test: add e2e pipeline integration tests; raise coverage floor to 80% (#93, #35, #97, #66)

.github/workflows/ci.yml

@@ -49,7 +49,7 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
       - run: uv sync --all-extras
-      - run: uv run pytest tests/ --cov=medcheck --cov-report=xml --cov-fail-under=55
+      - run: uv run pytest tests/ --cov=medcheck --cov-report=xml --cov-fail-under=80
       - uses: codecov/codecov-action@v6
         if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.13'
         with:

docker-compose.yml

@@ -4,7 +4,10 @@ services:
       context: .
       target: lite
     ports:
-      - "8080:8080"
+      # Published on loopback only by default: the API handles PHI and ships
+      # without auth unless MEDCHECK_API_KEY is set. To expose it on the
+      # network, change to "8080:8080" AND set MEDCHECK_API_KEY in .env.
+      - "127.0.0.1:8080:8080"
     env_file: .env
     volumes:
       - ./data:/data:ro

pyproject.toml

@@ -79,7 +79,7 @@ source = ["medcheck"]
 branch = true
 
 [tool.coverage.report]
-fail_under = 55
+fail_under = 80
 
 [tool.ruff]
 line-length = 120

src/medcheck/main.py

@@ -106,7 +106,11 @@ def analyze(
     source: str = typer.Argument(..., help="DICOM folder, ZIP file, or portal URL"),
     provider: str | None = typer.Option(None, "--provider", "-p", help="Data provider (auto-detected if omitted)"),
     code: str | None = typer.Option(None, "--code", help="Access code (for portal providers)"),
-    dob: str | None = typer.Option(None, "--dob", help="Date of birth (for portal providers)"),
+    dob: str | None = typer.Option(
+        None,
+        "--dob",
+        help="Date of birth (for portal providers; stored as a credential but NOT verified by MedCheck)",
+    ),
     symptoms: str | None = typer.Option(None, "--symptoms", help="Patient symptoms"),
     trauma: str | None = typer.Option(None, "--trauma", help="Trauma mechanism/history"),
     trauma_date: str | None = typer.Option(None, "--trauma-date", help="Date of trauma"),

tests/integration/test_pipeline_e2e.py

@@ -0,0 +1,137 @@
+"""End-to-end pipeline integration tests (no network, no optional ML deps).
+
+Runs the real WorkflowEngine over synthetic DICOM data through the
+ingest -> preprocess -> report steps and checks the generated artefacts.
+"""
+
+from __future__ import annotations
+
+import json
+import zipfile
+from pathlib import Path
+
+import numpy as np
+import pydicom
+import pytest
+from pydicom.dataset import FileDataset
+from pydicom.uid import ExplicitVRLittleEndian, generate_uid
+
+from medcheck.core.context import PipelineContext
+from medcheck.core.workflow import StepRegistry, WorkflowEngine
+from medcheck.pipeline.ingest import IngestStep
+from medcheck.pipeline.preprocess import PreprocessStep
+from medcheck.pipeline.report import ReportStep
+
+_STEPS = ["ingest", "preprocess", "report"]
+
+
+def _create_test_dicom(path: Path, series_desc: str, series_num: int, instance: int) -> None:
+    file_meta = pydicom.Dataset()
+    file_meta.MediaStorageSOPClassUID = "1.2.840.10008.5.1.4.1.1.4"
+    file_meta.MediaStorageSOPInstanceUID = generate_uid()
+    file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
+    ds = FileDataset(str(path), {}, file_meta=file_meta, preamble=b"\x00" * 128)
+    ds.PatientName = "Integration^Patient"
+    ds.PatientID = "INT-4711"
+    ds.PatientBirthDate = "19800101"
+    ds.PatientSex = "F"
+    ds.StudyDate = "20260601"
+    ds.StudyDescription = "Knee MRI"
+    ds.InstitutionName = "Integration Hospital"
+    ds.Manufacturer = "SIEMENS"
+    ds.ManufacturerModelName = "Avanto"
+    ds.MagneticFieldStrength = "1.5"
+    ds.Modality = "MR"
+    ds.SeriesDescription = series_desc
+    ds.SeriesNumber = series_num
+    ds.InstanceNumber = instance
+    ds.Rows = 32
+    ds.Columns = 32
+    ds.BitsAllocated = 16
+    ds.BitsStored = 16
+    ds.HighBit = 15
+    ds.PixelRepresentation = 0
+    ds.SamplesPerPixel = 1
+    ds.PhotometricInterpretation = "MONOCHROME2"
+    ds.PixelData = np.random.randint(0, 1000, (32, 32), dtype=np.uint16).tobytes()
+    ds.save_as(str(path))
+
+
+@pytest.fixture()
+def dicom_study(tmp_path: Path) -> Path:
+    study_dir = tmp_path / "study"
+    study_dir.mkdir()
+    for series, num in (("pd_sag_knee", 1), ("t1_cor_knee", 2)):
+        series_dir = study_dir / series
+        series_dir.mkdir()
+        for i in range(1, 4):
+            _create_test_dicom(series_dir / f"slice{i}.dcm", series, num, i)
+    return study_dir
+
+
+def _engine() -> WorkflowEngine:
+    registry = StepRegistry()
+    registry.register("ingest", IngestStep)
+    registry.register("preprocess", PreprocessStep)
+    registry.register("report", ReportStep)
+    return WorkflowEngine(registry)
+
+
+def _base_ctx(source: Path, output_dir: Path) -> PipelineContext:
+    ctx = PipelineContext()
+    ctx.source = str(source)
+    ctx.report_format = "json"
+    ctx.output_dir = str(output_dir)
+    return ctx
+
+
+def test_pipeline_directory_to_json_report(dicom_study: Path, tmp_path: Path) -> None:
+    out = tmp_path / "out"
+    ctx = _engine().run(steps=_STEPS, context=_base_ctx(dicom_study, out))
+
+    assert len(ctx.dicom_series) == 2
+    assert ctx.patient.patient_id == "INT-4711"
+    assert ctx.detected_anatomy == "knee"
+    assert ctx.report_path.endswith(".json")
+
+    data = json.loads(Path(ctx.report_path).read_text())
+    assert data["patient"]["name"] == "Integration^Patient"
+    assert data["study"]["institution"] == "Integration Hospital"
+    assert data["detected_anatomy"] == "knee"
+
+
+def test_pipeline_zip_source(dicom_study: Path, tmp_path: Path) -> None:
+    zip_path = tmp_path / "study.zip"
+    with zipfile.ZipFile(zip_path, "w") as zf:
+        for f in sorted(dicom_study.rglob("*.dcm")):
+            zf.write(f, f.relative_to(dicom_study))
+
+    out = tmp_path / "out"
+    ctx = _engine().run(steps=_STEPS, context=_base_ctx(zip_path, out))
+    assert len(ctx.dicom_series) == 2
+    assert Path(ctx.report_path).exists()
+
+
+def test_pipeline_deidentified_report(dicom_study: Path, tmp_path: Path) -> None:
+    out = tmp_path / "out"
+    base = _base_ctx(dicom_study, out)
+    base.deidentify = True
+    ctx = _engine().run(steps=_STEPS, context=base)
+
+    raw = Path(ctx.report_path).read_text()
+    assert "Integration^Patient" not in raw
+    assert "INT-4711" not in raw
+    assert "19800101" not in raw
+    data = json.loads(raw)
+    assert data["deidentified"] is True
+
+
+def test_pipeline_html_report(dicom_study: Path, tmp_path: Path) -> None:
+    out = tmp_path / "out"
+    base = _base_ctx(dicom_study, out)
+    base.report_format = "html"
+    base.report_language = "de"
+    ctx = _engine().run(steps=_STEPS, context=base)
+    assert ctx.report_path.endswith(".html")
+    html_text = Path(ctx.report_path).read_text()
+    assert 'lang="de"' in html_text