d3tales-api 0.2.0

API for parsing, database connection, and property calculations for D3taLES project

D³TaLES API

API designed for the D³TaLES project. Includes data processing, database access functions, and property calculators.

Website with full documentation for the D³TaLES API can be found here.

Modules

This API contains three modules:

• D3database: Interface for interacting with the D³TaLES databases. Includes queries, data insertion with validation, and a REST API interface.
• Processors: Processing code for extracting data from computational and experimental data files as well as ExpFlow run objects.
• Calculators: Property calculators and plotters for cyclic voltammetry
• Workflows: Fireworks workflow for the D³TaLES databases high throughput workflows

Installation

PIP Install

This module can be installed with pip install by running the following code:

pip install git+https://github.com/d3tales/d3tales_api.git

Installation Notes:

• If your python version is greater than 3.8, then you will need to install pymatgen directly into the environment you are working in. It is best to use conda for this.
• If you plan to use any NLP parsers, you will need to install ChemDataExtractor2 with pip install ChemDataExtractor2. Dependency conflicts make it necessary to install separately.

Environment Variables

Note that many operation require a DB_INFO_FILE environment variable. This environment variable should be a path to a JSON file containing connection information for the databases. The keys should be the database names such as frontend, backend, expflow, and fireworks. An example can be found at db_info_ex.json.

To set this variable run:

export DB_INFO_FILE=$PWD/db_infos_ex.json

You can also set a GROUP_FILE environment variable. This should point to a json file containing source_group tag names. This is optional.

To set this variable run:

export GROUP_FILE=$PWD/group_file_ex.json

REST API (d3tales_api.restapi.RESTAPI) will use UPLOAD_USER and UPLOAD_PASS environment variables if username and password arguments are not provided. These environment variables can be set in the same was as the DB_INFO_FILE variable.