From 07bc4c65535437b8e9e0744f08da8cea541d0116 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 7 Apr 2020 15:28:42 -0400
Subject: Add metadata validation with schema-salad

---
 bh20sequploader/bh20seq-schema.yml | 36 ++++++++++++++++++++++++++++++++++++
 bh20sequploader/main.py            |  7 +++++--
 bh20sequploader/qc_metadata.py     | 26 +++++++++++++++++---------
 3 files changed, 58 insertions(+), 11 deletions(-)
 create mode 100644 bh20sequploader/bh20seq-schema.yml

(limited to 'bh20sequploader')

diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
new file mode 100644
index 0000000..6e0973a
--- /dev/null
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -0,0 +1,36 @@
+$graph:
+
+- name: sampleInformationSchema
+  type: record
+  fields:
+    location: string
+    host: string
+    sequenceTechnology: string
+    assemblyMethod: string
+
+- name: InstituteInformationSchema
+  type: record
+  fields:
+    OriginatingLab: string
+    SubmittingLab: string
+
+- name: SubmitterInformationSchema
+  type: record
+  fields:
+    Submitter: string
+    submissionDate: string
+
+- name: VirusDetailSchema
+  type: record
+  fields:
+    VirusName: string
+    AccessionId: string
+
+- name: MainSchema
+  type: record
+  documentRoot: true
+  fields:
+    sampleInformation: sampleInformationSchema
+    InstituteInformation: InstituteInformationSchema
+    SubmitterInformation: SubmitterInformationSchema
+    VirusDetail: VirusDetailSchema
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index d3ebc0c..8b8fefe 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,6 +6,7 @@ import json
 import urllib.request
 import socket
 import getpass
+from .qc_metadata import qc_metadata
 
 ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -19,6 +20,8 @@ def main():
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
+    qc_metadata(args.metadata.name)
+
     col = arvados.collection.Collection(api_client=api)
 
     print("Reading FASTA")
@@ -29,8 +32,8 @@ def main():
             f.write(r)
             r = args.sequence.read(65536)
 
-    print("Reading JSONLD")
-    with col.open("metadata.jsonld", "w") as f:
+    print("Reading metadata")
+    with col.open("metadata.yaml", "w") as f:
         r = args.metadata.read(65536)
         print(r[0:20])
         while r:
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 0632777..78b31b2 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,13 +1,21 @@
-import yamale
+import schema_salad.schema
+import logging
+import pkg_resources
 
-## NOTE: this is just a DUMMY. Everything about this can and will change
 def qc_metadata(metadatafile):
-    print("Start metadata validation...")
-    schema = yamale.make_schema('../example/dummyschema.yaml')
-    data = yamale.make_data(metadatafile)
-    # Validate data against the schema. Throws a ValueError if data is invalid.
-    yamale.validate(schema, data)
-    print("...complete!")
+    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,
+     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)
 
-#qc_metadata("../example/metadata.yaml")
+    if not isinstance(avsc_names, schema_salad.avro.schema.Names):
+        print(avsc_names)
+        return False
 
+    try:
+        doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
+        return True
+    except:
+        return False
-- 
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