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-rw-r--r--bh20sequploader/bh20seq-schema.yml6
-rw-r--r--bh20sequploader/main.py2
-rw-r--r--bh20sequploader/qc_metadata.py29
3 files changed, 32 insertions, 5 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index cf9b015..a072bd7 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -174,9 +174,9 @@ $graph:
jsonldPredicate:
_id: "@id"
#_type: "@id"
- sequencefile:
- doc: The subject (eg the fasta/fastq file) that this metadata describes
+ id:
+ doc: The subject (eg the fasta/fastq file) that the metadata describes
type: string?
jsonldPredicate:
_id: "@id"
- _type: "@id" \ No newline at end of file
+ _type: "@id"
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index bfb8c51..2032508 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,7 +22,7 @@ def main():
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
- if not qc_metadata(args.metadata.name):
+ if not bh20sequploader.qc_metadata.qc_metadata(args.metadata.name):
print("Failed metadata qc")
exit(1)
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index ebe4dfc..38edcaa 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,12 +1,25 @@
import schema_salad.schema
+import schema_salad.ref_resolver
import logging
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")}
- (document_loader,
+ (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)
@@ -15,9 +28,23 @@ 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
except Exception as e:
+ traceback.print_exc()
logging.warn(e)
return False