Merge pull request #62 from bento-platform/features/configure-response

Features/configure response

bento_beacon/app.py

@@ -14,7 +14,7 @@
 from .authz.middleware import authz_middleware
 from .config_files.config import Config
 from .utils.beacon_response import beacon_error_response
-from .utils.beacon_request import save_request_data, validate_request
+from .utils.beacon_request import save_request_data, validate_request, verify_permissions
 from .utils.beacon_response import init_response_data
 from .utils.katsu_utils import katsu_censorship_settings
 
@@ -99,6 +99,7 @@
 @app.before_request
 def before_request():
     validate_request()
+    verify_permissions()
     save_request_data()
     init_response_data()
 

bento_beacon/authz/middleware.py

@@ -1,7 +1,7 @@
 from flask import request
 from bento_lib.auth.middleware.flask import FlaskAuthMiddleware
 from ..config_files.config import Config
-from ..utils.beacon_response import build_response_meta
+from ..utils.beacon_response import middleware_meta_callback
 
 __all__ = [
     "authz_middleware",
@@ -19,7 +19,7 @@
 authz_middleware = FlaskAuthMiddleware(
     Config.AUTHZ_URL,
     enabled=Config.AUTHZ_ENABLED,
-    beacon_meta_callback=build_response_meta,
+    beacon_meta_callback=middleware_meta_callback,
     debug_mode=Config.BENTO_DEBUG
 )
 

bento_beacon/config_files/config.py

@@ -1,14 +1,16 @@
 import json
 import os
 
+GA4GH_BEACON_REPO_URL = "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2"
+
 
 class Config:
     BEACON_SPEC_VERSION = "v2.0.0"
 
     # version of this implementation
     BENTO_BEACON_VERSION = os.environ.get("BENTO_BEACON_VERSION")
 
-    # max granularity for unauthorized users
+    # default when no requested granularity, as well as max granularity for anonymous users
     DEFAULT_GRANULARITY = {
         "individuals": "count",
         "variants": "count",
@@ -42,7 +44,7 @@ class Config:
             "defaultSchema": {
                 "id": "ga4gh-beacon-biosample-v2.0.0",
                 "name": "Default schema for biosamples",
-                    "referenceToSchemaDefinition": "https://github.com/ga4gh-beacon/beacon-v2/blob/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json",
+                    "referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json",
                     "schemaVersion": "v2.0.0"
             },
             "partOfSpecification": "Beacon v2.0.0"
@@ -54,7 +56,7 @@ class Config:
             "defaultSchema": {
                 "id": "ga4gh-beacon-cohort-v2.0.0",
                 "name": "Default schema for cohorts",
-                    "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json",
+                    "referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json",
                     "schemaVersion": "v2.0.0"
             },
             "partOfSpecification": "Beacon v2.0.0"
@@ -67,7 +69,7 @@ class Config:
             "defaultSchema": {
                 "id": "ga4gh-beacon-dataset-v2.0.0",
                 "name": "Default schema for datasets",
-                        "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json",
+                        "referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json",
                         "schemaVersion": "v2.0.0"
             },
             "partOfSpecification": "Beacon v2.0.0"
@@ -92,13 +94,41 @@ class Config:
             "defaultSchema": {
                 "id": "ga4gh-beacon-variant-v2.0.0",
                 "name": "Default schema for a genomic variation",
-                        "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json",
+                        "referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json",
                         "schemaVersion": "v2.0.0"
             },
             "partOfSpecification": "Beacon v2.0.0"
 
         }
     }
+
+    INFO_ENDPOINTS_SCHEMAS = {
+        "/":  {
+            "entityType": "info",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json"
+        },
+        "/configuration": {
+            "entityType": "configuration",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconConfigurationResponse.json"
+        },
+        "/entry_types": {
+            "entityType": "entryType",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconEntryTypesResponse.json"
+        },
+        "/filtering_terms": {
+            "entityType": "filteringTerm",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconFilteringTermsResponse.json"
+        },
+        "/info": {
+            "entityType": "info",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json"
+        },
+        "/map": {
+            "entityType": "map",
+            "schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconMapResponse.json"
+        },
+        "/overview": {}
+    }
 # -------------------
 # katsu
 

bento_beacon/constants.py

@@ -0,0 +1,3 @@
+GRANULARITY_BOOLEAN = "boolean"
+GRANULARITY_COUNT = "count"
+GRANULARITY_RECORD = "record"

bento_beacon/endpoints/biosamples.py

@@ -1,45 +1,17 @@
-from json import JSONDecodeError
-import requests
-from flask import Blueprint, jsonify, current_app
-from ..utils.exceptions import APIException, NotImplemented
-from ..utils.beacon_response import beacon_response, katsu_not_found
-from ..utils.beacon_mappings import katsu_biosample_to_beacon_biosample
+from flask import Blueprint
+from ..utils.exceptions import NotImplemented
 
-biosamples = Blueprint("biosamples", __name__)
 
+biosamples = Blueprint("biosamples", __name__)
 
-# TODO: pass beacon filtering terms as katsu queries
 
 @biosamples.route("/biosamples", methods=['GET', 'POST'])
 def get_biosamples():  # TODO: authz
-    # katsu_response = query_katsu(
-    #     current_app.config["KATSU_BIOSAMPLES_ENDPOINT"])
-
-    # current_app.logger.info(katsu_response)
-    # if katsu_not_found(katsu_response):
-    #     current_app.logger.info("katsu not found")
-    #     return beacon_response([])
-
-    # # expect response with properties "count", "next", "previous", "results"
-    # results = katsu_response.get("results")
-    # mapped_results = list(map(katsu_biosample_to_beacon_biosample, results))
-    # return beacon_response(mapped_results)
     raise NotImplemented()
 
 
 @biosamples.route("/biosamples/<id>", methods=['GET', 'POST'])
 def get_katsu_biosamples_by_id(id):  # TODO: authz
-    # katsu_response = query_katsu(
-    #     current_app.config["KATSU_BIOSAMPLES_ENDPOINT"], id)
-
-    # current_app.logger.info(katsu_response)
-
-    # if katsu_not_found(katsu_response):
-    #     current_app.logger.info("katsu returned 'not found'")
-    #     return beacon_response([])
-
-    # mapped_repsonse = katsu_biosample_to_beacon_biosample(katsu_response)
-    # return beacon_response([mapped_repsonse])
     raise NotImplemented()
 
 

bento_beacon/endpoints/cohorts.py

@@ -1,34 +1,28 @@
 from flask import Blueprint, current_app
 from ..authz.middleware import authz_middleware
-from ..utils.exceptions import NotImplemented
-from ..utils.beacon_response import beacon_response
+from ..utils.beacon_response import beacon_collections_response
 
 cohorts = Blueprint("cohorts", __name__)
 
 
 @cohorts.route("/cohorts", methods=['GET', 'POST'])
 @authz_middleware.deco_public_endpoint
 def get_cohorts():
-    granularity = current_app.config["DEFAULT_GRANULARITY"]["cohorts"]
-
-    cohort = current_app.config["BEACON_COHORT"]
-    results = {"collections": cohort}
-    return beacon_response(results, collection_response=True)
+    cohorts = current_app.config["BEACON_COHORT"]
+    return beacon_collections_response({"collections": cohorts})
 
 
 @cohorts.route("/cohorts/<id>", methods=['GET', 'POST'])
 @authz_middleware.deco_public_endpoint
 def get_cohort_by_id(id):
-    cohort = current_app.config["BEACON_COHORT"]
-    response = cohort if id == cohort.get("id") else {}
-    return beacon_response(response, collection_response=True)
-
-
-@cohorts.route("/cohorts/<id>/individuals", methods=['GET', 'POST'])
-def individuals_by_cohort(id):  # TODO: authz
-    raise NotImplemented()
+    cohorts = current_app.config["BEACON_COHORT"]
+    cohort_this_id = next((c for c in cohorts if c.get("id") == id), [])
+    return beacon_collections_response({"collections": cohort_this_id})
 
 
-@cohorts.route("/cohorts/<id>/filtering_terms", methods=['GET', 'POST'])
-def filtering_terms_by_cohort(id):  # TODO: authz
-    raise NotImplemented()
+# -------------------------------------------------------
+#       endpoints in beacon model not yet implemented:
+#
+#       /cohorts/<id>/individuals
+#       /cohorts/<id>/filtering_terms
+# -------------------------------------------------------

bento_beacon/endpoints/datasets.py

@@ -1,7 +1,6 @@
-from flask import Blueprint, current_app
+from flask import Blueprint
 from ..authz.middleware import authz_middleware
-from ..utils.exceptions import NotImplemented
-from ..utils.beacon_response import beacon_response
+from ..utils.beacon_response import beacon_collections_response
 from ..utils.katsu_utils import katsu_datasets
 from ..utils.beacon_mappings import katsu_to_beacon_dataset_mapping
 
@@ -11,39 +10,24 @@
 @datasets.route("/datasets", methods=['GET', 'POST'])
 @authz_middleware.deco_public_endpoint  # TODO: authz - more flexibility in what is visible (?)
 def get_datasets():
-    granularity = current_app.config["DEFAULT_GRANULARITY"]["datasets"]
-
     k_datasets = katsu_datasets()
-    datasets_beacon_format = list(
-        map(katsu_to_beacon_dataset_mapping, k_datasets))
-    results = {"collections": datasets_beacon_format}
-    return beacon_response(results, collection_response=True)
+    datasets_beacon_format = list(map(katsu_to_beacon_dataset_mapping, k_datasets))
+    return beacon_collections_response({"collections": datasets_beacon_format})
 
 
 @datasets.route("/datasets/<id>", methods=['GET', 'POST'])
 @authz_middleware.deco_public_endpoint  # TODO: authz - more flexibility in what is visible (?)
 def get_datasets_by_id(id):
     k_dataset = katsu_datasets(id)
-    dataset_beacon_format = katsu_to_beacon_dataset_mapping(
-        k_dataset) if k_dataset else {}
-    return beacon_response(dataset_beacon_format, collection_response=True)
-
-
-@datasets.route("/datasets/<id>/g_variants", methods=['GET', 'POST'])
-def variants_by_dataset(id):  # TODO: authz
-    raise NotImplemented()
-
-
-@datasets.route("/datasets/<id>/biosamples", methods=['GET', 'POST'])
-def biosamples_by_dataset(id):  # TODO: authz
-    raise NotImplemented()
-
-
-@datasets.route("/datasets/<id>/individuals", methods=['GET', 'POST'])
-def individuals_by_dataset(id):  # TODO: authz
-    raise NotImplemented()
-
-
-@datasets.route("/datasets/<id>/filtering_terms", methods=['GET', 'POST'])
-def filtering_terms_by_dataset(id):  # TODO: authz
-    raise NotImplemented()
+    dataset_beacon_format = katsu_to_beacon_dataset_mapping(k_dataset) if k_dataset else []
+    return beacon_collections_response({"collections": dataset_beacon_format})
+
+
+# -------------------------------------------------------
+#       endpoints in beacon model not yet implemented:
+#
+#       /datasets/<id>/g_variants
+#       /datasets/<id>/biosamples
+#       /datasets/<id>/individuals
+#       /datasets/<id>/filtering_terms
+# ---------------------------------------------------

bento_beacon/endpoints/individuals.py

@@ -1,17 +1,22 @@
 from flask import Blueprint
 from functools import reduce
-from ..authz.middleware import authz_middleware, PERMISSION_DOWNLOAD_DATA, PERMISSION_QUERY_DATA, check_permission
+from ..authz.middleware import (
+    authz_middleware,
+    PERMISSION_DOWNLOAD_DATA,
+    PERMISSION_QUERY_DATA,
+    check_permission
+)
 from ..utils.beacon_request import (
     query_parameters_from_request,
     summary_stats_requested,
 )
 from ..utils.beacon_response import (
-    beacon_response,
     add_info_to_response,
     add_stats_to_response,
     add_overview_stats_to_response,
     zero_count_response,
-    beacon_full_response
+    build_query_response,
+    beacon_result_set_response
 )
 from ..utils.katsu_utils import (
     katsu_filters_and_sample_ids_query,
@@ -27,9 +32,6 @@
 
 @individuals.route("/individuals", methods=['GET', 'POST'])
 def get_individuals():
-
-    full_response = check_permission(PERMISSION_QUERY_DATA)
-
     variants_query, phenopacket_filters, experiment_filters, config_filters = query_parameters_from_request()
 
     no_query = not (variants_query or phenopacket_filters or experiment_filters or config_filters)
@@ -43,7 +45,7 @@ def get_individuals():
         total_count = katsu_total_individuals_count()
         if summary_stats_requested():
             add_overview_stats_to_response()
-        return beacon_response({"count": total_count})
+        return build_query_response(numTotalResults=total_count)
 
     # ----------------------------------------------------------
     #  collect biosample ids from variant and experiment search
@@ -82,14 +84,11 @@ def get_individuals():
     if summary_stats_requested():
         add_stats_to_response(individual_ids)
 
-    if full_response:
-        return individuals_full_response(individual_ids)
-
-    return beacon_response({"count": len(individual_ids), "results": individual_ids})
+    return build_query_response(ids=individual_ids, full_record_handler=individuals_full_results)
 
 
 # TODO: pagination (ideally after katsu search gets paginated)
-def individuals_full_response(ids):
+def individuals_full_results(ids):
 
     # temp
     # if len(ids) > 100:
@@ -100,10 +99,12 @@ def individuals_full_response(ids):
     phenopackets_by_result_set = phenopackets_for_ids(ids).get("results", {})
     result_ids = list(phenopackets_by_result_set.keys())
     result_sets = {}
+    numTotalResults = 0
 
     for r_id in result_ids:
         results_this_id = phenopackets_by_result_set.get(r_id, {}).get("matches", [])
         results_count = len(results_this_id)
+        numTotalResults += results_count
         result = {
             "id": r_id,
             "setType": "individual",
@@ -116,14 +117,14 @@ def individuals_full_response(ids):
             result["resultsHandovers"] = handover_this_id
         result_sets[r_id] = result
 
-    return beacon_full_response(result_sets)
+    return result_sets, numTotalResults
 
 
 @individuals.route("/individuals/<id>", methods=['GET', 'POST'])
 @authz_middleware.deco_require_permissions_on_resource({PERMISSION_QUERY_DATA})
 def individual_by_id(id):
     # forbidden / unauthorized if no permissions
-    return individuals_full_response([id])
+    return beacon_result_set_response([id], 1)
 
 
 # -------------------------------------------------------