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@@ -1,5 +1,399 @@
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<?php
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+/**
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+ * Launchpad for feature administration.
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+ *
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+ * @ingroup tripal_feature
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+ */
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+function tripal_entities_admin_view() {
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+ $output = '';
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+
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+ // set the breadcrumb
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+ $breadcrumb = array();
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+ $breadcrumb[] = l('Home', '<front>');
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+ $breadcrumb[] = l('Administration', 'admin');
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+ $breadcrumb[] = l('Tripal', 'admin/tripal');
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+ $breadcrumb[] = l('Manage Data types', 'admin/tripal/data_types');
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+ drupal_set_breadcrumb($breadcrumb);
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+
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+/* // Add the view
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+ $view = views_embed_view('tripal_feature_admin_features','default');
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+ if (isset($view)) {
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+ $output .= $view;
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+ }
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+ else {
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+ $output .= '<p>The Feature module uses primarily views to provide an '
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+ . 'administrative interface. Currently one or more views needed for this '
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+ . 'administrative interface are disabled. <strong>Click each of the following links to '
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+ . 'enable the pertinent views</strong>:</p>';
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+ $output .= '<ul>';
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+ $output .= '<li>'.l('Features View', 'admin/tripal/chado/tripal_feature/views/features/enable').'</li>';
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+ $output .= '</ul>';
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+ }
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+
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+ // Add a summary chart.
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+ //-----------------------------------
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+ $output .= theme('tripal_feature_bar_chart_type_organism_summary');
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+ drupal_add_js('
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+ Drupal.behaviors.tripalFeature_moveAdminSummaryChart = {
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+ attach: function (context, settings) {
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+ jQuery("#tripal-feature-admin-summary").insertBefore( jQuery(".view-filters") );
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+ }};
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+ ', 'inline'); */
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+
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+ return $output;
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+}
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+
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+/**
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+ *
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+ * @param unknown $form
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+ * @param unknown $form_state
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+ * @return multitype:
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+ */
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+function tripal_entities_admin_publish_form($form, &$form_state) {
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+ $form = array();
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+
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+ // Set the defaults.
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+ $cv_id = NULL;
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+ $term_name = NULL;
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+
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+ // Set defaults using the form state.
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+ if (array_key_exists('values', $form_state)) {
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+ $cv_id = array_key_exists('cv_id', $form_state['values']) ? $form_state['values']['cv_id'] : NULL;
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+ $term_name = array_key_exists('term_name', $form_state['values']) ? $form_state['values']['term_name'] : NULL;
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+ }
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+
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+ // Let the user select the vocabulary and tripal_data but only if they haven't
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+ // already selected a tripal_data.
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+ $sql = "
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+ SELECT CV.cv_id, CV.name
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+ FROM {tripal_entity_type} TET
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+ INNER JOIN {cv} CV on CV.cv_id = TET.cv_id
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+ ORDER BY CV.name
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+ ";
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+ $vocabs = chado_query($sql);
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+ $cvs = array();
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+ while ($vocab = $vocabs->fetchObject()) {
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+ $cvs[$vocab->cv_id] = $vocab->name;
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+ }
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+ $form['cv_id'] = array(
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+ '#type' => 'select',
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+ '#title' => t('Vocabulary'),
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+ '#options' => $cvs,
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+ '#required' => TRUE,
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+ '#description' => t('Select a vocabulary that contains the term you would like to set as publishable. Only vocabularies that are linked to data are shown.'),
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+ '#default_value' => $cv_id,
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+ '#ajax' => array(
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+ 'callback' => "tripal_entities_admin_publish_form_ajax_callback",
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+ 'wrapper' => 'tripal_entities_admin_publish_form',
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+ 'effect' => 'fade',
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+ 'method' => 'replace'
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+ )
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+ );
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+
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+ // If we have a CV ID then we want to provide an autocomplete field
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+ if ($cv_id) {
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+ $form['cvterm_select']['term_name'] = array(
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+ '#title' => t('Data Type'),
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+ '#type' => 'textfield',
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+ '#description' => t("Please enter the name of the data type to set as publishable. The data type must be a valid term in the selected vocabulary. This field will autopopulate as you type to help find available data types."),
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+ '#required' => TRUE,
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+ '#default_value' => $term_name,
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+ '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
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+ );
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+
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+ $form['cvterm_select']['select_button'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Publish Data'),
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+ '#name' => 'publish',
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+ );
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+ }
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+
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+
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+ $form['#prefix'] = '<div id="tripal_entities_admin_publish_form">';
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+ $form['#suffix'] = '</div>';
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+ return $form;
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+}
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+
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+/**
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+ * An Ajax callback for the tripal_entities_admin_publish_form..
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+ */
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+function tripal_entities_admin_publish_form_ajax_callback($form, $form_state) {
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+ // return the form so Drupal can update the content on the page
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+ return $form;
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+}
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+/**
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+ * Implements hook_validate() for the tripal_entities_admin_publish_form.
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+ *
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+ */
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+function tripal_entities_admin_publish_form_validate($form, &$form_state) {
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+ $cv_id = $form_state['values']['cv_id'];
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+ $term_name = $form_state['values']['term_name'];
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+
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+ // Make sure the term_name is a real term in the vocabulary.
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+ $type = tripal_get_cvterm(array(
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+ 'name' => $term_name,
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+ 'cv_id' => $cv_id
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+ ));
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+ if (!$type) {
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+ form_set_error('term_name', t("The data type is not a valid name for the selected vocabulary."));
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+ }
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+
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+ // Make sure the term is used in the site:
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+ $values = array(
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+ 'cvterm_id' => $type->cvterm_id,
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+ );
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+ $bundles = chado_select_record('tripal_entity_bundle', array('bundle_id'), $values);
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+ if (count($bundles) == 0) {
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+ form_set_error('term_name', t("The data type, %type, is not associated with data on this site and thus cannot be set as publishable.", array('%type' => $term_name)));
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+ }
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+
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+ // Make sure the term is not already published.
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+ $values = array(
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+ 'cvterm_id' => $type->cvterm_id,
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+ 'publish' => 1,
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+ );
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+ $bundles = chado_select_record('tripal_entity_bundle', array('bundle_id'), $values);
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+ if (count($bundles) > 0) {
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+ form_set_error('term_name', t("This data type is already set as publishable."));
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+ }
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+}
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+/**
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+ * Implements hook_submit() for the tripal_entities_admin_publish_form.
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+ *
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+ */
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+function tripal_entities_admin_publish_form_submit($form, &$form_state) {
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+ $cv_id = $form_state['values']['cv_id'];
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+ $term_name = $form_state['values']['term_name'];
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+
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+ // Get the data type using the $term_name and $cv_id.
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+ $type = chado_generate_var('cvterm', array('cv_id' => $cv_id, 'name' => $term_name));
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+
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+
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+ // Start the transaction.
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+ $transaction = db_transaction();
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+ try {
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+
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+ // We don't need to check if the vocabulary is used because the
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+ // form only shows those vocabs that are used.
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+
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+ // Mark this entity as published.
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+ $match = array('cv_id' => $cv_id);
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+ $values = array('publish' => 1);
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+ $success = chado_update_record('tripal_entity_type', $match, $values);
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+ if (!$success) {
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+ throw new Exception('Cannot set the vocabulary as publishable');
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+ }
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+
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+ // We have already checked in the validate if the term already exists
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+ // as a bundle. So, if we're here we can enable it.
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+ $match = array('cvterm_id' => $type->cvterm_id);
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+ $values = array('publish' => 1);
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+ $success = chado_update_record('tripal_entity_bundle', $match, $values);
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+ if (!$success) {
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+ throw new Exception('Cannot set the data type as publishable');
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+ }
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+
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+ // Get the bundle
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+ $records = chado_select_record('tripal_entity_bundle', array('*'), $match);
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+ $bundle = $records[0];
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+ $bundle_name = $type->dbxref_id->db_id->name . '_' . $type->dbxref_id->accession;
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+ $entity_type_name = $type->dbxref_id->db_id->name;
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+
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+ // Get the list of tables where this cvterm is used.
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+ $values = array('bundle_id' => $bundle->bundle_id);
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+ $tables = chado_select_record('tripal_entity_bundle_source', array('*'), $values);
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+
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+ // Iterate through the tables.
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+ foreach ($tables as $table) {
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+ $tablename = $table->data_table;
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+
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+ // We only want to look at base tables.
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+ if ($tablename == 'cvterm_dbxref' || $tablename == 'cvterm_relationship' ||
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+ $tablename == 'cvtermpath' || $tablename == 'cvtermprop' || $tablename == 'chadoprop' ||
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+ $tablename == 'cvtermsynonym' || preg_match('/_relationship$/', $tablename) ||
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+ preg_match('/_cvterm$/', $tablename)) {
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+ continue;
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+ }
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+
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+ // Add in the bundle's fields.
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+ tripal_entities_add_bundle_fields($tablename, $entity_type_name, $bundle_name);
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+
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+ }
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+ drupal_set_message(t('Data type, %type, is now set as publishable.', array('%type' => $term_name)));
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+ }
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+ catch (Exception $e) {
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+ $transaction->rollback();
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+ drupal_set_message('Failure publishing this data type: ' . $e->getMessage(), 'error');
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+ watchdog_exception('trp_entities', $e);
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+ }
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+
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+}
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+
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+/**
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+ *
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+ * @param $table
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+ * @param $entity_type
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+ * @param $bundle_name
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+ */
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+function tripal_entities_add_bundle_fields($tablename, $entity_type_name, $bundle_name) {
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+
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+ // Iterate through the columns of the table and see if fields have been
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+ // created for each one. If not, then create them.
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+ $schema = chado_get_schema($tablename);
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+ $columns = $schema['fields'];
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+ foreach ($columns as $column_name => $details) {
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+ $field_name = $tablename . '__' . $column_name;
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+ $field = field_info_field($field_name);
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+
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+ // Skip the primary key field.
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+ if ($column_name == $schema['primary key'][0]) {
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+ continue;
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+ }
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+
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+ // Determine if the field is required.
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+ $is_required = 0;
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+ if (array_key_exists('not null', $details)) {
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+ $is_required = $details['not null'] ? 1 : 0;
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+ }
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+
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+ // Determine what type of field this should be.
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+ // Drupal data types are: https://www.drupal.org/node/159605.
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+ // Field types are here: https://www.drupal.org/node/1879542
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+ $field_type = '';
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+ $widget_type = '';
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+ $settings = array();
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+ $label = '';
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+ switch($details['type']) {
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+ case 'char':
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+ // unsupported by postgres
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+ break;
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+ case 'varchar':
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+ $field_type = 'text';
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+ $widget_type = 'text_textfield';
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+ $settings['max_length'] = $details['length'];
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+ break;
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+ case 'text':
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+ $field_type = 'text';
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+ $widget_type = 'text_textarea';
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+ $settings['max_length'] = '';
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+ break;
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+ case 'blob':
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+ // not sure how to support a blobl field.
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+ continue;
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+ break;
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+ case 'int':
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+ $field_type = 'number_integer';
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+ $widget_type = 'number';
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+ break;
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+ case 'float':
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+ $field_type = 'number_float';
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+ $widget_type = 'number';
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+ $settings['precision'] = 10;
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+ $settings['scale'] = 2;
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+ $settings['decimal_separator'] = '.';
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+ break;
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+ case 'numeric':
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+ $field_type = 'number_decimal';
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+ $widget_type = 'number';
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+ break;
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+ case 'serial':
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+ // Serial fields are not every added as fields.
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+ break;
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+ case 'boolean':
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+ // TODO: what is the proper field for booleans?????
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+ break;
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+ case 'datetime':
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+ // TODO: What is the proper datetime fields ??????
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+ break;
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+ default:
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+ drupal_set_message(t("Unhandled field type: %type", array('%type' => $details['type'])), 'warning');
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+ $field_type = 'text';
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+ $widget_type = 'text_textarea';
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+ if (array_key_exists('length', $details)) {
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+ $settings['max_length'] = $details['length'];
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+ }
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+ }
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+
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+ // If we don't have a field type then we don't need to create a field.
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+ if (!$field_type) {
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+ // If we don't have a field type but it is required and doesn't have
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+ // a default value then we are in trouble.
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+ if ($is_required and !array_key_exists('default', $details)) {
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+ throw new Exception(t('The %table.%field type, %type, is not yet supported for Entity fields, but it is required,',
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+ array('%table' => $tablename, '%field' => $column_name, '%type' => $details['type'])));
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+ }
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+ continue;
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+ }
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+
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+
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+ // If this field is a foreign key field then we will have a special custom
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+ // field provided by Tripal.
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+ $is_fk = FALSE;
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+ if (array_key_exists('foreign keys', $details)) {
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+ foreach ($details['foreign keys'] as $remote_table => $fk_details) {
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+ if (array_key_exists($field_name, $fk_details['columns'])) {
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+ $is_fk = TRUE;
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+ }
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+ }
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+ }
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+
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+ // If this column is a FK relationship then use a custom Tripal
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+ // defined field type for it.
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+ if ($is_fk) {
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+ // TODO: We need a better way to get the fields for FK relationships.
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+ // It's not a good idea to enumerate them all here. We need some sort
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+ // of hook or something that will let us lookup the correct field.
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+ switch ($column_name) {
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+ case 'organism_id':
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+ $field_type = 'organism_id';
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+ $label = 'Organism';
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+ break;
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+ }
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+ continue;
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+ }
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+
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+ // If the field doesn't exist then create it.
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+ if (!$field) {
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+ $field = array(
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+ 'field_name' => $field_name,
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+ 'type' => $field_type,
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+ 'cardinality' => 1,
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+ 'locked' => TRUE,
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+ 'storage' => array(
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+ 'type' => 'tripal_entities_storage'
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+ ),
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+ );
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+ field_create_field($field);
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+ }
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+
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+ // Attach the field to the bundle.
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+ $field_instance = array(
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+ 'field_name' => $field_name,
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+ 'label' => $label ? $label : ucwords(preg_replace('/_/', ' ', $column_name)),
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+ 'widget' => array(
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+ 'type' => $widget_type
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+ ),
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+ 'entity_type' => $entity_type_name,
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+ 'required' => $is_required,
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+ 'settings' => $settings,
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+ 'bundle' => $bundle_name,
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+ );
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+ field_create_instance($field_instance);
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+ }
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+}
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+/**
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+ *
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+ * @param unknown $form
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+ * @param unknown $form_state
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+ * @return multitype:
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+ */
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+function tripal_entities_admin_access_form($form, &$form_state) {
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+ $form = array();
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+
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+ return $form;
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+}
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+
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/**
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* This function populates the Tripal entity tables using existing
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* data in the database.
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Stephen Ficklin