From 3322a4023f954931b074678f5f78c7779d13a619 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 26 Apr 2024 09:42:32 -0400
Subject: [PATCH] FIX: Re-add run entity to electrodes.tsv (#1722)

* FIX: Re-add run entity to electrodes.tsv

* [ENH] Recommend electrodes usage/require inheritance

* SCHEMA: Add check to warn against excessive electrode specificity
---
 .../electroencephalography.md                     |  6 ++++++
 .../intracranial-electroencephalography.md        |  6 ++++++
 src/schema/rules/checks/electrodes.yaml           | 15 +++++++++++++++
 src/schema/rules/files/raw/channels.yaml          |  1 +
 4 files changed, 28 insertions(+)
 create mode 100644 src/schema/rules/checks/electrodes.yaml

diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md
index 6ba02cc13a..8a584bb7a0 100644
--- a/src/modality-specific-files/electroencephalography.md
+++ b/src/modality-specific-files/electroencephalography.md
@@ -308,6 +308,12 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_columns_table("eeg.EEGElectrodes") }}
 
+`*_electrodes.tsv` files SHOULD NOT be duplicated for each data file,
+for example, during multiple runs of a task.
+The [inheritance principle](../common-principles.md#the-inheritance-principle) MUST
+be used to find the appropriate electrode positions for a given data file.
+If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to indicate this.
+
 ### Example `*_electrodes.tsv`
 
 See also the corresponding [`electrodes.tsv` example](#example-channelstsv).
diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
index ae6a669a84..096b96f97d 100644
--- a/src/modality-specific-files/intracranial-electroencephalography.md
+++ b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -349,6 +349,12 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_columns_table("ieeg.iEEGElectrodes") }}
 
+`*_electrodes.tsv` files SHOULD NOT be duplicated for each data file,
+for example, during multiple runs of a task.
+The [inheritance principle](../common-principles.md#the-inheritance-principle) MUST
+be used to find the appropriate electrode positions for a given data file.
+If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to indicate this.
+
 ### Example `*_electrodes.tsv`
 
 ```Text
diff --git a/src/schema/rules/checks/electrodes.yaml b/src/schema/rules/checks/electrodes.yaml
new file mode 100644
index 0000000000..29f81d3d44
--- /dev/null
+++ b/src/schema/rules/checks/electrodes.yaml
@@ -0,0 +1,15 @@
+---
+ElectrodeSpecificity:
+  issue:
+    code: EXCESSIVE_ELECTRODE_SPECIFICITY
+    message: |
+      Run or acquisition entities detected in electrodes.tsv.
+      Electrode definitions should generally not vary within a session.
+      Consider creating a new session each time electrodes are reconfigured.
+    level: warning
+  selectors:
+    - suffix == 'electrodes'
+    - extension == '.tsv'
+  checks:
+    - '!("run" in entities)'
+    - '!("acquisition" in entities)'
diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml
index 06c213be17..25aa1deff3 100644
--- a/src/schema/rules/files/raw/channels.yaml
+++ b/src/schema/rules/files/raw/channels.yaml
@@ -70,6 +70,7 @@ electrodes:
     subject: required
     session: optional
     acquisition: optional
+    run: optional
     space: optional
 
 # MEG has an additional entity available