Merge branch '6.x-1617096-unify_coding_style' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-1617096-unify_coding_style

tripal_bulk_loader/tripal_bulk_loader.admin.inc

@@ -64,7 +64,56 @@ function tripal_bulk_loader_configuration_form($form_state = NULL) {
     '#default_value' => variable_get('tripal_bulk_loader_prepare', TRUE),
   );
 
-  $form['submit1'] = array(
+  $form['speed']['disable_triggers'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Delay Constraint Checking during loading job.'),
+    '#description' => t('This delays the constraint checking until the end of the
+    loading proccess.'),
+    '#default_value' => variable_get('tripal_bulk_loader_disable_triggers', TRUE),
+  );
+
+  $form['speed']['no_validate'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Skip Validation at the Tripal Core API level'),
+    '#description' => t('If an error is encountered, the Tripal core API will try
+      to provide informative error messages. With this turned off, you will not benifit
+      from these more informative error messages; however, your job will load faster
+      since it doesn\'t have to do the additional checking before inserting.'),
+    '#default_value' => variable_get('tripal_bulk_loader_skip_validation', FALSE),
+  );
+
+  $form['speed']['transactions'] = array(
+    '#type' => 'radios',
+    '#title' => t('Transaction Rollback when an error is encountered'),
+    '#options' => array(
+      'all' => t('Rollback the last constant set.'
+        .'<div class="description"If you added more then one constant set then the
+        successfully loaded constant sets will not be rolled back. However, once an error
+        is encountered no further constant sets will be loaded either.</div>'),
+      'row' => t('Only Rollback the last line of the input file.'
+        .'<div class="description">This option may allow you to restart the job after
+        fixing the error (manual intervention needed).</div>'),
+      'none' => t('Do not use transactions<div class="description">This is not recommended.</div>')
+    ),
+    '#default_value' => variable_get('tripal_bulk_loader_transactions','row')
+  );
+
+  $form['speed']['lock'] = array(
+    '#type' => 'radios',
+    '#title' => t('Lock Type'),
+    '#description' => t('The type of lock used by the bulk loading jobs. The lock is '
+      .'acquired at the beginning of the job and kept till the end. A lock of the type '
+      .'selected will be acquired for every table being inserted into.'),
+    '#options' => array(
+      'ROW EXCLUSIVE' => t('ROW EXCLUSIVE: The default lock type for insert queries.'),
+      'EXCLUSIVE' => t('EXCLUSIVE: Only Select Queries can access the table.'),
+      'ACCESS EXCLUSIVE' => t('ACCESS EXCLUSIVE: No other queries can access the table.'),
+    ),
+    '#default_value' => variable_get('tripal_bulk_loader_lock', 'ROW EXCLUSIVE'),
+  );
+
+
+ $form['submit1'] = array(
     '#type' => 'submit',
     '#value' => t('Save')
   );
@@ -78,6 +127,11 @@ function tripal_bulk_loader_configuration_form($form_state = NULL) {
 function tripal_bulk_loader_configuration_form_submit($form, $form_state) {
 
   variable_set('tripal_bulk_loader_prepare', $form_state['values']['prepare']);
+  variable_set('tripal_bulk_loader_disable_triggers', $form_state['values']['disable_triggers']);
+  variable_set('tripal_bulk_loader_skip_validation', $form_state['values']['no_validate']);
+  variable_set('tripal_bulk_loader_transactions',$form_state['values']['transactions']);
+  variable_set('tripal_bulk_loader_lock', $form_state['values']['lock']);
+
 }
 
 //////////////////////////////////////////////////////////////////////////////////////

tripal_bulk_loader/tripal_bulk_loader.admin.inc.orig

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

tripal_bulk_loader/tripal_bulk_loader.loader.inc

@@ -135,13 +135,18 @@ function tripal_bulk_loader_load_data($nid) {
   $default_data = array();
   $field2column = array();
   $record2priority = array();
+  $tables = array();
 
   foreach ($node->template->template_array as $priority => $record_array) {
     if (!is_array($record_array)) {
       continue;
     }
 
-    //watchdog('T_bulk_loader','1)'.$record_array['record_id']." => \n<pre>".print_r($record_array,TRUE).'</pre>', array(), WATCHDOG_NOTICE);
+    // Add tables being inserted into to a list to be treated differently
+    // this is used to acquire locks on these tables
+    if (preg_match('/insert/',$record_array['mode'])) {
+      $tables[$record_array['table']] = $record_array['table'];
+    }
 
     foreach ($record_array['fields'] as $field_index => $field_array) {
 
@@ -235,7 +240,11 @@ function tripal_bulk_loader_load_data($nid) {
     //print "\nField to Column Mapping: ".print_r($field2column, TRUE)."\n";
 
     // Parse File adding records as we go ========================================================
+
+    // Open File
     $file_handle = fopen($node->file, 'r');
+
+    // Set defaults
     if (preg_match('/(t|true|1)/', $node->file_has_header)) {
       fgets($file_handle, 4096);
     }
@@ -244,8 +253,38 @@ function tripal_bulk_loader_load_data($nid) {
     $num_errors = 0;
     $interval = intval($total_lines * 0.10);
     if ($interval == 0) {
-       $interval = 1;
-     }
+      $interval = 1;
+    }
+
+    // Start Transaction
+    switch (variable_get('tripal_bulk_loader_transactions','row')) {
+      case "none":
+        break;
+      case "all":
+        tripal_db_start_transaction();
+        $transactions = TRUE;
+        $savepoint = "";
+        break;
+      case "row":
+        tripal_db_start_transaction();
+        $transactions = TRUE;
+        $savepoint = "last_row_complete";
+        break;
+    }
+
+    // Disable triggers
+    $triggers_disabled = FALSE;
+    if ($transactions AND variable_get('tripal_bulk_loader_disable_triggers', TRUE)) {
+      $triggers_disabled = TRUE;
+      chado_query("SET CONSTRAINTS ALL DEFERRED");
+    }
+
+    // Acquire Locks
+    $lockmode = variable_get('tripal_bulk_loader_lock', 'ROW EXCLUSIVE');
+    foreach ($tables as $table) {
+      chado_query("LOCK TABLE %s IN %s MODE", $table, $lockmode);
+    }
+
     while (!feof($file_handle)) {
 
       // Clear variables
@@ -276,14 +315,6 @@ function tripal_bulk_loader_load_data($nid) {
         // and had a group percentage of 50% then the job progress would be
         // (2*100 + 50%) / 3 = 250%/3 = 83%
         $job_progress = round(((($group_index-1)*100)+$group_progress)/$total_num_groups);
-
-        /**
-          print "\nProgress Update:\n"
-            ."\t- ".$num_lines." lines have been processed for the current constant set.\n"
-            ."\t- ".$group_progress."% of the lines in the file have been processed for the current constant set.\n"
-            ."\t- ".$job_progress."% of the current job has been completed.\n";
-        */
-
         tripal_job_set_progress($node->job_id, $job_progress);
       }
 
@@ -293,11 +324,45 @@ function tripal_bulk_loader_load_data($nid) {
       foreach ($data_keys as $priority) {
         $status = process_data_array_for_line($priority, $data, $default_data, $field2column, $record2priority, $line, $nid, $num_lines, $group_index);
         if (!$status ) {
-          $loaded_without_errors = FALSE;
+          // Encountered an error
+          if ($transactions) {
+            tripal_db_rollback_transaction($savepoint);
+          }
+          $failed = TRUE;
+          break;
         }
       } // end of foreach table in default data array
 
+      if ($failed) {
+        break;
+      }
+      else {
+        // Row inserted successfully
+        // Set savepoint if supplied
+        if ($savepoint) {
+          if ($num_lines == 1) {
+            tripal_db_set_savepoint_transaction($savepoint);
+          }
+          else {
+            // Tell it to remove the previous savepoint of the same name
+            tripal_db_set_savepoint_transaction($savepoint, TRUE);
+          }
+        }
+      }
+
     } //end of foreach line of file
+
+    // END Transaction
+    if ($transactions) {
+      // end the transaction
+      tripal_db_commit_transaction();
+    }
+
+    if ($failed) {
+      $loaded_without_errors = FALSE;
+      break;
+    }
+
   } //end of foreach constant set
 
   // check that data was inserted and update job_status
@@ -310,11 +375,11 @@ function tripal_bulk_loader_load_data($nid) {
 
   // set the status of the job (in the node not the tripal jobs)
   if ($loaded_without_errors) {
-      $status = 'Loading Completed Successfully';
-    }
-    else {
-      $status = 'Errors Encountered';
-      }
+    $status = 'Loading Completed Successfully';
+  }
+  else {
+    $status = 'Errors Encountered';
+  }
   db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", $status, $nid);
 
 }
@@ -419,9 +484,9 @@ function process_data_array_for_line($priority, &$data, &$default_data, $field2c
 
 
   if (!preg_match('/select/', $table_data['mode'])) {
-    //watchdog('T_bulk_loader',$header.': Inserting:'.print_r($values, TRUE), array(), WATCHDOG_NOTICE);
+    // Use prepared statement?
     if (variable_get('tripal_bulk_loader_prepare',TRUE)) {
-      $options = array('statement_name' => $priority);
+      $options = array('statement_name' => 'record_'.$priority);
       if ($line_num == 1 && $group_index == 1) {
         $options['prepare'] = TRUE;
       }
@@ -430,6 +495,11 @@ function process_data_array_for_line($priority, &$data, &$default_data, $field2c
       $options = array();
     }
 
+    // Skip tripal_core_chado_insert() built-in validation?
+    if (variable_get('tripal_bulk_loader_skip_validation', FALSE)) {
+      $options['skip_validation'] = TRUE;
+    }
+
     $record = tripal_core_chado_insert($table, $values, $options);
 
     if (!$record) {
@@ -482,6 +552,7 @@ function process_data_array_for_line($priority, &$data, &$default_data, $field2c
       $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') No Matching record in ' . $table . ' where values:' . print_r($values, TRUE);
       watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
       $data[$priority]['error'] = TRUE;
+      $no_errors = FALSE;
     }
   }
   return $no_errors;

tripal_bulk_loader/tripal_bulk_loader.loader.inc.orig

@@ -1,733 +0,0 @@
-<?php
-
-/**
- * @file
- * @todo Add file header description
- */
-
-/**
- * Add Loader Job Form
- *
- * This form is meant to be included on the node page to allow users to submit/re-submit
- * loading jobs
- */
-function tripal_bulk_loader_add_loader_job_form($form_state, $node) {
-  $form = array();
-
-  $form['nid'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->nid,
-  );
-
-  $form['file'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->file
-  );
-
-  $form['job_id'] = array(
-    '#type' => 'hidden',
-    '#value' => $node->job_id,
-  );
-
-  $form['submit'] = array(
-    '#type' => 'submit',
-    '#value' => ($node->job_id) ? 'Re-Submit Job' : 'Submit Job',
-  );
-
-  $form['submit-cancel'] = array(
-    '#type' => ($node->job_id)? 'submit' : 'hidden',
-    '#value' => 'Cancel Job',
-  );
-
-  $form['submit-revert'] = array(
-    '#type' => ($node->job_id) ? 'submit' : 'hidden',
-    '#value' => 'Revert',
-  );
-
-  return $form;
-}
-
-/**
- * Add Loader Job Form (Submit)
- */
-function tripal_bulk_loader_add_loader_job_form_submit($form, $form_state) {
-  global $user;
-
-  if (preg_match('/Submit Job/', $form_state['values']['op'])) {
-    //Submit Tripal Job
-<<<<<<< HEAD
-    $job_args[1] = $form_state['values']['nid'];
-    if (is_readable($form_state['values']['file'])) {
-      $fname = basename($form_state['values']['file']);
-      $job_id = tripal_add_job("Bulk Loading Job: $fname", 'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
-
-      // add job_id to bulk_loader node
-      $success = db_query("UPDATE {tripal_bulk_loader} SET job_id=%d WHERE nid=%d", $job_id, $form_state['values']['nid']);
-
-      // change status
-      db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Submitted to Queue', $form_state['values']['nid']);
-    }
-    else {
-      drupal_set_message(t("Can not open %file. Job not scheduled.", array('%file' => $form_state['values']['file'])));
-    }
-  }
-  elseif (preg_match('/Re-Submit Job/', $form_state['values']['op'])) {
-=======
-		$job_args[1] = $form_state['values']['nid'];
-		if (is_readable($form_state['values']['file'])) {
-			$fname = basename($form_state['values']['file']);
-			$job_id = tripal_add_job("Bulk Loading Job: $fname",'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
-
-			// add job_id to bulk_loader node
-      $success = db_query("UPDATE {tripal_bulk_loader} SET job_id=%d WHERE nid=%d", $job_id, $form_state['values']['nid']);
-
-      // change status
-      db_query("UPDATE tripal_bulk_loader SET job_status='%s' WHERE nid=%d",'Submitted to Queue', $form_state['values']['nid']);
-		} else {
-			drupal_set_message("Can not open ".$form_state['values']['file'].". Job not scheduled.");
-		}
-  } elseif (preg_match('/Re-Submit Job/', $form_state['values']['op'])) {
->>>>>>> 6.x-0.4-dev
-    tripal_jobs_rerun($form_state['values']['job_id']);
-    db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Submitted to Queue', $form_state['values']['nid']);
-  }
-  elseif (preg_match('/Cancel Job/', $form_state['values']['op'])) {
-    db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Job Cancelled', $form_state['values']['nid']);
-    tripal_jobs_cancel($form_state['values']['job_id']);
-<<<<<<< HEAD
-  }
-  elseif (preg_match('/Revert/', $form_state['values']['op'])) {
-=======
-  } elseif (preg_match('/Revert/', $form_state['values']['op'])) {
->>>>>>> 6.x-0.4-dev
-
-    // Remove the records from the database that were already inserted
-    $resource = db_query('SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d ORDER BY tripal_bulk_loader_inserted_id DESC', $form_state['values']['nid']);
-    while ($r = db_fetch_object($resource)) {
-      $ids = preg_split('/,/', $r->ids_inserted);
-      db_query('DELETE FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted);
-      $result = db_fetch_object(db_query('SELECT true as present FROM %s WHERE %s IN (%s)', $r->table_inserted_into, $r->table_primary_key, $r->ids_inserted));
-      if (!$result->present) {
-        drupal_set_message(t('Successfully Removed data Inserted into the %tableto table.', array('%tableto' => $r->table_inserted_into)));
-        db_query('DELETE FROM {tripal_bulk_loader_inserted} WHERE tripal_bulk_loader_inserted_id=%d', $r->tripal_bulk_loader_inserted_id);
-      }
-      else {
-        drupal_set_message(t('Unable to remove data Inserted into the %tableto table!', array('%tableto' => $r->table_inserted_into)), 'error');
-      }
-    }
-
-    // reset status
-    db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Reverted -Data Deleted', $form_state['values']['nid']);
-  }
-
-}
-
-/**
- * Tripal Bulk Loader
- *
- * This is the function that's run by tripal_launch_jobs to bulk load chado data.
- *
- * @param $nid
- *   The Node ID of the bulk loading job node to be loaded. All other needed data is expected to be
- *   in the node (ie: template ID and file)
- *
- * Note: Instead of returning a value this function updates the tripal_bulk_loader.status.
- *   Errors are thrown through watchdog and can be viewed at admin/reports/dblog.
- */
-function tripal_bulk_loader_load_data($nid) {
-
-  // ensure no timeout
-  set_time_limit(0);
-
-  // set the status of the job (in the node not the tripal jobs)
-  db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", 'Loading...', $nid);
-
-
-<<<<<<< HEAD
-=======
-
->>>>>>> 6.x-0.4-dev
-  $node = node_load($nid);
-  print "Template: " . $node->template->name . " (" . $node->template_id . ")\n";
-
-  $total_lines = trim(`wc --lines < $node->file`);
-<<<<<<< HEAD
-  print "File: " . $node->file . " (" . $total_lines . " lines)\n";
-=======
-  print "File: ".$node->file." (".$total_lines." lines)\n";
->>>>>>> 6.x-0.4-dev
-
-  // Prep Work ==================================================================================
-  $loaded_without_errors = TRUE;
-
-  // Generate default values array
-  $default_data = array();
-  $field2column = array();
-  $record2priority = array();
-
-  foreach ($node->template->template_array as $priority => $record_array) {
-    if (!is_array($record_array)) {
-      continue;
-    }
-
-    //watchdog('T_bulk_loader','1)'.$record_array['record_id']." => \n<pre>".print_r($record_array,TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-    foreach ($record_array['fields'] as $field_index => $field_array) {
-
-      $default_data[$priority]['table'] = $record_array['table'];
-      $default_data[$priority]['mode'] = ($record_array['mode']) ? $record_array['mode'] : 'insert_unique';
-      $default_data[$priority]['record_id'] = $record_array['record_id'];
-      $record2priority[$record_array['record_id']] = $priority;
-      $default_data[$priority]['required'][$field_array['field']] = $field_array['required'];
-
-      $one = $default_data[$priority];
-      if (isset($field_array['regex'])) {
-        $default_data[$priority]['regex_transform'][$field_array['field']] = $field_array['regex'];
-      }
-
-      $two = $default_data[$priority];
-
-      if (preg_match('/table field/', $field_array['type'])) {
-        $default_data[$priority]['values_array'][$field_array['field']] = '';
-        $default_data[$priority]['need_further_processing'] = TRUE;
-        $field2column[$priority][$field_array['field']] = $field_array['spreadsheet column'];
-
-<<<<<<< HEAD
-      }
-      elseif (preg_match('/constant/', $field_array['type'])) {
-        $default_data[$priority]['values_array'][$field_array['field']] = $field_array['constant value'];
-
-      }
-      elseif (preg_match('/foreign key/', $field_array['type'])) {
-=======
-      } elseif (preg_match('/constant/', $field_array['type'])) {
-        $default_data[$priority]['values_array'][$field_array['field']] = $field_array['constant value'];
-
-      } elseif (preg_match('/foreign key/', $field_array['type'])) {
->>>>>>> 6.x-0.4-dev
-        $default_data[$priority]['values_array'][$field_array['field']] = array();
-        $default_data[$priority]['values_array'][$field_array['field']]['foreign record'] = $field_array['foreign key'];
-        $default_data[$priority]['need_further_processing'] = TRUE;
-
-<<<<<<< HEAD
-      }
-      else {
-        print 'WARNING: Unsupported type: ' . $field_array['type'] . ' for ' . $table . '.' . $field_array['field'] . "!\n";
-=======
-      } else {
-        print 'WARNING: Unsupported type: '. $field_array['type'] . ' for ' . $table . '.' . $field_array['field']."!\n";
->>>>>>> 6.x-0.4-dev
-      }
-
-      $three = $default_data[$priority];
-      //watchdog('T_bulk_loader','A)'.$field_index.':<pre>Field Array =>'.print_r($field_array,TRUE)."Initial => \n".print_r($one, TRUE)."\nAfter Regex =>".print_r($two, TRUE)."Final =>\n".print_r($three,TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-    } // end of foreach field
-    //watchdog('T_bulk_loader','2)'.$record_array['record_id'].':<pre>'.print_r($default_data[$priority], TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-  } //end of foreach record
-
-  ///////////////////////////////////////////////
-  // For each set of constants
-  ///////////////////////////////////////////////
-  $original_default_data = $default_data;
-  $group_index = 0;
-  $total_num_groups = sizeof($node->constants);
-  foreach ($node->constants as $group_id => $set) {
-    // revert default data array for next set of constants
-    $default_data = $original_default_data;
-    $group_index++;
-
-    // Add constants
-    if (!empty($set)) {
-      print "Constants:\n";
-      foreach ($set as $priority => $record) {
-        foreach ($record as $field_id => $field) {
-
-<<<<<<< HEAD
-          print "\t- " . $field['chado_table'] . '.' . $field['chado_field'] . ' = ' . $field['value'] . "\n";
-=======
-          print "\t- ".$field['chado_table'].'.'.$field['chado_field'].' = '.$field['value']."\n";
->>>>>>> 6.x-0.4-dev
-
-          if ($default_data[$priority]['table'] == $field['chado_table']) {
-            if (isset($default_data[$priority]['values_array'][$field['chado_field']])) {
-              if (isset($field2column[$priority][$field['chado_field']])) {
-                $field2column[$priority][$field['chado_field']] = $field['value'];
-              }
-              else {
-                $default_data[$priority]['values_array'][$field['chado_field']] = $field['value'];
-              }
-            }
-            else {
-              print "ERROR: Template has changed after constants were assigned!\n";
-              watchdog('T_bulk_loader', 'Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
-              exit(1);
-            }
-          }
-          else {
-            print "ERROR: Template has changed after constants were assigned!\n";
-            watchdog('T_bulk_loader', 'Template has changed after constants were assigned', array(), WATCHDOG_NOTICE);
-            exit(1);
-          }
-        }
-      }
-    }
-
-    //print "Default Data:".print_r($default_data,TRUE)."\n";
-    //watchdog('T_bulk_loader','Default Data:<pre>'.print_r($default_data, TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-    //print "\nDefault Values Array: ".print_r($default_data, TRUE)."\n";
-    //print "\nField to Column Mapping: ".print_r($field2column, TRUE)."\n";
-
-    // Parse File adding records as we go ========================================================
-    $file_handle = fopen($node->file, 'r');
-    if (preg_match('/(t|true|1)/', $node->file_has_header)) {
-      fgets($file_handle, 4096);
-    }
-    $num_records = 0;
-    $num_lines = 0;
-    $num_errors = 0;
-    $interval = intval($total_lines * 0.10);
-    if ($interval == 0) {
-       $interval = 1;
-     }
-    while (!feof($file_handle)) {
-
-      // Clear variables
-      // Was added to fix memory leak
-      unset($line);                     unset($raw_line);
-      unset($data);                     unset($data_keys);
-      unset($priority);                 unset($sql);
-      unset($result);
-
-      $raw_line = fgets($file_handle, 4096);
-      $raw_line = trim($raw_line);
-      if (empty($raw_line)) {
-        continue;
-      } // skips blank lines
-      $line = explode("\t", $raw_line);
-      $num_lines++;
-
-      // update the job status every 10% of lines processed for the current group
-      if ($node->job_id and $num_lines % $interval == 0) {
-        // percentage of lines processed for the current group
-        $group_progress = round(($num_lines/$total_lines)*100);
-
-        // percentage of lines processed for all groups
-        // <previous group index> * 100 + <current group progress>
-        // --------------------------------------------------------
-        //               <total number of groups>
-        // For example, if you were in the third group of 3 constant sets
-        // and had a group percentage of 50% then the job progress would be
-        // (2*100 + 50%) / 3 = 250%/3 = 83%
-        $job_progress = round(((($group_index-1)*100)+$group_progress)/$total_num_groups);
-
-        /**
-          print "\nProgress Update:\n"
-            ."\t- ".$num_lines." lines have been processed for the current constant set.\n"
-            ."\t- ".$group_progress."% of the lines in the file have been processed for the current constant set.\n"
-            ."\t- ".$job_progress."% of the current job has been completed.\n";
-        */
-
-<<<<<<< HEAD
-        tripal_job_set_progress($node->job_id, $job_progress);
-=======
-        tripal_job_set_progress($node->job_id,$job_progress);
->>>>>>> 6.x-0.4-dev
-      }
-
-      $data = $default_data;
-
-      $data_keys = array_keys($data);
-      foreach ($data_keys as $priority) {
-        $status = process_data_array_for_line($priority, $data, $default_data, $field2column, $record2priority, $line, $nid, $num_lines, $group_index);
-        if (!$status ) {
-          $loaded_without_errors = FALSE;
-        }
-      } // end of foreach table in default data array
-
-    } //end of foreach line of file
-  } //end of foreach constant set
-
-  // check that data was inserted and update job_status
-  $sql = 'SELECT count(*) as num_tables FROM {tripal_bulk_loader_inserted} WHERE nid=%d GROUP BY nid';
-  $result = db_fetch_object(db_query($sql, $nid));
-  if ($result->num_tables > 0) {
-    $node->job_status = 'Data Inserted';
-    drupal_write_record('node', $node, 'nid');
-  }
-
-  // set the status of the job (in the node not the tripal jobs)
-  if ($loaded_without_errors) {
-      $status = 'Loading Completed Successfully';
-    }
-    else {
-      $status = 'Errors Encountered';
-      }
-  db_query("UPDATE {tripal_bulk_loader} SET job_status='%s' WHERE nid=%d", $status, $nid);
-
-}
-
-/**
- *
- *
- */
-function process_data_array_for_line($priority, &$data, &$default_data, $field2column, $record2priority, $line, $nid, $line_num, $group_index) {
-  $table_data = $data[$priority];
-
-  $no_errors = TRUE;
-
-  $table = $table_data['table'];
-  $values = $table_data['values_array'];
-
-  //watchdog('T_bulk_loader','Original:<pre>'.print_r($table_data, TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-  //print 'default values:'.print_r($values,TRUE)."\n";
-  if ($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);
-    }
-
-    $values = tripal_bulk_loader_add_foreignkey_to_values($values, $data, $record2priority);
-    if (!$values) {
-      watchdog('T_bulk_loader', 'Line ' . $line_num . ' FK Added:<pre>' . print_r($values, TRUE) . print_r($data[$priority], TRUE) . '</pre>', array(), WATCHDOG_NOTICE);
-    }
-  }
-  $values = tripal_bulk_loader_regex_tranform_values($values, $table_data, $line);
-  if (!$values) {
-    watchdog('T_bulk_loader', 'Line ' . $line_num . ' Regex:<pre>' . print_r($values, TRUE) . print_r($table_data, TRUE) . '</pre>' . '</pre>', array(), WATCHDOG_NOTICE);
-  }
-
-  if (!$values) {
-<<<<<<< HEAD
-    $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') Aborted due to error in previous record. Values of current record:' . print_r($table_data['values_array'], TRUE);
-    watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
-    print "ERROR: " . $msg . "\n";
-=======
-    $msg = 'Line '.$line_num.' '.$table_data['record_id'].' ('.$table_data['mode'].') Aborted due to error in previous record. Values of current record:'.print_r($table_data['values_array'],TRUE);
-    watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
-    print "ERROR: ".$msg."\n";
->>>>>>> 6.x-0.4-dev
-    $data[$priority]['error'] = TRUE;
-    $no_errors = FALSE;
-  }
-
-<<<<<<< HEAD
-  $table_desc = module_invoke_all('chado_' . $table . '_schema');
-=======
-  $table_desc = module_invoke_all('chado_'.$table.'_schema');
->>>>>>> 6.x-0.4-dev
-  if (preg_match('/optional/', $table_array['mode'])) {
-    // Check all db required fields are set
-    $fields = $table_desc['fields'];
-    foreach ($fields as $field => $def) {
-      // a field is considered missing if it cannot be null and there is no default
-      // value for it or it is of type 'serial'
-<<<<<<< HEAD
-      if ($def['not null'] == 1 and !array_key_exists($field, $insert_values) and !isset($def['default']) and strcmp($def['type'], serial)!=0) {
-         $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') Missing Database Required Value: ' . $table . '.' . $field;
-=======
-      if($def['not null'] == 1 and !array_key_exists($field,$insert_values) and !isset($def['default']) and strcmp($def['type'],serial)!=0){
-         $msg = 'Line '.$line_num.' '.$table_data['record_id'].' ('.$table_data['mode'].') Missing Database Required Value: '.$table.'.'.$field;
->>>>>>> 6.x-0.4-dev
-         watchdog('T_bulk_loader', $msg, array(), WATCHDOG_NOTICE);
-         $data[$priority]['error'] = TRUE;
-      }
-    }
-  } //end of if optional record
-
-  // Check required fields are present
-  foreach ($table_data['required'] as $field => $required) {
-    if ($required) {
-      if (!isset($values[$field])) {
-<<<<<<< HEAD
-        $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') Missing Template Required Value: ' . $table . '.' . $field;
-=======
-        $msg = 'Line '.$line_num.' '.$table_data['record_id'].' ('.$table_data['mode'].') Missing Template Required Value: '.$table.'.'.$field;
->>>>>>> 6.x-0.4-dev
-        watchdog('T_bulk_loader', $msg, array(), WATCHDOG_NOTICE);
-        $data[$priority]['error'] = TRUE;
-      }
-    }
-  }
-
-  // add new values array into the data array
-  $data[$priority]['values_array'] = $values;
-
-  // check if it is already inserted
-  if ($table_data['inserted']) {
-    //watchdog('T_bulk_loader','Already Inserted:'.print_r($values,TRUE),array(),WATCHDOG_NOTICE);
-    return $no_errors;
-  }
-
-  // if there was an error already -> don't insert
-  if ($data[$priority]['error']) {
-    return $no_errors;
-  }
-
-  $header = '';
-  if (isset($values['feature_id'])) {
-    $header = $values['feature_id']['uniquename'] . ' ' . $table_data['record_id'];
-  }
-  else {
-    $header = $values['uniquename'] . ' ' . $table_data['record_id'];
-  }
-
-  // if insert unique then check to ensure unique
-  if (preg_match('/insert_unique/', $table_data['mode'])) {
-    $unique = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, array('has_record' => TRUE));
-    //print 'Unique?'.print_r(array('table' => $table, 'columns' => array_keys($table_desc['fields']), 'values' => $values),TRUE).' returns '.$unique."\n";
-    if ($unique > 0) {
-      //$default_data[$priority]['inserted'] = TRUE;
-      //watchdog('T_bulk_loader', $header.': Not unique ('.$unique.'):'.print_r($values,'values')."\n".print_r($data,TRUE),array(),WATCHDOG_NOTICE);;
-      return $no_errors;
-    }
-  }
-
-
-<<<<<<< HEAD
-  if (!preg_match('/select/', $table_data['mode'])) {
-=======
-  if (!preg_match('/select/',$table_data['mode'])) {
->>>>>>> 6.x-0.4-dev
-    //watchdog('T_bulk_loader',$header.': Inserting:'.print_r($values, TRUE), array(), WATCHDOG_NOTICE);
-    if (variable_get('tripal_bulk_loader_prepare',TRUE)) {
-      $options = array('statement_name' => $priority);
-      if ($line_num == 1 && $group_index == 1) {
-        $options['prepare'] = TRUE;
-      }
-    }
-    else {
-      $options = array();
-    }
-
-    $record = tripal_core_chado_insert($table, $values, $options);
-
-    if (!$record) {
-<<<<<<< HEAD
-      $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') Unable to insert record into ' . $table . ' where values:' . print_r($values, TRUE);
-      watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
-      print "ERROR: " . $msg . "\n";
-=======
-      $msg = 'Line '.$line_num.' '.$table_data['record_id'].' ('.$table_data['mode'].') Unable to insert record into '.$table.' where values:'.print_r($values,TRUE);
-      watchdog('T_bulk_loader', $msg, array(), WATCHDOG_ERROR);
-      print "ERROR: ".$msg."\n";
->>>>>>> 6.x-0.4-dev
-      $data[$priority]['error'] = TRUE;
-      $no_errors = FALSE;
-    }
-    else {
-      //add changes back to values array
-      $data[$priority]['values_array'] = $record;
-      $values = $record;
-
-      // if mode=insert_once then ensure we only insert it once
-      if (preg_match('/insert_once/', $table_data['mode'])) {
-        $default_data[$priority]['inserted'] = TRUE;
-      }
-
-      // add to tripal_bulk_loader_inserted
-      $insert_record = db_fetch_object(db_query(
-        "SELECT * FROM {tripal_bulk_loader_inserted} WHERE table_inserted_into='%s' AND nid=%d",
-        $table,
-        $nid
-      ));
-      if ($insert_record) {
-        $insert_record->ids_inserted .= ',' . $values[ $table_desc['primary key'][0] ];
-        drupal_write_record('tripal_bulk_loader_inserted', $insert_record, 'tripal_bulk_loader_inserted_id');
-        //print 'Update: '.print_r($insert_record,TRUE)."\n";
-        return $no_errors;
-      }
-      else {
-        $insert_record = array(
-          'nid' => $nid,
-          'table_inserted_into' => $table,
-          'table_primary_key' => $table_desc['primary key'][0],
-          'ids_inserted' => $values[ $table_desc['primary key'][0] ],
-        );
-        //print 'New: '.print_r($insert_record,TRUE)."\n";
-        $success = drupal_write_record('tripal_bulk_loader_inserted', $insert_record);
-        return $no_errors;
-      }//end of if insert record
-
-    } //end of if insert was successful
-  }
-  else {
-    $exists = tripal_core_chado_select($table, array_keys($table_desc['fields']), $values, array('has_record' => TRUE));
-    if (!$exists) {
-      // No record on select
-<<<<<<< HEAD
-      $msg = 'Line ' . $line_num . ' ' . $table_data['record_id'] . ' (' . $table_data['mode'] . ') No Matching record in ' . $table . ' where values:' . print_r($values, TRUE);
-=======
-      $msg = 'Line '.$line_num.' '.$table_data['record_id'].' ('.$table_data['mode'].') No Matching record in '.$table.' where values:'.print_r($values,TRUE);
->>>>>>> 6.x-0.4-dev
-      watchdog('T_bulk_loader', $msg, array(), WATCHDOG_WARNING);
-      $data[$priority]['error'] = TRUE;
-    }
-  }
-  return $no_errors;
-}
-
-/**
- * This function adds the file data to the values array
- *
- * @param $values
- *   The default values array -contains all constants
- * @param $line
- *   An array of values for the current line
- * @param $field2column
- *   An array mapping values fields to line columns
- * @return
- *   Supplemented values array
- */
-function tripal_bulk_loader_add_spreadsheetdata_to_values($values, $line, $field2column) {
-
-  foreach ($values as $field => $value) {
-<<<<<<< HEAD
-    if (is_array($value)) {
-      continue;
-    }
-
-    $column = $field2column[$field] - 1;
-    if ($column < 0) {
-      continue;
-    }
-
-    if (preg_match('/\S+/', $line[$column])) {
-=======
-    if (is_array($value)) { continue; }
-
-    $column = $field2column[$field] - 1;
-    if ($column < 0) { continue; }
-
-    if (preg_match('/\S+/',$line[$column])) {
->>>>>>> 6.x-0.4-dev
-      $values[$field] = $line[$column];
-    }
-    else {
-      unset($values[$field]);
-    }
-  }
-
-  return $values;
-}
-
-/**
- * Handles foreign keys in the values array.
- *
- * Specifically, if the value for a field is an array then it is assumed that the array contains
- * the name of the record whose values array should be substituted here. Thus the foreign
- * record is looked up and the values array is substituted in.
- *
- */
-function tripal_bulk_loader_add_foreignkey_to_values($values, $data, $record2priority) {
-
-  foreach ($values as $field => $value) {
-    if (is_array($value)) {
-      $foreign_record = $value['foreign record'];
-      $foreign_priority = $record2priority[$foreign_record];
-      $foreign_values = $data[$foreign_priority]['values_array'];
-
-      // add to current values array
-      $values[$field] = $foreign_values;
-    }
-  }
-
-  return $values;
-}
-
-/**
- * Uses a supplied regex to transform spreadsheet values
- *
- * @param $values
- *   The select/insert values array for the given table
- * @param $table_data
- *   The data array for the given table
- */
-function tripal_bulk_loader_regex_tranform_values($values, $table_data, $line) {
-
-  if (empty($table_data['regex_transform']) OR !is_array($table_data['regex_transform'])) {
-    return $values;
-  }
-
-<<<<<<< HEAD
-  //watchdog('T_bulk_loader','Regex Transformation:<pre>'.print_r($table_data['regex_transform'], TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-  foreach ($table_data['regex_transform'] as $field => $regex_array) {
-    if (!is_array($regex_array['replace'])) {
-       continue;
-     }
-=======
-  if (empty($table_data['regex_transform']) OR !is_array($table_data['regex_transform'])) { return $values; }
-
-  //watchdog('T_bulk_loader','Regex Transformation:<pre>'.print_r($table_data['regex_transform'], TRUE).'</pre>', array(), WATCHDOG_NOTICE);
-
-  foreach ($table_data['regex_transform'] as $field => $regex_array) {
-    if (!is_array($regex_array['replace'])) { continue; }
->>>>>>> 6.x-0.4-dev
-
-    //print 'Match:'.print_r($regex_array['pattern'],TRUE)."\n";
-    //print 'Replace:'.print_r($regex_array['replace'],TRUE)."\n";
-    //print 'Was:'.$values[$field]."\n";
-
-    // Check for <#column:\d+#> notation
-    // if present replace with that column in the current line
-    foreach ($regex_array['replace'] as $key => $replace) {
-      if (preg_match_all('/<#column:(\d+)#>/', $replace, $matches)) {
-        foreach ($matches[1] as $k => $column_num) {
-          $replace = preg_replace('/' . $matches[0][$k] .'/', $line[$column_num-1], $replace);
-        }
-        $regex_array['replace'][$key] = $replace;
-      }
-    }
-
-    // do the full replacement
-    $old_value = $values[$field];
-    $new_value = preg_replace($regex_array['pattern'], $regex_array['replace'], $old_value);
-    $values[$field] = $new_value;
-
-    if ($values[$field] === '') {
-      unset($values[$field]);
-    }
-    //print 'Now:'.$values[$field]."\n";
-  }
-
-
-
-  return $values;
-}
-
-/**
- * Flattens an array up to two levels
- * Used for printing of arrays without taking up much space
- */
-function tripal_bulk_loader_flatten_array($values) {
-  $flattened_values = array();
-
-  foreach ($values as $k => $v) {
-    if (is_array($v)) {
-      $vstr = array();
-      foreach ($v as $vk => $vv) {
-        if (strlen($vv) > 20) {
-          $vstr[] = $vk . '=>' . substr($vv, 0, 20) . '...';
-        }
-        else {
-          $vstr[] = $vk . '=>' . $vv;
-        }
-      }
-      $v = '{' . implode(',', $vstr) . '}';
-    }
-    elseif (strlen($v) > 20) {
-      $v = substr($v, 0, 20) . '...';
-    }
-    $flattened_values[] = $k . '=>' . $v;
-  }
-
-<<<<<<< HEAD
-  return implode(', ', $flattened_values);
-}
-=======
-  return implode(', ',$flattened_values);
-}
->>>>>>> 6.x-0.4-dev

tripal_bulk_loader/tripal_bulk_loader.module

@@ -55,9 +55,19 @@ function tripal_bulk_loader_menu() {
       'type' => MENU_NORMAL_ITEM,
       'file' => 'tripal_bulk_loader.admin.inc',
   );
+   $items['admin/tripal/tripal_bulk_loader_template/configure'] = array(
+      'title' => 'Configure',
+      'description' => 'Configuration of global options related to bulk loading jobs',
+      'page callback' => 'drupal_get_form',
+      'page arguments' => array('tripal_bulk_loader_configuration_form'),
+      'access arguments' => array('administer site configuration'),
+      'type' => MENU_NORMAL_ITEM,
+      'file' => 'tripal_bulk_loader.admin.inc',
+  );
+
   // Create/Edit Template -------
   $items['admin/tripal/tripal_bulk_loader_template/create'] = array(
-      'title' => 'Create Bulk Loader Template',
+      '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'),
@@ -66,7 +76,7 @@ function tripal_bulk_loader_menu() {
     'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/edit'] = array(
-      'title' => 'Edit Bulk Loader Template',
+      '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'),
@@ -103,7 +113,7 @@ function tripal_bulk_loader_menu() {
   );
   // Delete Template -----
   $items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
-      'title' => 'Delete Bulk Loader Template',
+      'title' => 'Delete Template',
       'description' => 'Delete bulk loader template',
       'page callback' => 'drupal_get_form',
       'page arguments' => array('tripal_bulk_loader_delete_template_base_form'),
@@ -113,7 +123,7 @@ function tripal_bulk_loader_menu() {
   );
   // Import/Export ---------
   $items['admin/tripal/tripal_bulk_loader_template/import'] = array(
-      'title' => 'Import Bulk Loader Template',
+      'title' => 'Import Template',
       'description' => 'Import Loaders',
       'page callback' => 'drupal_get_form',
       'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'import'),
@@ -122,7 +132,7 @@ function tripal_bulk_loader_menu() {
       'file' => 'tripal_bulk_loader.admin.inc',
   );
   $items['admin/tripal/tripal_bulk_loader_template/export'] = array(
-      'title' => 'Export Bulk Loader Template',
+      'title' => 'Export Template',
       'description' => 'Export Loaders',
       'page callback' => 'drupal_get_form',
       'page arguments' => array('tripal_bulk_loader_import_export_template_form', 'export'),

tripal_bulk_loader/tripal_bulk_loader.module.orig

@@ -1,647 +0,0 @@
-<?php
-
-include('tripal_bulk_loader.loader.inc');
-include('tripal_bulk_loader.constants.inc');
-
-/**
- * Implements hook_init
- * Used to add stylesheets and javascript files to the header
- */
-function tripal_bulk_loader_init() {
-  // Add javascript and style sheet
-  drupal_add_css(drupal_get_path('theme', 'tripal') . '/css/tripal_bulk_loader.css');
-  drupal_add_js(drupal_get_path('theme', 'tripal') . '/js/tripal_bulk_loader.js');
-}
-
-/**
- * Implements hook_menu
- */
-function tripal_bulk_loader_menu() {
-  $items = array();
-   // Show all loaders
-   $items['tripal_bulk_loaders'] = array(
-     'title' => 'Tripal Bulk Loaders',
-     'description' => 'Tripal bulk loaders for loading tab-delimited file into chado database',
-     'page callback' => 'tripal_bulk_loader_list',
-     'access arguments' => array('access tripal_bulk_loader'),
-     'type' => MENU_NORMAL_ITEM,
-   );
-   // Bulk Loading Job Node
-   $items['node/%node/constants/%/edit'] = array(
-      'title' => 'Edit Constant Set',
-      'description' => 'Edit a group of constants associated with the current bulk loader',
-      'page callback' => 'drupal_get_form',
-      'page arguments' => array('tripal_bulk_loader_edit_constant_set_form', 1, 3),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_CALLBACK,
-<<<<<<< HEAD
-      'file' => 'tripal_bulk_loader.constants.inc',
-=======
-		  'file' => 'tripal_bulk_loader.constants.inc',
->>>>>>> 6.x-0.4-dev
-   );
-   $items['node/%node/constants/%/delete'] = array(
-      'title' => 'Delete Constant Set',
-      'description' => 'Delete a group of constants associated with the current bulk loader',
-      'page callback' => 'drupal_get_form',
-      'page arguments' => array('tripal_bulk_loader_delete_constant_set_form', 1, 3),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_CALLBACK,
-<<<<<<< HEAD
-      'file' => 'tripal_bulk_loader.constants.inc',
-=======
-		  'file' => 'tripal_bulk_loader.constants.inc',
->>>>>>> 6.x-0.4-dev
-   );
-
-   // Admin page to create the template
-   $items['admin/tripal/tripal_bulk_loader_template'] = array(
-      'title' => 'Bulk Loader Template',
-      'description' => 'Templates for loading tab-delimited data',
-      'page callback' => 'tripal_bulk_loader_admin_template',
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_NORMAL_ITEM,
-<<<<<<< HEAD
-      'file' => 'tripal_bulk_loader.admin.inc',
-  );
-  // Create/Edit Template -------
-=======
-		  'file' => 'tripal_bulk_loader.admin.inc',
-	);
-   $items['admin/tripal/tripal_bulk_loader_template/configure'] = array(
-      'title' => 'Configuration',
-      'description' => 'Configure the Tripal Bulk Loader Module',
-    	'page callback' => 'drupal_get_form',
-    	'page arguments' => array('tripal_bulk_loader_configuration_form'),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_NORMAL_ITEM,
-		  'file' => 'tripal_bulk_loader.admin.inc',
-	);
-
-	// Create/Edit Template -------
->>>>>>> 6.x-0.4-dev
-  $items['admin/tripal/tripal_bulk_loader_template/create'] = array(
-      'title' => 'Create Bulk Loader 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,
-<<<<<<< HEAD
-    'file' => 'tripal_bulk_loader.admin.inc',
-=======
-		'file' => 'tripal_bulk_loader.admin.inc',
->>>>>>> 6.x-0.4-dev
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/edit'] = array(
-      'title' => 'Edit Bulk Loader 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,
-<<<<<<< HEAD
-      'file' => 'tripal_bulk_loader.admin.inc',
-=======
-		  'file' => 'tripal_bulk_loader.admin.inc',
->>>>>>> 6.x-0.4-dev
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/edit_record'] = array(
-      'title' => 'Edit Template Record',
-      'description' => 'Edit a record in an existing tripal bulk loader template.',
-      'page callback' => 'drupal_get_form',
-      'page arguments' => array('tripal_bulk_loader_edit_template_record_form'),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_CALLBACK,
-<<<<<<< HEAD
-    'file' => 'tripal_bulk_loader.admin.inc',
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
-=======
-		'file' => 'tripal_bulk_loader.admin.inc',
-	);
-	$items['admin/tripal/tripal_bulk_loader_template/add_field'] = array(
->>>>>>> 6.x-0.4-dev
-      'title' => 'Add Template Field',
-      'description' => 'Add a template field to an existing tripal bulk loader template.',
-      'page callback' => 'drupal_get_form',
-      'page arguments' => array('tripal_bulk_loader_add_template_field_form'),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_CALLBACK,
-<<<<<<< HEAD
-    'file' => 'tripal_bulk_loader.admin.inc',
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
-=======
-		'file' => 'tripal_bulk_loader.admin.inc',
-	);
-	$items['admin/tripal/tripal_bulk_loader_template/edit_field'] = array(
->>>>>>> 6.x-0.4-dev
-      'title' => 'Edit Template Field',
-      'description' => 'Edit an existing field from a tripal bulk loader template.',
-      'page callback' => 'drupal_get_form',
-      'page arguments' => array('tripal_bulk_loader_edit_template_field_form'),
-      'access arguments' => array('administer site configuration'),
-      'type' => MENU_CALLBACK,
-<<<<<<< HEAD
-    'file' => 'tripal_bulk_loader.admin.inc',
-  );
-  // Delete Template -----
-  $items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
-=======
-		'file' => 'tripal_bulk_loader.admin.inc',
-	);
-	// Delete Template -----
-	$items['admin/tripal/tripal_bulk_loader_template/delete'] = array(
->>>>>>> 6.x-0.4-dev
-      'title' => 'Delete Bulk Loader 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,
-<<<<<<< HEAD
-    'file' => 'tripal_bulk_loader.admin.inc',
-  );
-  // Import/Export ---------
-=======
-		'file' => 'tripal_bulk_loader.admin.inc',
-	);
-	// Import/Export ---------
->>>>>>> 6.x-0.4-dev
-  $items['admin/tripal/tripal_bulk_loader_template/import'] = array(
-      'title' => 'Import Bulk Loader 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,
-<<<<<<< HEAD
-      'file' => 'tripal_bulk_loader.admin.inc',
-=======
-		  'file' => 'tripal_bulk_loader.admin.inc',
->>>>>>> 6.x-0.4-dev
-  );
-  $items['admin/tripal/tripal_bulk_loader_template/export'] = array(
-      'title' => 'Export Bulk Loader 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,
-<<<<<<< HEAD
-      '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',
-  );
-=======
-		  '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',
-	);
->>>>>>> 6.x-0.4-dev
-
-  return $items;
-}
-
-
-/**
- * Implements hook_theme
- */
-function tripal_bulk_loader_theme() {
-  return array(
-    'tripal_bulk_loader_set_constants_form' => array(
-      'arguments' => array('form' => NULL),
-    ),
-    'tripal_bulk_loader_template' => array(
-      'arguments' => array('template_id' => NULL),
-      'template' => 'tripal_bulk_loader_template'
-    ),
-    'tripal_bulk_loader_modify_template_base_form' => array(
-      'arguments' => array('form' => NULL),
-      'template' => 'tripal_bulk_loader_modify_template_base_form',
-    ),
-    'tripal_bulk_loader_edit_template_field_form' => array(
-      'arguments' => array('form' => NULL),
-      'template' => 'tripal_bulk_loader_edit_template_field_form',
-    ),
-    'tripal_bulk_loader_add_template_field_form' => array(
-      'arguments' => array('form' => NULL),
-      'template' => 'tripal_bulk_loader_add_template_field_form',
-    ),
-  );
-}
-
-/**
- *  Implements hook_access
- */
-function tripal_bulk_loader_access($op, $node, $account) {
-  if ($op == 'create') {
-    if (!user_access('create tripal_bulk_loader', $account)) {
-         return FALSE;
-      }
-  }
-  if ($op == 'update') {
-    if (!user_access('edit tripal_bulk_loader', $account)) {
-      return FALSE;
-    }
-  }
-  if ($op == 'delete') {
-    if (!user_access('delete tripal_bulk_loader', $account)) {
-      return FALSE;
-    }
-  }
-  if ($op == 'view') {
-    if (!user_access('access tripal_bulk_loader', $account)) {
-      return FALSE;
-    }
-  }
-  return NULL;
-}
-
-/**
- * Implements hook_perm
- */
-function tripal_bulk_loader_perm() {
-  return array(
-      'access tripal_bulk_loader',
-      'create tripal_bulk_loader',
-      'delete tripal_bulk_loader',
-      'edit tripal_bulk_loader',
-  );
-}
-
-/**
- * Creates a listing page for all bulk loading jobs
- */
-function tripal_bulk_loader_list() {
-  $num_results_per_page = 50;
-  $output = '';
-
-<<<<<<< HEAD
-  $header = array('', 'Status', 'Loader', 'File');
-=======
-  $header = array('','Status','Loader','File');
->>>>>>> 6.x-0.4-dev
-  $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
-//////////////////////////////////////////////////////////////////////////////////////////////
-
-/**
- * Implements hook_node_info
- */
-function tripal_bulk_loader_node_info() {
-  $nodes = array();
-  $nodes['tripal_bulk_loader'] = array(
-      'name' => t('Bulk Loading Job'),
-      'module' => 'tripal_bulk_loader',
-      'description' => t('A bulk loader for inserting tab-delimited data into chado database'),
-      'has_title' => TRUE,
-      'has_body' => FALSE,
-      'locked' => TRUE
-  );
-  return $nodes;
-}
-
-/**
- * Implements node_form
- * Used to gather the extra details stored with a Bulk Loading Job Node
- */
-function tripal_bulk_loader_form($node, $form_state) {
-  $form = array();
-
-  if (isset($form_state['values'])) {
-    $node = $form_state['values'] + (array)$node;
-    $node = (object) $node;
-  }
-
-  $sql = "SELECT * FROM {tripal_bulk_loader_template}";
-  $results = db_query($sql);
-  $templates = array();
-  while ($template = db_fetch_object ($results)) {
-    $templates [$template->template_id] = $template->name;
-  }
-
-  if (!$templates) {
-    $form['label'] = array(
-    '#type' => 'item',
-      '#description' => t("Loader template needs to be created before any bulk loader can be added. Go to 'Tripal Management > Bulk Loader Template' to create the template."),
-      '#weight'        => -10,
-    );
-
-    return $form;
-  }
-
-  $form['loader'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Basic Details'),
-  );
-
-  $form['loader']['loader_name'] = array(
-    '#type'          => 'textfield',
-    '#title'         => t('Loading Job Name'),
-    '#weight'        => -10,
-    '#required'      => TRUE,
-    '#default_value' => $node->loader_name
-  );
-
-  $form['loader']['template_id'] = array(
-    '#type' => 'select',
-    '#title' => t('Template'),
-    '#description'   => t('Please specify a template for this loader'),
-    '#options'       => $templates,
-    '#weight'        => -9,
-    '#required'      => TRUE,
-    '#default_value' => $node->template_id,
-  );
-
-  $form['loader']['file']= array(
-    '#type'          => 'textfield',
-    '#title'         => t('Data File'),
-    '#description'   => t('Please specify the data file to be loaded.'),
-    '#weight'        => -8,
-    '#default_value' => $node->file
-  );
-
-  $form['loader']['has_header'] = array(
-    '#type' => 'radios',
-    '#title' => t('File has a Header'),
-    '#options' => array( 1 => 'Yes', 2 => 'No'),
-    '#weight' => -7,
-    '#default_value' => $node->file_has_header,
-  );
-
-  return $form;
-}
-
-
-/**
- * Implements node_load
- */
-function tripal_bulk_loader_load($node) {
-  $sql = "SELECT * FROM {tripal_bulk_loader} WHERE nid = %d";
-  $node = db_fetch_object(db_query($sql, $node->nid));
-
-<<<<<<< HEAD
-  $node->title = 'Bulk Loading Job: ' . $node->loader_name;
-
-  // Add the loader template
-  $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
-  $results = db_fetch_object(db_query($sql, $node->template_id));
-  $template = unserialize($results->template_array);
-  $node->template = $results;
-  $node->template->template_array = $template;
-=======
-	$node->title = 'Bulk Loading Job: '.$node->loader_name;
-
-	// Add the loader template
-	$sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
-	$results = db_fetch_object(db_query($sql, $node->template_id));
-	$template = unserialize($results->template_array);
-	$node->template = $results;
-	$node->template->template_array = $template;
->>>>>>> 6.x-0.4-dev
-
-  // Add inserted records
-  $sql = 'SELECT * FROM {tripal_bulk_loader_inserted} WHERE nid=%d';
-  $resource = db_query($sql, $node->nid);
-  while ($r = db_fetch_object($resource)) {
-<<<<<<< HEAD
-    $r->num_inserted = sizeof(preg_split('/,/', $r->ids_inserted));
-=======
-    $r->num_inserted = sizeof(preg_split('/,/',$r->ids_inserted));
->>>>>>> 6.x-0.4-dev
-    $node->inserted_records->{$r->table_inserted_into} = $r;
-  }
-
-  // Add exposed field list
-  $node->exposed_fields = array();
-  if ($template) {
-    foreach ($template as $record_id => $record) {
-      foreach ($record['fields'] as $field_id => $field) {
-        if ($field['exposed']) {
-          $node->exposed_fields[] = array(
-            'record_id' => $record_id,
-            'field_id' => $field_id,
-            'title' => $field['title'],
-          );
-        }
-      }
-    }
-
-    if (empty($node->exposed_fields)) {
-      $node->exposed_fields[] = array();
-    }
-  }
-
-
-  // Add constants
-  $sql = 'SELECT * FROM {tripal_bulk_loader_constants} WHERE nid=%d ORDER BY group_id, record_id, field_id';
-  $resource = db_query($sql, $node->nid);
-  while ($r = db_fetch_object($resource)) {
-    $node->constants[$r->group_id][$r->record_id][$r->field_id] = array(
-      'constant_id' => $r->constant_id,
-      'group_id' => $r->group_id,
-<<<<<<< HEAD
-      'chado_table' => $r->chado_table,
-      'chado_field' => $r->chado_field,
-      'record_id' => $r->record_id,
-      'field_id' => $r->field_id,
-      'value' => $r->value
-=======
-      'chado_table'=>$r->chado_table,
-      'chado_field'=>$r->chado_field,
-      'record_id'=>$r->record_id,
-      'field_id'=>$r->field_id,
-      'value'=>$r->value
->>>>>>> 6.x-0.4-dev
-    );
-  }
-  if (!$node->constants) {
-    $node->constants[] = array();
-  }
-
-<<<<<<< HEAD
-  return $node;
-=======
-	return $node;
->>>>>>> 6.x-0.4-dev
-}
-
-/**
- * Implements node_insert
- * Insert the data from the node form on Create content
- */
-<<<<<<< HEAD
-function tripal_bulk_loader_insert($node) {
-=======
-function tripal_bulk_loader_insert ($node) {
->>>>>>> 6.x-0.4-dev
-
-  // Insert into tripal_bulk_loader
-  $sql = "INSERT INTO {tripal_bulk_loader} (nid, loader_name, template_id, file, file_has_header, job_status) VALUES (%d, '%s', %d, '%s', %d, '%s')";
-  db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, 'Initialized');
-
-<<<<<<< HEAD
-  // Update title
-  $node->title =$node->loader_name;
-  drupal_write_record('node', $node, 'nid');
-  drupal_write_record('node_revision', $node, 'nid');
-=======
-	// Update title
-	$node->title =$node->loader_name;
-	drupal_write_record('node',$node,'nid');
-	drupal_write_record('node_revision',$node,'nid');
->>>>>>> 6.x-0.4-dev
-
-  drupal_set_message('After reviewing the details, please Submit this Job (by clicking the "Submit Job" button below). No data will be loaded until the submitted job is reached in the queue.');
-
-}
-
-/**
- * Implements node_delete
- * Deletes the data when the delete button on the node form is clicked
- */
-function tripal_bulk_loader_delete($node) {
-  $sql = "DELETE FROM {tripal_bulk_loader} WHERE nid = %d";
-  db_query($sql, $node->nid);
-}
-
-/**
- * Implements node_update
- * Updates the data submitted by the node form on edit
- */
-<<<<<<< HEAD
-function tripal_bulk_loader_update($node) {
-
-  // Update tripal_bulk_loader
-  $sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s' WHERE nid = %d";
-  db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, $node->nid);
-
-  // Add a job if the user want to load the data
-  global $user;
-  if ($node->job) {
-    $job_args[0] =$node->loader_name;
-    $job_args[1] = $node->template_id;
-    $job_args[2] = $node->file;
-    if (is_readable($node->file)) {
-      $fname = preg_replace("/.*\/(.*)/", "$1", $node->file);
-      tripal_add_job("Bulk Load: $fname", 'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
-    }
-    else {
-      drupal_set_message(t("Can not open %file. Job not scheduled.", array('%file' => $node->file)));
-    }
-  }
-=======
-function tripal_bulk_loader_update ($node) {
-
-  // Update tripal_bulk_loader
-	$sql = "UPDATE {tripal_bulk_loader} SET nid = %d, loader_name = '%s', template_id = %d, file = '%s', file_has_header = '%s' WHERE nid = %d";
-	db_query($sql, $node->nid, $node->loader_name, $node->template_id, $node->file, $node->has_header, $node->nid);
-
-	// Add a job if the user want to load the data
-	global $user;
-	if($node->job) {
-		$job_args[0] =$node->loader_name;
-		$job_args[1] = $node->template_id;
-		$job_args[2] = $node->file;
-		if (is_readable($node->file)) {
-			$fname = preg_replace("/.*\/(.*)/", "$1", $node->file);
-			tripal_add_job("Bulk Load: $fname",'tripal_bulk_loader', 'tripal_bulk_loader_load_data', $job_args, $user->uid);
-		} else {
-			drupal_set_message("Can not open $node->file. Job not scheduled.");
-		}
-	}
->>>>>>> 6.x-0.4-dev
-
-}
-
-///////////////////////////////////////////////////////////
-
-/**
- * Preprocessor function for the tripal_bulk_loader template
- */
-function tripal_bulk_loader_preprocess_tripal_bulk_loader_template(&$variables) {
-
-  $sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
-  $template = db_fetch_object(db_query($sql, $variables['template_id']));
-  $template->template_array = unserialize($template->template_array);
-  $variables['template'] = $template;
-
-<<<<<<< HEAD
-=======
-	$sql = "SELECT * FROM {tripal_bulk_loader_template} WHERE template_id=%d";
-	$template = db_fetch_object(db_query($sql, $variables['template_id']));
-	$template->template_array = unserialize($template->template_array);
-	$variables['template'] = $template;
-
->>>>>>> 6.x-0.4-dev
-}
-
-/**
- * Implements hook_job_describe_args()
- * Specifically to make viewing past tripal jobs more readable for jobs registered by this module
- *
- * @params $callback
- *   The callback passed into tripal_add_job()
- * @param $args
- *   The arguements passed into tripal_add_job()
- * @return
- *   An array where keys are the human readable headers describing each arguement
- *   and the value is the aguement passed in after formatting
- */
-function tripal_bulk_loader_job_describe_args($callback, $args) {
-
-  $new_args = array();
-  if ($callback == 'tripal_bulk_loader_load_data') {
-    //1st arg is the nid for a bulk loader node
-    $node = node_load($args[0]);
-    $new_args['Bulk Loading Job'] = l($node->title, 'node/' . $args[0]);
-    return $new_args;
-  }
-
-}
-

tripal_core/tripal_core.api.inc

@@ -71,6 +71,16 @@ require_once "tripal_core.schema.api.inc";
  *  The name of the chado table for inserting
  * @param $values
  *  An associative array containing the values for inserting.
+ * @param $options
+ *  An array of options such as:
+ *    -prepare: TRUE or FALSE. Whether or not to prepare the current statement.
+ *       statement_name must also be supplied.
+ *    -statement_name: the name of the prepared statement to use. If prepare is TRUE,
+ *       this indicates the name of the prepared statement to created; otherwise,
+ *       it indicates the name of the already prepared statement to use.
+ *    -skip_validation: TRUE or FALSE. If TRUE will skip all the validation steps and
+ *       just try to insert as is. This is much faster but results in unhandled
+ *       non user-friendly errors if the insert fails.
  *
  * @return
  *  On success this function returns TRUE. On failure, it returns FALSE.
@@ -102,13 +112,14 @@ require_once "tripal_core.schema.api.inc";
  *
  * @ingroup tripal_chado_api
  */
-function tripal_core_chado_insert($table, $values) {
+function tripal_core_chado_insert($table, $values, $options) {
   $insert_values = array();
   $chado_db = tripal_db_persistent_chado();
 
   // Determine plan of action
   if ($options['statement_name']) {
     $prepared = TRUE;
+    $connection = tripal_db_persistent_chado();
     if ($options['prepare']) {
       $build_sql = TRUE;
     }
@@ -120,6 +131,13 @@ function tripal_core_chado_insert($table, $values) {
     $build_sql = TRUE;
   }
 
+  if (array_key_exists('skip_validation', $options)) {
+    $validate = !$options['skip_validation'];
+  }
+  else {
+    $validate = TRUE;
+  }
+
   // get the table description
   $table_desc = module_invoke_all('chado_' . $table . '_schema');
   if (empty($table_desc)) {
@@ -148,48 +166,50 @@ function tripal_core_chado_insert($table, $values) {
     }
   }
 
-  // check for violation of any unique constraints
-  $ukeys = $table_desc['unique keys'];
-  $ukselect_cols = array();
-  $ukselect_vals = array();
-  if ($ukeys) {
-    foreach ($ukeys as $name => $fields) {
-      foreach ($fields as $index => $field) {
-        // build the arrays for performing a select that will check the contraint
-        array_push($ukselect_cols, $field);
-        $ukselect_vals[$field] = $insert_values[$field];
+  if ($validate) {
+
+    // check for violation of any unique constraints
+    $ukeys = $table_desc['unique keys'];
+    $ukselect_cols = array();
+    $ukselect_vals = array();
+    if ($ukeys) {
+      foreach ($ukeys as $name => $fields) {
+        foreach ($fields as $index => $field) {
+          // build the arrays for performing a select that will check the contraint
+          array_push($ukselect_cols, $field);
+          $ukselect_vals[$field] = $insert_values[$field];
+        }
+        // now check the constraint
+        if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals)) {
+          watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
+          return FALSE;
+        }
       }
-      // now check the constraint
-      if (tripal_core_chado_select($table, $ukselect_cols, $ukselect_vals)) {
-        watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate record into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
+    }
+
+    // if trying to insert a field that is the primary key, make sure it also is unique
+    $pkey = $table_desc['primary key'][0];
+    if ($insert_values[$pkey]) {
+      if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]))) {
+        watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
         return FALSE;
       }
     }
-  }
 
-  // if trying to insert a field that is the primary key, make sure it also is unique
-  $pkey = $table_desc['primary key'][0];
-  if ($insert_values[$pkey]) {
-    if (tripal_core_chado_select($table, array($pkey), array($pkey => $insert_values[$pkey]))) {
-      watchdog('tripal_core', "tripal_core_chado_insert: Cannot insert duplicate primary key into $table table: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
-      return FALSE;
+    // make sure required fields have a value
+    if (!is_array($table_desc['fields'])) {
+      $table_desc['fields'] = array();
+      watchdog('tripal_core', "tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
     }
-  }
-
-  // make sure required fields have a value
-  $fields = $table_desc['fields'];
-  if (!is_array($fields)) {
-    $fields = array();
-    watchdog('tripal_core', "tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
-  }
-  foreach ($fields as $field => $def) {
-    // a field is considered missing if it cannot be NULL and there is no default
-    // value for it or it is of type 'serial'
-    if ($def['not NULL'] == 1 and !array_key_exists($field, $insert_values) and !isset($def['default']) and strcmp($def['type'], serial) != 0) {
-      watchdog('tripal_core', "tripal_core_chado_insert: Field $table.$field cannot be NULL: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
-      return FALSE;
+    foreach ($table_desc['fields'] as $field => $def) {
+      // a field is considered missing if it cannot be NULL and there is no default
+      // value for it or it is of type 'serial'
+      if ($def['not NULL'] == 1 and !array_key_exists($field, $insert_values) and !isset($def['default']) and strcmp($def['type'], serial) != 0) {
+        watchdog('tripal_core', "tripal_core_chado_insert: Field $table.$field cannot be NULL: " . print_r($values, 1), array(), 'WATCHDOG_ERROR');
+        return FALSE;
+      }
     }
-  }
+  } //end of validation
 
   // Now build the insert SQL statement
   $ifields = array(); //contains the names of the fields
@@ -207,8 +227,9 @@ function tripal_core_chado_insert($table, $values) {
       $itypes[] = "NULL";
       $idatatypes[] = "NULL";
     }
-    elseif(strcmp($fields[$field]['type'],'serial')==0 or
-      strcmp($fields[$field]['type'],'int')==0){
+    elseif(strcasecmp($table_desc['fields'][$field]['type'],'serial')==0 or
+      strcasecmp($table_desc['fields'][$field]['type'],'int')==0 or
+      strcasecmp($table_desc['fields'][$field]['type'],'integer')==0){
       $itypes[] = "%d";
       $idatatypes[] = 'int';
     }
@@ -222,10 +243,7 @@ function tripal_core_chado_insert($table, $values) {
     // prepare the statement
     if ($prepared) {
       $prepare_sql = "PREPARE " . $options['statement_name'] . " (" . implode(', ', $idatatypes) . ") AS INSERT INTO {$table} (" . implode(", ", $ifields) . ") VALUES (" . implode(", ", $iplaceholders) . ")";
-
-      $previous_db = tripal_db_set_active('chado');
-      $status = db_query($prepare_sql);
-      tripal_db_set_active($previous_db);
+      $status = chado_query($prepare_sql);
 
       if (!$status) {
         watchdog('tripal_core',"tripal_core_chado_insert: not able to prepare '%name' statement for: %sql", array('%name' => $options['statement_name'], '%sql' => $sql), 'WATCHDOG ERROR');
@@ -240,10 +258,8 @@ function tripal_core_chado_insert($table, $values) {
   if ($prepared) {
 
     $sql = "EXECUTE " . $options['statement_name'] . "(" . implode(", ", $itypes) . ")";
+    $result = chado_query($sql, $ivalues);
 
-    $previous_db = tripal_db_set_active('chado');
-    $result = db_query($sql, $ivalues);
-    tripal_db_set_active($previous_db);
     if ($result) {
       // add primary keys to values before return
       $primary_key = array();
@@ -1406,10 +1422,17 @@ function tripal_core_exclude_field_from_feature_by_default() {
 }
 
 /**
- *  Use this function instead of db_query() to avoid switching databases
- *  when making query to the chado database
+ * Use this function instead of db_query() to avoid switching databases
+ * when making query to the chado database
+ *
+ * Will use a chado persistent connection if it already exists
+ *
+ * @param $sql
+ *   The sql statement to execute
  */
 function chado_query($sql) {
+  global $active_db;
+
   $args = func_get_args();
   array_shift($args);
   $sql = db_prefix_tables($sql);
@@ -1418,9 +1441,22 @@ function chado_query($sql) {
   }
   _db_query_callback($args, TRUE);
   $sql = preg_replace_callback(DB_QUERY_REGEXP, '_db_query_callback', $sql);
-  $previous_db = tripal_db_set_active('chado');
-  $results = _db_query($sql);
-  tripal_db_set_active($previous_db);
+
+  // Execute the query on the chado database/schema
+  // Use the persistent chado connection if it already exists
+  $persistent_connection = variable_get('tripal_perisistent_chado',NULL);
+  if ($persistent_connection) {
+    $previously_active_db = $active_db;
+    $active_db = $persistent_connection;
+    $results = _db_query($sql);
+    $active_db = $previously_active_db;
+  }
+  else {
+    $previous_db = tripal_db_set_active('chado');
+    $results = _db_query($sql);
+    tripal_db_set_active($previous_db);
+  }
+
   return $results;
 }
 
@@ -1860,7 +1896,7 @@ function tripal_db_set_active($dbname) {
  * @return
  *   A postgresql connection object which can be used by pg_prepare, pg_execute, etc.
  */
-function tripal_db_persistent_chado () {
+function tripal_db_persistent_chado() {
   global $db_url;
 
   // get connection if it already exists
@@ -1887,10 +1923,55 @@ function tripal_db_persistent_chado () {
 /**
  * Release a persistent chado connection
  */
-function tripal_db_release_persistent_chado () {
+function tripal_db_release_persistent_chado() {
   variable_del('tripal_perisistent_chado');
 }
 
+/**
+ * Start a transaction block. Ensures the use of a persistent chado connection
+ */
+function tripal_db_start_transaction() {
+  $connection = tripal_db_persistent_chado();
+  chado_query("BEGIN");
+}
+
+/**
+ * Set a savepoint to roll the current transaction back to if an error is encountered
+ */
+function tripal_db_set_savepoint_transaction($savepoint, $release = FALSE) {
+  // Postgresql requires a savepoint of the same name to be unset before re-use
+  if ($release) {
+    chado_query("RELEASE SAVEPOINT %s",$savepoint);
+  }
+  chado_query("SAVEPOINT %s",$savepoint);
+}
+
+/**
+ * Commit changes made during the current transaction
+ */
+function tripal_db_commit_transaction() {
+  chado_query("COMMIT");
+}
+
+/**
+ * Rollback changes.
+ *
+ * If $savepoint is NULL then rollback to the beginning of the transaction,
+ * Otherwise, rollback to the point at which the named $savepoint was created
+ *
+ * @param $savepoint
+ *   The name of the saved point in the transaction to rollback to
+ */
+function tripal_db_rollback_transaction($savepoint = NULL) {
+
+  if ($savepoint) {
+    chado_query("ROLLBACK TO SAVEPOINT %s",$savepoint);
+  }
+  else {
+    chado_query("ROLLBACK");
+  }
+
+}
 
 /**
  * Purpose: Get max rank for a given set of criteria

tripal_feature/tripal_feature.views.inc.orig

@@ -1,473 +0,0 @@
-<?php
-
-/**
- *  @file
- *  This file contains the basic functions for views integration of
- *  chado/tripal organism tables. Supplementary functions can be found in
- *  ./views/
- *
- *  Documentation on views integration can be found at
- *  http://views2.logrus.com/doc/html/index.html.
- */
-
-/**
- * @defgroup tripal_feature_views Feature Views Integration
- * @ingroup views
- * @ingroup tripal_feature
- */
-
-/**
- * Implements hook_views_data()
- *
- * Purpose: Describe chado/tripal tables & fields to views
- *
- * @return: a data array which follows the structure outlined in the
- *   views2 documentation for this hook. Essentially, it's an array of table
- *   definitions keyed by chado/tripal table name. Each table definition
- *   includes basic details about the table, fields in that table and
- *   relationships between that table and others (joins)
- *
- * @ingroup tripal_feature_views
- */
-function tripal_feature_views_data()  {
-  $data = array();
-
-<<<<<<< HEAD
-  if (module_exists('tripal_views')) {
-    $tables = array(
-      'feature',
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,TRUE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-
-    $tables = array(
-      'feature_cvterm',
-      'feature_cvterm_dbxref',
-      'feature_cvterm_pub',
-      'feature_cvtermprop',
-      'feature_dbxref',
-      'feature_pub',
-      'feature_pubprop',
-      'feature_relationship',
-      'feature_relationship_pub',
-      'feature_relationshipprop',
-      'feature_relationshipprop_pub',
-      'feature_synonym',
-      'featureloc',
-      'featureloc_pub',
-      'featureprop',
-      'featureprop_pub',
-      'featuremap',
-      'featuremap_pub',
-      'featurepos',
-      'featurerange'
-    );
-    foreach ($tables as $tablename) {
-      if (!tripal_views_is_integrated($tablename, 10)) {
-        $table_integration_array = tripal_views_get_integration_array_for_chado_table($tablename,FALSE);
-        tripal_views_integration_add_entry($table_integration_array);
-      }
-    }
-  }
-=======
-  $data = array_merge($data, retrieve_feature_views_data());
-  $data = array_merge($data, retrieve_chado_feature_views_data());
-  $data = array_merge($data, retrieve_feature_misc_tables_views_data());
->>>>>>> 6.x-0.4-dev
-
-  return $data;
-}
-
-/**
- * Implements hook_views_handlers()
- *
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- *
- * @return: An array of handler definitions
- *
- * @ingroup tripal_feature_views
- */
-function tripal_feature_views_handlers() {
- return array(
-   'info' => array(
-     'path' => drupal_get_path('module', 'tripal_feature') . '/views_handlers',
-   ),
-   'handlers' => array(
-     'views_handler_field_residues' => array(
-       'parent' => 'views_handler_field',
-     ),
-   ),
- );
-}
-
-/**
- * Implementation of hook_views_data_alter().
- */
-function tripal_feature_views_data_alter(&$data) {
-
-  if ( !(is_array($db_url) and array_key_exists('chado', $db_url)) ) {
-
-    // Add featuer relationship to node
-    $data['node']['feature_chado_nid'] = array(
-      'group' => 'Feature',
-      'title' => 'Feature Node',
-      'help' => 'Links Chado Feature Fields/Data to the Nodes in the current View.',
-      'real field' => 'nid',
-      'relationship' => array(
-        'handler' => 'views_handler_relationship',
-        'title' => t('Node => Chado'),
-        'label' => t('Node => Chado'),
-        'real field' => 'nid',
-        'base' => 'chado_feature',
-        'base field' => 'nid'
-      ),
-    );
-  }
-
-}
-
-/**
- *
- * @ingroup tripal_feature_views
- */
-function tripal_feature_views_default_views() {
-  $views = array();
-
-  // Main default view
-  // List all cvterms based on cv
-  $view = new view;
-  $view->name = 'all_features';
-  $view->description = 'A listing of all Sequence FEatures';
-  $view->tag = 'chado';
-  $view->view_php = '';
-  $view->base_table = 'feature';
-  $view->is_cacheable = FALSE;
-  $view->api_version = 2;
-  $view->disabled = FALSE; /* Edit this to true to make a default view disabled initially */
-  $handler = $view->new_display('default', 'Defaults', 'default');
-  $handler->override_option('fields', array(
-    'uniquename' => array(
-      'label' => 'Unique Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'uniquename',
-      'table' => 'feature',
-      'field' => 'uniquename',
-      'relationship' => 'none',
-    ),
-    'name' => array(
-      'label' => 'Name',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'name',
-      'table' => 'feature',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'common_name' => array(
-      'label' => 'Organism',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'name_3' => array(
-      'label' => 'Type',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'name_3',
-      'table' => 'cvterm',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'accession_link' => array(
-      'label' => 'External Reference',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'exclude' => 0,
-      'id' => 'accession_link',
-      'table' => 'dbxref',
-      'field' => 'accession_link',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
-      'label' => 'Library',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'name_1',
-      'table' => 'library',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'name_2' => array(
-      'label' => 'Analysis',
-      'alter' => array(
-        'alter_text' => 0,
-        'text' => '',
-        'make_link' => 0,
-        'path' => '',
-        'link_class' => '',
-        'alt' => '',
-        'prefix' => '',
-        'suffix' => '',
-        'target' => '',
-        'help' => '',
-        'trim' => 0,
-        'max_length' => '',
-        'word_boundary' => 1,
-        'ellipsis' => 1,
-        'html' => 0,
-        'strip_tags' => 0,
-      ),
-      'empty' => '',
-      'hide_empty' => 0,
-      'empty_zero' => 0,
-      'link_to_node' => 1,
-      'exclude' => 0,
-      'id' => 'name_2',
-      'table' => 'analysis',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('filters', array(
-    'common_name' => array(
-      'operator' => '=',
-      'value' => '<select organism>',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'common_name_op',
-        'identifier' => 'organism',
-        'label' => 'Organism',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'case' => 1,
-      'id' => 'common_name',
-      'table' => 'organism',
-      'field' => 'common_name',
-      'relationship' => 'none',
-    ),
-    'name' => array(
-      'operator' => 'contains',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_op',
-        'identifier' => 'name',
-        'label' => 'Name Contains',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name',
-      'table' => 'feature',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'name_1' => array(
-      'operator' => 'contains',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_1_op',
-        'identifier' => 'library',
-        'label' => 'Library Name Contains',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name_1',
-      'table' => 'library',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-    'name_2' => array(
-      'operator' => 'contains',
-      'value' => '',
-      'group' => '0',
-      'exposed' => TRUE,
-      'expose' => array(
-        'use_operator' => 0,
-        'operator' => 'name_2_op',
-        'identifier' => 'analysis',
-        'label' => 'Analysis Name Contains',
-        'optional' => 1,
-        'remember' => 0,
-      ),
-      'case' => 0,
-      'id' => 'name_2',
-      'table' => 'analysis',
-      'field' => 'name',
-      'relationship' => 'none',
-    ),
-  ));
-  $handler->override_option('access', array(
-    'type' => 'perm',
-    'perm' => 'access chado_feature content',
-  ));
-  $handler->override_option('cache', array(
-    'type' => 'none',
-  ));
-  $handler->override_option('title', 'Sequence Features');
-  $handler->override_option('empty', 'There are no features matching that criteria. Please select a different organism above.');
-  $handler->override_option('empty_format', '1');
-  $handler->override_option('items_per_page', 50);
-  $handler->override_option('style_plugin', 'table');
-  $handler = $view->new_display('page', 'Page', 'page_1');
-  $handler->override_option('path', 'features');
-  $handler->override_option('menu', array(
-    'type' => 'normal',
-    'title' => 'Sequence Features',
-    'description' => '',
-    'weight' => '0',
-    'name' => 'primary-links',
-  ));
-  $handler->override_option('tab_options', array(
-    'type' => 'none',
-    'title' => '',
-    'description' => '',
-    'weight' => 0,
-    'name' => 'navigation',
-  ));
-  $views[$view->name] = $view;
-
-  return $views;
-}

tripal_genetic/tripal_genetic.views.inc

@@ -38,7 +38,7 @@ function tripal_genetic_views_data()  {
 
     $tables = array(
       'environment_cvterm',
-      'feautre_genotype',
+      'feature_genotype',
       'phendesc',
       'phenotype_comparison'
     );

tripal_views/tripal_views.api.inc

@@ -134,7 +134,7 @@ function tripal_views_integration_add_entry($defn_array) {
     'name' => $defn_array['name'],
     'comment' => $defn_array['description'],
     'priority' => $defn_array['priority'],
-    'base_table' => ($defn_array['base_table']) ? 1 : 0,
+    'base_table' => $defn_array['base_table'],
   );
   if ($defn_array['type'] == 'mview') {
       $mview = db_fetch_object(db_query("SELECT mview_id FROM {tripal_mviews} WHERE mv_table='%s'", $defn_array['table']));
@@ -153,6 +153,16 @@ function tripal_views_integration_add_entry($defn_array) {
 
   if ($status) {
 
+    // Need to update the tripal_views record so base_table can be false
+    // this is a fix because drupal_write_record() puts in defaults if !isset()
+    // and a variable is considered not set if its null!
+    db_query(
+      "UPDATE {tripal_views} SET base_table=%d WHERE table_name='%s' AND priority=%d",
+      $defn_array['base_table'],
+      $defn_array['table'],
+      $defn_array['priority']
+    );
+
     // Insert Field Definitions
     foreach ($defn_array['fields'] as $field) {
       $field_record = array(

tripal_views/tripal_views.views.inc

@@ -4,6 +4,10 @@ include('views/handlers/views_handler_join_chado_through_linking.inc');
 include('views/handlers/views_handler_join_chado_aggregator.inc');
 include('tripal_views.api.inc');
 
+
+// TEMPORARY
+include('views/chado_linking.TMP.inc');
+
 /**
  * @file
  * Tripal Views Integration
@@ -204,7 +208,6 @@ function tripal_views_views_pre_render(&$view) {
   // custom form element which adds the file_path variable to the $_GET after the
   // view has populated the $view->exposed_input variable
   unset($view->exposed_input);
-  $query = $view->get_exposed_input();  // retrieves elements in $_GET array
 
   // we want to add to the bottom of the views the form for downloading
   // results in other formats (e.g. Excel, FASTA, CSV, etc.).  The Views Data
@@ -580,6 +583,10 @@ function tripal_views_views_data() {
     }
   }
 
+  // TEMPORARY: needed to join chado base tables to node linking tables
+  // currently done using old-style data arrays
+  $data = tripal_views_TEMPORARY_chado_linking_data($data);
+
   return $data;
 }
 
@@ -729,6 +736,7 @@ function tripal_views_data_export_download_form(&$form_state, $view, $display_id
       }
 
       $path = $display->display_options['path'];
+      $query = $view->get_exposed_input();  // retrieves elements in $_GET array
       $urls[$display->id]['path'] = $path;
       $urls[$display->id]['query'] = $query;
 
@@ -767,7 +775,6 @@ function tripal_views_data_export_download_form(&$form_state, $view, $display_id
       '#type' => 'submit',
     );
   }
-
   return $form;
 }
 

tripal_views/tripal_views_integration.inc

@@ -90,7 +90,7 @@ function tripal_views_integration_setup_list() {
   $rows = array();
 
   // get the list of materialized views
-  $tviews = db_query('SELECT tv.name, tv.table_name, tc.table_id, tv.priority, tv.comment '
+  $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tc.table_id, tv.priority, tv.comment '
                      .'FROM {tripal_views} tv '
                      .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
                      .'WHERE tv.mview_id IS NOT NULL '
@@ -107,7 +107,12 @@ function tripal_views_integration_setup_list() {
     );
   }
 
-  $output .= theme('table', $header, $rows);
+  if ($rows) {
+    $output .= theme('table', $header, $rows);
+  }
+  else {
+    $output .= '<p>There are currently no Materialized Views defined.</p>';
+  }
 
   // Now list non-mview custom tables
   $output .= '<br /><h3>Custom Tables</h3>';
@@ -115,7 +120,7 @@ function tripal_views_integration_setup_list() {
   $rows = array();
 
   // get the list of chado tables
-  $tviews = db_query('SELECT tv.name, tv.table_name, tv.priority, tv.comment '
+  $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
                      .'FROM {tripal_views} tv '
                      .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
                      .'WHERE mview_id IS NULL AND tc.table_id IS NOT NULL '
@@ -144,7 +149,7 @@ function tripal_views_integration_setup_list() {
   $rows = array();
 
   // get the list of chado tables
-  $tviews = db_query('SELECT tv.name, tv.table_name, tv.priority, tv.comment '
+  $tviews = db_query('SELECT tv.setup_id, tv.name, tv.table_name, tv.priority, tv.comment '
                      .'FROM {tripal_views} tv '
                      .'LEFT JOIN {tripal_custom_tables} tc ON tc.table_name=tv.table_name '
                      .'WHERE mview_id IS NULL AND tc.table_id IS NULL '

tripal_views/views/chado_linking.TMP.inc

@@ -0,0 +1,408 @@
+<?php
+
+/**
+ * This is a temporary function holding all the old-style views integration
+ * needed to link the base tables to their node. This will remain to keep things working
+ * until it has been best determined how to do this via the new tripal_views integration
+ *
+ * It's called att the bottom of tripal_views_views_data()
+ */
+function tripal_views_TEMPORARY_chado_linking_data($data) {
+  global $db_url;
+
+  // if the chado database is not local to the drupal database
+  // then we need to set the database name.  This should always
+  // be 'chado'.
+  if(is_array($db_url) and array_key_exists('chado',$db_url)){
+     // return empty data array b/c if chado is external then no join to the nodetable can be made
+     return $data;
+  }
+
+  // FEATURE ====================================
+  if (module_exists('tripal_feature')) {
+    // Basic table definition
+    $data['chado_feature']['table'] = array(
+      'field' => 'nid',
+      'group' => 'Chado Feature'
+    );
+
+    $data['chado_feature']['nid'] = array(
+      'title' => t('Feature Node ID'),
+      'help' => t('The node ID for this feature'),
+      'field' => array(
+        'handler' => 'views_handler_field_numeric',
+        'click sortable' => TRUE,
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_numeric',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+
+    // Note: No joins need to be made from $data['feature']['table']
+
+    // Join the chado feature table to feature
+    $data['chado_feature']['table']['join']['feature'] = array(
+      'left_field' => 'feature_id',
+      'field' => 'feature_id',
+    );
+
+    // Join the node table to chado feature
+    $data['node']['table']['join']['chado_feature'] = array(
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Join the node table to feature
+    $data['node']['table']['join']['feature'] = array(
+      'left_table' => 'chado_feature',
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Add relationship between chado_feature and feature
+    $data['chado_feature']['feature_nid'] = array(
+      'group' => 'Feature',
+      'title' => 'Feature Node',
+      'help' => 'Links Chado Feature Fields/Data to the Nodes in the current View.',
+      'real field' => 'feature_id',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Feature'),
+        'label' => t('Chado => Feature'),
+        'real field' => 'feature_id',
+        'base' => 'feature',
+        'base field' => 'feature_id'
+      ),
+    );
+
+    // Add node relationship to feature
+    $data['chado_feature']['feature_chado_nid'] = array(
+      'group' => 'Feature',
+      'title' => 'Feature Node',
+      'help' => 'Links Chado Feature Fields/Data to the Nodes in the current View.',
+      'real field' => 'nid',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Node'),
+        'label' => t('Chado => Node'),
+        'real field' => 'nid',
+        'base' => 'node',
+        'base field' => 'nid'
+      ),
+    );
+  }
+
+  // ANALYSIS ===================================
+  if (module_exists('tripal_analysis')) {
+    // Basic table definition
+    $data['chado_analysis']['table'] = array(
+      'field' => 'nid',
+      'group' => 'Chado Analysis'
+    );
+
+    $data['chado_analysis']['nid'] = array(
+      'title' => t('Analysis Node ID'),
+      'help' => t('The node ID for this analysis'),
+      'field' => array(
+        'handler' => 'views_handler_field_numeric',
+        'click sortable' => TRUE,
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_numeric',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+
+    // Note: No joins need to be made from $data['analysis']['table']
+
+    // Join the chado analysis table to analysis
+    $data['chado_analysis']['table']['join']['analysis'] = array(
+      'left_field' => 'analysis_id',
+      'field' => 'analysis_id',
+    );
+
+    // Join the node table to chado analysis
+    $data['node']['table']['join']['chado_analysis'] = array(
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Join the node table to analysis
+    $data['node']['table']['join']['analysis'] = array(
+      'left_table' => 'chado_analysis',
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Add relationship between chado_analysis and analysis
+    $data['chado_analysis']['analysis_nid'] = array(
+      'group' => 'Analysis',
+      'title' => 'Analysis Node',
+      'help' => 'Links Chado Analysis Fields/Data to the Nodes in the current View.',
+      'real field' => 'analysis_id',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Analysis'),
+        'label' => t('Chado => Analysis'),
+        'real field' => 'analysis_id',
+        'base' => 'analysis',
+        'base field' => 'analysis_id'
+      ),
+    );
+
+    // Add node relationship to analysis
+    $data['chado_analysis']['analysis_chado_nid'] = array(
+      'group' => 'Analysis',
+      'title' => 'Analysis Node',
+      'help' => 'Links Chado Analysis Fields/Data to the Nodes in the current View.',
+      'real field' => 'nid',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Node'),
+        'label' => t('Chado => Node'),
+        'real field' => 'nid',
+        'base' => 'node',
+        'base field' => 'nid'
+      ),
+    );
+  }
+
+  // ORGANISM ===================================
+  if (module_exists('tripal_organism')) {
+    // Basic table definition
+    $data['chado_organism']['table'] = array(
+      'field' => 'nid',
+      'group' => 'Chado Organism'
+    );
+
+    $data['chado_organism']['nid'] = array(
+      'title' => t('Organism Node ID'),
+      'help' => t('The node ID for this organism'),
+      'field' => array(
+        'handler' => 'views_handler_field_numeric',
+        'click sortable' => TRUE,
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_numeric',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+
+    // Note: No joins need to be made from $data['organism']['table']
+
+    // Join the chado organism table to organism
+    $data['chado_organism']['table']['join']['organism'] = array(
+      'left_field' => 'organism_id',
+      'field' => 'organism_id',
+    );
+
+    // Join the node table to chado organism
+    $data['node']['table']['join']['chado_organism'] = array(
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Join the node table to organism
+    $data['node']['table']['join']['organism'] = array(
+      'left_table' => 'chado_organism',
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Add relationship between chado_organism and organism
+    $data['chado_organism']['organism_id'] = array(
+      'group' => 'Organism',
+      'title' => 'Organism Node',
+      'help' => 'Links Chado Organism Fields/Data to the Nodes in the current View.',
+      'real field' => 'organism_id',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Organism'),
+        'label' => t('Chado => Organism'),
+        'real field' => 'organism_id',
+        'base' => 'organism',
+        'base field' => 'organism_id'
+      ),
+    );
+  /*
+    // Add node relationship to organism
+    $data['chado_organism']['nid'] = array(
+      'group' => 'Organism',
+      'title' => 'Organism Node',
+      'help' => 'Links Chado Organism Fields/Data to the Nodes in the current View.',
+      'real field' => 'nid',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Node'),
+        'label' => t('Chado => Node'),
+        'real field' => 'nid',
+        'base' => 'node',
+        'base field' => 'nid'
+      ),
+    );
+  */
+  }
+
+  // LIBRARY ====================================
+  if (module_exists('tripal_library')) {
+    // Basic table definition
+    $data['chado_library']['table'] = array(
+      'field' => 'nid',
+      'group' => 'Chado Library'
+    );
+
+    $data['chado_library']['nid'] = array(
+      'title' => t('Library Node ID'),
+      'help' => t('The node ID for this library'),
+      'field' => array(
+        'handler' => 'views_handler_field_numeric',
+        'click sortable' => TRUE,
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_numeric',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+
+    // Note: No joins need to be made from $data['library']['table']
+
+    // Join the chado library table to library
+    $data['chado_library']['table']['join']['library'] = array(
+      'left_field' => 'library_id',
+      'field' => 'library_id',
+    );
+
+    // Join the node table to chado library
+    $data['node']['table']['join']['chado_library'] = array(
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Join the node table to library
+    $data['node']['table']['join']['library'] = array(
+      'left_table' => 'chado_library',
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Add relationship between chado_library and library
+    $data['chado_library']['library_nid'] = array(
+      'group' => 'Library',
+      'title' => 'Library Node',
+      'help' => 'Links Chado Library Fields/Data to the Nodes in the current View.',
+      'real field' => 'library_id',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Library'),
+        'label' => t('Chado => Library'),
+        'real field' => 'library_id',
+        'base' => 'library',
+        'base field' => 'library_id'
+      ),
+    );
+
+    // Add node relationship to library
+    $data['chado_library']['library_chado_nid'] = array(
+      'group' => 'Library',
+      'title' => 'Library Node',
+      'help' => 'Links Chado Library Fields/Data to the Nodes in the current View.',
+      'real field' => 'nid',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Node'),
+        'label' => t('Chado => Node'),
+        'real field' => 'nid',
+        'base' => 'node',
+        'base field' => 'nid'
+      ),
+    );
+  }
+
+  // STOCK ======================================
+  if (module_exists('tripal_stock')) {
+    // Basic table definition
+    $data['chado_stock']['table'] = array(
+      'field' => 'stock_id',
+      'group' => 'Chado Stock',
+    );
+
+    $data['chado_stock']['nid'] = array(
+      'title' => t('Stock Node ID'),
+      'help' => t('The node ID for this analysis'),
+      'field' => array(
+        'handler' => 'views_handler_field_numeric',
+        'click sortable' => TRUE,
+      ),
+      'filter' => array(
+        'handler' => 'views_handler_filter_numeric',
+      ),
+      'sort' => array(
+        'handler' => 'views_handler_sort',
+      ),
+    );
+
+    // Note: No joins need to be made from $data['stock']['table']
+
+    // Join the chado stock table to stock
+    $data['chado_stock']['table']['join']['stock'] = array(
+      'left_field' => 'stock_id',
+      'field' => 'stock_id',
+    );
+
+    // Join the node table to chado stock
+    $data['node']['table']['join']['chado_stock'] = array(
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Join the node table to stock
+    $data['node']['table']['join']['stock'] = array(
+      'left_table' => 'chado_stock',
+      'left_field' => 'nid',
+      'field' => 'nid',
+    );
+
+    // Add relationship between chado_stock and stock
+    $data['chado_stock']['stock_nid'] = array(
+      'group' => 'Stock',
+      'title' => 'Stock Node',
+      'help' => 'Links Chado Stock Fields/Data to the Nodes in the current View.',
+      'real field' => 'stock_id',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Stock'),
+        'label' => t('Chado => Stock'),
+        'real field' => 'stock_id',
+        'base' => 'stock',
+        'base field' => 'stock_id'
+      ),
+    );
+
+    // Add node relationship to stock
+    $data['chado_stock']['stock_chado_nid'] = array(
+      'group' => 'Stock',
+      'title' => 'Stock Node',
+      'help' => 'Links Chado Stock Fields/Data to the Nodes in the current View.',
+      'real field' => 'nid',
+      'relationship' => array(
+        'handler' => 'views_handler_relationship',
+        'title' => t('Chado => Node'),
+        'label' => t('Chado => Node'),
+        'real field' => 'nid',
+        'base' => 'node',
+        'base field' => 'nid'
+      ),
+    );
+  }
+
+  return $data;
+}