diff options
| author | lltommy | 2020-04-22 18:37:35 +0200 |
|---|---|---|
| committer | lltommy | 2020-04-22 18:37:35 +0200 |
| commit | 5582ed4f4bd6bd5b03d20a0c88dc7fa27d2d5cde (patch) | |
| tree | 466dfc19d583aedb44f366ddacc6fa8e0b7a890e /bh20sequploader | |
| parent | b34531de1f49e4faa82a9c350f0c5d4169ccfeb4 (diff) | |
| parent | ce696b41b3476891ecb05185d64c289b140a73af (diff) | |
| download | bh20-seq-resource-5582ed4f4bd6bd5b03d20a0c88dc7fa27d2d5cde.tar.gz bh20-seq-resource-5582ed4f4bd6bd5b03d20a0c88dc7fa27d2d5cde.tar.lz bh20-seq-resource-5582ed4f4bd6bd5b03d20a0c88dc7fa27d2d5cde.zip | |
Merge branch 'master' of https://github.com/arvados/bh20-seq-resource
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 1 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-shex.rdf | 2 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 8 |
3 files changed, 7 insertions, 4 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml index 75308ab..1ceebe2 100644 --- a/bh20sequploader/bh20seq-schema.yml +++ b/bh20sequploader/bh20seq-schema.yml @@ -106,6 +106,7 @@ $graph: jsonldPredicate: _id: http://purl.obolibrary.org/obo/OBI_0001479 _type: "@id" + noLinkCheck: true sample_storage_conditions: doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh .... type: string? diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf index 59ee71b..31e714f 100644 --- a/bh20sequploader/bh20seq-shex.rdf +++ b/bh20sequploader/bh20seq-shex.rdf @@ -50,7 +50,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/> :technologyShape { obo:OBI_0600047 IRI {0,2} ; - obo:FLU_0000848 xsd:integer ?; + obo:FLU_0000848 xsd:double ?; efo:EFO_0002699 xsd:string ?; } diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index 49d012d..4c4711d 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) @@ -62,13 +63,14 @@ def main(): external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8') properties = { + "sequence_label": seqlabel, "upload_app": "bh20-seq-uploader", "upload_ip": external_ip, "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") |