Merge pull request #362 from statonlab/new_CI_and_test

Improved continuous integration, use Tripal Test Suite

.gitignore

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

.travis.yml

@@ -2,36 +2,79 @@ language: php
 
 services:
   - docker
+  - postgres
 
 sudo: required
 
+php:
+  - 5.6
+  - 7.0
+  - 7.1
+
+env:
+  - BASE_URL="http://localhost:8080"
+
+install:
+  - composer global require drush/drush:8
+
 before_script:
-  - docker pull statonlab/drupal7
+  - docker pull statonlab/tripal2
+  - psql -c "create database test_db encoding 'utf-8';" -U postgres
+  - psql -c "alter role postgres with password 'dbpass';" -U postgres
+  - cd ..
+
+  # Set additional environment variables
+  - export PATH="$HOME/.config/composer/vendor/bin:$PATH"
+  - export DRUPAL_ROOT="$(pwd)/drupal"
+
+  # Download and install Drupal
+  - drush dl drupal-7 -y
+  - mv drupal-7* drupal
+  - cd drupal
+  - drush si -y --db-url='pgsql://postgres:dbpass@localhost:5432/test_db'
+                --account-name='admin'
+                --account-pass='admin_pass'
+                --site-mail='admin@example.com'
+                --site-name='Tripal 3'
+
+  # Download Dependencies
+  - drush dl -y field_group, field_group_table, field_formatter_class, field_formatter_settings, ctools, date, devel,
+                ds, link, entity, libraries, redirect, token, uuid, jquery_update, views, webform
+
+  # Enable dependencies
+  - drush en -y field_group, field_group_table, field_formatter_class, field_formatter_settings, ctools, date, devel,
+              ds, link, entity, libraries, redirect, token uuid, jquery_update, views, webform
+
+  # Run the drush server
+  - drush runserver localhost:8080 &
 
 script:
-  # Set branch name
-  - export REPO=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_REPO_SLUG; else echo $TRAVIS_PULL_REQUEST_SLUG; fi)
-  - export BRANCH=$(if [ "$TRAVIS_PULL_REQUEST" == "false" ]; then echo $TRAVIS_BRANCH; else echo $TRAVIS_PULL_REQUEST_BRANCH; fi)
-  #  Travis does a shallow clone and we need a full clone to test Tripal v2 to v3 upgrade
-  - cd .. && rm -rf tripal && git clone https://github.com/$REPO.git tripal && cd tripal
-  - git checkout $BRANCH
-  # Test tripal 3 installation
-  - docker run -it -d --rm --name tripal3 -v "$(pwd)":/modules/tripal statonlab/drupal7
-  - sleep 15
-  - docker exec -it tripal3 drush en -y tripal tripal_chado tripal_chado_views tripal_ds tripal_ws
+  # Link our repo to the modules directory
+  - mv ../tripal sites/all/modules/tripal
+
+  # Run a docker container with tripal 2 pre-installed
+  - docker run -it -d --rm --name tripal2 -v "$(pwd)/tripal":/modules/tripal statonlab/tripal2
+
+  # Apply patches
+  - wget --no-check-certificate https://drupal.org/files/drupal.pgsql-bytea.27.patch
+  - patch -p1 < drupal.pgsql-bytea.27.patch
+  - cd sites/all/modules/views
+  - patch -p1 < ../tripal/tripal_chado_views/views-sql-compliant-three-tier-naming-1971160-30.patch
+  - cd ../tripal
+
+  # Install Tripal
+  - drush en -y tripal tripal_chado tripal_chado_views tripal_ds tripal_ws
+  - drush eval "module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install'); tripal_chado_load_drush_submit('Install Chado v1.3');"
+  - drush trp-run-jobs --username=admin
+
   # Prepare Chado
-  - docker exec -it tripal3 drush eval "module_load_include('inc', 'tripal_chado', 'includes/tripal_chado.install'); tripal_chado_load_drush_submit('Install Chado v1.3');"
-  - docker exec -it tripal3 drush trp-run-jobs --username=admin
-  # Prepare Drupal
-  - docker exec -it tripal3 drush eval "module_load_include('inc', 'tripal_chado', 'includes/setup/tripal_chado.setup'); tripal_chado_prepare_drush_submit();"
-  - docker exec -it tripal3 drush trp-run-jobs --username=admin
+  - drush eval "module_load_include('inc', 'tripal_chado', 'includes/setup/tripal_chado.setup'); tripal_chado_prepare_drush_submit();"
+  - drush trp-run-jobs --username=admin
+
   # Run PHPUnit tests
-  - docker exec -it tripal3 bash -c "cd /modules/tripal && composer install && DRUPAL_ROOT=/var/www/html ./vendor/bin/phpunit"
+  - composer update
+  - ./vendor/bin/phpunit
+
   # Test Tripal v2 to v3 upgrade steps
-  - git checkout 7.x-2.x
-  - docker run -it -d --rm --name tripal2 -v "$(pwd)":/modules/tripal statonlab/drupal7
-  - sleep 15
-  - docker exec -it tripal2 drush en -y tripal_core
   - docker exec -it tripal2 drush pm-disable tripal_core -y
-  - git checkout $BRANCH
   - docker exec -it tripal2 drush en -y tripal

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 +1,8 @@
 {
   "require-dev": {
-    "phpunit/phpunit": "^7"
+    "doctrine/instantiator": "1.0.*"
+  },
+  "require": {
+    "statonlab/tripal-test-suite": "1.0.*"
   }
 }

composer.lock

@@ -0,0 +1,1928 @@
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+    "_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#installing-dependencies",
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+            "extra": {
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+                    "dev-master": "1.8-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": "2018-04-26T10:06:28+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"
+        }
+    ],
+    "packages-dev": [],
+    "aliases": [],
+    "minimum-stability": "stable",
+    "stability-flags": [],
+    "prefer-stable": false,
+    "prefer-lowest": false,
+    "platform": [],
+    "platform-dev": []
+}

phpunit.xml

@@ -1,11 +1,33 @@
+<?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">./tests/</directory>
+        <testsuite name="tripal">
+            <directory suffix="Test.php">tests/tripal</directory>
+        </testsuite>
+        <testsuite name="tripal_chado">
+            <directory suffix="Test.php">tests/tripal_chado/</directory>
+        </testsuite>
+        <testsuite name="tripal_bulk_loader">
+            <directory suffix="Test.php">tests/tripal_bulk_loader/</directory>
+        </testsuite>
+        <testsuite name="tripal_chado_views">
+            <directory suffix="Test.php">tests/tripal_chado_views/</directory>
+        </testsuite>
+        <testsuite name="tripal_daemon">
+            <directory suffix="Test.php">tests/tripal_daemon/</directory>
+        </testsuite>
+        <testsuite name="tripal_ds">
+            <directory suffix="Test.php">tests/tripal_ds/</directory>
+        </testsuite>
+        <testsuite name="tripal_ws">
+            <directory suffix="Test.php">tests/tripal_ws/</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/bootstrap.php

@@ -1,39 +1,4 @@
 <?php
-// Set environment variables
-test_suite_read_and_set_environment_variables();
+require_once __DIR__.'/../vendor/autoload.php';
 
-// Get Drupal root path
-$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);
-  }
-}
+new \StatonLab\TripalTestSuite\TripalTestBootstrap();

tests/example.env

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

tests/TripalJobsTest.test → tests/tripal/api/TripalJobsApiTest.php

@@ -1,8 +1,12 @@
 <?php
+namespace Tests\tripal\api;
 
-use PHPUnit\Framework\TestCase;
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
 
-class TripalJobsTest extends TestCase {
+class TripalJobsApiTest extends TripalTestCase {
+
+  use DBTransaction;
 
   /**
    * Tests the ability to create a tripal job.
@@ -12,10 +16,5 @@ class TripalJobsTest extends TestCase {
   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/tripal_chado/api/TripalChadoAPITest.php

@@ -0,0 +1,69 @@
+<?php
+namespace Tests\tripal_chado\api;
+
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class TripalChadoAPITest extends TripalTestCase {
+
+  use DBTransaction;
+
+  /**
+   * Test the ability to publish Chado organism records as entities.
+   *
+   * @group api
+   */
+  public function test_tripal_chado_publish_records() {
+    $genus_string = 'a_genius_genus';
+    //create an organism, publish it
+    $organism = factory('chado.organism')->create([
+      'genus' => $genus_string,
+      'species' => 'fake_species',
+    ]);
+    //get bundle ID for organism
+    $bundle = db_select('public.chado_bundle', 'CB')
+      ->fields('CB', ['bundle_id'])
+      ->condition('data_table', 'organism')
+      ->execute()->fetchField();
+
+    $values = ['bundle_name' => 'bio_data_' . $bundle];
+
+    ob_start();//dont display the job message
+    $bool = tripal_chado_publish_records($values);
+    ob_end_clean();
+
+    $this->assertTrue($bool, 'Publishing a fake organism record failed');
+
+    //ensure that our entity was created
+    $query = db_select('chado.organism', 'O')
+      ->fields('O', ['organism_id']);
+    $query->join('public.chado_bio_data_' . $bundle, 'CBD', 'O.organism_id = CBD.record_id');
+    $query->condition('O.genus', $genus_string);
+    $organism_id = $query->execute()->fetchField();
+    $this->assertNotNull($organism_id, 'Organism with record ID not found in chado_bio_data table.');
+  }
+
+  /**
+   * Test chado_publish_records returns false given bad bundle.
+   *
+   * @group api
+   */
+  public function test_tripal_chado_publish_records_false_with_bad_bundle() {
+    putenv("TRIPAL_SUPPRESS_ERRORS=TRUE");//this will fail, so we suppress the tripal error reporter
+    $bool = tripal_chado_publish_records(['bundle_name' => 'never_in_a_million_years']);
+    $this->assertFalse($bool);
+    putenv("TRIPAL_SUPPRESS_ERRORS");//unset
+  }
+
+  /**
+   * calls tripal_get_chado_tokens.
+   *
+   * @group api
+   */
+  public function test_tripal_get_chado_tokens() {
+    $tokens = tripal_get_chado_tokens('organism');
+    $this->assertNotEmpty($tokens);
+    $this->assertArrayHasKey('[organism.organism_id]', $tokens);
+  }
+}

tests/tripal_chado/api/TripalChadoCustomTablesAPITest.php

@@ -0,0 +1,19 @@
+<?php
+namespace Tests\tripal_chado\api;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class TripalChadoCustomTablesAPITest extends TripalTestCase {
+  // Uncomment to auto start and rollback db transactions per test method.
+  // use DBTransaction;
+
+  /**
+   * 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/tripal_chado/api/TripalChadoOrganismAPITest.php

@@ -0,0 +1,113 @@
+<?php
+
+namespace Tests\tripal_chado\api;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class TripalChadoOrganismAPITest extends TripalTestCase {
+
+  use DBTransaction;
+
+  /**
+   * Test tripal_get_organism.
+   *
+   * @group api
+   */
+  public function test_tripal_get_organism() {
+    $genus_string = 'a_genius_genus';
+    $species_string = 'fake_species';
+
+    $organism = factory('chado.organism')->create([
+      'genus' => $genus_string,
+      'species' => $species_string,
+    ]);
+
+    $results = [];
+
+    $results[] = tripal_get_organism(['organism_id' => $organism->organism_id]);
+    $results[] = tripal_get_organism([
+      'genus' => $genus_string,
+      'species' => $species_string,
+    ]);
+
+    foreach ($results as $result) {
+      $this->assertNotFalse($result);
+      $this->assertNotNull($result);
+      $this->assertObjectHasAttribute('genus', $result);
+      $this->assertEquals($genus_string, $result->genus);
+    }
+  }
+
+  /**
+   * Test tripal_get_organism doesn't return anything
+   * when the organism doesn't exist.
+   */
+  public function test_tripal_get_organism_fails_gracefully() {
+    $result = tripal_get_organism([
+      'genus' => uniqid(),
+      'species' => uniqid(),
+    ]);
+
+    $this->assertNull($result);
+  }
+
+  /**
+   * Test tripal_get_organism_scientific_name
+   *
+   * @group  api
+   */
+  function test_tripal_get_organism_scientific_name() {
+    $genus_string = 'a_genius_genus';
+    $species_string = 'fake_species';
+    $infraspecific_name = "infrawhat?";
+    $term = factory('chado.cvterm')->create();
+
+    $organism = factory('chado.organism')->create([
+      'genus' => $genus_string,
+      'species' => $species_string,
+      'infraspecific_name' => $infraspecific_name,
+      'type_id' => $term->cvterm_id,
+    ]);
+
+    $sci_name = tripal_get_organism_scientific_name($organism);
+    $this->assertEquals(implode(" ", [
+      $genus_string,
+      $species_string,
+      $term->name,
+      $infraspecific_name,
+    ]), $sci_name);
+  }
+
+  //TODO: Can't test because it uses drupal_json_output.
+  //Need HTTP testing.
+  //
+  //  function test_tripal_autocomplete_organism(){
+  //
+  //    $genus_string = 'a_genius_genus';
+  //    $species_string = 'fake_species';
+  //
+  //    $organism = factory('chado.organism')->create([
+  //      'genus' => $genus_string,
+  //      'species' => $species_string,
+  //    ]);
+  //
+  //    tripal_autocomplete_organism(substr($genus_string, 0, 4));
+  //
+  //   //$this->assertEquals($genus_string, $auto_complete);
+  //  }
+
+  //This function is Tripal 2, and needs to be updated or deprecated
+
+  //  function test_tripal_get_organism_select_options_sycned_only_false(){
+  //
+  //    db_truncate('chado.organism');
+  //    factory('chado.organism', 20)->create();
+  //
+  //    $options = tripal_get_organism_select_options(FALSE);
+  //
+  //    $this->assertNotEmpty($options);
+  //    $this->assertGreaterThan(20, count($options));
+  //
+  //  }
+}

tripal/api/tripal.notice.api.inc

@@ -63,6 +63,10 @@ define('TRIPAL_DEBUG',7);
  */
 function tripal_report_error($type, $severity, $message, $variables = array(), $options = array()) {
 
+  $suppress = getenv('TRIPAL_SUPPRESS_ERRORS');
+
+  if(strtolower($suppress) === 'true') return;
+
   // Get human-readable severity string
   $severity_string = '';
   switch ($severity) {

tripal_chado/api/modules/tripal_chado.cv.api.inc

@@ -803,6 +803,8 @@ function tripal_update_cvtermpath_loop_increment(
         $matched_rows, $possible_start_of_loop, $no_loop_skip_test);
     }
   }
+
+
 }
 
 /**

tripal_chado/api/modules/tripal_chado.organism.api.inc

@@ -34,7 +34,7 @@
  * @return
  *   If unique values were passed in as an identifier then an object describing the organism
  *   will be returned (will be a chado variable from chado_generate_var()). Otherwise,
- *   FALSE will be returned.
+ *   NULL will be returned.
  *
  * @ingroup tripal_organism_api
  */
@@ -144,7 +144,7 @@ function tripal_get_organism_scientific_name($organism) {
     // For organism objects crated using chado_generate_var
     if (is_object($organism->type_id)) {
       if ($organism->type_id) {
-        $rank = $orgasnism->type_id->name;
+        $rank = $organism->type_id->name;
       }
     }
     else {
@@ -300,7 +300,7 @@ function tripal_autocomplete_organism($text) {
   $sql .= "ORDER BY genus, species ";
   $sql .= "LIMIT 25 OFFSET 0 ";
   $results = chado_query($sql, $args);
-  $items = array();
+  $items = array(['args' => [$sql => $args]]);
   foreach ($results as $organism) {
     $name = tripal_get_organism_scientific_name($organism);
     $items["$name [id: $organism->organism_id]"] = $name;