fixed code and add test

cgbeacon2/models/variant.py

@@ -12,8 +12,8 @@ def __init__(self, parsed_variant, datasetIds, genome_assembly="GRCh37"):
         self.end = parsed_variant["end"] # int
         self.endMin = parsed_variant["end"]  # int, for for querying imprecise positions
         self.endMax = parsed_variant["end"] # int, for for querying imprecise positions
-        self.referenceBases = parsed_variant["reference_bases"] # str, '^([ACGT]+|N)$'
-        self.alternateBases = parsed_variant["alternate_bases"] # str, '^([ACGT]+|N)$'
+        self.referenceBases = ''.join(parsed_variant["reference_bases"]) # str, '^([ACGT]+|N)$'
+        self.alternateBases = ''.join(parsed_variant["alternate_bases"]) # str, '^([ACGT]+|N)$'
         if parsed_variant.get("variant_type"):
             self.variantType = parsed_variant["variant_type"] # is used to denote structural variants: 'INS', 'DUP', 'DEL', 'INV'
         self.assemblyId = genome_assembly # str

tests/cli/add/test_add_variants.py

@@ -78,19 +78,32 @@ def test_add_variants_snv_vcf(mock_app, test_dataset_cli, database):
     # 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
     result =  runner.invoke(cli, [
         'add',
         'variants',
         '-ds', dataset["_id"],
         '-vcf', test_snv_vcf_path,
-        '-sample', 'ADM1059A1'
+        '-sample', sample
     ])
 
     # Then the command should NOT return error
     assert result.exit_code == 0
     assert f"variants loaded into the database" in result.output
 
-
-    #
+    # and variants parsed correctly have been saved to database
+    test_variant = database["variant"].find_one()
+    assert isinstance(test_variant["referenceName"], str)
+    assert isinstance(test_variant["start"], int)
+    assert isinstance(test_variant["startMin"], int)
+    assert isinstance(test_variant["startMax"], int)
+    assert isinstance(test_variant["end"], int)
+    assert isinstance(test_variant["endMin"], int)
+    assert isinstance(test_variant["endMax"], int)
+    assert isinstance(test_variant["referenceBases"], str)
+    assert isinstance(test_variant["alternateBases"], str)
+    assert test_variant["assemblyId"] == "GRCh37"
+    assert test_variant["datasetIds"] == [dataset["_id"]]
+    assert test_variant["sampleIds"] == [sample]