Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

VS-517 Use standard version of GetBQTableLastModifiedDatetime in GvsValidateVat #8024

Merged
merged 4 commits into from
Sep 21, 2022
Merged

VS-517 Use standard version of GetBQTableLastModifiedDatetime in GvsValidateVat #8024

Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
f4ddbbb
Pointing GvsValidateVAT at GvsUtils to use their version of GetBQTabl…
koncheto-broad Sep 12, 2022
6c93b16
Silly typo
koncheto-broad Sep 15, 2022
336c66f
Merge branch 'ah_var_store' into ah_vs517
koncheto-broad Sep 19, 2022
b80654a
cleanup dockstore branch
koncheto-broad Sep 19, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
49 changes: 3 additions & 46 deletions scripts/variantstore/variant_annotations_table/GvsValidateVAT.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,5 +1,7 @@
version 1.0

import "../wdl/GvsUtils.wdl" as Utils

workflow GvsValidateVat {
input {
String query_project_id
Expand All @@ -9,7 +11,7 @@ workflow GvsValidateVat {

String fq_vat_table = "~{query_project_id}.~{default_dataset}.~{vat_table_name}"

call GetBQTableLastModifiedDatetime {
call Utils.GetBQTableLastModifiedDatetime {
input:
query_project = query_project_id,
fq_table = fq_vat_table
Expand Down Expand Up @@ -170,51 +172,6 @@ workflow GvsValidateVat {
}
}

task GetBQTableLastModifiedDatetime {
# because this is being used to determine if the data has changed, never use call cache
meta {
volatile: true
}

input {
String query_project
String fq_table
}


# ------------------------------------------------
# try to get the last modified date for the table in question; fail if something comes back from BigQuery
# that isn't in the right format (e.g. an error)
command <<<
set -e

echo "project_id = ~{query_project}" > ~/.bigqueryrc

# bq needs the project name to be separate by a colon
DATASET_TABLE_COLON=$(echo ~{fq_table} | sed 's/\./:/')

LASTMODIFIED=$(bq --location=US --project_id=~{query_project} --format=json show ${DATASET_TABLE_COLON} | python3 -c "import sys, json; print(json.load(sys.stdin)['lastModifiedTime']);")
if [[ $LASTMODIFIED =~ ^[0-9]+$ ]]; then
echo $LASTMODIFIED
else
exit 1
fi
>>>

output {
String last_modified_timestamp = read_string(stdout())
}

runtime {
docker: "gcr.io/google.com/cloudsdktool/cloud-sdk:305.0.0"
memory: "3 GB"
disks: "local-disk 10 HDD"
preemptible: 3
cpu: 1
}

}

task EnsureVatTableHasVariants {
input {
String query_project_id
Expand Down