1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
|
import sys
import schema_salad.schema
import schema_salad.jsonld_context
from pyshex.evaluate import evaluate
path_yaml = sys.argv[1]
path_fasta = sys.argv[2]
path_schema_yaml = sys.argv[3]
path_shex_rdf = sys.argv[4]
with open(path_schema_yaml, "rb") as f:
cache = {
"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": f.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) = metadata_schema
if not isinstance(avsc_names, schema_salad.avro.schema.Names):
raise Exception(avsc_names)
with open(path_shex_rdf, "rb") as f:
shex = f.read().decode("utf-8")
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, path_yaml, True)
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)
# The sample_id in the FASTA header has to equal to the sample_id in the YAML file
sample_id_from_metadata = metadata['sample']['sample_id']
sample_id_from_fasta = ''
with open(path_fasta) as f:
for line in f:
sample_id_from_fasta = line.strip().split(' ')[0][1:]
break
if sample_id_from_metadata != sample_id_from_fasta:
raise ValueError(
f"sample_id in the YAML file '{sample_id_from_metadata}' is different from the sample_id in the FASTA '{sample_id_from_fasta}'"
)
|
