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@@ -0,0 +1,375 @@
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+<?php
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+/**
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+ * Purpose: Provide Guidance to new Tripal Admin
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+ *
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+ * @return
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+ * HTML Formatted text
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+function tripal_core_views_description_page() {
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+
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+ $text .= '<h3>Tripal Views Quick Links:</h3>';
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+ $text .= "<ul>
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+ <li><a href=\"".url("admin/tripal/views/mviews") . "\">List of Materialized Views (MViews)</a></li>
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+ <li><a href=\"".url("admin/tripal/views/mviews/new") . "\">Create a new MViews</a></li>
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+ <li><a href=\"".url("admin/tripal/views/integration/mviews") . "\">List of integrated MViews</a></li>
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+ <li><a href=\"".url("admin/tripal/views/integration/mviews/new"). "\">Integrate a MView</a></li>
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+ <li><a href=\"".url("admin/tripal/views/integration/chado"). "\">List of integrated Chado tables</a></li>
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+ <li><a href=\"".url("admin/tripal/views/integration/chado/new"). "\">Integrate a Chado tables</a></li>
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+ </ul>";
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+
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+ $text .= '<h3>Views Integartion Description:</h3>';
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+ $text .= '<p>Tripal Views provides an interface for integrating <a href="http://drupal.org/project/views">Drupal Views</a>
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+ with Tripal materialized views. This will allow site administrators to create custom queries for the materialized views
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+ and in turn provide custom content pages, custom blocks and custom search forms. The forms allow a site administrator
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+ to select a materialized view and associate other Chado tables on which the view can join. Usage of this module requires
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+ a good understanding of foreign-key relationships in Chado.
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+ </p>';
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+
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+ $text .= '<h3>Setup Instructions:</h3>';
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+ $text .= '<p>After installation of the Tripal core module. The following tasks should be performed
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+ <ol>
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+ <li><b>Set Permissions</b>: To allow access to site administrators for this module, simply
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+ <a href="'.url('admin/user/permissions').'">assign permissions</a> to the appropriate user roles for the
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+ permission type "manage tripal_views_integration". </li>
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+ </ol>
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+ </p>';
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+ $text .= '<h3>Usage Instructions:</h3>';
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+ $text .= "<p>To use Tripal Views integration follow these steps:
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+ <ol>
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+ <li><b>Identify or create a materialized view:</b> Using the <a href=\"".url("admin/tripal/views/mviews") . "\">
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+ Tripal materialized View</a> interface, identify the view you would like to integrate or create a new one.</li>
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+ <li><b>Setup the Views Integration</b>: Navigate to the <a href=\"".url("admin/tripal/views/integration/mviews/new") . "\">
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+ Tripal views integration setup page</a> to integrate the selected materialized view. Provide a user friendly name
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+ and description to help you remember the purpose for integrating the view. Next, select the view you want to integrate
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+ from the provided select box. If your materialized view has fields that can join with other Chado tables, you may
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+ provide those relationships in the provided form. Finally, if your fields require a special handler for display, you
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+ may select it from the drop down provided</li>
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+ <li><b>Create custom pages/block/search form</b>: After saving setup information from step 2 above, you will be redirected to the
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+ Drupal Views interface</a> where you can create a custom page, block or search form.</li>
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+ <li><b>Review your integrated views</b>: A page providing a
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+ <a href=\"".url("admin/tripal/views/integration/mviews/list") . "\">list of all integrated views</a> is provided. You may
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+ view this page to see all integrated views, but also to remove any unwanted integrations.</li>
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+ </ol>
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+
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+ </p>";
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+ return $text;
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+}
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+/**
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+function tripal_core_views_integration_admin_form(){
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+
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+ $form = array();
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+
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+ $form['#theme'] = 'tripal';
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+
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+ $query_results = db_query('SELECT * FROM public.tripal_views_integration;');
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+
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+ $header = array('Setup ID', 'Name', 'Materialized View ID', 'Base Table Name', 'Description');
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+ $rows = array();
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+
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+ $results = array();
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+ while($result = db_fetch_object($query_results)){
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+ $rows[] = array($result->setup_id, $result->name, $result->mview_id, $result->base_table_name, $result->description,);
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+ $results[] = $result;
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+ }
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+
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+ $options = array();
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+ foreach ($results as $key => $value) {
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+ if(!empty($value))
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+ $options[] = $value->setup_id;// . ' | ' . $value->name . ' | ' . $value->mview_id . ' | ' . $value->base_table_name;
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+ }
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+
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+ $form['existing_rows'] = array(
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+ '#type' => 'select',
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+ '#options' => $options,
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+ '#description' => '<strong>Select a View Setup to delete from the database.</strong>',
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+ '#prefix' => theme('table', $header, $rows),
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+ );
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+
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+ $form['submit'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Remove'),
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+ );
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+
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+ $form['new'] = array(
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+ '#type' => 'markup',
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+ '#value' => l(t(' Add a New MView'), 'admin/tripal/views/integration/mviews/new'),
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+ );
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+
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+ return $form;
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+}
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+
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+/**
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+function tripal_core_views_integration_admin_form_submit($form, &$form_state){
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+ $value = $form['existing_rows']['#options'][$form_state['values']['existing_rows']];
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+ db_query("DELETE FROM public.tripal_views_integration WHERE setup_id = $value;");
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+ db_query("DELETE FROM public.tripal_views_handlers WHERE setup_id = $value;");
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+ db_query("DELETE FROM public.tripal_mviews_join WHERE setup_id = $value;");
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+}
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+/**
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+
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+function tripal_core_views_integration_new_setup_form(&$form_state){
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+
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+ $form = array();
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+
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+ $data = array();
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+
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+ $form['#cache'] = TRUE;
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+
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+ //ahah_helper requires this to register the form with it's module
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+ ahah_helper_register($form, $form_state);
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+
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+ // field for the name of the
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+ $form['row_name'] = array(
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+ '#title' => t('Name'),
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+ '#type' => 'textfield',
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+ '#size' => 60,
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+ '#maxlength' => 128,
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+ '#description' => 'Name of the Views Setup',
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+ '#required' => TRUE,
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+ );
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+
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+ $form['row_description'] = array(
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+ '#title' => t('Description'),
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+ '#type' => 'textfield',
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+ '#size' => 60,
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+ '#maxlength' => 255,
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+ '#description' => 'Briefly describe in which view this will be used',
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+ '#required' => TRUE,
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+ );
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+
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+ $mview_query = db_query("SELECT mview_id,name FROM {tripal_mviews} ORDER BY name;");
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+ $mview_options = array();
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+ $mview_options['0'] = 'Select';
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+ while ($mview_option = db_fetch_array($mview_query)){
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+ $mview_options[$mview_option['mview_id']] = $mview_option['name'];
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+ }
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+
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+ $form['mview_id'] = array(
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+ '#title' => t('Materialized View'),
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+ '#type' => 'select',
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+ '#options' => $mview_options,
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+ '#description' => 'Which materialized view to use.',
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+ '#required' => TRUE,
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+ '#default_value' => $mview_default_value,
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+ '#ahah' => array(
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+ 'path' => ahah_helper_path(array('view_setup_table')),
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+ 'wrapper' => 'table-rows-div',
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+ 'effect' => 'fade',
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+ 'event' => 'change',
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+ 'method' => 'replace',
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+ ),
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+ );
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+
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+ // ignore this for now... we'll come back to it later -- spf
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+ // $form['row_base_table_name'] = array(
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+ // '#title' => t('Base Table Name'),
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+ // '#type' => 'select',
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+ // // '#options' => array('stub'),
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+ // '#options' => tripal_core_get_chado_tables(),
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+ // '#description' => 'Select which chado table to use for this view.',
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+ // '#required' => TRUE,
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+ // );
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+
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+ $form['view_setup_table'] = array(
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+ '#type' => 'item',
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+ '#prefix' => '<div id="table-rows-div">',
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+ '#suffix' => '</div>',
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+ );
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+
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+
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+ if ($form_state['storage']['mview_id']){
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+
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+ $mview_id = $form_state['storage']['mview_id'];
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+
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+ $form['view_setup_table'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => 'Join Selection',
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+ '#prefix' => '<div id="fieldset-table-rows-wrapper">',
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+ '#suffix' => '</div>',
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+ );
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+
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+ // get the columns in this materialized view. They are separated by commas
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+ // where the first word is the column name and the rest is the type
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+ $sql = "SELECT mv_specs FROM {tripal_mviews} WHERE mview_id = $mview_id";
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+ $mview = db_fetch_object(db_query($sql));
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+ $columns = explode(",",$mview->mv_specs);
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+
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+ $i=1;
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+ $chado_tables = tripal_core_get_chado_tables();
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+ $chado_tables = array_merge(array('',), $chado_tables);
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+
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+ $handlers_filters = array('<default>');
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+ $handlers_fields = array('<default>');
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+ $form['view_setup_table']["instructions"] = array(
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+ '#type' => 'markup',
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+ '#value' => "Select an optional table to which the fields of the materialized view can join. If a field does not need to join you may leave the selection blank.",
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+ );
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+ $form['view_setup_table']["fields_headers"] = array(
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+ '#type' => 'markup',
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+ '#value' => "<div class=\"field-headers\">".
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+ "<div class=\"column-id\">Field Name and Type</div>".
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+ "<div class=\"fields-column-join\">Join Table</div>".
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+ "<div class=\"fields-column-join-column\">Join Column</div>".
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+ "<div class=\"fields-filter-handler\">Filter Handler</div>".
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+ "<div class=\"fields-field-handler\">Field Handler</div></div>",
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+ );
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+
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+ $data['field_types'] = array();
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+
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+ foreach ($columns as $column){
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+ $column = trim($column); // trim trailing and leading spaces
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+ preg_match("/^(.*?)\ (.*?)$/",$column,$matches);
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+ $column_name = $matches[1];
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+ $column_type = $matches[2];
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+
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+ $form['view_setup_table']["fields_start_$mview_id-$i"] = array(
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+ '#type' => 'markup',
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+ '#value' => "<div class=\"fields-new-row\">",
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+ );
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+
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+ $form['view_setup_table']["fields_name_$mview_id-$i"] = array(
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+ '#type' => 'markup',
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+ '#attributes' => array('class' => 'fields-column-name'),
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+ '#value' => "<div class=\"column-id\"><span class=\"column-name\">$column_name</span>".
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+ "<br><span class=\"column-type\">$column_type</span></div>",
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+ );
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+
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+ $data['field_types'][$column_name] = $column_type;
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+
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+ $table = $form_state['storage']["fields_join_$mview_id-$i"];
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+ $form['view_setup_table']["fields_join_$mview_id-$i"] = array(
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+ '#type' => 'select',
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+ '#prefix' => "<div class=\"fields-column-join\">",
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+ '#suffix' => "</div>",
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+ '#options' => $chado_tables,
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+ '#required' => FALSE,
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+ '#default_value' => $table,
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+ '#ahah' => array(
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+ 'path' => ahah_helper_path(array("view_setup_table","fields_join_column_$mview_id-$i")),
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+ 'wrapper' => "fields-column-join-column-$mview_id-$i",
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+ 'effect' => 'fade',
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+ 'event' => 'change',
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+ 'method' => 'replace',
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+ ),
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+ );
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+ if($table){
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+ $table_desc = module_invoke_all('chado_'.$table.'_schema');
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+ $columns = array_keys($table_desc['fields']);
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+ } else {
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+ $columns = array();
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+ }
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+ $form['view_setup_table']["fields_join_column_$mview_id-$i"] = array(
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+ '#type' => 'select',
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+ '#prefix' => "<div id=\"fields-column-join-column-$mview_id-$i\" class=\"fields-column-join-column\">",
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+ '#suffix' => "</div>",
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+ '#options' => $columns,
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+ '#required' => FALSE,
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+ );
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+
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+ $form['view_setup_table']["fields_filter_handler_$mview_id-$i"] = array(
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+ '#type' => 'select',
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+ '#prefix' => "<div class=\"fields-filter-handler\">",
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+ '#suffix' => "</div>",
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+ '#options' => $handlers_filters,
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+ '#required' => FALSE,
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+ );
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+
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+ $form['view_setup_table']["fields_field_handler_$mview_id-$i"] = array(
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+ '#type' => 'select',
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+ '#prefix' => "<div class=\"fields-field-handler\">",
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+ '#suffix' => "</div>",
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+ '#options' => $handlers_fields,
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+ '#required' => FALSE,
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+ );
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+
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+ $form['view_setup_table']["fields_end_$i"] = array(
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+ '#type' => 'markup',
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+ '#value' => "</div>",
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+ );
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+ $i++;
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+ }
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+ $form['view_setup_table']['save'] = array(
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+ '#type' => 'submit',
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+ '#value' => t('Save'),
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+ );
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+
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+ $data['row_count'] = $i - 1;
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+ }
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+
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+ //use this to put values into $form_state['values']
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+ $form['data'] = array();
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+
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+ //need to find out if storing $form['data'][$key]['#value'] = $value <- is an issue
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+ //since it will give me errors if i try to stare an array instead of $value
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+ //and yet $value can be an array ie "field_types"
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+ foreach ($data as $key => $value) {
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+ $form['data'][$key] = array(
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+ '#type' => 'hidden',
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+ '#value' => $value,
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+ );
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+ }
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+
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+ return $form;
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+}
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+
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+
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+/**
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+function tripal_core_views_integration_new_setup_form_validate($form, &$form_state){
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+ $name_array = explode(" ", $form_state['values']['row_name']);
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+ if(count($name_array) > 1){
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+ form_set_error($form_state['values']['row_name'], 'Name must be ONE word only.');
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+ }
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+ //TODO: write validation function for this new form
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+}
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+/**
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+ *
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+ * @ingroup tripal_views_integration
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+ */
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+function tripal_core_views_integration_new_setup_form_submit($form, &$form_state){
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+ $name = $form_state['values']['row_name'];
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+ $mview_id = $form_state['values']['mview_id'];
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+ $tripal_views_integration_record = array(
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+ 'mview_id' => $mview_id,
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+ 'name' => $name,
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+ 'description' => $form_state['values']['row_description'],
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+ );
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+
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+ drupal_write_record('tripal_views_integration', $tripal_views_integration_record);
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+
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+ $i = 1;
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+ foreach ($form_state['values']['field_types'] as $key => $value){
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+ $mview_join_record = array(
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+ 'setup_id' => $tripal_views_integration_record['setup_id'],
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+ 'view_table' => $form['mview_id']['#options'][$form_state['values']['mview_id']],
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+ 'view_column' => $key,
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+ 'chado_table_join' => $form_state['values']["fields_join_$mview_id-$i"],
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+ 'chado_column' => $form['view_setup_table']["fields_join_column_$mview_id-$i"]['#options'][$form_state['values']["fields_join_column_$mview_id-$i"]],
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+ );
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+ drupal_write_record('tripal_mviews_join', $mview_join_record);
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+
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+ $handlers_record = array(
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+ 'setup_id' => $tripal_views_integration_record['setup_id'],
|
|
|
+ 'column_name' => $key,//TODO: should we change this to an mview_join_id from tripal_view_join?
|
|
|
+ 'handler_filter' => $form['view_setup_table']["fields_filter_handler_$mview_id-$i"]['#options'][$form_state['values']["fields_filter_handler_$mview_id-$i"]],
|
|
|
+ 'handler_field' => $form['view_setup_table']["fields_field_handler_$mview_id-$i"]['#options'][$form_state['values']["fields_field_handler_$mview_id-$i"]],
|
|
|
+ );
|
|
|
+ drupal_write_record('tripal_views_handlers', $handlers_record);
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+
|
spficklin