diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 14 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 6 |
2 files changed, 15 insertions, 5 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 8b8fefe..56cbe22 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -20,12 +20,18 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - qc_metadata(args.metadata.name) + if not qc_metadata(args.metadata.name): + print("Failed metadata qc") + exit(1) col = arvados.collection.Collection(api_client=api) - print("Reading FASTA") - with col.open("sequence.fasta", "w") as f: + if args.sequence.name.endswith("fasta") or args.sequence.name.endswith("fa"): + target = "sequence.fasta" + elif args.sequence.name.endswith("fastq") or args.sequence.name.endswith("fq"): + target = "reads.fastq" + + with col.open(target, "w") as f: r = args.sequence.read(65536) print(r[0:20]) while r: @@ -52,5 +58,7 @@ def main(): (properties['upload_user'], properties['upload_ip']), properties=properties, ensure_unique_name=True) + print("Done") + if __name__ == "__main__": main() diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 78b31b2..ebe4dfc 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,6 +1,7 @@ import schema_salad.schema import logging import pkg_resources +import logging def qc_metadata(metadatafile): schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") @@ -17,5 +18,6 @@ def qc_metadata(metadatafile): try: doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) return True - except: - return False + except Exception as e: + logging.warn(e) + return False |