Merge pull request #142 from c3g/bento-lib

Switch from chord_lib to bento_lib

chord_metadata_service/chord/serializers.py

@@ -1,4 +1,4 @@
-from chord_lib.schemas.chord import CHORD_DATA_USE_SCHEMA
+from bento_lib.schemas.bento import BENTO_DATA_USE_SCHEMA
 from chord_metadata_service.restapi.serializers import GenericSerializer
 from jsonschema import Draft7Validator, Draft4Validator
 from rest_framework import serializers
@@ -12,6 +12,10 @@
 __all__ = ["ProjectSerializer", "DatasetSerializer", "TableOwnershipSerializer", "TableSerializer"]
 
 
+BENTO_DATA_USE_SCHEMA_VALIDATOR = Draft7Validator(BENTO_DATA_USE_SCHEMA)
+LINKED_FIELD_SETS_SCHEMA_VALIDATOR = Draft7Validator(LINKED_FIELD_SETS_SCHEMA)
+
+
 #############################################################
 #                                                           #
 #              Project Management  Serializers              #
@@ -51,17 +55,17 @@ def validate_creators(self, value):
 
     # noinspection PyMethodMayBeStatic
     def validate_data_use(self, value):
-        validation = Draft7Validator(CHORD_DATA_USE_SCHEMA).is_valid(value)
+        validation = BENTO_DATA_USE_SCHEMA_VALIDATOR.is_valid(value)
         if not validation:
             raise serializers.ValidationError("Data use is not valid")
         return value
 
     # noinspection PyMethodMayBeStatic
     def validate_linked_field_sets(self, value):
-        v = Draft7Validator(LINKED_FIELD_SETS_SCHEMA)
-        validation = v.is_valid(value)
+        validation = LINKED_FIELD_SETS_SCHEMA_VALIDATOR.is_valid(value)
         if not validation:
-            raise serializers.ValidationError([str(error.message) for error in v.iter_errors(value)])
+            raise serializers.ValidationError([
+                str(error.message) for error in LINKED_FIELD_SETS_SCHEMA_VALIDATOR.iter_errors(value)])
         return value
 
     def validate(self, data):

chord_metadata_service/chord/views_ingest.py

@@ -1,24 +1,26 @@
 import json
-import jsonschema
-import jsonschema.exceptions
 import os
 import uuid
 
 from django.core.exceptions import ValidationError
 from django.db import transaction
+from jsonschema import Draft7Validator
 from rest_framework.decorators import api_view, permission_classes, renderer_classes
 from rest_framework.permissions import AllowAny
 from rest_framework.renderers import BaseRenderer
 from rest_framework.response import Response
 
-from chord_lib.schemas.chord import CHORD_INGEST_SCHEMA
-from chord_lib.responses import errors
-from chord_lib.workflows import get_workflow, get_workflow_resource, workflow_exists
+from bento_lib.schemas.bento import BENTO_INGEST_SCHEMA
+from bento_lib.responses import errors
+from bento_lib.workflows import get_workflow, get_workflow_resource, workflow_exists
 
 from .ingest import METADATA_WORKFLOWS, WORKFLOWS_PATH, WORKFLOW_INGEST_FUNCTION_MAP
 from .models import Table
 
 
+BENTO_INGEST_SCHEMA_VALIDATOR = Draft7Validator(BENTO_INGEST_SCHEMA)
+
+
 class WDLRenderer(BaseRenderer):
     media_type = "text/plain"
     format = "text"
@@ -65,9 +67,7 @@ def ingest(request):
     # TODO: Use serializers with basic objects and maybe some more complex ones too (but for performance, this might
     #  not be optimal...)
 
-    try:
-        jsonschema.validate(request.data, CHORD_INGEST_SCHEMA)
-    except jsonschema.exceptions.ValidationError:
+    if not BENTO_INGEST_SCHEMA_VALIDATOR.is_valid(request.data):
         return Response(errors.bad_request_error("Invalid ingest request body"), status=400)  # TODO: Validation errors
 
     table_id = request.data["table_id"]

chord_metadata_service/chord/views_search.py

@@ -2,6 +2,8 @@
 import json
 import uuid
 
+from bento_lib.responses import errors
+from bento_lib.search import build_search_response, postgres
 from collections import Counter
 from datetime import datetime
 from django.db import connection
@@ -12,8 +14,6 @@
 from rest_framework.response import Response
 from typing import Any, Callable, Dict
 
-from chord_lib.responses import errors
-from chord_lib.search import build_search_response, postgres
 from chord_metadata_service.experiments.models import Experiment
 from chord_metadata_service.experiments.serializers import ExperimentSerializer
 from chord_metadata_service.mcode.models import MCodePacket

chord_metadata_service/metadata/settings.py

@@ -87,7 +87,7 @@
     'django.middleware.common.CommonMiddleware',
     'django.middleware.csrf.CsrfViewMiddleware',
     'django.contrib.auth.middleware.AuthenticationMiddleware',
-    'chord_lib.auth.django_remote_user.CHORDRemoteUserMiddleware',
+    'bento_lib.auth.django_remote_user.BentoRemoteUserMiddleware',
     'django.contrib.messages.middleware.MessageMiddleware',
     'django.middleware.clickjacking.XFrameOptionsMiddleware',
 ]
@@ -168,7 +168,7 @@
 
 REST_FRAMEWORK = {
     'DEFAULT_AUTHENTICATION_CLASSES': [
-        'chord_lib.auth.django_remote_user.CHORDRemoteUserAuthentication'
+        'bento_lib.auth.django_remote_user.BentoRemoteUserAuthentication'
     ],
     'DEFAULT_PARSER_CLASSES': (
         # allows serializers to use snake_case field names, but parse incoming data as camelCase
@@ -199,7 +199,7 @@
 ]
 
 
-AUTHENTICATION_BACKENDS = ["chord_lib.auth.django_remote_user.CHORDRemoteUserBackend"] + (
+AUTHENTICATION_BACKENDS = ["bento_lib.auth.django_remote_user.BentoRemoteUserBackend"] + (
     ["django.contrib.auth.backends.ModelBackend"] if DEBUG else [])
 
 

requirements.txt

@@ -2,9 +2,9 @@ alabaster==0.7.12
 appdirs==1.4.4
 attrs==19.3.0
 Babel==2.8.0
+bento-lib==0.11.0
 certifi==2020.6.20
 chardet==3.0.4
-chord-lib==0.9.0
 codecov==2.1.7
 colorama==0.4.3
 coreapi==2.3.3

setup.py

@@ -16,7 +16,7 @@
 
     python_requires=">=3.6",
     install_requires=[
-        "chord_lib[django]==0.9.0",
+        "bento_lib[django]==0.11.0",
         "Django>=2.2.14,<3.0",
         "django-filter>=2.3,<3.0",
         "django-nose>=1.4,<2.0",