INCATools/tetool

Name: tetool

Owner: INCATools

Description: NPM CLI tool for creating and manipulating table-editor configuration files and directories

Created: 2017-06-21 19:21:15.0

Updated: 2017-07-01 01:41:33.0

Pushed: 2017-12-12 20:46:27.0

Homepage: null

Size: 19

Language: JavaScript

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README

tetool - Node CLI tool for managing table-editor configurations

tetool builds a static website that incorporates INCAForm to provide a way to edit CSV and TSV (collectively, XSV) files with guided autocomplete. The tool scans a source directory for DOSDPpatterns and corresponding XSV files and produces the resulting static website in a form that may be served via GitHub Pages or any other web hosting mechanism.

Requirements

• Node.js version 6.10.0 or higher

Installation

npm install -g tetool

Usage

tetool --help
tetool --site <targetSiteDir> --title <targetSiteTitle>
tetool --site <targetSiteDir> --source <ontologySourceDir>
tetool --site <targetSiteDir> --source <ontologySourceDir>@<branchName>

Examples

tetool --site ../exposure-inca-form/ --title 'Exposure Ontology'
tetool --site ../exposure-inca-form/ --source ../environmental-exposure-ontology/
tetool --site ../planteome-inca-form/ --source ../plant-trait-ontology/@clean-dp

Building the IncaForm site for exposure-inca-form

This example assumes that a single ontology repo will be used. For this example, the local copy of the environmental-exposure-ontology repo will be used as a source of patterns and XSVs.

• cd to the site directory, which may not yet contain a docs/ directory: cd exposure-inca-form/
• Use tetool to create a site directory: tetool –site ./
• This will create docs/, docs/configurations/, and docs/index.html
• Use tetool to augment the site directory with configurations based upon ontology source directories tetool –site ./ –source ../environmental-exposure-ontology/

Assumptions about the source directory structure

In order to simplify the use of tetool, we make the assumption that a source ontology repository has a hierarchy resembling that in https://github.com/EnvironmentOntology/environmental-exposure-ontology:

source-repo/
    src/
        ontology/
            a.csv
            b.csv
            ...
        patterns/
            a.yaml
            b.yaml
            ...

In order to support Planteome, this was kludged to support structures like those in https://github.com/Planteome/plant-trait-ontology:

source-repo/
    patterns/
        a.yaml
        a/
            a.csv
        b.yaml
        b/
            b.csv

Known Issues

The current GO ontology repo does not follow either of the file structures above, and therefore tetool will fail to find the appropriate patterns and XSV files when building the docs/ site. The workaround is to hand-edit the generated files to add any patterns or XSV that were not detected.

Longer term, tetool should be fixed to support a broader and perhaps a more general pattern-finding mechanism, or the user must have the ability to explicitly specify pattern files, rather than having them detected by tetool.

Developing tetool

• Clone the repo
• cd to the repo directory
• npm install # Install dependencies
• Invent!
• npm install -g # Install tetool globally, from the local working directory

Version History

0.0.1 - Initial version of tetool installed into NPM 0.0.2 - Adds –local option for ease of development. Adds 'Thing' as a global class available for autocomplete. Add 'src/ontology/patterns' as a possible location to discover pattern files. Add more documentation to README.