[REF] Rename Neurobagel-created session to ses-unnamed (#358)

* rename Neurobagel-created session --------- Co-authored-by: Sebastian Urchs <[email protected]>
neurobagel · Oct 9, 2024 · 7c82333 · 7c82333
1 parent 826bc93
commit 7c82333
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Showing 3 changed files with 8 additions and 6 deletions.
diff --git a/bagel/cli.py b/bagel/cli.py
@@ -18,8 +18,7 @@
     get_subject_instances,
 )
 
-# TODO: Coordinate with Nipoppy about what we want to name this
-CUSTOM_SESSION_LABEL = "ses-nb01"
+CUSTOM_SESSION_LABEL = "ses-unnamed"
 
 bagel = typer.Typer(
     help="""
@@ -128,7 +127,9 @@ def pheno(
 
         sessions = []
         for session_row_idx, session_row in _sub_pheno.iterrows():
-            # If there is no session column, we create a session with a custom label "ses-nb01" to assign each subject's phenotypic data to
+            # Our data model requires a session. To support phenotypic data without sessions,
+            # we create a session with a fixed, but unusual CUSTOM_SESSION_LABEL and add the
+            # phenotypic data to that session.
             if session_column is None:
                 session_label = CUSTOM_SESSION_LABEL
             else:
@@ -309,7 +310,8 @@ def bids(
                 continue
 
             # TODO: Currently if a subject has BIDS data but no "ses-" directories (e.g., only 1 session),
-            # we create a session for that subject with a custom label "ses-nb01" to be added to the graph.
+            # we create a session with a fixed, but unusual CUSTOM_SESSION_LABEL
+            # and add the imaging data info to a session with that label (or create it first).
             # However, we still provide the BIDS SUBJECT directory as the session path, instead of making up a path.
             # This should be revisited in the future as for these cases the resulting dataset object is not
             # an exact representation of what's on disk.

diff --git a/bagel/tests/test_cli_derivatives.py b/bagel/tests/test_cli_derivatives.py
@@ -197,7 +197,7 @@ def test_custom_imaging_sessions_created_for_missing_session_labels(
         for ses in sub["hasSession"]:
             if (
                 ses["schemaKey"] == "ImagingSession"
-                and ses["hasLabel"] == "ses-nb01"
+                and ses["hasLabel"] == "ses-unnamed"
             ):
                 custom_ses_completed_pipes[sub["hasLabel"]] = len(
                     ses["hasCompletedPipeline"]

diff --git a/bagel/tests/test_cli_pheno.py b/bagel/tests/test_cli_pheno.py
@@ -774,7 +774,7 @@ def test_pheno_session_created_for_missing_session_column(
     for sub in pheno["hasSamples"]:
         assert 1 == len(sub["hasSession"])
         assert sub["hasSession"][0]["schemaKey"] == "PhenotypicSession"
-        assert sub["hasSession"][0]["hasLabel"] == "ses-nb01"
+        assert sub["hasSession"][0]["hasLabel"] == "ses-unnamed"
 
 
 def test_multicolumn_diagnosis_annot_is_handled(