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[hailctl] allow passing arguments to hailctl batch submit scripts #12525

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merged 3 commits into from
Dec 3, 2022
Merged

[hailctl] allow passing arguments to hailctl batch submit scripts #12525

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f01af57
[hailctl] allow passing arguments to hailctl batch submit scripts
Dec 1, 2022
3937da2
Update build.yaml
danking Dec 2, 2022
2015cf4
Merge branch 'main' into hailctl-batch-submit-with-args
danking Dec 2, 2022
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51 changes: 51 additions & 0 deletions build.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -2671,6 +2671,57 @@ steps:
else
exit 1;
fi

cat >hail_with_args.py <<EOF
import hail as hl
import sys

with open('foo/baz.txt') as f:
print(f.read())

hl.init(app_name='test-hailctl-batch-submit-query')
assert hl.utils.range_table(int(sys.argv[1]))._force_count() == 100
EOF

BATCH_ID=$(hailctl batch submit --name=test-hailctl-batch-submit --files=foo -o json hail_with_args.py 100 | jq '.id')
STATUS=$(hailctl batch wait -o json $BATCH_ID | jq -jr '.state')
if [ "$STATUS" == "success" ]; then
exit 0;
else
exit 1;
fi
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I should have added such a test initially, but can you also test this with a bash script not just a python script?


cat >file.sh <<EOF
set -ex

cat foo
echo "Hello World!"
EOF

BATCH_ID=$(hailctl batch submit --name=test-hailctl-batch-submit --files=foo -o json file.sh | jq '.id')
STATUS=$(hailctl batch wait -o json $BATCH_ID | jq -jr '.state')
if [ "$STATUS" == "success" ]; then
exit 0;
else
exit 1;
fi

cat >file-with-args.sh <<EOF
set -ex

[[ $# -eq 2 ]]

cat foo
echo "Hello World! $1 $2"
EOF

BATCH_ID=$(hailctl batch submit --name=test-hailctl-batch-submit --files=foo -o json file-with-args.sh abc 123 | jq '.id')
STATUS=$(hailctl batch wait -o json $BATCH_ID | jq -jr '.state')
if [ "$STATUS" == "success" ]; then
exit 0;
else
exit 1;
fi
secrets:
- name: worker-deploy-config
namespace:
Expand Down
7 changes: 5 additions & 2 deletions hail/python/hailtop/hailctl/batch/submit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
import orjson
import os
import sys
from shlex import quote as shq

import hailtop.batch as hb
import hailtop.batch_client.client as bc
Expand All @@ -14,13 +15,14 @@


def init_parser(parser):
parser.add_argument('script', type=str, help='Path to script')
parser.add_argument('--name', type=str, default='', help='Batch name')
parser.add_argument('--image-name', type=str, required=False,
help='Name for Docker image. Defaults to hailgenetics/hail')
parser.add_argument('--files', nargs='+', action='append', default=[],
help='Comma-separated list of files or directories to add to the working directory of job')
parser.add_argument('-o', type=str, default='text', choices=['text', 'json'])
parser.add_argument('script', type=str, help='Path to script')
parser.add_argument('arguments', nargs='*', help='Arguments to script')


async def async_main(args):
Expand Down Expand Up @@ -59,7 +61,8 @@ def cloud_prefix(path):
j.env('HAIL_QUERY_BACKEND', 'batch')

command = 'python3' if script.endswith('.py') else 'bash'
j.command(f'{command} {script_file}')
script_arguments = " ".join(shq(x) for x in args.arguments)
j.command(f'{command} {script_file} {script_arguments}')
batch_handle: bc.Batch = b.run(wait=False, disable_progress_bar=quiet) # type: ignore

if args.o == 'text':
Expand Down