Test upload_dataset

Add custom option --upload-only to pytest.

The test will only run when that argument is passed. Skipped otherwise.

Minor changes to the test_parameters file.

.gitignore

@@ -1,4 +1,5 @@
 data/
+tests/test_local_parameters.json
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

README.md

@@ -12,3 +12,13 @@ please read the [CONTRIBUTING](CONTRIBUTING.md) page.
 Sample data for testing acquired from:
 [PROJECT: HumanCT  >  SUBJECT: VHFCT1mm-Pelvis  >  000-000-002](https://central.xnat.org/app/action/DisplayItemAction/search_element/xnat%3ActSessionData/search_field/xnat%3ActSessionData.ID/search_value/CENTRAL04_E04384/popup/false/project/HumanCT)
 and manually segmented using [Slicer3D](https://www.slicer.org/).
+
+## Tests
+
+Create a copy of the test_parameters where you will provide the mdai ids needed
+to upload and download the test data.
+
+`cp tests/test_parameters.json tests/test_local_parameters.json`
+
+We provide a tiny dataset that you can upload to a test dataset in your md.ai
+instance. Only needed to run once: `pytest tests -rP --upload-only`.

upload_dataset.py → mdai_utils/upload_dataset.py

@@ -36,13 +36,14 @@ def upload_dataset(mdai_dataset_id, dir_path, order_exams_by="default"):
         f"{order_exams_by}",
         f"{dir_path}",
     ]
-    return subprocess.run(
+    completed_process = subprocess.run(
         command,
         stdout=subprocess.PIPE,
-        stderr=subprocess.STDOUT,
         check=True,
-        encoding="utf-8",
     )
+    if completed_process.returncode or completed_process.stderr:
+        raise Exception(f"Error uploading dataset: {completed_process}.")
+    return completed_process
 
 
 if __name__ == "__main__":

tests/conftest.py

@@ -1,23 +1,66 @@
 import json
-import os
 from pathlib import Path
 
 import mdai
 import pytest
 
-_current_dir = Path(__file__).parent if "__file__" in locals() else Path(".")
+from mdai_utils.common import get_mdai_access_token
+
+
+def pytest_addoption(parser):
+    """Add a command line option to pytest."""
+    parser.addoption(
+        "--upload-only",
+        action="store_true",
+        default=False,
+        help="run only tests marked as upload_only",
+    )
+
+
+# Register the custom mark to avoid pytest warnings
+def pytest_configure(config):
+    config.addinivalue_line(
+        "markers", "upload_only: Mark test to run only when --upload-only is provided"
+    )
+
+
+@pytest.hookimpl(tryfirst=True)
+def pytest_runtest_setup(item):
+    """Hook that runs before a test is set up."""
+    is_upload_only_test = "upload_only" in item.keywords
+    upload_only_mode = item.config.getoption("--upload-only")
+
+    if upload_only_mode:
+        if not is_upload_only_test:
+            pytest.skip("Skipping non-upload tests in upload-only mode")
+    else:
+        if is_upload_only_test:
+            pytest.skip("Skipping upload-only tests in standard mode")
+
+
+_current_dir = Path(__file__).parent
 
 
 @pytest.fixture(scope="session")
-def mdai_setup(parameters_file=_current_dir / "test_parameters.json", input_token=None):
-    token = input_token or os.getenv("MDAI_TOKEN", "")
-    if token == "":
-        raise ValueError(
-            "Please set the MDAI_TOKEN environment variable with your MDAI credentials."
+def mdai_setup(
+    parameters_file=_current_dir / "test_local_parameters.json", input_token=None
+):
+    # Check if the parameters file exists
+    print(f"Parameters file: {parameters_file}")
+    if not parameters_file.exists():
+        existing_parameters_file = _current_dir / "test_parameters.json"
+        raise FileNotFoundError(
+            f"Parameters file {parameters_file} not found. Please create one, using {existing_parameters_file} as a template."
         )
+    token = input_token or get_mdai_access_token()
     with open(parameters_file) as f:
         parameters = json.load(f)
 
+    fixture_dir = _current_dir / "fixtures"
     mdai_domain = parameters.get("mdai_domain") or "md.ai"
     mdai_client = mdai.Client(domain=mdai_domain, access_token=token)
-    return {"mdai_client": mdai_client, "parameters": parameters}
+    return {
+        "mdai_client": mdai_client,
+        "parameters": parameters,
+        "fixture_dir": fixture_dir,
+    }

tests/test_parameters.json

@@ -1,17 +1,15 @@
 {
-    "mdai_domain": "uab.md.ai",
+    "mdai_domain": "md.ai",
     "mdai_token_env_variable": "MDAI_TOKEN",
     "mdai_project_id": "L1NprBvP",
     "mdai_dataset_id": "D_odXMLm",
-    "mdai_label_group_id": "G_P914xZ",
+    "mdai_label_group_id": "G_2Jy2yZ",
     "mdai_label_ids": {
-        "heart": "L_W4Xx64",
-        "inner-chest": "L_npal0d"
+        "mylabel": "L_W4XQKd"
     },
     "mdai_annotations_only": true,
     "mdai_no_fixing_metadata": false,
     "labels": [
-        "heart",
-        "inner-chest"
+        "mylabel",
     ]
 }

tests/upload_test.py

@@ -1,7 +1,29 @@
-# from mdai_utils.upload import upload_data_annotation_slice
+import pytest
 
+from mdai_utils.upload_dataset import upload_dataset
 
-def test_upload_mask_annotation(mdai_setup):
+
+def test_pytest_fixture(mdai_setup):
     mdai_parameters = mdai_setup["parameters"]
     mdai_project_id = mdai_parameters.get("mdai_project_id")
     assert mdai_project_id is not None
+
+
+@pytest.mark.upload_only(
+    reason="Only need to upload once. run pytest tests with --upload-only to run it."
+)
+def test_upload_dataset(mdai_setup):
+    mdai_parameters = mdai_setup["parameters"]
+    mdai_dataset_id = mdai_parameters.get("mdai_dataset_id")
+    fixture_dir = mdai_setup["fixture_dir"]
+    dicom_dir = fixture_dir / "humanct_0002_1000_1004"
+    assert fixture_dir.exists()
+    completed_process = upload_dataset(mdai_dataset_id, dicom_dir)
+    process_message = completed_process.stdout.strip()
+    print(process_message)
+    # Check the status of subprocess
+    assert completed_process.returncode == 0
+
+
+def test_upload_annotation(mdai_setup):
+    mdai_setup["parameters"]