Core, DB, CV legacy modules installable

legacy/tripal_core/tripal_core.drush.inc

@@ -33,19 +33,6 @@ function tripal_core_drush_help($command) {
       return dt('DEPRECATED. Please use: trp-rerun-job.');
       break;
 
-    // Tripal Materialized Views
-    case 'drush:tripal-update-mview':
-      return dt('Updates the specified materialized view.');
-      break;
-
-    // Chado Specific
-    case 'drush:tripal-chado-version':
-      return dt('Returns the current version of chado associated with this drupal site.');
-      break;
-    case 'drush:tripal-chadotable-desc':
-      return dt('Returns the table description as specified in the Tripal Schema API for the supplied table.');
-      break;
-
   }
 }
 
@@ -60,41 +47,6 @@ function tripal_core_drush_help($command) {
 function tripal_core_drush_command() {
   $items = array();
 
-  $items['trp-refresh-mview'] = array(
-    'description' => dt('Refreshes the contents of the specified materialized view.'),
-    'arguments' => array(),
-    'examples' => array(
-      'By Materialized View ID' => 'drush trp-refresh-mview --mview=5',
-      'By Table Name' => 'drush trp-refresh-mview --table=organism_feature_count'
-    ),
-    'options' => array(
-      'mview' => dt('The ID of the materialized view to update'),
-      'table' => dt('The name of the materialized view table to update.'),
-    ),
-  );
-
-  $items['trp-get-cversion'] = array(
-    'description' => dt('Returns the current installed version of Chado.'),
-    'arguments' => array(),
-    'examples' => array(
-      'Standard Example' => 'drush trp-get-cversion',
-    ),
-  );
-  $items['trp-get-table'] = array(
-    'description' => dt('Returns a table description in Drupal Schema API format.'),
-    'arguments' => array(),
-    'examples' => array(
-      'By Table Name' => 'drush trp-get-table --table=feature',
-      'By Section' => 'drush trp-get-table --table=feature --section=fields'
-    ),
-    'options' => array(
-      'table' => array(
-        'description' => dt('The name of the table. The table can be a true Chado table or a custom Chado table.'),
-        'required' => TRUE,
-      ),
-      'section' => dt('Only return the specified section of the schema array. Possible sections include: description, fields, primary key, unique keys, foreign keys, indexes, referring_tables.'),
-    ),
-  );
   $items['trp-clean-nodes'] = array(
     'description' => dt('Removes orphaned Drupal nodes.'),
     'arguments' => array(),
@@ -207,16 +159,6 @@ function drush_tripal_core_set_user($username) {
   drush_tripal_set_user($username);
 }
 
-/**
- * Executes jobs in the Tripal Jobs Queue.
- *
- * Executed when 'drush trp-run-job' is called.
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_run_jobs() {
-  drush_tripal_trp_run_jobs();
-}
 /**
  * DEPRECATED. Executes jobs in the Tripal Jobs Queue.
  *
@@ -247,17 +189,6 @@ function drush_tripal_core_tripal_jobs_launch($username) {
   }
 }
 
-/**
- * Executes jobs in the Tripal Jobs Queue.
- *
- * Executed when 'drush trp-rerun-job' is called.
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_rerun_job() {
-  drush_tripal_trp_rerun_job();
-}
-
 /**
  * DEPRECATED. Executes jobs in the Tripal Jobs Queue.
  *
@@ -276,17 +207,6 @@ function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
 
 }
 
-/**
- * Prints details about the current running job.
- *
- * Executed when 'drush trp-get-currjob' is called.
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_get_currjob() {
-  drush_tripal_trp_get_currjob();
-}
-
 /**
  * DEPRECATED. Prints details about the current running job.
  *
@@ -301,42 +221,6 @@ function drush_tripal_core_tripal_jobs_current() {
   drush_tripal_core_trp_get_currjob();
 }
 
-/**
- * Updates the specified materialized view
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_refresh_mview() {
-  $mview_id   = drush_get_option('mview');
-  $table_name = drush_get_option('table');
-
-  // Either table_name or mview is required
-  if (!$mview_id) {
-    if ($table_name) {
-      // if table_name supplied use that to get mview_id
-      $sql = "SELECT mview_id FROM {tripal_mviews} WHERE mv_table = :mv_table";
-      $results = db_query($sql, array(':mv_table' => $table_name));
-      $r = $resuls->fetchObject();
-      if (!$r->mview_id) {
-        drush_set_error('No Materialized View associated with that table_name.');
-      }
-      $mview_id=$r->mview_id;
-    }
-    else {
-      drush_set_error('Plese provide one option of --mview or --table.');
-    }
-  }
-
-  drush_print('Updating the Materialized View with ID=' . $mview_id);
-  $status = tripal_populate_mview($mview_id);
-  if ($status) {
-    drush_log('Materialized View Updated', 'ok');
-  }
-  else {
-    drush_set_error('Update failed.');
-  }
-}
-
 /**
  * DEPRECATED. Updates the specified materialized view.
  *
@@ -389,35 +273,6 @@ function drush_tripal_core_tripal_chado_version() {
   drush_tripal_core_trp_get_cversion();
 }
 
-/**
- * Returns the current version of chado.
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_get_cversion() {
-  $version = $GLOBALS["exact_chado_version"];
-  drush_print('Current Chado Version: ' . $version);
-}
-
-/**
- * Returns the Tripal Schema API Description of the given table
- *
- * @ingroup tripal_drush
- */
-function drush_tripal_core_trp_get_table() {
-  $section = drush_get_option('section');
-  $table_name = drush_get_option('table');
-
-  drush_print("Schema API Description for $table_name:");
-  $desc = chado_get_schema($table_name);
-
-  if (!empty($section)) {
-    drush_print("$section = " . print_r($desc[$section], TRUE));
-  }
-  else {
-    drush_print(print_r($desc, TRUE));
-  }
-}
 
 /**
  * DEPRECATED. Returns the Tripal Schema API Description of the given table.

legacy/tripal_core/tripal_core.install

@@ -20,15 +20,15 @@ function tripal_core_install() {
  */
 function tripal_core_schema() {
 
-  // get the schemas defined by this install file
+  // Get the schemas defined by this install file.
   $schema = tripal_core_get_schemas();
 
   // if this module is already installed and enabled, then we want to provide
   // the schemas for all of the custom tables.  This will allow Views to
   // see the schemas.  We check if the module is installed because during
-  // installation we don't want to make these custom tables available as we don't
-  // want them created in the Drupal database.  The custom tables go in the
-  // Chado database.
+  // installation we don't want to make these custom tables available as we
+  // don't want them created in the Drupal database.  The custom tables go in
+  // the Chado database.
   if (db_table_exists('tripal_custom_tables')) {
     $sql = 'SELECT * FROM {tripal_custom_tables}';
     $results = db_query($sql);
@@ -66,11 +66,7 @@ function tripal_core_uninstall() {
 function tripal_core_get_schemas() {
   $schema = array();
 
-  // get all the various schema parts and join them together
-  $temp = tripal_core_get_tripal_token_schema();
-  foreach ($temp as $table => $arr) {
-    $schema[$table] = $arr;
-  }
+  // Get all the various schema parts and join them together
   $temp = tripal_core_get_tripal_toc_schema();
   foreach ($temp as $table => $arr) {
     $schema[$table] = $arr;
@@ -84,7 +80,6 @@ function tripal_core_get_schemas() {
 }
 
 /**
- *
  *
  */
 function tripal_core_get_tripal_toc_schema() {
@@ -201,123 +196,4 @@ function tripal_core_get_tripal_vars_schema() {
   );
 
   return $schema;
-}
-
-/**
- * Adds an mview_id column to the tripal_custom_tables table and makes an assocation between the mview and the custom table
- *
- */
-function tripal_core_update_7200() {
-  try {
-    // add an mview column to the tripal_custom_tables table so we
-    // can associate which of the custom tables are also mviews
-    if (!db_field_exists('tripal_custom_tables', 'mview_id')) {
-      $spec = array(
-        'type' => 'int',
-        'not NULL' => FALSE
-      );
-      $keys = array(
-        'foreign keys' => array(
-          'tripal_mviews' => array(
-            'table' => 'tripal_mviews',
-            'columns' => array(
-              'mview_id' => 'mview_id'
-            ),
-          ),
-        ),
-      );
-      db_add_field('tripal_custom_tables', 'mview_id', $spec, $keys);
-
-      // the foreign key specification doesn't really add one to the
-      // Drupal schema, it is just used internally, but we want one
-      db_query('
-        ALTER TABLE {tripal_custom_tables}
-        ADD CONSTRAINT tripal_custom_tables_fk1
-        FOREIGN KEY (mview_id) REFERENCES {tripal_mviews} (mview_id)
-        ON DELETE CASCADE DEFERRABLE INITIALLY DEFERRED
-      ');
-    }
-
-    // now link the materialized view to it's custom table entry
-    $mviews = db_select('tripal_mviews', 'tmv')
-      ->fields('tmv', array('mview_id', 'mv_table'))
-      ->execute();
-    foreach ($mviews as $mview) {
-      db_update('tripal_custom_tables')
-       ->fields(array(
-         'mview_id' => $mview->mview_id
-       ))
-       ->condition('table_name', $mview->mv_table)
-       ->execute();
-    }
-  }
-  catch (\PDOException $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not update tripal_mviews table and link to custom tables: '. $error);
-  }
-}
-
-/**
- * Fixes missing language for nodes and URL aliases. This may take awhile...
- *
- */
-function tripal_core_update_7201() {
-
-  try {
-    $sql = "UPDATE {node} SET language = :language WHERE language = ''";
-    db_query($sql, array(':language' => LANGUAGE_NONE));
-    $sql = "UPDATE {url_alias} SET language = :language WHERE language = ''";
-    db_query($sql, array(':language' => LANGUAGE_NONE));
-  }
-  catch (\PDOException $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not reset language for nodes and url aliases: '. $error);
-  }
-}
-
-
-/**
- * Adds a tripal_token_formats table for custom page titles and URL paths
- */
-function tripal_core_update_7202() {
-  try {
-    $schema = drupal_get_schema_unprocessed('tripal_core', 'tripal_token_formats');
-    db_create_table('tripal_token_formats', $schema);
-  }
-  catch (Exception $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not add tripal_token_formats table: '. $error);
-  }
-}
-
-/**
- * Adds a tripal_toc table for customizing the table of contents on each Tripal page.
- */
-function tripal_core_update_7203() {
-  try {
-    $schema = drupal_get_schema_unprocessed('tripal_core', 'tripal_toc');
-    db_create_table('tripal_toc', $schema);
-  }
-  catch (Exception $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not add tripal_toc table: '. $error);
-
-  }
-}
-
-/**
- * Adds the tripal_variable_terms and a tripal_node_variables tables
- */
-function tripal_core_update_7204() {
-  try {
-    $schema = drupal_get_schema_unprocessed('tripal_core', 'tripal_variables');
-    db_create_table('tripal_variables', $schema);
-    $schema = drupal_get_schema_unprocessed('tripal_core', 'tripal_node_variables');
-    db_create_table('tripal_node_variables', $schema);
-  }
-  catch (Exception $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Could not add new tables table: '. $error);
-
-  }
 }

legacy/tripal_cv/tripal_cv.install

@@ -49,20 +49,6 @@ function tripal_cv_requirements($phase) {
  */
 function tripal_cv_install() {
 
-  // Add the cv_root_mview.
-  tripal_cv_add_cv_root_mview();
-
-  // Add defaults to the tables that correlate OBO files/references with
-  // a chado CV.
-  tripal_cv_add_obo_defaults();
-
-  // Add the Chado ontology CV.
-  $obo_path = '{tripal_cv}/files/cv_property.obo';
-  $obo_id = tripal_insert_obo('Chado CV Properties', $obo_path);
-  tripal_submit_obo_job(array('obo_id' => $obo_id));
-
-  // Create the temp table we will use for loading OBO files.
-  tripal_cv_create_tripal_obo_temp();
 }
 
 /**
@@ -72,240 +58,4 @@ function tripal_cv_install() {
  */
 function tripal_cv_uninstall() {
 
-  // drop the tripal_obo_temp table
-  if (db_table_exists('chado.tripal_obo_temp')) {
-    $sql = "DROP TABLE chado.tripal_obo_temp";
-    db_query($sql);
-  }
-}
-
-/**
- * Creates a temporary table to store obo details while loading an obo file
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_create_tripal_obo_temp() {
-  // the tripal_obo_temp table is used for temporary housing of records when loading OBO files
-  // we create it here using plain SQL because we want it to be in the chado schema but we
-  // do not want to use the Tripal Custom Table API because we don't want it to appear in the
-  // list of custom tables.  It needs to be available for the Tripal Chado API so we create it
-  // here and then define it in the tripal_cv/api/tripal_cv.schema.api.inc
-  if (!db_table_exists('chado.tripal_obo_temp')) {
-    $sql = "
-      CREATE TABLE {tripal_obo_temp} (
-        id character varying(255) NOT NULL,
-        stanza text NOT NULL,
-        type character varying(50) NOT NULL,
-        CONSTRAINT tripal_obo_temp_uq0 UNIQUE (id)
-      );
-    ";
-    chado_query($sql);
-    $sql = "CREATE INDEX tripal_obo_temp_idx0 ON {tripal_obo_temp} USING btree (id)";
-    chado_query($sql);
-    $sql = "CREATE INDEX tripal_obo_temp_idx1 ON {tripal_obo_temp} USING btree (type)";
-    chado_query($sql);
-  }
-}
-
-/**
- * Implementation of hook_schema().
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_schema() {
-  $schema = array();
-
-  tripal_cv_get_tripal_cv_obo_table($schema);
-  tripal_cv_get_tripal_cv_defaults_table($schema);
-
-  return $schema;
-}
-/**
- * Table definition for the tripal_cv_obo table
- * @param $schema
- */
-function tripal_cv_get_tripal_cv_obo_table(&$schema) {
-  $schema['tripal_cv_obo'] = array(
-    'fields' => array(
-      'obo_id' => array(
-        'type' => 'serial',
-        'unsigned' => TRUE,
-        'not null' => TRUE
-      ),
-      'name' => array(
-        'type' => 'varchar',
-         'length' => 255
-       ),
-      'path'  => array(
-        'type' => 'varchar',
-        'length' => 1024
-      ),
-    ),
-    'indexes' => array(
-      'tripal_cv_obo_idx1' => array('obo_id'),
-    ),
-    'primary key' => array('obo_id'),
-  );
-}
-
-/**
- * * Table definition for the tripal_cv_defaults table
- * @param unknown $schema
- */
-function tripal_cv_get_tripal_cv_defaults_table(&$schema) {
-  $schema['tripal_cv_defaults'] = array(
-    'fields' => array(
-      'cv_default_id' => array(
-        'type' => 'serial',
-        'unsigned' => TRUE,
-        'not null' => TRUE
-      ),
-      'table_name' => array(
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE,
-      ),
-      'field_name' => array(
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE,
-      ),
-      'cv_id' => array(
-        'type' => 'int',
-        'not null' => TRUE,
-      )
-    ),
-    'indexes' => array(
-      'tripal_cv_defaults_idx1' => array('table_name', 'field_name'),
-    ),
-    'unique keys' => array(
-      'tripal_cv_defaults_unq1' => array('table_name', 'field_name', 'cv_id'),
-    ),
-    'primary key' => array('cv_default_id')
-  );
-}
-
-/**
- * Add a materialized view of root terms for all chado cvs. This is needed for viewing cv trees
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_add_cv_root_mview() {
-  $mv_name = 'cv_root_mview';
-  $comment = 'A list of the root terms for all controlled vocabularies. This is needed for viewing CV trees';
-  $schema = array(
-    'table' => $mv_name,
-    'description' => $comment,
-    'fields' => array(
-      'name' => array(
-        'type' => 'varchar',
-        'length' => 255,
-        'not null' => TRUE,
-      ),
-      'cvterm_id' => array(
-        'type' => 'int',
-        'not null' => TRUE,
-      ),
-      'cv_id' => array(
-        'type' => 'int',
-        'not null' => TRUE,
-      ),
-      'cv_name' => array(
-        'type' => 'varchar',
-        'length' => 255,
-        'not null' => TRUE,
-      ),
-    ),
-    'indexes' => array(
-      'cv_root_mview_indx1' => array('cvterm_id'),
-      'cv_root_mview_indx2' => array('cv_id'),
-    ),
-  );
-
-  $sql = "
-    SELECT DISTINCT CVT.name,CVT.cvterm_id, CV.cv_id, CV.name
-    FROM cvterm_relationship CVTR
-      INNER JOIN cvterm CVT on CVTR.object_id = CVT.cvterm_id
-      INNER JOIN cv CV on CV.cv_id = CVT.cv_id
-    WHERE CVTR.object_id not in
-      (SELECT subject_id FROM cvterm_relationship)
-  ";
-
-  // Create the MView
-  tripal_add_mview($mv_name, 'tripal_cv', $schema, $sql, $comment);
-}
-
-/**
- * Add's defaults to the tripal_cv_obo table
- *
- * @ingroup tripal_cv
- */
-function tripal_cv_add_obo_defaults() {
-
-  // Insert commonly used ontologies into the tables.
-  $ontologies = array(
-    array('Relationship Ontology', 'http://purl.obolibrary.org/obo/ro.obo'),
-//    array('Relationship Ontology (older deprecated version)', 'http://www.obofoundry.org/ro/ro.obo'),
-    array('Sequence Ontology', 'https://github.com/The-Sequence-Ontology/SO-Ontologies/blob/master/so-xp-simple.obo'),
-    array('Gene Ontology', 'http://www.geneontology.org/ontology/gene_ontology.obo'),
-//    array('Cell Ontology', 'https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl.obo'),
-//    array('Plant Structure Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co'),
-//    array('Plant Growth and Development Stages Ontology', 'http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_temporal.obo?view=co')
-  );
-  foreach ($ontologies as $o) {
-    db_query("INSERT INTO {tripal_cv_obo} (name,path) VALUES (:name, :path)", array(':name' => $o[0], ':path' => $o[1]));
-  }
-}
-
-
-/**
- * This is the required update for tripal_cv when upgrading from Drupal core API 6.x.
- *
- */
-function tripal_cv_update_7200() {
-
-  // add in the new tripal_cv_defaults table
-  try {
-    $schema = array();
-    tripal_cv_get_tripal_cv_defaults_table($schema);
-    db_create_table('tripal_cv_defaults', $schema['tripal_cv_defaults']);
-  }
-  catch (\PDOException $e) {
-    $error = $e->getMessage();
-    throw new DrupalUpdateException('Failed to create tripal_cv_defaults table: '. $error);
-  }
-}
-
-/**
- * Fixes an error with the materialized view installation
- *
- */
-function tripal_cv_update_7201() {
-
-  // there is a bug in the Tripal v2.0-alpha release that didn't add the
-  // materialized view schema to the mviews table.
-  // get the schema for the materialized view from the custom_tables table
-  // as there is a copy there, but only if the schema is missing from the
-  // materialized view table
-  $view_name = 'cv_root_mview';
-  $schema = db_select('tripal_mviews', 'tm')
-    ->fields('tm', array('mv_schema'))
-    ->condition('name', $view_name)
-    ->execute()
-    ->fetchField();
-  if (!$schema or $schema == 'Array') {
-    $schema = db_select('tripal_custom_tables', 'tct')
-      ->fields('tct', array('schema'))
-      ->condition('table_name', $view_name)
-      ->execute()
-      ->fetchField();
-    $schema_str = var_export(unserialize($schema), TRUE);
-    $schema_str = preg_replace('/=>\s+\n\s+array/', '=> array', $schema_str);
-    db_update('tripal_mviews')
-      ->fields(array(
-        'mv_schema' => $schema_str
-      ))
-      ->condition('name', $view_name)
-      ->execute();
-  }
 }

legacy/tripal_cv/tripal_cv.module

@@ -14,12 +14,9 @@
  * @}
  */
 
-require_once 'api/tripal_cv.api.inc';
-require_once 'api/tripal_cv.schema.api.inc';
 require_once 'api/tripal_cv.DEPRECATED.inc';
 
 require_once 'includes/tripal_cv.admin.inc';
-require_once 'includes/tripal_cv.obo_loader.inc';
 require_once 'includes/tripal_cv.cv_form.inc';
 require_once 'includes/tripal_cv.cvterm_form.inc';
 require_once 'includes/tripal_cv.cvtermpath_form.inc';
@@ -258,10 +255,7 @@ function tripal_cv_help ($path, $arg) {
  */
 function tripal_cv_permission() {
   return array(
-    'administer controlled vocabularies' => array(
-      'title' => t('Administer controlled vocabularies (CVs).'),
-      'description' => t('Allow a user to add, edit and delete controlled vocabularies as well as add and edit terms.')
-    ),
+
   );
 }
 

tripal/tripal.module

@@ -246,6 +246,10 @@ function tripal_permission() {
       'title' => t('Administer Tripal data'),
       'description' => t('Edit and delete all tripal data'),
     ),
+    'administer controlled vocabularies' => array(
+      'title' => t('Administer controlled vocabularies (CVs).'),
+      'description' => t('Allow a user to add, edit and delete controlled vocabularies as well as add and edit terms.')
+    ),
   );
 }
 

tripal/tripal.views.inc

@@ -13,271 +13,5 @@
 function tripal_views_data() {
   $data = array();
 
-  // Job Management System
-  $data = tripal_views_data_jobs($data);
-
-  return $data;
-}
-
-/**
- * Provides the data array for the tripal job management system
- *
- * @param $data
- *   Previously generated tripal views data array
- * return
- *   $data array with job management system described
- *
- * @ingroup tripal
- */
-function tripal_views_data_jobs($data) {
-
-  $data['tripal_jobs']['table']['group'] = t('Tripal Jobs');
-  $data['tripal_jobs']['table']['base'] = array(
-    'field' => 'job_id', // This is the identifier field for the view.
-    'title' => t('Tripal Jobs'),
-    'help' => t('The Job Management system for Tripal.'),
-    'weight' => 10,
-  );
-
-  // Job ID
-  $data['tripal_jobs']['job_id'] = array(
-    'title' => t('Job ID'),
-    'help' => t('The job primary key.'),
-    'field' => array(
-      'handler' => 'views_handler_field_numeric',
-      'click sortable' => TRUE,
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_numeric',
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-  );
-
-  // User ID: Submitter
-  $data['tripal_jobs']['uid'] = array(
-    'title' => t('Job Submitter'),
-    'help' => t('The user who submitted the job.'),
-    'relationship' => array(
-      'base' => 'user', // The name of the table to join with.
-      'base field' => 'uid', // The name of the field on the joined table.
-      'handler' => 'views_handler_relationship',
-      'label' => t('Submitting User'),
-      'title' => t('Submitting User'),
-      'help' => t('The user who submitted the job'),
-    ),
-  );
-
-  // Job Name
-  $data['tripal_jobs']['job_name'] = array(
-    'title' => t('Job Name'),
-    'help' => t('The name of the job.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Module Name
-  $data['tripal_jobs']['modulename'] = array(
-    'title' => t('Module Name'),
-    'help' => t('The name of the module that submitted the job.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Callback
-  $data['tripal_jobs']['callback'] = array(
-    'title' => t('Callback'),
-    'help' => t('The callback executed when the job runs.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Arguments
-  $data['tripal_jobs']['arguments'] = array(
-    'title' => t('Arguements'),
-    'help' => t('Any arguements passed to the callback.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Progress
-  $data['tripal_jobs']['progress'] = array(
-    'title' => t('Progress'),
-    'help' => t('The current progress of the job.'),
-    'field' => array(
-      'handler' => 'views_handler_field_numeric',
-      'click sortable' => TRUE,
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_numeric',
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-  );
-
-  // Status
-  $data['tripal_jobs']['status'] = array(
-    'title' => t('Status'),
-    'help' => t('The current status of the job.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Submit Data
-  $data['tripal_jobs']['submit_date'] = array(
-    'title' => t('Submit Date'),
-    'help' => t('The date the job was submitted.'),
-    'field' => array(
-      'handler' => 'views_handler_field_date',
-      'click sortable' => TRUE,
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort_date',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_date',
-    ),
-  );
-
-  // Start Time
-  $data['tripal_jobs']['start_time'] = array(
-    'title' => t('Start Time'),
-    'help' => t('The time the job started.'),
-    'field' => array(
-      'handler' => 'views_handler_field_date',
-      'click sortable' => TRUE,
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort_date',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_date',
-    ),
-  );
-
-  // End Time
-  $data['tripal_jobs']['end_time'] = array(
-    'title' => t('End Time'),
-    'help' => t('The time the job ended.'),
-    'field' => array(
-      'handler' => 'views_handler_field_date',
-      'click sortable' => TRUE,
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort_date',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_date',
-    ),
-  );
-
-  // Error Message
-  $data['tripal_jobs']['error_msg'] = array(
-    'title' => t('Error Message '),
-    'help' => t('A short description of any error the job might have had.'),
-    'field' => array(
-      'handler' => 'views_handler_field',
-      'click sortable' => TRUE, // This is use by the table display plugin.
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_string',
-    ),
-    'argument' => array(
-      'handler' => 'views_handler_argument_string',
-    ),
-  );
-
-  // Unix Pid of the job
-  $data['tripal_jobs']['pid'] = array(
-    'title' => t('Job PID'),
-    'help' => t('The Unix PID of the job.'),
-    'field' => array(
-      'handler' => 'views_handler_field_numeric',
-      'click sortable' => TRUE,
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_numeric',
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-  );
-
-  // Priority
-  $data['tripal_jobs']['priority'] = array(
-    'title' => t('Priority'),
-    'help' => t('The priority of this job.'),
-    'field' => array(
-      'handler' => 'views_handler_field_numeric',
-      'click sortable' => TRUE,
-    ),
-    'filter' => array(
-      'handler' => 'views_handler_filter_numeric',
-    ),
-    'sort' => array(
-      'handler' => 'views_handler_sort',
-    ),
-  );
-
   return $data;
 }