Merge pull request #548 from statonlab/543-update_tests

543 update tests

README.md

@@ -121,3 +121,5 @@ DRUPAL_ROOT=/var/www/html
 Then run PHPUnit from your root Tripal directory.
 
 PHPUnit tests will also be run in the Travis CI build.
+
+Read our [testing guidelines](tests/README.md)

composer.json

@@ -1,7 +1,9 @@
 {
+  "name": "tripal",
+  "description": "Tripal is an toolkit to facilitate construction of online genomic, genetic (and other biological) websites.",
   "require-dev": {
     "doctrine/instantiator": "1.0.*",
-    "statonlab/tripal-test-suite": "^1.1"
+    "statonlab/tripal-test-suite": "1.*"
   },
   "require": {
   }

composer.lock

@@ -1,10 +1,10 @@
 {
     "_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",
+        "Read more about it at https://getcomposer.org/doc/01-basic-usage.md#installing-dependencies",
         "This file is @generated automatically"
     ],
-    "content-hash": "c8b425537daabed28cd865fb02a05684",
+    "content-hash": "fd3ab0a8fd06e0532a7764f20a9aa52b",
     "packages": [],
     "packages-dev": [
         {
@@ -63,16 +63,16 @@
         },
         {
             "name": "fzaninotto/faker",
-            "version": "v1.7.1",
+            "version": "v1.8.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/fzaninotto/Faker.git",
-                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d"
+                "reference": "f72816b43e74063c8b10357394b6bba8cb1c10de"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/fzaninotto/Faker/zipball/d3ed4cc37051c1ca52d22d76b437d14809fc7e0d",
-                "reference": "d3ed4cc37051c1ca52d22d76b437d14809fc7e0d",
+                "url": "https://api.github.com/repos/fzaninotto/Faker/zipball/f72816b43e74063c8b10357394b6bba8cb1c10de",
+                "reference": "f72816b43e74063c8b10357394b6bba8cb1c10de",
                 "shasum": ""
             },
             "require": {
@@ -80,7 +80,7 @@
             },
             "require-dev": {
                 "ext-intl": "*",
-                "phpunit/phpunit": "^4.0 || ^5.0",
+                "phpunit/phpunit": "^4.8.35 || ^5.7",
                 "squizlabs/php_codesniffer": "^1.5"
             },
             "type": "library",
@@ -109,7 +109,7 @@
                 "faker",
                 "fixtures"
             ],
-            "time": "2017-08-15T16:48:10+00:00"
+            "time": "2018-07-12T10:23:15+00:00"
         },
         {
             "name": "guzzlehttp/guzzle",
@@ -294,25 +294,28 @@
         },
         {
             "name": "myclabs/deep-copy",
-            "version": "1.7.0",
+            "version": "1.8.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/myclabs/DeepCopy.git",
-                "reference": "3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e"
+                "reference": "3e01bdad3e18354c3dce54466b7fbe33a9f9f7f8"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/myclabs/DeepCopy/zipball/3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e",
-                "reference": "3b8a3a99ba1f6a3952ac2747d989303cbd6b7a3e",
+                "url": "https://api.github.com/repos/myclabs/DeepCopy/zipball/3e01bdad3e18354c3dce54466b7fbe33a9f9f7f8",
+                "reference": "3e01bdad3e18354c3dce54466b7fbe33a9f9f7f8",
                 "shasum": ""
             },
             "require": {
-                "php": "^5.6 || ^7.0"
+                "php": "^7.1"
+            },
+            "replace": {
+                "myclabs/deep-copy": "self.version"
             },
             "require-dev": {
                 "doctrine/collections": "^1.0",
                 "doctrine/common": "^2.6",
-                "phpunit/phpunit": "^4.1"
+                "phpunit/phpunit": "^7.1"
             },
             "type": "library",
             "autoload": {
@@ -335,7 +338,7 @@
                 "object",
                 "object graph"
             ],
-            "time": "2017-10-19T19:58:43+00:00"
+            "time": "2018-06-11T23:09:50+00:00"
         },
         {
             "name": "phar-io/manifest",
@@ -593,16 +596,16 @@
         },
         {
             "name": "phpspec/prophecy",
-            "version": "1.7.6",
+            "version": "1.8.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/phpspec/prophecy.git",
-                "reference": "33a7e3c4fda54e912ff6338c48823bd5c0f0b712"
+                "reference": "4ba436b55987b4bf311cb7c6ba82aa528aac0a06"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/phpspec/prophecy/zipball/33a7e3c4fda54e912ff6338c48823bd5c0f0b712",
-                "reference": "33a7e3c4fda54e912ff6338c48823bd5c0f0b712",
+                "url": "https://api.github.com/repos/phpspec/prophecy/zipball/4ba436b55987b4bf311cb7c6ba82aa528aac0a06",
+                "reference": "4ba436b55987b4bf311cb7c6ba82aa528aac0a06",
                 "shasum": ""
             },
             "require": {
@@ -614,12 +617,12 @@
             },
             "require-dev": {
                 "phpspec/phpspec": "^2.5|^3.2",
-                "phpunit/phpunit": "^4.8.35 || ^5.7 || ^6.5"
+                "phpunit/phpunit": "^4.8.35 || ^5.7 || ^6.5 || ^7.1"
             },
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "1.7.x-dev"
+                    "dev-master": "1.8.x-dev"
                 }
             },
             "autoload": {
@@ -652,20 +655,20 @@
                 "spy",
                 "stub"
             ],
-            "time": "2018-04-18T13:57:24+00:00"
+            "time": "2018-08-05T17:53:17+00:00"
         },
         {
             "name": "phpunit/php-code-coverage",
-            "version": "6.0.4",
+            "version": "6.0.5",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/php-code-coverage.git",
-                "reference": "52187754b0eed0b8159f62a6fa30073327e8c2ca"
+                "reference": "4cab20a326d14de7575a8e235c70d879b569a57a"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/php-code-coverage/zipball/52187754b0eed0b8159f62a6fa30073327e8c2ca",
-                "reference": "52187754b0eed0b8159f62a6fa30073327e8c2ca",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-code-coverage/zipball/4cab20a326d14de7575a8e235c70d879b569a57a",
+                "reference": "4cab20a326d14de7575a8e235c70d879b569a57a",
                 "shasum": ""
             },
             "require": {
@@ -715,7 +718,7 @@
                 "testing",
                 "xunit"
             ],
-            "time": "2018-04-29T14:59:09+00:00"
+            "time": "2018-05-28T11:49:20+00:00"
         },
         {
             "name": "phpunit/php-file-iterator",
@@ -985,16 +988,16 @@
         },
         {
             "name": "phpunit/phpunit-mock-objects",
-            "version": "6.1.1",
+            "version": "6.1.2",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/phpunit-mock-objects.git",
-                "reference": "70c740bde8fd9ea9ea295be1cd875dd7b267e157"
+                "reference": "f9756fd4f43f014cb2dca98deeaaa8ce5500a36e"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/phpunit-mock-objects/zipball/70c740bde8fd9ea9ea295be1cd875dd7b267e157",
-                "reference": "70c740bde8fd9ea9ea295be1cd875dd7b267e157",
+                "url": "https://api.github.com/repos/sebastianbergmann/phpunit-mock-objects/zipball/f9756fd4f43f014cb2dca98deeaaa8ce5500a36e",
+                "reference": "f9756fd4f43f014cb2dca98deeaaa8ce5500a36e",
                 "shasum": ""
             },
             "require": {
@@ -1037,7 +1040,7 @@
                 "mock",
                 "xunit"
             ],
-            "time": "2018-04-11T04:50:36+00:00"
+            "time": "2018-05-29T13:54:20+00:00"
         },
         {
             "name": "psr/http-message",
@@ -1136,16 +1139,16 @@
         },
         {
             "name": "sebastian/comparator",
-            "version": "3.0.0",
+            "version": "3.0.2",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/comparator.git",
-                "reference": "ed5fd2281113729f1ebcc64d101ad66028aeb3d5"
+                "reference": "5de4fc177adf9bce8df98d8d141a7559d7ccf6da"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/comparator/zipball/ed5fd2281113729f1ebcc64d101ad66028aeb3d5",
-                "reference": "ed5fd2281113729f1ebcc64d101ad66028aeb3d5",
+                "url": "https://api.github.com/repos/sebastianbergmann/comparator/zipball/5de4fc177adf9bce8df98d8d141a7559d7ccf6da",
+                "reference": "5de4fc177adf9bce8df98d8d141a7559d7ccf6da",
                 "shasum": ""
             },
             "require": {
@@ -1196,20 +1199,20 @@
                 "compare",
                 "equality"
             ],
-            "time": "2018-04-18T13:33:00+00:00"
+            "time": "2018-07-12T15:12:46+00:00"
         },
         {
             "name": "sebastian/diff",
-            "version": "3.0.0",
+            "version": "3.0.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/diff.git",
-                "reference": "e09160918c66281713f1c324c1f4c4c3037ba1e8"
+                "reference": "366541b989927187c4ca70490a35615d3fef2dce"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/diff/zipball/e09160918c66281713f1c324c1f4c4c3037ba1e8",
-                "reference": "e09160918c66281713f1c324c1f4c4c3037ba1e8",
+                "url": "https://api.github.com/repos/sebastianbergmann/diff/zipball/366541b989927187c4ca70490a35615d3fef2dce",
+                "reference": "366541b989927187c4ca70490a35615d3fef2dce",
                 "shasum": ""
             },
             "require": {
@@ -1252,7 +1255,7 @@
                 "unidiff",
                 "unified diff"
             ],
-            "time": "2018-02-01T13:45:15+00:00"
+            "time": "2018-06-10T07:54:39+00:00"
         },
         {
             "name": "sebastian/environment",
@@ -1654,16 +1657,16 @@
         },
         {
             "name": "statonlab/tripal-test-suite",
-            "version": "1.1.0",
+            "version": "1.4.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/statonlab/TripalTestSuite.git",
-                "reference": "80b60a14b80f00d164ae5ba8511080d725526d38"
+                "reference": "e469f7fde2cf69303dc22315b142b46b027c9931"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/statonlab/TripalTestSuite/zipball/80b60a14b80f00d164ae5ba8511080d725526d38",
-                "reference": "80b60a14b80f00d164ae5ba8511080d725526d38",
+                "url": "https://api.github.com/repos/statonlab/TripalTestSuite/zipball/e469f7fde2cf69303dc22315b142b46b027c9931",
+                "reference": "e469f7fde2cf69303dc22315b142b46b027c9931",
                 "shasum": ""
             },
             "require": {
@@ -1698,20 +1701,20 @@
                     "email": "bcondon@utk.edu"
                 }
             ],
-            "time": "2018-05-25T13:17:31+00:00"
+            "time": "2018-08-06T19:38:14+00:00"
         },
         {
             "name": "symfony/console",
-            "version": "v4.0.9",
+            "version": "v4.1.3",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/console.git",
-                "reference": "3e820bc2c520a87ca209ad8fa961c97f42e0b4ae"
+                "reference": "ca80b8ced97cf07390078b29773dc384c39eee1f"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/console/zipball/3e820bc2c520a87ca209ad8fa961c97f42e0b4ae",
-                "reference": "3e820bc2c520a87ca209ad8fa961c97f42e0b4ae",
+                "url": "https://api.github.com/repos/symfony/console/zipball/ca80b8ced97cf07390078b29773dc384c39eee1f",
+                "reference": "ca80b8ced97cf07390078b29773dc384c39eee1f",
                 "shasum": ""
             },
             "require": {
@@ -1739,7 +1742,7 @@
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "4.0-dev"
+                    "dev-master": "4.1-dev"
                 }
             },
             "autoload": {
@@ -1766,20 +1769,20 @@
             ],
             "description": "Symfony Console Component",
             "homepage": "https://symfony.com",
-            "time": "2018-04-30T01:23:47+00:00"
+            "time": "2018-07-26T11:24:31+00:00"
         },
         {
             "name": "symfony/polyfill-mbstring",
-            "version": "v1.8.0",
+            "version": "v1.9.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/polyfill-mbstring.git",
-                "reference": "3296adf6a6454a050679cde90f95350ad604b171"
+                "reference": "d0cd638f4634c16d8df4508e847f14e9e43168b8"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/3296adf6a6454a050679cde90f95350ad604b171",
-                "reference": "3296adf6a6454a050679cde90f95350ad604b171",
+                "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/d0cd638f4634c16d8df4508e847f14e9e43168b8",
+                "reference": "d0cd638f4634c16d8df4508e847f14e9e43168b8",
                 "shasum": ""
             },
             "require": {
@@ -1791,7 +1794,7 @@
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "1.8-dev"
+                    "dev-master": "1.9-dev"
                 }
             },
             "autoload": {
@@ -1825,7 +1828,7 @@
                 "portable",
                 "shim"
             ],
-            "time": "2018-04-26T10:06:28+00:00"
+            "time": "2018-08-06T14:22:27+00:00"
         },
         {
             "name": "theseer/tokenizer",

tests/DataFactory.php

@@ -71,3 +71,27 @@ Factory::define('chado.feature', function (Faker\Generator $faker) {
         'type_id' => factory('chado.cvterm')->create()->cvterm_id,
     ];
 });
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('tripal_jobs', function (Faker\Generator $faker) {
+  return [
+    'uid' => 1,
+    'job_name' => $faker->sentence,
+    'modulename' => $faker->word,
+    'callback' => $faker->word,
+    'arguments' => serialize(['arg' => $faker->word]),
+    'progress' => 0,
+    'status' => $faker->randomElement([
+      'Waiting',
+      'Cancelled',
+      'Error',
+      'Completed',
+    ]),
+    'submit_date' => time(),
+    'start_time' => NULL,
+    'end_time' => NULL,
+    'error_msg' => NULL,
+    'pid' => $faker->numberBetween(1, 10000),
+    'priority' => $faker->numberBetween(1, 10),
+  ];
+}, 'job_id');

tests/README.md

@@ -11,6 +11,7 @@ For a basic introduction of Tripal Testing, please see the [Test Suite repo](htt
 
 After cloning the [Tripal github repo](https://github.com/tripal/tripal), you will need to install the developer dependencies required to run tests locally.  To do this, you'll need to [install Composer](https://getcomposer.org/doc/00-intro.md), and then execute `composer install` in your project root.
 
+Remember to run `composer update` to update TripalTestSuite before writing and running new tests. This is especially important when running pull requests that contribute unit tests. If tests are passing on the Travis environment but not on your machine, running composer update might resolve the problem.
 
 ## Testing criteria
 For facilitate accepting your pull requests, your code should include tests.  The tests should meet the following guidelines:

tests/tripal/api/TripalJobsApiTest.php

@@ -1,10 +1,11 @@
 <?php
+
 namespace Tests\tripal\api;
 
 use StatonLab\TripalTestSuite\DBTransaction;
 use StatonLab\TripalTestSuite\TripalTestCase;
 
-class TripalJobsApiTest extends TripalTestCase {
+class TripalJobsApiTest extends TripalTestCase{
 
   use DBTransaction;
 
@@ -13,8 +14,50 @@ class TripalJobsApiTest extends TripalTestCase {
    *
    * @test
    */
-  public function should_create_a_tripal_job() {
-    $job_id = tripal_add_job('Test adding jobs', 'tripal', 'tripal_tripal_cron_notification', [], 1);
+  public function testCreatingAJobWorks() {
+    $job_id = tripal_add_job('Test adding jobs', 'tripal',
+      'tripal_tripal_cron_notification', [], 1);
     $this->assertTrue(is_numeric($job_id));
   }
+
+  /** @test */
+  public function testRetrievingAJob() {
+    $job = factory('tripal_jobs')->create();
+
+    $job2 = tripal_get_job($job->job_id);
+
+    $this->assertNotEmpty($job2);
+    $this->assertObjectHasAttribute('job_id', $job2);
+    $this->assertEquals($job2->job_id, $job->job_id);
+  }
+
+  /** @test */
+  public function testRetrievingActiveJobs() {
+    factory('tripal_jobs')->create();
+    $jobs = tripal_get_active_jobs();
+
+    $this->assertNotEmpty($jobs);
+  }
+
+  /** @test */
+  public function testRetrievingActiveJobsWithAGivenModule() {
+    factory('tripal_jobs')->create([
+      'modulename' => 'tripal_test_suite',
+      'status' => 'Running',
+    ]);
+    $jobs = tripal_get_active_jobs('tripal_test_suite');
+
+    $this->assertNotEmpty($jobs);
+  }
+
+  /** @test */
+  public function testRetrievingCompletedJobsDoesNotHappen() {
+    factory('tripal_jobs')->create([
+      'modulename' => 'tripal_test_suite',
+      'status' => 'Completed',
+    ]);
+    $jobs = tripal_get_active_jobs('tripal_test_suite');
+
+    $this->assertEmpty($jobs);
+  }
 }

tests/tripal_chado/api/TripalChadoAPITest.php

@@ -1,11 +1,11 @@
 <?php
-namespace Tests\tripal_chado\api;
 
+namespace Tests\tripal_chado\api;
 
 use StatonLab\TripalTestSuite\DBTransaction;
 use StatonLab\TripalTestSuite\TripalTestCase;
 
-class TripalChadoAPITest extends TripalTestCase {
+class TripalChadoAPITest extends TripalTestCase{
 
   use DBTransaction;
 
@@ -17,33 +17,39 @@ class TripalChadoAPITest extends TripalTestCase {
    */
   public function test_tripal_chado_publish_records() {
     $genus_string = 'a_genius_genus';
-    //create an organism, publish it
+
+    // Create an organism, publish it
     $organism = factory('chado.organism')->create([
       'genus' => $genus_string,
       'species' => 'fake_species',
     ]);
-    //get bundle ID for organism
+
+    // Get bundle ID for organism
     $bundle = db_select('public.chado_bundle', 'CB')
       ->fields('CB', ['bundle_id'])
       ->condition('data_table', 'organism')
-      ->execute()->fetchField();
+      ->execute()
+      ->fetchField();
 
-    var_dump($bundle);
     $values = ['bundle_name' => 'bio_data_' . $bundle];
 
- //   ob_start();//dont display the job message
-    $bool = chado_publish_records($values);
-   // ob_end_clean();
+    // Don't display the job message
+    $bool = silent(function () use ($values) {
+      return chado_publish_records($values);
+    });
 
-    $this->assertTrue($bool, 'Publishing a fake organism record failed');
+    $this->assertTrue($bool->getReturnValue(),
+      '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');
+    // 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.');
+
+    $this->assertNotNull($organism_id,
+      'Organism with record ID not found in chado_bio_data table.');
   }
 
   /**
@@ -52,10 +58,11 @@ class TripalChadoAPITest extends TripalTestCase {
    * @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 = chado_publish_records(['bundle_name' => 'never_in_a_million_years']);
-    $this->assertFalse($bool);
-    putenv("TRIPAL_SUPPRESS_ERRORS");//unset
+    $bool = silent(function () {
+      return chado_publish_records(['bundle_name' => 'never_in_a_million_years']);
+    });
+
+    $this->assertFalse($bool->getReturnValue());
   }
 
   /**