redo test setup

.gitignore

@@ -1,4 +1,3 @@
 .DS_Store
-composer.lock
 vendor/*
 tests/.env

.travis.yml

@@ -7,6 +7,8 @@ sudo: required
 
 before_script:
   - docker pull statonlab/drupal7
+  - docker pull statonlab/tripal2
+  - docker pull statonlab/tripal3
 
 script:
   # Set branch name
@@ -28,8 +30,7 @@ script:
   # Run PHPUnit tests
   - docker exec -it tripal3 bash -c "cd /modules/tripal && composer install && DRUPAL_ROOT=/var/www/html ./vendor/bin/phpunit"
   # Test Tripal v2 to v3 upgrade steps
-  - git checkout 7.x-2.x
+  - docker run -it -d --rm --name tripal2 -v "$(pwd)":/modules/tripal statonlab/tripal2
-  - docker run -it -d --rm --name tripal2 -v "$(pwd)":/modules/tripal statonlab/drupal7
   - sleep 15
   - docker exec -it tripal2 drush en -y tripal_core
   - docker exec -it tripal2 drush pm-disable tripal_core -y

README.md

@@ -66,7 +66,7 @@ http://tripal.info/tutorials/v2.0/installation
 
 
 # Upgrade from Tripal v2.x to v3.x
-Note:  Upgrade can only be performed using 'drush' command.
+Note:  Upgrade can only be performed using the `drush` command.
 
 Note: Deprecated API functions from Tripal v1.x have been removed from Tripal
 v3.  Therefore, use of deprecated API functions in templates or custom 
@@ -80,24 +80,27 @@ Step 1: Put the site in maintenance mode.
 Step 2: Disable tripal modules. Disabling the core module will disable all
 other Tripal modules:
 
-  drush pm-disable tripal_core
+  `drush pm-disable tripal_core`
   
 Step 3: Remove old Tripal v2 package and replace with Tripal v3 package
 Step 4: Enable the tripal module
 
-  drush pm-enable tripal
+  `drush pm-enable tripal`
  
 Step 5: Enable the tripal_chado module  
 
-  drush pm-enable tripal_chado
+  `drush pm-enable tripal_chado`
   
 Step 6:  Tripal v2 modules are now called 'legacy modules'. these are the
 modules that were disabled in step #2.  For backwards compatibility, you 
 should re-enable these modules:
 
+```
   drush pm-enable tripal_core, tripal_views, tripal_db, tripal_cv, \
     tripal_analysis, tripal_organism, tripal_feature, tripal_pub, \
     tripal_stock
+```
+
 
 Be sure to enable any additional modules not included in the example
 drush command above.
@@ -117,7 +120,7 @@ Developer's Handbook for additional details.
 
 # Development Testing
 
-To run PHP unit tests on your local system, simply create a `.env` file in your `/Tests/` directory that defines the `DRUPAL_ROOT` variable, for example 
+To run PHP unit tests on your local system, run `composer install` to install developer-specific requirements.  Next, create a `.env` file in your `/Tests/` directory that defines the `DRUPAL_ROOT` variable, for example 
 
 ```
 DRUPAL_ROOT=/var/www/html

composer.json

@@ -1,5 +1,6 @@
 {
   "require-dev": {
-    "phpunit/phpunit": "^7"
+    "phpunit/phpunit": "^7",
+    "statonlab/tripal-test-suite": "^0.3.0"
   }
 }

composer.lock

@@ -0,0 +1,1696 @@
+{
+    "_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"
+    ],
+    "content-hash": "9a8fda4f357b1982844a9b7df2d3b1ba",
+    "packages": [],
+    "packages-dev": [
+        {
+            "name": "doctrine/instantiator",
+            "version": "1.1.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/doctrine/instantiator.git",
+                "reference": "185b8868aa9bf7159f5f953ed5afb2d7fcdc3bda"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/doctrine/instantiator/zipball/185b8868aa9bf7159f5f953ed5afb2d7fcdc3bda",
+                "reference": "185b8868aa9bf7159f5f953ed5afb2d7fcdc3bda",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1"
+            },
+            "require-dev": {
+                "athletic/athletic": "~0.1.8",
+                "ext-pdo": "*",
+                "ext-phar": "*",
+                "phpunit/phpunit": "^6.2.3",
+                "squizlabs/php_codesniffer": "^3.0.2"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.2.x-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Doctrine\\Instantiator\\": "src/Doctrine/Instantiator/"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Marco Pivetta",
+                    "email": "ocramius@gmail.com",
+                    "homepage": "http://ocramius.github.com/"
+                }
+            ],
+            "description": "A small, lightweight utility to instantiate objects in PHP without invoking their constructors",
+            "homepage": "https://github.com/doctrine/instantiator",
+            "keywords": [
+                "constructor",
+                "instantiate"
+            ],
+            "time": "2017-07-22T11:58:36+00:00"
+        },
+        {
+            "name": "fzaninotto/faker",
+            "version": "v1.7.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/fzaninotto/Faker.git",
+                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/fzaninotto/Faker/zipball/d3ed4cc37051c1ca52d22d76b437d14809fc7e0d",
+                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.3.3 || ^7.0"
+            },
+            "require-dev": {
+                "ext-intl": "*",
+                "phpunit/phpunit": "^4.0 || ^5.0",
+                "squizlabs/php_codesniffer": "^1.5"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.8-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Faker\\": "src/Faker/"
+                }
+            },
+            "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": "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": "phar-io/manifest",
+            "version": "1.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phar-io/manifest.git",
+                "reference": "2df402786ab5368a0169091f61a7c1e0eb6852d0"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phar-io/manifest/zipball/2df402786ab5368a0169091f61a7c1e0eb6852d0",
+                "reference": "2df402786ab5368a0169091f61a7c1e0eb6852d0",
+                "shasum": ""
+            },
+            "require": {
+                "ext-dom": "*",
+                "ext-phar": "*",
+                "phar-io/version": "^1.0.1",
+                "php": "^5.6 || ^7.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Arne Blankerts",
+                    "email": "arne@blankerts.de",
+                    "role": "Developer"
+                },
+                {
+                    "name": "Sebastian Heuer",
+                    "email": "sebastian@phpeople.de",
+                    "role": "Developer"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "Developer"
+                }
+            ],
+            "description": "Component for reading phar.io manifest information from a PHP Archive (PHAR)",
+            "time": "2017-03-05T18:14:27+00:00"
+        },
+        {
+            "name": "phar-io/version",
+            "version": "1.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phar-io/version.git",
+                "reference": "a70c0ced4be299a63d32fa96d9281d03e94041df"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phar-io/version/zipball/a70c0ced4be299a63d32fa96d9281d03e94041df",
+                "reference": "a70c0ced4be299a63d32fa96d9281d03e94041df",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.6 || ^7.0"
+            },
+            "type": "library",
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Arne Blankerts",
+                    "email": "arne@blankerts.de",
+                    "role": "Developer"
+                },
+                {
+                    "name": "Sebastian Heuer",
+                    "email": "sebastian@phpeople.de",
+                    "role": "Developer"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "Developer"
+                }
+            ],
+            "description": "Library for handling version information and constraints",
+            "time": "2017-03-05T17:38:23+00:00"
+        },
+        {
+            "name": "phpdocumentor/reflection-common",
+            "version": "1.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/ReflectionCommon.git",
+                "reference": "21bdeb5f65d7ebf9f43b1b25d404f87deab5bfb6"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phpDocumentor/ReflectionCommon/zipball/21bdeb5f65d7ebf9f43b1b25d404f87deab5bfb6",
+                "reference": "21bdeb5f65d7ebf9f43b1b25d404f87deab5bfb6",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.5"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^4.6"
+            },
+            "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": "4.3.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/ReflectionDocBlock.git",
+                "reference": "94fd0001232e47129dd3504189fa1c7225010d08"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phpDocumentor/ReflectionDocBlock/zipball/94fd0001232e47129dd3504189fa1c7225010d08",
+                "reference": "94fd0001232e47129dd3504189fa1c7225010d08",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0",
+                "phpdocumentor/reflection-common": "^1.0.0",
+                "phpdocumentor/type-resolver": "^0.4.0",
+                "webmozart/assert": "^1.0"
+            },
+            "require-dev": {
+                "doctrine/instantiator": "~1.0.5",
+                "mockery/mockery": "^1.0",
+                "phpunit/phpunit": "^6.4"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "4.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"
+                }
+            ],
+            "description": "With this component, a library can provide support for annotations via DocBlocks or otherwise retrieve information that is embedded in a DocBlock.",
+            "time": "2017-11-30T07:14:17+00:00"
+        },
+        {
+            "name": "phpdocumentor/type-resolver",
+            "version": "0.4.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/phpDocumentor/TypeResolver.git",
+                "reference": "9c977708995954784726e25d0cd1dddf4e65b0f7"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phpDocumentor/TypeResolver/zipball/9c977708995954784726e25d0cd1dddf4e65b0f7",
+                "reference": "9c977708995954784726e25d0cd1dddf4e65b0f7",
+                "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",
+                "reference": "33a7e3c4fda54e912ff6338c48823bd5c0f0b712"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/phpspec/prophecy/zipball/33a7e3c4fda54e912ff6338c48823bd5c0f0b712",
+                "reference": "33a7e3c4fda54e912ff6338c48823bd5c0f0b712",
+                "shasum": ""
+            },
+            "require": {
+                "doctrine/instantiator": "^1.0.2",
+                "php": "^5.3|^7.0",
+                "phpdocumentor/reflection-docblock": "^2.0|^3.0.2|^4.0",
+                "sebastian/comparator": "^1.1|^2.0|^3.0",
+                "sebastian/recursion-context": "^1.0|^2.0|^3.0"
+            },
+            "require-dev": {
+                "phpspec/phpspec": "^2.5|^3.2",
+                "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"
+        },
+        {
+            "name": "phpunit/php-code-coverage",
+            "version": "6.0.4",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/php-code-coverage.git",
+                "reference": "52187754b0eed0b8159f62a6fa30073327e8c2ca"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-code-coverage/zipball/52187754b0eed0b8159f62a6fa30073327e8c2ca",
+                "reference": "52187754b0eed0b8159f62a6fa30073327e8c2ca",
+                "shasum": ""
+            },
+            "require": {
+                "ext-dom": "*",
+                "ext-xmlwriter": "*",
+                "php": "^7.1",
+                "phpunit/php-file-iterator": "^1.4.2",
+                "phpunit/php-text-template": "^1.2.1",
+                "phpunit/php-token-stream": "^3.0",
+                "sebastian/code-unit-reverse-lookup": "^1.0.1",
+                "sebastian/environment": "^3.1",
+                "sebastian/version": "^2.0.1",
+                "theseer/tokenizer": "^1.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.0"
+            },
+            "suggest": {
+                "ext-xdebug": "^2.6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "6.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.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": "2018-04-29T14:59:09+00:00"
+        },
+        {
+            "name": "phpunit/php-file-iterator",
+            "version": "1.4.5",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/php-file-iterator.git",
+                "reference": "730b01bc3e867237eaac355e06a36b85dd93a8b4"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-file-iterator/zipball/730b01bc3e867237eaac355e06a36b85dd93a8b4",
+                "reference": "730b01bc3e867237eaac355e06a36b85dd93a8b4",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.3"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.4.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": "FilterIterator implementation that filters files based on a list of suffixes.",
+            "homepage": "https://github.com/sebastianbergmann/php-file-iterator/",
+            "keywords": [
+                "filesystem",
+                "iterator"
+            ],
+            "time": "2017-11-27T13:52:08+00:00"
+        },
+        {
+            "name": "phpunit/php-text-template",
+            "version": "1.2.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/php-text-template.git",
+                "reference": "31f8b717e51d9a2afca6c9f046f5d69fc27c8686"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-text-template/zipball/31f8b717e51d9a2afca6c9f046f5d69fc27c8686",
+                "reference": "31f8b717e51d9a2afca6c9f046f5d69fc27c8686",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.3"
+            },
+            "type": "library",
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Simple template engine.",
+            "homepage": "https://github.com/sebastianbergmann/php-text-template/",
+            "keywords": [
+                "template"
+            ],
+            "time": "2015-06-21T13:50:34+00:00"
+        },
+        {
+            "name": "phpunit/php-timer",
+            "version": "2.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/php-timer.git",
+                "reference": "8b8454ea6958c3dee38453d3bd571e023108c91f"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-timer/zipball/8b8454ea6958c3dee38453d3bd571e023108c91f",
+                "reference": "8b8454ea6958c3dee38453d3bd571e023108c91f",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "2.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Utility class for timing",
+            "homepage": "https://github.com/sebastianbergmann/php-timer/",
+            "keywords": [
+                "timer"
+            ],
+            "time": "2018-02-01T13:07:23+00:00"
+        },
+        {
+            "name": "phpunit/php-token-stream",
+            "version": "3.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/php-token-stream.git",
+                "reference": "21ad88bbba7c3d93530d93994e0a33cd45f02ace"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-token-stream/zipball/21ad88bbba7c3d93530d93994e0a33cd45f02ace",
+                "reference": "21ad88bbba7c3d93530d93994e0a33cd45f02ace",
+                "shasum": ""
+            },
+            "require": {
+                "ext-tokenizer": "*",
+                "php": "^7.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Wrapper around PHP's tokenizer extension.",
+            "homepage": "https://github.com/sebastianbergmann/php-token-stream/",
+            "keywords": [
+                "tokenizer"
+            ],
+            "time": "2018-02-01T13:16:43+00:00"
+        },
+        {
+            "name": "phpunit/phpunit",
+            "version": "7.1.5",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/phpunit.git",
+                "reference": "ca64dba53b88aba6af32aebc6b388068db95c435"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/phpunit/zipball/ca64dba53b88aba6af32aebc6b388068db95c435",
+                "reference": "ca64dba53b88aba6af32aebc6b388068db95c435",
+                "shasum": ""
+            },
+            "require": {
+                "ext-dom": "*",
+                "ext-json": "*",
+                "ext-libxml": "*",
+                "ext-mbstring": "*",
+                "ext-xml": "*",
+                "myclabs/deep-copy": "^1.6.1",
+                "phar-io/manifest": "^1.0.1",
+                "phar-io/version": "^1.0",
+                "php": "^7.1",
+                "phpspec/prophecy": "^1.7",
+                "phpunit/php-code-coverage": "^6.0.1",
+                "phpunit/php-file-iterator": "^1.4.3",
+                "phpunit/php-text-template": "^1.2.1",
+                "phpunit/php-timer": "^2.0",
+                "phpunit/phpunit-mock-objects": "^6.1.1",
+                "sebastian/comparator": "^3.0",
+                "sebastian/diff": "^3.0",
+                "sebastian/environment": "^3.1",
+                "sebastian/exporter": "^3.1",
+                "sebastian/global-state": "^2.0",
+                "sebastian/object-enumerator": "^3.0.3",
+                "sebastian/resource-operations": "^1.0",
+                "sebastian/version": "^2.0.1"
+            },
+            "require-dev": {
+                "ext-pdo": "*"
+            },
+            "suggest": {
+                "ext-xdebug": "*",
+                "phpunit/php-invoker": "^2.0"
+            },
+            "bin": [
+                "phpunit"
+            ],
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "7.1-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "The PHP Unit Testing framework.",
+            "homepage": "https://phpunit.de/",
+            "keywords": [
+                "phpunit",
+                "testing",
+                "xunit"
+            ],
+            "time": "2018-04-29T15:09:19+00:00"
+        },
+        {
+            "name": "phpunit/phpunit-mock-objects",
+            "version": "6.1.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/phpunit-mock-objects.git",
+                "reference": "70c740bde8fd9ea9ea295be1cd875dd7b267e157"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/phpunit-mock-objects/zipball/70c740bde8fd9ea9ea295be1cd875dd7b267e157",
+                "reference": "70c740bde8fd9ea9ea295be1cd875dd7b267e157",
+                "shasum": ""
+            },
+            "require": {
+                "doctrine/instantiator": "^1.0.5",
+                "php": "^7.1",
+                "phpunit/php-text-template": "^1.2.1",
+                "sebastian/exporter": "^3.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.0"
+            },
+            "suggest": {
+                "ext-soap": "*"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "6.1-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Mock Object library for PHPUnit",
+            "homepage": "https://github.com/sebastianbergmann/phpunit-mock-objects/",
+            "keywords": [
+                "mock",
+                "xunit"
+            ],
+            "time": "2018-04-11T04:50:36+00:00"
+        },
+        {
+            "name": "sebastian/code-unit-reverse-lookup",
+            "version": "1.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/code-unit-reverse-lookup.git",
+                "reference": "4419fcdb5eabb9caa61a27c7a1db532a6b55dd18"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/code-unit-reverse-lookup/zipball/4419fcdb5eabb9caa61a27c7a1db532a6b55dd18",
+                "reference": "4419fcdb5eabb9caa61a27c7a1db532a6b55dd18",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.6 || ^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^5.7 || ^6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Looks up which function or method a line of code belongs to",
+            "homepage": "https://github.com/sebastianbergmann/code-unit-reverse-lookup/",
+            "time": "2017-03-04T06:30:41+00:00"
+        },
+        {
+            "name": "sebastian/comparator",
+            "version": "3.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/comparator.git",
+                "reference": "ed5fd2281113729f1ebcc64d101ad66028aeb3d5"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/comparator/zipball/ed5fd2281113729f1ebcc64d101ad66028aeb3d5",
+                "reference": "ed5fd2281113729f1ebcc64d101ad66028aeb3d5",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1",
+                "sebastian/diff": "^3.0",
+                "sebastian/exporter": "^3.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.1"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Jeff Welch",
+                    "email": "whatthejeff@gmail.com"
+                },
+                {
+                    "name": "Volker Dusch",
+                    "email": "github@wallbash.com"
+                },
+                {
+                    "name": "Bernhard Schussek",
+                    "email": "bschussek@2bepublished.at"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Provides the functionality to compare PHP values for equality",
+            "homepage": "https://github.com/sebastianbergmann/comparator",
+            "keywords": [
+                "comparator",
+                "compare",
+                "equality"
+            ],
+            "time": "2018-04-18T13:33:00+00:00"
+        },
+        {
+            "name": "sebastian/diff",
+            "version": "3.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/diff.git",
+                "reference": "e09160918c66281713f1c324c1f4c4c3037ba1e8"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/diff/zipball/e09160918c66281713f1c324c1f4c4c3037ba1e8",
+                "reference": "e09160918c66281713f1c324c1f4c4c3037ba1e8",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^7.0",
+                "symfony/process": "^2 || ^3.3 || ^4"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Kore Nordmann",
+                    "email": "mail@kore-nordmann.de"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Diff implementation",
+            "homepage": "https://github.com/sebastianbergmann/diff",
+            "keywords": [
+                "diff",
+                "udiff",
+                "unidiff",
+                "unified diff"
+            ],
+            "time": "2018-02-01T13:45:15+00:00"
+        },
+        {
+            "name": "sebastian/environment",
+            "version": "3.1.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/environment.git",
+                "reference": "cd0871b3975fb7fc44d11314fd1ee20925fce4f5"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/environment/zipball/cd0871b3975fb7fc44d11314fd1ee20925fce4f5",
+                "reference": "cd0871b3975fb7fc44d11314fd1ee20925fce4f5",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^6.1"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.1.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Provides functionality to handle HHVM/PHP environments",
+            "homepage": "http://www.github.com/sebastianbergmann/environment",
+            "keywords": [
+                "Xdebug",
+                "environment",
+                "hhvm"
+            ],
+            "time": "2017-07-01T08:51:00+00:00"
+        },
+        {
+            "name": "sebastian/exporter",
+            "version": "3.1.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/exporter.git",
+                "reference": "234199f4528de6d12aaa58b612e98f7d36adb937"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/exporter/zipball/234199f4528de6d12aaa58b612e98f7d36adb937",
+                "reference": "234199f4528de6d12aaa58b612e98f7d36adb937",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0",
+                "sebastian/recursion-context": "^3.0"
+            },
+            "require-dev": {
+                "ext-mbstring": "*",
+                "phpunit/phpunit": "^6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.1.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Jeff Welch",
+                    "email": "whatthejeff@gmail.com"
+                },
+                {
+                    "name": "Volker Dusch",
+                    "email": "github@wallbash.com"
+                },
+                {
+                    "name": "Bernhard Schussek",
+                    "email": "bschussek@2bepublished.at"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                },
+                {
+                    "name": "Adam Harvey",
+                    "email": "aharvey@php.net"
+                }
+            ],
+            "description": "Provides the functionality to export PHP variables for visualization",
+            "homepage": "http://www.github.com/sebastianbergmann/exporter",
+            "keywords": [
+                "export",
+                "exporter"
+            ],
+            "time": "2017-04-03T13:19:02+00:00"
+        },
+        {
+            "name": "sebastian/global-state",
+            "version": "2.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/global-state.git",
+                "reference": "e8ba02eed7bbbb9e59e43dedd3dddeff4a56b0c4"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/global-state/zipball/e8ba02eed7bbbb9e59e43dedd3dddeff4a56b0c4",
+                "reference": "e8ba02eed7bbbb9e59e43dedd3dddeff4a56b0c4",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^6.0"
+            },
+            "suggest": {
+                "ext-uopz": "*"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "2.0-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Snapshotting of global state",
+            "homepage": "http://www.github.com/sebastianbergmann/global-state",
+            "keywords": [
+                "global state"
+            ],
+            "time": "2017-04-27T15:39:26+00:00"
+        },
+        {
+            "name": "sebastian/object-enumerator",
+            "version": "3.0.3",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/object-enumerator.git",
+                "reference": "7cfd9e65d11ffb5af41198476395774d4c8a84c5"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/object-enumerator/zipball/7cfd9e65d11ffb5af41198476395774d4c8a84c5",
+                "reference": "7cfd9e65d11ffb5af41198476395774d4c8a84c5",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0",
+                "sebastian/object-reflector": "^1.1.1",
+                "sebastian/recursion-context": "^3.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Traverses array structures and object graphs to enumerate all referenced objects",
+            "homepage": "https://github.com/sebastianbergmann/object-enumerator/",
+            "time": "2017-08-03T12:35:26+00:00"
+        },
+        {
+            "name": "sebastian/object-reflector",
+            "version": "1.1.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/object-reflector.git",
+                "reference": "773f97c67f28de00d397be301821b06708fca0be"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/object-reflector/zipball/773f97c67f28de00d397be301821b06708fca0be",
+                "reference": "773f97c67f28de00d397be301821b06708fca0be",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.1-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Allows reflection of object attributes, including inherited and non-public ones",
+            "homepage": "https://github.com/sebastianbergmann/object-reflector/",
+            "time": "2017-03-29T09:07:27+00:00"
+        },
+        {
+            "name": "sebastian/recursion-context",
+            "version": "3.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/recursion-context.git",
+                "reference": "5b0cd723502bac3b006cbf3dbf7a1e3fcefe4fa8"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/recursion-context/zipball/5b0cd723502bac3b006cbf3dbf7a1e3fcefe4fa8",
+                "reference": "5b0cd723502bac3b006cbf3dbf7a1e3fcefe4fa8",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "3.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Jeff Welch",
+                    "email": "whatthejeff@gmail.com"
+                },
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                },
+                {
+                    "name": "Adam Harvey",
+                    "email": "aharvey@php.net"
+                }
+            ],
+            "description": "Provides functionality to recursively process PHP variables",
+            "homepage": "http://www.github.com/sebastianbergmann/recursion-context",
+            "time": "2017-03-03T06:23:57+00:00"
+        },
+        {
+            "name": "sebastian/resource-operations",
+            "version": "1.0.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/resource-operations.git",
+                "reference": "ce990bb21759f94aeafd30209e8cfcdfa8bc3f52"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/resource-operations/zipball/ce990bb21759f94aeafd30209e8cfcdfa8bc3f52",
+                "reference": "ce990bb21759f94aeafd30209e8cfcdfa8bc3f52",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.6.0"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de"
+                }
+            ],
+            "description": "Provides a list of PHP built-in functions that operate on resources",
+            "homepage": "https://www.github.com/sebastianbergmann/resource-operations",
+            "time": "2015-07-28T20:34:47+00:00"
+        },
+        {
+            "name": "sebastian/version",
+            "version": "2.0.1",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/sebastianbergmann/version.git",
+                "reference": "99732be0ddb3361e16ad77b68ba41efc8e979019"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/sebastianbergmann/version/zipball/99732be0ddb3361e16ad77b68ba41efc8e979019",
+                "reference": "99732be0ddb3361e16ad77b68ba41efc8e979019",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.6"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "2.0.x-dev"
+                }
+            },
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Sebastian Bergmann",
+                    "email": "sebastian@phpunit.de",
+                    "role": "lead"
+                }
+            ],
+            "description": "Library that helps with managing the version number of Git-hosted PHP projects",
+            "homepage": "https://github.com/sebastianbergmann/version",
+            "time": "2016-10-03T07:35:21+00:00"
+        },
+        {
+            "name": "statonlab/tripal-test-suite",
+            "version": "0.3.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/statonlab/TripalTestSuite.git",
+                "reference": "260d5bf0fc68adff44354ce1dd66598daf6d61db"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/statonlab/TripalTestSuite/zipball/260d5bf0fc68adff44354ce1dd66598daf6d61db",
+                "reference": "260d5bf0fc68adff44354ce1dd66598daf6d61db",
+                "shasum": ""
+            },
+            "require": {
+                "fzaninotto/faker": "^1.7",
+                "phpunit/phpunit": "^5 || ^6 || ^7.0",
+                "symfony/console": "^3 || ^4.0"
+            },
+            "bin": [
+                "tripaltest"
+            ],
+            "type": "library",
+            "autoload": {
+                "psr-4": {
+                    "StatonLab\\TripalTestSuite\\": "src/"
+                },
+                "files": [
+                    "src/Helpers/helpers.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "GPL-3.0"
+            ],
+            "authors": [
+                {
+                    "name": "Abdullah Almsaeed",
+                    "email": "aalmsaee@utk.edu"
+                },
+                {
+                    "name": "Bradford Condon",
+                    "email": "bcondon@utk.edu"
+                }
+            ],
+            "time": "2018-04-18T15:56:58+00:00"
+        },
+        {
+            "name": "symfony/console",
+            "version": "v4.0.9",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/symfony/console.git",
+                "reference": "3e820bc2c520a87ca209ad8fa961c97f42e0b4ae"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/symfony/console/zipball/3e820bc2c520a87ca209ad8fa961c97f42e0b4ae",
+                "reference": "3e820bc2c520a87ca209ad8fa961c97f42e0b4ae",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1.3",
+                "symfony/polyfill-mbstring": "~1.0"
+            },
+            "conflict": {
+                "symfony/dependency-injection": "<3.4",
+                "symfony/process": "<3.3"
+            },
+            "require-dev": {
+                "psr/log": "~1.0",
+                "symfony/config": "~3.4|~4.0",
+                "symfony/dependency-injection": "~3.4|~4.0",
+                "symfony/event-dispatcher": "~3.4|~4.0",
+                "symfony/lock": "~3.4|~4.0",
+                "symfony/process": "~3.4|~4.0"
+            },
+            "suggest": {
+                "psr/log-implementation": "For using the console logger",
+                "symfony/event-dispatcher": "",
+                "symfony/lock": "",
+                "symfony/process": ""
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "4.0-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Symfony\\Component\\Console\\": ""
+                },
+                "exclude-from-classmap": [
+                    "/Tests/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Fabien Potencier",
+                    "email": "fabien@symfony.com"
+                },
+                {
+                    "name": "Symfony Community",
+                    "homepage": "https://symfony.com/contributors"
+                }
+            ],
+            "description": "Symfony Console Component",
+            "homepage": "https://symfony.com",
+            "time": "2018-04-30T01:23:47+00:00"
+        },
+        {
+            "name": "symfony/polyfill-mbstring",
+            "version": "v1.7.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/symfony/polyfill-mbstring.git",
+                "reference": "78be803ce01e55d3491c1397cf1c64beb9c1b63b"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/78be803ce01e55d3491c1397cf1c64beb9c1b63b",
+                "reference": "78be803ce01e55d3491c1397cf1c64beb9c1b63b",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.3"
+            },
+            "suggest": {
+                "ext-mbstring": "For best performance"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.7-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Symfony\\Polyfill\\Mbstring\\": ""
+                },
+                "files": [
+                    "bootstrap.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Nicolas Grekas",
+                    "email": "p@tchwork.com"
+                },
+                {
+                    "name": "Symfony Community",
+                    "homepage": "https://symfony.com/contributors"
+                }
+            ],
+            "description": "Symfony polyfill for the Mbstring extension",
+            "homepage": "https://symfony.com",
+            "keywords": [
+                "compatibility",
+                "mbstring",
+                "polyfill",
+                "portable",
+                "shim"
+            ],
+            "time": "2018-01-30T19:27:44+00:00"
+        },
+        {
+            "name": "theseer/tokenizer",
+            "version": "1.1.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/theseer/tokenizer.git",
+                "reference": "cb2f008f3f05af2893a87208fe6a6c4985483f8b"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/theseer/tokenizer/zipball/cb2f008f3f05af2893a87208fe6a6c4985483f8b",
+                "reference": "cb2f008f3f05af2893a87208fe6a6c4985483f8b",
+                "shasum": ""
+            },
+            "require": {
+                "ext-dom": "*",
+                "ext-tokenizer": "*",
+                "ext-xmlwriter": "*",
+                "php": "^7.0"
+            },
+            "type": "library",
+            "autoload": {
+                "classmap": [
+                    "src/"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "BSD-3-Clause"
+            ],
+            "authors": [
+                {
+                    "name": "Arne Blankerts",
+                    "email": "arne@blankerts.de",
+                    "role": "Developer"
+                }
+            ],
+            "description": "A small library for converting tokenized PHP source code into XML and potentially other formats",
+            "time": "2017-04-07T12:08:54+00:00"
+        },
+        {
+            "name": "webmozart/assert",
+            "version": "1.3.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/webmozart/assert.git",
+                "reference": "0df1908962e7a3071564e857d86874dad1ef204a"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/webmozart/assert/zipball/0df1908962e7a3071564e857d86874dad1ef204a",
+                "reference": "0df1908962e7a3071564e857d86874dad1ef204a",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^5.3.3 || ^7.0"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "^4.6",
+                "sebastian/version": "^1.0.1"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.3-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Webmozart\\Assert\\": "src/"
+                }
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Bernhard Schussek",
+                    "email": "bschussek@gmail.com"
+                }
+            ],
+            "description": "Assertions to validate method input/output with nice error messages.",
+            "keywords": [
+                "assert",
+                "check",
+                "validate"
+            ],
+            "time": "2018-01-29T19:49:41+00:00"
+        }
+    ],
+    "aliases": [],
+    "minimum-stability": "stable",
+    "stability-flags": [],
+    "prefer-stable": false,
+    "prefer-lowest": false,
+    "platform": [],
+    "platform-dev": []
+}

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/DatabaseSeedersTable.php

@@ -0,0 +1,61 @@
+<?php
+
+namespace Tests\DatabaseSeeders;
+
+use StatonLab\TripalTestSuite\Database\Seeder;
+
+class UsersTableSeeder extends Seeder
+{
+    /**
+     * Whether to run the seeder automatically before
+     * starting our tests and destruct them automatically
+     * once the tests are completed.
+     *
+     * If you set this to false, you can run the seeder
+     * from your tests directly using UsersTableSeeder::seed()
+     * which returns an instance of the class the you can use
+     * to run the down() method whenever required.
+     *
+     * @var bool
+     */
+    public $auto_run = true;
+
+    /**
+     * The users that got created.
+     * We save this here to have them easily deleted
+     * in the down() method.
+     *
+     * @var array
+     */
+    protected $users = [];
+
+    /**
+     * 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.
+        $this->users[] = user_save(new \stdClass(), $new_user);
+    }
+
+    /**
+     * Cleans up the database from the created users.
+     */
+    public function down()
+    {
+        foreach ($this->users as $user) {
+            user_delete($user->uid);
+        }
+    }
+}

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/TripalJobsTest.test

@@ -1,21 +0,0 @@
-<?php
-
-use PHPUnit\Framework\TestCase;
-
-class TripalJobsTest extends TestCase {
-
-  /**
-   * Tests the ability to create a tripal job.
-   *
-   * @test
-   */
-  public function should_create_a_tripal_job() {
-    $job_id = tripal_add_job('Test adding jobs', 'tripal', 'tripal_tripal_cron_notification', [], 1);
-    $this->assertTrue(is_numeric($job_id));
-
-    // Clean up
-    if($job_id) {
-      db_query('DELETE FROM {tripal_jobs} WHERE job_id = :id', [':id' => $job_id]);
-    }
-  }
-}

tests/bootstrap.php

@@ -1,39 +1,4 @@
 <?php
-// Set environment variables
+require_once __DIR__.'/../vendor/autoload.php';
-test_suite_read_and_set_environment_variables();
 
-// Get Drupal root path
+new \StatonLab\TripalTestSuite\TripalTestBootstrap();
-$drupal_root = getenv('DRUPAL_ROOT');
-define('DRUPAL_ROOT', $drupal_root ?: '/var/www/html');
-
-// Get Drupal bootstrap functions
-require_once DRUPAL_ROOT.'/includes/bootstrap.inc';
-$_SERVER['REMOTE_ADDR'] = '127.0.0.1';
-
-// Bootstrap Drupal.
-$current_dir = getcwd();
-chdir(DRUPAL_ROOT);
-drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);
-chdir($current_dir);
-
-/**
- * Get and set environment variables from .env file if it exists.
- *
- * @throws \Exception
- */
-function test_suite_read_and_set_environment_variables() {
-  $filename = __DIR__.'/.env';
-  if(file_exists($filename)) {
-    $file = fopen($filename, 'r');
-    while ($line = str_replace("\n", '', fgets($file))) {
-      // break line into key value
-      $env = explode('=', $line);
-      if(count($env) === 2) {
-        putenv($line);
-      } else {
-        throw new Exception('Invalid environment line: ' . $line);
-      }
-    }
-    fclose($file);
-  }
-}

tests/example.env

@@ -0,0 +1,2 @@
+DRUPAL_ROOT=/var/www/html
+FAKER_LOCALE=en_US