Merge branch '6.x-0.4-dev' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-0.4-dev

tripal_bulk_loader/tripal_bulk_loader.admin.inc

@@ -2,7 +2,7 @@
 
 /**
  * @file
- * Handles Create/Edit/Delete Template Admin Forms
+ * Bulk Loader Administration (Miscellaneous)
  */
 
 /**
@@ -12,12 +12,42 @@ function tripal_bulk_loader_admin_template() {
   $output = '';
 
   $output .= '<br /><h3>Quick Links:</h3>';
-  $output .= l(t('Create a new bulk loader template'), 'admin/tripal/tripal_bulk_loader_template/create') . "<br />";
-  $output .= l(t('Edit a bulk loader template'), 'admin/tripal/tripal_bulk_loader_template/edit') . "<br />";
-  $output .= l(t('Delete a bulk loader template'), 'admin/tripal/tripal_bulk_loader_template/delete') . "<br />";
-  $output .= l(t('Export a bulk loader template'), 'admin/tripal/tripal_bulk_loader_template/export') . "<br />";
-  $output .= l(t('Import a bulk loader template'), 'admin/tripal/tripal_bulk_loader_template/import') . "<br />";
-  $output .= '<br />';
+  $output .= '<ul>'
+    . '<li>'
+      . t('<a href="@link">Configure settings</a>',
+        array('@link' => url('admin/tripal/tripal_bulk_loader_template/configure')))
+      . '</li>'
+    . '<li>'
+      . t('List <a href="@link">Bulk Loader Jobs</a>',
+      array('@link' => url('admin/tripal/tripal_bulk_loader_template/jobs')))
+      . '</li>'
+    . '<li>'
+      . t('List <a href="@link">Manage Templates</a>',
+      array('@link' => url('admin/tripal/tripal_bulk_loader_template/manage_templates')))
+      . '</li>'
+      . '<ul>'
+      . '<li>'
+        . t('<a href="@create">Create</a> a new template',
+        array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@edit">Edit</a> an existing template',
+        array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@delete">Delete</a> an existing template',
+        array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@import">Import</a> a new template',
+        array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@export">Export</a> an existing template',
+        array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
+        . '</li>'
+      . '</ul>'
+    . '</ul>';
 
   $output .= '<h3>Module Description:</h3>';
   $output .= '<p>This module provides the ability to create loading templates for any tab-delimited '
@@ -43,6 +73,91 @@ function tripal_bulk_loader_admin_template() {
   return $output;
 }
 
+/**
+ * Provides a description page and quick links for template management
+ */
+function tripal_bulk_loader_admin_manage_templates() {
+  $output = '';
+
+  $output .= '<br /><h3>Quick Links:</h3>';
+  $output .= '<ul>'
+    . '<li>'
+      . t('<a href="@create">Create</a> a new template',
+      array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@edit">Edit</a> an existing template',
+      array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@delete">Delete</a> an existing template',
+      array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@import">Import</a> a new template',
+      array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@export">Export</a> an existing template',
+      array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
+      . '</li>'
+    . '</ul>';
+
+  $output .= '<p>' . t('Templates, as the term is used for this module, refer to plans
+  describing how the columns in the data file supplied to a bulk loading job map to tables
+  and fields in chado. Templates are created independently of bulk loading jobs so that
+  they can be re-used. Thus you only need one template to load any number of files of the
+  same format.') . '</p>';
+
+
+
+  return $output;
+}
+
+/**
+ * Provides a listing of bulk loader jobs and links for administration
+ */
+function tripal_bulk_loader_admin_jobs() {
+  $output = '';
+  $num_jobs_per_page = 50;
+
+  $output .= '<p>' . t('Jobs are not automatically submitted to the tripal jobs management
+  system when they are first created. Any jobs listed below with a status of "Initialized"
+  will not have a Job ID until you go to the bulk loader page and submit the job.') . '</p>';
+
+  $header = array(
+    array('data' => 'Job ID', 'field' => 'job_id', 'sort' => 'DESC'),
+    array('data' => 'Name', 'field' => 'loader_name'),
+    array('data' =>  'Template', 'field' => 'template_name'),
+    array('data' =>  'Status', 'field' => 'job_status'),
+    '');
+  $rows = array();
+  $resource = pager_query("SELECT n.*, t.name as template_name
+    FROM {tripal_bulk_loader} n
+    LEFT JOIN {tripal_bulk_loader_template} t ON cast(n.template_id as integer)=t.template_id"
+    . tablesort_sql($header),
+    $num_jobs_per_page);
+  while ($n = db_fetch_object($resource)) {
+    $rows[] = array(
+      l($n->job_id, 'admin/tripal/tripal_jobs/view/' . $n->job_id),
+      l($n->loader_name, 'node/' . $n->nid),
+      l($n->template_name, 'admin/tripal/tripal_bulk_loader_template/manage_templates/edit', array('query' => 'template_id=' . $n->template_id)),
+      $n->job_status,
+      l('View', 'node/' . $n->nid) . ' | ' .  l('Edit', 'node/' . $n->nid . '/edit')
+    );
+  }
+  $output .= theme_table($header, $rows);
+
+  $output .= theme('pager');
+
+  return $output;
+}
+
+/**
+ * @section
+ * Configuration Form
+ */
+
 /**
  * A Configuration form for this module
  */
@@ -132,2138 +247,3 @@ function tripal_bulk_loader_configuration_form_submit($form, $form_state) {
   variable_set('tripal_bulk_loader_lock', $form_state['values']['lock']);
 
 }
-
-//////////////////////////////////////////////////////////////////////////////////////
-// Modify Template
-//////////////////////////////////////////////////////////////////////////////////////
-
-
-/**
- * The main form reached at admin/tripal/tripal_bulk_loader/create and /edit
- */
-function tripal_bulk_loader_modify_template_base_form($form_state = NULL, $mode) {
-  $form = array();
-
-   // get template id from path and rebuild form
-  if ($_GET['template_id']) {
-    if (preg_match('/^\d+$/', $_GET['template_id'])) {
-      $form_state['storage']['template_id'] = $_GET['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;
-    }
-  }
-
-  $form['mode'] = array(
-    '#type' => 'hidden',
-    '#value' => $mode,
-  );
-
-  if ($form_state['storage']['template_id']) {
-    $form['template_name'] = array(
-      '#type' => 'item',
-      '#title' => 'Template',
-      '#value' => $form_state['storage']['template_name'],
-      '#weight' => 1,
-    );
-  }
-  else {
-    if (preg_match('/create/', $mode)) {
-      $form['new_template_name'] = array(
-        '#type' => 'textfield',
-        '#title' => 'Template Name',
-        '#weight' => 1,
-      );
-    }
-    elseif (preg_match('/edit/', $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,
-      );
-    }
-  }
-
-  $form['records'] = array(
-    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
-    '#title' => t('Current Records'),
-    '#collapsible' => TRUE,
-    '#weight' => 2,
-  );
-
-  $form['records']['description'] = array(
-    '#type' => 'item',
-    '#value' => 'Records will be inserted into the chado database in the order listed below. To '
-      .'change this order: <ul><li>Drag the rows into the correct order OR</li><li>Enter '
-      .'the numbers 1 and up in the Order textboxes to indicate the correct order.</li></ul>',
-  );
-
-  $form['records']['records-data'] = array(
-    '#tree' => TRUE,
-  );
-
-  $form['records']['no_records'] = array(
-    '#type' => 'hidden',
-    '#value' => TRUE,
-  );
-
-  $form['records']['submit-new_record'] = array(
-    '#type' => 'submit',
-    '#value' => 'New Record/Field',
-  );
-
-  $form['records']['submit-reorder'] = array(
-    '#type' => 'submit',
-    '#value' => 'Save Order',
-  );
-
-  $form['fields'] = array(
-    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
-    '#title' => t('Current Fields'),
-    '#collapsible' => TRUE,
-    '#weight' => 3,
-  );
-
-  $form['fields']['fields-data'] = array(
-    '#tree' => TRUE,
-  );
-
-  if ($form_state['storage']['template']) {
-
-    // List Current Fields -------------------------------------------------------------
-    $i=1;
-    foreach ($form_state['storage']['template'] as $priority => $table_array) {
-      if (!is_array($table_array)) {
-      continue; }
-
-        $form['records']['no_records']['#value'] = FALSE;
-
-        $form['records']['records-data'][$priority] = array(
-          'title' => array(
-            '#type' => 'markup',
-            '#value' => filter_xss($table_array['record_id']),
-          ),
-          'chado_table' => array(
-            '#type' => 'markup',
-            '#value' => filter_xss($table_array['table']),
-          ),
-          'mode' => array(
-            '#type' => 'item',
-            '#value' => ($table_array['mode']) ? $table_array['mode'] : 'insert_unique',
-          ),
-          'new_priority' => array(
-            '#type' => 'select',
-            '#options' => range(1, sizeof($form_state['storage']['template'])),
-            '#default_value' => $priority,
-          ),
-          'old_priority' => array(
-            '#type' => 'hidden',
-            '#value' => $priority,
-          ),
-          'id'  => array(
-            '#type' => 'hidden',
-            '#value' => $priority,
-          ),
-          'submit-edit_record' => array(
-            '#type' => 'submit',
-            '#name' => (string)$priority,
-            '#value' => 'Edit Record',
-          ),
-          'submit-add_field' => array(
-            '#type' => 'submit',
-            '#name' => (string)$priority,
-            '#value' => 'Add Field',
-          ),
-          'submit-duplicate_record' => array(
-            '#type' => 'submit',
-            '#name' => (string)$priority,
-            '#value' => 'Duplicate Record'
-          ),
-        );
-
-        foreach ($table_array['fields'] as $field_index => $field) {
-
-          $form['fields']['fields-data'][$i] = array(
-            'record_id' => array(
-              '#type' => 'item',
-              '#value' => $table_array['record_id'],
-            ),
-            'priority_hidden' => array(
-              '#type' => 'hidden',
-              '#value' => $priority,
-            ),
-            'field_name' => array(
-              '#type' => 'item',
-              '#value' => $field['title'],
-            ),
-            'chado_table_name' => array(
-              '#type' => 'item',
-              '#value' => $table_array['table'],
-            ),
-            'chado_table_hidden' => array(
-              '#type' => 'hidden',
-              '#value' => $table_array['table'],
-            ),
-            'chado_field_name' => array(
-              '#type' => 'item',
-              '#value' => $field['field'],
-            ),
-            'sheet_name' => array(
-              '#type' => 'item',
-              '#value' => $field['spreadsheet sheet'],
-            ),
-            'column_num' => array(
-              '#type' => 'item',
-              '#value' => $field['spreadsheet column'],
-            ),
-            'constant_value' => array(
-              '#type' => 'item',
-              '#value' => $field['constant value'],
-            ),
-            'field_index' => array(
-              '#type' => 'hidden',
-              '#value' => $field_index
-            ),
-            'foreign_record_id' => array(
-              '#type' => 'item',
-              '#value' => $field['foreign key'],
-            ),
-            'edit_submit' => array(
-              '#type' => 'submit',
-              '#name' => (string)$i,
-              '#value' => "Edit Field",
-            ),
-            'delete_submit' => array(
-              '#type' => 'submit',
-              '#name' => (string)$i,
-              '#value' => "Delete Field",
-            ),
-          );
-
-          $i++;
-        }
-    }
-    $form['fields']['total_fields'] = array(
-      '#type' => 'item',
-      '#value' => $i,
-    );
-
-  }
-
-  if ($form['records']['no_records']['#value']) {
-    $form['records']['description'] = array(
-      '#type' => 'item',
-      '#value' => 'There are currently no records.',
-    );
-    unset($form['records']['submit-reorder']);
-
-    $form['fields']['description'] = array(
-      '#type' => 'item',
-      '#value' => 'There are currently no fields.',
-    );
-
-  }
-
-  $mode_title = (preg_match('/create/', $mode)) ? 'Create Template' : 'Edit Template';
-  $value = ($form_state['storage']['template_id'])? 'Save Template' : $mode_title;
-  $form['submit'] = array(
-    '#type' => 'submit',
-    '#value' => $value,
-    '#weight' => 4,
-  );
-
-  return $form;
-}
-
-/**
- * Submit for tripal_bulk_loader_modify_template_base_form
- */
-function tripal_bulk_loader_modify_template_base_form_submit($form, &$form_state) {
-
-  $form_state['rebuild'] = TRUE;
-  if ($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) {
-        if (preg_match('/\d+/', $priority)) {
-          unset($new_template[$priority]);
-        }
-      }
-      //set elements in new order
-      foreach ($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(
-        'template_id' => $form_state['storage']['template_id'],
-        'record_id' => 'NEW',
-      );
-      drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
-    break;
-
-    case 'Edit Record':
-      $query = array(
-        'template_id' => $form_state['storage']['template_id'],
-        'record_id' => $form_state['clicked_button']['#name'],
-      );
-      drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_record', $query);
-    break;
-
-    case 'Add Field':
-      $query = array(
-        'template_id' => $form_state['storage']['template_id'],
-        '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(
-        'template_id' => $form_state['storage']['template_id'],
-        '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(t('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(t('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,
-  );
-
-  $form['submit'] = array(
-    '#type' => 'submit',
-    '#value' => 'Delete Template',
-  );
-
-  return $form;
-}
-
-/**
- * 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(t('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 $form_state
- *   Contains the values and storage for the form
- * @return
- *   A form array to be rendered by drupal_get_form
- */
-function tripal_bulk_loader_edit_template_record_form(&$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 $form;
-  }
-
-  // Pre-process values/defaults ---------------------------
-
-  // If this is the first load of the form (no form state) we need to initialize some variables
-  if (!$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'];
-  }
-  else {
-    $table = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['table'];
-  }
-
-  //dpm($form_state, 'form state');
-
-   // Form Proper -------------------------------------------
-  $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,
-    '#default_value' => $priority_default,
-    '#required' => TRUE,
-  );
-
-  $form['edit_record']['record_name'] = array(
-    '#type' => 'textfield',
-    '#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(t('Successfully Updated Template Record'));
-        drupal_set_message(t('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], $query);
-      }
-      else {
-        drupal_set_message(t('Unable to Save Template!'), 'error');
-        watchdog('T_bulk_loader',
-          'Unable to save bulk loader template: %template',
-          array('%template' => print_r($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();
-  $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 $form;
-  }
-
-  // Pre-set Variables needed for form proper------------------------------------------
-
-   // If this is the first load of the form (no form state) we need to initialize some variables
-  if (!$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 = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
-    $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 $form_state
- *   The values and storage for the form
- */
-function tripal_bulk_loader_add_template_field_form_submit($form, &$form_state) {
-
-  $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;
-
-      }
-      else {
-        $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' => $form_state['values']['constant_validate'],
-        );
-      }
-      elseif ($form_state['values']['field_type'] == 'foreign key') {
-        $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(t('Successfully Added Field to Template'));
-        drupal_set_message(t('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], $query);
-      }
-      else {
-        drupal_set_message(t('Unable to Save Template!'), 'error');
-        watchdog('T_bulk_loader',
-          'Unable to save bulk loader template: %template',
-          array('%template' => print_r($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], $query);
-    }
-    elseif ($op == 'Add Transformation') {
-
-      // Add transformation rule to original field
-      $form_state['storage']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
-      $form_state['storage']['regex']['replace'][] = $form_state['values']['replace'];
-      drupal_set_message(t('Successfully Added Transformation Rule'));
-
-    }
-    elseif ($op == 'Save Transformation Rule Order') {
-
-      // 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'] = $new_regex;
-    }
-    elseif ($op == 'Delete Transformation') {
-
-      // Unset regex rule
-      $index = $form_state['clicked_button']['#name'];
-      unset($form_state['storage']['regex']['pattern'][$index]);
-      unset($form_state['storage']['regex']['replace'][$index]);
-
-    }
-    elseif ($op == 'Test Transformation Rules') {
-
-      $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();
-  $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 $form;
-  }
-
-  // Pre-set Variables needed for form proper------------------------------------------
-
-  // If this is the first load of the form (no form state) we need to initialize some variables
-  if (!$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'];
-  }
-  else {
-    $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_' . $table . '_schema');
-  if ($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 = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
-    $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;
-
-      }
-      else {
-        $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'] = $form_state['values']['constant_exposed'];
-      }
-      elseif ($form_state['values']['field_type'] == 'foreign key') {
-          $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(t('Successfully Updated Field'));
-        drupal_set_message(t('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], $query);
-      }
-      else {
-        drupal_set_message(t('Unable to Save Template!'), 'error');
-        watchdog('T_bulk_loader',
-          'Unable to save bulk loader template: %template',
-          array('%template' => print_r($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], $query);
-
-    }
-    elseif ($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(t('Successfully Added Transformation Rule'));
-        drupal_set_message(t('Template Saved.'));
-      }
-      else {
-        drupal_set_message(t('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 == 'Save Transformation Rule Order') {
-
-      // 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(t('Successfully Reordered Transformation Rules'));
-        drupal_set_message(t('Template Saved.'));
-      }
-      else {
-        drupal_set_message(t('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 == 'Delete Transformation') {
-
-      // 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(t('Successfully Reordered Transformation Rules'));
-        drupal_set_message(t('Template Saved.'));
-      }
-      else {
-        drupal_set_message(t('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 == 'Test Transformation Rules') {
-
-      $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);
-  $form_build_id = filter_xss($_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);
-  $form_build_id = filter_xss($_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();
-
-}

tripal_bulk_loader/tripal_bulk_loader.admin.templates.inc

@@ -0,0 +1,2150 @@
+<?php
+
+/**
+ * @file
+ * All functions in this file pertain to administrative management of bulk loader templates
+ */
+
+/**
+ * @section
+ * Modify Template
+ * The main form for creating/editing templates as a whole
+ */
+
+
+/**
+ * The main form reached at admin/tripal/tripal_bulk_loader/create and /edit
+ */
+function tripal_bulk_loader_modify_template_base_form($form_state = NULL, $mode) {
+  $form = array();
+
+   // get template id from path and rebuild form
+  if ($_GET['template_id']) {
+    if (preg_match('/^\d+$/', $_GET['template_id'])) {
+      $form_state['storage']['template_id'] = $_GET['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;
+    }
+  }
+
+  $form['mode'] = array(
+    '#type' => 'hidden',
+    '#value' => $mode,
+  );
+
+  if ($form_state['storage']['template_id']) {
+    $form['template_name'] = array(
+      '#type' => 'item',
+      '#title' => 'Template',
+      '#value' => $form_state['storage']['template_name'],
+      '#weight' => 1,
+    );
+  }
+  else {
+    if (preg_match('/create/', $mode)) {
+      $form['new_template_name'] = array(
+        '#type' => 'textfield',
+        '#title' => 'Template Name',
+        '#weight' => 1,
+      );
+    }
+    elseif (preg_match('/edit/', $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,
+      );
+    }
+  }
+
+  $form['records'] = array(
+    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
+    '#title' => t('Current Records'),
+    '#collapsible' => TRUE,
+    '#weight' => 2,
+  );
+
+  $form['records']['description'] = array(
+    '#type' => 'item',
+    '#value' => 'Records will be inserted into the chado database in the order listed below. To '
+      .'change this order: <ul><li>Drag the rows into the correct order OR</li><li>Enter '
+      .'the numbers 1 and up in the Order textboxes to indicate the correct order.</li></ul>',
+  );
+
+  $form['records']['records-data'] = array(
+    '#tree' => TRUE,
+  );
+
+  $form['records']['no_records'] = array(
+    '#type' => 'hidden',
+    '#value' => TRUE,
+  );
+
+  $form['records']['submit-new_record'] = array(
+    '#type' => 'submit',
+    '#value' => 'New Record/Field',
+  );
+
+  $form['records']['submit-reorder'] = array(
+    '#type' => 'submit',
+    '#value' => 'Save Order',
+  );
+
+  $form['fields'] = array(
+    '#type' => ($form_state['storage']['template_id'])? 'fieldset' : 'hidden',
+    '#title' => t('Current Fields'),
+    '#collapsible' => TRUE,
+    '#weight' => 3,
+  );
+
+  $form['fields']['fields-data'] = array(
+    '#tree' => TRUE,
+  );
+
+  if ($form_state['storage']['template']) {
+
+    // List Current Fields -------------------------------------------------------------
+    $i=1;
+    foreach ($form_state['storage']['template'] as $priority => $table_array) {
+      if (!is_array($table_array)) {
+      continue; }
+
+        $form['records']['no_records']['#value'] = FALSE;
+
+        $form['records']['records-data'][$priority] = array(
+          'title' => array(
+            '#type' => 'markup',
+            '#value' => filter_xss($table_array['record_id']),
+          ),
+          'chado_table' => array(
+            '#type' => 'markup',
+            '#value' => filter_xss($table_array['table']),
+          ),
+          'mode' => array(
+            '#type' => 'item',
+            '#value' => ($table_array['mode']) ? $table_array['mode'] : 'insert_unique',
+          ),
+          'new_priority' => array(
+            '#type' => 'select',
+            '#options' => range(1, sizeof($form_state['storage']['template'])),
+            '#default_value' => $priority,
+          ),
+          'old_priority' => array(
+            '#type' => 'hidden',
+            '#value' => $priority,
+          ),
+          'id'  => array(
+            '#type' => 'hidden',
+            '#value' => $priority,
+          ),
+          'submit-edit_record' => array(
+            '#type' => 'submit',
+            '#name' => (string)$priority,
+            '#value' => 'Edit Record',
+          ),
+          'submit-add_field' => array(
+            '#type' => 'submit',
+            '#name' => (string)$priority,
+            '#value' => 'Add Field',
+          ),
+          'submit-duplicate_record' => array(
+            '#type' => 'submit',
+            '#name' => (string)$priority,
+            '#value' => 'Duplicate Record'
+          ),
+        );
+
+        foreach ($table_array['fields'] as $field_index => $field) {
+
+          $form['fields']['fields-data'][$i] = array(
+            'record_id' => array(
+              '#type' => 'item',
+              '#value' => $table_array['record_id'],
+            ),
+            'priority_hidden' => array(
+              '#type' => 'hidden',
+              '#value' => $priority,
+            ),
+            'field_name' => array(
+              '#type' => 'item',
+              '#value' => $field['title'],
+            ),
+            'chado_table_name' => array(
+              '#type' => 'item',
+              '#value' => $table_array['table'],
+            ),
+            'chado_table_hidden' => array(
+              '#type' => 'hidden',
+              '#value' => $table_array['table'],
+            ),
+            'chado_field_name' => array(
+              '#type' => 'item',
+              '#value' => $field['field'],
+            ),
+            'sheet_name' => array(
+              '#type' => 'item',
+              '#value' => $field['spreadsheet sheet'],
+            ),
+            'column_num' => array(
+              '#type' => 'item',
+              '#value' => $field['spreadsheet column'],
+            ),
+            'constant_value' => array(
+              '#type' => 'item',
+              '#value' => $field['constant value'],
+            ),
+            'field_index' => array(
+              '#type' => 'hidden',
+              '#value' => $field_index
+            ),
+            'foreign_record_id' => array(
+              '#type' => 'item',
+              '#value' => $field['foreign key'],
+            ),
+            'edit_submit' => array(
+              '#type' => 'submit',
+              '#name' => (string)$i,
+              '#value' => "Edit Field",
+            ),
+            'delete_submit' => array(
+              '#type' => 'submit',
+              '#name' => (string)$i,
+              '#value' => "Delete Field",
+            ),
+          );
+
+          $i++;
+        }
+    }
+    $form['fields']['total_fields'] = array(
+      '#type' => 'item',
+      '#value' => $i,
+    );
+
+  }
+
+  if ($form['records']['no_records']['#value']) {
+    $form['records']['description'] = array(
+      '#type' => 'item',
+      '#value' => 'There are currently no records.',
+    );
+    unset($form['records']['submit-reorder']);
+
+    $form['fields']['description'] = array(
+      '#type' => 'item',
+      '#value' => 'There are currently no fields.',
+    );
+
+  }
+
+  $mode_title = (preg_match('/create/', $mode)) ? 'Create Template' : 'Edit Template';
+  $value = ($form_state['storage']['template_id'])? 'Save Template' : $mode_title;
+  $form['submit'] = array(
+    '#type' => 'submit',
+    '#value' => $value,
+    '#weight' => 4,
+  );
+
+  return $form;
+}
+
+/**
+ * Submit for tripal_bulk_loader_modify_template_base_form
+ */
+function tripal_bulk_loader_modify_template_base_form_submit($form, &$form_state) {
+
+  $form_state['rebuild'] = TRUE;
+  if ($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) {
+        if (preg_match('/\d+/', $priority)) {
+          unset($new_template[$priority]);
+        }
+      }
+      //set elements in new order
+      foreach ($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(
+        'template_id' => $form_state['storage']['template_id'],
+        'record_id' => 'NEW',
+      );
+      drupal_goto('admin/tripal/tripal_bulk_loader_template/add_field', $query);
+    break;
+
+    case 'Edit Record':
+      $query = array(
+        'template_id' => $form_state['storage']['template_id'],
+        'record_id' => $form_state['clicked_button']['#name'],
+      );
+      drupal_goto('admin/tripal/tripal_bulk_loader_template/edit_record', $query);
+    break;
+
+    case 'Add Field':
+      $query = array(
+        'template_id' => $form_state['storage']['template_id'],
+        '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(
+        'template_id' => $form_state['storage']['template_id'],
+        '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(t('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(t('Template Saved.'));
+
+}
+
+/**
+ * @section
+ * 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,
+  );
+
+  $form['submit'] = array(
+    '#type' => 'submit',
+    '#value' => 'Delete Template',
+  );
+
+  return $form;
+}
+
+/**
+ * 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']);
+}
+
+/**
+ * @section
+ * 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(t('Successfully imported Tripal Bulk Loader Template.'));
+      }
+    break;
+  }
+}
+
+/**
+ * @section
+ * 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 $form_state
+ *   Contains the values and storage for the form
+ * @return
+ *   A form array to be rendered by drupal_get_form
+ */
+function tripal_bulk_loader_edit_template_record_form(&$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 $form;
+  }
+
+  // Pre-process values/defaults ---------------------------
+
+  // If this is the first load of the form (no form state) we need to initialize some variables
+  if (!$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'];
+  }
+  else {
+    $table = $form_state['storage']['template_array'][$form_state['storage']['original_priority']]['table'];
+  }
+
+  //dpm($form_state, 'form state');
+
+   // Form Proper -------------------------------------------
+  $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,
+    '#default_value' => $priority_default,
+    '#required' => TRUE,
+  );
+
+  $form['edit_record']['record_name'] = array(
+    '#type' => 'textfield',
+    '#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 file',
+      '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(t('Successfully Updated Template Record'));
+        drupal_set_message(t('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], $query);
+      }
+      else {
+        drupal_set_message(t('Unable to Save Template!'), 'error');
+        watchdog('T_bulk_loader',
+          'Unable to save bulk loader template: %template',
+          array('%template' => print_r($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);
+    }
+  }
+
+}
+
+/**
+ * @section
+ * 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();
+  $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 $form;
+  }
+
+  // Pre-set Variables needed for form proper------------------------------------------
+
+   // If this is the first load of the form (no form state) we need to initialize some variables
+  if (!$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('Data: A Field which maps to a column in the supplied file.'),
+      'constant' => t('Constant: Field which remains Constant throughout the file'),
+      '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 file',
+    '#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'],
+  );
+
+  // loading file data column
+  $form['add_fields']['columns'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Data File Column'),
+    '#collapsible' => TRUE,
+    '#collapsed' => ($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 data 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 data file value.'),
+    '#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',
+  );
+
+  $form['add_fields']['additional']['regex_transform'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Transform Data File Value Rules',
+    '#collapsible' => TRUE,
+    '#collapsed' => (!$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 data file) 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 data file 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 = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
+    $form['add_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
+      .'The following references are also available for data file fields: <b><#column:<i>number</i>#></b>. '
+      .'This allows you to substitute other data file 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 $form_state
+ *   The values and storage for the form
+ */
+function tripal_bulk_loader_add_template_field_form_submit($form, &$form_state) {
+
+  $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;
+
+      }
+      else {
+        $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 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' => $form_state['values']['constant_validate'],
+        );
+      }
+      elseif ($form_state['values']['field_type'] == 'foreign key') {
+        $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(t('Successfully Added Field to Template'));
+        drupal_set_message(t('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], $query);
+      }
+      else {
+        drupal_set_message(t('Unable to Save Template!'), 'error');
+        watchdog('T_bulk_loader',
+          'Unable to save bulk loader template: %template',
+          array('%template' => print_r($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], $query);
+    }
+    elseif ($op == 'Add Transformation') {
+
+      // Add transformation rule to original field
+      $form_state['storage']['regex']['pattern'][] = '/' . $form_state['values']['pattern'] . '/';
+      $form_state['storage']['regex']['replace'][] = $form_state['values']['replace'];
+      drupal_set_message(t('Successfully Added Transformation Rule'));
+
+    }
+    elseif ($op == 'Save Transformation Rule Order') {
+
+      // 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'] = $new_regex;
+    }
+    elseif ($op == 'Delete Transformation') {
+
+      // Unset regex rule
+      $index = $form_state['clicked_button']['#name'];
+      unset($form_state['storage']['regex']['pattern'][$index]);
+      unset($form_state['storage']['regex']['replace'][$index]);
+
+    }
+    elseif ($op == 'Test Transformation Rules') {
+
+      $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();
+  $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 $form;
+  }
+
+  // Pre-set Variables needed for form proper------------------------------------------
+
+  // If this is the first load of the form (no form state) we need to initialize some variables
+  if (!$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'];
+  }
+  else {
+    $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_' . $table . '_schema');
+  if ($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('Data Field: Fields which maps to a data file column'),
+      'constant' => t('Constant: Field which remains Constant throughout the data file'),
+      '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 data file',
+    '#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'],
+  );
+
+  // data file column
+  $form['edit_fields']['columns'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Data File Column'),
+    '#collapsible' => TRUE,
+    '#collapsed' => ($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'],
+  );
+  */
+
+  $form['edit_fields']['columns']['column_number'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Column'),
+    '#description' => t('Specify the column in the data file that this field maps to where the first column is 1.'),
+    '#size' => 5,
+    '#default_value' => ($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,
+  );
+
+  $form['edit_fields']['constant']['constant_value'] = array(
+    '#type' => 'textfield',
+    '#title' => t('Constant Value'),
+    '#description' => t('Specify the value you wish this field to have regardless of data file value.'),
+    '#default_value' => ($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'],
+  );
+
+  $form['edit_fields']['additional']['regex_transform'] = array(
+    '#type' => 'fieldset',
+    '#title' => 'Transform Data File Value Rules',
+    '#collapsible' => TRUE,
+    '#collapsed' => (!$template_field['regex']['pattern']) ? TRUE : FALSE,
+  );
+
+  $transformation_msg = '<p>A transformation rule allows you to transform the original value '
+      .'(usually from a user submitted data file) 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 data file 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 = '&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp&nbsp';
+    $form['edit_fields']['additional']['regex_transform']['new_regex']['replace']['#description'] .= '<p>'
+      .'The following references are also available for data file fields: <b><#column:<i>number</i>#></b>. '
+      .'This allows you to substitute other data file 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;
+
+      }
+      else {
+        $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 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'] = $form_state['values']['constant_exposed'];
+      }
+      elseif ($form_state['values']['field_type'] == 'foreign key') {
+          $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(t('Successfully Updated Field'));
+        drupal_set_message(t('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], $query);
+      }
+      else {
+        drupal_set_message(t('Unable to Save Template!'), 'error');
+        watchdog('T_bulk_loader',
+          'Unable to save bulk loader template: %template',
+          array('%template' => print_r($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], $query);
+
+    }
+    elseif ($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(t('Successfully Added Transformation Rule'));
+        drupal_set_message(t('Template Saved.'));
+      }
+      else {
+        drupal_set_message(t('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 == 'Save Transformation Rule Order') {
+
+      // 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(t('Successfully Reordered Transformation Rules'));
+        drupal_set_message(t('Template Saved.'));
+      }
+      else {
+        drupal_set_message(t('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 == 'Delete Transformation') {
+
+      // 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(t('Successfully Reordered Transformation Rules'));
+        drupal_set_message(t('Template Saved.'));
+      }
+      else {
+        drupal_set_message(t('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 == 'Test Transformation Rules') {
+
+      $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;
+    }
+  }
+
+}
+
+/**
+ * @section
+ * 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);
+  $form_build_id = filter_xss($_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);
+  $form_build_id = filter_xss($_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();
+
+}

tripal_bulk_loader/tripal_bulk_loader.constants.inc

@@ -143,7 +143,7 @@ function tripal_bulk_loader_set_constants_form($form_state, $node) {
       '#type' => 'item',
       '#value' => t('You have already added constants to this bulk loading job. Each '
         .'row in the following table represents a set of constants. Each set will be used '
-        .'to load your spreadsheet with the specified template resulting in the each record '
+        .'to load your data file with the specified template resulting in the each record '
         .'in the template to be loaded x number of times where there are x sets of '
         .'constants (rows in the following table).')
     );
@@ -167,7 +167,7 @@ function tripal_bulk_loader_set_constants_form($form_state, $node) {
 
       $form['exposed_fields']['existing'][$group]['delete'] = array(
         '#type' => 'markup',
-        '#value' => filter_xss(l(t('Edit'), 'node/' . $node->nid . '/constants/' . $group . '/edit') . '&nbsp&nbsp|&nbsp&nbsp'  .
+        '#value' => filter_xss(l(t('Edit'), 'node/' . $node->nid . '/constants/' . $group . '/edit') . '  |  '  .
           l(t('Delete'), 'node/' . $node->nid . '/constants/' . $group . '/delete')),
       );
 
@@ -211,7 +211,7 @@ function tripal_bulk_loader_set_constants_form($form_state, $node) {
             $form['exposed_fields']['new'][$record_id . '-' . $field_id] = array(
               '#type' => 'textfield',
               '#title' => t('%title', array('%title' => $field['title']) ),
-              '#description' => t('Enter the case-sensitive value of this constant for your spreadsheet'),
+              '#description' => t('Enter the case-sensitive value of this constant for your data file'),
               '#default_value' => (isset($node->constants[$record_id][$field_id]['value'])) ? $node->constants[$record_id][$field_id]['value'] : $field['constant value'],
             );
           break;
@@ -440,7 +440,7 @@ function tripal_bulk_loader_edit_constant_set_form($form_state, $node, $group_id
             $form[$record_id . '-' . $field_id] = array(
               '#type' => 'textfield',
               '#title' => t('%title', array('%title' => $field['title'])),
-              '#description' => t('Enter the case-sensitive value of this constant for your spreadsheet'),
+              '#description' => t('Enter the case-sensitive value of this constant for your data file'),
               '#default_value' => (isset($node->constants[$group_id][$record_id][$field_id]['value'])) ? $node->constants[$group_id][$record_id][$field_id]['value'] : $field['constant value'],
             );
           break;

tripal_bulk_loader/tripal_bulk_loader.loader.inc

@@ -402,7 +402,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $field2c
   if ($table_data['need_further_processing']) {
     $values = tripal_bulk_loader_add_spreadsheetdata_to_values($values, $line, $field2column[$priority]);
     if (!$values) {
-      watchdog('T_bulk_loader', 'Line ' . $line_num . ' Spreadsheet Added:' . print_r($values, TRUE), array(), WATCHDOG_NOTICE);
+      watchdog('T_bulk_loader', 'Line ' . $line_num . ' Data File Added:' . print_r($values, TRUE), array(), WATCHDOG_NOTICE);
     }
 
     $values = tripal_bulk_loader_add_foreignkey_to_values($values, $data, $record2priority);

tripal_bulk_loader/tripal_bulk_loader.module

@@ -2,6 +2,8 @@
 
 include('tripal_bulk_loader.loader.inc');
 include('tripal_bulk_loader.constants.inc');
+include('tripal_bulk_loader.admin.inc');
+include('tripal_bulk_loader.admin.templates.inc');
 
 /**
  * Implements hook_init
@@ -34,7 +36,6 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_edit_constant_set_form', 1, 3),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.constants.inc',
   );
   $items['node/%node/constants/%/delete'] = array(
     'title' => 'Delete Constant Set',
@@ -43,17 +44,15 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_delete_constant_set_form', 1, 3),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.constants.inc',
   );
 
-  // Admin page to create the template
+  // Admin pages -----------------
   $items['admin/tripal/tripal_bulk_loader_template'] = array(
-    'title' => 'Bulk Loader Template',
+    'title' => 'Bulk Loader',
     'description' => 'Templates for loading tab-delimited data',
     'page callback' => 'tripal_bulk_loader_admin_template',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/configure'] = array(
     'title' => 'Configure',
@@ -62,27 +61,38 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_configuration_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
+  );
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates'] = array(
+    'title' => 'Manage Templates',
+    'description' => 'Create/Update/Delete/Import/Export Templates',
+    'page callback' => 'tripal_bulk_loader_admin_manage_templates',
+    'access arguments' => array('administer site configuration'),
+    'type' => MENU_NORMAL_ITEM,
+  );
+  $items['admin/tripal/tripal_bulk_loader_template/jobs'] = array(
+    'title' => 'Jobs',
+    'description' => 'Listing of Bulk Loading Jobs',
+    'page callback' => 'tripal_bulk_loader_admin_jobs',
+    'access arguments' => array('administer site configuration'),
+    'type' => MENU_NORMAL_ITEM,
   );
 
-  // Create/Edit Template -------
-  $items['admin/tripal/tripal_bulk_loader_template/create'] = array(
+  // Create/Edit Template --------
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/create'] = array(
     'title' => 'Create Template',
     'description' => 'Create loader template for loading tab-delimited data',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'create'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
-  $items['admin/tripal/tripal_bulk_loader_template/edit'] = array(
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/edit'] = array(
     'title' => 'Edit Template',
     'description' => 'Edit loader template for loading tab-delimited data',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_modify_template_base_form', 'edit'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_record'] = array(
     'title' => 'Edit Template Record',
@@ -91,7 +101,6 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_edit_template_record_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
     'title' => 'Add Template Field',
@@ -100,7 +109,6 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_add_template_field_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
     'title' => 'Edit Template Field',
@@ -109,49 +117,43 @@ function tripal_bulk_loader_menu() {
     'page arguments' => array('tripal_bulk_loader_edit_template_field_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   // Delete Template -----
-  $items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/delete'] = array(
     'title' => 'Delete Template',
     'description' => 'Delete bulk loader template',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_delete_template_base_form'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   // Import/Export ---------
-  $items['admin/tripal/tripal_bulk_loader_template/import'] = array(
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/import'] = array(
     'title' => 'Import Template',
     'description' => 'Import Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'import'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
-  $items['admin/tripal/tripal_bulk_loader_template/export'] = array(
+  $items['admin/tripal/tripal_bulk_loader_template/manage_templates/export'] = array(
     'title' => 'Export Template',
     'description' => 'Export Loaders',
     'page callback' => 'drupal_get_form',
     'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'export'),
     'access arguments' => array('administer site configuration'),
     'type' => MENU_NORMAL_ITEM,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   // AHAH ---------
   $items['admin/tripal/tripal_bulk_loader_template/add_field_ahah'] = array(
     'page callback' => 'tripal_bulk_loader_add_field_ahah',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit_field_ahah'] = array(
     'page callback' => 'tripal_bulk_loader_edit_field_ahah',
     'access arguments' => array('administer site configuration'),
     'type' => MENU_CALLBACK,
-    'file' => 'tripal_bulk_loader.admin.inc',
   );
 
   return $items;
@@ -224,35 +226,6 @@ function tripal_bulk_loader_perm() {
   );
 }
 
-/**
- * Creates a listing page for all bulk loading jobs
- */
-function tripal_bulk_loader_list() {
-  $num_results_per_page = 50;
-  $output = '';
-
-  $header = array('', 'Status', 'Loader', 'File');
-  $rows = array();
-
-  $query = 'SELECT * FROM {tripal_bulk_loader} l '
-    .'LEFT JOIN {node} n ON n.nid = l.nid '
-    .'LEFT JOIN {tripal_bulk_loader_template} t ON t.template_id = cast(l.template_id as integer)';
-  $resource = pager_query($query, $num_results_per_page, 0, NULL);
-  while ($r = db_fetch_object($resource)) {
-    $row = array(
-      l($r->title, 'node/' . $r->nid),
-      $r->job_status,
-      $r->name,
-      $r->file
-    );
-    $rows[] = $row;
-  }
-
-  $output .= theme('table', $header, $rows);
-  return $output;
-
-}
-
 //////////////////////////////////////////////////////////////////////////////////////////////
 // Node Functions
 //////////////////////////////////////////////////////////////////////////////////////////////
@@ -328,7 +301,7 @@ function tripal_bulk_loader_form($node, $form_state) {
   $form['loader']['file']= array(
     '#type'          => 'textfield',
     '#title'         => t('Data File'),
-    '#description'   => t('Please specify the data file to be loaded.'),
+    '#description'   => t('Please specify the data file to be loaded. This must be a tab-delimited text file with UNIX line endings.'),
     '#weight'        => -8,
     '#default_value' => $node->file
   );

tripal_views/tripal_views.views.inc

@@ -727,8 +727,15 @@ function tripal_views_data_export_download_form(&$form_state, $view, $display_id
   $displays = $view->display;
   $options = array();
   $default = '';
+  $current_display = $view->current_display;
   foreach ($displays as $name => $display) {
     if (preg_match("/^views_data_export/", $name)) {
+    
+      // only add this display to the form if it is attached 
+      $display_options = $display->display_options;
+      if(strcmp($display_options['displays'][$current_display],$current_display)!=0){
+         continue;
+      } 
 
       // set the first item as default
       if (!$default) {

tripal_views/views/handlers/views_handler_filter_chado_select_string.inc

@@ -44,6 +44,12 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
       '#default_value' => (isset($this->options['max_length'])) ? $this->options['max_length'] : 40,
 
     );
+    $form['max_length'] = array(
+      '#type' => 'markup',
+      '#value' => t('<strong><font color="red">Note:</font></strong> If another filter exists for the same table then '.
+                    'the values shown in the drop box will only include those from rows that are not filtered.'),
+
+    );
 
   }
 
@@ -64,19 +70,43 @@ class views_handler_filter_chado_select_string extends views_handler_filter_stri
     }
     else {
 
-      // Get Options
-      if ($this->options['optional']) {
-        //$options['<select '.$this->table.'>'] = '--None--';
-        $options['All'] = '--Any--';
+      // build a where clause that will filter the list in the drop box
+      // using fields that are not exposed and that are for the table
+      // from whcih the values in the drop box will be slected and
+      // we only want to use non-exposed fields because these are not
+      // available to the user to edit--their fixed.
+      $where = '';
+      $filters = $this->view->filter;
+      foreach($filters as $filter_name => $details){
+         // we only want to inclue non-exposed filters 
+         if($details->options['exposed'] == FALSE){
+            // we only want to filter on the table we're getting the list from
+            if(strcmp($details->table,$this->table)==0){
+              $where .= "$details->field $details->operator ". $details->value['value'];
+              $where .= ' AND ';
+            }
+         }
+      } 
+      if($where){
+         $where = "WHERE $where";
+         $where = substr($where,0,-5); # remove the final ' AND '
       }
-      $sql = "SELECT $this->field FROM $this->table ORDER BY $this->field ASC";
+
+      // get the values from the table
+      $sql = "SELECT $this->real_field FROM $this->table $where ORDER BY $this->field ASC";
       $previous_db = tripal_db_set_active('chado');  // use chado database
       $results = db_query($sql);
       tripal_db_set_active($previous_db);  // now use drupal database
+
+      // Build the select box options
       $max_length = $this->options['max_length'];
       if (!$max_length) {
         $max_length = 40;
       }
+      if ($this->options['optional']) {
+        //$options['<select '.$this->table.'>'] = '--None--';
+        $options['All'] = '--Any--';
+      }
       while ($r = db_fetch_object($results)) {
         if (drupal_strlen($r->{$this->field}) > $max_length) {
           $options[$r->{$this->field}] = drupal_substr($r->{$this->field}, 0, $max_length) . '...';