fix an error and increase coverage

cgbeacon2/cli/add.py

@@ -203,7 +203,6 @@ def variants(ds, vcf, sample, panel):
     )
 
     if vcf_obj is None:
-        click.echo(f"Coundn't extract variants from provided VCF file")
         raise click.Abort()
 
     nr_variants = count_variants(vcf_obj)

cgbeacon2/utils/parse.py

@@ -37,7 +37,15 @@ def extract_variants(vcf_file, samples=None, filter=None):
             temp_intersections_file.close()
 
         else:
-            vcf_obj = VCF(vcf_file, samples=list(samples))
+            try:
+                vcf_obj = VCF(vcf_file, samples=list(samples))
+            except Exception as ex:
+                vcf_obj = VCF(vcf_file)
+                LOG.error(
+                    f"Invalid VCF or samples. Valid samples are:{vcf_obj.samples}"
+                )
+                return
+
     except Exception as err:
         LOG.error(f"Error while creating VCF iterator from variant file:{err}")
         return

cgbeacon2/utils/update.py

@@ -23,7 +23,7 @@ def update_dataset(database, dataset_id, samples, add):
     n_variants = update_dataset_variant_count(database, dataset_id)
 
     # Update number of allele calls for this dataset
-    n_alleles = update_dataset_allele_count(database, dataset_obj)
+    n_alleles = update_dataset_allele_count(database, dataset_id, list(updated_samples))
 
     result = database["dataset"].find_one_and_update(
         {"_id": dataset_id},
@@ -82,12 +82,13 @@ def update_dataset_variant_count(database, dataset_id):
     return n_variants
 
 
-def update_dataset_allele_count(database, dataset_obj):
+def update_dataset_allele_count(database, dataset_id, samples):
     """Count how many allele calls are present for a dataset and update dataset object with this number
 
     Accepts:
         database(pymongo.database.Database)
-        dataset_obj(dict): a dataset object
+        dataset_id(str): id of dataset to be updated
+        samples(list): list of dataset samples
 
     Returns:
         updated_dataset(obj): the updated dataset
@@ -106,34 +107,35 @@ def update_dataset_allele_count(database, dataset_obj):
 
     # Else count calls for each sample of this dataset in variant collection and sum them up
     else:
-        allele_count = _samples_calls(variant_collection, dataset_obj)
+        allele_count = _samples_calls(variant_collection, dataset_id, samples)
 
     return allele_count
 
 
-def _samples_calls(variant_collection, dataset_obj):
+def _samples_calls(variant_collection, dataset_id, samples):
     """Count all allele calls for a dataset in variants collection
 
     Accepts:
         variant_collection(pymongo.database.Database.Collection)
-        dataset_obj(dict): a dataset object
+        dataset_id(str): id of dataset to be updated
+        samples(list): list of dataset samples
     Returns:
-
+        allele_count(int)
     """
     allele_count = 0
-    samples = dataset_obj.get("samples", [])
 
     for sample in samples:
         pipe = [
             {
                 "$group": {
                     "_id": None,
                     "alleles": {
-                        "$sum": f"$datasetIds.test_public.samples.{sample}.allele_count"
+                        "$sum": f"$datasetIds.{dataset_id}.samples.{sample}.allele_count"
                     },
                 }
             }
         ]
+        LOG.error(f"PIPE IS {pipe}")
         aggregate_res = variant_collection.aggregate(pipeline=pipe)
         for res in aggregate_res:
             allele_count += res.get("alleles")

tests/cli/add/test_add_variants.py

@@ -315,8 +315,6 @@ def test_add_same_variant_different_datasets(
     hit_dset2 = {".".join(["datasetIds", registered_dataset["_id"]]): {"$exists": True}}
     test_variant = database["variant"].find_one({"$and": [hit_dset1, hit_dset2]})
 
-    assert test_variant is not None
-
     # Variant should countain callCount for each sample
     callCount1 = test_variant["datasetIds"][public_dataset["_id"]]["samples"][
         samples[0]
@@ -328,6 +326,13 @@ def test_add_same_variant_different_datasets(
     # And a cumulative call count as well
     assert test_variant["call_count"] == callCount1 + callCount2
 
+    # Both dataset objects should be updated with the right number of samples, variants and calls:
+    for ds in datasets:
+        updated_dataset = database["dataset"].find_one({"_id": ds["_id"]})
+        assert len(updated_dataset["samples"]) == 1
+        assert updated_dataset["variant_count"] > 0
+        assert updated_dataset["allele_count"] > 0
+
 
 def test_add_sv_variants(mock_app, public_dataset, database):
     """Test adding SV variants for one sample"""