diff --git a/integrationtests/test-profile/profile.yml b/integrationtests/test-profile/profile.yml index 2c285731b79dd45ff9022f3ef1553d80495efb9e..ee669196cce69f89d01af0f82bd0f6b5502cd6ef 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 3123de13ffd88b84daa29ac4a6ae1259bd8f980f..4866654338dfdee16f1b7635a72da6c8f7928e19 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 71956f998cb7c88b486823c675743faa803aa3f3..61099cc8c57b7df1c96779aeea97655fd3300540 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: