translator-testing-framework

This repo is a prototype to demonstrate how Behave can be utilized to write tests in natural language. The interpretation and behavior of the natural language statements are handled by Python code.

Getting started

Clone this repository,

git clone --recursive https://github.com/deepakunni3/translator-testing-framework.git

Note: Be sure to use --recursive flag to clone the NCATS-Tangerine/NCATS-ReasonerStdAPI-diff dependency.

After cloning the repo, set up a virtual environment using Python 3's venv module,

python3 -m venv my-working-environment

Then, activate my-working-environment,

source my-working-environment/bin/activate

Now install required packages,

pip install -r requirements.txt

Running Behave tests

To run the Behave tests,

behave

To successfully run all the defined tests, be sure to run the reasoner_diff/server.py first. reasoner_diff/server.py will start a local server on http://0.0.0.0:9999.

Writing Behave tests

Write your tests similar to how you would type out a testing behavior.

For example,

Feature: Compare answers between reasoners

    Scenario: Compare answers between RTX and ROBOKOP
        Given an answer graph from "RTX"
        Given an answer graph from "ROBOKOP"
        When we compare the answer graphs
        Then the response should contain "graph_diff"
        Then the response should have some JSONPath "graph_diff.intersection.edges[*].source_id" containing "string" "HP:0002105"
        Then the response should have some JSONPath "graph_diff.intersection.edges[*].relation" containing "string" "RO:0002200"
        Then the response should have some JSONPath "graph_diff.intersection.edges[*].relation_label" containing "string" "has phenotype"
        Then the response should have some JSONPath "graph_diff.intersection.edges[*].target_id" containing "string" "MONDO:0018076"

Each suite of tests is called a Feature. You can group similar tests into one Feature.

Each Feature can have one (or more) Scenario.

In the above Scenario, there are two Given statements, one When statement and five Then statements.

Each of these statements are backed by Python code that handles what behavior you would like to see. The code itself resides in features/steps folder.

Take a look at the implementation,

• Code that handles the behavior for Given an answer graph from ...
• Code that handles the behavior for When we compare the answer graphs
• Code that handles the behavior for Then the response should contain ...
• Code that handles the behavior for Then the response should have some JSONPath ... containing ...

The above statements are defined in a flexible way such that they can be reused for different scenarios.

If there are new statements that originate from your scenarios, then add these statements to features/steps.

Motivation

The motivation for this framework originated from the Knowledge Graph Standardization call.

Objectives

• Testing reasoners
• Validate reasoner response against a minimal ground truth answers
• Validate answers according to input questions
• Allow for strict as well as fuzzy validation
• Easy for Subject Matter Experts (SMEs) to write tests
• Easy for programmers to codify testing behavior

Fork purpose

The purpose of this fork is to extend the Translator Testing Framework's capabilities to incorporate TranQL queries.

TranQL is a query language for interactive exploration of federated knowledge graphs. Its queries may span multiple reasoners, namely, ICEES, Gamma, RTX, and (partially) Indigo.

To only run TranQL specific tests, run behave features/tranql-invalid-schema.feature features/tranql-reasoners.feature in the root directory.

To run the TranQL tests, you must run the TranQL dev server. You need to use this fork. To run the dev server, follow the installation and usage guide in the repository's readme file. You only need to run the backplane and API.