Importer instead of form

includes/TripalImporter/EutilsImporter.inc

@@ -0,0 +1,137 @@
+<?php
+
+/**
+ * EUtils Importer for loading remote NCBI accessions.
+ */
+class EutilsImporter extends TripalImporter {
+
+
+  public static $name = 'NCBI EUtils Accession loader';
+  public static $description = 'Import a BLAST XML file into Chado';
+  public static $machine_name = 'eutils_loader';
+  public static $use_analysis = FALSE;
+  public static $button_text = 'Import NCBI Record';
+  public static $methods = [
+    'file_upload' => FALSE,
+    'file_local' => FALSE,
+    'file_remote' => FALSE,
+  ];
+  public static $file_required = FALSE;
+
+  /**
+   * Implements hook_form().
+   *
+   * @see TripalImporter::form()
+   */
+  public function form($form, &$form_state) {
+
+    $form['instructions'] = [
+      '#markup' => t('<p>Please enter an accession and specify a database.</p>
+                  <p>Press the <b>Preview Record</b> button to view the 
+                  retrieved data and metadata.  Pressing <b>Create Chado 
+                  Record</b> will create the record.</p>'),
+    ];
+
+    $db_choices = [
+      'bioproject' => 'BioProject',
+      'biosample' => 'Biosample',
+      'assembly' => 'Assembly',
+    ];
+
+    $form['db'] = [
+      '#type' => 'radios',
+      '#title' => t('NCBI Database'),
+      '#description' => t('The database to query.'),
+      '#options' => $db_choices,
+    ];
+
+    $form['accession'] = [
+      '#type' => 'textfield',
+      '#title' => t('NCBI Accession Number'),
+      '#description' => t('Valid examples: (BioSample 744358 120060 SAMN02261463), (Assembly 91111, 751381, GCA_000516895.1), (BioProject 12384, 394253, 66853, PRJNA185471)'),
+    ];
+
+    $form['callback'] = [
+      '#type' => 'button',
+      '#value' => "Preview Record",
+    ];
+
+    if (isset($form_state['values']['parsed'])) {
+      $form['data'] = [
+        '#type' => 'fieldset',
+        '#title' => 'Data',
+      ];
+
+      $form['data'][] = $form_state['values']['parsed'];
+
+    }
+
+    $form['options'] = [
+      '#type' => 'fieldset',
+      '#title' => "Options",
+    ];
+
+    $form['options']['linked_records'] = [
+      '#type' => 'checkbox',
+      '#title' => t('Create Linked Records'),
+      '#description' => t('Each accession links to other NCBI databases: 
+                          you can create those chado records as well.'),
+      '#default_value' => 1,
+    ];
+
+    return $form;
+  }
+
+  /**
+   * Validate form keys and check the accession on NCBI.
+   *
+   * @see TripalImporter::formValidate()
+   * TODO only run the EUTils check if submitted.
+   */
+  public function formValidate($form, &$form_state) {
+
+    $vals = $form_state['values'];
+
+    $db = $vals['db'];
+    $accession = $vals['accession'];
+
+    if (!$db) {
+      form_set_error('db', 'please select a valid db');
+    }
+
+    if (!$accession) {
+      form_set_error('accession', 'please enter an accession');
+    }
+
+    if (!$db or !$accession) {
+      return;
+    }
+
+    $connection = new \EUtils();
+    try {
+      $connection->setPreview();
+      $parsed = $connection->get($db, $accession);
+      $form_state['values']['parsed'] = $parsed;
+    }
+    catch (\Exception $e) {
+      tripal_set_message($e->getMessage(), TRIPAL_ERROR);
+      return;
+    }
+  }
+
+  /**
+   * Runs the importer.
+   *
+   * @see TripalImporter::run()
+   */
+  public function run() {
+    $arguments = $this->arguments['run_args'];
+    $db = $arguments['db'];
+    $accession = $arguments['accession'];
+    $create_linked_records = $arguments['linked_records'];
+
+    tripal_eutils_create_records($db, $accession, $create_linked_records);
+
+  }
+
+}

tests/ImportFormTest.php

@@ -16,7 +16,7 @@ class ImportFormTest extends TripalTestCase {
   public function testAccessibilityToImportForm() {
     $this->actingAs(1);
 
-    $response = $this->get('admin/tripal/loaders/eutils_ncbi_import');
+    $response = $this->get('admin/tripal/loaders/eutils_loader');
     $response->assertSuccessful()
     ->assertSee('NCBI Accession Number');
   }