diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 15 | ||||
| -rw-r--r-- | bh20sequploader/qc_fasta.py | 5 |
2 files changed, 15 insertions, 5 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 2cd15c2..a2e62fa 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -31,16 +31,23 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) - log.debug("Checking metadata") - if not qc_metadata(args.metadata.name): - log.warning("Failed metadata qc") + try: + log.debug("Checking metadata") + if not qc_metadata(args.metadata.name): + log.warning("Failed metadata qc") + exit(1) + except ValueError as e: + log.debug(e) + log.debug("Failed metadata qc") + print(e) exit(1) try: log.debug("Checking FASTA QC") target = qc_fasta(args.sequence) except ValueError as e: - log.warning("Failed FASTA qc") + log.debug(e) + log.debug("Failed FASTA qc") print(e) exit(1) diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py index 16cf2c9..5c8cf3a 100644 --- a/bh20sequploader/qc_fasta.py +++ b/bh20sequploader/qc_fasta.py @@ -6,6 +6,8 @@ import tempfile import logging import re +log = logging.getLogger(__name__ ) + def read_fasta(sequence): entries = 0 bases = [] @@ -17,11 +19,12 @@ def read_fasta(sequence): else: bases.append(line) if entries > 1: + log.debug("FASTA file contains multiple entries") raise ValueError("FASTA file contains multiple entries") - break return label, bases def qc_fasta(sequence): + log.debug("Starting qc_fasta") schema_resource = pkg_resources.resource_stream(__name__, "validation/formats") with tempfile.NamedTemporaryFile() as tmp: tmp.write(schema_resource.read()) |