diff options
| -rw-r--r-- | bh20seqanalyzer/main.py | 11 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 36 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 7 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 26 | ||||
| -rw-r--r-- | example/dummyschema.yaml | 16 | ||||
| -rw-r--r-- | setup.py | 3 |
6 files changed, 68 insertions, 31 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py index 2513ea3..78e32c9 100644 --- a/bh20seqanalyzer/main.py +++ b/bh20seqanalyzer/main.py @@ -6,12 +6,14 @@ import subprocess import tempfile import json import logging +import ruamel.yaml +from bh20sequploader.qc_metadata import qc_metadata logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S", level=logging.INFO) logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) -def validate_upload(api, collection, validated_project, latest_result_uuid): +def validate_upload(api, collection, validated_project): col = arvados.collection.Collection(collection["uuid"]) # validate the collection here. Check metadata, etc. @@ -20,9 +22,12 @@ def validate_upload(api, collection, validated_project, latest_result_uuid): if "sequence.fasta" not in col: valid = False logging.warn("Upload '%s' missing sequence.fasta", collection["name"]) - if "metadata.jsonld" not in col: - logging.warn("Upload '%s' missing metadata.jsonld", collection["name"]) + if "metadata.yaml" not in col: + logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) valid = False + else: + metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) + valid = qc_metadata(metadata_content) and valid dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], ["portable_data_hash", "=", col.portable_data_hash()]]).execute() diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml new file mode 100644 index 0000000..6e0973a --- /dev/null +++ b/bh20sequploader/bh20seq-schema.yml @@ -0,0 +1,36 @@ +$graph: + +- name: sampleInformationSchema + type: record + fields: + location: string + host: string + sequenceTechnology: string + assemblyMethod: string + +- name: InstituteInformationSchema + type: record + fields: + OriginatingLab: string + SubmittingLab: string + +- name: SubmitterInformationSchema + type: record + fields: + Submitter: string + submissionDate: string + +- name: VirusDetailSchema + type: record + fields: + VirusName: string + AccessionId: string + +- name: MainSchema + type: record + documentRoot: true + fields: + sampleInformation: sampleInformationSchema + InstituteInformation: InstituteInformationSchema + SubmitterInformation: SubmitterInformationSchema + VirusDetail: VirusDetailSchema diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py index d3ebc0c..8b8fefe 100644 --- a/bh20sequploader/main.py +++ b/bh20sequploader/main.py @@ -6,6 +6,7 @@ import json import urllib.request import socket import getpass +from .qc_metadata import qc_metadata ARVADOS_API_HOST='lugli.arvadosapi.com' ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' @@ -19,6 +20,8 @@ def main(): api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + qc_metadata(args.metadata.name) + col = arvados.collection.Collection(api_client=api) print("Reading FASTA") @@ -29,8 +32,8 @@ def main(): f.write(r) r = args.sequence.read(65536) - print("Reading JSONLD") - with col.open("metadata.jsonld", "w") as f: + print("Reading metadata") + with col.open("metadata.yaml", "w") as f: r = args.metadata.read(65536) print(r[0:20]) while r: diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py index 0632777..78b31b2 100644 --- a/bh20sequploader/qc_metadata.py +++ b/bh20sequploader/qc_metadata.py @@ -1,13 +1,21 @@ -import yamale +import schema_salad.schema +import logging +import pkg_resources -## NOTE: this is just a DUMMY. Everything about this can and will change def qc_metadata(metadatafile): - print("Start metadata validation...") - schema = yamale.make_schema('../example/dummyschema.yaml') - data = yamale.make_data(metadatafile) - # Validate data against the schema. Throws a ValueError if data is invalid. - yamale.validate(schema, data) - print("...complete!") + 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")} + (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) -#qc_metadata("../example/metadata.yaml") + if not isinstance(avsc_names, schema_salad.avro.schema.Names): + print(avsc_names) + return False + try: + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) + return True + except: + return False diff --git a/example/dummyschema.yaml b/example/dummyschema.yaml deleted file mode 100644 index e428324..0000000 --- a/example/dummyschema.yaml +++ /dev/null @@ -1,16 +0,0 @@ -#sampleInformation: include('sampleInformation') -#InstituteInformation: include('InstituteInformation') ---- -sampleInformation: - location : str() - host : str() - sequenceTechnology: str() - assemblyMethod: str() - -InstituteInformation: - OriginatingLab: str() - SubmittingLab: str() - -VirusDetail: - VirusName: str() - AccessionId: str() diff --git a/setup.py b/setup.py index 0685d37..48c25aa 100644 --- a/setup.py +++ b/setup.py @@ -15,7 +15,7 @@ try: except ImportError: tagger = egg_info_cmd.egg_info -install_requires = ["arvados-python-client"] +install_requires = ["arvados-python-client", "schema-salad"] needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else [] @@ -30,6 +30,7 @@ setup( author_email="peter.amstutz@curii.com", license="Apache 2.0", packages=["bh20sequploader", "bh20seqanalyzer"], + package_data={"bh20sequploader": ["bh20seq-schema.yml"]}, install_requires=install_requires, setup_requires=[] + pytest_runner, tests_require=["pytest<5"], |