Minor fixes (#129)

samuelbray32 · web-flow · commit 6dcbc9786227 · 2025-08-06T08:16:27.000-07:00
* use int instead of string for ref group

* update capitalization in virus names

* update no ref test
diff --git a/src/trodes_to_nwb/convert_yaml.py b/src/trodes_to_nwb/convert_yaml.py
@@ -300,7 +300,7 @@ def add_electrode_groups(
     for nwb_group in list(electrode_table["group_name"]):
         # use the refference electrode map and defined electrode table to find index of the reference electrode
         ref_group, ref_electrode = ref_electrode_map[str(nwb_group)]
-        if ref_group == "-1":
+        if ref_group == -1:
             # handle case where no reference electrode is defined
             ref_electrode_id.append(-1)
             continue
diff --git a/src/trodes_to_nwb/device_metadata/virus_metadata/AAV-1-Ef1a-DIO-ChRmine-mScarlet.yml b/src/trodes_to_nwb/device_metadata/virus_metadata/AAV-1-Ef1a-DIO-ChRmine-mScarlet.yml
@@ -1,4 +1,4 @@
-virus_name : AAV-1-Ef1a-DIO-ChRmine-mScarlet-WPRE
-construct_name : AAV-1-Ef1a-DIO-ChRmine-mScarlet-WPRE
+virus_name : AAV-1-EF1a-DIO-ChRmine-mScarlet-WPRE
+construct_name : AAV-1-EF1a-DIO-ChRmine-mScarlet-WPRE
 description : Cre-Dependent excitatory optogenetic construct for ChRmine-mScarlet expression
 manufacturer : AddGene
diff --git a/src/trodes_to_nwb/device_metadata/virus_metadata/AAV-8-Ef1a-DIO-ChRmine-mScarlet.yml b/src/trodes_to_nwb/device_metadata/virus_metadata/AAV-8-Ef1a-DIO-ChRmine-mScarlet.yml
@@ -1,4 +1,4 @@
-virus_name : AAV-8-Ef1a-DIO-ChRmine-mScarlet-WPRE
-construct_name : AAV-8-Ef1a-DIO-ChRmine-mScarlet-WPRE
+virus_name : AAV-8-EF1a-DIO-ChRmine-mScarlet-WPRE
+construct_name : AAV-8-EF1a-DIO-ChRmine-mScarlet-WPRE
 description : Cre-Dependent excitatory optogenetic construct for ChRmine-mScarlet expression
 manufacturer : Stanford University
diff --git a/src/trodes_to_nwb/tests/test_convert_yaml.py b/src/trodes_to_nwb/tests/test_convert_yaml.py
@@ -252,7 +252,7 @@ def test_no_reference_electrode():
         metadata, rec_header.find("SpikeConfiguration")
     )
     # set one tetrode to no reference
-    ref_electrode_map["0"] = ("-1", -1)
+    ref_electrode_map["0"] = (-1, -1)
     convert_yaml.add_electrode_groups(
         nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map
     )

Original file line number	Diff line number	Diff line change
`@@ -252,7 +252,7 @@ def test_no_reference_electrode():`
`252`	`252`	`metadata, rec_header.find("SpikeConfiguration")`
`253`	`253`	`)`
`254`	`254`	`# set one tetrode to no reference`
`255`		`- ref_electrode_map["0"] = ("-1", -1)`
	`255`	`+ ref_electrode_map["0"] = (-1, -1)`
`256`	`256`	`convert_yaml.add_electrode_groups(`
`257`	`257`	`nwbfile, metadata, probe_metadata, hw_channel_map, ref_electrode_map`
`258`	`258`	`)`