diff options
Diffstat (limited to 'bh20sequploader')
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 6 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 2 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 29 |
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 |