Merge pull request #52 from bento-platform/features/handle-get

handle GET parameters

bento_beacon/config_files/config.py

@@ -18,6 +18,8 @@ class Config:
         "info": "record"
     }
 
+    DEFAULT_PAGINATION_PAGE_SIZE = 10
+
     BENTO_DOMAIN = os.environ.get("BENTOV2_DOMAIN")
     BEACON_BASE_URL = os.environ.get("BEACON_BASE_URL")
     BENTO_PUBLIC_URL = os.environ.get("BENTOV2_PUBLIC_URL")

bento_beacon/utils/beacon_request.py

@@ -10,7 +10,7 @@ def request_defaults():
         "includeResultsetResponses": "ALL",
         "pagination": {
             "skip": 0,
-            "limit": 0
+            "limit": current_app.config["DEFAULT_PAGINATION_PAGE_SIZE"]
         },
         "requestedSchemas": []
     }
@@ -21,16 +21,9 @@ def expand_path(id):
     return id.replace("/", ".[item].")
 
 
-# request read from flask request context
 def query_parameters_from_request():
-    if request.method == "POST":
-        beacon_args = request.get_json() or {}
-    else:
-        beacon_args = {}
-
-    variants_query = beacon_args.get("query", {}).get(
-        "requestParameters", {}).get("g_variant") or {}
-    filters = beacon_args.get("query", {}).get("filters") or []
+    variants_query = g.request_data.get("requestParameters", {}).get("g_variant") or {}
+    filters = g.request_data.get("filters") or []
 
     # reject if too many filters
     max_filters = current_app.config["MAX_FILTERS"]
@@ -41,7 +34,7 @@ def query_parameters_from_request():
     phenopacket_filters = list(filter(lambda f: f["id"].startswith("phenopacket."), filters))
     experiment_filters = list(filter(lambda f: f["id"].startswith("experiment."), filters))
     config_filters = [f for f in filters if f not in phenopacket_filters and f not in experiment_filters]
-    
+
     # strip filter prefixes and convert remaining ids to bento format
     phenopacket_filters = list(map(lambda f:  {"id": expand_path(f["id"])[len("phenopacket."):],
                                                "operator": f["operator"], "value": f["value"]}, phenopacket_filters))
@@ -50,26 +43,69 @@ def query_parameters_from_request():
     return variants_query, phenopacket_filters, experiment_filters, config_filters
 
 
+# structure GET params so they match the nested structure in POST
+def package_get_params(params):
+    param_keys = list(params)
+
+    query_params_primitives = ("includeResultsetResponses", "requestedGranularity", "testMode")
+    variant_params_primitives = ("alternateBases", "aminoacidChange", "assemblyId", "geneId", "genomicAlleleShortForm",
+                                 "mateName", "referenceBases", "referenceName", "variantMaxLength", "variantMinLength",
+                                 "variantType")
+    variant_params_arrays = ("start", "end")
+    pagination_params = ("skip", "limit")
+
+    meta = {}
+    if ["apiVersion"] in param_keys:
+        meta["apiVersion"] = params["apiVersion"]
+
+    pagination = {}
+    for key in pagination_params:
+        if key in param_keys:
+            pagination[key] = params[key]
+
+    g_variant = {}
+    for key in variant_params_primitives:
+        if key in param_keys:
+            g_variant[key] = params[key]
+    for key in variant_params_arrays:
+        if key in param_keys:
+            g_variant[key] = params.getlist(key)
+
+    query = {"requestParameters": {"g_variant": g_variant}, "pagination": pagination}
+    for key in query_params_primitives:
+        if key in param_keys:
+            query[key] = params[key]
+    if "filters" in param_keys:
+        query["filters"] = params.getlist("filters")
+
+    return {"meta": meta, "query": query}
+
+
 def save_request_data():
     defaults = request_defaults()
 
-    # queries only use POST for now
-    # if GET, it's a call to an info endpoint, can ignore anything here for now
     if request.method == "POST":
         request_args = request.get_json() or {}
     else:
-        request_args = {}
+        request_args = package_get_params(request.args)
 
     request_meta = request_args.get("meta", {})
     request_query = request_args.get("query", {})
     request_bento = request_args.get("bento", {})
+    query_request_parameters = request_query.get("requestParameters")
+    query_filters = request_query.get("filters")
 
     request_data = {
         "apiVersion": request_meta.get("apiVersion", defaults["apiVersion"]),
         "requestedSchemas": request_meta.get("requestedSchemas", defaults["requestedSchemas"]),
         "pagination": {**defaults["pagination"], **request_query.get("pagination", {})},
         "requestedGranularity": request_query.get("requestedGranularity", defaults["granularity"]),
     }
+    if query_request_parameters:
+        request_data["requestParameters"] = query_request_parameters
+
+    if query_filters:
+        request_data["filters"] = query_filters
 
     if request_bento:
         request_data["bento"] = request_bento
@@ -81,7 +117,7 @@ def validate_request():
     if request.method == "POST":
         request_args = request.get_json() or {}
     else:
-        # GET currently used for info endpoints only, so no request payload
+        # GET params are not bound by the beaconRequestBody schema
         return
 
     # file path resolver for local json schema