fix bug loading taxonomy importer

composer.json

@@ -1,7 +1,7 @@
 {
   "require-dev": {
     "doctrine/instantiator": "1.0.*",
-    "statonlab/tripal-test-suite": "^1.1"
+    "statonlab/tripal-test-suite": "^1.3"
   },
   "require": {
   }

composer.lock

@@ -4,7 +4,7 @@
         "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": "c8b425537daabed28cd865fb02a05684",
+    "content-hash": "adeee18e119693b993349d81c922f961",
     "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": "1.3.0",
             "source": {
                 "type": "git",
                 "url": "https://github.com/statonlab/TripalTestSuite.git",
-                "reference": "80b60a14b80f00d164ae5ba8511080d725526d38"
+                "reference": "1e616e426faf46b2c2c7cecc43741ee462387433"
             },
             "dist": {
                 "type": "zip",
-                "url": "https://api.github.com/repos/statonlab/TripalTestSuite/zipball/80b60a14b80f00d164ae5ba8511080d725526d38",
-                "reference": "80b60a14b80f00d164ae5ba8511080d725526d38",
+                "url": "https://api.github.com/repos/statonlab/TripalTestSuite/zipball/1e616e426faf46b2c2c7cecc43741ee462387433",
+                "reference": "1e616e426faf46b2c2c7cecc43741ee462387433",
                 "shasum": ""
             },
             "require": {
@@ -1698,20 +1701,20 @@
                     "email": "bcondon@utk.edu"
                 }
             ],
-            "time": "2018-05-25T13:17:31+00:00"
+            "time": "2018-08-03T14:20:13+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/tripal_chado/loaders/GFF3ImporterTest.php

@@ -52,7 +52,6 @@ class GFF3ImporterTest extends TripalTestCase {
 
   /**
    * @group gff
-   * @group failing
    * @ticket 77
    *
    */
@@ -119,12 +118,13 @@ class GFF3ImporterTest extends TripalTestCase {
   }
 
   private function runGFFLoader($run_args, $file) {
-    module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/GFF3Importer');
-    $importer = new \GFF3Importer();
-    $importer->create($run_args, $file);
-    $importer->prepareFiles();
-    $importer->run();
-
+   // silent(function ($run_args, $file) {
+      module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/GFF3Importer');
+      $importer = new \GFF3Importer();
+      $importer->create($run_args, $file);
+      $importer->prepareFiles();
+      $importer->run();
+  //  });
   }
 
   private function loadLandmarks($analysis, $organism) {
@@ -146,10 +146,13 @@ class GFF3ImporterTest extends TripalTestCase {
       'parent_type' => NULL,
     ];
     module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/FASTAImporter');
-    $importer = new \FASTAImporter();
-    $importer->create($run_args, $landmark_file);
-    $importer->prepareFiles();
-    $importer->run();
+    //silent(function ($run_args, $landmark_file) {
+      $importer = new \FASTAImporter();
+      $importer->create($run_args, $landmark_file);
+      $importer->prepareFiles();
+      $importer->run();
+   // });
+
   }
 
 }

tests/tripal_chado/loaders/TaxonomyImporterTest.php

@@ -5,12 +5,9 @@ namespace Tests\tripal_chado;
 use StatonLab\TripalTestSuite\DBTransaction;
 use StatonLab\TripalTestSuite\TripalTestCase;
 
-//require_once(__DIR__ . '/../../tripal_chado/includes/TripalImporter/TaxonomyImporter.inc');
-
-module_load_include('inc', 'tripal_chado', 'TripalImporter/TaxonomyImporter.inc');
-
 
 class TaxonomyImporterTest extends TripalTestCase {
+
   use DBTransaction;
 
 
@@ -19,16 +16,18 @@ class TaxonomyImporterTest extends TripalTestCase {
    *
    */
   public function testImportExistingTaxonomyLoader() {
+    module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/TaxonomyImporter');
+
     $org = [
       'genus' => 'Armadillo',
       'species' => 'officinalis',
       'abbreviation' => 'A. officinalis',
       'common_name' => 'pillbug',
-      'type_id' => null
+      'type_id' => NULL,
     ];
 
     $organism = factory('chado.organism')->create($org);
-  //  $this->publish('organism');
+    //  $this->publish('organism');
     $file = [];
     $run_args = ['import_existing' => TRUE];
     $importer = new \TaxonomyImporter();
@@ -48,7 +47,8 @@ class TaxonomyImporterTest extends TripalTestCase {
   }
 
   /**
-   * the importer can also load an array of pubmed ids.  We use the pillbug again.
+   * the importer can also load an array of pubmed ids.  We use the pillbug
+   * again.
    *
    * https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96821
    *
@@ -56,6 +56,8 @@ class TaxonomyImporterTest extends TripalTestCase {
    */
   public function testImportOrganismFromTaxID() {
 
+    module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/TaxonomyImporter');
+
     $file = [];
     $run_args = ['taxonomy_ids' => '96821']; //its the pillbug again!
     $importer = new \TaxonomyImporter();

tripal_chado/includes/TripalImporter/GFF3Importer.inc

@@ -102,12 +102,12 @@ class GFF3Importer extends TripalImporter {
     );
 
 
-    $form['advanced']['skip_proteins'] = array(
+    $form['advanced']['skip_protein'] = array(
       '#type' => 'checkbox',
       '#title' => t('Skip automatic protein creation'),
       '#required' => FALSE,
       '#description' => t('The GFF loader will automatically create a protein feature for each transcript in the GFF file if a protein feature is missing in the GFF file. Check this box to disable this functionality. Protein features that are specifically present in the GFF will always be created.'),
-      '#default_value' => FALSE
+      '#default_value' => 0
     );
 
 
@@ -414,7 +414,7 @@ class GFF3Importer extends TripalImporter {
       $add_only = 0, $update = 1, $refresh = 0, $remove = 0, $use_transaction = 1,
       $target_organism_id = NULL, $target_type = NULL,  $create_target = 0,
       $start_line = 1, $landmark_type = '', $alt_id_attr = '',  $create_organism = FALSE,
-      $re_mrna = '', $re_protein = '', $skip_protein = FALSE) {
+      $re_mrna = '', $re_protein = '', $skip_protein = 0) {
 
     $ret = array();
     $date = getdate();
@@ -961,7 +961,7 @@ class GFF3Importer extends TripalImporter {
               $pfmin += $min_phase[0]->phase;
             }
 
-            if ($skip_protein === 0){
+            if ($skip_protein == 0){
               // Add the new protein record.
               $feature = $this->loadFeature($organism, $analysis_id,
                 $protein_cvterm, $uname, $name, '', 'f', 'f', 1, 0);