adding assemblyId required if refName is chr

beacon/connections/mongo/filters.py

@@ -812,7 +812,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, col
                 elif filter.value == 'Y':
                     dict_regex['$regex']='^NC_0000'+'24'
                 else:
-                    dict_regex['$regex']='^NC_0000'+filter.value+'.'+'10:g'+'|'+'^NC_0000'+filter.value+'.'+'11:g'+'|'+'^NC_0000'+filter.value+'.'+'9:g'
+                    dict_regex['$regex']='^NC_0000'+filter.value
             elif '>' in filter.value:# pragma: no cover
                 dict_regex=filter.value
             elif '.' in filter.value:# pragma: no cover

beacon/connections/mongo/reindex.py

@@ -65,13 +65,12 @@
 #client.beacon.genomicVariations.create_index([("caseLevelData.biosampleId", 1)])
 #client.beacon.genomicVariations.create_index([("variation.location.interval.end.value", -1), ("variation.location.interval.start.value", 1)])
 client.beacon.genomicVariations.create_index([("datasetId", 1)])
-#client.beacon.genomicVariations.create_index([("variantInternalId", 1)])
+client.beacon.genomicVariations.create_index([("variantInternalId", 1)])
 client.beacon.genomicVariations.create_index([("variation.location.interval.start.value", 1)])
 #client.beacon.genomicVariations.create_index([("variation.location.interval.start.value", 1), ("variation.location.interval.end.value", -1)])
-#client.beacon.genomicVariations.create_index([("identifiers.genomicHGVSId", 1), ("variation.location.interval.start.value", 1), ("caseLevelData.biosampleId", 1), ("variation.referenceBases", 1), ("variation.alternateBases", 1)])
-#client.beacon.genomicVariations.create_index([("variation.location.interval.end.value", -1), ("variation.location.interval.start.value", 1), ("variation.referenceBases", 1), ("variation.alternateBases", 1)])
+client.beacon.genomicVariations.create_index([("identifiers.genomicHGVSId", 1)])
 #client.beacon.genomicVariations.create_index([("datasetId", 1), ("variation.location.interval.start.value", 1), ("variation.referenceBases", 1), ("variation.alternateBases", 1)])
-client.beacon.genomicVariations.create_index([("molecularAttributes.geneIds", 1), ("variantInternalId", 1), ("variation.variantType", 1)])
+client.beacon.genomicVariations.create_index([("molecularAttributes.geneIds", 1), ("variation.variantType", 1)])
 #client.beacon.individuals.create_index([("$**", "text")])
 #client.beacon.runs.create_index([("$**", "text")])
 #collection_name = client.beacon.analyses

beacon/request/parameters.py

@@ -4,7 +4,8 @@
     ValidationError,
     field_validator,
     Field,
-    PrivateAttr
+    PrivateAttr,
+    model_validator
 )
 from strenum import StrEnum
 from typing import List, Optional, Union
@@ -92,7 +93,22 @@ class SequenceQuery(BaseModel):
     referenceBases: str
     clinicalRelevance: Optional[str] =None
     mateName: Optional[str] =None
-    assemblyId: Optional[str] ='GRCh38'
+    assemblyId: Optional[str] =None
+    @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',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+            try:
+                if values.assemblyId == None:
+                    err = 'if referenceName is just the chromosome: assemblyId parameter is required'
+                    errcode=400
+                    raise_exception(err, errcode)
+                else:
+                    pass
+            except Exception as e:
+                raise ValueError
+        else:
+            raise ValueError
 
 class RangeQuery(BaseModel):
     referenceName: Union[str,int]
@@ -105,7 +121,22 @@ class RangeQuery(BaseModel):
     variantMaxLength: Optional[int] =None
     clinicalRelevance: Optional[str] =None
     mateName: Optional[str] =None
-    assemblyId: Optional[str] ='GRCh38'
+    assemblyId: Optional[str] =None
+    @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',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+            try:
+                if values.assemblyId == None:
+                    err = 'if referenceName is just the chromosome: assemblyId parameter is required'
+                    errcode=400
+                    raise_exception(err, errcode)
+                else:
+                    pass
+            except Exception as e:
+                raise ValueError
+        else:
+            raise ValueError
 
 class DatasetsRequested(BaseModel):
     datasets: list
@@ -117,7 +148,6 @@ class GeneIdQuery(BaseModel):
     aminoacidChange: Optional[str] =None
     variantMinLength: Optional[int] =None
     variantMaxLength: Optional[int] =None
-    assemblyId: Optional[str] ='GRCh38'
 
 class BracketQuery(BaseModel):
     referenceName: Union[str,int]
@@ -126,7 +156,7 @@ class BracketQuery(BaseModel):
     variantType: Optional[str] =None
     clinicalRelevance: Optional[str] =None
     mateName: Optional[str] =None
-    assemblyId: Optional[str] ='GRCh38'
+    assemblyId: Optional[str] =None
     @field_validator('start')
     @classmethod
     def start_must_be_array_of_integers(cls, v: list) -> list:
@@ -143,15 +173,28 @@ def end_must_be_array_of_integers(cls, v: list) -> list:
                 pass
             else:
                 raise ValueError
+    @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',1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23]:
+            try:
+                if values.assemblyId == None:
+                    err = 'if referenceName is just the chromosome: assemblyId parameter is required'
+                    errcode=400
+                    raise_exception(err, errcode)
+                else:
+                    pass
+            except Exception as e:
+                raise ValueError
+        else:
+            raise ValueError
 
 class GenomicAlleleQuery(BaseModel):
     genomicAlleleShortForm: str
-    assemblyId: Optional[str] ='GRCh38'
 
 class AminoacidChangeQuery(BaseModel):
     aminoacidChange: str
     geneId: str
-    assemblyId: Optional[str] ='GRCh38'
 
 class RequestParams(CamelModel):
     meta: RequestMeta = RequestMeta()