fix spelling

INCF · May 18, 2024 · 08eef1c · 08eef1c
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diff --git a/.github/workflows/publishdocs.yaml b/.github/workflows/publishdocs.yaml
@@ -4,7 +4,9 @@ on:
   push:
     branches:
     - main
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 jobs:
   build:
     name: Deploy docs

diff --git a/.github/workflows/update_spreadsheet.yml b/.github/workflows/update_spreadsheet.yml
@@ -1,5 +1,9 @@
 name: Update spreadsheet
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches: [ main ]

diff --git a/.github/workflows/validate.yml b/.github/workflows/validate.yml
@@ -1,5 +1,9 @@
 name: validate jsonld
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches:

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -18,3 +18,9 @@ repos:
     rev: "v3.8.2"
     hooks:
         - id: reorder-python-imports
+
+# Checks for spelling errors
+-   repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+    -   id: codespell
diff --git a/README.md b/README.md
@@ -15,8 +15,8 @@ The goal of the ARTEM-IS is to use insights derived from systematic reviews and
 3. Once logged in, by clicking `Create` in the top right corner, you can create a new, blank template.
 4. You can navigate a template by using the menu on top and answer the questions corresponding to the study you are reporting on. This is meant to ensure that you have not forgotten any of the essential information during data collection or later in the methods and results parts of your article.
 5. Click `Save` in the top right corner to save any changes.
-6. You can view your own saved templates using `My templates` option. For each template, you have the options to make them publically (in)visible to others, download a human-readable PDF output and download a machine-readable JSON output. All templates are set to private in the beginning.
-7. You can view and download publically available templates by other members using `Browse` menu.
+6. You can view your own saved templates using `My templates` option. For each template, you have the options to make them publicly (in)visible to others, download a human-readable PDF output and download a machine-readable JSON output. All templates are set to private in the beginning.
+7. You can view and download publicly available templates by other members using `Browse` menu.
 8. You can upload a previously downloaded (in JSON format) templates to your account using `Upload` menu.
 
 You can find output examples on the [OSF page of this project](https://osf.io/ahp3t/).

diff --git a/inputs/tsv/acquisition.tsv b/inputs/tsv/acquisition.tsv
@@ -1,37 +1,37 @@
 sub_section	preamble	question	unit	details	field_type	choices	item_pref_label	visibility	item_order	include	mandatory	activity_pref_label	activity_order	BIDS_status	BIDS_key_for_unit	BIDS_key	BIDS_file	Change_log
-Acquisition software	In this section you will descibe acquisition set-up, which software you have used, impedance upper treschold, what type of online reference, recording channels, VEOG and HEOG and online filters.   NOTE: If you notice a bug, or have a suggestion, we'd be grateful if you posted an issue on GitHub: https://github.com/INCF/artem-is/	What software did you use for the acquisition?			select	preset:meeg_acquisition_softwares	acquisition_software	1	1	1	1	Acquisition	4			SoftwareVersions	*_eeg.json	
-Acquisition software		Specify software version if applicable, and software name and version if "other" was selected.			text		acquisition_software_details	1	2	1	1	Acquisition	4			SoftwareVersions	*_eeg.json	
-Data quality		Did you document impedances, or an alternative data aquisition quality measure? 			radio	preset:boolean	acquisition_quality_measure_exists	1	3	1	1	Acquisition	4					
-Data quality		What is the appropriate acquisition data quality measure for the recording equipment?			radio	impedance upper threshold | impedance range | a data quality measure alternative to impedances	acquisition_quality_measure	acquisition_quality_measure_exists == 1	4	1	1	Acquisition	4			status	*_channels.tsv	
-Data quality		What was the upper threshold of impedance that was registered in this study?	kilo-ohms		integer		impedance_threshold	acquisition_quality_measure == 0	5	1	1	Acquisition	4					
-Data quality		What was the lowest impedance registered in this study?	kilo-ohms		integer		impedance_lower_end	acquisition_quality_measure == 1	6	1	1	Acquisition	4					
-Data quality		What was the highest impedance registered in this study?	kilo-ohms		integer		impedance_higher_end	acquisition_quality_measure == 1	7	1	1	Acquisition	4					
-Data quality		Report data quality measures provided by the recording system alternative to impedances.			textarea		impedance_alternative	acquisition_quality_measure == 2	8	1	1	Acquisition	4					
-Online (recording) reference		Was voltage measured relative to an online reference for EEG electrodes (as opposed to alternative solutions such as Driven Right Leg (DRL))?			radio	preset:boolean	online_reference_exists	1	9	1	1	Acquisition	4					
-Online (recording) reference		Location of the EEG online reference electrode(s)			select	preset:eeg_reference_electrodes	online_reference_type	online_reference_exists == 1	10	1	1	Acquisition	4			EEGReference // reference	*_eeg.json // *_channels.tsv	
-Online (recording) reference		What alternative to an EEG online reference (for example DRL) was used?			text		alternatives_to_reference	online_reference_exists == 0	11	1	1	Acquisition	4					
-Online (recording) reference		EEG online reference location other than listed			text		online_reference_type_other	online_reference_type == 9	12	1	1	Acquisition	4					
-Online (recording) reference		Location of the ground electrode during recording			text		location_ground	online_reference_exists == 1	13	1	1	Acquisition	4			EEGGround	*_eeg.json	
-Online (recording) reference		Online reference for VEOG electrodes			radio	bipolar (lower - upper VEOG) | the same reference as EEG electrodes | other | VEOG was not recorded	online_reference_VEOG	1	14	1	1	Acquisition	4					
-Online (recording) reference		Which other reference was used for VEOG recording?			text		online_reference_VEOG_other	online_reference_VEOG == 2	15	1	1	Acquisition	4					
-Online (recording) reference		Online reference for HEOG electrodes			radio	bipolar (left - right HEOG) | bipolar (right - left HEOG) | the same reference as EEG electrodes | other | HEOG was not recorded	online_reference_HEOG	1	16	1	1	Acquisition	4					
+Acquisition software	In this section you will describe acquisition set-up, which software you have used, impedance upper treschold, what type of online reference, recording channels, VEOG and HEOG and online filters.   NOTE: If you notice a bug, or have a suggestion, we'd be grateful if you posted an issue on GitHub: https://github.com/INCF/artem-is/	What software did you use for the acquisition?			select	preset:meeg_acquisition_softwares	acquisition_software	1	1	1	1	Acquisition	4			SoftwareVersions	*_eeg.json
+Acquisition software		Specify software version if applicable, and software name and version if "other" was selected.			text		acquisition_software_details	1	2	1	1	Acquisition	4			SoftwareVersions	*_eeg.json
+Data quality		Did you document impedances, or an alternative data acquisition quality measure? 			radio	preset:boolean	acquisition_quality_measure_exists	1	3	1	1	Acquisition	4
+Data quality		What is the appropriate acquisition data quality measure for the recording equipment?			radio	impedance upper threshold | impedance range | a data quality measure alternative to impedances	acquisition_quality_measure	acquisition_quality_measure_exists == 1	4	1	1	Acquisition	4			status	*_channels.tsv
+Data quality		What was the upper threshold of impedance that was registered in this study?	kilo-ohms		integer		impedance_threshold	acquisition_quality_measure == 0	5	1	1	Acquisition	4
+Data quality		What was the lowest impedance registered in this study?	kilo-ohms		integer		impedance_lower_end	acquisition_quality_measure == 1	6	1	1	Acquisition	4
+Data quality		What was the highest impedance registered in this study?	kilo-ohms		integer		impedance_higher_end	acquisition_quality_measure == 1	7	1	1	Acquisition	4
+Data quality		Report data quality measures provided by the recording system alternative to impedances.			textarea		impedance_alternative	acquisition_quality_measure == 2	8	1	1	Acquisition	4
+Online (recording) reference		Was voltage measured relative to an online reference for EEG electrodes (as opposed to alternative solutions such as Driven Right Leg (DRL))?			radio	preset:boolean	online_reference_exists	1	9	1	1	Acquisition	4
+Online (recording) reference		Location of the EEG online reference electrode(s)			select	preset:eeg_reference_electrodes	online_reference_type	online_reference_exists == 1	10	1	1	Acquisition	4			EEGReference // reference	*_eeg.json // *_channels.tsv
+Online (recording) reference		What alternative to an EEG online reference (for example DRL) was used?			text		alternatives_to_reference	online_reference_exists == 0	11	1	1	Acquisition	4
+Online (recording) reference		EEG online reference location other than listed			text		online_reference_type_other	online_reference_type == 9	12	1	1	Acquisition	4
+Online (recording) reference		Location of the ground electrode during recording			text		location_ground	online_reference_exists == 1	13	1	1	Acquisition	4			EEGGround	*_eeg.json
+Online (recording) reference		Online reference for VEOG electrodes			radio	bipolar (lower - upper VEOG) | the same reference as EEG electrodes | other | VEOG was not recorded	online_reference_VEOG	1	14	1	1	Acquisition	4
+Online (recording) reference		Which other reference was used for VEOG recording?			text		online_reference_VEOG_other	online_reference_VEOG == 2	15	1	1	Acquisition	4
+Online (recording) reference		Online reference for HEOG electrodes			radio	bipolar (left - right HEOG) | bipolar (right - left HEOG) | the same reference as EEG electrodes | other | HEOG was not recorded	online_reference_HEOG	1	16	1	1	Acquisition	4
 Online (recording) reference		Which other reference was used for HEOG recording?			text		online_reference_HEOG_other	online_reference_HEOG == 3	17	1	1	Acquisition	4					27.11.2023 Angela rephrased question and options
 Online (recording) reference		Online reference for other non-EEG (and non-EOG) electrodes			radio	the same reference as EEG electrodes | other | no non-EEG non-EOG electrodes were used	online_reference_other_non-EEG	1	18	1	1	Acquisition	4					25.08.2023 Angela: this question was a text question by mistake, changed to radio  27.11.2023 Angela rephrased question and options
 Online (recording) reference		Which other reference was used for other non-EEG (and non-EOG) electrodes?			text		online_reference_other_non-EEG_other	online_reference_other_non-EEG == 1	19	1	1	Acquisition	4					27.11.2023 Angela rephrased question and options
 Online filters		Which of the following online filters were used?		Select "none" to mark this question as answered if you did not use any online filters. Please note that this case is highly unlikely given that acquisition systems normally have at least an anti-aliasing low-pass filter.	radio_multiple	high pass | low pass | notch | none	online_filters	1	20	1	1	Acquisition	4			online_filters	*_eeg.json	25.08.2023 Angela: added additional instructions in the "details" section
-Online filters		High-pass filter cut-off used during recording	Hz		float		online_filters_high_pass_cut_off	online_filters.includes(0)	21	1	1	Acquisition	4			high_cutoff 	*_channels.tsv	
-Online filters		Type of online high-pass filter cut-off			radio	half-amplitude | half-power	online_filters_high_pass_cutoff_unit	online_filters.includes(0)	22	1	1	Acquisition	4					
-Online filters		High-pass filter roll off used during recording	dB/octave		float		online_filters_high_pass_roll_off	online_filters.includes(0)	23	1	1	Acquisition	4					
-Online filters		High-pass filter impulse response during recording			radio	finite impulse response (FIR) | infinite impulse response (IIR)	online_filters_high_pass_impulse	online_filters.includes(0)	24	1	1	Acquisition	4					
-Online filters		Type of online low-pass filter cut-off			radio	half-amplitude | half-power	online_filters_low_pass_cutoff_unit	online_filters.includes(1)	25	1	1	Acquisition	4					
-Online filters		Low-pass filter cut-off used during recording	Hz		float		online_filters_low_pass_cut_off	online_filters.includes(1)	26	1	1	Acquisition	4					
-Online filters		Low-pass filter roll off used during recording	dB/octave		float		online_filters_low_pass_roll_off	online_filters.includes(1)	27	1	1	Acquisition	4			low_cutoff 	*_channels.tsv	
-Online filters		Low-pass filter impulse response during recording			radio	finite impulse response (FIR) | infinite impulse response (IIR)	online_filters_low_pass_impulse	online_filters.includes(1)	28	1	1	Acquisition	4					
-Offline filters		What notch filter was applied online (during recording)?			radio	50 Hz | 60 Hz | other	online_notch_filter_type	online_filters.includes(2)	29	1	1	Acquisition	4					
-Offline filters		Center frequency of the online notch filter	Hz		text		online_notch_filter_type_details	online_notch_filter_type == 2	30	1	1	Acquisition	4					
-Offline filters		In which format do you want to report the width of the offline notch filter?			radio	distance between 3 dB points | number of removed frequencies in a decrete Fourier transform	online_notch_filter_width	online_filters.includes(2)	31	1	1	Acquisition	4					
-Offline filters		Distance between 3 dB points	Hz		float		online_notch_filter_width_distance	online_notch_filter_width == 0	32	1	1	Acquisition	4					
-Offline filters		Number of removed frequencies in a descrete Fourier transform			float		online_notch_filter_width_number_frequencies	online_notch_filter_width == 1	33	1	1	Acquisition	4					
-Offline filters		Were any harmonics also removed by the online notch filter?			radio	preset:boolean	online_notch_filter_harmonics	online_filters.includes(2)	34	1	1	Acquisition	4					
-Offline filters		Which harmonics were removed by the online notch filter? List center frequencies separated by a semicolon and a space			text		online_notch_filter_harmonics_which	online_notch_filter_harmonics == 1	35	1	1	Acquisition	4					
-Sampling		Acquisition sampling rate	Hz		float		recording_samping_frequency	1	36	1	1	Acquisition	4			sampling_frequency	*_channels.tsv	
+Online filters		High-pass filter cut-off used during recording	Hz		float		online_filters_high_pass_cut_off	online_filters.includes(0)	21	1	1	Acquisition	4			high_cutoff 	*_channels.tsv
+Online filters		Type of online high-pass filter cut-off			radio	half-amplitude | half-power	online_filters_high_pass_cutoff_unit	online_filters.includes(0)	22	1	1	Acquisition	4
+Online filters		High-pass filter roll off used during recording	dB/octave		float		online_filters_high_pass_roll_off	online_filters.includes(0)	23	1	1	Acquisition	4
+Online filters		High-pass filter impulse response during recording			radio	finite impulse response (FIR) | infinite impulse response (IIR)	online_filters_high_pass_impulse	online_filters.includes(0)	24	1	1	Acquisition	4
+Online filters		Type of online low-pass filter cut-off			radio	half-amplitude | half-power	online_filters_low_pass_cutoff_unit	online_filters.includes(1)	25	1	1	Acquisition	4
+Online filters		Low-pass filter cut-off used during recording	Hz		float		online_filters_low_pass_cut_off	online_filters.includes(1)	26	1	1	Acquisition	4
+Online filters		Low-pass filter roll off used during recording	dB/octave		float		online_filters_low_pass_roll_off	online_filters.includes(1)	27	1	1	Acquisition	4			low_cutoff 	*_channels.tsv
+Online filters		Low-pass filter impulse response during recording			radio	finite impulse response (FIR) | infinite impulse response (IIR)	online_filters_low_pass_impulse	online_filters.includes(1)	28	1	1	Acquisition	4
+Offline filters		What notch filter was applied online (during recording)?			radio	50 Hz | 60 Hz | other	online_notch_filter_type	online_filters.includes(2)	29	1	1	Acquisition	4
+Offline filters		Center frequency of the online notch filter	Hz		text		online_notch_filter_type_details	online_notch_filter_type == 2	30	1	1	Acquisition	4
+Offline filters		In which format do you want to report the width of the offline notch filter?			radio	distance between 3 dB points | number of removed frequencies in a decrete Fourier transform	online_notch_filter_width	online_filters.includes(2)	31	1	1	Acquisition	4
+Offline filters		Distance between 3 dB points	Hz		float		online_notch_filter_width_distance	online_notch_filter_width == 0	32	1	1	Acquisition	4
+Offline filters		Number of removed frequencies in a discrete Fourier transform			float		online_notch_filter_width_number_frequencies	online_notch_filter_width == 1	33	1	1	Acquisition	4
+Offline filters		Were any harmonics also removed by the online notch filter?			radio	preset:boolean	online_notch_filter_harmonics	online_filters.includes(2)	34	1	1	Acquisition	4
+Offline filters		Which harmonics were removed by the online notch filter? List center frequencies separated by a semicolon and a space			text		online_notch_filter_harmonics_which	online_notch_filter_harmonics == 1	35	1	1	Acquisition	4
+Sampling		Acquisition sampling rate	Hz		float		recording_samping_frequency	1	36	1	1	Acquisition	4			sampling_frequency	*_channels.tsv