add tests for fasta importer

tests/tripal_chado/data/two_prots.fasta

@@ -0,0 +1,4 @@
+>FRAEX38873_v2_000000010.1
+MDQNQFANELISSYFLQQWRHNSQTLTLNPTPSNSGTESDSARSDLEYEDEGEEFPTELDTVNSSGGFSVVGPGKLSVLYPNVNLHGHDVGVVHANCAAPSKRLLYYFEMYVKNAGAKGQIAIGFITSAFKVRRHPGWEANTYGYHGDDGLLYRGRGKGESFGPMYTTDDTKYTTGDTVGGGINYATQEFFFTKNGVVVGTVSKDVKSPVFPTVAVHSQGEEVTVNFGKDPFVFDIKAYEAEQRAIQQEKIDCISIPLDAGHGLVRSYLQHYGYEGTLEFFDMASKSTAPPISLVPENGFNEEDNVYAMNRRTLRELIRHGEIDETFAKLRELYPQIVQDDRSSICFLLHTQKFIELVRVGKLEEAVLYGRSEFEKFKRRSEFDDLVKDCAALLAYERPDNSSVGYLLRESQRELVADAVNAIILATNPNVKDPKCCLQSRLERLLRQLTACFLEKRSLNGGDGEAFHLRRILKSGKKG
+>FRAEX38873_v2_000000010.2
+MDQNQFANELISSYFLQQWRHNSQTLTLNPTPSNSGTESDSARSDLEYEDEGEEFPTELDTVNSSGGFSVVGPGKLSVLYPNVNLHGHDVGVVHANCAAPSKRLLYYFEMYVKNAGAKGQIAIGFITSAFKVRRHPGWEANTYGYHGDDGLLYRGRGKGESFGPMYTTDDTKYTTGDTVGGGINYATQEFFFTKNGVVVGTVSKDVKSPVFPTVAVHSQGEEVTVNFGKDPFVFDIKAYEAEQRAIQQEKIDCISIPLDAGHGLVRSYLQHYGYEGTLEFFDMASKSTAPPISLVPENGFNEEDNVYAMNRRTLRELIRHGEIDETFAKLRELYPQIVQDDRSSICFLLHTQKFIELVRVGKLEEAVLYGRSEFEKFKRRSEFDDLVKDCAALLAYERPDNSSVGYLLRESQRELVADAVNAIILATNPNVKDPKCCLQSRLERLLRQLTACFLEKRSLNGGDGEAFHLRRILKSGKKG

tests/tripal_chado/loaders/FASTAImporterTest.php

@@ -0,0 +1,87 @@
+<?php
+
+namespace Tests;
+
+use StatonLab\TripalTestSuite\DBTransaction;
+use StatonLab\TripalTestSuite\TripalTestCase;
+
+class FASTAImporterTest 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.
+   */
+
+  /**
+   * @group fasta
+   * @group chado
+   */
+  public function testImporterAssociatesParentWithoutRegexp() {
+    module_load_include('inc', 'tripal_chado', 'includes/TripalImporter/FASTAImporter');
+    $importer = new \FASTAImporter();
+
+    //this test will first create an organism and mrna features with the same name as devseed proteins.
+    //It will then load the devseed protein fasta via the importer.
+    //Finally it will ensure feature_relationships exist with the test mrna.
+
+    $organism = factory('chado.organism')->create();
+    $mrna_term = chado_get_cvterm(['id' => 'SO:0000234']);
+    $analysis = factory('chado.analysis')->create();
+    $mrna_1 = factory('chado.feature')->create([
+      'type_id' => $mrna_term->cvterm_id,
+      'organism_id' => $organism->organism_id,
+      'name' => 'FRAEX38873_v2_000000010.1',
+      'uniquename' => 'FRAEX38873_v2_000000010.1',
+    ]);
+    $mrna_2 = factory('chado.feature')->create([
+      'type_id' => $mrna_term->cvterm_id,
+      'organism_id' => $organism->organism_id,
+      'name' => 'FRAEX38873_v2_000000010.2',
+      'uniquename' => 'FRAEX38873_v2_000000010.2',
+    ]);
+    $file = ['file_local' => __DIR__ . '/../data/two_prots.fasta'];
+
+    $run_args = [
+      'analysis_id' => $analysis->analysis_id,
+      'organism_id' => $organism->organism_id,
+      'seqtype' => 'polypeptide',
+      'parent_type' => "mRNA",
+      'rel_type' => "derives_from",
+      'method' => '2',
+      'match_type' => '1',
+      're_name' => "",
+      're_uname' => "",
+      're_accession' => "",
+      'db_id' => "",
+      're_subject' => "",
+      'match_type' => "1",
+    ];
+
+    $importer->create($run_args, $file);
+    $importer->prepareFiles();
+    $importer->run();
+
+
+    $result = db_select('chado.feature', 'f')
+      ->fields('f')
+      ->condition('f.organism_id', $organism->organism_id)
+      ->execute()
+      ->fetchAll();
+
+    $this->assertNotEquals(2, count($result), 'The child features were not loaded when a regexp was not provided.');
+
+
+    $result = db_select('chado.feature_relationship', 'fr')
+      ->fields('fr')
+      ->condition('fr.object_id', $mrna_1->feature_id)
+      ->join('chado.feature', 'f', 'f.feature_id = fr.subject_id')
+      ->execute()
+      ->fetchObject();
+
+    $this->assertNotFalse($result, 'relationship was not added to parente feature when regexp not provided (same parent/child name).');
+  }
+}

tripal_chado/includes/TripalImporter/FASTAImporter.inc

@@ -320,7 +320,6 @@ class FASTAImporter extends TripalImporter {
    * @see TripalImporter::run()
    */
   public function run() {
-
     $arguments = $this->arguments['run_args'];
     $file_path = $this->arguments['files'][0]['file_path'];
 
@@ -534,7 +533,7 @@ class FASTAImporter extends TripalImporter {
         }
 
         // Get the relationship subject
-         $subject = $name;
+         $subject = $name ? $name : $uname;
         if (!empty($re_subject)) {
           preg_match("/$re_subject/", $line, $matches);
           $subject = trim($matches[1]);