diff options
Diffstat (limited to 'bh20seqanalyzer')
| -rw-r--r-- | bh20seqanalyzer/main.py | 36 |
1 files changed, 19 insertions, 17 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 794ce27..9164190 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -39,22 +39,25 @@ def validate_upload(api, collection, validated_project, logging.warn("Failed metadata qc") if valid: - tgt = None - paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"} - for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): - if n not in col: - continue - with col.open(n, 'rb') as qf: - tgt = qc_fasta(qf)[0] - if tgt != n and tgt != paired.get(n): - logging.info("Expected %s but magic says it should be %s", n, tgt) - valid = False - elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): - start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n) - return False - if tgt is None: + try: + tgt = None + paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"} + for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): + if n not in col: + continue + with col.open(n, 'rb') as qf: + tgt = qc_fasta(qf)[0] + if tgt != n and tgt != paired.get(n): + logging.info("Expected %s but magic says it should be %s", n, tgt) + valid = False + elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"): + start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n) + return False + if tgt is None: + valid = False + logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"]) + except ValueError as v: valid = False - logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"]) dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], ["portable_data_hash", "=", col.portable_data_hash()]]).execute() @@ -70,9 +73,8 @@ def validate_upload(api, collection, validated_project, "owner_uuid": validated_project, "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute() else: - pass # It is invalid, delete it. - #logging.warn("Deleting '%s'" % collection["name"]) + logging.warn("Suggest deleting '%s'" % collection["name"]) #api.collections().delete(uuid=collection["uuid"]).execute() return valid |