variantgrid-api 1.1.1__tar.gz → 1.2.0__tar.gz

{variantgrid_api-1.1.1/src/variantgrid_api.egg-info → variantgrid_api-1.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.1.1
+Version: 1.2.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.1.1 → variantgrid_api-1.2.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "variantgrid_api"
-version = "1.1.1"
+version = "1.2.0"
 description = "A Python API client for VariantGrid"
 authors = [
     { name = "Dave Lawrence", email = "davmlaw@gmail.com" }

{variantgrid_api-1.1.1 → variantgrid_api-1.2.0}/src/variantgrid_api/data_models.py

@@ -25,6 +25,30 @@ class SequencerModel:
     manufacturer: Manufacturer
     data_naming_convention: str # 'M' or 'H' for (HiSeq only)
 
+    # (prefix, model_name, data_naming_convention)
+    _ILLUMINA_PREFIXES = [
+        ("LH", "NovaSeq X",    "M"),
+        ("NB", "NextSeq",      "M"),
+        ("NS", "NextSeq",      "M"),
+        ("A",  "NovaSeq 6000", "M"),
+        ("H",  "HiSeq",        "H"),
+        ("M",  "MiSeq",        "M"),
+    ]
+
+    @classmethod
+    def from_sequencer_name(cls, sequencer_name: str) -> 'SequencerModel':
+        """Infer SequencerModel from an Illumina sequencer instrument name.
+
+        Illumina instrument names begin with a letter code that identifies the
+        platform (e.g. ``M02027`` → MiSeq, ``A01234`` → NovaSeq 6000).
+        Returns an Unknown model when no prefix matches.
+        """
+        illumina = Manufacturer(name="Illumina")
+        for prefix, model_name, convention in cls._ILLUMINA_PREFIXES:
+            if sequencer_name.startswith(prefix):
+                return cls(model=model_name, manufacturer=illumina, data_naming_convention=convention)
+        return cls(model="Unknown", manufacturer=illumina, data_naming_convention="U")
+
 
 @dataclass_json
 @dataclass

variantgrid_api-1.2.0/src/variantgrid_api/mock_variantgrid_api.py

@@ -0,0 +1,134 @@
+"""
+Mock replacement for variantgrid_api.api_client.VariantGridAPI.
+
+Records every call so tests can assert on what was sent without making any
+
+Usage::
+
+    api = MockVariantGridAPI()
+    api.create_experiment("HAEM_25_080")
+    api.assert_called_once("create_experiment")
+    api.assert_not_called("sequencing_run_has_vcf")
+"""
+from __future__ import annotations
+
+import copy
+from typing import Any, List, Optional, Tuple
+
+
+class MockVariantGridAPI:
+    """Drop-in replacement for VariantGridAPI that records all calls."""
+
+    def __init__(self):
+        # List of (method_name, args, kwargs) in call order
+        self.calls: List[Tuple[str, tuple, dict]] = []
+        self._return_values: dict = {}
+
+    # ------------------------------------------------------------------ #
+    # Introspection helpers                                               #
+    # ------------------------------------------------------------------ #
+
+    def _record(self, method: str, *args, **kwargs):
+        self.calls.append((method, args, kwargs))
+
+    def _ret(self, method: str, default: Any) -> Any:
+        return copy.deepcopy(self._return_values.get(method, default))
+
+    def set_return(self, method: str, value: Any) -> None:
+        """Override the default return value for a given method."""
+        self._return_values[method] = value
+
+    def get_calls(self, method: str) -> List[Tuple[tuple, dict]]:
+        """Return all (args, kwargs) pairs recorded for *method*."""
+        return [(a, kw) for name, a, kw in self.calls if name == method]
+
+    def call_count(self, method: str) -> int:
+        return len(self.get_calls(method))
+
+    def assert_called_once(self, method: str) -> None:
+        n = self.call_count(method)
+        assert n == 1, f"Expected {method!r} called once, was called {n} times"
+
+    def assert_not_called(self, method: str) -> None:
+        n = self.call_count(method)
+        assert n == 0, f"Expected {method!r} not called, was called {n} times"
+
+    def reset(self) -> None:
+        self.calls.clear()
+
+    # ------------------------------------------------------------------ #
+    # API surface — mirrors VariantGridAPI public methods exactly         #
+    # ------------------------------------------------------------------ #
+
+    def create_experiment(self, experiment):
+        self._record("create_experiment", experiment)
+        return self._ret("create_experiment", {"name": experiment})
+
+    def create_enrichment_kit(self, enrichment_kit):
+        self._record("create_enrichment_kit", enrichment_kit)
+        return self._ret("create_enrichment_kit", {
+            "name": enrichment_kit.name,
+            "version": enrichment_kit.version,
+            "gene_list": {
+                "genelistgenesymbol_set": [
+                    {"gene_symbol": "BRCA1"},
+                    {"gene_symbol": "BRCA2"},
+                ]
+            },
+        })
+
+    def create_sequencer_model(self, sequencer_model):
+        self._record("create_sequencer_model", sequencer_model)
+        return self._ret("create_sequencer_model", {"model": sequencer_model.model})
+
+    def create_sequencer(self, sequencer):
+        self._record("create_sequencer", sequencer)
+        return self._ret("create_sequencer", {"name": sequencer.name})
+
+    def create_sequencing_run(self, sequencing_run):
+        self._record("create_sequencing_run", sequencing_run)
+        return self._ret("create_sequencing_run", {"name": sequencing_run.name})
+
+    def create_sample_sheet(self, sample_sheet):
+        self._record("create_sample_sheet", sample_sheet)
+        return self._ret("create_sample_sheet", {"path": sample_sheet.path})
+
+    def create_sample_sheet_combined_vcf_file(self, sscvf):
+        self._record("create_sample_sheet_combined_vcf_file", sscvf)
+        return self._ret("create_sample_sheet_combined_vcf_file", {"path": sscvf.path})
+
+    def create_sequencing_data(self, sample_sheet_lookup, sequencing_files):
+        self._record("create_sequencing_data", sample_sheet_lookup, sequencing_files)
+        return self._ret("create_sequencing_data", {"created": len(sequencing_files)})
+
+    def create_qc_gene_list(self, qc_gene_list):
+        self._record("create_qc_gene_list", qc_gene_list)
+        return self._ret("create_qc_gene_list", {})
+
+    def create_multiple_qc_gene_lists(self, qc_gene_lists):
+        self._record("create_multiple_qc_gene_lists", qc_gene_lists)
+        return self._ret("create_multiple_qc_gene_lists", {"created": len(qc_gene_lists)})
+
+    def create_qc_exec_stats(self, qc_exec_stats):
+        self._record("create_qc_exec_stats", qc_exec_stats)
+        return self._ret("create_qc_exec_stats", {})
+
+    def create_multiple_qc_exec_stats(self, qc_exec_stats):
+        self._record("create_multiple_qc_exec_stats", qc_exec_stats)
+        return self._ret("create_multiple_qc_exec_stats", {"created": len(qc_exec_stats)})
+
+    def create_multiple_qc_gene_coverage(self, qc_gene_coverage_list):
+        self._record("create_multiple_qc_gene_coverage", qc_gene_coverage_list)
+        return self._ret("create_multiple_qc_gene_coverage", {"created": len(qc_gene_coverage_list)})
+
+    def upload_file(self, filename):
+        self._record("upload_file", filename)
+        return self._ret("upload_file", {"path": filename, "status": "ok"})
+
+    def sequencing_run_has_vcf(self, sequencing_run, path=None):
+        self._record("sequencing_run_has_vcf", sequencing_run, path)
+        return self._ret("sequencing_run_has_vcf", True)
+
+    def sequencing_run_name_has_vcf(self, sequencing_run_name, path=None):
+        self._record("sequencing_run_name_has_vcf", sequencing_run_name, path)
+        return self._ret("sequencing_run_name_has_vcf", True)

{variantgrid_api-1.1.1 → variantgrid_api-1.2.0/src/variantgrid_api.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: variantgrid_api
-Version: 1.1.1
+Version: 1.2.0
 Summary: A Python API client for VariantGrid
 Author-email: Dave Lawrence <davmlaw@gmail.com>
 License: MIT License

{variantgrid_api-1.1.1 → variantgrid_api-1.2.0}/src/variantgrid_api.egg-info/SOURCES.txt

@@ -3,6 +3,7 @@ README.md
 pyproject.toml
 src/variantgrid_api/api_client.py
 src/variantgrid_api/data_models.py
+src/variantgrid_api/mock_variantgrid_api.py
 src/variantgrid_api.egg-info/PKG-INFO
 src/variantgrid_api.egg-info/SOURCES.txt
 src/variantgrid_api.egg-info/dependency_links.txt
@@ -11,4 +12,6 @@ src/variantgrid_api.egg-info/top_level.txt
 tests/test_api_client.py
 tests/test_api_client_bulk.py
 tests/test_api_client_validation.py
-tests/test_data_models.py
+tests/test_data_models.py
+tests/test_mock_variantgrid_api.py
+tests/test_sequencer_model_from_name.py

variantgrid_api-1.2.0/tests/test_mock_variantgrid_api.py

@@ -0,0 +1,141 @@
+"""Tests for MockVariantGridAPI — verifies call recording, return-value
+overrides, and assertion helpers work correctly."""
+import pytest
+
+from variantgrid_api.mock_variantgrid_api import MockVariantGridAPI
+
+
+@pytest.fixture
+def mock_api():
+    return MockVariantGridAPI()
+
+
+# ------------------------------------------------------------------ #
+# Call recording                                                       #
+# ------------------------------------------------------------------ #
+
+def test_calls_are_recorded(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    assert mock_api.call_count("create_experiment") == 1
+    assert mock_api.call_count("create_sequencing_run") == 0
+
+
+def test_multiple_calls_accumulate(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.create_experiment(vg_objects["experiment"])
+    assert mock_api.call_count("create_experiment") == 2
+
+
+def test_get_calls_returns_args(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    calls = mock_api.get_calls("create_experiment")
+    assert len(calls) == 1
+    args, kwargs = calls[0]
+    assert args[0] == vg_objects["experiment"]
+
+
+def test_calls_from_different_methods_are_independent(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.create_sequencing_run(vg_objects["sequencing_run"])
+    assert mock_api.call_count("create_experiment") == 1
+    assert mock_api.call_count("create_sequencing_run") == 1
+    assert mock_api.call_count("create_sample_sheet") == 0
+
+
+# ------------------------------------------------------------------ #
+# Assertion helpers                                                    #
+# ------------------------------------------------------------------ #
+
+def test_assert_called_once_passes(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.assert_called_once("create_experiment")  # should not raise
+
+
+def test_assert_called_once_fails_when_not_called(mock_api):
+    with pytest.raises(AssertionError):
+        mock_api.assert_called_once("create_experiment")
+
+
+def test_assert_called_once_fails_when_called_twice(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.create_experiment(vg_objects["experiment"])
+    with pytest.raises(AssertionError):
+        mock_api.assert_called_once("create_experiment")
+
+
+def test_assert_not_called_passes(mock_api):
+    mock_api.assert_not_called("create_experiment")  # should not raise
+
+
+def test_assert_not_called_fails_when_called(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    with pytest.raises(AssertionError):
+        mock_api.assert_not_called("create_experiment")
+
+
+# ------------------------------------------------------------------ #
+# Default return values                                                #
+# ------------------------------------------------------------------ #
+
+def test_default_return_create_experiment(mock_api, vg_objects):
+    result = mock_api.create_experiment(vg_objects["experiment"])
+    assert result == {"name": vg_objects["experiment"]}
+
+
+def test_default_return_sequencing_run_has_vcf(mock_api, vg_objects):
+    result = mock_api.sequencing_run_has_vcf(vg_objects["sequencing_run"])
+    assert result is True
+
+
+def test_default_return_create_sequencing_data(mock_api, vg_objects):
+    result = mock_api.create_sequencing_data(
+        vg_objects["sample_sheet_lookup"], vg_objects["sequencing_files"]
+    )
+    assert result == {"created": len(vg_objects["sequencing_files"])}
+
+
+def test_default_return_create_multiple_qc_gene_lists(mock_api, vg_objects):
+    result = mock_api.create_multiple_qc_gene_lists(vg_objects["qc_gene_lists"])
+    assert result == {"created": len(vg_objects["qc_gene_lists"])}
+
+
+# ------------------------------------------------------------------ #
+# set_return overrides                                                 #
+# ------------------------------------------------------------------ #
+
+def test_set_return_overrides_default(mock_api, vg_objects):
+    mock_api.set_return("create_experiment", {"name": "overridden", "id": 99})
+    result = mock_api.create_experiment(vg_objects["experiment"])
+    assert result == {"name": "overridden", "id": 99}
+
+
+def test_set_return_is_deep_copied(mock_api, vg_objects):
+    sentinel = {"name": "exp", "extra": []}
+    mock_api.set_return("create_experiment", sentinel)
+    r1 = mock_api.create_experiment(vg_objects["experiment"])
+    r1["extra"].append("mutated")
+    r2 = mock_api.create_experiment(vg_objects["experiment"])
+    assert r2["extra"] == [], "set_return should return independent copies each call"
+
+
+def test_set_return_sequencing_run_has_vcf_false(mock_api, vg_objects):
+    mock_api.set_return("sequencing_run_has_vcf", False)
+    assert mock_api.sequencing_run_has_vcf(vg_objects["sequencing_run"]) is False
+
+
+# ------------------------------------------------------------------ #
+# reset                                                                #
+# ------------------------------------------------------------------ #
+
+def test_reset_clears_calls(mock_api, vg_objects):
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.reset()
+    assert mock_api.call_count("create_experiment") == 0
+
+
+def test_reset_preserves_return_overrides(mock_api, vg_objects):
+    mock_api.set_return("create_experiment", {"id": 7})
+    mock_api.create_experiment(vg_objects["experiment"])
+    mock_api.reset()
+    result = mock_api.create_experiment(vg_objects["experiment"])
+    assert result == {"id": 7}

variantgrid_api-1.2.0/tests/test_sequencer_model_from_name.py

@@ -0,0 +1,32 @@
+import pytest
+from variantgrid_api.data_models import SequencerModel
+
+
+@pytest.mark.parametrize("name,expected_model,expected_convention", [
+    ("M02027",  "MiSeq",        "M"),
+    ("H001",    "HiSeq",        "H"),
+    ("NB551234","NextSeq",      "M"),
+    ("NS500123","NextSeq",      "M"),
+    ("A01234",  "NovaSeq 6000", "M"),
+    ("LH00999", "NovaSeq X",    "M"),
+    ("XYZ999",  "Unknown",      "U"),
+])
+def test_from_sequencer_name(name, expected_model, expected_convention):
+    sm = SequencerModel.from_sequencer_name(name)
+    assert sm.model == expected_model
+    assert sm.data_naming_convention == expected_convention
+    assert sm.manufacturer.name == "Illumina"
+
+
+def test_from_sequencer_name_matches_conftest_example():
+    # The conftest uses sequencer "SN1101" which doesn't match any prefix → Unknown
+    # But the run name contains "M02027" as the instrument — verify MiSeq detection
+    sm = SequencerModel.from_sequencer_name("M02027")
+    assert sm.model == "MiSeq"
+
+
+def test_lh_prefix_not_matched_as_h():
+    """NovaSeq X instruments start with LH — must not be classified as HiSeq."""
+    sm = SequencerModel.from_sequencer_name("LH00187")
+    assert sm.model == "NovaSeq X"
+    assert sm.data_naming_convention == "M"