fixed ^M endings in tripal_bulk_loader.admin.inc

tripal_bulk_loader/tripal_bulk_loader.admin.inc

@@ -1,268 +1,268 @@
-<?php
-
-/**
- * @file
- * Bulk Loader Administration (Miscellaneous)
- */
-
-/**
- * Provides a description page and quick links for the bulk loader
- */
-function tripal_bulk_loader_admin_template() {
-  $output = '';
-
-  $output .= '<br /><h3>Quick Links:</h3>';
-  $output .= '<ul>'
-    . '<li>'
-      . t('<a href="@link">Configure settings</a>',
-        array('@link' => url('admin/tripal/tripal_bulk_loader_template/configure')))
-      . '</li>'
-    . '<li>'
-      . t('List <a href="@link">Bulk Loader Jobs</a>',
-      array('@link' => url('admin/tripal/tripal_bulk_loader_template/jobs')))
-      . '</li>'
-    . '<li>'
-      . t('List <a href="@link">Manage Templates</a>',
-      array('@link' => url('admin/tripal/tripal_bulk_loader_template/manage_templates')))
-      . '</li>'
-      . '<ul>'
-      . '<li>'
-        . t('<a href="@create">Create</a> a new template',
-        array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@edit">Edit</a> an existing template',
-        array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@delete">Delete</a> an existing template',
-        array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@import">Import</a> a new template',
-        array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
-        . '</li>'
-      . '<li>'
-        . t('<a href="@export">Export</a> an existing template',
-        array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
-        . '</li>'
-      . '</ul>'
-    . '</ul>';
-
-  $output .= '<h3>Module Description:</h3>';
-  $output .= '<p>This module provides the ability to create loading templates for any tab-delimited '
-    . '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(t('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;
-}
-
-/**
- * Provides a description page and quick links for template management
- */
-function tripal_bulk_loader_admin_manage_templates() {
-  $output = '';
-
-  $output .= '<br /><h3>Quick Links:</h3>';
-  $output .= '<ul>'
-    . '<li>'
-      . t('<a href="@create">Create</a> a new template',
-      array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
-      . '</li>'
-    . '<li>'
-      . t('<a href="@edit">Edit</a> an existing template',
-      array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
-      . '</li>'
-    . '<li>'
-      . t('<a href="@delete">Delete</a> an existing template',
-      array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
-      . '</li>'
-    . '<li>'
-      . t('<a href="@import">Import</a> a new template',
-      array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
-      . '</li>'
-    . '<li>'
-      . t('<a href="@export">Export</a> an existing template',
-      array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
-      . '</li>'
-    . '</ul>';
-
-  $output .= '<p>' . t('Templates, as the term is used for this module, refer to plans
-  describing how the columns in the data file supplied to a bulk loading job map to tables
-  and fields in chado. Templates are created independently of bulk loading jobs so that
-  they can be re-used. Thus you only need one template to load any number of files of the
-  same format.') . '</p>';
-
-
-
-  return $output;
-}
-
-/**
- * Provides a listing of bulk loader jobs and links for administration
- */
-function tripal_bulk_loader_admin_jobs() {
-  $output = '';
-  $num_jobs_per_page = 50;
-
-  $output .= '<p>' . t('Jobs are not automatically submitted to the tripal jobs management
-  system when they are first created. Any jobs listed below with a status of "Initialized"
-  will not have a Job ID until you go to the bulk loader page and submit the job.') . '</p>';
-
-  $header = array(
-    array('data' => 'Job ID', 'field' => 'job_id', 'sort' => 'DESC'),
-    array('data' => 'Name', 'field' => 'loader_name'),
-    array('data' =>  'Template', 'field' => 'template_name'),
-    array('data' =>  'Status', 'field' => 'job_status'),
-    array('data' => 'Progress', 'field' => 'progress'),
-    '');
-  $rows = array();
-  $resource = pager_query("SELECT n.*, t.name as template_name, j.progress
-    FROM {tripal_bulk_loader} n
-    LEFT JOIN {tripal_bulk_loader_template} t ON cast(n.template_id as integer) = t.template_id
-    LEFT JOIN {tripal_jobs} j ON n.job_id = j.job_id"
-    . tablesort_sql($header),
-    $num_jobs_per_page);
-  while ($n = db_fetch_object($resource)) {
-    $rows[] = array(
-      l($n->job_id, 'admin/tripal/tripal_jobs/view/' . $n->job_id),
-      l($n->loader_name, 'node/' . $n->nid),
-      l($n->template_name, 'admin/tripal/tripal_bulk_loader_template/manage_templates/edit', array('query' => 'template_id=' . $n->template_id)),
-      $n->job_status,
-      ($n->progress) ? $n->progress . '%' : '',
-      l('View', 'node/' . $n->nid) . ' | ' .  l('Edit', 'node/' . $n->nid . '/edit')
-    );
-  }
-  $output .= theme_table($header, $rows);
-
-  $output .= theme('pager');
-
-  return $output;
-}
-
-/**
- * @section
- * Configuration Form
- */
-
-/**
- * A Configuration form for this module
- */
-function tripal_bulk_loader_configuration_form($form_state = NULL) {
-  $form = array();
-
-  $form['space'] = array(
-    '#type' => 'fieldset',
-    '#title' => t('Enable/Disable Functionality'),
-  );
-
-  $form['space']['keep_track_inserted'] = array(
-    '#type' => 'checkbox',
-    '#title' => t('Keep track of inserted record IDs'),
-    '#description' => t('This enables the ability to revert an entire loading job even if '
-      .'it completed successfully. Furthermore, it displays the number of records '
-      .'successfully inserted into each table.'),
-    '#default_value' => variable_get('tripal_bulk_loader_keep_track_inserted', FALSE),
-  );
-
-  $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['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')
-  );
-
-  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']);
-  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']);
-
-  variable_set('tripal_bulk_loader_keep_track_inserted', $form_state['values']['keep_track_inserted']);
-
-}
+<?php
+
+/**
+ * @file
+ * Bulk Loader Administration (Miscellaneous)
+ */
+
+/**
+ * Provides a description page and quick links for the bulk loader
+ */
+function tripal_bulk_loader_admin_template() {
+  $output = '';
+
+  $output .= '<br /><h3>Quick Links:</h3>';
+  $output .= '<ul>'
+    . '<li>'
+      . t('<a href="@link">Configure settings</a>',
+        array('@link' => url('admin/tripal/tripal_bulk_loader_template/configure')))
+      . '</li>'
+    . '<li>'
+      . t('List <a href="@link">Bulk Loader Jobs</a>',
+      array('@link' => url('admin/tripal/tripal_bulk_loader_template/jobs')))
+      . '</li>'
+    . '<li>'
+      . t('List <a href="@link">Manage Templates</a>',
+      array('@link' => url('admin/tripal/tripal_bulk_loader_template/manage_templates')))
+      . '</li>'
+      . '<ul>'
+      . '<li>'
+        . t('<a href="@create">Create</a> a new template',
+        array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@edit">Edit</a> an existing template',
+        array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@delete">Delete</a> an existing template',
+        array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@import">Import</a> a new template',
+        array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
+        . '</li>'
+      . '<li>'
+        . t('<a href="@export">Export</a> an existing template',
+        array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
+        . '</li>'
+      . '</ul>'
+    . '</ul>';
+
+  $output .= '<h3>Module Description:</h3>';
+  $output .= '<p>This module provides the ability to create loading templates for any tab-delimited '
+    . '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(t('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;
+}
+
+/**
+ * Provides a description page and quick links for template management
+ */
+function tripal_bulk_loader_admin_manage_templates() {
+  $output = '';
+
+  $output .= '<br /><h3>Quick Links:</h3>';
+  $output .= '<ul>'
+    . '<li>'
+      . t('<a href="@create">Create</a> a new template',
+      array('@create' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/create')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@edit">Edit</a> an existing template',
+      array('@edit' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/edit')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@delete">Delete</a> an existing template',
+      array('@delete' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/delete')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@import">Import</a> a new template',
+      array('@import' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/import')))
+      . '</li>'
+    . '<li>'
+      . t('<a href="@export">Export</a> an existing template',
+      array('@export' => url('admin/tripal/tripal_bulk_loader_template/manage_templates/export')))
+      . '</li>'
+    . '</ul>';
+
+  $output .= '<p>' . t('Templates, as the term is used for this module, refer to plans
+  describing how the columns in the data file supplied to a bulk loading job map to tables
+  and fields in chado. Templates are created independently of bulk loading jobs so that
+  they can be re-used. Thus you only need one template to load any number of files of the
+  same format.') . '</p>';
+
+
+
+  return $output;
+}
+
+/**
+ * Provides a listing of bulk loader jobs and links for administration
+ */
+function tripal_bulk_loader_admin_jobs() {
+  $output = '';
+  $num_jobs_per_page = 50;
+
+  $output .= '<p>' . t('Jobs are not automatically submitted to the tripal jobs management
+  system when they are first created. Any jobs listed below with a status of "Initialized"
+  will not have a Job ID until you go to the bulk loader page and submit the job.') . '</p>';
+
+  $header = array(
+    array('data' => 'Job ID', 'field' => 'job_id', 'sort' => 'DESC'),
+    array('data' => 'Name', 'field' => 'loader_name'),
+    array('data' =>  'Template', 'field' => 'template_name'),
+    array('data' =>  'Status', 'field' => 'job_status'),
+    array('data' => 'Progress', 'field' => 'progress'),
+    '');
+  $rows = array();
+  $resource = pager_query("SELECT n.*, t.name as template_name, j.progress
+    FROM {tripal_bulk_loader} n
+    LEFT JOIN {tripal_bulk_loader_template} t ON cast(n.template_id as integer) = t.template_id
+    LEFT JOIN {tripal_jobs} j ON n.job_id = j.job_id"
+    . tablesort_sql($header),
+    $num_jobs_per_page);
+  while ($n = db_fetch_object($resource)) {
+    $rows[] = array(
+      l($n->job_id, 'admin/tripal/tripal_jobs/view/' . $n->job_id),
+      l($n->loader_name, 'node/' . $n->nid),
+      l($n->template_name, 'admin/tripal/tripal_bulk_loader_template/manage_templates/edit', array('query' => 'template_id=' . $n->template_id)),
+      $n->job_status,
+      ($n->progress) ? $n->progress . '%' : '',
+      l('View', 'node/' . $n->nid) . ' | ' .  l('Edit', 'node/' . $n->nid . '/edit')
+    );
+  }
+  $output .= theme_table($header, $rows);
+
+  $output .= theme('pager');
+
+  return $output;
+}
+
+/**
+ * @section
+ * Configuration Form
+ */
+
+/**
+ * A Configuration form for this module
+ */
+function tripal_bulk_loader_configuration_form($form_state = NULL) {
+  $form = array();
+
+  $form['space'] = array(
+    '#type' => 'fieldset',
+    '#title' => t('Enable/Disable Functionality'),
+  );
+
+  $form['space']['keep_track_inserted'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Keep track of inserted record IDs'),
+    '#description' => t('This enables the ability to revert an entire loading job even if '
+      .'it completed successfully. Furthermore, it displays the number of records '
+      .'successfully inserted into each table.'),
+    '#default_value' => variable_get('tripal_bulk_loader_keep_track_inserted', FALSE),
+  );
+
+  $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['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')
+  );
+
+  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']);
+  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']);
+
+  variable_set('tripal_bulk_loader_keep_track_inserted', $form_state['values']['keep_track_inserted']);
+
+}