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authorPeter Amstutz2020-07-08 17:10:10 -0400
committerPeter Amstutz2020-07-08 17:10:10 -0400
commite821857e7a9403739f321feb7418d33d6bd8b2c7 (patch)
tree1b72a737b50e60346aefaf009ac2488d45c8abe0 /bh20sequploader
parentbfcebbd349687ebe2d1d47185db9fda38803b674 (diff)
downloadbh20-seq-resource-upload-download-status.tar.gz
bh20-seq-resource-upload-download-status.tar.lz
bh20-seq-resource-upload-download-status.zip
Give uploader an option to trust local validation (for batch imports)upload-download-status
Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
Diffstat (limited to 'bh20sequploader')
-rw-r--r--bh20sequploader/main.py17
-rw-r--r--bh20sequploader/qc_metadata.py10
2 files changed, 19 insertions, 8 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 56e0150..f744a8c 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,7 +22,7 @@ ARVADOS_API_HOST='lugli.arvadosapi.com'
UPLOADER_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
ANONYMOUS_API_TOKEN='5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh'
UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
-VALIDATED_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
+VALIDATED_PROJECT='lugli-j7d0g-5ct8p1i1wrgyjvp'
def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
failed = False
@@ -69,9 +69,14 @@ def main():
parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTQ pair')
parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check")
+ parser.add_argument("--trusted", action="store_true", help="Trust local validation and add directly to validated project")
args = parser.parse_args()
- api = arvados.api(host=ARVADOS_API_HOST, token=UPLOADER_API_TOKEN, insecure=True)
+ if args.trusted:
+ # Use credentials from environment
+ api = arvados.api()
+ else:
+ api = arvados.api(host=ARVADOS_API_HOST, token=UPLOADER_API_TOKEN, insecure=True)
target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc)
seqlabel = target[0][1]
@@ -116,7 +121,13 @@ def main():
print("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
exit(1)
- col.save_new(owner_uuid=UPLOAD_PROJECT, name="%s uploaded by %s from %s" %
+ if args.trusted:
+ properties["status"] = "validated"
+ owner_uuid = VALIDATED_PROJECT
+ else:
+ owner_uuid = UPLOAD_PROJECT
+
+ col.save_new(owner_uuid=owner_uuid, name="%s uploaded by %s from %s" %
(seqlabel, properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 0a0c780..27657b1 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -16,12 +16,12 @@ def qc_metadata(metadatafile):
if metadata_schema is None:
schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")}
- metadata_schema = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
+ metadata_schema = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
- (document_loader,
- avsc_names,
- schema_metadata,
- metaschema_loader) = metadata_schema
+ (document_loader,
+ avsc_names,
+ schema_metadata,
+ metaschema_loader) = metadata_schema
shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8")