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@@ -0,0 +1,2427 @@
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+<?php
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+
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+/**
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+ * @file
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+ * Handles Create/Edit/Delete Template Admin Forms
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+ */
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+
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+/**
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+ * Provides a description page and quick links for the bulk loader
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+ */
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+<<<<<<< HEAD
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+function tripal_bulk_loader_admin_template() {
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+ $output = '';
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+
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+ $output .= '<br><h3>Quick Links:</h3>';
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+ $output .= l('Create a new bulk loader template', 'admin/tripal/tripal_bulk_loader_template/create') . "<br>";
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+ $output .= l('Edit a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/edit') . "<br>";
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+ $output .= l('Delete a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/delete') . "<br>";
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+ $output .= l('Export a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/export') . "<br>";
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+ $output .= l('Import a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/import') . "<br>";
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+=======
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+function tripal_bulk_loader_admin_template () {
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+ $output = '';
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+
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+ $output .= '<br><h3>Quick Links:</h3>';
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+ $output .= l('Create a new bulk loader template', 'admin/tripal/tripal_bulk_loader_template/create')."<br>";
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+ $output .= l('Edit a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/edit')."<br>";
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+ $output .= l('Delete a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/delete')."<br>";
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+ $output .= l('Export a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/export')."<br>";
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+ $output .= l('Import a bulk loader template', 'admin/tripal/tripal_bulk_loader_template/import')."<br>";
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+>>>>>>> 6.x-0.4-dev
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+ $output .= '<br>';
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+
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+ $output .= '<h3>Module Description:</h3>';
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+ $output .= '<p>This module provides the ability to create loading templates for any tab-delimited '
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+ . 'data file allowing it to be loaded into chado. The Loading Templates are a direct mapping '
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+ . 'between the columns in your file and the columns in chado tables. As such to use this tool '
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+ . 'you need to be very familar with the chado schema -See '
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+ . l('Chado -Getting Started', 'http://gmod.org/wiki/Chado_-_Getting_Started')
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+ . '. The ability to add constants and specify foreign key contraints is also provided '
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+ . 'in order for the loader to fill chado columns which may be required but are not specified '
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+ . 'in your input file.</p>';
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+ $output .= '<br>';
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+
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+ $output .= '<h3>Setup Instructions</h3>';
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+ $output .= '<p>After intallation of the bulk loader module, the following tasks should be performed:</p>';
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+ $output .= '<ol>';
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+ $output .= '<li><b>Install Theme:</b> In order for Bulk Loading pages to be displayed correctly, '
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+ .'the contents of the Tripal Bulk Loader theme directory ([drupal root]/sites/all/modules/tripal/tripal_bulk_loader/theme) '
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+ .'should be moved to the base directory of the Tripal theme ([drupal root]/sites/all/themes/tripal). '
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+ .'Finally the drupal cache should be cleared for the new theme to take effect -navigate to admin/settings/performance '
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+ .'and click the Clear Cached Data button.</li>';
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+ $output .= '</ol>';
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+
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+ return $output;
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+}
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+
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+/**
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+ * A Configuration form for this module
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+ */
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+function tripal_bulk_loader_configuration_form($form_state = NULL) {
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+ $form = array();
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+
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+ $form['speed'] = array(
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+ '#type' => 'fieldset',
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+ '#title' => t('Possible Speed Improvements'),
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+ );
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+
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+ $form['speed']['prepare'] = array(
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+ '#type' => 'checkbox',
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+ '#title' => t('Use Prepared Statements'),
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+ '#description' => t('SQL Prepared Statements allow for SQL queries which will be run '
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+ .'many times to be parsed, rewritten and planned only once rather then every time '
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+ .'the query is run. In the case of the bulk loader, this ensures that planning only '
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+ .'occurs once for each "record" in your bulk loading template.'),
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+ '#default_value' => variable_get('tripal_bulk_loader_prepare', TRUE),
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+ );
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+
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+ $form['submit1'] = 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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+ return $form;
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+}
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+
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+/**
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+ * A Configuration form for this module (Submit)
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+ */
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+function tripal_bulk_loader_configuration_form_submit($form, $form_state) {
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+
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+ variable_set('tripal_bulk_loader_prepare', $form_state['values']['prepare']);
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+}
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+
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+//////////////////////////////////////////////////////////////////////////////////////
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+// Modify Template
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+//////////////////////////////////////////////////////////////////////////////////////
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+
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+
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+/**
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+ * The main form reached at admin/tripal/tripal_bulk_loader/create and /edit
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+ */
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+function tripal_bulk_loader_modify_template_base_form($form_state = NULL, $mode) {
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+ $form = array();
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+
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+ // get template id from path and rebuild form
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+ if ($_GET['template_id']) {
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+ if (preg_match('/^\d+$/', $_GET['template_id'])) {
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+ $form_state['storage']['template_id'] = $_GET['template_id'];
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+ }
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+
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+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
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+ $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
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+ $form_state['storage']['template'] = unserialize($result->template_array);
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+ $form_state['storage']['template_name'] = $result->name;
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+
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+ $form_state['storage']['record2priority'] = array();
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+ foreach ($form_state['storage']['template'] as $priority => $record_array) {
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+ if (!is_array($record_array)) {
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+ continue; }
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+ $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
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+ }
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+ }
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+
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+ $form['mode'] = array(
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+ '#type' => 'hidden',
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+ '#value' => $mode,
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+ );
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+
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+ if ($form_state['storage']['template_id']) {
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+ $form['template_name'] = array(
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+ '#type' => 'item',
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+ '#title' => 'Template',
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+ '#value' => $form_state['storage']['template_name'],
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+ '#weight' => 1,
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+ );
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+ }
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+ else {
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+ if (preg_match('/create/', $mode)) {
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+ $form['new_template_name'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Template Name',
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+ '#weight' => 1,
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+ );
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+ }
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+ elseif (preg_match('/edit/', $mode)) {
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+ $sql = "SELECT * FROM {tripal_bulk_loader_template}";
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+ $resource = db_query($sql);
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+ $templates = array();
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+ $templates[''] = 'Select a Template';
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+ while ($r = db_fetch_object($resource)) {
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+ $templates[$r->template_id] = $r->name;
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+ }
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+
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+ $form['template_id'] = array(
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+ '#title' => t('Template'),
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+ '#description' => t('Please select the template you would like to edit.'),
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+ '#type' => 'select',
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+ '#options' => $templates,
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+ '#default_value' => $form_state['storage']['template_id'],
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+ '#weight' => 0,
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+ '#required' => TRUE,
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+ '#weight' => 1,
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+ );
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+ }
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+ }
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+
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+ $form['records'] = array(
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+<<<<<<< HEAD
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+ '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
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+ '#title' => t('Current Records'),
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+ '#collapsible' => TRUE,
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+ '#weight' => 2,
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+=======
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+ '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
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+ '#title' => t('Current Records'),
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+ '#collapsible' => TRUE,
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+ '#weight' => 2,
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+>>>>>>> 6.x-0.4-dev
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+ );
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+
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+ $form['records']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => 'Records will be inserted into the chado database in the order listed below. To '
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+ .'change this order: <ul><li>Drag the rows into the correct order OR</li><li>Enter '
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+ .'the numbers 1 and up in the Order textboxes to indicate the correct order.</li></ul>',
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+ );
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+
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+ $form['records']['records-data'] = array(
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+ '#tree' => TRUE,
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+ );
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+
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+ $form['records']['no_records'] = array(
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+ '#type' => 'hidden',
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+ '#value' => TRUE,
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+ );
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+
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+ $form['records']['submit-new_record'] = array(
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+ '#type' => 'submit',
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+ '#value' => 'New Record/Field',
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+ );
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+
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+ $form['records']['submit-reorder'] = array(
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+ '#type' => 'submit',
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+ '#value' => 'Save Order',
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+ );
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+
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+<<<<<<< HEAD
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+ $form['fields'] = array(
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+ '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
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+ '#title' => t('Current Fields'),
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+ '#collapsible' => TRUE,
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+ '#weight' => 3,
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+ );
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+=======
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+ $form['fields'] = array(
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+ '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
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+ '#title' => t('Current Fields'),
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+ '#collapsible' => TRUE,
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+ '#weight' => 3,
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+ );
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+>>>>>>> 6.x-0.4-dev
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+
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+ $form['fields']['fields-data'] = array(
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+ '#tree' => TRUE,
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+ );
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+
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+<<<<<<< HEAD
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+ if ($form_state['storage']['template']) {
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+=======
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+ if ($form_state['storage']['template']) {
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+>>>>>>> 6.x-0.4-dev
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+
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+ // List Current Fields -------------------------------------------------------------
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+ $i=1;
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+ foreach ($form_state['storage']['template'] as $priority => $table_array) {
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+<<<<<<< HEAD
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+ if (!is_array($table_array)) {
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+ continue; }
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+=======
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+ if (!is_array($table_array)) { continue; }
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+>>>>>>> 6.x-0.4-dev
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+
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+ $form['records']['no_records']['#value'] = FALSE;
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+
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+ $form['records']['records-data'][$priority] = array(
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+ 'title' => array(
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+ '#type' => 'markup',
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+ '#value' => $table_array['record_id'],
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+ ),
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+ 'chado_table' => array(
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+ '#type' => 'markup',
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+ '#value' => $table_array['table'],
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+ ),
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+ 'mode' => array(
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+ '#type' => 'item',
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+ '#value' => ($table_array['mode']) ? $table_array['mode'] : 'insert_unique',
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+ ),
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+ 'new_priority' => array(
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+ '#type' => 'select',
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+ '#options' => range(1, sizeof($form_state['storage']['template'])),
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+ '#default_value' => $priority,
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+ ),
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+ 'old_priority' => array(
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+ '#type' => 'hidden',
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+ '#value' => $priority,
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+ ),
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+ 'id' => array(
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+ '#type' => 'hidden',
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+ '#value' => $priority,
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+ ),
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+ 'submit-edit_record' => array(
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+ '#type' => 'submit',
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+ '#name' => (string)$priority,
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+ '#value' => 'Edit Record',
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+ ),
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+ 'submit-add_field' => array(
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+ '#type' => 'submit',
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+ '#name' => (string)$priority,
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+ '#value' => 'Add Field',
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+ ),
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+ 'submit-duplicate_record' => array(
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+ '#type' => 'submit',
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+ '#name' => (string)$priority,
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+ '#value' => 'Duplicate Record'
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+ ),
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+ );
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+
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+ foreach ($table_array['fields'] as $field_index => $field) {
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+
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+ $form['fields']['fields-data'][$i] = array(
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+ 'record_id' => array(
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+ '#type' => 'item',
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+ '#value' => $table_array['record_id'],
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+ ),
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+ 'priority_hidden' => array(
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+ '#type' => 'hidden',
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+ '#value' => $priority,
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+ ),
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+ 'field_name' => array(
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+ '#type' => 'item',
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+ '#value' => $field['title'],
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+ ),
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+ 'chado_table_name' => array(
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+ '#type' => 'item',
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+ '#value' => $table_array['table'],
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+ ),
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+ 'chado_table_hidden' => array(
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+ '#type' => 'hidden',
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+ '#value' => $table_array['table'],
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+ ),
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+ 'chado_field_name' => array(
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+ '#type' => 'item',
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+ '#value' => $field['field'],
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+ ),
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+ 'sheet_name' => array(
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+ '#type' => 'item',
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+ '#value' => $field['spreadsheet sheet'],
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+ ),
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+ 'column_num' => array(
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+ '#type' => 'item',
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+ '#value' => $field['spreadsheet column'],
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+ ),
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+ 'constant_value' => array(
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+ '#type' => 'item',
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+ '#value' => $field['constant value'],
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+ ),
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+ 'field_index' => array(
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+ '#type' => 'hidden',
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+ '#value' => $field_index
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+ ),
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+ 'foreign_record_id' => array(
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+ '#type' => 'item',
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+ '#value' => $field['foreign key'],
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+ ),
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+ 'edit_submit' => array(
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+ '#type' => 'submit',
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+ '#name' => (string)$i,
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+ '#value' => "Edit Field",
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+ ),
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+ 'delete_submit' => array(
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+ '#type' => 'submit',
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+ '#name' => (string)$i,
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+ '#value' => "Delete Field",
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+ ),
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+ );
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+
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+ $i++;
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+ }
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+ }
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+ $form['fields']['total_fields'] = array(
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+ '#type' => 'item',
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+ '#value' => $i,
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+ );
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+
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+ }
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+
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+ if ($form['records']['no_records']['#value']) {
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+ $form['records']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => 'There are currently no records.',
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+ );
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+ unset($form['records']['submit-reorder']);
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+
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+ $form['fields']['description'] = array(
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+ '#type' => 'item',
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+ '#value' => 'There are currently no fields.',
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+ );
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+
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+ }
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+
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+<<<<<<< HEAD
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+ $mode_title = (preg_match('/create/', $mode)) ? 'Create Template' : 'Edit Template';
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+ $value = ($form_state['storage']['template_id'])? 'Save Template' : $mode_title;
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+ $form['submit'] = array(
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+ '#type' => 'submit',
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+ '#value' => $value,
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+ '#weight' => 4,
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+ );
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+ return $form;
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+=======
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+ $mode_title = (preg_match('/create/',$mode)) ? 'Create Template' : 'Edit Template';
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+ $value = ($form_state['storage']['template_id'])? 'Save Template' : $mode_title;
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+ $form['submit'] = array(
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+ '#type' => 'submit',
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+ '#value' => $value,
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+ '#weight' => 4,
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+ );
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+
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+ return $form;
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+>>>>>>> 6.x-0.4-dev
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+}
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+
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+/**
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+ * Submit for tripal_bulk_loader_modify_template_base_form
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+ */
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+function tripal_bulk_loader_modify_template_base_form_submit($form, &$form_state) {
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+
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+ $form_state['rebuild'] = TRUE;
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|
|
+ if ($form_state['storage']['template_id']) {
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
|
|
|
+ $form_state['storage']['template'] = unserialize($result->template_array);
|
|
|
+ }
|
|
|
+
|
|
|
+ $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];
|
|
|
+ switch ($op) {
|
|
|
+ // Initialize after template is chosen ----------------------------------------
|
|
|
+ case 'Edit Template':
|
|
|
+ $form_state['storage']['template_id'] = $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ $result = db_fetch_object(db_query($sql, $form_state['storage']['template_id']));
|
|
|
+ $form_state['storage']['template'] = unserialize($result->template_array);
|
|
|
+ $form_state['storage']['template_name'] = $result->name;
|
|
|
+
|
|
|
+ $form_state['storage']['record2priority'] = array();
|
|
|
+ foreach ($form_state['storage']['template'] as $priority => $record_array) {
|
|
|
+ if (!is_array($record_array)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
|
|
|
+ }
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Create Template':
|
|
|
+ $record = array(
|
|
|
+ 'name' => $form_state['values']['new_template_name'],
|
|
|
+ 'template_array' => array(),
|
|
|
+ );
|
|
|
+ drupal_write_record('tripal_bulk_loader_template', $record);
|
|
|
+ $form_state['storage']['template_id'] = $record['template_id'];
|
|
|
+ $form_state['storage']['template_name'] = $record['name'];
|
|
|
+ $form_state['storage']['template'] = array();
|
|
|
+ break;
|
|
|
+
|
|
|
+ // Save Reordered Records -----------------------------------------------------
|
|
|
+ case 'Save Order':
|
|
|
+ $new_template = $form_state['storage']['template'];
|
|
|
+ // unset old elements
|
|
|
+ $form_state['storage']['record2priority'] = array();
|
|
|
+ foreach ($new_template as $priority => $record_array) {
|
|
|
+<<<<<<< HEAD
|
|
|
+ if (preg_match('/\d+/', $priority)) {
|
|
|
+ unset($new_template[$priority]);
|
|
|
+ }
|
|
|
+=======
|
|
|
+ if (preg_match('/\d+/', $priority)) { unset($new_template[$priority]); }
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ }
|
|
|
+ //set elements in new order
|
|
|
+ foreach ($form_state['values']['records-data'] as $item) {
|
|
|
+ $new_template[$item['new_priority']] = $form_state['storage']['template'][$item['old_priority']];
|
|
|
+ $record_name = $new_template[$item['new_priority']]['record_id'];
|
|
|
+ $form_state['storage']['record2priority'][$record_name] = $item['new_priority'];
|
|
|
+ }
|
|
|
+ ksort($new_template);
|
|
|
+ $form_state['storage']['template'] = $new_template;
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'New Record/Field':
|
|
|
+ $query = array(
|
|
|
+<<<<<<< HEAD
|
|
|
+ 'template_id' => $form_state['storage']['template_id'],
|
|
|
+=======
|
|
|
+ 'template_id'=> $form_state['storage']['template_id'],
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ 'record_id' => 'NEW',
|
|
|
+ );
|
|
|
+ drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Edit Record':
|
|
|
+ $query = array(
|
|
|
+<<<<<<< HEAD
|
|
|
+ 'template_id' => $form_state['storage']['template_id'],
|
|
|
+=======
|
|
|
+ 'template_id'=> $form_state['storage']['template_id'],
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ 'record_id' => $form_state['clicked_button']['#name'],
|
|
|
+ );
|
|
|
+ drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_record', $query);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Add Field':
|
|
|
+ $query = array(
|
|
|
+<<<<<<< HEAD
|
|
|
+ 'template_id' => $form_state['storage']['template_id'],
|
|
|
+=======
|
|
|
+ 'template_id'=> $form_state['storage']['template_id'],
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ 'record_id' => $form_state['clicked_button']['#name'],
|
|
|
+ );
|
|
|
+ drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Duplicate Record':
|
|
|
+ // original record (one to be duplicated)
|
|
|
+ $orig_priority = $form_state['clicked_button']['#name'];
|
|
|
+ $record = $form_state['storage']['template'][ $orig_priority ];
|
|
|
+
|
|
|
+ // new record
|
|
|
+ $new_priority = sizeof($form_state['storage']['template']) + 1;
|
|
|
+ $record['record_id'] = $record['record_id'] . '_' . date('YzHi');
|
|
|
+ $form_state['storage']['template'][ $new_priority ] = $record;
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Edit Field':
|
|
|
+ $field_data_index = $form_state['clicked_button']['#name'];
|
|
|
+ $query = array(
|
|
|
+<<<<<<< HEAD
|
|
|
+ 'template_id' => $form_state['storage']['template_id'],
|
|
|
+=======
|
|
|
+ 'template_id'=> $form_state['storage']['template_id'],
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ 'record_id' => $form_state['values']['fields-data'][$field_data_index]['priority_hidden'],
|
|
|
+ 'field_index' => $form_state['values']['fields-data'][$field_data_index]['field_index'],
|
|
|
+ );
|
|
|
+ drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_field', $query);
|
|
|
+ break;
|
|
|
+
|
|
|
+ case 'Delete Field':
|
|
|
+ $field_data = $form_state['values']['fields-data'][$form_state['clicked_button']['#name']];
|
|
|
+ $priority = $field_data['priority_hidden'];
|
|
|
+ $field_key = $field_data['field_index'];
|
|
|
+ unset($form_state['storage']['template'][$priority]['fields'][$field_key]);
|
|
|
+ if (!$form_state['storage']['template'][$priority]['fields']) {
|
|
|
+ unset($form_state['storage']['record2priority'][$form_state['storage']['template'][$priority]['record_id']]);
|
|
|
+ unset($form_state['storage']['template'][$priority]);
|
|
|
+ }
|
|
|
+ drupal_set_message('Deleted Field from Template.');
|
|
|
+ break;
|
|
|
+ } //end of switch
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $record = array(
|
|
|
+ 'template_id' => $form_state['storage']['template_id'],
|
|
|
+ 'template_array' => serialize($form_state['storage']['template'])
|
|
|
+ );
|
|
|
+ drupal_write_record('tripal_bulk_loader_template', $record, array('template_id'));
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+// Delete Template
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+/**
|
|
|
+ * Delete Template Form
|
|
|
+ * This form allows admin to delete already existing templates
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_delete_template_base_form() {
|
|
|
+ $form = array();
|
|
|
+
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template}";
|
|
|
+ $resource = db_query($sql);
|
|
|
+ $templates = array();
|
|
|
+ $templates[''] = 'Select a Template';
|
|
|
+ while ($r = db_fetch_object($resource)) {
|
|
|
+ $templates[$r->template_id] = $r->name;
|
|
|
+ }
|
|
|
+ $form['template_name'] = array(
|
|
|
+ '#title' => t('Template'),
|
|
|
+ '#description' => t('Please select the template you would like to delete.'),
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => $templates,
|
|
|
+ '#weight' => 0,
|
|
|
+ '#required' => TRUE,
|
|
|
+<<<<<<< HEAD
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['submit'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Delete Template',
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+=======
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['submit'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Delete Template',
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Delete Template Form Submit
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form that was submitted
|
|
|
+ * @param $form_state
|
|
|
+ * The values and storage that were submitted
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_delete_template_base_form_submit($form, &$form_state) {
|
|
|
+ $sql = "DELETE FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ db_query($sql, $form_state['values']['template_name']);
|
|
|
+}
|
|
|
+
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+// Import/Export Template
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+/**
|
|
|
+ * Import/Export Template Form
|
|
|
+ *
|
|
|
+ * On export, simply selects the serialized array from the db for a given template
|
|
|
+ * and presents it to the user. On import, a serialized template array and a name is
|
|
|
+ * supplied and a template record is created.
|
|
|
+ *
|
|
|
+ * @todo Make array presented to the user more readable. (ie: unserialize and print to the screen)
|
|
|
+ *
|
|
|
+ * @param $form_state
|
|
|
+ * The values and storage for the form
|
|
|
+ * @param $mode
|
|
|
+ * Either 'import' or 'export' to indicate which function is being performed
|
|
|
+ * @return
|
|
|
+ * A form array to be rendered by drupal_get_form
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_import_export_template_form($form_state = NULL, $mode) {
|
|
|
+ $form = array();
|
|
|
+
|
|
|
+ $form['mode'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $mode,
|
|
|
+ );
|
|
|
+
|
|
|
+ if (preg_match('/import/', $mode)) {
|
|
|
+ $form['new_template_name'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Template Name',
|
|
|
+ '#weight' => 1,
|
|
|
+ );
|
|
|
+ }
|
|
|
+ elseif (preg_match('/export/', $mode)) {
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template}";
|
|
|
+ $resource = db_query($sql);
|
|
|
+ $templates = array();
|
|
|
+ $templates[''] = 'Select a Template';
|
|
|
+ while ($r = db_fetch_object($resource)) {
|
|
|
+ $templates[$r->template_id] = $r->name;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['template_id'] = array(
|
|
|
+ '#title' => t('Template'),
|
|
|
+ '#description' => t('Please select the template you would like to edit.'),
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => $templates,
|
|
|
+ '#default_value' => $form_state['storage']['template_id'],
|
|
|
+ '#weight' => 0,
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#weight' => 1,
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['template_array'] = array(
|
|
|
+ '#type' => 'textarea',
|
|
|
+ '#title' => 'Template Array',
|
|
|
+ '#default_value' => $form_state['storage']['template_array'],
|
|
|
+ '#weight' => 2,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['submit'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Submit',
|
|
|
+ '#weight' => 10,
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Import/Export Template Form Submit
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form that was submitted
|
|
|
+ * @param $form_state
|
|
|
+ * The values and storage that were submitted
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_import_export_template_form_submit($form, &$form_state) {
|
|
|
+ switch ($form_state['values']['mode']) {
|
|
|
+ case 'export':
|
|
|
+ $record = db_fetch_object(db_query("SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d", $form_state['values']['template_id']));
|
|
|
+ $form_state['storage']['template_array'] = $record->template_array;
|
|
|
+ $form_state['storage']['template_id'] = $form_state['values']['template_id'];
|
|
|
+ break;
|
|
|
+ case 'import':
|
|
|
+ $record = array(
|
|
|
+ 'name' => $form_state['values']['new_template_name'],
|
|
|
+ 'template_array' => $form_state['values']['template_array'],
|
|
|
+ );
|
|
|
+ drupal_write_record('tripal_bulk_loader_template', $record);
|
|
|
+ if ($record->template_id) {
|
|
|
+ drupal_set_message('Successfully imported Tripal Bulk Loader Template.');
|
|
|
+ }
|
|
|
+ break;
|
|
|
+ }
|
|
|
+}
|
|
|
+
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+// Edit Record Form
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+/**
|
|
|
+ * Edit Record Form
|
|
|
+ *
|
|
|
+ * This form is meant to be called from a bulk loader form. The following should be set
|
|
|
+ * in the query section of the path:
|
|
|
+ * - template_id=\d+: the template which the edited record is part of
|
|
|
+ * - record_id=\d+: the priority or key in the template array of the record to be edited
|
|
|
+ *
|
|
|
+ * @param $form_state
|
|
|
+ * Contains the values and storage for the form
|
|
|
+ * @return
|
|
|
+ * A form array to be rendered by drupal_get_form
|
|
|
+ */
|
|
|
+<<<<<<< HEAD
|
|
|
+function tripal_bulk_loader_edit_template_record_form(&$form_state = NULL) {
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id'] !== NULL) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+=======
|
|
|
+function tripal_bulk_loader_edit_template_record_form (&$form_state = NULL) {
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id'] !== NULL) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Pre-process values/defaults ---------------------------
|
|
|
+
|
|
|
+ // If this is the first load of the form (no form state) we need to initialize some variables
|
|
|
+ if (!$form_state['storage']['template']) {
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ $template = db_fetch_object(db_query($sql, $template_id));
|
|
|
+ $form_state['storage']['template_array'] = unserialize($template->template_array);
|
|
|
+ $form_state['storage']['template'] = $template;
|
|
|
+
|
|
|
+ $form_state['storage']['record2priority'] = array();
|
|
|
+ foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
|
|
|
+ if (!is_array($record_array)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $template = $form_state['storage']['template'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the record_id from the path
|
|
|
+ if ($_GET['record_id'] !== NULL) {
|
|
|
+ $form_state['values']['field_group'] = $_GET['record_id'];
|
|
|
+ $form_state['storage']['original_priority'] = $_GET['record_id'];
|
|
|
+ }
|
|
|
+
|
|
|
+
|
|
|
+ // Tables and default table
|
|
|
+ $tables = tripal_core_get_chado_tables();
|
|
|
+ if ($form_state['values']['chado_table']) {
|
|
|
+ $table = $form_state['values']['chado_table'];
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $table = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['table'];
|
|
|
+ }
|
|
|
+
|
|
|
+ //dpm($form_state, 'form state');
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ // Form Proper -------------------------------------------
|
|
|
+=======
|
|
|
+ // Form Proper -------------------------------------------
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $form['template_name'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#title' => 'Template',
|
|
|
+ '#value' => $template->name,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['template_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $template_id,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ );
|
|
|
+
|
|
|
+ // check template array for records then add one more
|
|
|
+ if (!$form_state['storage']['record2priority']) {
|
|
|
+ $groups = array();
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $groups = array_flip($form_state['storage']['record2priority']);
|
|
|
+ }
|
|
|
+ $priority_default = $form_state['values']['field_group'];
|
|
|
+ $form['edit_record']['field_group'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => 'Record',
|
|
|
+ '#description' => 'By Changing the record here, you can move all the fields from the current record into the selected record.',
|
|
|
+ '#options' => $groups,
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|
+ '#default_value' => $priority_default,
|
|
|
+ '#required' => TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record']['record_name'] = array(
|
|
|
+ '#type' => 'textfield',
|
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|
+ '#title' => 'Unique Record Name',
|
|
|
+ '#default_value' => $groups[$priority_default],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record']['chado_table'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Chado Table'),
|
|
|
+ '#description' => 'This changes the chado table for all fields in this record.',
|
|
|
+ '#options' => $tables,
|
|
|
+ '#default_value' => $table,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record']['mode'] = array(
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#title' => 'Action to take when Loading Record',
|
|
|
+ '#options' => array(
|
|
|
+ 'select' => 'SELECT: Don\'t insert this record: it\'s used to define a foreign key in another record',
|
|
|
+ 'insert' => 'INSERT: Insert the record',
|
|
|
+ 'optional' => 'OPTIONAL: Record will only be inserted if all required data is filled in',
|
|
|
+ 'insert_once' => 'INSERT ONCE: Record will be inserted once for the entire spreadsheet',
|
|
|
+ 'insert_unique' => 'INSERT UNIQUE: Only insert record if there isn\'t a record with the same values',
|
|
|
+ ),
|
|
|
+ '#default_value' => 'insert_unique'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record']['submit-edit_record'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Edit Record'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_record']['submit-cancel'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Cancel'
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+
|
|
|
+/**
|
|
|
+ * Edit Record Form Submit
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form that was submitted
|
|
|
+ * @param $form_state
|
|
|
+ * Contains the values and storage for the form
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_edit_template_record_form_submit($form, &$form_state) {
|
|
|
+ //dpm($form_state, 'form state -start submit');
|
|
|
+
|
|
|
+ if (!$form_state['ahah_submission']) {
|
|
|
+ if ($form_state['values']['op'] == 'Edit Record') {
|
|
|
+
|
|
|
+ $template = $form_state['storage']['template_array'];
|
|
|
+
|
|
|
+ // Edit Record
|
|
|
+ $record = $template[ $form_state['storage']['original_priority'] ];
|
|
|
+ $record['record_id'] = $form_state['values']['record_name'];
|
|
|
+ $record['mode'] = $form_state['values']['mode'];
|
|
|
+ $record['table'] = $form_state['values']['chado_table'];
|
|
|
+
|
|
|
+ if ($form_state['storage']['original_priority'] != $form_state['values']['field_group']) {
|
|
|
+ $record['fields'] = array_merge($record['fields'], $template[ $form_state['values']['field_group'] ]['fields']);
|
|
|
+ $template[ $form_state['values']['field_group'] ] = $record;
|
|
|
+ unset($template[ $form_state['storage']['original_priority'] ]);
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $template[ $form_state['storage']['original_priority'] ] = $record;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $form_state['storage']['template']->template_array = serialize($template);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Updated Template Record');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+=======
|
|
|
+ $path = explode('?',$form_state['storage']['referring URL']);
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['op'] == 'Cancel') {
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ //dpm('Redirecting to: '.$path[0].'?'.print_r($query,TRUE).' where the referring URL:'.$form_state['storage']['referring URL']);
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+// Add/Edit Field Forms
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add Field Form
|
|
|
+ *
|
|
|
+ * This form is meant to be called from a bulk loader form. Blank Defaults are in place but you
|
|
|
+ * can use the following in the query of the path to set defaults for a given template:
|
|
|
+ * - template_id=\d+: the template to add the field to
|
|
|
+ * - record_id=\d+: the priority or key in the template array of the record to add the field to
|
|
|
+ *
|
|
|
+ * @param $form_state
|
|
|
+ * Contains the values and storage for the form
|
|
|
+ * @return
|
|
|
+ * A form array to be rendered by drupal_get_form
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_add_template_field_form(&$form_state = NULL) {
|
|
|
+ $form = array();
|
|
|
+<<<<<<< HEAD
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+=======
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Pre-set Variables needed for form proper------------------------------------------
|
|
|
+
|
|
|
+ // If this is the first load of the form (no form state) we need to initialize some variables
|
|
|
+ if (!$form_state['storage']['template']) {
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ $template = db_fetch_object(db_query($sql, $template_id));
|
|
|
+ $form_state['storage']['template_array'] = unserialize($template->template_array);
|
|
|
+ $form_state['storage']['template'] = $template;
|
|
|
+
|
|
|
+ $form_state['storage']['record2priority'] = array();
|
|
|
+ foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
|
|
|
+ if (!is_array($record_array)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $template = $form_state['storage']['template'];
|
|
|
+ }
|
|
|
+
|
|
|
+ $field_type = ($form_state['values']['field_type'])? $form_state['values']['field_type'] : 'table field';
|
|
|
+
|
|
|
+ // Tables and default table
|
|
|
+ $tables = tripal_core_get_chado_tables();
|
|
|
+ if ($form_state['values']) {
|
|
|
+ if (!preg_match('/^' . current($tables) . '$/', $form_state['values']['chado_table'])) {
|
|
|
+ $table = $form_state['values']['chado_table'];
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['record_name']) {
|
|
|
+ $record_name = $form_state['values']['record_name'];
|
|
|
+ $priority = $form_state['storage']['record2priority'][$record_name];
|
|
|
+ $table = $form_state['storage']['template_array'][$priority]['table'];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $priority = $form_state['values']['field_group'];
|
|
|
+ $table = $form_state['storage']['template_array'][$priority]['table'];
|
|
|
+ }
|
|
|
+ }
|
|
|
+ if (!$table) {
|
|
|
+ $table = reset($tables);
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the record_id from the path
|
|
|
+ if ($_GET['record_id'] !== NULL) {
|
|
|
+ $form_state['values']['field_group'] = $_GET['record_id'];
|
|
|
+ if (preg_match('/\d+/', $_GET['record_id'])) {
|
|
|
+ $priority = $form_state['values']['field_group'];
|
|
|
+ $table = $form_state['storage']['template_array'][$priority]['table'];
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ // Fields and foreign key mappings
|
|
|
+ $chado_fields = array();
|
|
|
+ $fk_options = array();
|
|
|
+ $fk_options['NULL'] = 'None';
|
|
|
+ $table_description = module_invoke_all('chado_' . $table . '_schema');
|
|
|
+ //dpm($table_description, 'table description for |'.$table.'|');
|
|
|
+ if ($field_type == 'foreign key') {
|
|
|
+ $foreign_field2table = array();
|
|
|
+ foreach ($table_description['foreign keys'] as $key_table => $key_array) {
|
|
|
+ foreach ($key_array['columns'] as $left_field => $right_field) {
|
|
|
+ $chado_fields[$left_field] = $left_field;
|
|
|
+ $foreign_field2table[$left_field] = $key_table;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ reset($chado_fields);
|
|
|
+
|
|
|
+ // set default field
|
|
|
+ if (empty($chado_fields)) {
|
|
|
+ $field = NULL;
|
|
|
+ }
|
|
|
+ elseif ($chado_fields[$form_state['values']['chado_field']]) {
|
|
|
+ $field = $form_state['values']['chado_field'];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $field = current($chado_fields);
|
|
|
+ }
|
|
|
+
|
|
|
+ // Foreign key options
|
|
|
+ $foreign_table = $foreign_field2table[$field];
|
|
|
+ if ($foreign_table) {
|
|
|
+ foreach ($form_state['storage']['record2priority'] as $record_name => $priority ) {
|
|
|
+ if (preg_match('/^' . $foreign_table . '$/', $form_state['storage']['template_array'][$priority]['table'])) {
|
|
|
+ $fk_options[$record_name] = $record_name;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ foreach ($table_description['fields'] as $field_name => $field_array) {
|
|
|
+ $chado_fields[$field_name] = $field_name;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ $variables = array(
|
|
|
+ 'form_state' => $form_state,
|
|
|
+ 'tables' => $tables,
|
|
|
+ 'default table' => $table,
|
|
|
+ 'fields' => $chado_fields,
|
|
|
+ 'default_field' => $field,
|
|
|
+ 'priority' => $priority,
|
|
|
+ 'record_name' => $record_name,
|
|
|
+ 'table description' => $table_description,
|
|
|
+ 'foreign key options' => $fk_options,
|
|
|
+ 'foreign field=>table' => $foreign_field2table,
|
|
|
+ 'foreign table' => $foreign_table,
|
|
|
+ );
|
|
|
+ //dpm($variables, 'variables');
|
|
|
+
|
|
|
+ // Start of Form Proper--------------------------------------------------------------
|
|
|
+ //dpm($form_state, 'Form State');
|
|
|
+
|
|
|
+ $form['template_name'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#title' => 'Template',
|
|
|
+ '#value' => $template->name,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['template_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $template_id,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#prefix' => '<div id="tripal_bulk_loader_template-add_field">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['field_type'] = array(
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#title' => t('Type of Field'),
|
|
|
+ '#options' => array(
|
|
|
+ 'table field' => t('Spreadsheet: Fields which maps to a Spreadsheet Column'),
|
|
|
+ 'constant' => t('Constant: Field which remains Constant throughout the Spreadsheet'),
|
|
|
+ 'foreign key' => t('Foreign Key: Fields which map to a record in another table'),
|
|
|
+ ),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_value' => $field_type,
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-add_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ // check template array for records then add one more
|
|
|
+ if (!$form_state['storage']['record2priority']) {
|
|
|
+ $groups = array();
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $groups = array_flip($form_state['storage']['record2priority']);
|
|
|
+ }
|
|
|
+ $groups['NONE'] = 'Select a Record';
|
|
|
+ $groups['NEW'] = 'New Record';
|
|
|
+ $form['add_fields']['field_group'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => 'Record',
|
|
|
+ '#description' => 'This is used to group a set of fields together allowing '
|
|
|
+ .'multiple records to be inserted into the same table per line of the spreadsheet',
|
|
|
+ '#options' => $groups,
|
|
|
+ '#default_value' => (preg_match('/\w+.*/', $form_state['values']['field_group'])) ? $form_state['values']['field_group'] : 'NONE',
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-add_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ '#required' => TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['record_name'] = array(
|
|
|
+ '#type' => (preg_match('/NEW/', $form_state['values']['field_group'])) ? 'textfield' : 'hidden',
|
|
|
+ '#title' => 'Unique Record Name',
|
|
|
+ '#prefix' => '<div id="tripal_bulk_loader_template-add_record">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ '#default_value' => $form_state['values']['record_name'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['field_title'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Human-readable Title for Field'),
|
|
|
+ '#default_value' => $form_state['values']['field_title'],
|
|
|
+ );
|
|
|
+
|
|
|
+ // Spreadsheet column
|
|
|
+ $form['add_fields']['columns'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Spreadsheet Column'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'table field')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['columns']['sheet_name'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Worksheet'),
|
|
|
+ '#description' => t('Specify the name of the worksheet.'),
|
|
|
+ '#size' => 5,
|
|
|
+ '#default_value' => ($form_state['values']['sheet_name'])? $form_state['values']['sheet_name'] : 'Sheet1',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['columns']['column_number'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Column'),
|
|
|
+ '#description' => t('Specify the column in the spreadsheet that this field maps to where the first column is 1.'),
|
|
|
+ '#size' => 5,
|
|
|
+ '#default_value' => $form_state['values']['column_number'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['columns']['column_exposed'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Allow Column to be set for each Bulk Loading Job'),
|
|
|
+ '#description' => t('Adds a textbox field to the Bulk Loader Page to allow users to set this value.'),
|
|
|
+ '#default_value' => ($form_state['values']['column_exposed']) ? $form_state['values']['column_exposed'] : $template_field['exposed'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['columns']['column_exposed_desc'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Description for exposed field on bulk loading job'),
|
|
|
+ '#description' => t('This description should tell the user what column should be entered here.'),
|
|
|
+ '#default_value' => ($form_state['values']['column_exposed_desc']) ? $form_state['values']['column_exposed_desc'] : $template_field['exposed_description'],
|
|
|
+ );
|
|
|
+
|
|
|
+ // Global Value
|
|
|
+ $form['add_fields']['constant'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Constant'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'constant')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['constant']['constant_value'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Constant Value'),
|
|
|
+ '#description' => t('Specify the value you wish this field to have regardless of spreadsheet data.'),
|
|
|
+ '#default_value' => $form_state['values']['constant_value']
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['constant']['constant_exposed'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Allow Constant to be set for each Bulk Loading Job'),
|
|
|
+ '#description' => t('Adds a textbox field to the Create Bulk Loader Form to allow users to set this value.')
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['constant']['constant_validate'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Ensure value is in table'),
|
|
|
+ '#description' => t('Checks the database when a bulk loading job is created to ensure the value entered already exists in the database.'),
|
|
|
+ );
|
|
|
+
|
|
|
+ // Foreign Key
|
|
|
+ $form['add_fields']['foreign_key'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Foreign Key',
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'foreign key')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['foreign_key']['foreign_record'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => 'Record to refer to',
|
|
|
+ '#descripion' => 'Select the record that this foreign key shouold refer to. The record needs to already exist and be of the correct table.',
|
|
|
+ '#options' => $fk_options,
|
|
|
+ );
|
|
|
+
|
|
|
+ // Chado Field
|
|
|
+ $form['add_fields']['chado'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Chado Field/Column Details'),
|
|
|
+ '#description' => t('Specify the Table/Field in chado that this field maps to.'),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['chado']['chado_table'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Chado Table'),
|
|
|
+ '#options' => $tables,
|
|
|
+ '#default_value' => $table,
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-add_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['chado']['chado_field'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Chado Field/Column'),
|
|
|
+ '#options' => $chado_fields,
|
|
|
+ '#default_value' => $form_state['values']['chado_field'],
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/add_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-add_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Additional Options',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['required'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => 'Make this file required',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Transform Spreadsheet Value Rules',
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => (!$form_state['storage']['regex']['pattern']) ? TRUE : FALSE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['regex_description'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => 'A transformation rule allows you to transform the original value '
|
|
|
+ .'(usually from a user submitted spreadsheet) into the form you would like it stored '
|
|
|
+ .'in the chado database. Each rule consists of a match pattern (a php regular expression '
|
|
|
+ .'which determines which replacement patterns are applied and captures regions of the '
|
|
|
+ .'original value) and a replacement pattern (a string which may contain capture references '
|
|
|
+ .'that describes what the new value should be). Each rule is applied to the result of the '
|
|
|
+ .'previous rule.'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['regex-data'] = array(
|
|
|
+ '#tree' => TRUE,
|
|
|
+ );
|
|
|
+ if (!$form_state['storage']['regex']['pattern']) {
|
|
|
+ $form_state['storage']['regex']['pattern'] = array();
|
|
|
+ }
|
|
|
+ foreach ($form_state['storage']['regex']['pattern'] as $index => $pattern) {
|
|
|
+ $data_element = array(
|
|
|
+ 'pattern' => array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $pattern,
|
|
|
+ ),
|
|
|
+ 'replace' => array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $form_state['storage']['regex']['replace'][$index],
|
|
|
+ ),
|
|
|
+ 'old_index' => array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $index,
|
|
|
+ ),
|
|
|
+ 'new_index' => array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => range(0, sizeof($form_state['storage']['regex']['pattern'])-1),
|
|
|
+ '#default_value' => $index,
|
|
|
+ ),
|
|
|
+ 'id' => array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $index,
|
|
|
+ ),
|
|
|
+ 'submit-delete' => array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Delete Transformation',
|
|
|
+ '#name' => $index,
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $form['add_fields']['additional']['regex_transform']['regex-data'][$index] = $data_element;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['submit-reorder_regex'] = array(
|
|
|
+ '#type' => ($form_state['storage']['regex']['pattern']) ? 'submit' : 'hidden',
|
|
|
+ '#value' => 'Save Transformation Rule Order'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['new_regex'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Add a new Transformation Rule',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['new_regex']['pattern'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Match Pattern',
|
|
|
+ '#description' => 'You can use standard php regular expressions in this field to specify a '
|
|
|
+ .'pattern. Only if this pattern matches the value in the spreadsheet does the replacement '
|
|
|
+ .'pattern get applied to the value. To capture a section of your value for use in the '
|
|
|
+ .'replacement patten surround with round brackets. For example, <i>GI:(\d+)</i> will match '
|
|
|
+ .' NCBI gi numbers and will capture the numerical digits for use in the replacement pattern. '
|
|
|
+ .' To match and capture any value use <i>.*</i>',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['new_regex']['replace'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Replacement Pattern',
|
|
|
+ '#description' => 'This pattern should contain the text you want to replace the match pattern '
|
|
|
+ .'mentioned above. It can include references of the form \n where n is the number of the '
|
|
|
+ .'capture in the match pattern. For example, \1 will be replaced with the text matched in your '
|
|
|
+ .'first set of round brackets.',
|
|
|
+ );
|
|
|
+
|
|
|
+ if ($field_type == 'table field') {
|
|
|
+ $tab = '        ';
|
|
|
+ $form['add_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
|
|
|
+ .'The following references are also available for spreadsheet fields: <b><#column:<i>number</i>#></b>. '
|
|
|
+ .'This allows you to substitute other spreadsheet values into the current field. For example, '
|
|
|
+ .'if you had the following line:<br>'
|
|
|
+ . $tab . 'SNP' . $tab . '15-Jan-2011' . $tab . '1' . $tab . '54' . $tab . 'Contig34355'
|
|
|
+ .'<br> and your current field is for column #1 and you\'re inserting into the chado field '
|
|
|
+ .'feature.uniquename then you might want to add in the data to ensure your uniquename is '
|
|
|
+ .'unique. The Match Pattern is (.*) to select all the first column and the Replacement '
|
|
|
+ .'Pattern could be \1_<#column:2#> which would insert SNP_15-Jan-2011 into the database.</p>';
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['new_regex']['submit-add_transform'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Add Transformation',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['test_regex'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Test Transformation Rules',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['test_regex']['test_string'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Test Value',
|
|
|
+ '#description' => 'This should be a value that you expect the above transformation rules '
|
|
|
+ .'to be applied to.',
|
|
|
+ '#default_value' => $form_state['storage']['test_regex_test'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['test_regex']['test_result'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Test Result',
|
|
|
+ '#description' => 'This is the value that would be saved to the database after the above transformation '
|
|
|
+ .'riles were applied to the Test Value.',
|
|
|
+ '#default_value' => $form_state['storage']['test_regex_result'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['additional']['regex_transform']['test_regex']['submit-test'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Test Transformation Rules'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['submit-add_field'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Add Field'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['add_fields']['submit-cancel'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Cancel'
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Add Field Submit
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form that was submitted
|
|
|
+ * @param $form_state
|
|
|
+ * The values and storage for the form
|
|
|
+ */
|
|
|
+<<<<<<< HEAD
|
|
|
+function tripal_bulk_loader_add_template_field_form_submit($form, &$form_state) {
|
|
|
+=======
|
|
|
+function tripal_bulk_loader_add_template_field_form_submit ($form, &$form_state) {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];
|
|
|
+
|
|
|
+ if (!$form_state['ahah_submission']) {
|
|
|
+ if ($op == 'Add Field') {
|
|
|
+
|
|
|
+ $template = $form_state['storage']['template_array'];
|
|
|
+
|
|
|
+ // If new record
|
|
|
+ if (preg_match('/NEW/', $form_state['values']['field_group'])) {
|
|
|
+ $record_name = $form_state['values']['record_name'];
|
|
|
+ $priority = sizeof($form_state['storage']['template_array']) + 1;
|
|
|
+ $record2priority[$record_name] = $priority;
|
|
|
+ $template[$priority]['table'] = $form_state['values']['chado_table'];
|
|
|
+ $template[$priority]['record_id'] = $record_name;
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $priority = $form_state['values']['field_group'];
|
|
|
+ $record_name = $record2priority[$priority];
|
|
|
+ }
|
|
|
+
|
|
|
+ // Add field to template array
|
|
|
+ if ($form_state['values']['field_type'] == 'table field') {
|
|
|
+ $field = array(
|
|
|
+ 'type' => 'table field',
|
|
|
+ 'title' => $form_state['values']['field_title'],
|
|
|
+ 'field' => $form_state['values']['chado_field'],
|
|
|
+ 'required' => $form_state['values']['required'],
|
|
|
+ //'allowed values' => empty by default,
|
|
|
+ 'spreadsheet sheet' => $form_state['values']['sheet_name'],
|
|
|
+ 'spreadsheet column' => $form_state['values']['column_number'],
|
|
|
+ 'exposed' => $form_state['values']['column_exposed'],
|
|
|
+ 'exposed_description' => $form_state['values']['column_exposed_desc'],
|
|
|
+ );
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['field_type'] == 'constant') {
|
|
|
+ $field = array(
|
|
|
+ 'type' => 'constant',
|
|
|
+ 'title' => $form_state['values']['field_title'],
|
|
|
+ 'field' => $form_state['values']['chado_field'],
|
|
|
+ 'required' => $form_state['values']['required'],
|
|
|
+ //'allowed values' => empty by default,
|
|
|
+ 'constant value' => $form_state['values']['constant_value'],
|
|
|
+ 'exposed' => $form_state['values']['constant_exposed'],
|
|
|
+ 'exposed_validate' => $form_state['values']['constant_validate'],
|
|
|
+ );
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['field_type'] == 'foreign key') {
|
|
|
+=======
|
|
|
+ } elseif ($form_state['values']['field_type'] == 'foreign key') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $field = array(
|
|
|
+ 'type' => 'foreign key',
|
|
|
+ 'title' => $form_state['values']['field_title'],
|
|
|
+ 'field' => $form_state['values']['chado_field'],
|
|
|
+ 'foreign key' => $form_state['values']['foreign_record'],
|
|
|
+ 'required' => $form_state['values']['required'],
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+ // Deal with any additional options
|
|
|
+ if ($form_state['storage']['regex']) {
|
|
|
+ $field['regex'] = $form_state['storage']['regex'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $template[$priority]['fields'][] = $field;
|
|
|
+ $form_state['storage']['template']->template_array = serialize($template);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Added Field to Template');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+=======
|
|
|
+ $path = explode('?',$form_state['storage']['referring URL']);
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+ }
|
|
|
+ elseif ($op == 'Cancel') {
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Add Transformation') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Add Transformation') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Add transformation rule to original field
|
|
|
+ $form_state['storage']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
|
|
|
+ $form_state['storage']['regex']['replace'][] = $form_state['values']['replace'];
|
|
|
+ drupal_set_message('Successfully Added Transformation Rule');
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Save Transformation Rule Order') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Save Transformation Rule Order') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Generate new regex array
|
|
|
+ $new_regex = array();
|
|
|
+ $old_regex = $form_state['storage']['regex'];
|
|
|
+ foreach ($form_state['values']['regex-data'] as $key => $element) {
|
|
|
+ $new_regex['pattern'][ $element['new_index'] ] = $old_regex['pattern'][ $element['old_index'] ];
|
|
|
+ $new_regex['replace'][ $element['new_index'] ] = $old_regex['replace'][ $element['old_index'] ];
|
|
|
+ }
|
|
|
+
|
|
|
+ // sort new regex arrays
|
|
|
+ asort($new_regex['pattern']);
|
|
|
+ asort($new_regex['replace']);
|
|
|
+
|
|
|
+ $form_state['storage']['regex'] = $new_regex;
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Delete Transformation') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Delete Transformation') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Unset regex rule
|
|
|
+ $index = $form_state['clicked_button']['#name'];
|
|
|
+ unset($form_state['storage']['regex']['pattern'][$index]);
|
|
|
+ unset($form_state['storage']['regex']['replace'][$index]);
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Test Transformation Rules') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Test Transformation Rules') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ $patterns = $form_state['storage']['regex']['pattern'];
|
|
|
+ $replaces = $form_state['storage']['regex']['replace'];
|
|
|
+ $test_string = $form_state['values']['test_string'];
|
|
|
+ $form_state['storage']['test_regex_result'] = preg_replace($patterns, $replaces, $test_string);
|
|
|
+ $form_state['storage']['test_regex_test'] = $test_string;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Edit Field Form
|
|
|
+ *
|
|
|
+ * This form is meant to be called from a bulk loader form. The following should be set
|
|
|
+ * in the query section of the path:
|
|
|
+ * - template_id=\d+: the template which the edited field is part of
|
|
|
+ * - record_id=\d+: the priority or key in the template array of the record the field
|
|
|
+ * is currently part of
|
|
|
+ * - field_index=\d+: the key of the field in the fields array of the previously
|
|
|
+ * specified record
|
|
|
+ *
|
|
|
+ * @param $form_state
|
|
|
+ * Contains the values and storage for the form
|
|
|
+ * @return
|
|
|
+ * A form array to be rendered by drupal_get_form
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_edit_template_field_form(&$form_state = NULL) {
|
|
|
+ $form = array();
|
|
|
+<<<<<<< HEAD
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+=======
|
|
|
+ $form['#cache'] = TRUE; // Make sure the form is cached.
|
|
|
+
|
|
|
+ // get template id from path
|
|
|
+ $template_id = ($_GET['template_id']) ? $_GET['template_id'] : $form_state['values']['template_id'];
|
|
|
+
|
|
|
+ // if there is no template supplied don't return rest of form
|
|
|
+ if (!$template_id) {
|
|
|
+ return $form;
|
|
|
+ }
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Pre-set Variables needed for form proper------------------------------------------
|
|
|
+
|
|
|
+ // If this is the first load of the form (no form state) we need to initialize some variables
|
|
|
+ if (!$form_state['storage']['template']) {
|
|
|
+ $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
|
|
|
+ $template = db_fetch_object(db_query($sql, $template_id));
|
|
|
+ $form_state['storage']['template_array'] = unserialize($template->template_array);
|
|
|
+ $form_state['storage']['template'] = $template;
|
|
|
+
|
|
|
+ $form_state['storage']['record2priority'] = array();
|
|
|
+ foreach ($form_state['storage']['template_array'] as $priority => $record_array) {
|
|
|
+ if (!is_array($record_array)) {
|
|
|
+ continue;
|
|
|
+ }
|
|
|
+ $form_state['storage']['record2priority'][$record_array['record_id']] = $priority;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form_state['storage']['referring URL'] = $_SERVER["HTTP_REFERER"];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $template = $form_state['storage']['template'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // get the field from the path
|
|
|
+ if (!($_GET['record_id']===NULL || $_GET['field_index']===NULL)) {
|
|
|
+ $priority = $_GET['record_id'];
|
|
|
+ $field_index = $_GET['field_index'];
|
|
|
+ $template_field = $form_state['storage']['template_array'][$priority]['fields'][$field_index];
|
|
|
+ $form_state['storage']['original_field'] = $template_field;
|
|
|
+ $form_state['storage']['original_field']['priority'] = $priority;
|
|
|
+ $form_state['storage']['original_field']['field_index'] = $field_index;
|
|
|
+ }
|
|
|
+
|
|
|
+ $field_type = ($form_state['values']['field_type'])? $form_state['values']['field_type'] : $template_field['type'];
|
|
|
+
|
|
|
+ // Tables and default table
|
|
|
+ $tables = tripal_core_get_chado_tables();
|
|
|
+ if ($form_state['values']) {
|
|
|
+ $table = $form_state['values']['chado_table'];
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $table = $form_state['storage']['template_array'][$priority]['table'];
|
|
|
+ }
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+ $table = $form_state['storage']['template_array'][$priority]['table'];
|
|
|
+ }
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+
|
|
|
+ // Fields and foreign key mappings
|
|
|
+ $chado_fields = array();
|
|
|
+ $fk_options = array();
|
|
|
+ $fk_options['NULL'] = 'None';
|
|
|
+ $table_description = module_invoke_all('chado_' . $table . '_schema');
|
|
|
+ if ($field_type == 'foreign key') {
|
|
|
+ $foreign_field2table = array();
|
|
|
+ foreach ($table_description['foreign keys'] as $key_table => $key_array) {
|
|
|
+ foreach ($key_array['columns'] as $left_field => $right_field) {
|
|
|
+ $chado_fields[$left_field] = $left_field;
|
|
|
+ $foreign_field2table[$left_field] = $key_table;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ reset($chado_fields);
|
|
|
+
|
|
|
+ // set default field
|
|
|
+ if (empty($chado_fields)) {
|
|
|
+ $field = NULL;
|
|
|
+ }
|
|
|
+ elseif ($chado_fields[$form_state['values']['chado_field']]) {
|
|
|
+ $field = $form_state['values']['chado_field'];
|
|
|
+ }
|
|
|
+ elseif ($template_field['field']) {
|
|
|
+ $field = $template_field['field'];
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $field = current($chado_fields);
|
|
|
+ }
|
|
|
+ //dpm($field, 'field');
|
|
|
+
|
|
|
+ // Foreign key options
|
|
|
+ $foreign_table = $foreign_field2table[$field];
|
|
|
+ if ($foreign_table) {
|
|
|
+ foreach ($form_state['storage']['record2priority'] as $record_name_ => $priority_ ) {
|
|
|
+ if (preg_match('/^' . $foreign_table . '$/', $form_state['storage']['template_array'][$priority_]['table'])) {
|
|
|
+ $fk_options[$record_name_] = $record_name_;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ foreach ($table_description['fields'] as $field_name => $field_array) {
|
|
|
+ $chado_fields[$field_name] = $field_name;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+// dpm(array( 'tables' => $tables, 'default table' => $table, 'record name' => $record_name, 'priority' => $priority,
|
|
|
+// 'fields' => $chad_fields, 'default field' => $field, 'foreign field=>table' => $foreign_field2table,
|
|
|
+// 'table desc' => $table_description, 'foreign record options' => $fk_options, 'foreign table' => $foreign_table
|
|
|
+// ), 'Variables');
|
|
|
+
|
|
|
+ // Start of Form Proper--------------------------------------------------------------
|
|
|
+
|
|
|
+ $form['template_name'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#title' => 'Template',
|
|
|
+ '#value' => $template->name,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['template_id'] = array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $template_id,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#prefix' => '<div id="tripal_bulk_loader_template-edit_field">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['field_type'] = array(
|
|
|
+ '#type' => 'radios',
|
|
|
+ '#title' => t('Type of Field'),
|
|
|
+ '#options' => array(
|
|
|
+ 'table field' => t('Spreadsheet: Fields which maps to a Spreadsheet Column'),
|
|
|
+ 'constant' => t('Constant: Field which remains Constant throughout the Spreadsheet'),
|
|
|
+ 'foreign key' => t('Foreign Key: Fields which map to a record in another table'),
|
|
|
+ ),
|
|
|
+ '#required' => TRUE,
|
|
|
+ '#default_value' => $field_type,
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-edit_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ // check template array for records then edit one more
|
|
|
+ if (!$form_state['storage']['record2priority']) {
|
|
|
+ $groups = array();
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $groups = array_flip($form_state['storage']['record2priority']);
|
|
|
+ }
|
|
|
+ $groups['NONE'] = 'Select a Record';
|
|
|
+ $groups['NEW'] = 'New Record';
|
|
|
+ $form['edit_fields']['field_group'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => 'Record',
|
|
|
+ '#description' => 'This is used to group a set of fields together allowing '
|
|
|
+ .'multiple records to be inserted into the same table per line of the spreadsheet',
|
|
|
+ '#options' => $groups,
|
|
|
+ '#default_value' => (preg_match('/(\d+|\w+)/', $form_state['values']['field_group'])) ? $form_state['values']['field_group'] : $priority,
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-edit_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ '#required' => TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['record_name'] = array(
|
|
|
+ '#type' => (preg_match('/NEW/', $form_state['values']['field_group'])) ? 'textfield' : 'hidden',
|
|
|
+ '#title' => 'Unique Record Name',
|
|
|
+ '#prefix' => '<div id="tripal_bulk_loader_template-edit_record">',
|
|
|
+ '#suffix' => '</div>',
|
|
|
+ '#default_value' => $form_state['values']['record_name'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['field_title'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Human-readable Title for Field'),
|
|
|
+ '#default_value' => ($form_state['values']['field_title']) ? $form_state['values']['field_title'] : $template_field['title'],
|
|
|
+ );
|
|
|
+
|
|
|
+ // Spreadsheet column
|
|
|
+ $form['edit_fields']['columns'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Spreadsheet Column'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'table field')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['columns']['sheet_name'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Worksheet'),
|
|
|
+ '#description' => t('Specify the name of the worksheet.'),
|
|
|
+ '#size' => 5,
|
|
|
+ '#default_value' => ($form_state['values']['sheet_name'])? $form_state['values']['sheet_name'] : $template_field['spreadsheet sheet'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['columns']['column_number'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Column'),
|
|
|
+ '#description' => t('Specify the column in the spreadsheet that this field maps to where the first column is 1.'),
|
|
|
+ '#size' => 5,
|
|
|
+ '#default_value' => ($form_state['values']['column_number']) ? $form_state['values']['column_number'] : $template_field['spreadsheet column'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['columns']['column_exposed'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Allow Column to be set for each Bulk Loading Job'),
|
|
|
+ '#description' => t('Adds a textbox field to the Bulk Loader Page to allow users to set this value.'),
|
|
|
+ '#default_value' => ($form_state['values']['column_exposed']) ? $form_state['values']['column_exposed'] : $template_field['exposed'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['columns']['column_exposed_desc'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Description for exposed field on bulk loading job'),
|
|
|
+ '#description' => t('This description should tell the user what column should be entered here.'),
|
|
|
+ '#default_value' => ($form_state['values']['column_exposed_desc']) ? $form_state['values']['column_exposed_desc'] : $template_field['exposed_description'],
|
|
|
+ );
|
|
|
+
|
|
|
+ // Global Value
|
|
|
+ $form['edit_fields']['constant'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Constant'),
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'constant')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['constant']['constant_value'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Constant Value'),
|
|
|
+ '#description' => t('Specify the value you wish this field to have regardless of spreadsheet data.'),
|
|
|
+ '#default_value' => ($form_state['values']['constant_value']) ? $form_state['values']['constant_value'] : $template_field['constant value'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['constant']['constant_exposed'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Allow Constant to be set for each Bulk Loading Job'),
|
|
|
+ '#description' => t('Adds a textbox field to the Create Bulk Loader Form to allow users to set this value.'),
|
|
|
+ '#default_value' => ($form_state['values']['constant_exposed']) ? $form_state['values']['constant_exposed'] : $template_field['exposed'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['constant']['constant_validate'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Ensure value is in table'),
|
|
|
+ '#description' => t('Checks the database when a bulk loading job is created to ensure the value entered already exists in the database.'),
|
|
|
+ '#default_value' => ($form_state['values']['constant_validate']) ? $form_state['values']['constant_validate'] : $template_field['exposed_validate'],
|
|
|
+ );
|
|
|
+
|
|
|
+ // Foreign Key
|
|
|
+ $form['edit_fields']['foreign_key'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Foreign Key',
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => ($field_type == 'foreign key')? FALSE : TRUE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['foreign_key']['foreign_record'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => 'Record to refer to',
|
|
|
+ '#descripion' => 'Select the record that this foreign key shouold refer to. The record needs to already exist and be of the correct table.',
|
|
|
+ '#options' => $fk_options,
|
|
|
+ );
|
|
|
+
|
|
|
+ // Chado Field
|
|
|
+ $form['edit_fields']['chado'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => t('Chado Field/Column Details'),
|
|
|
+ '#description' => t('Specify the Table/Field in chado that this field maps to.'),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['chado']['chado_table'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Chado Table'),
|
|
|
+ '#options' => $tables,
|
|
|
+ '#default_value' => $table,
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-edit_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['chado']['chado_field'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Chado Field/Column'),
|
|
|
+ '#options' => $chado_fields,
|
|
|
+ '#default_value' => ($form_state['values']['chado_field']) ? $form_state['values']['chado_field'] : $template_field['field'],
|
|
|
+ '#ahah' => array(
|
|
|
+ 'path' => 'admin/tripal/tripal_bulk_loader_template/edit_field_ahah',
|
|
|
+ 'wrapper' => 'tripal_bulk_loader_template-edit_field',
|
|
|
+ 'effect' => 'fade'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Additional Options',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['required'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => 'Make this file required',
|
|
|
+ '#default_value' => $template_field['required'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Transform Spreadsheet Value Rules',
|
|
|
+ '#collapsible' => TRUE,
|
|
|
+ '#collapsed' => (!$template_field['regex']['pattern']) ? TRUE : FALSE,
|
|
|
+ );
|
|
|
+
|
|
|
+ $transformation_msg = '<p>A transformation rule allows you to transform the original value '
|
|
|
+ .'(usually from a user submitted spreadsheet) into the form you would like it stored '
|
|
|
+ .'in the chado database. Each rule consists of a match pattern (a php regular expression '
|
|
|
+ .'which determines which replacement patterns are applied and captures regions of the '
|
|
|
+ .'original value) and a replacement pattern (a string which may contain capture references '
|
|
|
+ .'that describes what the new value should be). Each rule is applied to the result of the '
|
|
|
+ .'previous rule.<p>';
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['regex_description'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $transformation_msg,
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['regex-data'] = array(
|
|
|
+ '#tree' => TRUE,
|
|
|
+ );
|
|
|
+ foreach ($template_field['regex']['pattern'] as $index => $pattern) {
|
|
|
+ $data_element = array(
|
|
|
+ 'pattern' => array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $pattern,
|
|
|
+ ),
|
|
|
+ 'replace' => array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#value' => $template_field['regex']['replace'][$index],
|
|
|
+ ),
|
|
|
+ 'old_index' => array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $index,
|
|
|
+ ),
|
|
|
+ 'new_index' => array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#options' => range(0, sizeof($template_field['regex']['pattern'])-1),
|
|
|
+ '#default_value' => $index,
|
|
|
+ ),
|
|
|
+ 'id' => array(
|
|
|
+ '#type' => 'hidden',
|
|
|
+ '#value' => $index,
|
|
|
+ ),
|
|
|
+ 'submit-delete' => array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Delete Transformation',
|
|
|
+ '#name' => $index,
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['regex-data'][$index] = $data_element;
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['submit-reorder_regex'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Save Transformation Rule Order'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['new_regex'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Add a new Transformation Rule',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['new_regex']['pattern'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Match Pattern',
|
|
|
+ '#description' => 'You can use standard <b>php regular expressions</b> in this field to specify a '
|
|
|
+ .'pattern. Only if this pattern matches the value in the spreadsheet does the replacement '
|
|
|
+ .'pattern get applied to the value. To capture a section of your value for use in the '
|
|
|
+ .'replacement patten surround with round brackets. For example, <i>GI:(\d+)</i> will match '
|
|
|
+ .' NCBI gi numbers and will capture the numerical digits for use in the replacement pattern. '
|
|
|
+ .' To match and capture any value use <i>.*</i>',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['new_regex']['replace'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Replacement Pattern',
|
|
|
+ '#description' => '<p>This pattern should contain the text you want to replace the match pattern '
|
|
|
+ .'mentioned above. It can include references of the form <b>\n</b> where n is the number of the '
|
|
|
+ .'capture in the match pattern. For example, \1 will be replaced with the text matched in your '
|
|
|
+ .'first set of round brackets.</p>',
|
|
|
+ );
|
|
|
+
|
|
|
+ if ($field_type == 'table field') {
|
|
|
+ $tab = '        ';
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
|
|
|
+ .'The following references are also available for spreadsheet fields: <b><#column:<i>number</i>#></b>. '
|
|
|
+ .'This allows you to substitute other spreadsheet values into the current field. For example, '
|
|
|
+ .'if you had the following line:<br>'
|
|
|
+ . $tab . 'SNP' . $tab . '15-Jan-2011' . $tab . '1' . $tab . '54' . $tab . 'Contig34355'
|
|
|
+ .'<br> and your current field is for column #1 and you\'re inserting into the chado field '
|
|
|
+ .'feature.uniquename then you might want to add in the data to ensure your uniquename is '
|
|
|
+ .'unique. The Match Pattern is (.*) to select all the first column and the Replacement '
|
|
|
+ .'Pattern could be \1_<#column:2#> which would insert SNP_15-Jan-2011 into the database.</p>';
|
|
|
+ }
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['new_regex']['submit-add_transform'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Add Transformation',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['test_regex'] = array(
|
|
|
+ '#type' => 'fieldset',
|
|
|
+ '#title' => 'Test Transformation Rules',
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['test_regex']['test_string'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Test Value',
|
|
|
+ '#description' => 'This should be a value that you expect the above transformation rules '
|
|
|
+ .'to be applied to.',
|
|
|
+ '#default_value' => $form_state['storage']['test_regex_test'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['test_regex']['test_result'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => 'Test Result',
|
|
|
+ '#description' => 'This is the value that would be saved to the database after the above transformation '
|
|
|
+ .'riles were applied to the Test Value.',
|
|
|
+ '#default_value' => $form_state['storage']['test_regex_result'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['additional']['regex_transform']['test_regex']['submit-test'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Test Transformation Rules'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['submit-edit_field'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Edit Field'
|
|
|
+ );
|
|
|
+
|
|
|
+ $form['edit_fields']['submit-cancel'] = array(
|
|
|
+ '#type' => 'submit',
|
|
|
+ '#value' => 'Cancel'
|
|
|
+ );
|
|
|
+
|
|
|
+ return $form;
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * Edit Field Form Submit
|
|
|
+ *
|
|
|
+ * @param $form
|
|
|
+ * The form that was submitted
|
|
|
+ * @param $form_state
|
|
|
+ * The values and storage for the form
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_edit_template_field_form_submit($form, &$form_state) {
|
|
|
+
|
|
|
+ $op = $form_state['values'][ $form_state['clicked_button']['#name'] ];
|
|
|
+ //dpm($op, 'Operation Submitted');
|
|
|
+
|
|
|
+ //Clear Test
|
|
|
+ $form_state['storage']['test_regex_result'] = NULL;
|
|
|
+ $form_state['storage']['test_regex_test'] = NULL;
|
|
|
+
|
|
|
+ if (!$form_state['ahah_submission']) {
|
|
|
+ if ($op == 'Edit Field') {
|
|
|
+
|
|
|
+ // If new record
|
|
|
+ if (preg_match('/NEW/', $form_state['values']['field_group'])) {
|
|
|
+ // add new record
|
|
|
+ $record_name = $form_state['values']['record_name'];
|
|
|
+ $priority = sizeof($form_state['storage']['template_array']) + 1;
|
|
|
+ $old_priority = $form_state['storage']['original_field']['priority'];
|
|
|
+ $field_index = $form_state['storage']['original_field']['field_index'];
|
|
|
+ $form_state['storage']['record2priority'][$record_name] = $priority;
|
|
|
+ $form_state['storage']['template_array'][$priority]['table'] = $form_state['values']['chado_table'];
|
|
|
+ $form_state['storage']['template_array'][$priority]['record_id'] = $record_name;
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $priority = $form_state['values']['field_group'];
|
|
|
+ $old_priority = $form_state['storage']['original_field']['priority'];
|
|
|
+ $field_index = $form_state['storage']['original_field']['field_index'];
|
|
|
+ $record_name = $form_state['storage']['record2priority'][$priority];
|
|
|
+ }
|
|
|
+
|
|
|
+ $field = $form_state['storage']['original_field'];
|
|
|
+ if ($form_state['values']['field_type'] == 'table field') {
|
|
|
+ $field['type'] = 'table field';
|
|
|
+ $field['title'] = $form_state['values']['field_title'];
|
|
|
+ $field['field'] = $form_state['values']['chado_field'];
|
|
|
+ $field['required'] = $form_state['values']['required'];
|
|
|
+ //$field['allowed values'] = empty by default;
|
|
|
+ $field['spreadsheet sheet'] = $form_state['values']['sheet_name'];
|
|
|
+ $field['spreadsheet column'] = $form_state['values']['column_number'];
|
|
|
+ $field['exposed'] = $form_state['values']['column_exposed'];
|
|
|
+ $field['exposed_description'] = $form_state['values']['column_exposed_desc'];
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['field_type'] == 'constant') {
|
|
|
+ $field['type'] = 'constant';
|
|
|
+ $field['title'] = $form_state['values']['field_title'];
|
|
|
+ $field['field'] = $form_state['values']['chado_field'];
|
|
|
+ $field['required'] = $form_state['values']['required'];
|
|
|
+ //$field['allowed values'] = empty by default;
|
|
|
+ $field['constant value'] = $form_state['values']['constant_value'];
|
|
|
+ $field['exposed_validate'] = $form_state['values']['constant_validate'];
|
|
|
+ $field['exposed'] = $form_state['values']['constant_exposed'];
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($form_state['values']['field_type'] == 'foreign key') {
|
|
|
+=======
|
|
|
+ } elseif ($form_state['values']['field_type'] == 'foreign key') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ $field['type'] = 'foreign key';
|
|
|
+ $field['title'] = $form_state['values']['field_title'];
|
|
|
+ $field['field'] = $form_state['values']['chado_field'];
|
|
|
+ $field['foreign key'] = $form_state['values']['foreign_record'];
|
|
|
+ $field['required'] = $form_state['values']['required'];
|
|
|
+ }
|
|
|
+
|
|
|
+ // Deal with any additional options
|
|
|
+
|
|
|
+ // if the record has changed...
|
|
|
+ $form_state['storage']['template_array'][$priority]['table'] = $form_state['values']['chado_table'];
|
|
|
+ if ($old_priority != $priority) {
|
|
|
+ $form_state['storage']['template_array'][$priority]['fields'][] = $field;
|
|
|
+ unset($form_state['storage']['template_array'][$old_priority]['fields'][$field_index]);
|
|
|
+
|
|
|
+ // if there are no fields left delete the old record
|
|
|
+ if (!$form_state['storage']['template_array'][$old_priority]['fields']) {
|
|
|
+ unset($form_state['storage']['template_array'][$old_priority]);
|
|
|
+ }
|
|
|
+ }
|
|
|
+ else {
|
|
|
+ $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $field;
|
|
|
+ }
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Updated Field');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Cancel') {
|
|
|
+
|
|
|
+ $path = explode('?', $form_state['storage']['referring URL']);
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Cancel') {
|
|
|
+
|
|
|
+ $path = explode('?',$form_state['storage']['referring URL']);
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ parse_str($path[1], $query);
|
|
|
+ $query['template_id'] = $form_state['storage']['template']->template_id;
|
|
|
+ drupal_goto($path[0], $query);
|
|
|
+
|
|
|
+ }
|
|
|
+ elseif ($op == 'Add Transformation') {
|
|
|
+
|
|
|
+ // Add transformation rule to original field
|
|
|
+ $form_state['storage']['original_field']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
|
|
|
+ $form_state['storage']['original_field']['regex']['replace'][] = $form_state['values']['replace'];
|
|
|
+
|
|
|
+ // Add original field back into template
|
|
|
+ $priority = $form_state['storage']['original_field']['priority'];
|
|
|
+ $field_index = $form_state['storage']['original_field']['field_index'];
|
|
|
+ $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Added Transformation Rule');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Save Transformation Rule Order') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Save Transformation Rule Order') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Generate new regex array
|
|
|
+ $new_regex = array();
|
|
|
+ $old_regex = $form_state['storage']['original_field']['regex'];
|
|
|
+ foreach ($form_state['values']['regex-data'] as $key => $element) {
|
|
|
+ $new_regex['pattern'][ $element['new_index'] ] = $old_regex['pattern'][ $element['old_index'] ];
|
|
|
+ $new_regex['replace'][ $element['new_index'] ] = $old_regex['replace'][ $element['old_index'] ];
|
|
|
+ }
|
|
|
+
|
|
|
+ // sort new regex arrays
|
|
|
+ asort($new_regex['pattern']);
|
|
|
+ asort($new_regex['replace']);
|
|
|
+
|
|
|
+ // Add back to original field
|
|
|
+ $form_state['storage']['original_field']['regex'] = $new_regex;
|
|
|
+ $priority = $form_state['storage']['original_field']['priority'];
|
|
|
+ $field_index = $form_state['storage']['original_field']['field_index'];
|
|
|
+ $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Reordered Transformation Rules');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Delete Transformation') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Delete Transformation') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ // Unset regex rule
|
|
|
+ $index = $form_state['clicked_button']['#name'];
|
|
|
+ unset($form_state['storage']['original_field']['regex']['pattern'][$index]);
|
|
|
+ unset($form_state['storage']['original_field']['regex']['replace'][$index]);
|
|
|
+
|
|
|
+ $priority = $form_state['storage']['original_field']['priority'];
|
|
|
+ $field_index = $form_state['storage']['original_field']['field_index'];
|
|
|
+ $form_state['storage']['template_array'][$priority]['fields'][$field_index] = $form_state['storage']['original_field'];
|
|
|
+
|
|
|
+ // Save Template
|
|
|
+ $form_state['storage']['template']->template_array = serialize($form_state['storage']['template_array']);
|
|
|
+ $success = drupal_write_record('tripal_bulk_loader_template', $form_state['storage']['template'], array('template_id'));
|
|
|
+
|
|
|
+ if ($success) {
|
|
|
+ drupal_set_message('Successfully Reordered Transformation Rules');
|
|
|
+ drupal_set_message('Template Saved.');
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ else {
|
|
|
+=======
|
|
|
+ } else {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+ drupal_set_message('Unable to Save Template!', 'error');
|
|
|
+ watchdog('T_bulk_loader',
|
|
|
+ 'Unable to save bulk loader template: %template',
|
|
|
+ array('%template' => print_r($form_state['storage']['template'], TRUE)),
|
|
|
+ WATCHDOG_ERROR
|
|
|
+ );
|
|
|
+ }
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+ }
|
|
|
+ elseif ($op == 'Test Transformation Rules') {
|
|
|
+=======
|
|
|
+ } elseif ($op == 'Test Transformation Rules') {
|
|
|
+>>>>>>> 6.x-0.4-dev
|
|
|
+
|
|
|
+ $patterns = $form_state['storage']['original_field']['regex']['pattern'];
|
|
|
+ $replaces = $form_state['storage']['original_field']['regex']['replace'];
|
|
|
+ $test_string = $form_state['values']['test_string'];
|
|
|
+ $form_state['storage']['test_regex_result'] = preg_replace($patterns, $replaces, $test_string);
|
|
|
+ $form_state['storage']['test_regex_test'] = $test_string;
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+// AHAH Callbacks
|
|
|
+//////////////////////////////////////////////////////////////////////////////////////
|
|
|
+
|
|
|
+/**
|
|
|
+ * AHAH Function: Replace $form['add_fields'] in tripal_bulk_loader_add_template_field_form
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * JSON Data printed to the screen
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_add_field_ahah() {
|
|
|
+
|
|
|
+ $form_state = array('storage' => NULL, 'submitted' => FALSE);
|
|
|
+ $form_build_id = $_POST['form_build_id'];
|
|
|
+ $form = form_get_cache($form_build_id, $form_state);
|
|
|
+ $args = $form['#parameters'];
|
|
|
+ $form_id = array_shift($args);
|
|
|
+ $form_state['post'] = $form['#post'] = $_POST;
|
|
|
+
|
|
|
+ // Enable the submit/validate handlers to determine whether AHAH-submittted.
|
|
|
+ $form_state['ahah_submission'] = TRUE;
|
|
|
+
|
|
|
+ $form['#programmed'] = $form['#redirect'] = FALSE;
|
|
|
+ drupal_process_form($form_id, $form, $form_state);
|
|
|
+ $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);
|
|
|
+
|
|
|
+ $form_element = $form['add_fields'];
|
|
|
+ // Remove the wrapper so we don't double it up.
|
|
|
+ //unset($form_element['#prefix'], $form_element['#suffix']);
|
|
|
+
|
|
|
+ $output = theme('status_messages');
|
|
|
+ $output .= drupal_render($form_element);
|
|
|
+
|
|
|
+ // Final rendering callback.
|
|
|
+ print drupal_json(array('status' => TRUE, 'data' => $output));
|
|
|
+ exit();
|
|
|
+
|
|
|
+}
|
|
|
+
|
|
|
+/**
|
|
|
+ * AHAH Function: Replace $form['edit_fields'] in tripal_bulk_loader_edit_template_field_form
|
|
|
+ *
|
|
|
+ * @return
|
|
|
+ * JSON Data printed to the screen
|
|
|
+ */
|
|
|
+function tripal_bulk_loader_edit_field_ahah() {
|
|
|
+
|
|
|
+ $form_state = array('storage' => NULL, 'submitted' => FALSE);
|
|
|
+ $form_build_id = $_POST['form_build_id'];
|
|
|
+ $form = form_get_cache($form_build_id, $form_state);
|
|
|
+ $args = $form['#parameters'];
|
|
|
+ $form_id = array_shift($args);
|
|
|
+ $form_state['post'] = $form['#post'] = $_POST;
|
|
|
+
|
|
|
+ // Enable the submit/validate handlers to determine whether AHAH-submittted.
|
|
|
+ $form_state['ahah_submission'] = TRUE;
|
|
|
+
|
|
|
+ $form['#programmed'] = $form['#redirect'] = FALSE;
|
|
|
+ drupal_process_form($form_id, $form, $form_state);
|
|
|
+ $form = drupal_rebuild_form($form_id, $form_state, $args, $form_build_id);
|
|
|
+
|
|
|
+ $form_element = $form['edit_fields'];
|
|
|
+ // Remove the wrapper so we don't double it up.
|
|
|
+ unset($form_element['#prefix'], $form_element['#suffix']);
|
|
|
+
|
|
|
+ $output = theme('status_messages');
|
|
|
+ $output .= drupal_render($form_element);
|
|
|
+
|
|
|
+ // Final rendering callback.
|
|
|
+ print drupal_json(array('status' => TRUE, 'data' => $output));
|
|
|
+ exit();
|
|
|
+
|
|
|
+<<<<<<< HEAD
|
|
|
+}
|
|
|
+=======
|
|
|
+}
|
|
|
+>>>>>>> 6.x-0.4-dev
|
laceysanderson