Test utility for inserting mapped variants to DB

Author: bencap

tests/helpers/constants.py

@@ -637,6 +637,20 @@
 }
 
 
+TEST_MINIMAL_PRE_MAPPED_METADATA = {
+    "genomic": {"sequence_id": "ga4gh:SQ.em9khDCUYXrVWBfWr9r8fjBUrTjj1aig", "sequence_type": "dna"}
+}
+
+
+TEST_MINIMAL_POST_MAPPED_METADATA = {
+    "genomic": {
+        "sequence_id": "ga4gh:SQ.em9khDCUYXrVWBfWr9r8fjBUrTjj1aig",
+        "sequence_type": "dna",
+        "sequence_accessions": [VALID_ACCESSION],
+        "sequence_genes": [VALID_GENE],
+    }
+}
+
 TEST_VARIANT_MAPPING_SCAFFOLD = {
     "metadata": {},
     "computed_genomic_reference_sequence": {
@@ -656,6 +670,17 @@
 }
 
 
+TEST_MINIMAL_MAPPED_VARIANT = {
+    "pre_mapped": {},
+    "post_mapped": {},
+    "modification_date": datetime.isoformat(datetime.now()),
+    "mapped_date": datetime.isoformat(datetime.now()),
+    "current": True,
+    "vrs_version": "2.0",
+    "mapping_api_version": "pytest.0.0",
+}
+
+
 TEST_SCORESET_RANGE = {
     "wt_score": 1.0,
     "ranges": [

tests/helpers/util.py

@@ -11,9 +11,13 @@
 from mavedb.lib.validation.dataframe import validate_and_standardize_dataframe_pair
 from mavedb.models.contributor import Contributor
 from mavedb.models.enums.processing_state import ProcessingState
+from mavedb.models.enums.mapping_state import MappingState
+from mavedb.models.mapped_variant import MappedVariant
 from mavedb.models.score_set import ScoreSet as ScoreSetDbModel
 from mavedb.models.license import License
+from mavedb.models.target_gene import TargetGene
 from mavedb.models.user import User
+from mavedb.models.variant import Variant
 from mavedb.view_models.collection import Collection
 from mavedb.view_models.experiment import Experiment, ExperimentCreate
 from mavedb.view_models.score_set import ScoreSet, ScoreSetCreate
@@ -23,7 +27,10 @@
     TEST_COLLECTION,
     TEST_MINIMAL_ACC_SCORESET,
     TEST_MINIMAL_EXPERIMENT,
+    TEST_MINIMAL_PRE_MAPPED_METADATA,
+    TEST_MINIMAL_POST_MAPPED_METADATA,
     TEST_MINIMAL_SEQ_SCORESET,
+    TEST_MINIMAL_MAPPED_VARIANT,
 )
 
 
@@ -185,6 +192,25 @@ def mock_worker_variant_insertion(client, db, data_provider, score_set, scores_c
     return client.get(f"/api/v1/score-sets/{score_set['urn']}").json()
 
 
+def create_mapped_variants_for_score_set(db, score_set_urn):
+    score_set = db.scalar(select(ScoreSetDbModel).where(ScoreSetDbModel.urn == score_set_urn))
+    targets = db.scalars(select(TargetGene).where(TargetGene.score_set_id == score_set.id))
+    variants = db.scalars(select(Variant).where(Variant.score_set_id == score_set.id)).all()
+
+    for variant in variants:
+        mv = MappedVariant(**TEST_MINIMAL_MAPPED_VARIANT, variant_id=variant.id)
+        db.add(mv)
+
+    for target in targets:
+        target.pre_mapped_metadata = TEST_MINIMAL_PRE_MAPPED_METADATA
+        target.post_mapped_metadata = TEST_MINIMAL_POST_MAPPED_METADATA
+        db.add(target)
+
+    score_set.mapping_state = MappingState.complete
+    db.commit()
+    return
+
+
 def create_seq_score_set_with_variants(
     client, db, data_provider, experiment_urn, scores_csv_path, update=None, counts_csv_path=None
 ):

tests/routers/conftest.py

@@ -28,6 +28,7 @@
     create_acc_score_set_with_variants,
     create_experiment,
     create_seq_score_set_with_variants,
+    create_mapped_variants_for_score_set,
     publish_score_set,
 )
 
@@ -76,6 +77,7 @@ def setup_seq_scoreset(setup_router_db, session, data_provider, client, data_fil
     score_set = create_seq_score_set_with_variants(
         client, session, data_provider, experiment["urn"], data_files / "scores.csv"
     )
+    create_mapped_variants_for_score_set(session, score_set["urn"])
     publish_score_set(client, score_set["urn"])