Merge pull request #1880 from effigies/fix/check-issues

fix(schema): Add issue definitions for all checks

src/metaschema.json

@@ -315,7 +315,7 @@
                       "$ref": "#/definitions/ruleTypes/expressionList"
                     }
                   },
-                  "required": ["checks", "selectors"],
+                  "required": ["checks", "selectors", "issue"],
                   "additionalProperties": false
                 }
               }

src/schema/meta/context.yaml

@@ -209,6 +209,16 @@ 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

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

src/schema/rules/checks/nirs.yaml

@@ -1,16 +1,29 @@
 ---
 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"
   checks:
     - 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
@@ -22,34 +35,63 @@ 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
   checks:
     - 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
   checks:
     - 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
   checks:
     - 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'
   checks:
     - 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"

src/schema/rules/checks/references.yaml

@@ -1,40 +1,76 @@
 ---
 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"
   checks:
     - 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"
   checks:
     - 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"
   checks:
     - 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"
   checks:
     - 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"
   checks:
     - 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"