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| author | Peter Amstutz | 2020-04-20 12:50:03 -0400 |
|---|---|---|
| committer | Peter Amstutz | 2020-04-20 12:50:03 -0400 |
| commit | 1219eaf496c899f3043b90e30eb956f0f363bfb3 (patch) | |
| tree | a0735d5df88e608c5461d5b3cb9a3c6bb2f0f32e /bh20sequploader/main.py | |
| parent | a2d19fa7b34170abab3759cdff14d8b052178a8a (diff) | |
| download | bh20-seq-resource-1219eaf496c899f3043b90e30eb956f0f363bfb3.tar.gz bh20-seq-resource-1219eaf496c899f3043b90e30eb956f0f363bfb3.tar.lz bh20-seq-resource-1219eaf496c899f3043b90e30eb956f0f363bfb3.zip | |
Add ShEx validation
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20sequploader/main.py')
| -rw-r--r-- | bh20sequploader/main.py | 11 |
1 files changed, 10 insertions, 1 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index e0a6a9a..49d012d 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -21,16 +21,25 @@ def main(): parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ') parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') + parser.add_argument("--validate", action="store_true", help="Dry run, validate only") args = parser.parse_args() api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - target = qc_fasta(args.sequence) + try: + target = qc_fasta(args.sequence) + except ValueError as e: + print(e) + exit(1) if not qc_metadata(args.metadata.name): print("Failed metadata qc") exit(1) + if args.validate: + print("Valid") + exit(0) + col = arvados.collection.Collection(api_client=api) with col.open(target, "w") as f: |