Merge pull request #173 from EGA-archive/urgentfixes

Patch to fix referenceName=X and referenceName=Y queries + pointing to map schema in $schema under /map

Author: costero-e

beacon/conf/api_version.yml

@@ -1 +1 @@
-api_version: v2.1.1
+api_version: v2.1.2

beacon/connections/mongo/data/test/genomicVariations.json

@@ -75,7 +75,7 @@ def at_least_one_not_none(cls, values):
         return values
 
 class MapSchema(BaseModel):
-    schema: str = Field(alias="$schema", default="https://raw.githubusercontent.com/ga4gh-beacon/beacon-framework-v2/main/configuration/beaconConfigurationSchema.json")
+    schema: str = Field(alias="$schema", default="https://raw.githubusercontent.com/ga4gh-beacon/beacon-framework-v2/main/configuration/beaconMapSchema.json")
     endpointSets: EndpointEntries
     def populate_endpoints(self):
         # Load all_modules and do a loop per populating EndpointEntries(loaded_module=Endpoint...) and loading the variables _lookup = True by name, getting endpoint_names per each lookup = True.

beacon/framework/validator/v2_0_0/map.py

@@ -8,7 +8,7 @@ def parse_request_parameters(self, query, filter):
     # Processing the request parameters as filters, checking which is the id of the property mapped by the request parameter (where the requestParameter points at, several can apply to one property)
     if filter.id == "identifiers.genomicHGVSId":
         # Initialize a dictionary to use for the chromosome query and create the list of chromosome values accepted that come from requestParameters
-        list_chromosomes = ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','X','Y','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chr24','chrX','chrY']
+        list_chromosomes = ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chr24','chrX','chrY']
         dict_regex={}
         # Check if the value of the chromosome is accepted
         if filter.value in list_chromosomes:
@@ -25,18 +25,18 @@ def parse_request_parameters(self, query, filter):
                     prehgvs='^NC_00000'
                 if filter.value == 'X':
                     if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36':
-                        dict_regex['$regex']='^NC_000023'+filter.value+'.'+'9:g'
+                        dict_regex['$regex']='^NC_000023'+'.'+'9:g'
                     elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37':
-                        dict_regex['$regex']='^NC_000023'+filter.value+'.'+'10:g'
+                        dict_regex['$regex']='^NC_000023'+'.'+'10:g'
                     elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38':
-                        dict_regex['$regex']='^NC_000023'+filter.value+'.'+'11:g'
+                        dict_regex['$regex']='^NC_000023'+'.'+'11:g'
                 elif filter.value == 'Y':
                     if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36':
-                        dict_regex['$regex']='^NC_000024'+filter.value+'.'+'8:g'
+                        dict_regex['$regex']='^NC_000024'+'.'+'8:g'
                     elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh37':
-                        dict_regex['$regex']='^NC_000024'+filter.value+'.'+'9:g'
+                        dict_regex['$regex']='^NC_000024'+'.'+'9:g'
                     elif RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'GRCh38':
-                        dict_regex['$regex']='^NC_000024'+filter.value+'.'+'10:g'
+                        dict_regex['$regex']='^NC_000024'+'.'+'10:g'
                 elif filter.value in ['14', '21']:
                     if RequestAttributes.qparams.query.requestParameters["assemblyId"] == 'NCBI36':
                         dict_regex['$regex']=prehgvs+filter.value+'.'+'7:g'

beacon/models/ga4gh/beacon_v2_default_model/connections/mongo/filters/request_parameters/alphanumeric.py

@@ -39,7 +39,7 @@ class SequenceQuery(BaseModel, extra='forbid'):
     @model_validator(mode='after')
     @classmethod
     def referenceName_must_have_assemblyId_if_not_HGVSId(cls, values):
-        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chr24','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]:
             if values.assemblyId == None:
                 raise ValueError('if referenceName is just the chromosome: assemblyId parameter is required')
         else:
@@ -67,7 +67,7 @@ class RangeQuery(BaseModel, extra='forbid'):
     @model_validator(mode='after')
     @classmethod
     def referenceName_must_have_assemblyId_if_not_HGVSId_2(cls, values):
-        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chr24','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]:
             if values.assemblyId == None:
                 raise ValueError('if referenceName is just the chromosome: assemblyId parameter is required')
         else:
@@ -129,7 +129,7 @@ def end_must_be_array_of_integers(cls, v: list) -> list:
     @model_validator(mode='after')
     @classmethod
     def referenceName_must_have_assemblyId_if_not_HGVSId_3(cls, values):
-        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+        if values.referenceName in ['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','23','24','X','Y','MT','chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chr23','chr24','chrX','chrY','chrMT',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24]:
             if values.assemblyId == None:
                 raise ValueError('if referenceName is just the chromosome: assemblyId parameter is required')
         else:

beacon/request/parameters.py

@@ -1026,7 +1026,7 @@ async def test_check_cohorts_g_variants_endpoint_is_working():
                 responsetext=await resp.text()
                 responsedict=json.loads(responsetext)
                 assert responsedict["responseSummary"]["exists"] == True
-                assert responsedict["responseSummary"]["numTotalResults"] == 40
+                assert responsedict["responseSummary"]["numTotalResults"] == 41
             loop.run_until_complete(test_check_cohorts_g_variants_endpoint_is_working())
             loop.run_until_complete(client.close())
     def test_main_check_datasets_with_limit_endpoint_is_working(self):
@@ -1089,7 +1089,7 @@ async def test_check_datasets_g_variants_endpoint_is_working():
                 responsetext=await resp.text()
                 responsedict=json.loads(responsetext)
                 assert responsedict["responseSummary"]["exists"] == True
-                assert responsedict["responseSummary"]["numTotalResults"] == 40
+                assert responsedict["responseSummary"]["numTotalResults"] == 41
             loop.run_until_complete(test_check_datasets_g_variants_endpoint_is_working())
             loop.run_until_complete(client.close())
     def test_main_check_datasets_biosamples_endpoint_is_working(self):
@@ -1511,7 +1511,7 @@ async def test_check_datasets_g_variants_endpoint_is_working():
                 assert resp.status == 200
                 responsetext=await resp.text()
                 responsedict=json.loads(responsetext)
-                assert responsedict["responseSummary"]["numTotalResults"] == 40
+                assert responsedict["responseSummary"]["numTotalResults"] == 41
             loop.run_until_complete(test_check_datasets_g_variants_endpoint_is_working())
             loop.run_until_complete(client.close())
     def test_main_check_alphanumeric_equal_query_is_working(self):
@@ -2881,20 +2881,36 @@ async def test_check_g_variants_endpoint_with_parameters_is_working():
                 assert resp.status == 200
                 responsetext=await resp.text()
                 responsedict=json.loads(responsetext)
-                assert responsedict["responseSummary"]["exists"] == False
+                assert responsedict["responseSummary"]["exists"] == True
+                assert responsedict["responseSummary"]["numTotalResults"] == 1
             loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working())
             loop.run_until_complete(client.close())
-    def test_main_check_g_variants_range_query_chrY(self):
+    def test_main_check_g_variants_sequence_query_chrX(self):
         with loop_context() as loop:
             app = create_app()
             client = TestClient(TestServer(app), loop=loop)
             loop.run_until_complete(client.start_server())
             async def test_check_g_variants_endpoint_with_parameters_is_working():
-                resp = await client.get(conf_override.config.uri_subpath+"/"+genomicVariant["genomicVariant"]["endpoint_name"]+"?start=31120923&referenceName=Y&assemblyId=GRCh37&end=31121924&testMode=true")
+                resp = await client.get(conf_override.config.uri_subpath+"/"+genomicVariant["genomicVariant"]["endpoint_name"]+"?start=31121923&referenceName=X&assemblyId=GRCh37&referenceBases=T&alternateBases=C&testMode=true")
                 assert resp.status == 200
                 responsetext=await resp.text()
                 responsedict=json.loads(responsetext)
-                assert responsedict["responseSummary"]["exists"] == False
+                assert responsedict["responseSummary"]["exists"] == True
+                assert responsedict["responseSummary"]["numTotalResults"] == 1
+            loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working())
+            loop.run_until_complete(client.close())
+    def test_main_check_g_variants_range_sequence_chrY(self):
+        with loop_context() as loop:
+            app = create_app()
+            client = TestClient(TestServer(app), loop=loop)
+            loop.run_until_complete(client.start_server())
+            async def test_check_g_variants_endpoint_with_parameters_is_working():
+                resp = await client.get(conf_override.config.uri_subpath+"/"+genomicVariant["genomicVariant"]["endpoint_name"]+"?start=14191773&referenceBases=A&alternateBases=G&assemblyId=GRCh37&referenceName=Y")
+                assert resp.status == 200
+                responsetext=await resp.text()
+                responsedict=json.loads(responsetext)
+                assert responsedict["responseSummary"]["exists"] == True
+                assert responsedict["responseSummary"]["numTotalResults"] == 1
             loop.run_until_complete(test_check_g_variants_endpoint_with_parameters_is_working())
             loop.run_until_complete(client.close())
     def test_main_check_limit_query_is_working(self):