Merge pull request #15 from Australian-Imaging-Service/simple-dir-data

Simple dir data

scripts/add_data.py

@@ -2,4 +2,4 @@
 from xnat4tests.data import add_data
 
 start_xnat()
-add_data("user-training")
+add_data("simple-dir")

tests/test_data.py

@@ -44,3 +44,29 @@ def test_add_nifti(config, launched_xnat):
         assert sorted(s.type for s in xsess2.scans.values()) == [
             "t1w",
         ]
+
+
+def test_simple_dir(config, launched_xnat):
+
+    add_data("simple-dir", config_name=config)
+
+    with connect(config) as login:
+        xsess1 = (
+            login.projects["SIMPLE_DIR"]
+            .subjects["subject01"]
+            .experiments["subject01_1"]
+        )
+
+        assert sorted(s.type for s in xsess1.scans.values()) == [
+            "a-directory",
+        ]
+
+        xsess2 = (
+            login.projects["SIMPLE_DIR"]
+            .subjects["subject02"]
+            .experiments["subject02_1"]
+        )
+
+        assert sorted(s.type for s in xsess2.scans.values()) == [
+            "a-directory",
+        ]

xnat4tests/data.py

@@ -81,36 +81,41 @@ def add_data(dataset: str, config_name: str or dict = "default"):
             project_id="OPENNEURO_T1W",
             subject_id="subject01",
             session_id="subject01_MR01",
+            resource_name="NIFTI",
         )
         _upload_directly(
             {"t1w": openneuro_t1w()},
             config,
             project_id="OPENNEURO_T1W",
             subject_id="subject02",
             session_id="subject02_MR01",
+            resource_name="NIFTI",
         )
 
     elif dataset == "simple-dir":
 
         tmp_dir = Path(tempfile.mkdtemp())
         a_dir = tmp_dir / "a-dir"
+        a_dir.mkdir()
         for i in range(3):
             a_file = a_dir / f"file{i + 1}.txt"
-            a_file.write_text("A dummy file - {i}\n")
+            a_file.write_text(f"A dummy file - {i + 1}\n")
 
         _upload_directly(
             {"a-directory": a_dir},
             config,
-            project_id="SIMPLEDIR",
+            project_id="SIMPLE_DIR",
             subject_id="subject01",
             session_id="subject01_1",
+            resource_name="DIRECTORY",
         )
         _upload_directly(
             {"a-directory": a_dir},
             config,
-            project_id="SIMPLEDIR",
+            project_id="SIMPLE_DIR",
             subject_id="subject02",
             session_id="subject02_1",
+            resource_name="DIRECTORY",
         )
 
     elif dataset == "user-training":
@@ -186,7 +191,7 @@ def add_data(dataset: str, config_name: str or dict = "default"):
 
 
 def _upload_dicom_data(
-    to_upload: Path or ty.List[Path] or str,
+    to_upload: ty.Union[Path, ty.List[Path], str],
     config: dict,
     project_id: str,
     subject_id: str,
@@ -281,6 +286,7 @@ def _upload_directly(
     project_id: str,
     subject_id: str,
     session_id: str,
+    resource_name: str,
 ):
 
     with connect(config) as login:
@@ -325,6 +331,6 @@ def _upload_directly(
         for i, (scan_type, fspath) in enumerate(to_upload.items(), start=1):
             xdataset = login.classes.MrScanData(id=i, type=scan_type, parent=xsession)
             resource = xdataset.create_resource(
-                "NIFTI"
+                resource_name
             )  # TODO get this resource name from somewhere else
             resource.upload_dir(fspath.parent, method="tar_file")