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| author | Peter Amstutz | 2020-07-08 20:51:14 +0000 |
|---|---|---|
| committer | Peter Amstutz | 2020-07-08 20:52:48 +0000 |
| commit | bfcebbd349687ebe2d1d47185db9fda38803b674 (patch) | |
| tree | 1c9780c034f9f9c23df828ca2e155259d8881f92 | |
| parent | ae8991618927f81343038f235c3e3f76932f80ea (diff) | |
| download | bh20-seq-resource-bfcebbd349687ebe2d1d47185db9fda38803b674.tar.gz bh20-seq-resource-bfcebbd349687ebe2d1d47185db9fda38803b674.tar.lz bh20-seq-resource-bfcebbd349687ebe2d1d47185db9fda38803b674.zip | |
Uploader checks for duplicates
| -rw-r--r-- | Dockerfile | 2 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 14 |
2 files changed, 13 insertions, 3 deletions
@@ -13,7 +13,7 @@ ADD bh20seqanalyzer /app/bh20simplewebuploader ADD bh20sequploader /app/bh20sequploader ADD bh20simplewebuploader /app/bh20simplewebuploader -RUN pip3 install -e . +RUN pip3 install -e .[web] ENV PORT 8080 CMD ["gunicorn", "-w", "4", "-b", "0.0.0.0:8080", "bh20simplewebuploader.main:app"] diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index fd0278d..56e0150 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-n5clictpuvwk8aa' def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True): failed = False @@ -69,7 +71,7 @@ def main(): parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check") args = parser.parse_args() - api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + 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] @@ -106,6 +108,14 @@ def main(): "upload_user": "%s@%s" % (username, socket.gethostname()) } + 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) + 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) |