Merge pull request #324 from EGA-archive/develop

Handling errors
EGA-archive · May 14, 2024 · 196c930 · 196c930
2 parents c3102c9 + dcef8c4
commit 196c930
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Showing 10 changed files with 398 additions and 283 deletions.
diff --git a/beacon/request/handlers.py b/beacon/request/handlers.py
diff --git a/beacon/request/model.py b/beacon/request/model.py
@@ -6,6 +6,7 @@
 from beacon import conf
 from humps.main import camelize
 from aiohttp.web_request import Request
+from aiohttp import web
 
 LOG = logging.getLogger(__name__)
 
@@ -97,8 +98,10 @@ def from_request(self, request: Request) -> Self:
                     self.query.pagination.limit = int(v)
                 elif k == "includeResultsetResponses":
                     self.query.include_resultset_responses = IncludeResultsetResponses(v)
-                else:
+                elif k == 'filters' or k in ["start", "end", "assemblyId", "referenceName", "referenceBases", "alternateBases", "variantType","variantMinLength","variantMaxLength","geneId","genomicAlleleShortForm","aminoacidChange","clinicalRelevance"]:
                     self.query.request_parameters[k] = v
+                else:
+                    raise web.HTTPBadRequest(text='request parameter introduced is not allowed')
         return self
 
     def summary(self):

diff --git a/beacon/request/routes.py b/beacon/request/routes.py
@@ -2,7 +2,7 @@
 
 from beacon.db import analyses, biosamples, cohorts, datasets, g_variants, individuals, runs, filtering_terms
 from beacon.request.handlers import collection_handler, generic_handler, filtering_terms_handler
-from beacon.response import framework, info, service_info
+from beacon.response import framework, info, service_info, error
 
 routes = [
 
@@ -76,6 +76,9 @@
     web.get('/api/runs/{id}/g_variants', generic_handler(db_fn=runs.get_variants_of_run)),
     web.get('/api/runs/{id}/analyses', generic_handler(db_fn=runs.get_analyses_of_run)),
 
+    web.get('/api/{tail:.*}', error.handler),
+    web.get('/{tail:.*}', error.handler),
+
 
 
     ########################################
@@ -136,4 +139,7 @@
     web.post('/api/runs/{id}/g_variants', generic_handler(db_fn=runs.get_variants_of_run)),
     web.post('/api/runs/{id}/analyses', generic_handler(db_fn=runs.get_analyses_of_run)),
 
+    web.post('/api/{tail:.*}', error.handler),
+    web.post('/{tail:.*}', error.handler)
+
 ]
diff --git a/beacon/response/build_response.py b/beacon/response/build_response.py
@@ -15,14 +15,22 @@ def build_meta(qparams: RequestParams, entity_schema: Optional[DefaultSchemas],
 
     We assume that receivedRequest is the evaluated request (qparams) sent by the user.
     """
-
-    meta = {
-        'beaconId': conf.beacon_id,
-        'apiVersion': conf.api_version,
-        'returnedGranularity': returned_granularity,
-        'receivedRequestSummary': qparams.summary(),
-        'returnedSchemas': [entity_schema.value] if entity_schema is not None else []
-    }
+    try:
+        meta = {
+            'beaconId': conf.beacon_id,
+            'apiVersion': conf.api_version,
+            'returnedGranularity': returned_granularity,
+            'receivedRequestSummary': qparams.summary(),
+            'returnedSchemas': [entity_schema.value] if entity_schema is not None else []
+        }
+    except Exception:
+        meta = {
+            'beaconId': conf.beacon_id,
+            'apiVersion': conf.api_version,
+            'returnedGranularity': returned_granularity,
+            'receivedRequestSummary': qparams,
+            'returnedSchemas': [entity_schema.value] if entity_schema is not None else []
+        }
     return meta
 
 def build_response_summary(exists, num_total_results):
@@ -253,6 +261,22 @@ def build_beacon_info_response(data, qparams, func_response_type, authorized_dat
 
     return beacon_response
 
+########################################
+# Error Response
+########################################
+
+def build_beacon_error_response(errorCode, qparams, errorMessage):
+
+    beacon_response = {
+        'meta': build_meta(qparams, None, Granularity.RECORD),
+        'error': {
+            'errorCode': str(errorCode),
+            'errorMessage': str(errorMessage)
+        }
+    }
+
+    return beacon_response
+
 ########################################
 # Service Info Response
 ########################################
@@ -300,6 +324,18 @@ def build_filtering_terms_response(data,
         # TODO: 'extendedInfo': build_extended_info(),
         'response': {
             'filteringTerms': data,
+            'resources': [{"id": "hp","name": "Human Phenotype Ontology","url": "https://purl.obolibrary.org/obo/hp.owl","version": "27-03-2020","namespacePrefix": "HP","iriPrefix": "https://purl.obolibrary.org/obo/HP_"},
+                {"id": "icd10","name": "International Classification of Diseaes 10th edition","version": "17-03-2008","namespacePrefix": "ICD10"},
+                {"id": "ncit","name": "National Cancer Institute Thesaurus","url": "https://purl.obolibrary.org/obo/ncit.owl","version": "19-10-2023","namespacePrefix": "NCIT","iriPrefix": "https://purl.obolibrary.org/obo/NCIT_"},
+                {"id": "loinc","name": "Logical Observation Identifiers Names and Codes","url": "https://loinc.org/download/loinc-complete/","version": "19-10-2023","namespacePrefix": "LOINC"},
+                {"id": "gaz","name": "Gazetteer","url": "https://purl.obolibrary.org/obo/gaz.owl","namespacePrefix": "GAZ","iriPrefix": "https://purl.obolibrary.org/obo/GAZ_"},
+                {"id": "opcs4","name": "Office of Population Censuses and Surveys 4th revision","version": "01-04-2023","namespacePrefix": "OPCS4"},
+                {"id": "genepio","name": "Genomic Epidemiology Ontology","version": "19-08-2023","namespacePrefix": "GENEPIO"},
+                {"id": "obi","name": "Ontology for Biomedical Investigations","url": "http://purl.obolibrary.org/obo/obi.owl","version": "19-01-2024","namespacePrefix": "OBI","iriPrefix": "https://purl.obolibrary.org/obo/OBI_"},
+                {"id": "efo","name": "Experimental Factor Ontology","version": "15-04-2024","namespacePrefix": "EFO"},
+                {"id": "uberon","name": "Uber-anatomy ontology","version": "22-03-2024","namespacePrefix": "UBERON"},
+                {"id": "doid","name": "Human Disease Ontology","url": "http://purl.obolibrary.org/obo/doid.owl","version": "28-03-2024","namespacePrefix": "DOID","iriPrefix": "https://purl.obolibrary.org/obo/DOID_"},
+                {"id": "geno","name": "GENO ontology","version": "08-10-2023","namespacePrefix": "GENO"}]
         },
         'beaconHandovers': beacon_handovers(),
     }

diff --git a/beacon/response/error.py b/beacon/response/error.py
@@ -0,0 +1,21 @@
+import subprocess
+import logging
+import json
+from aiohttp.web_request import Request
+from beacon.db.datasets import get_datasets
+from beacon.request import RequestParams
+from beacon.response.build_response import build_beacon_error_response
+from beacon.utils.auth import resolve_token
+from beacon.utils.stream import json_stream
+from bson import json_util
+
+LOG = logging.getLogger(__name__)
+
+async def handler(request: Request):
+    LOG.error('Running an error request')
+
+    # Fetch datasets info
+    qparams = ''
+
+    response_converted= build_beacon_error_response(404, qparams, 'Not Found')
+    return await json_stream(request, response_converted)
diff --git a/beacon/response/info.py b/beacon/response/info.py
@@ -16,54 +16,67 @@
 from aiohttp.web_request import Request
 from beacon.db.datasets import get_datasets
 from beacon.request import RequestParams
-from beacon.response.build_response import build_beacon_info_response
+from beacon.response.build_response import build_beacon_info_response, build_beacon_error_response
 from beacon.utils.auth import resolve_token
 from beacon.utils.stream import json_stream
 from bson import json_util
 
 LOG = logging.getLogger(__name__)
 
 async def handler(request: Request):
-    LOG.info('Running a GET info request')
+    try:
+        LOG.info('Running a GET info request')
 
-    # Fetch datasets info
-    json_body = await request.json() if request.method == "POST" and request.has_body and request.can_read_body else {}
-    qparams = RequestParams(**json_body).from_request(request)
-    _, _, datasets = get_datasets(None, qparams)
-    beacon_datasets = [ r for r in datasets ]
-
-    all_datasets = [ r['_id'] for r in beacon_datasets]
-    specific_datasets = [ r['id'] for r in beacon_datasets]
-    LOG.debug(specific_datasets)
+        # Fetch datasets info
+        json_body = await request.json() if request.method == "POST" and request.has_body and request.can_read_body else {}
+        qparams = RequestParams(**json_body).from_request(request)
+        _, _, datasets = get_datasets(None, qparams)
+        beacon_datasets = [ r for r in datasets ]
+            
+        all_datasets = [ r['_id'] for r in beacon_datasets]
+        specific_datasets = [ r['id'] for r in beacon_datasets]
+        LOG.debug(specific_datasets)
 
-    search_datasets = []
-    authenticated=False
-    access_token = request.headers.get('Authorization')
-    LOG.debug(access_token)
-    if access_token is not None:
-        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)
-        LOG.debug('all datasets:  %s', all_datasets)
-        LOG.info('resolved datasets:  %s', authorized_datasets)
-        LOG.debug(authenticated)
+        search_datasets = []
+        authenticated=False
+        access_token = request.headers.get('Authorization')
+        LOG.debug(access_token)
+        if access_token is not None:
+            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)
+            LOG.debug('all datasets:  %s', all_datasets)
+            LOG.info('resolved datasets:  %s', authorized_datasets)
+            LOG.debug(authenticated)
 
-        specific_datasets_authorized = []
+            specific_datasets_authorized = []
 
-        if not specific_datasets:
-            for auth_element in authorized_datasets:
-                specific_datasets_authorized = [ r for r in beacon_datasets if r['id'] == auth_element]
+            if not specific_datasets:
+                for auth_element in authorized_datasets:
+                    specific_datasets_authorized = [ r for r in beacon_datasets if r['id'] == auth_element]
+            else:
+                for element in specific_datasets:
+                    if element in authorized_datasets:
+                        specific_datasets_authorized = [ r for r in beacon_datasets if r['id'] == element]
         else:
-            for element in specific_datasets:
-                if element in authorized_datasets:
-                    specific_datasets_authorized = [ r for r in beacon_datasets if r['id'] == element]
-    else:
-        specific_datasets_authorized = []
+            specific_datasets_authorized = []
 
-
-    response_converted = build_beacon_info_response(specific_datasets_authorized,
-                                                                qparams,
-                                                                lambda x,y,z: x,
-                                                                authorized_datasets if authenticated else [])
+
+        response_converted = build_beacon_info_response(specific_datasets_authorized,
+                                                                    qparams,
+                                                                    lambda x,y,z: x,
+                                                                    authorized_datasets if authenticated else [])
+    except Exception as err:
+        qparams = ''
+        if str(err) == 'Not Found':
+            response_converted = build_beacon_error_response(404, qparams, str(err))
+        elif str(err) == 'Bad Request':
+            response_converted = build_beacon_error_response(400, qparams, str(err)+':'+str(err.text))
+        elif str(err) == 'Bad Gateway':
+            response_converted = build_beacon_error_response(502, qparams, str(err))
+        elif str(err) == 'Method Not Allowed':
+            response_converted = build_beacon_error_response(405, qparams, str(err))
+        else:
+            response_converted = build_beacon_error_response(500, qparams, str(err))
     return await json_stream(request, response_converted)
diff --git a/beacon/response/service_info.py b/beacon/response/service_info.py
@@ -1,11 +1,20 @@
 import logging
 from aiohttp.web_request import Request
-from beacon.response.build_response import build_beacon_service_info_response
+from beacon.response.build_response import build_beacon_service_info_response, build_beacon_error_response
 from beacon.utils.stream import json_stream
 
 LOG = logging.getLogger(__name__)
 
 async def handler(request: Request):
-    LOG.info('Running a GET service info request')
-    response_converted = build_beacon_service_info_response()
+    try:
+        LOG.info('Running a GET service info request')
+        response_converted = build_beacon_service_info_response()
+    except Exception as err:
+        qparams = ''
+        if str(err) == 'Not Found':
+            response_converted = build_beacon_error_response(404, qparams, str(err))
+        elif str(err) == 'Bad Request':
+            response_converted = build_beacon_error_response(400, qparams, str(err))
+        else:
+            response_converted = build_beacon_error_response(500, qparams, str(err))
     return await json_stream(request, response_converted)
diff --git a/deploy/Makefile b/deploy/Makefile
@@ -9,22 +9,6 @@ build:
 	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.genomicVariations.deleteMany({})"'
 	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.individuals.deleteMany({})"'
 	docker exec rimongo /bin/bash -c 'mongo beacon -u root -p example --authenticationDatabase admin --eval "db.runs.deleteMany({})"'
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/analyses.json rimongo:tmp/analyses.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/biosamples.json rimongo:tmp/biosamples.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/cohorts.json rimongo:tmp/cohorts.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/datasets.json rimongo:tmp/datasets.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/genomicVariations.json rimongo:tmp/genomicVariations.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/individuals.json rimongo:tmp/individuals.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/runs.json rimongo:tmp/runs.json
-	docker cp /data/vault/bio-scratch/arnau/beacon/beacon2-ri-tools-v2_test_anot/filtering_terms.json rimongo:tmp/filtering_terms.json
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
-	docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/filtering_terms.json --collection filtering_terms
 	docker cp data/analyses.json rimongo:tmp/analyses.json
 	docker cp data/biosamples.json rimongo:tmp/biosamples.json
 	docker cp data/cohorts.json rimongo:tmp/cohorts.json

diff --git a/deploy/README.md b/deploy/README.md
@@ -40,23 +40,23 @@ With `mongo-express` we can see the contents of the database at [http://localhos
 To load the database we execute the following commands:
 
 ```bash
-docker cp /path/to/analyses.json deploy_db_1:tmp/analyses.json
-docker cp /path/to/biosamples.json deploy_db_1:tmp/biosamples.json
-docker cp /path/to/cohorts.json deploy_db_1:tmp/cohorts.json
-docker cp /path/to/datasets.json deploy_db_1:tmp/datasets.json
-docker cp /path/to/genomicVariations.json deploy_db_1:tmp/genomicVariations.json
-docker cp /path/to/individuals.json deploy_db_1:tmp/individuals.json
-docker cp /path/to/runs.json deploy_db_1:tmp/runs.json
+docker cp /path/to/analyses.json rimongo:tmp/analyses.json
+docker cp /path/to/biosamples.json rimongo:tmp/biosamples.json
+docker cp /path/to/cohorts.json rimongo:tmp/cohorts.json
+docker cp /path/to/datasets.json rimongo:tmp/datasets.json
+docker cp /path/to/genomicVariations.json rimongo:tmp/genomicVariations.json
+docker cp /path/to/individuals.json rimongo:tmp/individuals.json
+docker cp /path/to/runs.json rimongo:tmp/runs.json
 ```
 
 ```bash
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
-docker exec deploy_db_1 mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/datasets.json --collection datasets
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/analyses.json --collection analyses
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/biosamples.json --collection biosamples
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/cohorts.json --collection cohorts
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/genomicVariations.json --collection genomicVariations
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/individuals.json --collection individuals
+docker exec rimongo mongoimport --jsonArray --uri "mongodb://root:[email protected]:27017/beacon?authSource=admin" --file /tmp/runs.json --collection runs
 ```
 
 This loads the JSON files inside of the `data` folder into the MongoDB database container. Each time you import data you will have to create indexes for the queries to run smoothly. Please, check the next point about how to Create the indexes.

diff --git a/deploy/docker-compose.yml b/deploy/docker-compose.yml
@@ -39,6 +39,7 @@ services:
   db:
     image: mongo:5
     hostname: mongo
+    container_name: rimongo
     ports:
       - 27017:27017
     environment:
@@ -79,6 +80,7 @@ services:
       - ./conf.py:/beacon/beacon/conf.py
       - ./logger.yml:/beacon/beacon/logger.yml
       - ../beacon/request/datasets.yml:/beacon/beacon/request/datasets.yml
+      - ../beacon/request/cohorts.yml:/beacon/beacon/request/cohorts.yml
       - ../beacon/request/response_type.yml:/beacon/beacon/request/response_type.yml
     ports:
       - "5050:5050"