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Centaur reference image test should validate symlinks [VS-796] #6996

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merged 5 commits into from
Feb 9, 2023
Merged

Centaur reference image test should validate symlinks [VS-796] #6996

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b7bb440
test for reference image symlink validity
mcovarr Feb 2, 2023
73dbae8
Update link to corrected Nirvana image
mcovarr Feb 2, 2023
222c3f3
assert for metachar Nirvana files too
mcovarr Feb 2, 2023
0255fde
boop
mcovarr Feb 2, 2023
50b7821
Trigger CI
jgainerdewar Feb 8, 2023
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48 changes: 30 additions & 18 deletions centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.wdl
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Original file line number Diff line number Diff line change
@@ -1,26 +1,38 @@
version 1.0

task check_if_localized_as_symlink {
task check_if_localized_with_valid_symlink {
input {
File broad_reference_file_input
File nirvana_reference_file_input
File nirvana_reference_file_metachar_input
}
String broad_input_symlink = "broad_input_symlink.txt"
String nirvana_input_symlink = "nirvana_input_symlink.txt"
String nirvana_metachar_input_symlink = "nirvana_metachar_input_symlink.txt"
command {
# Print true if input is a symlink, otherwise print false.
if test -h ~{broad_reference_file_input}; then echo true; else echo false; fi > ~{broad_input_symlink}
if test -h ~{nirvana_reference_file_input}; then echo true; else echo false; fi > ~{nirvana_input_symlink}
String broad_input_valid_symlink = "broad_input_valid_symlink.txt"
String nirvana_input_valid_symlink = "nirvana_input_valid_symlink.txt"
String nirvana_metachar_input_valid_symlink = "nirvana_metachar_input_valid_symlink.txt"
command <<<
PS4='\D{+%F %T} \w $ '
set -o nounset -o pipefail -o xtrace

# Quotes added here due to the metachar in the filename.
if test -h "~{nirvana_reference_file_metachar_input}"; then echo true; else echo false; fi > ~{nirvana_metachar_input_symlink}
}
# Echo true to stdout if the argument is a symlink pointing to an extant file, otherwise echo false.
check_if_valid_symlink() {
local reference_input="$1"

if [[ -h "${reference_input}" && -f $(readlink "${reference_input}") ]]; then
echo true
else
echo false
fi
}

check_if_valid_symlink "~{broad_reference_file_input}" > ~{broad_input_valid_symlink}
check_if_valid_symlink "~{nirvana_reference_file_input}" > ~{nirvana_input_valid_symlink}
check_if_valid_symlink "~{nirvana_reference_file_metachar_input}" > ~{nirvana_metachar_input_valid_symlink}

>>>
output {
Boolean is_broad_input_symlink = read_boolean("~{broad_input_symlink}")
Boolean is_nirvana_input_symlink = read_boolean("~{nirvana_input_symlink}")
Boolean is_nirvana_metachar_input_symlink = read_boolean("~{nirvana_metachar_input_symlink}")
Boolean is_broad_input_valid_symlink = read_boolean("~{broad_input_valid_symlink}")
Boolean is_nirvana_input_valid_symlink = read_boolean("~{nirvana_input_valid_symlink}")
Boolean is_nirvana_metachar_input_valid_symlink = read_boolean("~{nirvana_metachar_input_valid_symlink}")
}
runtime {
docker: "ubuntu:latest"
Expand All @@ -34,15 +46,15 @@ workflow wf_reference_disk_test {
File nirvana_reference_file_input
File nirvana_reference_file_metachar_input
}
call check_if_localized_as_symlink {
call check_if_localized_with_valid_symlink {
input:
broad_reference_file_input = broad_reference_file_input,
nirvana_reference_file_input = nirvana_reference_file_input,
nirvana_reference_file_metachar_input = nirvana_reference_file_metachar_input
}
output {
Boolean is_broad_input_file_a_symlink = check_if_localized_as_symlink.is_broad_input_symlink
Boolean is_nirvana_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_input_symlink
Boolean is_nirvana_metachar_input_file_a_symlink = check_if_localized_as_symlink.is_nirvana_metachar_input_symlink
Boolean is_broad_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_broad_input_valid_symlink
Boolean is_nirvana_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_input_valid_symlink
Boolean is_nirvana_metachar_input_file_a_valid_symlink = check_if_localized_with_valid_symlink.is_nirvana_metachar_input_valid_symlink
}
}
5 changes: 3 additions & 2 deletions centaur/src/main/resources/standardTestCases/reference_disk_false_options.test
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Expand Up @@ -11,6 +11,7 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
}
5 changes: 3 additions & 2 deletions centaur/src/main/resources/standardTestCases/reference_disk_true_options.test
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Expand Up @@ -11,6 +11,7 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": true
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": true
"outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": true
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": true
"outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": true
}
5 changes: 3 additions & 2 deletions centaur/src/main/resources/standardTestCases/reference_disk_unspecified_options.test
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@ files {
metadata {
workflowName: wf_reference_disk_test
status: Succeeded
"outputs.wf_reference_disk_test.is_broad_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_symlink": false
"outputs.wf_reference_disk_test.is_broad_input_file_a_valid_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_input_file_a_valid_symlink": false
"outputs.wf_reference_disk_test.is_nirvana_metachar_input_file_a_valid_symlink": false
}
2 changes: 1 addition & 1 deletion src/ci/resources/papi_v2_reference_image_manifest.conf
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Expand Up @@ -192,7 +192,7 @@ reference-disk-localization-manifests = [
]
},
{
"imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-01-03",
"imageIdentifier" : "projects/broad-dsde-cromwell-dev/global/images/nirvana-3-18-1-references-2023-02-01",
"diskSizeGb" : 55,
"files" : [ {
"path" : "broad-public-datasets/gvs/vat-annotations/Nirvana/3.18.1/SupplementaryAnnotation/GRCh38/phyloP_hg38.npd",
Expand Down