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A meteor-based table-building application for epidemiology, and mechanistic data used in the human-health assessment of chemicals.

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shapiromatron/tblBuilder

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Table builder

DOI

Building evidence tables to justify decisions for human-health decisions can be cumbersome, and often times the data which are entered in these tables can be reused for subsequent analyses. However, the tables impose certain formatting conventions for conciseness in the table.

This application attempts to create a simple web-application for adding data to a table, and will allow for customized Excel reports for downloading the data in both formatted-tables and raw-tabular format which is more amenable for statistical modeling.

Development notes

Global installation requirements:

  1. install meteor
  2. install mongodb
  3. install python 3.6 or higher

In the root directory of the application:

  1. install Python3 dependencies with pip install -r requirements.txt
  2. install R and R dependencies with bash requirements.sh
  3. install Javascript dependencies with cd src && meteor npm install

Editing the settings.json

Modify settings in ./settings/settings.json to reflect your environment. For an example of what's required, see the ./settings/settings.example.json file.

  • public.context is one of: ["ntp", "iarc", or "demo"]
  • scripts_path is the absolute path to the ./src/private/scripts folder.

Create admin user

To create an admin in the database, modify bin/createSuperuser.js with the username, email address and password you would like to use. Then run meteor shell to open up the meteor shell and run .load ./bin/createSuperuser.js to create your admin user.

Loading dev database

If you've been supplied with a development database, move it to your desktop and make sure Mongo is running, then load it into Mongo by running the commands:

unzip ~/Desktop/'Backup-Date'-backup.zip -d ~/Desktop/_extracted
mongorestore --drop --host localhost:3001 -d meteor ~/Desktop/_extracted
rm –rf ~/Desktop/_extracted

Running the dev environment

A basic dev environment using tmux is set up with the Makefile. Start the dev environment by running make dev.

Production notes

Deploy using docker; view the docker-compose.yml for more details.

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A meteor-based table-building application for epidemiology, and mechanistic data used in the human-health assessment of chemicals.

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