variantgrid-api 0.1.4__tar.gz → 0.1.5__tar.gz

{variantgrid_api-0.1.4 → variantgrid_api-0.1.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: variantgrid_api
-Version: 0.1.4
+Version: 0.1.5
 Summary: API to connect to VariantGrid
 Home-page: https://bitbucket.org/sacgf/variantgrid_api
 Author: David Lawrence

variantgrid_api-0.1.5/variantgrid_api/__init__.py

@@ -0,0 +1,2 @@
+
+__version__ = '0.1.5'

{variantgrid_api-0.1.4 → variantgrid_api-0.1.5}/variantgrid_api/add_classification.py

@@ -12,5 +12,7 @@ def add_classification_handle_args(args):
     elif args.variant:
         classification = api.add_classifications_for_variant(args.variant, args.classification, args.public)
 
-        print("created classification: %s" % classification)
-
+    if classification:
+        pk = classification["id"]
+        gvc_url = "%s/variantclassification/view_genomic_variant_classification/%d" % (api.url, pk) 
+        print("Created classification: %s" % gvc_url)

{variantgrid_api-0.1.4 → variantgrid_api-0.1.5}/variantgrid_api/api.py

@@ -97,24 +97,29 @@ class VariantGridAPI(object):
         return self._get_classification_json(url, classification)
 
 
-    def _add_classification_json(self, path, classification, public):
+    def _add_classification_json(self, path, classification, dbsnp=None, variant=None, public=False):
         url_path = os.path.join(self.url, path) + ".json"
         data = {"classification" : classification,
                 "public" : public}
+        if dbsnp:
+            data["dbsnp_string"] = dbsnp
+        elif variant:
+            data["variant_string"] = variant
+        else:
+            msg = "Need to specify either 'dbsnp' or 'variant'"
+            raise ValueError(msg)
         
         r = requests.post(url_path, auth=self.auth, json=data)
         r.raise_for_status()
-        return r.text
+        return json.loads(r.text)
 
-    def add_classifications_for_dbsnp(self, dbsnp, classification, public=False):
-        params = {'dbsnp' : dbsnp}
-        url = 'variantclassification/api/add_classification/dbsnp/%(dbsnp)s' % params   
-        return self._add_classification_json(url, classification, public)
+    def add_classifications_for_dbsnp(self, dbsnp, classification, public):
+        url = 'variantclassification/api/add_classification'   
+        return self._add_classification_json(url, classification, dbsnp=dbsnp, public=public)
 
-    def add_classifications_for_variant(self, variant_string, classification, public=False):
-        params = {'variant_string' : variant_string,}
-        url = 'variantclassification/api/add_classification/variant/%(variant_string)s' % params   
-        return self._add_classification_json(url, classification, public)
+    def add_classifications_for_variant(self, variant_string, classification, public):
+        url = 'variantclassification/api/add_classification'   
+        return self._add_classification_json(url, classification, variant=variant_string, public=public)
 
 
 

{variantgrid_api-0.1.4 → variantgrid_api-0.1.5}/variantgrid_api.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.0
 Name: variantgrid-api
-Version: 0.1.4
+Version: 0.1.5
 Summary: API to connect to VariantGrid
 Home-page: https://bitbucket.org/sacgf/variantgrid_api
 Author: David Lawrence

variantgrid_api-0.1.4/variantgrid_api/__init__.py

@@ -1,2 +0,0 @@
-
-__version__ = '0.1.4'