From d781e42c9adac07253cb928ae66e9b7314710267 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Mon, 20 Apr 2020 12:55:18 -0400 Subject: Move workflows into main repo Arvados-DCO-1.1-Signed-off-by: Peter Amstutz --- workflows/pangenome-generate/merge-metadata.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 workflows/pangenome-generate/merge-metadata.py (limited to 'workflows/pangenome-generate/merge-metadata.py') diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py new file mode 100644 index 0000000..64275b1 --- /dev/null +++ b/workflows/pangenome-generate/merge-metadata.py @@ -0,0 +1,17 @@ +import schema_salad.schema +import schema_salad.jsonld_context + +metadataSchema = '$(inputs.metadataSchema.path)' +metadata = $(inputs.metadata) +subjects = $(inputs.subjects) + +(document_loader, + avsc_names, + schema_metadata, + metaschema_loader) = schema_salad.schema.load_schema(metadataSchema) + +for i, m in enumerate(metadata): + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, m["path"], True) + doc["id"] = subjects[i] + g = schema_salad.jsonld_context.makerdf(subjects[i], doc, document_loader.ctx) + print(g.serialize(format="ntriples").decode("utf-8")) -- cgit v1.2.3