Merge branch '7.x-2.x' of git.drupal.org:project/tripal into 7.x-2.x

tripal_bulk_loader/api/tripal_bulk_loader.api.templates.inc

@@ -157,9 +157,13 @@ function tripal_insert_bulk_loader_template($options, &$errors, &$warnings) {
     // do nothing it's in PHP serialized format
   }
   // The typical format is JSON
-  elseif (preg_match('/^\{/', $template_array)) {
+  elseif (json_decode($template_array)) {
     $template_array = serialize(json_decode($template_array, TRUE));
   }
+  else {
+    $errors['template_array'] = t('Unrecognized array type.');
+    return FALSE;
+  }
 
   $record = array(
     'name' => $template_name,

tripal_bulk_loader/includes/tripal_bulk_loader.admin.templates.inc

@@ -807,7 +807,7 @@ function tripal_bulk_loader_export_template_form($form, &$form_state) {
   if ($template_id > 0) {
     $result = db_select('tripal_bulk_loader_template','t')
       ->fields('t')
-      ->condition('t.template_id',$template_id)
+      ->condition('t.template_id', $template_id)
       ->execute();
     $template = $result->fetchObject();
     $form_state['storage']['template_array'] = $template->template_array;
@@ -822,7 +822,7 @@ function tripal_bulk_loader_export_template_form($form, &$form_state) {
   $form['template_array'] = array(
     '#type' => 'textarea',
     '#title' => 'Export',
-    '#default_value' => json_encode(unserialize($form_state['storage']['template_array'])),
+    '#default_value' => json_encode(unserialize($template->template_array)),
     '#description' => t('Use this JSON array for import of this bulk loader template into another Tripal site.'),
     '#rows' => 30,
     '#weight' => 5,

tripal_core/includes/tripal_core.mviews.inc

@@ -76,6 +76,7 @@ function tripal_mview_report($mview_id) {
   $update_url = url("admin/tripal/schema/mviews/action/update/$mview->mview_id");
   $delete_url = url("admin/tripal/schema/mviews/action/delete/$mview->mview_id");
   $edit_url = url("admin/tripal/schema/mviews/edit/$mview->mview_id");
+  $export_url = url("admin/tripal/schema/mviews/export/$mview->mview_id");
   $rows[] = array('Actions', "<a href='$update_url'>Populate</a>, <a href='$edit_url'>Edit</a>,  <a href='$delete_url'>Delete</a>");
 
   if ($mview->last_update > 0) {

tripal_core/tripal_core.drush.inc

@@ -21,7 +21,7 @@
  */
 function tripal_core_drush_help($command) {
   switch ($command) {
-    
+
     // TRIPAL JOBS
     case 'trp-run-jobs':
       return dt('Launches pending jobs waiting in the queue.');
@@ -101,14 +101,16 @@ function tripal_core_drush_command() {
   $items['trp-run-jobs'] = array(
     'description' => dt('Launches jobs waiting in the queue. Only one job can execute at a time unless the --parllel=1 option is provided.'),
     'examples' => array(
-      'Single Job' => 'drush trp-run-jobs --user=administrator',
-      'Parallel Job' => 'drush trp-run-jobs --user=administrator --parallel=1'
+      'Single Job' => 'drush trp-run-jobs --username=administrator',
+      'Parallel Job' => 'drush trp-run-jobs --username=administrator --parallel=1'
     ),
     'arguments' => array(),
     'options' => array(
       'user' => array(
+        'description' => dt('DEPRECATED. Conflicts with Drush 7.x --user argument. Please use the --username argument.'),
+      ),
+      'username' => array(
         'description' => dt('The Drupal user name for which the job should be run.  The permissions for this user will be used.'),
-        'required' => TRUE,
       ),
       'parallel' => dt('Normally jobs are executed one at a time. But if you are certain no conflicts will occur with other currently running jobs you may set this argument to a value of 1 to make the job run in parallel with other running jobs.'),
       'job_id' => dt('Provide a job_id to run a specific job. Only jobs that have not been run already can be used'),
@@ -117,14 +119,16 @@ function tripal_core_drush_command() {
   $items['trp-rerun-job'] = array(
     'description' => dt('Re-run a specific job from the queue.'),
     'examples' => array(
-      'Single Job' => 'drush trp-rerun-job --user=administrator --job_id=2',
-      'Parallel Job' => 'drush trp-rerun-job --user=administrator  --job_id=2 --parallel=1'
+      'Single Job' => 'drush trp-rerun-job --username=administrator --job_id=2',
+      'Parallel Job' => 'drush trp-rerun-job --username=administrator  --job_id=2 --parallel=1'
     ),
     'arguments' => array(),
     'options' => array(
       'user' => array(
+        'description' => dt('DEPRECATED. Conflicts with Drush 7.x --user argument. Please use the --username argument.'),
+      ),
+      'username' => array(
         'description' => dt('The Drupal user name for which the job should be run.  The permissions for this user will be used.'),
-        'required' => TRUE,
       ),
       'job_id' => array(
         'description' => dt('The job ID to run.'),
@@ -199,7 +203,7 @@ function tripal_core_drush_command() {
       'Parallel Job' => 'drush tripal-jobs-launch admin --parallel=1'
     ),
     'arguments' => array(
-      'user' => dt('The Drupal username under which the job should be run.  The permissions for this user will be used.'),
+      'username' => dt('The Drupal username under which the job should be run.  The permissions for this user will be used.'),
     ),
     'options' => array(
       'parallel' => dt('Normally jobs are executed one at a time. But if you are certain no conflicts will occur with other currently running jobs you may set this argument to a value of 1 to make the job run in parallel with other running jobs.'),
@@ -214,7 +218,7 @@ function tripal_core_drush_command() {
       'Parallel Job' => 'drush tripal-jobs-rerun admin  2 --parallel=1'
     ),
     'arguments' => array(
-      'user' => dt('The Drupal username under which the job should be run.  The permissions for this user will be used.'),
+      'username' => dt('The Drupal username under which the job should be run.  The permissions for this user will be used.'),
       'job_id' => dt('The job ID to run.'),
     ),
     'options' => array(
@@ -269,7 +273,7 @@ function drush_tripal_core_set_user($username) {
     $results = db_query($sql, array(':name' => $username));
     $u = $results->fetchObject();
     if (!$u) {
-      drush_print('ERROR: Please provide a valid username for running this job.');
+      drush_print('ERROR: Please provide a valid username (--username argument) for running this job.');
       exit;
     }
     global $user;
@@ -277,7 +281,7 @@ function drush_tripal_core_set_user($username) {
     return $u->uid;
   }
   else {
-    drush_print('ERROR: Please provide a username for running this job.');
+    drush_print('ERROR: Please provide a username (--username argument) for running this job.');
     exit;
   }
 }
@@ -290,10 +294,25 @@ function drush_tripal_core_set_user($username) {
  * @ingroup tripal_drush
  */
 function drush_tripal_core_trp_run_jobs() {
-  $username = drush_get_option('user');
   $parallel = drush_get_option('parallel');
   $job_id   = drush_get_option('job_id');
 
+  // Unfortunately later versions of Drush use the '--user' argument which
+  // makes it incompatible with how Tripal was using it.  For backwards
+  // compatabiliy we will accept --user with a non numeric value only. The
+  // numeric value should be for Drush. Tripal will instead use the
+  // --username argument for the fture.
+  $user = drush_get_option('user');
+  $uname = drush_get_option('username');
+  if ($user and is_numeric($user)) {
+  }
+  elseif ($user) {
+    $username = $user;
+  }
+  if ($uname) {
+    $username = $uname;
+  }
+
   drush_tripal_core_set_user($username);
 
   if ($parallel) {
@@ -321,7 +340,7 @@ function drush_tripal_core_tripal_jobs_launch($username) {
   $job_id = drush_get_option('job_id');
 
   drush_tripal_core_set_user($username);
-  
+
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
     "continue to work but please consider using the 'trp-run-jobs' command.\n\n");
 
@@ -347,10 +366,26 @@ function drush_tripal_core_tripal_jobs_launch($username) {
  * @ingroup tripal_drush
  */
 function drush_tripal_core_trp_rerun_job() {
-  $username = drush_get_option('user');
+  // Unfortunately later versions of Drush use the '--user' argument which
+  // makes it incompatible with how Tripal was using it.  For backwards
+  // compatabiliy we will accept --user with a non numeric value only. The
+  // numeric value should be for Drush. Tripal will instead use the
+  // --username argument for the fture.
+  $user = drush_get_option('user');
+  $uname = drush_get_option('username');
+  print "USER: '$user', UNAME: '$uname'\n";
+  if ($user and is_numeric($user)) {
+  }
+  elseif ($user) {
+    $username = $user;
+  }
+  if ($uname) {
+    $username = $uname;
+  }
+
   $parallel = drush_get_option('parallel');
   $job_id   = drush_get_option('job_id');
-  
+
   drush_tripal_core_set_user($username);
   $new_job_id = tripal_rerun_job($job_id, FALSE);
 
@@ -377,10 +412,10 @@ function drush_tripal_core_trp_rerun_job() {
  * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_jobs_rerun($username, $job_id) {
-  
+
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
       "continue to work but please consider using the 'trp-rerun-job' command.\n\n");
-  
+
   drush_tripal_core_set_user($username);
   $new_job_id = tripal_rerun_job($job_id, FALSE);
   drush_tripal_core_tripal_jobs_launch($username, $new_job_id);
@@ -430,7 +465,7 @@ function drush_tripal_core_trp_get_currjob() {
 function drush_tripal_core_tripal_jobs_current() {
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
       "continue to work but please consider using the 'trp-get-currjob' command.\n\n");
-  
+
   drush_tripal_core_trp_get_currjob();
 }
 
@@ -476,10 +511,10 @@ function drush_tripal_core_trp_refresh_mview() {
  * @ingroup tripal_drush
  */
 function drush_tripal_core_tripal_update_mview() {
-  
+
   $mview_id = drush_get_option('mview_id');
   $table_name = drush_get_option('table_name');
-  
+
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
       "continue to work but please consider using the 'trp-refresh-mview' command.\n\n");
 
@@ -518,7 +553,7 @@ function drush_tripal_core_tripal_update_mview() {
 function drush_tripal_core_tripal_chado_version() {
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
       "continue to work but please consider using the 'trp-get-cversion' command.\n\n");
-  
+
   drush_tripal_core_trp_get_cversion();
 }
 
@@ -562,7 +597,7 @@ function drush_tripal_core_trp_get_table() {
  */
 function drush_tripal_core_tripal_chadotable_desc($table_name) {
   $section = drush_get_option('section');
-  
+
   drush_print("\n\nDEPRECATED: This drush command is outdated.\nIt will ".
       "continue to work but please consider using the 'trp-get-table' command.\n\n");
 
@@ -584,7 +619,7 @@ function drush_tripal_core_tripal_chadotable_desc($table_name) {
  */
 function drush_tripal_core_trp_clean_nodes() {
   $table = drush_get_option('table');
-  
+
   chado_cleanup_orphaned_nodes($table, 0);
 }
 

tripal_core/tripal_core.module

@@ -313,6 +313,24 @@ function tripal_core_menu() {
     'access arguments' => array('administer tripal'),
     'type' => MENU_CALLBACK,
   );
+  // TODO: complete the code for exporting and importing of MViews.
+  // Need to address security issues of sharing SQL.
+  $items['admin/tripal/schema/mviews/import'] = array(
+    'title' => 'Import MView',
+    'description' => 'Import a materialized view from another Tripal instance.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_mviews_import_form'),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_CALLBACK,
+  );
+  $items['admin/tripal/schema/mviews/%tblid/export'] = array(
+    'title' => 'Export MView',
+    'description' => 'Export a materialized view for use by another Tripal instance.',
+    'page callback' => 'drupal_get_form',
+    'page arguments' => array('tripal_mviews_export_form', 5),
+    'access arguments' => array('administer tripal'),
+    'type' => MENU_CALLBACK,
+  );
 
   // Custom Tables
   $items['admin/tripal/schema/custom_tables'] = array(