Merge pull request #238 from EGA-archive/develop

last changes adding introspection and GDI changes

beacon/conf.py

@@ -102,7 +102,7 @@
 #
 # Permissions server configuration
 #
-permissions_url = 'http://beacon-permissions'
+permissions_url = 'http://beacon-permissions:5051/'
 #permissions_url = 'http://localhost:5051/'
 
 #

beacon/db/extract_filtering_terms.py

@@ -20,14 +20,44 @@
 import numpy as np
 from utils import get_filtering_documents
 
+import sys
+import os
+
+
+current = os.path.dirname(os.path.realpath(__file__))
+
+
+parent = os.path.dirname(current)
+
+
+sys.path.append(parent)
+
+
+import conf
+
 
 ONTOLOGY_REGEX = re.compile(r"([_A-Za-z0-9]+):([_A-Za-z0-9^\-]+)")
 
+client = MongoClient(
+        #"mongodb://127.0.0.1:27017/"
+        "mongodb://{}:{}@{}:{}/{}?authSource={}".format(
+            conf.database_user,
+            conf.database_password,
+            conf.database_host,
+            conf.database_port,
+            conf.database_name,
+            conf.database_auth_source,
+        )
+    )
+
+'''
+client = MongoClient(
 client = MongoClient(
     #"mongodb://127.0.0.1:27017/"
     "mongodb://root:example@mongo:27017/beacon?authSource=admin"
 
 )
+'''
 
 class MyProgressBar:
     def __init__(self):

beacon/request/handlers.py

@@ -6,6 +6,7 @@
 from bson import json_util
 from beacon import conf
 import yaml
+import jwt
 
 from beacon.request import ontologies
 from beacon.request.model import Granularity, RequestParams
@@ -66,6 +67,9 @@ async def wrapper(request: Request):
             except Exception:
                 specific_datasets = []
             access_token = access_token[7:]  # cut out 7 characters: len('Bearer ')
+
+
+
 
             authorized_datasets, authenticated = await resolve_token(access_token, search_datasets)
             LOG.debug(authorized_datasets)
@@ -178,6 +182,24 @@ async def wrapper(request: Request):
 
 
         qparams = RequestParams(**json_body).from_request(request)
+
+        if access_token is not None:
+            decoded = jwt.decode(access_token, options={"verify_signature": False})
+            LOG.debug(decoded)
+            token_username = decoded['preferred_username']
+            with open("/beacon/beacon/request/response_type.yml", 'r') as response_type_file:
+                response_type_dict = yaml.safe_load(response_type_file)
+
+            response_type = response_type_dict[token_username]
+            if response_type is not None:
+                for response_typed in response_type:    
+                    LOG.debug(response_typed)        
+                    if response_typed == 'boolean':
+                        qparams.query.requested_granularity = Granularity.BOOLEAN
+                    elif response_typed == 'count':
+                        qparams.query.requested_granularity = Granularity.COUNT
+                    elif response_typed == 'record':
+                        qparams.query.requested_granularity = Granularity.RECORD
 
 
         entry_id = request.match_info.get('id', None)
@@ -200,6 +222,8 @@ async def wrapper(request: Request):
             finish_record = limit*skip + limit
 
         response_converted = records
+
+        LOG.debug(qparams.query.requested_granularity)
 
         if qparams.query.requested_granularity == Granularity.BOOLEAN:
             response = build_beacon_boolean_response(response_converted, count, qparams, lambda x, y: x, entity_schema)
@@ -242,6 +266,11 @@ async def wrapper(request: Request):
             except Exception:
                 specific_datasets = []
             access_token = access_token[7:]  # cut out 7 characters: len('Bearer ')
+
+
+            decoded = jwt.decode(access_token, options={"verify_signature": False})
+            LOG.debug(decoded)
+            token_username = decoded['preferred_username']
 
             authorized_datasets, authenticated = await resolve_token(access_token, search_datasets)
             LOG.debug(authorized_datasets)

beacon/request/public_datasets.yml

@@ -1,3 +1,2 @@
 public_datasets:
- - CINECA_synthetic_cohort_EUROPE_UK1
- - AV_Dataset
+- AV_Dataset

beacon/request/response_type.yml

@@ -0,0 +1,2 @@
+new_user:
+- record

beacon/utils/auth.py

@@ -27,7 +27,7 @@ async def resolve_token(token, requested_datasets_ids):
     # * return _all_ the datasets the user has access to, in case the datasets list is empty
     async with ClientSession() as session:
         async with session.post(
-                'http://beacon-permissions:5051/',
+                permissions_url,
                 headers={'Authorization': 'Bearer ' + token,
                          'Accept': 'application/json'},
                 json={'datasets': requested_datasets_ids},  # will set the Content-Type to application/json

deploy/conf.py

@@ -99,7 +99,7 @@
 #
 # Permissions server configuration
 #
-permissions_url = 'http://beacon-permissions'
+permissions_url = 'http://beacon-permissions:5051/'
 
 #
 # IdP endpoints (OpenID Connect/Oauth2)