
dockerfile_content <- .insert_materials_dir(dockerfile_content)
}
writeLines(dockerfile_content, file.path(output_dir, "Dockerfile"))
.write_dockerfile(dockerfile_content, file.path(output_dir, "Dockerfile"))
.generate_docker_readme(output_dir = output_dir,image = image)
invisible(output_dir)
}
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