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Make .query_sysreqs_bioc testable #91

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merged 3 commits into from
Feb 26, 2023
Merged

Make .query_sysreqs_bioc testable #91

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b74107d
Make .query_sysreqs_bioc testable
chainsawriot Feb 26, 2023
af96e40
Reduce locs and improve tests
chainsawriot Feb 26, 2023
a4c4135
Add tests
chainsawriot Feb 26, 2023
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14 changes: 11 additions & 3 deletions R/resolve.R
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Original file line number Diff line number Diff line change
Expand Up @@ -475,13 +475,18 @@ query_sysreqs <- function(rang, os = "ubuntu-20.04") {
}
pkgs <- .memo_search_bioc(bioc_version = "release")
raw_sys_reqs <- pkgs$SystemRequirements[pkgs$Package %in% handles]
baseurl <- "https://sysreqs.r-hub.io/map/"
singleline_sysreqs <- paste0(raw_sys_reqs[!is.na(raw_sys_reqs)], collapse = ", ")
singleline_sysreqs <- gsub("\\n", " ", singleline_sysreqs)
.query_singleline_sysreqs(singleline_sysreqs = singleline_sysreqs, arch = arch)
}

.query_singleline_sysreqs <- function(singleline_sysreqs, arch = "DEB") {
baseurl <- "https://sysreqs.r-hub.io/map/"
url <- utils::URLencode(paste0(baseurl, singleline_sysreqs))
checkable_cmds <- vapply(jsonlite::read_json(url), .extract_sys_package, character(1), arch = arch)
query_res <- jsonlite::read_json(url)
checkable_cmds <- vapply(query_res, .extract_sys_package, character(1), arch = arch)
uncheckable_cmds <- .extract_uncheckable_sysreqs(singleline_sysreqs, arch = arch)
return(c(checkable_cmds, uncheckable_cmds))
c(checkable_cmds[!is.na(checkable_cmds)], uncheckable_cmds)
}

## Not everything can be check from sysreqs DB, especially Bioc packages
Expand All @@ -506,6 +511,9 @@ query_sysreqs <- function(rang, os = "ubuntu-20.04") {
} else {
sys_pkg <- output[["buildtime"]]
}
if (is.null(sys_pkg)) {
return(NA_character_)
}
if (arch == "DEB") {
return(paste0("apt-get install -y ", sys_pkg))
}
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Binary file added tests/testdata/sysreqs_gmp.RDS
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10 changes: 10 additions & 0 deletions tests/testthat/test_resolve.R
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Expand Up @@ -225,10 +225,20 @@ test_that(".query_sysreqs_bioc with uncheckable info", {
expect_true("apt-get install -y libbz2-dev" %in% x) ## uncheckable
expect_true("apt-get install -y liblzma-dev" %in% x)
expect_true("apt-get install -y make" %in% x) ## checkable
expect_false("apt-get install -y" %in% x) ## the null response from C++
x <- .query_sysreqs_bioc("Rhtslib", "centos-7")
expect_true("yum install -y libbz2-devel" %in% x)
expect_true("yum install -y xz-devel" %in% x)
expect_true("yum install -y make" %in% x)
expect_false("yum install -y" %in% x) ## the null response from C++
x <- .query_singleline_sysreqs("libxml2", "DEB")
expect_equal(x, "apt-get install -y libxml2-dev")
x <- .query_singleline_sysreqs("C++", "DEB")
expect_equal(x, character(0))
x <- readRDS("../testdata/sysreqs_gmp.RDS")
## buildtime / runtime requirements
expect_equal(.extract_sys_package(x[[1]], arch = "DEB"),
"apt-get install -y libgmp-dev")
})

test_that("issue 89", {
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