Upading master

beacon/__main__.py

@@ -66,7 +66,7 @@ async def main(path=None):
     #)
 
     beacon = web.Application(
-        middlewares=[web.normalize_path_middleware(), middlewares.error_middleware, cors_middleware(origins=["https://beacon-network-test.ega-archive.org", "https://beacon-network-test2.ega-archive.org", "https://beacon-network-demo.ega-archive.org","https://beacon-network-demo2.ega-archive.org", "http://localhost:3000", "http://localhost:3010", "https://beacon-network-cineca-demo.ega-archive.org", "https://cancer-beacon-demo.ega-archive.org"])]
+        middlewares=[web.normalize_path_middleware(), middlewares.error_middleware, cors_middleware(origins=["https://beacon-network-test.ega-archive.org", "https://beacon-network-test2.ega-archive.org", "https://beacon-network-demo.ega-archive.org","https://beacon-network-demo2.ega-archive.org", "http://localhost:3000", "http://localhost:3010", "https://beacon-network-cineca-demo.ega-archive.org", "https://beacon.ega-archive.org", "https://cancer-beacon-demo.ega-archive.org"])]
     )
 
 
@@ -116,6 +116,11 @@ async def main(path=None):
             expose_headers="*",
             allow_methods=("POST", "PATCH", "GET", "OPTIONS"),
             allow_headers=DEFAULT_ALLOW_HEADERS),
+        "https://beacon.ega-archive.org":
+            aiohttp_cors.ResourceOptions(allow_credentials=True,
+            expose_headers="*",
+            allow_methods=("POST", "PATCH", "GET", "OPTIONS"),
+            allow_headers=DEFAULT_ALLOW_HEADERS),
         "http://localhost:3010":
             aiohttp_cors.ResourceOptions(allow_credentials=True,
             expose_headers="*",

beacon/api_version.yml

@@ -1 +1 @@
-api_version: v2.0-b8fa53a
+api_version: v2.0-b50b1ac

beacon/conf.py

@@ -126,6 +126,6 @@
 #
 ontologies_folder = "ontologies"
 
-alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration']
+alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']
 
 ontology_files={"NCIT": "http://purl.obolibrary.org/obo/NCIT.obo"}

beacon/db/analyses.py

@@ -45,7 +45,7 @@ def get_analyses(entry_id: Optional[str], qparams: RequestParams, dataset: str):
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_analysis_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'analyses'
@@ -63,7 +63,7 @@ def get_analysis_with_id(entry_id: Optional[str], qparams: RequestParams, datase
     if limit > 100 or limit == 0:
         limit = 100
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_variants_of_analysis(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'analyses'
@@ -86,7 +86,7 @@ def get_variants_of_analysis(entry_id: Optional[str], qparams: RequestParams, da
         limit = 100
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_filtering_terms_of_analyse(entry_id: Optional[str], qparams: RequestParams):
     query = {'scopes': 'analysis'}

beacon/db/biosamples.py

@@ -45,7 +45,7 @@ def get_biosamples(entry_id: Optional[str], qparams: RequestParams, dataset: str
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_biosample_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -64,7 +64,7 @@ def get_biosample_with_id(entry_id: Optional[str], qparams: RequestParams, datas
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_variants_of_biosample(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'g_variants'
@@ -82,7 +82,7 @@ def get_variants_of_biosample(entry_id: Optional[str], qparams: RequestParams, d
         limit = 100
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_analyses_of_biosample(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -102,7 +102,7 @@ def get_analyses_of_biosample(entry_id: Optional[str], qparams: RequestParams, d
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_runs_of_biosample(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'biosamples'
@@ -120,7 +120,7 @@ def get_runs_of_biosample(entry_id: Optional[str], qparams: RequestParams, datas
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_filtering_terms_of_biosample(entry_id: Optional[str], qparams: RequestParams):
     query = {'scopes': 'biosample'}

beacon/db/g_variants.py

@@ -6,6 +6,7 @@
 from beacon.request.model import AlphanumericFilter, Operator, RequestParams
 from beacon.db import client
 import yaml
+import time
 from aiohttp import web
 
 
@@ -238,6 +239,7 @@ def apply_request_parameters(query: Dict[str, List[dict]], qparams: RequestParam
 
 
 def get_variants(entry_id: Optional[str], qparams: RequestParams, dataset: str):
+    LOG.debug(time.time())
     collection = 'g_variants'
     mongo_collection = client.beacon.genomicVariations
     parameters_as_filters=False
@@ -267,7 +269,8 @@ def get_variants(entry_id: Optional[str], qparams: RequestParams, dataset: str):
         datasets_dict = yaml.safe_load(datasets_file)
     #LOG.debug(query)
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    LOG.debug(time.time())
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_variant_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -287,7 +290,7 @@ def get_variant_with_id(entry_id: Optional[str], qparams: RequestParams, dataset
         limit = 100
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_biosamples_of_variant(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -323,7 +326,7 @@ def get_biosamples_of_variant(entry_id: Optional[str], qparams: RequestParams, d
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_runs_of_variant(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'g_variants'
@@ -358,7 +361,7 @@ def get_runs_of_variant(entry_id: Optional[str], qparams: RequestParams, dataset
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_analyses_of_variant(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -394,7 +397,7 @@ def get_analyses_of_variant(entry_id: Optional[str], qparams: RequestParams, dat
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_filtering_terms_of_genomicvariation(entry_id: Optional[str], qparams: RequestParams):
     query = {'scopes': 'genomicVariation'}
@@ -447,4 +450,4 @@ def get_individuals_of_variant(entry_id: Optional[str], qparams: RequestParams,
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset

beacon/db/individuals.py

@@ -8,6 +8,7 @@
 from beacon.db.utils import query_id, get_count, get_documents
 from beacon.request.model import RequestParams
 from beacon.db.g_variants import apply_request_parameters
+import time
 import yaml
 from aiohttp import web
 
@@ -18,6 +19,7 @@ def include_resultset_responses(query: Dict[str, List[dict]], qparams: RequestPa
     return query
 
 def get_individuals(entry_id: Optional[str], qparams: RequestParams, dataset: str):
+    LOG.debug(time.time())
     collection = 'individuals'
     mongo_collection = client.beacon.individuals
     parameters_as_filters=False
@@ -45,7 +47,7 @@ def get_individuals(entry_id: Optional[str], qparams: RequestParams, dataset: st
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_individual_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -65,7 +67,7 @@ def get_individual_with_id(entry_id: Optional[str], qparams: RequestParams, data
     if limit > 100 or limit == 0:
         limit = 100
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_variants_of_individual(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -89,7 +91,7 @@ def get_variants_of_individual(entry_id: Optional[str], qparams: RequestParams,
         limit = 100
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_biosamples_of_individual(entry_id: Optional[str], qparams: RequestParams, dataset: str):
@@ -109,7 +111,7 @@ def get_biosamples_of_individual(entry_id: Optional[str], qparams: RequestParams
         limit = 100
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 def get_filtering_terms_of_individual(entry_id: Optional[str], qparams: RequestParams):
@@ -144,7 +146,7 @@ def get_runs_of_individual(entry_id: Optional[str], qparams: RequestParams, data
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_analyses_of_individual(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'individuals'
@@ -163,4 +165,4 @@ def get_analyses_of_individual(entry_id: Optional[str], qparams: RequestParams,
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset

beacon/db/runs.py

@@ -41,7 +41,7 @@ def get_runs(entry_id: Optional[str], qparams: RequestParams, dataset: str):
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_run_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'runs'
@@ -59,7 +59,7 @@ def get_run_with_id(entry_id: Optional[str], qparams: RequestParams, dataset: st
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 
 
@@ -83,7 +83,7 @@ def get_variants_of_run(entry_id: Optional[str], qparams: RequestParams, dataset
         limit = 100
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_analyses_of_run(entry_id: Optional[str], qparams: RequestParams, dataset: str):
     collection = 'runs'
@@ -102,7 +102,7 @@ def get_analyses_of_run(entry_id: Optional[str], qparams: RequestParams, dataset
         limit = 100
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(include, query, datasets_dict, dataset, limit, skip, mongo_collection, idq)
-    return schema, count, dataset_count, docs
+    return schema, count, dataset_count, docs, dataset
 
 def get_filtering_terms_of_run(entry_id: Optional[str], qparams: RequestParams):
     query = {'scopes': 'run'}

beacon/request/handlers.py

@@ -8,6 +8,7 @@
 import yaml
 import jwt
 import requests
+import concurrent.futures
 from concurrent.futures import ThreadPoolExecutor
 from beacon.request import ontologies
 from beacon.request.model import Granularity, RequestParams
@@ -59,8 +60,6 @@ async def wrapper(request: Request):
                     [r for r in records] if records else []
                 )
                 LOG.debug(entity_schema)
-                LOG.debug(response_converted)
-                LOG.debug(type(response_converted))
                 response = build_beacon_collection_response(
                     response_converted, count, qparams, lambda x, y: x, entity_schema
                 )
@@ -221,11 +220,12 @@ async def wrapper(request: Request):
                 #LOG.debug(response_datasets)
                 new_count=0
                 loop = asyncio.get_running_loop()
-                for dataset in response_datasets:
-                    with ThreadPoolExecutor() as pool:
-                        entity_schema, count, dataset_count, records = await loop.run_in_executor(pool, db_fn, entry_id, qparams, dataset)
-                    #LOG.debug(dataset)
-
+                with ThreadPoolExecutor() as pool:
+                    done, pending = await asyncio.wait(fs=[loop.run_in_executor(pool, db_fn, entry_id, qparams, dataset) for dataset in response_datasets],
+                    return_when=asyncio.ALL_COMPLETED
+                    )
+                for task in done:
+                    entity_schema, count, dataset_count, records, dataset = task.result()
                     if dataset_count != -1:
                         new_count+=dataset_count
                         datasets_docs[dataset]=records

deploy/conf.py

@@ -126,6 +126,6 @@
 #
 ontologies_folder = "ontologies"
 
-alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration']
+alphanumeric_terms = ['libraryStrategy', 'molecularAttributes.geneIds', 'diseases.ageOfOnset.iso8601duration', 'molecularAttributes.aminoacidChanges']
 
 ontology_files={"NCIT": "http://purl.obolibrary.org/obo/NCIT.obo"}

permissions/public_datasets.yml

@@ -3,5 +3,4 @@ public_datasets:
 - CINECA_dataset
 - AV_Dataset
 - rd-connect_dataset
-- coadread_tcga_pan_can_atlas_2018
-- B1MG-COADREAD
+- coadread_tcga_pan_can_atlas_2018