save SVs to beacon database

cgbeacon2/resources/__init__.py

@@ -2,12 +2,14 @@
 
 ###### Files ######
 test_snv_vcf = "resources/demo/643594.clinical.vcf.gz"
+test_sv_vcf = "resources/demo/643594.clinical.SV.vcf.gz"
 empty_vcf = "resources/demo/empty.clinical.SV.vcf.gz"
 panel1 = "resources/demo/panel1.bed"
 panel2 = "resources/demo/panel2.bed"
 
 ###### Paths ######
 test_snv_vcf_path = pkg_resources.resource_filename("cgbeacon2", test_snv_vcf)
+test_sv_vcf_path = pkg_resources.resource_filename("cgbeacon2", test_sv_vcf)
 test_empty_vcf_path = pkg_resources.resource_filename("cgbeacon2", empty_vcf)
 panel1_path = pkg_resources.resource_filename("cgbeacon2", panel1)
 panel2_path = pkg_resources.resource_filename("cgbeacon2", panel2)

cgbeacon2/utils/add.py

@@ -92,16 +92,17 @@ def add_variants(database, vcf_obj, samples, assembly, dataset_id, nr_variants):
             if len(sample_calls) == 0:
                 continue  # variant was not called in samples of interest
 
-            if vcf_variant.var_type == "sv":  # otherwise snp or indel
-                parsed_variant["variant_type"] = "sv"  # fix later, this is not OK yet
-
             parsed_variant = dict(
                 chromosome=vcf_variant.CHROM,
                 start=vcf_variant.start,
                 end=vcf_variant.end,
                 reference_bases=vcf_variant.REF,
                 alternate_bases=vcf_variant.ALT,
             )
+
+            if vcf_variant.var_type == "sv":
+                parsed_variant["variant_type"] = vcf_variant.get("SVTYPE")
+
             dataset_dict = {dataset_id: {"samples": sample_calls}}
             # Create standard variant object with specific _id
             variant = Variant(parsed_variant, dataset_dict, assembly)

tests/server/blueprints/api_v1/test_request_errors.py

@@ -0,0 +1,122 @@
+# -*- coding: utf-8 -*-
+import json
+from cgbeacon2.constants import (
+    NO_MANDATORY_PARAMS,
+    NO_SECONDARY_PARAMS,
+    NO_POSITION_PARAMS,
+    NO_SV_END_PARAM,
+    INVALID_COORD_RANGE,
+    BUILD_MISMATCH,
+)
+
+BASE_ARGS = "query?assemblyId=GRCh37&referenceName=1&referenceBases=TA"
+
+################## TESTS FOR HANDLING WRONG REQUESTS ################
+
+
+def test_query_get_request_missing_mandatory_params(mock_app):
+    """Test the query endpoint by sending a request without mandatory params:
+    referenceName, referenceBases, assemblyId
+    """
+
+    # When a request missing one or more required params is sent to the server
+    response = mock_app.test_client().get("/apiv1.0/query?")
+
+    # Then it should return error
+    assert response.status_code == 400
+    data = json.loads(response.data)
+    assert data["message"]["error"] == NO_MANDATORY_PARAMS
+    assert data["message"]["exists"] == None
+    assert data["message"]["datasetAlleleResponses"] == []
+    assert data["message"]["beaconId"]
+    assert data["message"]["apiVersion"] == "1.0.0"
+
+
+def test_query_get_request_build_mismatch(mock_app, test_dataset_cli):
+    """Test the query endpoint by sending a request with build mismatch between queried datasets and genome build"""
+
+    # Having a dataset with genome build GRCh38 in the database:
+    database = mock_app.db
+    test_dataset_cli["assembly_id"] = "GRCh38"
+    database["dataset"].insert_one(test_dataset_cli)
+
+    # When a request with genome build GRCh37 and detasetIds with genome build GRCh38 is sent to the server:
+    query_string = "&".join([BASE_ARGS, f"datasetIds={test_dataset_cli['_id']}"])
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+
+    # Then it should return error
+    assert response.status_code == 400
+    data = json.loads(response.data)
+    assert data["message"]["error"] == BUILD_MISMATCH
+
+
+def test_query_get_request_missing_secondary_params(mock_app):
+    """Test the query endpoint by sending a request without secondary params:
+    alternateBases, variantType
+    """
+    # When a request missing alternateBases or variantType params is sent to the server
+    query_string = BASE_ARGS
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+
+    # Then it should return error
+    assert response.status_code == 400
+    data = json.loads(response.data)
+    assert data["message"]["error"] == NO_SECONDARY_PARAMS
+
+
+def test_query_get_request_missing_positions_params(mock_app):
+    """Test the query endpoint by sending a request missing coordinate params:
+        Either stat or startMin + startMax + endMin + endMax
+
+    """
+    # When a request missing start position and all the 4 range position coordinates (startMin, startMax, endMin, endMax)
+    query_string = "&".join(
+        [BASE_ARGS, "alternateBases=T&startMin=2&startMax=6&endMin=4"]
+    )
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+    data = json.loads(response.data)
+    # Then it should return error
+    assert response.status_code == 400
+    assert data["message"]["error"] == NO_POSITION_PARAMS
+
+
+def test_query_get_request_non_numerical_sv_coordinates(mock_app):
+    """Test the query endpoint by sending a request missing SV coordinates params:
+        provide only start but no end param
+
+    """
+    query_string = "&".join([BASE_ARGS, "start=4&variantType=DUP"])
+    # When a request for SV variants is missing stop position parameter
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+    data = json.loads(response.data)
+    # Then it should return error
+    assert response.status_code == 400
+    assert data["message"]["error"] == NO_SV_END_PARAM
+
+
+def test_query_get_request_non_increasing_sv_coordinates(mock_app):
+    """Test the query endpoint by sending a request with non-ordered range coordinates"""
+
+    range_coords = "&variantType=DUP&startMin=2&startMax=4&endMin=7&endMax=5"
+    query_string = "&".join([BASE_ARGS, range_coords])
+
+    # When a request for range coordinates doesn't contain ordered coordinates
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+    data = json.loads(response.data)
+    # Then it should return error
+    assert response.status_code == 400
+    assert data["message"]["error"] == INVALID_COORD_RANGE
+
+
+def test_query_get_request_non_numerical_range_coordinates(mock_app):
+    """Test the query endpoint by sending a request with non-numerical range coordinates"""
+
+    range_coords = "&variantType=DUP&startMin=2&startMax=3&endMin=6&endMax=FOO"
+    query_string = "&".join([BASE_ARGS, range_coords])
+
+    # When a request for range coordinates doesn't contain integers
+    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
+    data = json.loads(response.data)
+    # Then it should return error
+    assert response.status_code == 400
+    assert data["message"]["error"] == INVALID_COORD_RANGE

tests/server/blueprints/api_v1/test_views.py

@@ -12,7 +12,6 @@
 BASE_ARGS = "query?assemblyId=GRCh37&referenceName=1&referenceBases=TA"
 COORDS_ARGS = "start=235826381&end=235826383"
 ALT_ARG = "alternateBases=T"
-DATASET_ARGS = "datasetIds=foo&datasetIds=test_ds"
 
 
 def test_info(mock_app):
@@ -29,117 +28,6 @@ def test_info(mock_app):
         assert data[field] is not None
 
 
-################## TESTS FOR HANDLING WRONG REQUESTS ################
-
-
-def test_query_get_request_missing_mandatory_params(mock_app):
-    """Test the query endpoint by sending a request without mandatory params:
-    referenceName, referenceBases, assemblyId
-    """
-
-    # When a request missing one or more required params is sent to the server
-    response = mock_app.test_client().get("/apiv1.0/query?")
-
-    # Then it should return error
-    assert response.status_code == 400
-    data = json.loads(response.data)
-    assert data["message"]["error"] == NO_MANDATORY_PARAMS
-    assert data["message"]["exists"] == None
-    assert data["message"]["datasetAlleleResponses"] == []
-    assert data["message"]["beaconId"]
-    assert data["message"]["apiVersion"] == "1.0.0"
-
-
-def test_query_get_request_build_mismatch(mock_app, test_dataset_cli):
-    """Test the query endpoint by sending a request with build mismatch between queried datasets and genome build"""
-
-    # Having a dataset with genome build GRCh38 in the database:
-    database = mock_app.db
-    test_dataset_cli["assembly_id"] = "GRCh38"
-    database["dataset"].insert_one(test_dataset_cli)
-
-    # When a request with genome build GRCh37 and detasetIds with genome build GRCh38 is sent to the server:
-    query_string = "&".join([BASE_ARGS, f"datasetIds={test_dataset_cli['_id']}"])
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-
-    # Then it should return error
-    assert response.status_code == 400
-    data = json.loads(response.data)
-    assert data["message"]["error"] == BUILD_MISMATCH
-
-
-def test_query_get_request_missing_secondary_params(mock_app):
-    """Test the query endpoint by sending a request without secondary params:
-    alternateBases, variantType
-    """
-    # When a request missing alternateBases or variantType params is sent to the server
-    query_string = BASE_ARGS
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-
-    # Then it should return error
-    assert response.status_code == 400
-    data = json.loads(response.data)
-    assert data["message"]["error"] == NO_SECONDARY_PARAMS
-
-
-def test_query_get_request_missing_positions_params(mock_app):
-    """Test the query endpoint by sending a request missing coordinate params:
-        Either stat or startMin + startMax + endMin + endMax
-
-    """
-    # When a request missing start position and all the 4 range position coordinates (startMin, startMax, endMin, endMax)
-    query_string = "&".join(
-        [BASE_ARGS, "alternateBases=T&startMin=2&startMax=6&endMin=4"]
-    )
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-    data = json.loads(response.data)
-    # Then it should return error
-    assert response.status_code == 400
-    assert data["message"]["error"] == NO_POSITION_PARAMS
-
-
-def test_query_get_request_non_numerical_sv_coordinates(mock_app):
-    """Test the query endpoint by sending a request missing SV coordinates params:
-        provide only start but no end param
-
-    """
-    query_string = "&".join([BASE_ARGS, "start=4&variantType=DUP"])
-    # When a request for SV variants is missing stop position parameter
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-    data = json.loads(response.data)
-    # Then it should return error
-    assert response.status_code == 400
-    assert data["message"]["error"] == NO_SV_END_PARAM
-
-
-def test_query_get_request_non_increasing_sv_coordinates(mock_app):
-    """Test the query endpoint by sending a request with non-ordered range coordinates"""
-
-    range_coords = "&variantType=DUP&startMin=2&startMax=4&endMin=7&endMax=5"
-    query_string = "&".join([BASE_ARGS, range_coords])
-
-    # When a request for range coordinates doesn't contain ordered coordinates
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-    data = json.loads(response.data)
-    # Then it should return error
-    assert response.status_code == 400
-    assert data["message"]["error"] == INVALID_COORD_RANGE
-
-
-def test_query_get_request_non_numerical_range_coordinates(mock_app):
-    """Test the query endpoint by sending a request with non-numerical range coordinates"""
-
-    range_coords = "&variantType=DUP&startMin=2&startMax=3&endMin=6&endMax=FOO"
-    query_string = "&".join([BASE_ARGS, range_coords])
-
-    # When a request for range coordinates doesn't contain integers
-    response = mock_app.test_client().get("".join(["/apiv1.0/", query_string]))
-    data = json.loads(response.data)
-    # Then it should return error
-    assert response.status_code == 400
-    assert data["message"]["error"] == INVALID_COORD_RANGE
-
-
 ################## TESTS FOR HANDLING SNV REQUESTS ################