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[DOC] adding comments file to team description
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bclenet committed Oct 10, 2023
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Expand Up @@ -6,20 +6,22 @@ It is a conversion into tsv format (tab-separated values) of the [original .xlsx

The file `narps_open/data/description/analysis_pipelines_derived_descriptions.tsv` contains for each team a set of programmatically usable data based on the textual descriptions of the previous file. This data is available in the `derived` sub dictionary (see examples hereafter).

The file `narps_open/data/description/analysis_pipelines_comments.tsv` contains for each team a set of comments made by the NARPS Open Pipelines team about reproducibility and exclusions of the pipeline. This data is available in the `comments` sub dictionary (see examples hereafter).

The class `TeamDescription` of module `narps_open.data.description` acts as a parser for these two files.

You can use the command-line tool as so. Option `-t` is for the team id, option `-d` allows to print only one of the sub parts of the description among : `general`, `exclusions`, `preprocessing`, `analysis`, and `categorized_for_analysis`. Options `--json` and `--md` allow to choose the export format you prefer between JSON and Markdown.
You can use the command-line tool as so. Option `-t` is for the team id, option `-d` allows to print only one of the sub parts of the description among : `general`, `exclusions`, `preprocessing`, `analysis`, `categorized_for_analysis`, `derived`, and `comments`. Options `--json` and `--md` allow to choose the export format you prefer between JSON and Markdown.

```bash
python narps_open/data/description -h
# usage: __init__.py [-h] -t TEAM [-d {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived}]
# usage: __init__.py [-h] -t TEAM [-d {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived,comments}]
#
# Get description of a NARPS pipeline.
#
# options:
# -h, --help show this help message and exit
# -t TEAM, --team TEAM the team ID
# -d {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived}, --dictionary {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived}
# -d {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived,comments}, --dictionary {general,exclusions,preprocessing,analysis,categorized_for_analysis,derived,comments}
# the sub dictionary of team description
# --json output team description as JSON
# --md output team description as Markdown
Expand Down Expand Up @@ -91,6 +93,7 @@ description.preprocessing
description.analysis
description.categorized_for_analysis
description.derived
description.comments
# Access values of sub dictionaries
description.general['teamID']
# Other keys in general are: ['teamID', 'NV_collection_link', 'results_comments', 'preregistered', 'link_preregistration_form', 'regions_definition', 'softwares', 'general_comments']
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