[ENH] schema - specify what is valid at the root of a dataset

src/schema/rules/associated_data.yaml

@@ -2,10 +2,18 @@
 # This file describes the requirement levels of directories which may appear
 # within a dataset directory without following BIDS format.
 code:
+  pattern: 'code'
+  type: 'directory'
   required: false
 derivatives:
+  pattern: 'derivatives'
+  type: 'directory'
   required: false
 sourcedata:
+  pattern: 'sourcedata'
+  type: 'directory'
   required: false
 stimuli:
+  pattern: 'stimuli'
+  type: 'directory'
   required: false

src/schema/rules/checks/func.yaml

@@ -1,5 +1,5 @@
-# Rules for functional data that are not defined in tables.
 ---
+# Rules for functional data that are not defined in tables.
 PhaseSuffixDeprecated:
   issue:
     code: PHASE_SUFFIX_DEPRECATED

src/schema/rules/filenames.yaml

@@ -0,0 +1,119 @@
+---
+root:
+  type: 'directory'
+  # you can call datasets whetever you want.
+  pattern: '.*'
+  children:
+  - subject_dirs
+  - $ref: rules.top_level_files
+  - $ref: rules.associated_data
+
+subject_dirs:
+  type: 'directory'
+  entities:
+  - subject
+  children:
+  - session_dirs
+  - datatype_dirs
+  - $ref: rules.tabular_metadata
+
+session_dirs:
+  type: 'directory'
+  entities:
+  - session
+  children:
+  - datatype_dirs
+
+datatype_dirs:
+- pattern: 'anat'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.anat.nonparametric
+  - $ref: rules.datatypes.anat.parametric
+  - $ref: rules.datatypes.anat.defacemask
+  - $ref: rules.datatypes.anat.multiecho
+  - $ref: rules.datatypes.anat.multiflip
+  - $ref: rules.datatypes.anat.multiinversion
+  - $ref: rules.datatypes.anat.mp2rage
+  - $ref: rules.datatypes.anat.vfamt
+  - $ref: rules.datatypes.anat.mtr
+- pattern: 'beh'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.beh.timeseries
+  - $ref: rules.datatypes.beh.noncontinuous
+- pattern: 'dwi'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.dwi.dwi
+  - $ref: rules.datatypes.dwi.sbref
+  - $ref: rules.datatypes.dwi.timeseries
+- pattern: 'eeg'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.eeg.eeg
+  - $ref: rules.datatypes.eeg.channels
+  - $ref: rules.datatypes.eeg.coordsystem
+  - $ref: rules.datatypes.eeg.electrodes
+  - $ref: rules.datatypes.eeg.events
+  - $ref: rules.datatypes.eeg.photo
+  - $ref: rules.datatypes.eeg.timeseries
+- pattern: 'fmap'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.fmap.fieldmaps
+  - $ref: rules.datatypes.fmap.pepolar
+  - $ref: rules.datatypes.fmap.TB1DAM
+  - $ref: rules.datatypes.fmap.TB1EPI
+  - $ref: rules.datatypes.fmap.RFFieldMaps
+  - $ref: rules.datatypes.fmap.TB1SRGE
+  - $ref: rules.datatypes.fmap.parametric
+- pattern: 'func'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.func.func
+  - $ref: rules.datatypes.func.phase
+  - $ref: rules.datatypes.func.events
+  - $ref: rules.datatypes.func.timeseries
+- pattern: 'ieeg'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.ieeg.ieeg
+  - $ref: rules.datatypes.ieeg.channels
+  - $ref: rules.datatypes.ieeg.coordsystem
+  - $ref: rules.datatypes.ieeg.electrodes
+  - $ref: rules.datatypes.ieeg.events
+  - $ref: rules.datatypes.ieeg.photo
+  - $ref: rules.datatypes.ieeg.timeseries
+- pattern: 'meg'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.meg.meg
+  - $ref: rules.datatypes.meg.calibration
+  - $ref: rules.datatypes.meg.crosstalk
+  - $ref: rules.datatypes.meg.headshape
+  - $ref: rules.datatypes.meg.markers
+  - $ref: rules.datatypes.meg.coordsystem
+  - $ref: rules.datatypes.meg.channels
+  - $ref: rules.datatypes.meg.events
+  - $ref: rules.datatypes.meg.photo
+  - $ref: rules.datatypes.meg.timeseries
+- pattern: 'micr'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.micr.microscopy
+  - $ref: rules.datatypes.micr.photo
+- pattern: 'perf'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.perf.asl
+  - $ref: rules.datatypes.perf.aslcontext
+  - $ref: rules.datatypes.perf.asllabeling
+  - $ref: rules.datatypes.perf.timeseries
+- pattern: 'pet'
+  type: 'directory'
+  children:
+  - $ref: rules.datatypes.pet.pet
+  - $ref: rules.datatypes.pet.blood
+  - $ref: rules.datatypes.pet.events
+  - $ref: rules.datatypes.pet.timeseries

src/schema/rules/top_level_files.yaml

@@ -1,34 +1,41 @@
 ---
 README:
   required: true
+  pattern: 'README'
   extensions:
   - None
   - .md
   - .rst
   - .txt
 CHANGES:
   required: true
+  pattern: 'CHANGES'
   extensions:
   - None
 LICENSE:
   required: false
+  pattern: 'LICENSE'
   extensions:
   - None
 dataset_description:
   required: true
+  pattern: 'dataset_description'
   extensions:
   - .json
 genetic_info:
   required: false
+  pattern: 'genetic_info'
   extensions:
   - .json
 participants:
   required: false
+  pattern: 'participants'
   extensions:
   - .tsv
   - .json
 samples:
   required: false
+  pattern: 'samples'
   extensions:
   - .tsv
   - .json