From 7f63953f6b9b84aeb811352d1d1b03eb514ff3e7 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:25:11 -0400
Subject: [PATCH 1/4] fix(metaschema): Require issues for checks

---
 src/metaschema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index c0462edcaf..f6e5a62d25 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -315,7 +315,7 @@
                       "$ref": "#/definitions/ruleTypes/expressionList"
                     }
                   },
-                  "required": ["checks", "selectors"],
+                  "required": ["checks", "selectors", "issue"],
                   "additionalProperties": false
                 }
               }

From e23714770c88590fffdb699eca599e3dd84d127d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:26:07 -0400
Subject: [PATCH 2/4] fix(schema): Add issues for file reference checks

---
 src/schema/rules/checks/references.yaml | 42 +++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/src/schema/rules/checks/references.yaml b/src/schema/rules/checks/references.yaml
index b0f1dd6e9d..191dcb6d4f 100644
--- a/src/schema/rules/checks/references.yaml
+++ b/src/schema/rules/checks/references.yaml
@@ -1,5 +1,11 @@
 ---
 SubjectRelativeIntendedForString:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be subject-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype != "ieeg"
     - type(sidecar.IntendedFor) == "string"
@@ -7,6 +13,12 @@ SubjectRelativeIntendedForString:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "subject") == 1
 
 SubjectRelativeIntendedForArray:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be subject-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype != "ieeg"
     - type(sidecar.IntendedFor) == "array"
@@ -14,6 +26,12 @@ SubjectRelativeIntendedForArray:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "subject") == length(sidecar.IntendedFor)
 
 DatasetRelativeIntendedForString:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "ieeg"
     - type(sidecar.IntendedFor) == "string"
@@ -21,6 +39,12 @@ DatasetRelativeIntendedForString:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "dataset") == 1
 
 DatasetRelativeIntendedForArray:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "ieeg"
     - type(sidecar.IntendedFor) == "array"
@@ -28,6 +52,12 @@ DatasetRelativeIntendedForArray:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "dataset") == length(sidecar.IntendedFor)
 
 AssociatedEmptyRoomString:
+  issue:
+    code: ASSOCIATED_EMPTY_ROOM
+    message: |
+      'AssociatedEmptyRoom' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "meg"
     - type(sidecar.AssociatedEmptyRoom) == "string"
@@ -35,6 +65,12 @@ AssociatedEmptyRoomString:
     - exists(sidecar.AssociatedEmptyRoom, "bids-uri") + exists(sidecar.AssociatedEmptyRoom, "dataset") == 1
 
 AssociatedEmptyRoomArray:
+  issue:
+    code: ASSOCIATED_EMPTY_ROOM
+    message: |
+      'AssociatedEmptyRoom' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "meg"
     - type(sidecar.AssociatedEmptyRoom) == "array"
@@ -44,6 +80,12 @@ AssociatedEmptyRoomArray:
       == length(sidecar.AssociatedEmptyRoom)
 
 Sources:
+  issue:
+    code: SOURCE_FILE_EXIST
+    message: |
+      'Sources' field needs to point to existing files.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivatives"
     - type(sidecar.Sources) != "null"

From c5cb8eed6ef6179cc239a960d0fdf20f5c0d02f1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:47:19 -0400
Subject: [PATCH 3/4] fix(schema): Add issues for resolution/density object
 checks

---
 src/schema/rules/checks/common_derivatives.yaml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/schema/rules/checks/common_derivatives.yaml b/src/schema/rules/checks/common_derivatives.yaml
index 723ddf0e59..6d9cd2eda7 100644
--- a/src/schema/rules/checks/common_derivatives.yaml
+++ b/src/schema/rules/checks/common_derivatives.yaml
@@ -1,18 +1,32 @@
 ---
 ResInSidecar:
+  issue:
+    code: MISSING_RESOLUTION_DESCRIPTION
+    message: |
+      The Resolution metadata object does not contain an entry for the file's
+      res-<label> entity.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
     - intersects([modality], ["mri", "pet"])
     - match(extension, '^\.nii(\.gz)?$')
+    - type(entities.resolution) != 'null'
     - type(sidecar.Resolution) == "object"
   checks:
     - entities.resolution in sidecar.Resolution
 
 DenInSidecar:
+  issue:
+    code: MISSING_DENSITY_DESCRIPTION
+    message: |
+      The Density metadata object does not contain an entry for the file's
+      res-<label> entity.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
     - intersects([modality], ["mri", "pet"])
     - match(extension, '^\.nii(\.gz)?$')
+    - type(entities.density) != 'null'
     - type(sidecar.Density) == "object"
   checks:
     - entities.density in sidecar.Density

From 02049c56bc5dfff6b09f5792ebc7cc540dc0d910 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 2 Aug 2024 00:23:38 -0400
Subject: [PATCH 4/4] fix(schema): Add issues for NIRS checks

---
 src/schema/meta/context.yaml      | 10 +++++
 src/schema/rules/checks/nirs.yaml | 62 +++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 280ae7b933..a1881df37b 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -212,6 +212,16 @@ properties:
             type: array
             items:
               type: string
+          short_channel:
+            description: 'Contents of the short_channel column'
+            type: array
+            items:
+              type: string
+          sampling_frequency:
+            description: 'Contents of the sampling_frequency column'
+            type: array
+            items:
+              type: string
       coordsystem:
         description: 'Coordinate system file'
         type: object
diff --git a/src/schema/rules/checks/nirs.yaml b/src/schema/rules/checks/nirs.yaml
index e4cabe3291..b4038b9d34 100644
--- a/src/schema/rules/checks/nirs.yaml
+++ b/src/schema/rules/checks/nirs.yaml
@@ -1,5 +1,11 @@
 ---
 NASamplingFreq:
+  issue:
+    code: NIRS_SAMPLING_FREQUENCY
+    message: |
+      Sampling frequency must be defined in the sidecar, or else as a sampling_frequency
+      column of channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - sidecar.SamplingFrequency == "n/a"
@@ -7,10 +13,17 @@ NASamplingFreq:
     - associations.channels.sampling_frequency != null
 
 NIRSChannelCount:
+  issue:
+    code: NIRS_CHANNEL_COUNT
+    message: |
+      NIRSChannelCount metadata must equal the number of channels with type NIRS*,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "nirs"
     - match(extension, '\.nii(\.gz)?$')
+    - type(sidecar.NIRSChannelCount) != 'null'
   checks:
     - |
       sidecar.NIRSChannelCount
@@ -22,6 +35,12 @@ NIRSChannelCount:
       +  count(associations.channels.type, "NIRSCWMUA")
 
 ACCELChannelCountReq:
+  issue:
+    code: ACCEL_CHANNEL_COUNT
+    message: |
+      ACCELChannelCount metadata must equal the number of channels with type ACCEL,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "ACCEL") > 0
@@ -29,6 +48,12 @@ ACCELChannelCountReq:
     - sidecar.ACCELChannelCount == count(associations.channels.type, "ACCEL")
 
 GYROChannelCountReq:
+  issue:
+    code: GYRO_CHANNEL_COUNT
+    message: |
+      GYROChannelCount metadata must equal the number of channels with type GYRO,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "GYRO") > 0
@@ -36,6 +61,12 @@ GYROChannelCountReq:
     - sidecar.GYROChannelCount == count(associations.channels.type, "GYRO")
 
 MAGNChannelCountReq:
+  issue:
+    code: MAGN_CHANNEL_COUNT
+    message: |
+      MAGNChannelCount metadata must equal the number of channels with type MAGN,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "MAGN") > 0
@@ -43,6 +74,12 @@ MAGNChannelCountReq:
     - sidecar.MAGNChannelCount == count(associations.channels.type, "MAGN")
 
 ShortChannelCountReq:
+  issue:
+    code: SHORT_CHANNEL_COUNT
+    message: |
+      ShortChannelCount metadata must equal the number of channels with the value `true`
+      in the `short_channel` column of channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - '"ShortChannelCount" in sidecar'
@@ -50,6 +87,11 @@ ShortChannelCountReq:
     - sidecar.ShortChannelCount == count(associations.channels.short_channel, "true")
 
 Component:
+  issue:
+    code: COMPONENT_COLUMN_REQUIRED
+    message: |
+      ACCEL, GYRO, and MAGN columns require a `component` column in channels.tsv.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "channels"
@@ -71,6 +113,11 @@ RecommendedChannels:
     - associations.channels != null
 
 RequiredTemplateX:
+  issue:
+    code: REQUIRED_TEMPLATE_X
+    message: |
+      The `template_x` column MUST be defined if the `x` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -80,6 +127,11 @@ RequiredTemplateX:
     - columns.template_x != null
 
 RequiredTemplateY:
+  issue:
+    code: REQUIRED_TEMPLATE_Y
+    message: |
+      The `template_y` column MUST be defined if the `y` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -89,6 +141,11 @@ RequiredTemplateY:
     - columns.template_y != null
 
 RequiredTemplateZ:
+  issue:
+    code: REQUIRED_TEMPLATE_Z
+    message: |
+      The `template_z` column MUST be defined if the `z` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -98,6 +155,11 @@ RequiredTemplateZ:
     - columns.template_z != null
 
 RequiredCoordsystem:
+  issue:
+    code: REQUIRED_COORDSYSTEM
+    message: |
+      If an optodes.tsv file is provided, an associated coordsystem.json must also be present.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"