Merge pull request #92 from arvados/upload-download-status

Split upload tab.  Add upload status tab.  Also a bunch of QC and uploader improvements.

1 files changed, 12 insertions, 3 deletions

diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 2b57991..27657b1 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -8,15 +8,20 @@ import traceback
 from rdflib import Graph, Namespace
 from pyshex.evaluate import evaluate
 
+metadata_schema = None
 
 def qc_metadata(metadatafile):
+    global metadata_schema
     log = logging.getLogger(__name__ )
-    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")}
+    if metadata_schema is None:
+        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")}
+        metadata_schema = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache)
+
     (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)
+     metaschema_loader) = metadata_schema
 
     shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8")
 
@@ -27,6 +32,10 @@ def qc_metadata(metadatafile):
     g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx)
     rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape")
 
+    # As part of QC make sure serialization works too, this will raise
+    # an exception if there are invalid URIs.
+    g.serialize(format="ntriples")
+
     if not rslt:
         raise Exception(reason)