From 48247ad8a4d7680f4911036b2a8d59a5a9aa359f Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Tue, 14 Feb 2023 22:04:46 +0100
Subject: [PATCH] wip
---
integrationtests/test-profile/profile.yml | 2 +-
src/bids-cfood/cfood.yml | 30 +++++++++++------------
src/bids-cfood/model.yml | 29 ++++++++++++++++++++--
3 files changed, 43 insertions(+), 18 deletions(-)
diff --git a/integrationtests/test-profile/profile.yml b/integrationtests/test-profile/profile.yml
index 2c28573..ee66919 100644
--- a/integrationtests/test-profile/profile.yml
+++ b/integrationtests/test-profile/profile.yml
@@ -22,7 +22,7 @@ default:
# list of `NAME: PATH` pairs or a single path.
extroot:
# "": "paths/extroot"
- "": "../../unittests/test_data/valid_dataset/"
+ "": "../../bids-examples/"
#
# "base": "/path/to/base/dir"
# "other": "/path/to/other"
diff --git a/src/bids-cfood/cfood.yml b/src/bids-cfood/cfood.yml
index 3123de1..4866654 100644
--- a/src/bids-cfood/cfood.yml
+++ b/src/bids-cfood/cfood.yml
@@ -175,6 +175,9 @@ Converters:
BIDSFUNCDirectory:
package: bidsconverter.bids_dir_converter
converter: BIDSFUNCDirConverter
+ BIDSSessionDirectory:
+ package: bidsconverter.bids_dir_converter
+ converter: BIDSSessionDirConverter
project_level:
type: Directory
match: ^(?P<name>.*)$
@@ -202,15 +205,16 @@ project_level:
Authors:
type: DictListElement
match_name: ^Authors$
- debug_match: True
match_value: ^(.*)$
subtree:
Author:
type: TextElement
match_value: ^(?P<val>((?!,).)*)$
records:
+ # TODO how to deal with those two case and identifiable
Person:
- name: $val
+ firstName: ""
+ lastName: $val
Dataset:
Author: +$Person
AuthorSplit:
@@ -307,15 +311,16 @@ project_level:
Subject: +$Subject
subtree:
session_level:
- type: Directory
- match: ^(ses-(?P<seslabel>[a-zA-Z0-9]+))$
+ type: BIDSSessionDirectory
+ match: ^.*$
+ debug_match: True
records:
Session:
label: $seslabel
Subject:
Session: +$Session
subtree:
- func:
+ func: &func_subtree
type: BIDSFUNCDirectory
match: ^(?P<datatype>func)$
subtree:
@@ -342,15 +347,13 @@ project_level:
- suffix: "((?!events|bold|cbv|sbref|stim)((?!_).)*?)"
parent: "RawData"
- anat:
+ anat: &anat_subtree
type: BIDSANATDirectory
match: ^(?P<datatype>anat)$
- debug_match: False
subtree:
series_list:
type: ListElement
match_name: (?P<series_no>.*)
- debug_match: False
records:
AnatomyImaging:
parents: [AnatomyImaging]
@@ -398,15 +401,13 @@ project_level:
parent: "MagnetizationTransferRatio"
- suffix: "(?!defacemask|MERGE|MESE|VFA|ITR1|MP2RAGE|MPM|MTS|T1w|MTR)"
parent: "RawData"
- meg:
+ meg: &meg_subtree
type: BIDSMEGDirectory
match: ^(?P<datatype>meg)$
- debug_match: False
subtree:
series_list:
type: ListElement
match_name: (?P<series_no>.*)
- debug_match: False
records:
Magnetoencephalography:
parents: [AnatomyImaging]
@@ -434,15 +435,14 @@ project_level:
parent: "PhotoFile"
- suffix: "headshape"
parent: "HeadshapeFile"
- eeg:
+ eeg: &eeg_subtree
type: BIDSEEGDirectory
match: ^(?P<datatype>eeg)$
- debug_match: False
subtree:
series_list:
type: ListElement
match_name: (?P<series_no>.*)
- debug_match: False
+ debug_match: True
records:
Electroencephalography:
parents: [Electroencephalography]
@@ -466,7 +466,7 @@ project_level:
parent: "ElectrodeFile"
- suffix: "photo"
parent: "PhotoFile"
- fmap:
+ fmap: &fmap_subtree
type: BIDSDirectory
match: ^(?P<datatype>fmap)$
debug_match: False
diff --git a/src/bids-cfood/model.yml b/src/bids-cfood/model.yml
index 71956f9..61099cc 100644
--- a/src/bids-cfood/model.yml
+++ b/src/bids-cfood/model.yml
@@ -6,10 +6,35 @@ Dataset:
recommended_properties:
Subject:
DataSetDescription:
+ description: JSON file that describes the dataset
+ BIDSVersion:
+ datatype: TEXT
ParticipantsTable:
description: tsv files that lists the participants/subjects
-DataSetDescription:
- description: JSON file that describes the dataset
+ Author:
+ datatype: Person
+ License:
+ datatype: TEXT
+ DatasetType:
+ datatype: TEXT
+ Acknowledgements:
+ datatype: TEXT
+ HowToAcknowledge:
+ datatype: TEXT
+ DatasetDOI:
+ datatype: TEXT
+ ReferencesAndLinks:
+ datatype: TEXT
+ EthicsApproval:
+ datatype: TEXT
+ HEDVersion:
+ datatype: TEXT
+Person:
+ recommended_properties:
+ firstName:
+ datatype: TEXT
+ lastName:
+ datatype: TEXT
Subject:
description: single subject data
recommended_properties:
--
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