Merge pull request #1417 from tripal/t4g1-1400-generic_vocab_classes

Deafult (non Chado) Vocabulary and IdSpace Plugin.

tripal/src/Plugin/TripalVocabulary/TripalDefaultVocabulary.php

@@ -0,0 +1,275 @@
+<?php
+
+namespace Drupal\tripal\Plugin\TripalVocabulary;
+
+use Drupal\tripal\TripalVocabTerms\TripalVocabularyBase;
+
+/**
+ * Default implementation of the TripalVocabularyBase.
+ *
+ *  @TripalVocabulary(
+ *    id = "tripal_default_vocabulary",
+ *    label = @Translation("Deafult Tripal Vocabulary Plugin"),
+ *  )
+ */
+class TripalDefaultVocabulary extends TripalVocabularyBase {
+  /**
+   * An instance of the TripalLogger.
+   *
+   * @var \Drupal\tripal\Services\TripalLogger
+   */
+  protected $messageLogger = NULL;
+
+  /**
+   * A simple boolean to prevent Chado queries if the vocabulary isn't valid.
+   *
+   * @var bool
+   */
+  protected $is_valid = False;
+
+  /**
+   * {@inheritdoc}
+   */
+  public function __construct(array $configuration, $plugin_id, $plugin_definition) {
+    parent::__construct($configuration, $plugin_id, $plugin_definition);
+
+    // Instantiate the TripalLogger
+    $this->messageLogger = \Drupal::service('tripal.logger');
+  }
+
+  /**
+   * Loads the vocabulary record.
+   *
+   * @return
+   *   An associative array containing the list of vocabularies.
+   */
+  protected function loadVocab() {
+
+    $conn = \Drupal::service('database');
+    $query = $conn->select('tripal_terms_vocabs', 'vocabs')
+      ->condition('name', $this->getName(), '=')
+      ->fields('vocabs', ['name', 'label', 'url', 'idspaces']);
+    $result = $query->execute();
+    if ($result) {
+      return $result->fetchAssoc();
+    }
+    return NULL;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function getIdSpaceNames() {
+    $cv = $this->loadVocab();
+    $idspaces = unserialize($cv['idspaces']);
+    return $idspaces;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function getLabel() {
+    $cv = $this->loadVocab();
+    return $cv['label'];
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function recordExists() {
+   $cv = $this->loadVocab();
+   if ($cv and $cv['name'] == $this->getName()) {
+      return True;
+    }
+    return False;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function isValid() {
+
+    // Make sure the name of this collection does not exceeed the allowed size in Chado.
+    $name = $this->getName();
+    if (!empty($name) AND (strlen($name) > 255)) {
+      $this->messageLogger->error('TripalDefaultVocabulary: The vocabulary name must not be longer than @size characters. ' +
+          'The value provided was: @value',
+	  ['@size' => 255, '@value' => $this->getName()]);
+      $this->is_valid = FALSE;
+      return FALSE;
+    }
+    $this->is_valid = TRUE;
+    return TRUE;
+  }
+
+  /**
+   * Returns the namespace of the vocabulary
+   *
+   * This should be identical to the name of the collection, and
+   * therefore, there is no setter function.
+   *
+   * @return string $namespace
+   *   The namespace of the vocabulary.
+   */
+  public function getNameSpace() {
+    return $this->getName();
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function destroy() {
+    $this->messageLogger->warning('The TripalDefaultVocabulary::destroy() function is currently not implemented');
+  }
+
+    /**
+   * {@inheritdoc}
+   */
+  public function getTerms($name, $exact = True){
+    $this->messageLogger->warning('The TripalDefaultVocabulary::getTerms() function is currently not implemented');
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function setURL($url) {
+    // @todo there may be a problem in the future if we are able to
+    // associate borrowed terms with a vocabulary.  If we
+    // add the ID space of borrowed terms to a vocabulary then
+    // setting the URL will be incorrect for those ID spaces.
+
+    // Don't set a value for a vocabulary that isn't valid.
+    if (!$this->is_valid) {
+      return False;
+    }
+
+    // Don't exceed the expected size of the URL for the database.
+    if (strlen($url) > 255) {
+      $this->messageLogger->error('TripalDefaultVocabulary: The vocabulary name must not be longer than @size characters. ' +
+          'The value provided was: @value',
+          ['@size' => 255, '@value' => $this->getName()]);
+          return False;
+    }
+
+    // If we don't have any ID spaces then there is no URL.
+    $id_spaces = $this->getIdSpaceNames();
+    if (count($id_spaces) == 0) {
+      $this->messageLogger->error('TripalDefaultVocabulary: Cannot set the URL when no ID spaces are present for the vocabulary.');
+      return False;
+    }
+
+    // Update the record in the table for the URL for all ID spaces.
+    $conn = \Drupal::service('database');
+    $update = $conn->update('tripal_terms_vocabs');
+    $update = $update->fields(['url' => $url]);
+    $update = $update->condition('name', $this->getName(), '=');
+    $num_updated = $update->execute();
+    if ($num_updated != 1) {
+      $this->messageLogger->error(t('TripalDefaultVocabulary: The URL could not be updated for the vocabulary, "@vocab.',
+          ['@vocab' => $this->getName()]));
+      return False;
+    }
+    return True;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function getURL() {
+    $cv = $this->loadVocab();
+    return $cv['url'];
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function setLabel($label) {
+    // Don't set a value for a vocabulary that isn't valid.
+    if (!$this->is_valid) {
+      return False;
+    }
+
+    // Make sure the label is not too long.
+    if (empty($label)) {
+      $this->messageLogger->error('TripalDeafultVocabulary: You must provide a label when calling setLabel().');
+      return False;
+    }
+    if (strlen($label) > 255) {
+      $this->messageLogger->error('TripalDeafultVocabulary: The label for the vocabulary must not be longer than @size characters. ' +
+          'The value provided was: @value',
+          ['@size' => 255, '@value' => $label]);
+      return False;
+    }
+
+
+    // Update the record.
+    $chado = \Drupal::service('database');
+    $update = $chado->update('tripal_terms_vocabs');
+    $update = $update->fields(['label' => $label]);
+    $update = $update->condition('name', $this->getName(), '=');
+    $num_updated = $update->execute();
+    if ($num_updated != 1) {
+      $this->messageLogger->error('TripalDefaultVocabulary: The label could not be updated for the vocabulary.');
+      return False;
+    }
+    return True;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function create() {
+
+    // Check if the record already exists in the database, if it
+    // doesn't then insert it.  We don't yet have the definition,
+    // but that's okay, the name is all that isrequired to create
+    // a record in the `cv` table.
+    $conn = \Drupal::service('database');
+    $vocab = $this->loadVocab();
+    if (!$vocab) {
+      $query = $conn->insert('tripal_terms_vocabs');
+      $query = $query->fields([
+        'name' => $this->getName(),
+        'idspaces' => serialize([]),
+      ]);
+      $query->execute();
+    }
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function addIdSpace($idSpace) {
+
+    // Get the ID collection for this idSpace and if it exists 
+    // then add the idSpace to our list.
+    $idsmanager = \Drupal::service('tripal.collection_plugin_manager.idspace');
+    $id = $idsmanager->loadCollection($idSpace);
+    if ($id) {
+      $idspaces = $this->getIdSpaceNames();
+      $idspaces[] = $idSpace;
+      $conn = \Drupal::service('database');
+      $update = $conn->update('tripal_terms_vocabs');
+      $update = $update->fields(['idspaces' => serialize($idspaces)]);
+      $update = $update->condition('name', $this->getName(), '=');
+      $update->execute();
+      return True;
+    }
+    return False;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  public function removeIdSpace($idSpace) {
+    $idspaces = $this->getIdSpaceNames();
+    if (in_array($idSpace, $idspaces)) {
+      $idspaces = array_diff($idspaces, [$idSpace]);
+      $conn = \Drupal::service('database');
+      $update = $conn->update('tripal_terms_vocabs');
+      $update = $update->fields(['idspaces' => serialize($idspaces)]);
+      $update = $update->condition('name', $this->getName(), '=');
+      $update->execute();
+    }
+  }
+}

tripal/tests/src/Functional/Plugin/TripalDefaultIdSpaceTest.php

@@ -0,0 +1,100 @@
+<?php
+
+namespace Drupal\Tests\tripal\Functional\Plugin;
+
+use Drupal\Core\Database\Database;
+use Drupal\Tests\tripal\Functional\TripalTestBrowserBase;
+use Drupal\Core\Test\FunctionalTestSetupTrait;
+use Drupal\tripal\TripalVocabTerms\TripalTerm;
+
+
+
+/**
+ * Tests for the TripalDefaultIdSpace classes
+ *
+ * @group Tripal
+ * @group TripalDefaultIdSpace
+ */
+class TripalDefaultIdSpaceTest extends TripalTestBrowserBase {
+
+
+  /**
+   * A helper function to retrieve an id_space record.
+   *
+   * @param string $dbname
+   *   The name of the id_space to lookup.
+   *
+   * @return A database query result.
+   */
+  protected function getIdSpace($id_space) {
+
+    $conn = \Drupal::service('database');
+    $query = $conn->select('tripal_terms_idspaces', 'idspace');
+    $query = $query->condition('name', $id_space, '=');
+    $query = $query->fields('idspace');
+    $result = $query->execute();
+    if (!$result) {
+      return [];
+    }
+    return $result->fetchAssoc();
+  }
+
+  /**
+   * Tests the TripalDefaultIdSpace and TripalDefaultVocabulary Classes
+   *
+   */
+  public function testTripaDefaultIdSpace() {
+
+    // Create Collection managers.
+    $idsmanager = \Drupal::service('tripal.collection_plugin_manager.idspace');
+    $vmanager = \Drupal::service('tripal.collection_plugin_manager.vocabulary');
+
+    // These are the values we'll use for the ID space and vocablary.
+    $GO_idspace = 'GO';
+    $GO_cc_namespace = 'cellular_component';
+    $GO_bp_namespace = 'biological_process';
+    $GO_mf_namespace = 'molecular_function';
+    $GO_description = "The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes";
+    $GO_cc_label = 'Gene Ontology Cellular Component Vocabulary';
+    $GO_bp_label = 'Gene Ontology Biological Process Vocabulary';
+    $GO_mf_label = 'Gene Ontology Molecular Function Vocabulary';
+    $GO_urlprefix = "http://amigo.geneontology.org/amigo/term/{db}:{accession}";
+    $GO_url = 'http://geneontology.org/';
+
+    //
+    // Testing TripalDefaultIdSpace Functionality
+    //
+
+    // Create the ID space object and make sure a Chado record got created.
+    $GO = $idsmanager->createCollection($GO_idspace, "tripal_default_id_space");
+    $db = $this->getIdSpace($GO_idspace);
+    $this->assertTrue($db['name'] == $GO_idspace, 'The name was not set correctly by the TripaDefaultIdSpace object.');
+    $this->assertEmpty($db['description'], 'The description should not be set by the TripaDefaultIdSpace object just yet.');
+    $this->assertEmpty($db['urlprefix'], 'The URL prefix should not be set by the TripaDefaultIdSpace object just yet.');
+
+    // Set the description to make sure it gets set in Chado.
+    $GO->setDescription($GO_description);
+    $db = $this->getIdSpace($GO_idspace);
+    $this->assertTrue($db['name'] == $GO_idspace, 'The name was not set correctly after updating by the TripaDefaultIdSpace object.');
+    $this->assertTrue($db['description'] == $GO_description, 'The description was not set correctly by the TripaDefaultIdSpace object.');
+    $this->assertEmpty($db['urlprefix'], 'The URL prefix should not be set by the TripaDefaultIdSpace object just yet.');
+
+    // Set the URL prefix to make sure it gets set in Chado.
+    $GO->setURLPrefix($GO_urlprefix);
+    $db = $this->getIdSpace($GO_idspace);
+    $this->assertTrue($db['name'] == $GO_idspace, 'The name was not set correctly after updating by the TripaDefaultIdSpace object.');
+    $this->assertTrue($db['description'] == $GO_description, 'The description was not set correctly after updating by the TripaDefaultIdSpace object.');
+    $this->assertTrue($db['urlprefix'] == $GO_urlprefix, 'The URL prefix was not set correctly by the TripaDefaultIdSpace object.');
+
+    // Make sure the getters work.
+    $this->assertTrue($GO->getURLPrefix() == $GO_urlprefix, "The TripaDefaultIdSpace object did not return a correct URL prefix.");
+    $this->assertTrue($GO->getDescription() == $GO_description, "The TripaDefaultIdSpace object did not return a correct description.");
+
+    // Change the description and URL prefix and make sure it updates
+    $GO->setDescription('Changed');
+    $GO->setURLPrefix('Changed');
+    $this->assertTrue($GO->getDescription() == 'Changed', "The TripaDefaultIdSpace object did not update the description.");
+    $this->assertTrue($GO->getURLPrefix() == 'Changed', "The TripaDefaultIdSpace object did not update the URL prefix.");
+
+  }
+}