Added missing file ripal_chado.vocab_storage.inc

tripal_chado/includes/tripal_chado.vocab_storage.inc

@@ -0,0 +1,227 @@
+<?php
+/**
+ * Implements hook_vocab_storage_info().
+ *
+ * This hook is created by the Tripal module and is not a Drupal hook.
+ */
+function tripal_chado_vocab_storage_info() {
+  return array(
+    'term_chado_storage' => array(
+      'label' => t('Chado storage'),
+      'module' => 'tripal_chado',
+      'description' => t('Integrates terms stored in the local Chado database
+          with Tripal entities.'),
+      'settings' => array(),
+    ),
+  );
+}
+
+/**
+ * Implements hook_vocab_get_term().
+ *
+ * This hook is created by the Tripal module and is not a Drupal hook.
+ */
+function tripal_chado_vocab_get_term($vocabulary, $accession) {
+  // Create an empty term array for returning if there is a problem.
+  $empty_term = array(
+    'vocabulary' => $vocabulary,
+    'accession'  => $accession,
+    'name'       => '',
+    'definition' => 'Term is undefined.',
+    'url'  => '',
+    // The following are not required for the returned array but we'll
+    // add these for convenience later when we look at the TripalTerm
+    // objects and these will be there.
+    'cvterm'     => NULL,
+  );
+
+  // It's possible that Chado is not available (i.e. it gets renamed
+  // for copying) but Tripal has already been prepared and the
+  // entities exist.  If this is the case we don't want to run the
+  // commands below.
+  if (!chado_table_exists('cvterm')) {
+    return $empty_term;
+  }
+  $match = array(
+    'dbxref_id' => array(
+      'db_id' => array(
+        'name' => $vocabulary,
+      ),
+      'accession' => $accession,
+    ),
+  );
+  $cvterm = chado_generate_var('cvterm', $match);
+  if (!$cvterm) {
+    return $empty_term;
+  }
+  $cvterm = chado_expand_var($cvterm, 'field', 'cvterm.definition');
+  $term = array(
+    'vocabulary' => $cvterm->dbxref_id->db_id->name,
+    'accession'  => $cvterm->dbxref_id->accession,
+    'name'       => $cvterm->name,
+    'url'        => '',
+    'definition' => (isset($cvterm->definition)) ? $cvterm->definition : '',
+    // The following are not required for the returned array but we'll
+    // add these for convenience later when we look at the TripalTerm
+    // objects and these will be there.
+    'cvterm'     => $cvterm,
+  );
+  if ($cvterm->dbxref_id->db_id->urlprefix) {
+    $term['url'] = $cvterm->dbxref_id->db_id->urlprefix .
+      $cvterm->dbxref_id->db_id->name . ':' . $cvterm->dbxref_id->accession;
+  }
+  return $term;
+}
+
+/**
+ * Implements hook_vocab_import_form();
+ */
+function tripal_chado_vocab_import_form($form, &$form_state) {
+  module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader');
+  return tripal_cv_obo_form($form, $form_state);
+}
+/**
+ * Implements hook_vocab_import_form_validate();
+ */
+function tripal_chado_vocab_import_form_validate($form, &$form_state) {
+  module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader');
+  return tripal_cv_obo_form_validate($form, $form_state);
+}
+/**
+ * Implements hook_vocab_import_form_submit();
+ */
+function tripal_chado_vocab_import_form_submit($form, &$form_state) {
+  module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.obo_loader');
+  return tripal_cv_obo_form_submit($form, $form_state);
+}
+/**
+ * Implements hook_vocab_select_term_form().
+ */
+function tripal_chado_vocab_select_term_form($form, &$form_state) {
+  $term_name = array_key_exists('values', $form_state) ? $form_state['values']['term_name'] : '';
+
+  // If no term has been selected yet then provide the auto complete field.
+  $form['term_name'] = array(
+    '#title'       => t('Content Type'),
+    '#type'        => 'textfield',
+    '#description' => t("The content type must be the name of a term in
+        a controlled vocabulary and the controlled vocabulary should
+        already be loaded into Tripal.  For example, to create a content
+        type for storing 'genes', use the 'gene' term from the
+        Sequence Ontology (SO)."),
+    '#required'    => TRUE,
+    '#default_value' => $term_name,
+    '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/cvterm/",
+  );
+  $form['select_button'] = array(
+    '#type' => 'submit',
+    '#value' => t('Lookup Term'),
+    '#name' => 'select_cvterm',
+    '#ajax' => array(
+      'callback' => "tripal_chado_vocab_select_term_form_ajax_callback",
+      'wrapper' => "tripal-chado-vocab-select-form",
+      'effect' => 'fade',
+      'method' => 'replace'
+    ),
+  );
+
+  if ($term_name) {
+    $form['terms_list'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Matching Terms'),
+      '#description' => t('Please select the term the best matches the
+          content type you want to create. If the same term exists in
+          multiple vocabularies you will see more than one option below.')
+    );
+    $match = array(
+      'name' => $term_name,
+    );
+    $terms = chado_generate_var('cvterm', $match, array('return_array' => TRUE));
+    $terms = chado_expand_var($terms, 'field', 'cvterm.definition');
+    $num_terms = 0;
+    foreach ($terms as $term) {
+      // Save the user a click by setting the default value as 1 if there's
+      // only one matching term.
+      $default = FALSE;
+      $attrs = array();
+      if ($num_terms == 0 and count($terms) == 1) {
+        $default = TRUE;
+        $attrs = array('checked' => 'checked');
+      }
+       $form['terms_list']['term-' . $term->cvterm_id] = array(
+         '#type' => 'checkbox',
+         '#title' =>  $term->name,
+         '#default_value' => $default,
+         '#attributes' => $attrs,
+         '#description' => '<b>Vocabulary:</b> ' . $term->cv_id->name .
+             '<br><b>Term: </b> ' . $term->dbxref_id->db_id->name . ':' . $term->dbxref_id->accession . '.  ' .
+             '<br><b>Definition:</b>  ' . $term->definition,
+       );
+       $num_terms++;
+    }
+    if ($num_terms == 0) {
+      $form['terms_list']['none'] = array(
+        '#type' => 'item',
+        '#markup' => '<i>' . t('There is no term that matches the entered text.') . '</i>'
+      );
+    }
+    // Add in the button for the cases of no terms or too many.
+    $form['submit_button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Use this term'),
+      '#name' => 'use_cvterm'
+    );
+  }
+
+  $form['#prefix'] = '<div id = "tripal-chado-vocab-select-form">';
+  $form['#suffix'] = '</div>';
+
+  return $form;
+}
+
+/**
+ * Implements an AJAX callback for the tripal_chado_vocab_select_term_form.
+ */
+function tripal_chado_vocab_select_term_form_ajax_callback($form, $form_state) {
+  return $form;
+}
+
+/**
+ * Implements hook_vocab_select_term_form_validate().
+ */
+function tripal_chado_vocab_select_term_form_validate($form, &$form_state) {
+
+  if (array_key_exists('clicked_button', $form_state) and
+      $form_state['clicked_button']['#name'] =='use_cvterm') {
+
+    $cvterm_id = NULL;
+
+    // Make sure we have a cvterm selected
+    $num_selected = 0;
+    foreach ($form_state['values'] as $key => $value) {
+      $matches = array();
+      if (preg_match("/^term-(\d+)$/", $key, $matches) and
+          $form_state['values']['term-' . $matches[1]]) {
+        $cvterm_id = $matches[1];
+        $term = chado_generate_var('cvterm', array('cvterm_id' => $cvterm_id));
+        $num_selected++;
+      }
+    }
+    if ($num_selected == 0) {
+      form_set_error('', 'Please select at least one term.');
+    }
+    else if ($num_selected > 1) {
+      form_set_error('term-' . $cvterm_id, 'Please select only one term from the list below.');
+    }
+    else {
+      $form_state['storage']['vocabulary'] = $term->dbxref_id->db_id->name;
+      $form_state['storage']['accession'] = $term->dbxref_id->accession;
+      $form_state['storage']['term_name'] = $term->name;
+    }
+  }
+  // For any other button click it's an AJAX call and we just want to reubild
+  // the form.
+  else {
+    $form_state['rebuild'] = TRUE;
+  }
+}