diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/main.py | 27 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 15 |
2 files changed, 36 insertions, 6 deletions
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index fd0278d..f744a8c 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -19,8 +19,10 @@ log = logging.getLogger(__name__ ) log.debug("Entering sequence uploader") ARVADOS_API_HOST='lugli.arvadosapi.com' -ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +UPLOADER_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +ANONYMOUS_API_TOKEN='5o42qdxpxp5cj15jqjf7vnxx5xduhm4ret703suuoa3ivfglfh' UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' +VALIDATED_PROJECT='lugli-j7d0g-5ct8p1i1wrgyjvp' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): failed = False @@ -67,9 +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=ARVADOS_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] @@ -106,7 +113,21 @@ def main(): "upload_user": "%s@%s" % (username, socket.gethostname()) } - col.save_new(owner_uuid=UPLOAD_PROJECT, name="%s uploaded by %s from %s" % + api2 = arvados.api(host=ARVADOS_API_HOST, token=ANONYMOUS_API_TOKEN, insecure=True) + dup = api2.collections().list(filters=[["owner_uuid", "in", [VALIDATED_PROJECT, UPLOAD_PROJECT]], + ["portable_data_hash", "=", col.portable_data_hash()]]).execute() + if dup["items"]: + # This exact collection has been uploaded before. + print("Duplicate of %s" % ([d["uuid"] for d in dup["items"]])) + exit(1) + + 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 2b57991..27657b1 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -8,15 +8,20 @@ import traceback from rdflib import Graph, Namespace from pyshex.evaluate import evaluate +metadata_schema = None def qc_metadata(metadatafile): + global metadata_schema log = logging.getLogger(__name__ ) - 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")} + 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) + (document_loader, avsc_names, schema_metadata, - metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) + metaschema_loader) = metadata_schema shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8") @@ -27,6 +32,10 @@ def qc_metadata(metadatafile): g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx) rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape") + # As part of QC make sure serialization works too, this will raise + # an exception if there are invalid URIs. + g.serialize(format="ntriples") + if not rslt: raise Exception(reason) |