Merge pull request #1893 from effigies/fix/schema-types

fix(schema): Minor issues

Author: effigies

src/metaschema.json

@@ -68,6 +68,7 @@
         "versions": {
           "type": "array",
           "items": {
+            "type": "string",
             "pattern": "^[0-9]+\\.[0-9]+\\.[0-9]+$"
           }
         }
@@ -470,7 +471,7 @@
               "properties": {
                 "datatypes": {
                   "type": "array",
-                  "items": { "pattern": "^[a-z]+$" }
+                  "items": { "type": "string", "pattern": "^[a-z]+$" }
                 }
               },
               "required": ["datatypes"],
@@ -661,7 +662,7 @@
         "level": { "enum": ["optional", "recommended", "required"] },
         "datatypes": {
           "type": "array",
-          "items": { "pattern": "^[a-z]+$" }
+          "items": { "type": "string", "pattern": "^[a-z]+$" }
         },
         "stem": { "type": "string" },
         "extensions": { "type": "array", "items": { "type": "string" } }
@@ -675,11 +676,11 @@
         "level": { "enum": ["optional", "recommended", "required"] },
         "datatypes": {
           "type": "array",
-          "items": { "pattern": "^[a-z]+$" }
+          "items": { "type": "string", "pattern": "^[a-z]+$" }
         },
         "suffixes": {
           "type": "array",
-          "items": { "pattern": "^[a-zA-Z0-9]+$" }
+          "items": { "type": "string", "pattern": "^[a-zA-Z0-9]+$" }
         },
         "extensions": { "type": "array", "items": { "type": "string" } },
         "entities": {

src/schema/meta/context.yaml

@@ -155,7 +155,7 @@ properties:
       events:
         description: 'Events file'
         type: object
-        required: [path, onset]
+        required: [path]
         additionalProperties: false
         properties:
           path:
@@ -169,7 +169,7 @@ properties:
       aslcontext:
         description: 'ASL context file'
         type: object
-        required: [path, n_rows, volume_type]
+        required: [path, n_rows]
         additionalProperties: false
         properties:
           path:
@@ -248,7 +248,7 @@ properties:
       channels:
         description: 'Channels file'
         type: object
-        required: [path, type]
+        required: [path]
         additionalProperties: false
         properties:
           path:
@@ -292,7 +292,7 @@ properties:
   gzip:
     description: 'Parsed contents of gzip header'
     type: object
-    required: [timestamp, filename]
+    required: [timestamp]
     additionalProperties: false
     properties:
       timestamp:

src/schema/rules/checks/func.yaml

@@ -40,7 +40,9 @@ RepetitionTimeMismatch:
     - type(sidecar.RepetitionTime) != "null"
     - type(nifti_header) != "null"
   checks:
-    - sidecar.RepetitionTime == nifti_header.pixdim[4]
+    # Implement millisecond rounding via AND
+    - sidecar.RepetitionTime - nifti_header.pixdim[4] < 0.001
+    - sidecar.RepetitionTime - nifti_header.pixdim[4] > -0.001
 
 # 54
 BoldNot4d:

src/schema/rules/checks/privacy.yaml

@@ -1,17 +1,41 @@
 ---
-GzipHeaderFields:
+GzipHeaderMtime:
   issue:
-    code: GZIP_HEADER_DATA
+    code: GZIP_HEADER_MTIME
     message: |
-      The gzip header contains a non-zero timestamp or a non-empty filename and/or comment field.
-      These may leak sensitive information or indicate a non-reproducible conversion process.
+      The gzip header contains a non-zero timestamp.
+      This may leak sensitive information or indicate a non-reproducible conversion process.
     level: warning
   selectors:
     - match(extension, ".gz$")
     - gzip != null
   checks:
     - gzip.timestamp == 0
+
+GzipHeaderFilename:
+  issue:
+    code: GZIP_HEADER_FILENAME
+    message: |
+      The gzip header contains a non-empty filename.
+      This may leak sensitive information or indicate a non-reproducible conversion process.
+    level: warning
+  selectors:
+    - match(extension, ".gz$")
+    - gzip.filename
+  checks:
     - gzip.filename == ""
+
+GzipHeaderComment:
+  issue:
+    code: GZIP_HEADER_COMMENT
+    message: |
+      The gzip header contains a non-empty comment field.
+      This may leak sensitive information or indicate a non-reproducible conversion process.
+    level: warning
+  selectors:
+    - match(extension, ".gz$")
+    - gzip.comment
+  checks:
     - gzip.comment == ""
 
 CheckAge89:

src/schema/rules/sidecars/beh.yaml

@@ -8,6 +8,7 @@
 # Metadata for either beh or events files
 BEHTaskInformation:
   selectors:
+    - datatype == "beh"
     - intersects([suffix], ["beh", "events"])
   fields:
     TaskName: recommended
@@ -18,6 +19,7 @@ BEHTaskInformation:
 
 BEHInstitutionInformation:
   selectors:
+    - datatype == "beh"
     - intersects([suffix], ["beh", "events"])
   fields:
     InstitutionName: recommended

src/schema/rules/sidecars/entity_rules.yaml

@@ -10,12 +10,14 @@
 EntitiesTaskMetadata:
   selectors:
     - '"task" in entities'
+    - suffix != 'events'
   fields:
     TaskName: recommended
 
 EntitiesCeMetadata:
   selectors:
     - '"ce" in entities'
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     ContrastBolusIngredient: optional
 
@@ -30,24 +32,28 @@ EntitiesStainMetadata:
 EntitiesEchoMetadata:
   selectors:
     - '"echo" in entities'
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     EchoTime: required
 
 EntitiesFlipMetadata:
   selectors:
     - '"flip" in entities'
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     FlipAngle: required
 
 EntitiesInvMetadata:
   selectors:
     - '"inv" in entities'
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     InversionTime: required
 
 EntitiesMTMetadata:
   selectors:
     - '"mt" in entities'
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     MTState: required
 

src/schema/rules/sidecars/func.yaml

@@ -47,6 +47,7 @@ MRIFuncTimingParameters:
   selectors:
     - datatype == "func"
     - suffix == "bold"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     NumberOfVolumesDiscardedByScanner: recommended
     NumberOfVolumesDiscardedByUser: recommended
@@ -64,6 +65,7 @@ MRIFuncTaskInformation:
   selectors:
     - datatype == "func"
     - suffix == "bold"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     Instructions:
       level: recommended

src/schema/rules/sidecars/mri.yaml

@@ -9,6 +9,7 @@
 MRIHardware:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     Manufacturer:
       level: recommended
@@ -57,6 +58,7 @@ MRIChunkPosition:
 MRISample:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     BodyPart:
       level: optional
@@ -69,12 +71,14 @@ MRIScannerHardwareASL:
     - datatype == "perf"
     - suffix == "asl"
     - intersects([suffix], ["asl", "m0scan"])
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     MagneticFieldStrength: required
 
 MRISequenceSpecifics:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     PulseSequenceType: recommended
     ScanningSequence: recommended
@@ -105,13 +109,15 @@ PETMRISequenceSpecifics:
   selectors:
     - modality == "mri"
     - intersects(dataset.modalities, ["pet"])
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     NonlinearGradientCorrection: required
 
 ASLMRISequenceSpecifics:
   selectors:
     - datatype == "perf"
     - suffix == "asl"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     MRAcquisitionType: required
 
@@ -147,6 +153,7 @@ SpoilingGradient:
 MRISpatialEncoding:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     NumberShots: recommended
     ParallelReductionFactorInPlane: recommended
@@ -164,6 +171,7 @@ PhaseEncodingDirectionRec:
   selectors:
     - modality == "mri"
     - suffix != "epi"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     PhaseEncodingDirection:
       level: recommended
@@ -201,27 +209,24 @@ PhaseEncodingDirectionReq:
 MRITimingParameters:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     EchoTime:
       level: recommended
       level_addendum: |
         required if corresponding fieldmap data is present,
         or the data comes from a multi-echo sequence or Arterial Spin Labeling.
-      issue:
-        code: ECHO_TIME_NOT_DEFINED
-        message: |
-          You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE)
-          for the acquisition, specified in seconds. Corresponds to DICOM Tag
-          0018, 0081 Echo Time (please note that the DICOM term is in milliseconds
-          not seconds). The data type number may apply to files from any MRI modality
-          concerned with a single value for this field, or to the files in a file
-          collection where the value of this field is iterated using the echo entity.
-          The data type array provides a value for each volume in a 4D dataset and
-          should only be used when the volume timing is critical for interpretation
-          of the data, such as in ASL or variable echo time fMRI sequences.
     InversionTime: recommended
     DwellTime: recommended
 
+EchoTimeRequiredASL:
+  selectors:
+    - modality == "mri"
+    - datatype == "perf"
+    - match(extension, "^\.nii(\.gz)?$")
+  fields:
+    EchoTime: required
+
 SliceTimingMRI:
   selectors:
     - modality == "mri"
@@ -240,7 +245,6 @@ SliceTimingASL:
     - intersects([suffix], ["asl", "m0scan"])
     - sidecar.MRAcquisitionType == "2D"
   fields:
-    EchoTime: required
     SliceTiming:
       level: required
       issue:
@@ -260,16 +264,10 @@ SliceTimingASL:
           final entry in the `SliceTiming` list is the time of acquisition of slice 0.
           Without this parameter slice time correction will not be possible.
 
-# This is technically for sparse sequences only, but I don't know how to encode that.
-# SliceTimingSparse:
-#    selectors:
-#    - modality == "mri"
-#    fields:
-#        SliceTiming: required
-
 MRIRFandContrast:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     NegativeContrast: optional
 
@@ -307,13 +305,15 @@ MRIFlipAngleLookLockerTrue:
 MRISliceAcceleration:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     MultibandAccelerationFactor: recommended
 
 MRIAnatomicalLandmarks:
   selectors:
     - datatype == "anat"
     - intersects(dataset.datatypes, ["meg"])
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     AnatomicalLandmarkCoordinates__mri: recommended
 
@@ -328,12 +328,14 @@ MRIEchoPlanarImagingAndB0FieldSource:
   selectors:
     - intersects(datatype, ['dwi', 'func', 'perf'])
     - intersects(dataset.datatypes, ['fmap'])
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     B0FieldSource: recommended
 
 MRIInstitutionInformation:
   selectors:
     - modality == "mri"
+    - match(extension, "^\.nii(\.gz)?$")
   fields:
     InstitutionName:
       level: recommended