Workshop Docker image

.datajoint_config.json

@@ -0,0 +1,15 @@
+{
+    "database.host": "tutorial-db.datajoint.io",
+    "database.port": 3306,
+    "database.reconnect": true,
+    "connection.init_function": null,
+    "connection.charset": "",
+    "loglevel": "INFO",
+    "safemode": true,
+    "fetch_format": "array",
+    "display.limit": 12,
+    "display.width": 14,
+    "display.show_tuple_count": true,
+    "database.use_tls": null,
+    "enable_python_native_blobs": true
+}

.gitignore

@@ -119,3 +119,6 @@ Diagram.ipynb
 
 # vscode
 .vscode/settings.json
+
+# Mac
+.DS_Store

requirements.txt

@@ -1,6 +1,6 @@
 datajoint>=0.13.0
-element-array-ephys 
-element-lab 
-element-animal 
-element-session 
-ipykernel
+element-array-ephys
+element-lab
+element-animal
+element-session
+ipykernel

tests/__init__.py

@@ -13,6 +13,8 @@
 
 # ------------------- SOME CONSTANTS -------------------
 
+_tear_down = True
+
 test_user_data_dir = pathlib.Path('./tests/user_data')
 test_user_data_dir.mkdir(exist_ok=True)
 
@@ -84,7 +86,8 @@ def pipeline():
            'session': pipeline.session,
            'get_ephys_root_data_dir': pipeline.get_ephys_root_data_dir}
 
-    pipeline.subject.Subject.delete()
+    if _tear_down:
+        pipeline.subject.Subject.delete()
 
 
 @pytest.fixture
@@ -197,7 +200,8 @@ def kilosort_paramset(pipeline):
 
     yield params_ks
 
-    (ephys.ClusteringParamSet & 'paramset_idx = 0').delete()
+    if _tear_down:
+        (ephys.ClusteringParamSet & 'paramset_idx = 0').delete()
 
 
 @pytest.fixture
@@ -208,7 +212,8 @@ def ephys_recordings(pipeline, ingest_sessions):
 
     yield
 
-    ephys.EphysRecording.delete()
+    if _tear_down:
+        ephys.EphysRecording.delete()
 
 
 @pytest.fixture
@@ -225,11 +230,13 @@ def clustering_tasks(pipeline, kilosort_paramset, ephys_recordings):
         kilosort_dir = next(recording_dir.rglob('spike_times.npy')).parent
         ephys.ClusteringTask.insert1({**ephys_rec_key,
                                       'paramset_idx': 0,
-                                      'clustering_output_dir': kilosort_dir.as_posix()})
+                                      'clustering_output_dir': kilosort_dir.as_posix()},
+                                     skip_duplicates=True)
 
     yield
 
-    ephys.ClusteringTask.delete()
+    if _tear_down:
+        ephys.ClusteringTask.delete()
 
 
 @pytest.fixture
@@ -240,7 +247,8 @@ def clustering(clustering_tasks, pipeline):
 
     yield
 
-    ephys.Clustering.delete()
+    if _tear_down:
+        ephys.Clustering.delete()
 
 
 @pytest.fixture
@@ -252,4 +260,5 @@ def curations(clustering, pipeline):
 
     yield
 
-    ephys.Curation.delete()
+    if _tear_down:
+        ephys.Curation.delete()

workflow_array_ephys/ingest.py

@@ -21,7 +21,7 @@ def ingest_sessions(session_csv_path='./user_data/sessions.csv'):
     root_data_dir = get_ephys_root_data_dir()
 
     # ---------- Insert new "Session" and "ProbeInsertion" ---------
-    with open(session_csv_path, newline= '') as f:
+    with open(session_csv_path, newline='') as f:
         input_sessions = list(csv.DictReader(f, delimiter=','))
 
     # Folder structure: root / subject / session / probe / .ap.meta

workflow_array_ephys/pipeline.py

@@ -22,6 +22,7 @@
 
 subject.activate(db_prefix + 'subject', linking_module=__name__)
 
+Experimenter = lab.User
 session.activate(db_prefix + 'session', linking_module=__name__)
 
 # ----------- Declare table SkullReference for use in element-array-ephys ---------