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-rw-r--r--bh20sequploader/main.py15
-rw-r--r--bh20sequploader/qc_fasta.py5
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())