variantgrid-api 1.6.0__tar.gz → 1.8.0__tar.gz

{variantgrid_api-1.6.0/src/variantgrid_api.egg-info → variantgrid_api-1.8.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.6.0
+Version: 1.8.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "variantgrid_api"
-version = "1.6.0"
+version = "1.8.0"
 description = "A Python API client for VariantGrid"
 authors = [
     { name = "Dave Lawrence", email = "davmlaw@gmail.com" }

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/src/variantgrid_api/api_client.py

@@ -243,8 +243,20 @@ class VariantGridAPI:
         for sf in sequencing_files:
             # The server requires both paths - catch it here, naming the record, rather than a 400 for the batch
             self._validate_string(f"SequencingFile '{sf.sample_name}' bam_file.path", sf.bam_file and sf.bam_file.path)
-            self._validate_string(f"SequencingFile '{sf.sample_name}' vcf_file.path", sf.vcf_file and sf.vcf_file.path)
+            vcf_files = sf.get_vcf_files()
+            self._validate_list(f"SequencingFile '{sf.sample_name}' vcf_files", vcf_files)
+            for i, vcf_file in enumerate(vcf_files):
+                self._validate_string(f"SequencingFile '{sf.sample_name}' vcf_files[{i}].path",
+                                      vcf_file and vcf_file.path)
+            # The server keeps one VCF per BAM and caller - a repeated caller would silently replace a path
+            callers = [f"{vc.name} {vc.version}" for vcf_file in vcf_files
+                       if vcf_file and (vc := vcf_file.variant_caller)]
+            if repeated := {c for c in callers if callers.count(c) > 1}:
+                raise ValueError(f"SequencingFile '{sf.sample_name}' has more than one VCF from variant caller(s) "
+                                 f"{', '.join(sorted(repeated))} - each VCF off a BAM needs its own caller")
             data = sf.to_dict()
+            data.pop("vcf_file", None)
+            data.pop("vcf_files", None)
             # put into hierarchial JSON DRF expects
             fastq_r1 = data.pop("fastq_r1", None)
             fastq_r2 = data.pop("fastq_r2", None)
@@ -255,8 +267,10 @@ class VariantGridAPI:
                 data["unaligned_reads"] = unaligned_reads
             elif fastq_r2:
                 raise ValueError(f"SequencingFile '{sf.sample_name}' has fastq_r2 without fastq_r1")
-            # No FastQs (BAM-first run) - server resolves the sample from sample_name
-            records.append(data)
+            # No FastQs (BAM-first run) - server resolves the sample from sample_name.
+            # The server takes one VCF per record, so each is a record sharing the BAM and FastQs
+            for vcf_file in vcf_files:
+                records.append({**data, "vcf_file": vcf_file.to_dict() if vcf_file else None})
 
         json_data = {
             "sample_sheet": sample_sheet_lookup.to_dict(),

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/src/variantgrid_api/data_models.py

@@ -196,12 +196,33 @@ class VCFFile(SingleSampleVCF):
 @dataclass_json
 @dataclass
 class SequencingFile:
-    """ FastQs are optional - BAM-first runs (sequencer emits BAM, or FastQs not kept) send just BAM + VCF """
+    """ FastQs are optional - BAM-first runs (sequencer emits BAM, or FastQs not kept) send just BAM + VCF
+
+        vcf_files: the VCFs called off this BAM, one per variant caller, eg DRAGEN TSO 500's small variant VCF and
+        its gene-level CNV VCF. The server keeps one VCF per BAM and caller, so a second with the same caller
+        would replace the first - create_sequencing_data() raises instead.
+
+        vcf_file is deprecated - use vcf_files. It still works (set it and it is sent, read it back as before),
+        and get_vcf_files() gives both """
     sample_name: str
     bam_file: BamFile
-    vcf_file: SingleSampleVCF
+    vcf_file: Optional[SingleSampleVCF] = field(default=None, metadata=config(exclude=lambda x: x is None))
     fastq_r1: Optional[str] = field(default=None, metadata=config(exclude=lambda x: x is None))
     fastq_r2: Optional[str] = field(default=None, metadata=config(exclude=lambda x: x is None))
+    vcf_files: Optional[List[SingleSampleVCF]] = field(default=None, metadata=config(exclude=lambda x: x is None))
+
+    def __post_init__(self):
+        if self.vcf_file is not None:
+            warnings.warn(
+                "SequencingFile.vcf_file is deprecated; use vcf_files instead.",
+                DeprecationWarning,
+                stacklevel=3,
+            )
+
+    def get_vcf_files(self) -> List[SingleSampleVCF]:
+        """ vcf_file (deprecated) then vcf_files """
+        vcf_files = [self.vcf_file] if self.vcf_file is not None else []
+        return vcf_files + list(self.vcf_files or [])
 
 
 @dataclass_json
@@ -473,6 +494,7 @@ class UploadFileType(_ServerName):
     BED = "bed"
     DRAGEN_TSO500_ALL_FUSIONS = "dragen_tso500_all_fusions"
     DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT = "dragen_tso500_combined_variant_output"
+    DRAGEN_TSO500_METRICS_OUTPUT = "dragen_tso500_metrics_output"
     GENE_COVERAGE = "gene_coverage"
     GENE_LIST = "gene_list"
     GENE_LEVEL_CNV_VCF = "gene_level_cnv_vcf"

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/src/variantgrid_api/mock_variantgrid_api.py

@@ -30,6 +30,7 @@ MOCK_CAPABILITIES = ServerCapabilities(
     upload_file_types=frozenset({UploadFileType.VCF, UploadFileType.GENE_COVERAGE,
                                  UploadFileType.DRAGEN_TSO500_ALL_FUSIONS,
                                  UploadFileType.DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT,
+                                 UploadFileType.DRAGEN_TSO500_METRICS_OUTPUT,
                                  UploadFileType.GENE_LEVEL_CNV_VCF}),
 )
 

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0/src/variantgrid_api.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.6.0
+Version: 1.8.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/tests/test_api_client.py

@@ -7,7 +7,7 @@ import pytest
 import responses
 
 from variantgrid_api.api_client import VariantGridAPI, DateTimeEncoder, EmptyInputPolicy
-from variantgrid_api.data_models import BamFile, SingleSampleVCF
+from variantgrid_api.data_models import BamFile, SequencingFile, SingleSampleVCF, VariantCaller
 
 
 def _last_json():
@@ -67,19 +67,21 @@ def test_create_sequencing_data_fastq_r2_without_r1_raises(api, vg_objects):
     with pytest.raises(ValueError):
         api.create_sequencing_data(vg_objects["sample_sheet_lookup"], [sf])
 
-@pytest.mark.parametrize("field, value", [
-    ("vcf_file", None),
-    ("vcf_file", SingleSampleVCF(path=None)),
-    ("vcf_file", SingleSampleVCF(path="")),
-    ("bam_file", None),
-    ("bam_file", BamFile(path=None)),
+@pytest.mark.parametrize("changes, name", [
+    ({"vcf_files": None}, "vcf_files"),
+    ({"vcf_files": []}, "vcf_files"),
+    ({"vcf_files": [None]}, r"vcf_files\[0\].path"),
+    ({"vcf_files": [SingleSampleVCF(path=None)]}, r"vcf_files\[0\].path"),
+    ({"vcf_files": [SingleSampleVCF(path="")]}, r"vcf_files\[0\].path"),
+    ({"bam_file": None}, "bam_file.path"),
+    ({"bam_file": BamFile(path=None)}, "bam_file.path"),
 ])
 @responses.activate
-def test_create_sequencing_data_missing_path_names_record(api, vg_objects, field, value):
+def test_create_sequencing_data_missing_path_names_record(api, vg_objects, changes, name):
     """ SACGF/variantgrid_api#23 - caught before sending, naming the record, rather than a 400 for the batch """
     sequencing_files = list(vg_objects["sequencing_files"])
-    sequencing_files[1] = dataclasses.replace(sequencing_files[1], **{field: value})
-    with pytest.raises(ValueError, match=f"SequencingFile 'fake_sample_2' {field}.path"):
+    sequencing_files[1] = dataclasses.replace(sequencing_files[1], **changes)
+    with pytest.raises(ValueError, match=f"SequencingFile 'fake_sample_2' {name}"):
         api.create_sequencing_data(vg_objects["sample_sheet_lookup"], sequencing_files)
     assert len(responses.calls) == 0
 
@@ -89,10 +91,55 @@ def test_create_sequencing_data_missing_vcf_path_warns_and_posts(server, api_tok
     url = f"{server}/seqauto/api/v1/sequencing_files/bulk_create"
     responses.add(responses.POST, url, json={"created": 2}, status=200)
     sequencing_files = list(vg_objects["sequencing_files"])
-    sequencing_files[0] = dataclasses.replace(sequencing_files[0], vcf_file=SingleSampleVCF(path=None))
+    sequencing_files[0] = dataclasses.replace(sequencing_files[0], vcf_files=[SingleSampleVCF(path=None)])
     api.create_sequencing_data(vg_objects["sample_sheet_lookup"], sequencing_files)
     assert len(responses.calls) == 1
-    assert any("SequencingFile 'fake_sample_1' vcf_file.path" in r.message for r in caplog.records)
+    assert any("SequencingFile 'fake_sample_1' vcf_files[0].path" in r.message for r in caplog.records)
+
+@responses.activate
+def test_create_sequencing_data_vcf_files_share_the_bam(api, server, vg_objects):
+    """ eg DRAGEN TSO 500's CNV VCF beside its small variant VCF - one record per VCF, same BAM and FastQs """
+    url = f"{server}/seqauto/api/v1/sequencing_files/bulk_create"
+    responses.add(responses.POST, url, json={"created": 3}, status=200)
+    cnv_vcf = SingleSampleVCF(path="/data/fake_sample_1.cnv.vcf", variant_caller=VariantCaller(name="cnv", version="1"))
+    sequencing_files = list(vg_objects["sequencing_files"])
+    sf = sequencing_files[0]
+    sequencing_files[0] = dataclasses.replace(sf, vcf_files=sf.vcf_files + [cnv_vcf])
+    api.create_sequencing_data(vg_objects["sample_sheet_lookup"], sequencing_files)
+
+    records = _last_json()["records"]
+    assert [r["sample_name"] for r in records] == ["fake_sample_1", "fake_sample_1", "fake_sample_2"]
+    first, second = records[0], records[1]
+    assert "vcf_files" not in first
+    assert first["vcf_file"]["path"] == sf.vcf_files[0].path
+    assert second["vcf_file"]["path"] == "/data/fake_sample_1.cnv.vcf"
+    assert second["bam_file"] == first["bam_file"]
+    assert second["unaligned_reads"] == first["unaligned_reads"]
+
+def test_create_sequencing_data_vcf_files_same_caller_raises(api, vg_objects):
+    """ The server keeps one VCF per BAM and caller, so the second would silently replace the first's path """
+    sf = vg_objects["sequencing_files"][0]
+    same_caller = SingleSampleVCF(path="/data/other.vcf", variant_caller=sf.vcf_files[0].variant_caller)
+    sf = dataclasses.replace(sf, vcf_files=sf.vcf_files + [same_caller])
+    with pytest.raises(ValueError, match="fake_sample_1.*more than one VCF"):
+        api.create_sequencing_data(vg_objects["sample_sheet_lookup"], [sf])
+
+@responses.activate
+def test_create_sequencing_data_deprecated_vcf_file_still_sent(api, server, vg_objects):
+    """ vcf_file is deprecated for vcf_files, but a client still using it sends the same records as before """
+    url = f"{server}/seqauto/api/v1/sequencing_files/bulk_create"
+    responses.add(responses.POST, url, json={"created": 2}, status=200)
+    old_style = []
+    for sf in vg_objects["sequencing_files"]:
+        with pytest.warns(DeprecationWarning, match="vcf_file is deprecated"):
+            old_style.append(SequencingFile(sample_name=sf.sample_name, bam_file=sf.bam_file,
+                                            vcf_file=sf.vcf_files[0], fastq_r1=sf.fastq_r1, fastq_r2=sf.fastq_r2))
+    api.create_sequencing_data(vg_objects["sample_sheet_lookup"], old_style)
+    old_records = _last_json()["records"]
+
+    api.create_sequencing_data(vg_objects["sample_sheet_lookup"], vg_objects["sequencing_files"])
+    assert old_records == _last_json()["records"]
+    assert old_style[0].vcf_file.path == old_style[0].get_vcf_files()[0].path
 
 def assert_post(api_call, url):
     responses.add(responses.POST, url, json={"ok": True}, status=200)

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/tests/test_api_client_capabilities.py

@@ -60,12 +60,15 @@ def test_capabilities_accept_enums(api, capabilities_url, capabilities_json):
 
     assert all(api.supports(feature) for feature in ServerFeature)
     assert api.accepts_upload(UploadFileType.DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT)
+    assert api.accepts_upload(UploadFileType.DRAGEN_TSO500_METRICS_OUTPUT)
     assert not api.accepts_upload(UploadFileType.GENE_LIST)
 
 
 def test_enums_are_their_server_names():
     assert ServerFeature.PATIENTS == "patients"
     assert str(UploadFileType.DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT) == CVO
+    # SACGF/variantgrid_api#24 - the server's UploadedFileTypes.DRAGEN_TSO500_METRICS_OUTPUT in lower case
+    assert str(UploadFileType.DRAGEN_TSO500_METRICS_OUTPUT) == "dragen_tso500_metrics_output"
     assert f"'{ServerFeature.UPLOAD_METADATA}'" == "'upload_metadata'"
     for enum_class in (ServerFeature, UploadFileType):
         for member in enum_class:

{variantgrid_api-1.6.0 → variantgrid_api-1.8.0}/tests/test_mock_variantgrid_api.py

@@ -245,6 +245,7 @@ def test_mock_default_capabilities_accept_enums(mock_api):
     assert mock_api.supports("upload_status")
     assert mock_api.accepts_upload(UploadFileType.DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT)
     assert not mock_api.accepts_upload(UploadFileType.PED)
+    assert mock_api.accepts_upload(UploadFileType.DRAGEN_TSO500_METRICS_OUTPUT)
     mock_api.upload_file("cvo.tsv", path=None, file_type=UploadFileType.DRAGEN_TSO500_COMBINED_VARIANT_OUTPUT)
     mock_api.assert_called_once("upload_file")