Update test suite and a test for aliases

composer.lock

@@ -229,32 +229,33 @@
         },
         {
             "name": "guzzlehttp/psr7",
-            "version": "1.4.2",
+            "version": "1.5.2",
             "source": {
                 "type": "git",
                 "url": "https://github.com/guzzle/psr7.git",
-                "reference": "f5b8a8512e2b58b0071a7280e39f14f72e05d87c"
+                "reference": "9f83dded91781a01c63574e387eaa769be769115"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/guzzle/psr7/zipball/f5b8a8512e2b58b0071a7280e39f14f72e05d87c",
-                "reference": "f5b8a8512e2b58b0071a7280e39f14f72e05d87c",
+                "url": "https://api.github.com/repos/guzzle/psr7/zipball/9f83dded91781a01c63574e387eaa769be769115",
+                "reference": "9f83dded91781a01c63574e387eaa769be769115",
                 "shasum": ""
             },
             "require": {
                 "php": ">=5.4.0",
-                "psr/http-message": "~1.0"
+                "psr/http-message": "~1.0",
+                "ralouphie/getallheaders": "^2.0.5"
             },
             "provide": {
                 "psr/http-message-implementation": "1.0"
             },
             "require-dev": {
-                "phpunit/phpunit": "~4.0"
+                "phpunit/phpunit": "~4.8.36 || ^5.7.27 || ^6.5.8"
             },
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "1.4-dev"
+                    "dev-master": "1.5-dev"
                 }
             },
             "autoload": {
@@ -284,13 +285,14 @@
             "keywords": [
                 "http",
                 "message",
+                "psr-7",
                 "request",
                 "response",
                 "stream",
                 "uri",
                 "url"
             ],
-            "time": "2017-03-20T17:10:46+00:00"
+            "time": "2018-12-04T20:46:45+00:00"
         },
         {
             "name": "myclabs/deep-copy",
@@ -810,16 +812,16 @@
         },
         {
             "name": "phpunit/php-timer",
-            "version": "2.0.0",
+            "version": "2.1.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/php-timer.git",
-                "reference": "8b8454ea6958c3dee38453d3bd571e023108c91f"
+                "reference": "8b389aebe1b8b0578430bda0c7c95a829608e059"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/php-timer/zipball/8b8454ea6958c3dee38453d3bd571e023108c91f",
-                "reference": "8b8454ea6958c3dee38453d3bd571e023108c91f",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-timer/zipball/8b389aebe1b8b0578430bda0c7c95a829608e059",
+                "reference": "8b389aebe1b8b0578430bda0c7c95a829608e059",
                 "shasum": ""
             },
             "require": {
@@ -831,7 +833,7 @@
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "2.0-dev"
+                    "dev-master": "2.1-dev"
                 }
             },
             "autoload": {
@@ -855,20 +857,20 @@
             "keywords": [
                 "timer"
             ],
-            "time": "2018-02-01T13:07:23+00:00"
+            "time": "2019-02-20T10:12:59+00:00"
         },
         {
             "name": "phpunit/php-token-stream",
-            "version": "3.0.0",
+            "version": "3.0.1",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/php-token-stream.git",
-                "reference": "21ad88bbba7c3d93530d93994e0a33cd45f02ace"
+                "reference": "c99e3be9d3e85f60646f152f9002d46ed7770d18"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/php-token-stream/zipball/21ad88bbba7c3d93530d93994e0a33cd45f02ace",
-                "reference": "21ad88bbba7c3d93530d93994e0a33cd45f02ace",
+                "url": "https://api.github.com/repos/sebastianbergmann/php-token-stream/zipball/c99e3be9d3e85f60646f152f9002d46ed7770d18",
+                "reference": "c99e3be9d3e85f60646f152f9002d46ed7770d18",
                 "shasum": ""
             },
             "require": {
@@ -904,7 +906,7 @@
             "keywords": [
                 "tokenizer"
             ],
-            "time": "2018-02-01T13:16:43+00:00"
+            "time": "2018-10-30T05:52:18+00:00"
         },
         {
             "name": "phpunit/phpunit",
@@ -1092,6 +1094,46 @@
             ],
             "time": "2016-08-06T14:39:51+00:00"
         },
+        {
+            "name": "ralouphie/getallheaders",
+            "version": "2.0.5",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/ralouphie/getallheaders.git",
+                "reference": "5601c8a83fbba7ef674a7369456d12f1e0d0eafa"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/ralouphie/getallheaders/zipball/5601c8a83fbba7ef674a7369456d12f1e0d0eafa",
+                "reference": "5601c8a83fbba7ef674a7369456d12f1e0d0eafa",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3"
+            },
+            "require-dev": {
+                "phpunit/phpunit": "~3.7.0",
+                "satooshi/php-coveralls": ">=1.0"
+            },
+            "type": "library",
+            "autoload": {
+                "files": [
+                    "src/getallheaders.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Ralph Khattar",
+                    "email": "ralph.khattar@gmail.com"
+                }
+            ],
+            "description": "A polyfill for getallheaders.",
+            "time": "2016-02-11T07:05:27+00:00"
+        },
         {
             "name": "sebastian/code-unit-reverse-lookup",
             "version": "1.0.1",
@@ -1203,23 +1245,23 @@
         },
         {
             "name": "sebastian/diff",
-            "version": "3.0.1",
+            "version": "3.0.2",
             "source": {
                 "type": "git",
                 "url": "https://github.com/sebastianbergmann/diff.git",
-                "reference": "366541b989927187c4ca70490a35615d3fef2dce"
+                "reference": "720fcc7e9b5cf384ea68d9d930d480907a0c1a29"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/sebastianbergmann/diff/zipball/366541b989927187c4ca70490a35615d3fef2dce",
-                "reference": "366541b989927187c4ca70490a35615d3fef2dce",
+                "url": "https://api.github.com/repos/sebastianbergmann/diff/zipball/720fcc7e9b5cf384ea68d9d930d480907a0c1a29",
+                "reference": "720fcc7e9b5cf384ea68d9d930d480907a0c1a29",
                 "shasum": ""
             },
             "require": {
                 "php": "^7.1"
             },
             "require-dev": {
-                "phpunit/phpunit": "^7.0",
+                "phpunit/phpunit": "^7.5 || ^8.0",
                 "symfony/process": "^2 || ^3.3 || ^4"
             },
             "type": "library",
@@ -1255,7 +1297,7 @@
                 "unidiff",
                 "unified diff"
             ],
-            "time": "2018-06-10T07:54:39+00:00"
+            "time": "2019-02-04T06:01:07+00:00"
         },
         {
             "name": "sebastian/environment",
@@ -1657,16 +1699,16 @@
         },
         {
             "name": "statonlab/tripal-test-suite",
-            "version": "1.5.1",
+            "version": "1.5.2",
             "source": {
                 "type": "git",
                 "url": "https://github.com/tripal/TripalTestSuite.git",
-                "reference": "c652f62c0e8302e00cf25a39c95a605b0266656f"
+                "reference": "2c89b5919e3a48c8ecd63744e5879b00fac03bd7"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/tripal/TripalTestSuite/zipball/c652f62c0e8302e00cf25a39c95a605b0266656f",
-                "reference": "c652f62c0e8302e00cf25a39c95a605b0266656f",
+                "url": "https://api.github.com/repos/tripal/TripalTestSuite/zipball/2c89b5919e3a48c8ecd63744e5879b00fac03bd7",
+                "reference": "2c89b5919e3a48c8ecd63744e5879b00fac03bd7",
                 "shasum": ""
             },
             "require": {
@@ -1701,30 +1743,34 @@
                     "email": "bcondon@utk.edu"
                 }
             ],
-            "time": "2018-09-25T19:08:14+00:00"
+            "time": "2019-01-10T13:18:54+00:00"
         },
         {
             "name": "symfony/console",
-            "version": "v4.1.4",
+            "version": "v4.2.4",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/console.git",
-                "reference": "ca80b8ced97cf07390078b29773dc384c39eee1f"
+                "reference": "9dc2299a016497f9ee620be94524e6c0af0280a9"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/console/zipball/ca80b8ced97cf07390078b29773dc384c39eee1f",
-                "reference": "ca80b8ced97cf07390078b29773dc384c39eee1f",
+                "url": "https://api.github.com/repos/symfony/console/zipball/9dc2299a016497f9ee620be94524e6c0af0280a9",
+                "reference": "9dc2299a016497f9ee620be94524e6c0af0280a9",
                 "shasum": ""
             },
             "require": {
                 "php": "^7.1.3",
+                "symfony/contracts": "^1.0",
                 "symfony/polyfill-mbstring": "~1.0"
             },
             "conflict": {
                 "symfony/dependency-injection": "<3.4",
                 "symfony/process": "<3.3"
             },
+            "provide": {
+                "psr/log-implementation": "1.0"
+            },
             "require-dev": {
                 "psr/log": "~1.0",
                 "symfony/config": "~3.4|~4.0",
@@ -1734,7 +1780,7 @@
                 "symfony/process": "~3.4|~4.0"
             },
             "suggest": {
-                "psr/log-implementation": "For using the console logger",
+                "psr/log": "For using the console logger",
                 "symfony/event-dispatcher": "",
                 "symfony/lock": "",
                 "symfony/process": ""
@@ -1742,7 +1788,7 @@
             "type": "library",
             "extra": {
                 "branch-alias": {
-                    "dev-master": "4.1-dev"
+                    "dev-master": "4.2-dev"
                 }
             },
             "autoload": {
@@ -1769,20 +1815,146 @@
             ],
             "description": "Symfony Console Component",
             "homepage": "https://symfony.com",
-            "time": "2018-07-26T11:24:31+00:00"
+            "time": "2019-02-23T15:17:42+00:00"
+        },
+        {
+            "name": "symfony/contracts",
+            "version": "v1.0.2",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/symfony/contracts.git",
+                "reference": "1aa7ab2429c3d594dd70689604b5cf7421254cdf"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/symfony/contracts/zipball/1aa7ab2429c3d594dd70689604b5cf7421254cdf",
+                "reference": "1aa7ab2429c3d594dd70689604b5cf7421254cdf",
+                "shasum": ""
+            },
+            "require": {
+                "php": "^7.1.3"
+            },
+            "require-dev": {
+                "psr/cache": "^1.0",
+                "psr/container": "^1.0"
+            },
+            "suggest": {
+                "psr/cache": "When using the Cache contracts",
+                "psr/container": "When using the Service contracts",
+                "symfony/cache-contracts-implementation": "",
+                "symfony/service-contracts-implementation": "",
+                "symfony/translation-contracts-implementation": ""
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.0-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Symfony\\Contracts\\": ""
+                },
+                "exclude-from-classmap": [
+                    "**/Tests/"
+                ]
+            },
+            "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": "A set of abstractions extracted out of the Symfony components",
+            "homepage": "https://symfony.com",
+            "keywords": [
+                "abstractions",
+                "contracts",
+                "decoupling",
+                "interfaces",
+                "interoperability",
+                "standards"
+            ],
+            "time": "2018-12-05T08:06:11+00:00"
+        },
+        {
+            "name": "symfony/polyfill-ctype",
+            "version": "v1.10.0",
+            "source": {
+                "type": "git",
+                "url": "https://github.com/symfony/polyfill-ctype.git",
+                "reference": "e3d826245268269cd66f8326bd8bc066687b4a19"
+            },
+            "dist": {
+                "type": "zip",
+                "url": "https://api.github.com/repos/symfony/polyfill-ctype/zipball/e3d826245268269cd66f8326bd8bc066687b4a19",
+                "reference": "e3d826245268269cd66f8326bd8bc066687b4a19",
+                "shasum": ""
+            },
+            "require": {
+                "php": ">=5.3.3"
+            },
+            "suggest": {
+                "ext-ctype": "For best performance"
+            },
+            "type": "library",
+            "extra": {
+                "branch-alias": {
+                    "dev-master": "1.9-dev"
+                }
+            },
+            "autoload": {
+                "psr-4": {
+                    "Symfony\\Polyfill\\Ctype\\": ""
+                },
+                "files": [
+                    "bootstrap.php"
+                ]
+            },
+            "notification-url": "https://packagist.org/downloads/",
+            "license": [
+                "MIT"
+            ],
+            "authors": [
+                {
+                    "name": "Symfony Community",
+                    "homepage": "https://symfony.com/contributors"
+                },
+                {
+                    "name": "Gert de Pagter",
+                    "email": "backendtea@gmail.com"
+                }
+            ],
+            "description": "Symfony polyfill for ctype functions",
+            "homepage": "https://symfony.com",
+            "keywords": [
+                "compatibility",
+                "ctype",
+                "polyfill",
+                "portable"
+            ],
+            "time": "2018-08-06T14:22:27+00:00"
         },
         {
             "name": "symfony/polyfill-mbstring",
-            "version": "v1.9.0",
+            "version": "v1.10.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/symfony/polyfill-mbstring.git",
-                "reference": "d0cd638f4634c16d8df4508e847f14e9e43168b8"
+                "reference": "c79c051f5b3a46be09205c73b80b346e4153e494"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/d0cd638f4634c16d8df4508e847f14e9e43168b8",
-                "reference": "d0cd638f4634c16d8df4508e847f14e9e43168b8",
+                "url": "https://api.github.com/repos/symfony/polyfill-mbstring/zipball/c79c051f5b3a46be09205c73b80b346e4153e494",
+                "reference": "c79c051f5b3a46be09205c73b80b346e4153e494",
                 "shasum": ""
             },
             "require": {
@@ -1828,7 +2000,7 @@
                 "portable",
                 "shim"
             ],
-            "time": "2018-08-06T14:22:27+00:00"
+            "time": "2018-09-21T13:07:52+00:00"
         },
         {
             "name": "theseer/tokenizer",
@@ -1872,20 +2044,21 @@
         },
         {
             "name": "webmozart/assert",
-            "version": "1.3.0",
+            "version": "1.4.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/webmozart/assert.git",
-                "reference": "0df1908962e7a3071564e857d86874dad1ef204a"
+                "reference": "83e253c8e0be5b0257b881e1827274667c5c17a9"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/webmozart/assert/zipball/0df1908962e7a3071564e857d86874dad1ef204a",
-                "reference": "0df1908962e7a3071564e857d86874dad1ef204a",
+                "url": "https://api.github.com/repos/webmozart/assert/zipball/83e253c8e0be5b0257b881e1827274667c5c17a9",
+                "reference": "83e253c8e0be5b0257b881e1827274667c5c17a9",
                 "shasum": ""
             },
             "require": {
-                "php": "^5.3.3 || ^7.0"
+                "php": "^5.3.3 || ^7.0",
+                "symfony/polyfill-ctype": "^1.8"
             },
             "require-dev": {
                 "phpunit/phpunit": "^4.6",
@@ -1918,7 +2091,7 @@
                 "check",
                 "validate"
             ],
-            "time": "2018-01-29T19:49:41+00:00"
+            "time": "2018-12-25T11:19:39+00:00"
         }
     ],
     "aliases": [],

tests/tripal_chado/api/ChadoQueryTest.php

@@ -68,6 +68,7 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_chado_db_select_works_for_chado_tables() {
     $analysis_record = factory('chado.analysis')->create();
@@ -92,6 +93,7 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_chado_db_select_should_throw_an_exception_if_table_is_undefined() {
     $this->expectException(\Exception::class);
@@ -101,9 +103,11 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_chado_db_select_recognizes_non_chado_tables() {
-    $query = chado_db_select('users');
+    $query = chado_db_select('users', '');
+    $query->fields('u');
     $query->range(0, 1);
     $results = $query->execute()->fetchAll();
 
@@ -113,6 +117,21 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
+   */
+  public function test_chado_db_select_handles_aliases_correctly() {
+    $query = chado_db_select('public.users');
+    $query->fields('public_users');
+    $query->range(0, 1);
+    $results = $query->execute()->fetchAll();
+
+    $this->assertNotEmpty($results);
+  }
+
+  /**
+   * @group api
+   * @group chado
+   * @group chado_db_select
    */
   public function test_joining_chado_tables_in_chado_db_select() {
     $feature = factory('chado.feature')->create();
@@ -122,7 +141,7 @@ class ChadoQueryTest extends TripalTestCase {
     $feature_cvterm = chado_insert_record('feature_cvterm', [
       'feature_id' => $feature->feature_id,
       'cvterm_id' => $cvterm->cvterm_id,
-      'pub_id' => $pub->pub_id
+      'pub_id' => $pub->pub_id,
     ]);
 
     $query = chado_db_select('feature', 'f');
@@ -139,6 +158,7 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_left_joining_chado_tables_in_chado_db_select() {
     $feature = factory('chado.feature')->create();
@@ -148,7 +168,7 @@ class ChadoQueryTest extends TripalTestCase {
     $feature_cvterm = chado_insert_record('feature_cvterm', [
       'feature_id' => $feature->feature_id,
       'cvterm_id' => $cvterm->cvterm_id,
-      'pub_id' => $pub->pub_id
+      'pub_id' => $pub->pub_id,
     ]);
 
     $query = chado_db_select('feature', 'f');
@@ -165,6 +185,7 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_right_joining_chado_tables_in_chado_db_select() {
     $feature = factory('chado.feature')->create();
@@ -174,7 +195,7 @@ class ChadoQueryTest extends TripalTestCase {
     $feature_cvterm = chado_insert_record('feature_cvterm', [
       'feature_id' => $feature->feature_id,
       'cvterm_id' => $cvterm->cvterm_id,
-      'pub_id' => $pub->pub_id
+      'pub_id' => $pub->pub_id,
     ]);
 
     $query = chado_db_select('feature', 'f');
@@ -191,6 +212,7 @@ class ChadoQueryTest extends TripalTestCase {
   /**
    * @group api
    * @group chado
+   * @group chado_db_select
    */
   public function test_inner_joining_chado_tables_in_chado_db_select() {
     $feature = factory('chado.feature')->create();
@@ -200,7 +222,7 @@ class ChadoQueryTest extends TripalTestCase {
     $feature_cvterm = chado_insert_record('feature_cvterm', [
       'feature_id' => $feature->feature_id,
       'cvterm_id' => $cvterm->cvterm_id,
-      'pub_id' => $pub->pub_id
+      'pub_id' => $pub->pub_id,
     ]);
 
     $query = chado_db_select('feature', 'f');