diff options
Diffstat (limited to 'bh20sequploader/qc_metadata.py')
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 29 |
1 files changed, 28 insertions, 1 deletions
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 |