diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 36 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 7 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 26 |
3 files changed, 58 insertions, 11 deletions
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 |