Merge branch 'master' into mri-redundancies-really

.gitignore

@@ -42,6 +42,9 @@ share/python-wheels/
 *.egg
 MANIFEST
 
+# Poetry requirements / packaging
+/pyproject.toml
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

src/schema/SCHEMA_VERSION

@@ -1 +1 @@
-0.4.1-dev
+0.5.0-dev

src/schema/meta/context.yaml

@@ -20,6 +20,9 @@
 context:
   type: object
   properties:
+    schema:
+      description: 'The BIDS specification schema'
+      type: object
     dataset:
       description: 'Properties and contents of the entire dataset'
       type: object
@@ -36,6 +39,9 @@ context:
         ignored:
           description: 'Set of ignored files'
           type: array
+        datatypes:
+          description: 'Data types present in the dataset'
+          type: array
         modalities:
           description: 'Modalities present in the dataset'
           type: array

src/schema/rules/checks/asl.yaml

@@ -22,7 +22,7 @@ ASLLabelingDurationNiftiLength:
     - '"LabelingDuration" in sidecar'
     - type(sidecar.LabelingDuration) == 'array'
   checks:
-    - nifti_header.dim[4] == sidecar.LabelingDuration.length
+    - length(sidecar.LabelingDuration) == nifti_header.dim[4]
 
 # 165
 ASLContextConsistent:
@@ -57,7 +57,7 @@ ASLFlipAngleNiftiLength:
     - '"FlipAngle" in sidecar'
     - type(sidecar.FlipAngle) == 'array'
   checks:
-    - nifti_header.dim[4] == sidecar.FlipAngle.length
+    - length(sidecar.FlipAngle) == nifti_header.dim[4]
 
 # 172
 ASLFlipAngleASLContextLength:
@@ -79,7 +79,7 @@ ASLFlipAngleASLContextLength:
     - '"FlipAngle" in sidecar'
     - type(sidecar.FlipAngle) == 'array'
   checks:
-    - aslcontext.n_rows == sidecar.FlipAngle.length
+    - length(sidecar.FlipAngle) == aslcontext.n_rows
 
 # 173
 ASLPostLabelingDelayNiftiLength:
@@ -103,7 +103,7 @@ ASLPostLabelingDelayNiftiLength:
     - '"aslcontext" in associations'
     - type(sidecar.PostLabelingDelay) == 'array'
   checks:
-    - nifti_header.pixdim[4] == sidecar.PostLabelingDelay.length
+    - length(sidecar.PostLabelingDelay) == nifti_header.dim[4]
 
 # 174
 ASLPostLabelingDelayASLContextLength:
@@ -127,7 +127,7 @@ ASLPostLabelingDelayASLContextLength:
     - '"aslcontext" in associations'
     - type(sidecar.PostLabelingDelay) == 'array'
   checks:
-    - aslcontext.n_rows == sidecar.PostLabelingDelay.length
+    - length(sidecar.PostLabelingDelay) == aslcontext.n_rows
 
 # 175
 ASLLabelingDurationASLContextLength:
@@ -153,7 +153,7 @@ ASLLabelingDurationASLContextLength:
     - '"LabelingDuration" in sidecar'
     - type(sidecar.LabelingDuration) == 'array'
   checks:
-    - aslcontext.n_rows == sidecar.LabelingDuration.length
+    - length(sidecar.LabelingDuration) == aslcontext.n_rows
 
 # 177
 ASLRepetitionTimePreparationASLContextLength:
@@ -174,7 +174,7 @@ ASLRepetitionTimePreparationASLContextLength:
     - '"RepetitionTimePreparation" in sidecar'
     - type(sidecar.RepetitionTimePreparation) == 'array'
   checks:
-    - aslcontext.n_rows == sidecar.RepetitionTimePreparation.length
+    - length(sidecar.RepetitionTimePreparation) == aslcontext.n_rows
 
 # 180
 ASLBackgroundSuppressionNumberPulses:
@@ -192,7 +192,7 @@ ASLBackgroundSuppressionNumberPulses:
     - '"BackgroundSuppressionPulseTime" in sidecar'
     - type(sidecar.BackgroundSuppressionPulseTime) == 'array'
   checks:
-    - sidecar.BackgroundSuppressionPulseTime.length == sidecar.BackgroundSuppressionNumberPulses
+    - length(sidecar.BackgroundSuppressionPulseTime) == sidecar.BackgroundSuppressionNumberPulses
 
 # 181
 ASLTotalAcquiredVolumesASLContextLength:
@@ -226,7 +226,7 @@ ASLEchoTimeASLContextLength:
     - '"EchoTime" in sidecar'
     - type(sidecar.EchoTime) == 'array'
   checks:
-    - aslcontext.n_rows == sidecar.EchoTime.length
+    - length(sidecar.EchoTime) == aslcontext.n_rows
 
 # 198
 ASLM0TypeAbsentScan:
@@ -256,7 +256,7 @@ ASLM0TypeAbsentASLContext:
   selectors:
     - suffix == "asl"
     - '"aslcontext" in associations'
-    - aslcontext.volume_type.includes('"m0scan")
+    - intersects(aslcontext.volume_type, ["m0scan"])
     - '"M0Type" in sidecar'
   checks:
     - sidecar.M0Type != "absent"

src/schema/rules/checks/dwi.yaml

@@ -2,11 +2,12 @@
 ---
 # 29
 DWIVolumeCount:
-  code: VOLUME_COUNT_MISMATCH
-  description: |
-    The number of volumes in this scan does not match the number of volumes in the
-    corresponding .bvec and .bval files.
-  level: error
+  issue:
+    code: VOLUME_COUNT_MISMATCH
+    message: |
+      The number of volumes in this scan does not match the number of volumes in the
+      corresponding .bvec and .bval files.
+    level: error
   selectors:
     - suffix == "dwi"
     - '"bval" in associations'
@@ -17,43 +18,47 @@ DWIVolumeCount:
 
 # 30
 DWIBvalRows:
-  code: BVAL_MULTIPLE_ROWS
-  description: |
-    '.bval' files should contain exactly one row of volumes.
-  level: error
+  issue:
+    code: BVAL_MULTIPLE_ROWS
+    message: |
+      '.bval' files should contain exactly one row of volumes.
+    level: error
   selectors:
     - extension == "bval"
   checks:
     - data.n_rows == 1
 
 # 31
 DWIBvecRows:
-  code: BVEC_NUMBER_ROWS
-  description: |
-    '.bvec' files should contain exactly three rows of volumes.
-  level: error
+  issue:
+    code: BVEC_NUMBER_ROWS
+    message: |
+      '.bvec' files should contain exactly three rows of volumes.
+    level: error
   selectors:
     - extension == "bvec"
   checks:
     - data.n_rows == 3
 
 # 32
 DWIMissingBvec:
-  code: DWI_MISSING_BVEC
-  description: |
-    DWI scans must have a corresponding .bvec file.
-  level: error
+  issue:
+    code: DWI_MISSING_BVEC
+    message: |
+      DWI scans must have a corresponding .bvec file.
+    level: error
   selectors:
     - suffix == "dwi"
   checks:
     - '"bvec" in associations'
 
 # 33
 DWIMissingBval:
-  code: DWI_MISSING_BVAL
-  description: |
-    DWI scans must have a corresponding .bval file.
-  level: error
+  issue:
+    code: DWI_MISSING_BVAL
+    message: |
+      DWI scans must have a corresponding .bval file.
+    level: error
   selectors:
     - suffix == "dwi"
   checks:

src/schema/rules/checks/events.yaml

@@ -10,7 +10,7 @@ EventsMissing:
     level: warning # could be an error with the proper selectors, I think
   selectors:
     - '"task" in entities'
-    - '!(entities.task.includes("rest"))'
+    - '!matches(entities.task, "rest")'
     - suffix != "events"
   checks:
     - '"events" in associations'

src/schema/rules/checks/func.yaml

@@ -13,4 +13,4 @@ PhaseSuffixDeprecated:
   selectors:
     - datatype == "func"
   checks:
-    - '!(suffix == "phase")'
+    - suffix != "phase"

src/schema/rules/checks/mri.yaml

@@ -0,0 +1,14 @@
+---
+PhasePartUnits:
+  issue:
+    code: PHASE_UNITS
+    message: |
+      Phase images (with the `part-phase` entity) must have units
+      "rad" or "arbitrary".
+    level: error
+  selectors:
+    - modality == "mri"
+    - entities.part == "phase"
+    - '"Units" in sidecar'
+  checks:
+    - intersects([sidecar.Units], ["rad", "arbitrary"])

src/schema/rules/common_derivatives_validation.yaml

@@ -2,17 +2,17 @@
 ResInSidecar:
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - '["mri", "pet"].includes(modality)'
-    - '["nii", " nii.gz"].includes(extension)'
+    - intersects([modality], ["mri", "pet"])
+    - match(extension, '^\.nii(\.gz)?$')
     - type(sidecar.Resolution) == "object"
   checks:
     - entities.resolution in sidecar.Resolution
 
 DenInSidecar:
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
-    - '["mri", "pet"].includes(modality)'
-    - '[".nii", ".nii.gz"].includes(extension)'
+    - intersects([modality], ["mri", "pet"])
+    - match(extension, '^\.nii(\.gz)?$')
     - type(sidecar.Density) == "object"
   checks:
     - entities.density in sidecar.Density

src/schema/rules/dataset_metadata.yaml

@@ -42,7 +42,7 @@ derivative_description:
 dataset_description_with_genetics:
   selectors:
     - path == "/dataset_description.json"
-    - 'dataset.files.includes("/genetic_info.json")'
+    - intersects(dataset.files, ["/genetic_info.json"])
   fields:
     Genetics: required
     Genetics{}.Dataset:

src/schema/rules/errors.yaml

@@ -9,7 +9,7 @@ NiftiHeaderUnreadable:
     Please ensure it is not corrupted or mislabeled.
   level: error
   selectors:
-    - '[".nii", ".nii.gz"].includes(extension)'
+    - match(extension, '^\.nii(\.gz)?$')
 
 # BIDS Validator Original Issue Code #27
 JsonInvalid:
@@ -27,7 +27,7 @@ GzNotGzipped:
     This file ends in the .gz extension but is not actually gzipped.
   level: error
   selectors:
-    - extension.includes(".gz")
+    - match(extension, '\.gz$')
 
 # BIDS Validator Original Issue Code #30
 BvalMultipleRows:
@@ -54,7 +54,7 @@ NiftiTooSmall:
     This file is too small to contain the minimal NIfTI header.
   level: error
   selectors:
-    - '[".nii", ".nii.gz"].includes(extension)'
+    - match(extension, '^\.nii(\.gz)?$')
 
 # BIDS Validator Original Issue Code #43
 OrphanedSymlink:
@@ -90,7 +90,7 @@ BFile:
     and contain only numerical values.
   level: error
   selectors:
-    - '[".bval", ".bvec"].includes(extension)'
+    - intersects([extension], [".bval", ".bvec"])
 
 # BIDS Validator Original Issue Code #55
 JsonSchemaValidationError:
@@ -175,7 +175,7 @@ BrainvisionLinksBroken:
     and *.vmrk) are broken or some files do not exist.
   level: error
   selectors:
-    - '[ ".eeg", ".vhdr", ".vmrk"].includes(extension)'
+    - intersects([extension], [".eeg", ".vhdr", ".vmrk"])
 
 # BIDS Validator Original Issue Code #104
 HedError:

src/schema/rules/sidecars/anat.yaml

@@ -9,7 +9,7 @@
 
 MRIAnatomyCommonMetadataFields:
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "anat"
   fields:
     ContrastBolusIngredient: optional
@@ -18,15 +18,15 @@ MRIAnatomyCommonMetadataFields:
 
 PhaseEntityUnits:
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "anat"
     - entities.part == "phase"
   fields:
     Units: required
 
 PhaseSuffixUnits:
   selectors:
-    - modality == "MRI"
+    - modality == "mri"
     - datatype == "anat"
     - suffix == "phase"
   fields: