variantgrid-api 1.3.2__tar.gz → 1.4.0__tar.gz

{variantgrid_api-1.3.2/src/variantgrid_api.egg-info → variantgrid_api-1.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.3.2
+Version: 1.4.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.3.2 → variantgrid_api-1.4.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "variantgrid_api"
-version = "1.3.2"
+version = "1.4.0"
 description = "A Python API client for VariantGrid"
 authors = [
     { name = "Dave Lawrence", email = "davmlaw@gmail.com" }

{variantgrid_api-1.3.2 → variantgrid_api-1.4.0}/src/variantgrid_api/data_models.py

@@ -132,6 +132,14 @@ class VariantCaller:
     run_params: Optional[str] = None
 
 
+@dataclass_json
+@dataclass
+class SequencingSampleLookup:
+    """ Only used as arguments to find existing sequencing sample on server - not enough details to create one """
+    sample_sheet_lookup: SampleSheetLookup = field(metadata=config(field_name="sample_sheet"))
+    sample_name: str
+
+
 @dataclass_json
 @dataclass
 class JointCalledVCF:
@@ -139,6 +147,10 @@ class JointCalledVCF:
     path: str
     sample_sheet_lookup: SampleSheetLookup = field(metadata=config(field_name="sample_sheet"))
     variant_caller: VariantCaller
+    # Set for joint calls that draw samples from more than one sequencing run, eg a family trio.
+    # sample_sheet_lookup stays the owning run - the one the path sits under.
+    sequencing_samples: Optional[List[SequencingSampleLookup]] = \
+        field(default=None, metadata=config(exclude=lambda x: x is None))
 
 
 @dataclass_json
@@ -190,14 +202,6 @@ class SequencingFile:
     vcf_file: SingleSampleVCF
 
 
-@dataclass_json
-@dataclass
-class SequencingSampleLookup:
-    """ Only used as arguments to find existing sequencing sample on server - not enough details to create one """
-    sample_sheet_lookup: SampleSheetLookup = field(metadata=config(field_name="sample_sheet"))
-    sample_name: str
-
-
 @dataclass_json
 @dataclass
 class QC:

{variantgrid_api-1.3.2 → variantgrid_api-1.4.0/src/variantgrid_api.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.3.2
+Version: 1.4.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.3.2 → variantgrid_api-1.4.0}/tests/test_api_client.py

@@ -97,6 +97,26 @@ def test_create_joint_called_vcf_posts_json(api, server, vg_objects):
         url
     )
     assert body["path"].endswith(".vcf.gz")
+    # A single-run joint call leaves the key off entirely, so the server keeps its existing behaviour
+    assert "sequencing_samples" not in body
+
+
+@responses.activate
+def test_create_joint_called_vcf_posts_cross_run_members(api, server, vg_objects):
+    url = f"{server}/seqauto/api/v1/joint_called_vcf/"
+    body = assert_post(
+        lambda: api.create_joint_called_vcf(
+            vg_objects["cross_run_joint_called_vcf"]
+        ),
+        url
+    )
+    members = body["sequencing_samples"]
+    assert [m["sample_name"] for m in members] == ["fake_sample_1", "fake_sample_mum", "fake_sample_dad"]
+    # Members carry their own sample sheet, so two of them point at the run that sequenced the parents
+    runs = {m["sample_sheet"]["sequencing_run"] for m in members}
+    assert len(runs) == 2
+    # The owning sheet is still the run the path sits under
+    assert body["sample_sheet"]["sequencing_run"] == vg_objects["SEQUENCING_RUN_NAME"]
 
 
 @responses.activate