1 files changed, 33 insertions, 4 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 9132453..8a6794e 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -47,6 +47,7 @@ def type_to_heading(type_name):
     Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading.
     """
 
+    print(type_name,file=sys.stderr)
     # Remove camel case
     decamel = re.sub('([A-Z])', r' \1', type_name)
     # Split
@@ -227,8 +228,13 @@ def generate_form(schema, options):
 
 
 # At startup, we need to load the metadata schema from the uploader module, so we can make a form for it
-METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
-METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+if os.path.isfile("bh20sequploader/bh20seq-schema.yml"):
+    METADATA_SCHEMA = yaml.safe_load(open("bh20sequploader/bh20seq-schema.yml","r").read())
+    METADATA_OPTION_DEFINITIONS = yaml.safe_load(open("bh20sequploader/bh20seq-options.yml","r").read())
+else:
+    METADATA_SCHEMA = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-schema.yml"))
+    METADATA_OPTION_DEFINITIONS = yaml.safe_load(pkg_resources.resource_stream("bh20sequploader", "bh20seq-options.yml"))
+# print(METADATA_SCHEMA,file=sys.stderr)
 FORM_ITEMS = generate_form(METADATA_SCHEMA, METADATA_OPTION_DEFINITIONS)
 
 @app.route('/')
@@ -505,7 +511,7 @@ def status_page():
     Processing status
     """
 
-    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
+    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True)
     pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", UPLOADER_PROJECT]])
     out = []
     status = {}
@@ -567,11 +573,34 @@ baseURL='http://sparql.genenetwork.org/sparql/'
 
 @app.route('/api/getCount', methods=['GET'])
 def getCount():
-    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN)
+    """
+    Get sequence counts from Arvados record
+    """
+    api = arvados.api(host=ARVADOS_API, token=ANONYMOUS_TOKEN, insecure=True)
     c = api.collections().list(filters=[["owner_uuid", "=", VALIDATED_PROJECT]], limit=1).execute()
 
     return jsonify({'sequences': c["items_available"]})
 
+@app.route('/api/getCountDB', methods=['GET'])
+def getCountDB():
+    """
+    Get sequence counts from Virtuoso DB
+    """
+    query="""
+    PREFIX pubseq: <http://biohackathon.org/bh20-seq-schema#MainSchema/>
+    select (COUNT(distinct ?dataset) as ?num)
+    {
+    ?dataset pubseq:submitter ?id .
+    ?id ?p ?submitter
+    }
+    """
+    payload = {'query': query, 'format': 'json'}
+    r = requests.get(baseURL, params=payload)
+    result = r.json()['results']['bindings']
+    # [{'num': {'type': 'typed-literal', 'datatype': 'http://www.w3.org/2001/XMLSchema#integer', 'value': '1352'}}]
+    # print(result, file=sys.stderr)
+    return jsonify({'sequences': int(result[0]["num"]["value"])})
+
 @app.route('/api/getAllaccessions', methods=['GET'])
 def getAllaccessions():
     query="""SELECT DISTINCT ?fasta ?value WHERE {?fasta ?x[ <http://edamontology.org/data_2091> ?value ]}"""