Set-up the testing environment using [TripalTestSuite v1.1](https://github.com/statonlab/TripalTestSuite).

Specifically, I ran:
1. `composer require statonlab/tripal-test-suite --dev`
2. `./vendor/bin/tripaltest init tripal_blast`
3. Added to my .gitignore as suggested by #2.
That's All! Look how easy TripalTestSuite makes it to get started!

.gitignore

@@ -2,3 +2,8 @@
 # Ignore an internal CViTjs installation.
 # Assumes it's been cloned in the js directory
 js/*
+
+## Ignore PHPUnit Test vendor scripts & environment info.
+.env
+vendor/
+

.travis.yml

@@ -0,0 +1,20 @@
+language: php
+
+# Add php version so composer doesn't complain
+php:
+  - 7.1
+
+services:
+  - docker
+
+env:
+  - DRUPAL_ROOT=/var/www/html
+
+before_script:
+  - docker pull statonlab/tripal3
+
+script:
+  - docker run -it -d --rm --name tripal -v "$(pwd)":/modules/tripal_blast statonlab/tripal3
+  - sleep 30 # We pause here so postgres and apache complete booting up
+  - docker exec -it tripal drush pm-enable -y tripal_blast
+  - docker exec -it tripal bash -c "cd /modules/tripal_blast && composer install && DRUPAL_ROOT=/var/www/html ./vendor/bin/phpunit"

composer.json

@@ -0,0 +1,5 @@
+{
+    "require-dev": {
+        "statonlab/tripal-test-suite": "^1.1"
+    }
+}

composer.lock

@@ -0,0 +1,1953 @@
+{
+    "_readme": [
+        "This file locks the dependencies of your project to a known state",
+        "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#composer-lock-the-lock-file",
+        "This file is @generated automatically"
+    ],
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+            "version": "1.0.5",
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+                "url": "https://github.com/doctrine/instantiator.git",
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+            },
+            "dist": {
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+                "reference": "8e884e78f9f0eb1329e445619e04456e64d8051d",
+                "shasum": ""
+            },
+            "require": {
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+            },
+            "require-dev": {
+                "athletic/athletic": "~0.1.8",
+                "ext-pdo": "*",
+                "ext-phar": "*",
+                "phpunit/phpunit": "~4.0",
+                "squizlabs/php_codesniffer": "~2.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
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+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
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+                    "email": "ocramius@gmail.com",
+                    "homepage": "http://ocramius.github.com/"
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+            ],
+            "description": "A small, lightweight utility to instantiate objects in PHP without invoking their constructors",
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+            "keywords": [
+                "constructor",
+                "instantiate"
+            ],
+            "time": "2015-06-14T21:17:01+00:00"
+        },
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+            "version": "v1.7.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/fzaninotto/Faker.git",
+                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d"
+            },
+            "dist": {
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+                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d",
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+            },
+            "require": {
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+            },
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+                "squizlabs/php_codesniffer": "^1.5"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
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+                }
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+                "psr-4": {
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+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "François Zaninotto"
+                }
+            ],
+            "description": "Faker is a PHP library that generates fake data for you.",
+            "keywords": [
+                "data",
+                "faker",
+                "fixtures"
+            ],
+            "time": "2017-08-15T16:48:10+00:00"
+        },
+        {
+            "name": "guzzlehttp/guzzle",
+            "version": "6.3.3",
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+                "type": "git",
+                "url": "https://github.com/guzzle/guzzle.git",
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+            },
+            "dist": {
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+                "reference": "407b0cb880ace85c9b63c5f9551db498cb2d50ba",
+                "shasum": ""
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+                "guzzlehttp/psr7": "^1.4",
+                "php": ">=5.5"
+            },
+            "require-dev": {
+                "ext-curl": "*",
+                "phpunit/phpunit": "^4.8.35 || ^5.7 || ^6.4 || ^7.0",
+                "psr/log": "^1.0"
+            },
+            "suggest": {
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+            },
+            "type": "library",
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+                }
+            },
+            "autoload": {
+                "files": [
+                    "src/functions_include.php"
+                ],
+                "psr-4": {
+                    "GuzzleHttp\\": "src/"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
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+                    "email": "mtdowling@gmail.com",
+                    "homepage": "https://github.com/mtdowling"
+                }
+            ],
+            "description": "Guzzle is a PHP HTTP client library",
+            "homepage": "http://guzzlephp.org/",
+            "keywords": [
+                "client",
+                "curl",
+                "framework",
+                "http",
+                "http client",
+                "rest",
+                "web service"
+            ],
+            "time": "2018-04-22T15:46:56+00:00"
+        },
+        {
+            "name": "guzzlehttp/promises",
+            "version": "v1.3.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/guzzle/promises.git",
+                "reference": "a59da6cf61d80060647ff4d3eb2c03a2bc694646"
+            },
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+                "reference": "a59da6cf61d80060647ff4d3eb2c03a2bc694646",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.5.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^4.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.4-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "GuzzleHttp\\Promise\\": "src/"
+                },
+                "files": [
+                    "src/functions_include.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Michael Dowling",
+                    "email": "mtdowling@gmail.com",
+                    "homepage": "https://github.com/mtdowling"
+                }
+            ],
+            "description": "Guzzle promises library",
+            "keywords": [
+                "promise"
+            ],
+            "time": "2016-12-20T10:07:11+00:00"
+        },
+        {
+            "name": "guzzlehttp/psr7",
+            "version": "1.4.2",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/guzzle/psr7.git",
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+                "psr/http-message": "~1.0"
+            },
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+            },
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+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.4-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "GuzzleHttp\\Psr7\\": "src/"
+                },
+                "files": [
+                    "src/functions_include.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Michael Dowling",
+                    "email": "mtdowling@gmail.com",
+                    "homepage": "https://github.com/mtdowling"
+                },
+                {
+                    "name": "Tobias Schultze",
+                    "homepage": "https://github.com/Tobion"
+                }
+            ],
+            "description": "PSR-7 message implementation that also provides common utility methods",
+            "keywords": [
+                "http",
+                "message",
+                "request",
+                "response",
+                "stream",
+                "uri",
+                "url"
+            ],
+            "time": "2017-03-20T17:10:46+00:00"
+        },
+        {
+            "name": "myclabs/deep-copy",
+            "version": "1.7.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/myclabs/DeepCopy.git",
+                "reference": "3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/myclabs/DeepCopy/zipball/3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e",
+                "reference": "3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.6 || ^7.0"
+            },
+            "require-dev": {
+                "doctrine/collections": "^1.0",
+                "doctrine/common": "^2.6",
+                "phpunit/phpunit": "^4.1"
+            },
+            "type": "library",
+            "autoload": {
+                "psr-4": {
+                    "DeepCopy\\": "src/DeepCopy/"
+                },
+                "files": [
+                    "src/DeepCopy/deep_copy.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "description": "Create deep copies (clones) of your objects",
+            "keywords": [
+                "clone",
+                "copy",
+                "duplicate",
+                "object",
+                "object graph"
+            ],
+            "time": "2017-10-19T19:58:43+00:00"
+        },
+        {
+            "name": "phpdocumentor/reflection-common",
+            "version": "1.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/ReflectionCommon.git",
+                "reference": "21bdeb5f65d7ebf9f43b1b25d404f87deab5bfb6"
+            },
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+                "shasum": ""
+            },
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+                "php": ">=5.5"
+            },
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+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "phpDocumentor\\Reflection\\": [
+                        "src"
+                    ]
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Jaap van Otterdijk",
+                    "email": "opensource@ijaap.nl"
+                }
+            ],
+            "description": "Common reflection classes used by phpdocumentor to reflect the code structure",
+            "homepage": "http://www.phpdoc.org",
+            "keywords": [
+                "FQSEN",
+                "phpDocumentor",
+                "phpdoc",
+                "reflection",
+                "static analysis"
+            ],
+            "time": "2017-09-11T18:02:19+00:00"
+        },
+        {
+            "name": "phpdocumentor/reflection-docblock",
+            "version": "3.3.2",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/ReflectionDocBlock.git",
+                "reference": "bf329f6c1aadea3299f08ee804682b7c45b326a2"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phpDocumentor/ReflectionDocBlock/zipball/bf329f6c1aadea3299f08ee804682b7c45b326a2",
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+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.6 || ^7.0",
+                "phpdocumentor/reflection-common": "^1.0.0",
+                "phpdocumentor/type-resolver": "^0.4.0",
+                "webmozart/assert": "^1.0"
+            },
+            "require-dev": {
+                "mockery/mockery": "^0.9.4",
+                "phpunit/phpunit": "^4.4"
+            },
+            "type": "library",
+            "autoload": {
+                "psr-4": {
+                    "phpDocumentor\\Reflection\\": [
+                        "src/"
+                    ]
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Mike van Riel",
+                    "email": "me@mikevanriel.com"
+                }
+            ],
+            "description": "With this component, a library can provide support for annotations via DocBlocks or otherwise retrieve information that is embedded in a DocBlock.",
+            "time": "2017-11-10T14:09:06+00:00"
+        },
+        {
+            "name": "phpdocumentor/type-resolver",
+            "version": "0.4.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/TypeResolver.git",
+                "reference": "9c977708995954784726e25d0cd1dddf4e65b0f7"
+            },
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+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.5 || ^7.0",
+                "phpdocumentor/reflection-common": "^1.0"
+            },
+            "require-dev": {
+                "mockery/mockery": "^0.9.4",
+                "phpunit/phpunit": "^5.2||^4.8.24"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "phpDocumentor\\Reflection\\": [
+                        "src/"
+                    ]
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Mike van Riel",
+                    "email": "me@mikevanriel.com"
+                }
+            ],
+            "time": "2017-07-14T14:27:02+00:00"
+        },
+        {
+            "name": "phpspec/prophecy",
+            "version": "1.7.6",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpspec/prophecy.git",
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+                "sebastian/recursion-context": "^1.0|^2.0|^3.0"
+            },
+            "require-dev": {
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+                "phpunit/phpunit": "^4.8.35 || ^5.7 || ^6.5"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.7.x-dev"
+                }
+            },
+            "autoload": {
+                "psr-0": {
+                    "Prophecy\\": "src/"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Konstantin Kudryashov",
+                    "email": "ever.zet@gmail.com",
+                    "homepage": "http://everzet.com"
+                },
+                {
+                    "name": "Marcello Duarte",
+                    "email": "marcello.duarte@gmail.com"
+                }
+            ],
+            "description": "Highly opinionated mocking framework for PHP 5.3+",
+            "homepage": "https://github.com/phpspec/prophecy",
+            "keywords": [
+                "Double",
+                "Dummy",
+                "fake",
+                "mock",
+                "spy",
+                "stub"
+            ],
+            "time": "2018-04-18T13:57:24+00:00"
+        },
+        {
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+            "version": "4.0.8",
+            "source": {
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+                "url": "https://github.com/sebastianbergmann/php-code-coverage.git",
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+            },
+            "require": {
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+                "phpunit/php-file-iterator": "^1.3",
+                "phpunit/php-text-template": "^1.2",
+                "phpunit/php-token-stream": "^1.4.2 || ^2.0",
+                "sebastian/code-unit-reverse-lookup": "^1.0",
+                "sebastian/environment": "^1.3.2 || ^2.0",
+                "sebastian/version": "^1.0 || ^2.0"
+            },
+            "require-dev": {
+                "ext-xdebug": "^2.1.4",
+                "phpunit/phpunit": "^5.7"
+            },
+            "suggest": {
+                "ext-xdebug": "^2.5.1"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "4.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sb@sebastian-bergmann.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Library that provides collection, processing, and rendering functionality for PHP code coverage information.",
+            "homepage": "https://github.com/sebastianbergmann/php-code-coverage",
+            "keywords": [
+                "coverage",
+                "testing",
+                "xunit"
+            ],
+            "time": "2017-04-02T07:44:40+00:00"
+        },
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+            "version": "1.4.5",
+            "source": {
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+    "stability-flags": [],
+    "prefer-stable": false,
+    "prefer-lowest": false,
+    "platform": [],
+    "platform-dev": []
+}

phpunit.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:noNamespaceSchemaLocation="phpunit.xsd"
+         convertErrorsToExceptions="true"
+         convertNoticesToExceptions="true"
+         convertWarningsToExceptions="true"
+         bootstrap="tests/bootstrap.php"
+         verbose="true"
+         colors="true">
+  <testsuites>
+    <testsuite name="default">
+      <directory suffix="Test.php">tests</directory>
+    </testsuite>
+  </testsuites>
+</phpunit>

tests/DataFactory.php

@@ -0,0 +1,73 @@
+<?php
+
+use StatonLab\TripalTestSuite\Database\Factory;
+
+/**
+ * Data Factory
+ * -----------------------------------------------------------
+ * This is where you can define factories for use in tests and
+ * database seeders.
+ *
+ * @docs https://github.com/statonlab/TripalTestSuite
+ */
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.cv', function (Faker\Generator $faker) {
+    return [
+        'name' => $faker->name,
+        'definition' => $faker->text,
+    ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.db', function (Faker\Generator $faker) {
+    return [
+        'name' => $faker->name,
+        'description' => $faker->text,
+        'urlprefix' => $faker->url,
+        'url' => $faker->url,
+    ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.dbxref', function (Faker\Generator $faker) {
+    return [
+        'db_id' => factory('chado.db')->create()->db_id,
+        'accession' => $faker->numberBetween(),
+        'version' => $faker->numberBetween(),
+        'description' => $faker->text,
+    ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.cvterm', function (Faker\Generator $faker) {
+    return [
+        'cv_id' => factory('chado.cv')->create()->cv_id,
+        'dbxref_id' => factory('chado.dbxref')->create()->dbxref_id,
+        'name' => $faker->name,
+        'definition' => $faker->text,
+        'is_obsolete' => 0,
+        'is_relationshiptype' => 0,
+    ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.organism', function (Faker\Generator $faker) {
+    return [
+        'abbreviation' => $faker->name,
+        'genus' => $faker->name,
+        'species' => $faker->name,
+        'common_name' => $faker->name,
+        'type_id' => factory('chado.cvterm')->create()->cvterm_id,
+    ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.feature', function (Faker\Generator $faker) {
+    return [
+        'name' => $faker->name,
+        'uniquename' => $faker->unique()->name,
+        'organism_id' => factory('chado.organism')->create()->organism_id,
+        'type_id' => factory('chado.cvterm')->create()->cvterm_id,
+    ];
+});

tests/DatabaseSeeders/UsersTableSeeder.php

@@ -0,0 +1,28 @@
+<?php
+
+namespace Tests\DatabaseSeeders;
+
+use StatonLab\TripalTestSuite\Database\Seeder;
+
+class UsersTableSeeder extends Seeder
+{
+    /**
+     * Seeds the database with users.
+     */
+    public function up()
+    {
+        $new_user = [
+            'name' => 'test user',
+            'pass' => 'secret',
+            'mail' => 'test@example.com',
+            'status' => 1,
+            'init' => 'Email',
+            'roles' => [
+                DRUPAL_AUTHENTICATED_RID => 'authenticated user',
+            ],
+        ];
+
+        // The first parameter is sent blank so a new user is created.
+        user_save(new \stdClass(), $new_user);
+    }
+}

tests/ExampleTest.php

@@ -0,0 +1,25 @@
+<?php
+
+namespace Tests;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+/**
+ * Class ExampleTest
+ *
+ * Note that test classes must have a suffix of Test.php and the filename
+ * must match the class name.
+ *
+ * @package Tests
+ */
+class ExampleTest extends TripalTestCase {
+  /**
+   * Basic test example.
+   * Tests must begin with the word "test".
+   * See https://phpunit.readthedocs.io/en/latest/ for more information.
+   */
+  public function testBasicExample() {
+    $this->assertTrue(true);
+  }
+}

tests/bootstrap.php

@@ -0,0 +1,4 @@
+<?php
+require_once __DIR__.'/../vendor/autoload.php';
+
+new \StatonLab\TripalTestSuite\TripalTestBootstrap();

tests/example.env

@@ -0,0 +1,3 @@
+BASE_URL=http://localhost
+DRUPAL_ROOT=/var/www/html
+FAKER_LOCALE=en_US