Initialize test suite.

.gitignore

@@ -3,3 +3,5 @@
 
 vendor/
 _build/
+
+.env

.travis.yml

@@ -0,0 +1,20 @@
+language: php
+
+# Add php version so composer doesn't complain
+php:
+  - 7.1
+
+services:
+  - docker
+
+env:
+  - DRUPAL_ROOT=/var/www/html
+
+before_script:
+  - docker pull statonlab/tripal3
+
+script:
+  - docker run -it -d --rm --name tripal -v "$(pwd)":/modules/tripal_jbrowse statonlab/tripal3
+  - sleep 30 # We pause here so postgres and apache complete booting up
+  - docker exec -it tripal drush pm-enable -y tripal_jbrowse
+  - docker exec -it tripal bash -c "cd /modules/tripal_jbrowse && composer install && DRUPAL_ROOT=/var/www/html ./vendor/bin/phpunit"

composer.json

@@ -0,0 +1,5 @@
+{
+    "require-dev": {
+        "statonlab/tripal-test-suite": "^1.5"
+    }
+}

composer.lock

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+}

phpunit.xml

@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<phpunit xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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+         convertWarningsToExceptions="true"
+         bootstrap="tests/bootstrap.php"
+         verbose="true"
+         colors="true">
+  <testsuites>
+    <testsuite name="default">
+      <directory suffix="Test.php">tests</directory>
+    </testsuite>
+  </testsuites>
+</phpunit>

tests/DataFactory.php

@@ -0,0 +1,190 @@
+<?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->unique()->word .  uniqid(),
+   // 'name' => $faker->unique($reset = TRUE)->word ,
+    'definition' => $faker->text,
+  ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.db', function (Faker\Generator $faker) {
+  return [
+    'name' => $faker->unique()->word .  uniqid(),
+    '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->word,
+    'definition' => $faker->text,
+    'is_obsolete' => 0,
+    'is_relationshiptype' => 0,
+  ];
+});
+
+/** @see  StatonLab\TripalTestSuite\Database\Factory::define() */
+Factory::define('chado.organism', function (Faker\Generator $faker) {
+
+  $genus = $faker->word;
+  $species = $faker->word;
+
+  $abbr = substr($genus, 0) + ". " + $species;
+
+  return [
+    'abbreviation' => $abbr,
+    'genus' => $genus,
+    'species' => $faker->name,
+    'common_name' => $faker->word,
+    '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->word,
+    'uniquename' => $faker->unique()->word,
+    'organism_id' => factory('chado.organism')->create()->organism_id,
+    'type_id' => factory('chado.cvterm')->create()->cvterm_id,
+  ];
+});
+
+
+Factory::define('chado.analysis', function (Faker\Generator $faker) {
+  return [
+    'name' => $faker->word,
+    'description' => $faker->text,
+    'program' => $faker->unique()->word,
+    'programversion' => $faker->unique()->word,
+    'sourcename' => $faker->unique()->word,
+    'algorithm' => $faker->word,
+    'sourcename' => $faker->word,
+    'sourceversion' => $faker->word,
+    'sourceuri' => $faker->word,
+    // 'timeexecuted' => $faker->time()// needs to match 2018-03-23 15:08:00.000000
+  ];
+});
+
+Factory::define('chado.contact', function (Faker\Generator $faker) {
+  return [
+    'type_id' => factory('chado.cvterm')->create()->cvterm_id,
+    'name' => $faker->name,
+    'description' => $faker->text,
+  ];
+});
+
+
+Factory::define('chado.biomaterial', function (Faker\Generator $faker) {
+  return [
+
+    'taxon_id' => factory('chado.organism')->create()->organism_id,
+    'biosourceprovider_id' => factory('chado.contact')->create()->contact_id,
+    'dbxref_id' => factory('chado.dbxref')->create()->dbxref_id,
+    'name' => $faker->unique()->word,
+    'description' => $faker->text,
+
+  ];
+});
+
+
+Factory::define('chado.featuremap', function (Faker\Generator $faker) {
+  return [
+
+    'name' => $faker->unique()->word,
+    'description' => $faker->text,
+    'unittype_id' => factory('chado.cvterm')->create()->cvterm_id,
+  ];
+});
+
+Factory::define('chado.featurepos', function (Faker\Generator $faker) {
+  return [
+    'featuremap_id' => factory('chado.featuremap')->create()->featuremap_id,
+    'feature_id' => factory('chado.feature')->create()->feature_id,
+    'map_feature_id' => factory('chado.feature')->create()->feature_id,
+    'mappos' => $faker->randomFloat,
+  ];
+});
+
+
+// IMPORTANT!!!!
+// IF you use this factory, call 
+//
+//  $prev_db = chado_set_active('chado');
+//
+// beforehand, and 
+//
+//  chado_set_active($prev_db);
+//
+// afterwards.
+
+
+Factory::define('chado.featureloc', function (Faker\Generator $faker) {
+  
+
+ $a = $faker->randomNumber;
+ $b = $faker->randomNumber;
+
+ return [
+
+   'feature_id' => factory('chado.feature')->create()->feature_id,
+   'srcfeature_id' => factory('chado.feature')->create()->feature_id,
+   'fmin' => min([$a, $b]),
+   'is_fmin_partial' => 0,
+   'fmax' => max([$a, $b]),
+   'is_fmax_partial' => 0,
+   'strand' => NULL,
+   'phase' => NULL,
+   'residue_info' => $faker->word,
+   'locgroup' => 0,
+   'rank' => 0,
+  ];
+  
+});
+
+Factory::define('chado.library', function (Faker\Generator $faker) {
+  return [
+    'organism_id' => factory('chado.organism')->create()->organism_id,
+    'name' => $faker->word,
+    'uniquename' => $faker->unique()->word,
+    'type_id' => factory('chado.cvterm')->create()->cvterm_id,
+    'is_obsolete' => 0,
+  ];
+});
+
+Factory::define('chado.project', function (Faker\Generator $faker) {
+  return [
+
+    'name' => $faker->word,
+    'description' => $faker->text,
+  ];
+});

tests/DatabaseSeeders/examples/DevSeedSeeder.php

@@ -0,0 +1,383 @@
+<?php
+
+namespace Tests\DatabaseSeeders;
+
+use StatonLab\TripalTestSuite\Database\Seeder;
+use \Exception;
+
+class DevSeedSeeder extends Seeder
+{
+    /**
+     * Part one:
+     * Chado records.
+     * These are records used by many of the below importers.
+     * ALL importers require an organism.
+     * The expression data loader will associate the data with the
+     * $expression_analysis record. All other importers associate data with the
+     * $sequence_analysis. Uncomment the array to create that chado record.
+     */
+
+protected $organism = [
+        'common_name' => 'F. excelsior miniature',
+        'genus' => 'Fraxinus',
+        'species' => 'excelsior',
+        'abbreviation' => 'F. excelsor',
+        'comment' => 'Loaded with TripalDev Seed.',
+      ];
+
+protected $sequence_analysis = [
+      'name' => 'Fraxinus exclesior miniature dataset',
+      'description' => 'Tripal Dev Seed',
+    ];
+
+    protected $expression_analysis = [
+
+      'name' => 'Fraxinus exclesior miniature dataset Expression Analysis',
+      'description' => 'Tripal Dev Seed',
+    ];
+
+  protected $blastdb = [
+    'name' => 'DevSeed Database: TREMBL',
+    'description' => 'A dummy database created by DevSeed',
+  ];
+
+    /**
+     * Part 2:
+     * Files.
+     * Each importer will take a file argument.  This argument should be an array
+     * with one of the following two keys: file_remote => url where the file is
+     * located file_local => server path where the file is located.
+     */
+
+    protected $landmark_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/sequences/empty_landmarks.fasta'];
+
+    protected $landmark_type = 'supercontig';
+
+    protected $mRNA_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/sequences/mrna_mini.fasta'];
+
+    protected $protein_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/sequences/polypeptide_mini.fasta'];
+
+    protected $gff_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/gff/filtered.gff'];
+
+    protected $blast_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/gff/filtered.gff'];
+
+    protected $biomaterial_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/biomaterials/biomaterials.xml'];
+
+    protected $expression_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/expression/expression.tsv'];
+
+    protected $interpro_file = ['file_remote' => 'https://raw.githubusercontent.com/statonlab/tripal_dev_seed/master/Fexcel_mini/ips/polypeptide_mini.fasta.xml'];
+
+    // Regular expression that will link the protein name to the mRNA parent feature name.
+   // protected $prot_regexp = '/(FRA.*?)(?=:)/';
+
+    protected $prot_regexp = null;
+
+    public function __construct()
+    {
+
+        if ($this->organism) {
+
+            try {
+                $organism = $this->fetch_chado_record('chado.organism', [
+                    'common_name',
+                    'organism_id',
+                ], $this->organism);
+            } catch (\Exception $e) {
+                echo $e->getMessage();
+                exit;
+            }
+
+            $this->organism = $organism;
+
+            if ($this->sequence_analysis) {
+
+                try {
+                    $seq_analysis = $this->fetch_chado_record('chado.analysis', ['analysis_id'],
+                        $this->sequence_analysis);
+                } catch (\Exception $e) {
+                    echo $e->getMessage();
+                    exit;
+                }
+                $this->sequence_analysis = $seq_analysis;
+            }
+
+            if ($this->expression_analysis) {
+                try {
+                    $expression_analysis = $this->fetch_chado_record('chado.analysis', ['analysis_id'],
+                        $this->expression_analysis);
+                } catch (\Exception $e) {
+                    echo $e->getMessage();
+                    exit;
+                }
+
+                $this->expression_analysis = $expression_analysis;
+            }
+        }
+
+        if ($this->blastdb) {
+            try {
+                $blastdb = $this->fetch_chado_record('chado.db', ['db_id'], $this->blastdb);
+            } catch (\Excetion $e) {
+                echo $e->getMessage();
+            }
+
+            $this->blastdb = $blastdb;
+        }
+    }
+
+    /**
+     * Runs all loaders.
+     * Will only run loaders where the files have been uncommented at the start
+     * of the class.
+     */
+    public function up()
+    {
+
+        if ($this->landmark_file) {
+
+            $run_args = [
+                'organism_id' => $this->organism->organism_id,
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                'seqtype' => $this->landmark_type,
+                'method' => 2, //default insert and update
+                'match_type' => 1, //unique name default
+                //optional
+                're_name' => null,
+                're_uname' => null,
+                're_accession' => null,
+                'db_id' => null,
+                'rel_type' => null,
+                're_subject' => null,
+                'parent_type' => null,
+            ];
+            $this->load_landmarks($run_args, $this->landmark_file);
+        }
+
+        if ($this->gff_file) {
+            $run_args = [
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                'organism_id' => $this->organism->organism_id,
+                'use_transaction' => 1,
+                'add_only' => 0,
+                'update' => 1,
+                'create_organism' => 0,
+                'create_target' => 0,
+
+                ///regexps for mRNA and protein.
+                're_mrna' => null,
+                're_protein' => $this->prot_regexp,
+                //optional
+                'target_organism_id' => null,
+                'target_type' => null,
+                'start_line' => null,
+                'landmark_type' => null,
+                'alt_id_attr' => null,
+            ];
+            $this->load_GFF($run_args, $this->gff_file);
+        }
+
+        if ($this->mRNA_file) {
+
+            $run_args = [
+                'organism_id' => $this->organism->organism_id,
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                'seqtype' => 'mRNA',
+                'method' => 2, //default insert and update
+                'match_type' => 1, //unique name default
+                //optional
+                're_name' => null,
+                're_uname' => null,
+                're_accession' => null,
+                'db_id' => null,
+                'rel_type' => null,
+                're_subject' => null,
+                'parent_type' => null,
+            ];
+            $this->load_mRNA_FASTA($run_args, $this->mRNA_file);
+        }
+
+        if ($this->protein_file) {
+            $run_args = [
+                'organism_id' => $this->organism->organism_id,
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                'seqtype' => 'polypeptide',
+                'method' => 2,
+                'match_type' => 1,
+                //optional
+                're_name' => null,
+                're_uname' => null,
+                're_accession' => null,
+                'db_id' => null,
+            ];
+
+            if ($this->prot_regexp) {
+                //links polypeptide to mRNA
+                $run_args['rel_type'] = 'derives_from';
+                $run_args['re_subject'] = $this->prot_regexp;
+                $run_args['parent_type'] = 'mRNA';
+            }
+            $this->load_polypeptide_FASTA($run_args, $this->protein_file);
+        }
+
+        if ($this->interpro_file) {
+
+            $run_args = [
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                //optional
+                'query_type' => 'mRNA',
+                'query_re' => $this->prot_regexp,
+                'query_uniquename' => null,
+                'parsego' => true,
+            ];
+
+            $this->load_interpro_annotations($run_args, $this->interpro_file);
+        }
+
+        if ($this->blast_file) {
+            $run_args = [
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                'no_parsed' => 25,//number results to parse
+                'query_type' => 'mRNA',
+                //optional
+                'blastdb' => $this->blastdb->db_id,
+                'blastfile_ext' => null,
+                'is_concat' => 0,
+                'query_re' => null,
+                'query_uniquename' => 0,
+            ];
+
+            $this->load_blast_annotations($run_args, $this->blast_file);
+        }
+
+        if ($this->biomaterial_file) {
+            $run_args = [
+                'organism_id' => $this->organism->organism_id,
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+            ];
+            //optional: specifies specific CVterms for properties/property values.  Not used here.
+            //'cvterm_configuration' => NULL,
+            //'cvalue_configuration' => NULL];
+
+            $this->load_biomaterials($run_args, $this->biomaterial_file);
+        }
+
+        if ($this->expression_file) {
+            $run_args = [
+                'filetype' => 'mat', //matrix file type
+                'organism_id' => $this->organism->organism_id,
+                'analysis_id' => $this->sequence_analysis->analysis_id,
+                //optional
+                'fileext' => null,
+                'feature_uniquenames' => 'uniq',
+                're_start' => null,
+                're_stop' => null,
+                'feature_uniquenames' => null,
+                'quantificationunits' => null,
+            ];
+            $this->load_expression($run_args, $this->expression_file);
+        }
+    }
+
+    private function load_landmarks($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/FASTAImporter');
+
+        $importer = new \FASTAImporter();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_mRNA_FASTA($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/FASTAImporter');
+
+        $importer = new \FASTAImporter();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_polypeptide_FASTA($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/FASTAImporter');
+
+        $importer = new \FASTAImporter();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_interpro_annotations($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_analysis_interpro', 'includes/TripalImporter/InterProImporter');
+
+        $importer = new \InterProImporter();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_GFF($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/GFF3Importer');
+
+        $importer = new \GFF3Importer();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_blast_annotations($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_analysis_blast', 'includes/TripalImporter/BlastImporter');
+
+        $importer = new \BlastImporter();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_biomaterials($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_biomaterial', 'includes/TripalImporter/tripal_biomaterial_loader_v3');
+
+        $importer = new \tripal_biomaterial_loader_v3();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function load_expression($run_args, $file)
+    {
+        module_load_include('inc', 'tripal_analysis_expression',
+            'includes/TripalImporter/tripal_expression_data_loader');
+
+        $importer = new \tripal_expression_data_loader();
+        $importer->create($run_args, $file);
+        $importer->prepareFiles();
+        $importer->run();
+    }
+
+    private function fetch_chado_record($table, $fields, $factory_array)
+    {
+        $query = db_select($table, 't')->fields('t', $fields);
+
+        foreach ($factory_array as $key => $value) {
+            $query->condition($key, $value);
+        }
+
+        $count_query = $query;
+        $count = (int) $count_query->countQuery()->execute()->fetchField();
+
+        if ($count === 0) {
+            return factory($table)->create($factory_array);
+        }
+
+        if ($count === 1) {
+            return $query->execute()->fetchObject();
+        }
+
+        throw new Exception("Error creating object for: ".$table.".\n Array supplied matches ".$count_query." results, must match 1.");
+    }
+}

tests/DatabaseSeeders/examples/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

@@ -0,0 +1,4 @@
+<?php
+require_once __DIR__.'/../vendor/autoload.php';
+
+new \StatonLab\TripalTestSuite\TripalTestBootstrap();

tests/example.env

@@ -0,0 +1,3 @@
+BASE_URL=http://localhost
+DRUPAL_ROOT=/var/www/html
+FAKER_LOCALE=en_US