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-rw-r--r--bh20sequploader/qc_metadata.py26
1 files changed, 1 insertions, 25 deletions
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 38edcaa..e477f21 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -5,21 +5,10 @@ import pkg_resources
import logging
import traceback
-class CustomFetcher(schema_salad.ref_resolver.DefaultFetcher):
- def check_exists(sup, url):
- if url.startswith("keep:"):
- return True
- else:
- return super().check_exists(url)
-
- def supported_schemes(self): # type: () -> List[str]
- return ["file", "http", "https", "mailto", "keep"]
-
-
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")}
- (loader,
+ (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)
@@ -28,19 +17,6 @@ def qc_metadata(metadatafile):
print(avsc_names)
return False
- document_loader = schema_salad.ref_resolver.Loader(
- loader.ctx,
- schemagraph=loader.graph,
- foreign_properties=loader.foreign_properties,
- idx=loader.idx,
- cache=loader.cache,
- fetcher_constructor=CustomFetcher,
- skip_schemas=loader.skip_schemas,
- url_fields=loader.url_fields,
- allow_attachments=loader.allow_attachments,
- session=loader.session,
- )
-
try:
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
return True