Merge 57b3082 into 7397aca

CHANGELOG.md

@@ -16,3 +16,4 @@
 - Added repository codeowners
 - Added tests for queries with datasetAlleleResponses == HIT and MISS
 - No conflicts between queried assembly and the assembly or queried datasets
+- Parse SVs and add save them to 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.INFO["SVTYPE"]
+
             dataset_dict = {dataset_id: {"samples": sample_calls}}
             # Create standard variant object with specific _id
             variant = Variant(parsed_variant, dataset_dict, assembly)

tests/cli/add/test_add_variants.py

@@ -2,6 +2,7 @@
 import pytest
 from cgbeacon2.resources import (
     test_snv_vcf_path,
+    test_sv_vcf_path,
     test_empty_vcf_path,
     panel1_path,
     panel2_path,
@@ -264,3 +265,93 @@ def test_add_other_sample_variants(mock_app, test_dataset_cli, database):
     assert sample in dataset_obj["samples"]
     assert sample2 in dataset_obj["samples"]
     assert "updated" in dataset_obj
+
+
+def test_add_sv_variants(mock_app, test_dataset_cli, database):
+    """Test adding SV variants for one sample"""
+
+    runner = mock_app.test_cli_runner()
+
+    # Having a database containing a dataset
+    dataset = test_dataset_cli
+    database["dataset"].insert_one(dataset)
+
+    sample = "ADM1059A1"
+
+    # When invoking the add variants from a VCF file for the first time
+    result = runner.invoke(
+        cli,
+        [
+            "add",
+            "variants",
+            "-ds",
+            dataset["_id"],
+            "-vcf",
+            test_sv_vcf_path,
+            "-sample",
+            sample,
+        ],
+    )
+
+    # Then a number of variants should have been saved to database
+    saved_vars = list(database["variant"].find())
+    assert len(saved_vars) > 0
+
+    valid_types = ["INS", "DUP", "DEL", "INV"]
+    # AND all of them should have a valid SV variant type
+    for var in saved_vars:
+        assert var["variantType"] in valid_types
+
+
+def test_add_snv_sv_variants(mock_app, test_dataset_cli, database):
+    """Test adding snv + sv variants for one sample"""
+
+    runner = mock_app.test_cli_runner()
+
+    # Having a database containing a dataset
+    dataset = test_dataset_cli
+    database["dataset"].insert_one(dataset)
+
+    sample = "ADM1059A1"
+
+    # When invoking the add variants from a VCF file for the first time
+    # filtering using 2 gene panels
+    result = runner.invoke(
+        cli,
+        [
+            "add",
+            "variants",
+            "-ds",
+            dataset["_id"],
+            "-vcf",
+            test_snv_vcf_path,
+            "-sample",
+            sample,
+            "-panel",
+            panel1_path,
+            "-panel",
+            panel2_path,
+        ],
+    )
+
+    # Then a number of SNV variants should have been saved to database
+    saved_snvs = sum(1 for i in database["variant"].find())
+
+    # WHEN variants from a another VCF file containing SVs are added
+    result = runner.invoke(
+        cli,
+        [
+            "add",
+            "variants",
+            "-ds",
+            dataset["_id"],
+            "-vcf",
+            test_sv_vcf_path,
+            "-sample",
+            sample,
+        ],
+    )
+
+    # THEN more variants should have been added to the database
+    new_saved_vars = sum(1 for i in database["variant"].find())
+    assert new_saved_vars > saved_snvs

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