bh20sequploader/qc_metadata.py


1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21

import schema_salad.schema
import logging
import pkg_resources

def qc_metadata(metadatafile):
    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)

    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