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-rw-r--r--bh20sequploader/bh20seq-schema.yml4
-rw-r--r--bh20sequploader/main.py7
2 files changed, 6 insertions, 5 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 75308ab..ebca35b 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -162,12 +162,12 @@ $graph:
_id: http://www.ebi.ac.uk/efo/EFO_0002699
sequencing_coverage:
doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x)
- type: float?
+ type: ["null", float, int]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
sequencing_coverage2:
doc: If a second sequence technology was used you can submit its coverage here
- type: float?
+ type: ["null", float, int]
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
additional_technology_information:
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 49d012d..2fda347 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -44,7 +44,8 @@ def main():
with col.open(target, "w") as f:
r = args.sequence.read(65536)
- print(r[0:20])
+ seqlabel = r[1:r.index("\n")]
+ print(seqlabel)
while r:
f.write(r)
r = args.sequence.read(65536)
@@ -67,8 +68,8 @@ def main():
"upload_user": "%s@%s" % (getpass.getuser(), socket.gethostname())
}
- col.save_new(owner_uuid=UPLOAD_PROJECT, name="Uploaded by %s from %s" %
- (properties['upload_user'], properties['upload_ip']),
+ col.save_new(owner_uuid=UPLOAD_PROJECT, name="%s uploaded by %s from %s" %
+ (seqlabel, properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
print("Done")