Merge branch 'develop' into frontend

EGA-archive · Oct 10, 2023 · 668dcff · 668dcff
2 parents 1b5e835 + 8f576dc
commit 668dcff
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Showing 68 changed files with 88 additions and 38,619 deletions.
diff --git a/beacon/conf.py b/beacon/conf.py
@@ -12,7 +12,7 @@
 beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
 beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
-uri = 'https://beacon-apis-test.ega-archive.org/api/'
+uri = 'https://beacon-apis-demo.ega-archive.org/api/'
 
 #
 # Beacon granularity
@@ -34,7 +34,7 @@
               '08003 Barcelona, Spain')
 org_welcome_url = 'https://ega-archive.org/'
 org_contact_url = 'mailto:[email protected]'
-org_logo_url = 'https://ega-archive.org/images/logo.png'
+org_logo_url = 'https://legacy.ega-archive.org/images/logo.png'
 org_info = ''
 
 #

diff --git a/beacon/db/individuals.py b/beacon/db/individuals.py
@@ -44,6 +44,7 @@ def include_resultset_responses(query: Dict[str, List[dict]], qparams: RequestPa
 
 def apply_request_parameters(query: Dict[str, List[dict]], qparams: RequestParams):
     LOG.debug("Request parameters len = {}".format(len(qparams.query.request_parameters)))
+    v_list=[]
     query_2={}
     for k, v in qparams.query.request_parameters.items():
         LOG.debug(k)
@@ -81,6 +82,17 @@ def apply_request_parameters(query: Dict[str, List[dict]], qparams: RequestParam
                             query_2["$or"].append({'id': case["biosampleId"]})
 
                 LOG.debug(query_2)
+
+            elif ',' in v:
+                v_list =v.split(',')
+                LOG.debug(v_list)
+            else:
+                v_list.append(v)
+            for id in v_list:
+                v_dict={}
+                v_dict['id']=id
+                qparams.query.filters.append(v_dict)
+
 
 
 

diff --git a/beacon/response/framework.py b/beacon/response/framework.py
@@ -26,7 +26,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.ANALYSES.value['schema'],
                 "name": "Default schema for a bioinformatics analysis",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/analyses/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/analyses/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "additionallySupportedSchemas": []
@@ -43,7 +43,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.BIOSAMPLES.value['schema'],
                 "name": "Default schema for a biological sample",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/biosamples/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "additionallySupportedSchemas": []
@@ -60,7 +60,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.COHORTS.value['schema'],
                 "name": "Default schema for cohorts",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/cohorts/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "aCollectionOf": [{"id": "individual", "name": "Individuals"}],
@@ -78,7 +78,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.DATASETS.value['schema'],
                 "name": "Default schema for datasets",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/datasets/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "aCollectionOf": [{"id": "genomicVariation", "name": "Genomic Variants"}],
@@ -96,7 +96,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.GENOMICVARIATIONS.value['schema'],
                 "name": "Default schema for a genomic variation",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/genomicVariations/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "additionallySupportedSchemas": []
@@ -113,7 +113,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.INDIVIDUALS.value['schema'],
                 "name": "Default schema for an individual",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/individuals/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/individuals/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "additionallySupportedSchemas": []
@@ -130,7 +130,7 @@ def get_entry_types():
             "defaultSchema": {
                 "id": DefaultSchemas.RUNS.value['schema'],
                 "name": "Default schema for a sequencing run",
-                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/runs/defaultSchema.json",
+                "referenceToSchemaDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/runs/defaultSchema.json",
                 "schemaVersion": "v2.0.0"
             },
             "additionallySupportedSchemas": []
@@ -200,7 +200,7 @@ async def beacon_map(request):
         "endpointSets": {
             "analysis": {
                 "entryType": "analysis",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/analyses/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/analyses/endpoints.json",
                 "rootUrl": conf.uri + "analyses",
                 "singleEntryUrl": conf.uri + "analyses/{id}",
                 "endpoints": {
@@ -212,7 +212,7 @@ async def beacon_map(request):
             },
             "biosample": {
                 "entryType": "biosample",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/biosamples/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/biosamples/endpoints.json",
                 "rootUrl": conf.uri + "biosamples",
                 "singleEntryUrl": conf.uri + "biosamples/{id}",
                 "endpoints": {
@@ -232,7 +232,7 @@ async def beacon_map(request):
             },
             "cohort": {
                 "entryType": "cohort",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/cohorts/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/cohorts/endpoints.json",
                 "rootUrl": conf.uri + "cohorts",
                 "singleEntryUrl": conf.uri + "cohorts/{id}",
                 "filteringTermsUrl": conf.uri + "cohorts/filtering_terms",
@@ -253,7 +253,7 @@ async def beacon_map(request):
             },
             "dataset": {
                 "entryType": "dataset",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/datasets/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/datasets/endpoints.json",
                 "rootUrl": conf.uri + "datasets",
                 "singleEntryUrl": conf.uri + "datasets/{id}",
                 "filteringTermsUrl": conf.uri + "datasets/filtering_terms",
@@ -282,7 +282,7 @@ async def beacon_map(request):
             },
             "genomicVariant": {
                 "entryType": "genomicVariant",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/genomicVariations/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/genomicVariations/endpoints.json",
                 "rootUrl": conf.uri + "g_variants",
                 "singleEntryUrl": conf.uri + "g_variants/{variantInternalId}",
                 "endpoints": {
@@ -306,7 +306,7 @@ async def beacon_map(request):
             },
             "individual": {
                 "entryType": "individual",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/individuals/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/individuals/endpoints.json",
                 "rootUrl": conf.uri + "individuals",
                 "singleEntryUrl": conf.uri + "individuals/{id}",
                 "filteringTermsUrl": conf.uri + "individuals/filtering_terms",
@@ -331,7 +331,7 @@ async def beacon_map(request):
             },
             "run": {
                 "entryType": "run",
-                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2-Models/main/BEACON-V2-Model/runs/endpoints.json",
+                "openAPIEndpointsDefinition": "https://raw.githubusercontent.com/ga4gh-beacon/beacon-v2/main/models/json/beacon-v2-default-model/runs/endpoints.json",
                 "rootUrl": conf.uri + "runs",
                 "singleEntryUrl": conf.uri + "runs/{id}",
                 "endpoints": {

diff --git a/deploy/conf.py b/deploy/conf.py
@@ -6,7 +6,7 @@
 beacon_id = 'org.ega-archive.ga4gh-approval-beacon-test'  # ID of the Beacon
 beacon_name = 'GA4GH Approval Beacon Test'  # Name of the Beacon service
 api_version = 'v2.0.0'  # Version of the Beacon implementation
-uri = 'https://beacon-apis-test.ega-archive.org/api/'
+uri = 'https://beacon-apis-demo.ega-archive.org/api/'
 
 #
 # Beacon granularity
@@ -28,7 +28,7 @@
               '08003 Barcelona, Spain')
 org_welcome_url = 'https://ega-archive.org/'
 org_contact_url = 'mailto:[email protected]'
-org_logo_url = 'https://ega-archive.org/images/logo.png'
+org_logo_url = 'https://legacy.ega-archive.org/images/logo.png'
 org_info = ''
 
 #