made session_id equal to subject_visit

xnat_ingest/cli/stage.py

@@ -150,7 +150,7 @@ def stage(
     associated_files: AssociatedFiles,
     project_field: str,
     subject_field: str,
-    session_field: str,
+    visit_field: str,
     project_id: str | None,
     delete: bool,
     log_level: str,
@@ -175,7 +175,7 @@ def stage(
         dicoms_path=dicoms_path,
         project_field=project_field,
         subject_field=subject_field,
-        session_field=session_field,
+        visit_field=visit_field,
         project_id=project_id,
     )
 

xnat_ingest/cli/upload.py

@@ -129,8 +129,10 @@
     "--use-manifest/--dont-use-manifest",
     default=None,
     envvar="XNAT_INGEST_REQUIRE_MANIFEST",
-    help=("Whether to use the manifest file in the staged sessions to load the "
-          "directory structure. By default it is used if present and ignore if not there"),
+    help=(
+        "Whether to use the manifest file in the staged sessions to load the "
+        "directory structure. By default it is used if present and ignore if not there"
+    ),
     type=bool,
 )
 def upload(
@@ -158,26 +160,30 @@ def upload(
 
     with xnat_repo.connection:
 
-        def xnat_session_exists(project_id, subject_id, session_id):
+        def xnat_session_exists(project_id, subject_id, visit_id):
             try:
                 xnat_repo.connection.projects[project_id].subjects[
                     subject_id
-                ].experiments[session_id]
+                ].experiments[
+                    ImagingSession.make_session_id(project_id, subject_id, visit_id)
+                ]
             except KeyError:
                 return False
             else:
                 logger.info(
                     "Skipping session '%s-%s-%s' as it already exists on XNAT",
                     project_id,
                     subject_id,
-                    session_id,
+                    visit_id,
                 )
                 return True
 
         if staged.startswith("s3://"):
             # List sessions stored in s3 bucket
             s3 = boto3.resource(
-                "s3", aws_access_key_id=store_credentials[0], aws_secret_access_key=store_credentials[1]
+                "s3",
+                aws_access_key_id=store_credentials[0],
+                aws_secret_access_key=store_credentials[1],
             )
             bucket_name, prefix = staged[5:].split("/", 1)
             bucket = s3.Bucket(bucket_name)
@@ -186,7 +192,7 @@ def xnat_session_exists(project_id, subject_id, session_id):
             for obj in all_objects:
                 if obj.key.endswith("/"):
                     continue
-                path_parts = obj.key[len(prefix):].split("/")
+                path_parts = obj.key[len(prefix) :].split("/")
                 session_ids = tuple(path_parts[:3])
                 session_objs[session_ids].append((path_parts[3:], obj))
 
@@ -212,7 +218,7 @@ def iter_staged_sessions():
                     session_tmp_dir.mkdir(parents=True, exist_ok=True)
                     for relpath, obj in tqdm(
                         objs,
-                        desc=f"Downloading scans in {':'.join(ids)} session from S3 bucket"
+                        desc=f"Downloading scans in {':'.join(ids)} session from S3 bucket",
                     ):
                         obj_path = session_tmp_dir.joinpath(*relpath)
                         obj_path.parent.mkdir(parents=True, exist_ok=True)
@@ -237,14 +243,18 @@ def iter_staged_sessions():
                         ):
                             sessions.append(session_dir)
             num_sessions = len(sessions)
-            logger.info("Found %d sessions in staging directory '%s'", num_sessions, staged)
+            logger.info(
+                "Found %d sessions in staging directory '%s'", num_sessions, staged
+            )
 
         for session_staging_dir in tqdm(
             sessions,
             total=num_sessions,
             desc=f"Processing staged sessions found in '{staged}'",
         ):
-            session = ImagingSession.load(session_staging_dir, use_manifest=use_manifest)
+            session = ImagingSession.load(
+                session_staging_dir, use_manifest=use_manifest
+            )
             try:
                 if "MR" in session.modalities:
                     SessionClass = xnat_repo.connection.classes.MrSessionData
@@ -282,7 +292,7 @@ def iter_staged_sessions():
                         )
                     xsession = SessionClass(label=session.session_id, parent=xsubject)
                 session_path = (
-                    f"{session.project_id}:{session.subject_id}:{session.session_id}"
+                    f"{session.project_id}:{session.subject_id}:{session.visit_id}"
                 )
 
                 # Access Arcana dataset associated with project

xnat_ingest/session.py

@@ -58,7 +58,7 @@ def scans_converter(
 class ImagingSession:
     project_id: str
     subject_id: str
-    session_id: str
+    visit_id: str
     scans: ty.Dict[str, ImagingScan] = attrs.field(
         factory=dict,
         converter=scans_converter,
@@ -72,11 +72,19 @@ def __getitem__(self, fieldname: str) -> ty.Any:
 
     @property
     def name(self):
-        return f"{self.project_id}-{self.subject_id}-{self.session_id}"
+        return f"{self.project_id}-{self.subject_id}-{self.visit_id}"
 
     @property
     def staging_relpath(self):
-        return [self.project_id, self.subject_id, self.session_id]
+        return [self.project_id, self.subject_id, self.visit_id]
+
+    @property
+    def session_id(self):
+        return self.make_session_id(self.project_id, self.subject_id, self.visit_id)
+
+    @classmethod
+    def make_session_id(cls, project_id, subject_id, visit_id):
+        return f"{subject_id}_{visit_id}"
 
     @cached_property
     def modalities(self) -> ty.Set[str]:
@@ -189,7 +197,7 @@ def from_dicoms(
         dicoms_path: str | Path,
         project_field: str = "StudyID",
         subject_field: str = "PatientID",
-        session_field: str = "AccessionNumber",
+        visit_field: str = "AccessionNumber",
         project_id: str | None = None,
     ) -> ty.List["ImagingSession"]:
         """Loads all imaging sessions from a list of DICOM files
@@ -205,7 +213,7 @@ def from_dicoms(
         subject_field : str
             the name of the DICOM field that is to be interpreted as the corresponding
             XNAT project
-        session_field : str
+        visit_field : str
             the name of the DICOM field that is to be interpreted as the corresponding
             XNAT project
         project_id : str
@@ -248,7 +256,7 @@ def from_dicoms(
                 "SOPInstanceUID",  # used in ordering the contents of the dicom series
                 project_field.keyword,
                 subject_field.keyword,
-                session_field.keyword,
+                visit_field.keyword,
             ],
         ):
             # Restrict the metadata fields that are loaded (others are ignored),
@@ -298,7 +306,7 @@ def get_id(field):
                     scans=scans,
                     project_id=(project_id if project_id else get_id(project_field)),
                     subject_id=get_id(subject_field),
-                    session_id=get_id(session_field),
+                    visit_id=get_id(visit_field),
                 )
             )
 
@@ -330,7 +338,7 @@ def load(cls, session_dir: Path, use_manifest: ty.Optional[bool] = None) -> "Ima
         """
         project_id = session_dir.parent.parent.name
         subject_id = session_dir.parent.name
-        session_id = session_dir.name
+        visit_id = session_dir.name
         yaml_file = session_dir / cls.MANIFEST_FILENAME
         if yaml_file.exists() and use_manifest is not False:
             # Load session from YAML file metadata
@@ -363,7 +371,7 @@ def load(cls, session_dir: Path, use_manifest: ty.Optional[bool] = None) -> "Ima
             session = cls(
                 project_id=project_id,
                 subject_id=subject_id,
-                session_id=session_id,
+                visit_id=visit_id,
                 **dct,
             )
         elif use_manifest is not True:
@@ -387,7 +395,7 @@ def load(cls, session_dir: Path, use_manifest: ty.Optional[bool] = None) -> "Ima
                 scans=scans,
                 project_id=project_id,
                 subject_id=subject_id,
-                session_id=session_id,
+                visit_id=visit_id,
             )
         else:
             raise FileNotFoundError(
@@ -417,7 +425,7 @@ def save(self, save_dir: Path, just_manifest: bool = False) -> "ImagingSession":
         scans = {}
         saved = deepcopy(self)
         session_dir = (
-            save_dir / self.project_id / self.subject_id / self.session_id
+            save_dir / self.project_id / self.subject_id / self.visit_id
         ).absolute()
         session_dir.mkdir(parents=True, exist_ok=True)
         for scan in self.scans.values():
@@ -506,7 +514,7 @@ def stage(
             )
         staged_scans = []
         staged_metadata = {}
-        session_dir = dest_dir / self.project_id / self.subject_id / self.session_id
+        session_dir = dest_dir / self.project_id / self.subject_id / self.visit_id
         session_dir.mkdir(parents=True)
         for scan in tqdm(
             self.scans.values(), f"Staging DICOM sessions to {session_dir}"
@@ -652,7 +660,7 @@ def stage(
         staged = type(self)(
             project_id=self.project_id,
             subject_id=self.subject_id,
-            session_id=self.session_id,
+            visit_id=self.visit_id,
             scans=staged_scans,
         )
         staged.save(dest_dir, just_manifest=True)

xnat_ingest/tests/test_cli.py

@@ -57,15 +57,15 @@ def test_stage_and_upload(
         os.unlink(log_file)
 
     # Delete any existing sessions from previous test runs
-    session_ids = []
+    visit_ids = []
     with xnat4tests.connect() as xnat_login:
         for i, c in enumerate("abc"):
             first_name = f"First{c.upper()}"
             last_name = f"Last{c.upper()}"
             PatientName = f"{first_name}^{last_name}"
             PatientID = f"subject{i}"
             AccessionNumber = f"98765432{i}"
-            session_ids.append(AccessionNumber)
+            visit_ids.append(AccessionNumber)
 
             StudyInstanceUID = (
                 f"1.3.12.2.1107.5.1.4.10016.3000002308242209356530000001{i}"
@@ -227,8 +227,8 @@ def test_stage_and_upload(
 
     with xnat4tests.connect() as xnat_login:
         xproject = xnat_login.projects[xnat_project]
-        for session_id in session_ids:
-            xsession = xproject.experiments[session_id]
+        for visit_id in visit_ids:
+            xsession = xproject.experiments[visit_id]
             scan_ids = sorted(xsession.scans)
 
             assert scan_ids == [

xnat_ingest/tests/test_session.py

@@ -52,7 +52,7 @@ def imaging_session() -> ImagingSession:
     return ImagingSession(
         project_id="PROJECTID",
         subject_id="SUBJECTID",
-        session_id="SESSIONID",
+        visit_id="SESSIONID",
         scans=scans,
     )