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tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt.api.inc

@@ -78,13 +78,15 @@ function tripal_jbrowse_mgmt_get_instances($conditions = NULL) {
     }
     $instance->organism = $organisms[$instance->organism_id];
 
-    if (!isset($analysis[$instance->analysis_id])){
-      $instance[$instance->analysis_id] = chado_query('SELECT * FROM {analysis} WHERE analysis_id=:id'
-        [':id' => $instance->analysis_id])->fetchObject();
+    if($instance->analysis_id){
+      if (!isset($analysis[$instance->analysis_id])){
+        $analysis[$instance->analysis_id] = chado_query('SELECT * FROM {analysis} WHERE analysis_id=:id',
+          [':id' => $instance->analysis_id])->fetchObject();
+      }
+      $instance->analysis = $analysis[$instance->analysis_id];
     }
-    $instance->analysis = $analysis[$instance->analysis_id];
-  }
 
+  }
   return $instances;
 }
 
@@ -99,7 +101,6 @@ function tripal_jbrowse_mgmt_get_instances($conditions = NULL) {
  */
 function tripal_jbrowse_mgmt_create_instance($data) {
   global $user;
-  dpm($data, '$data in tripal_jbrowse_mgmt_create_instance');
   // Check that required fields are provided.
   $required = ['organism_id', 'created_at'];
   foreach ($required as $key) {

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_add.form.inc

@@ -63,7 +63,7 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
 
   $form['analysis'] = [
     '#title' => t('Analysis'),
-    '#description' => t('Select the analysis to which this instance will be related.'),
+    '#description' => 'Select the analysis to which this instance will be related. Analysis can be created in '.l('Add Tripal Content', 'bio_data/add/3').' if wanted analysis is not available.<br><strong>Please choose analysis carefully</strong> since it can not change once instance is created.',
     '#type' => 'textfield',
     '#autocomplete_path' => 'admin/tripal/extension/tripal_jbrowse/management/instances/analysis/autocomplete',
   ];
@@ -177,7 +177,6 @@ function tripal_jbrowse_mgmt_add_form($form, &$form_state) {
  * @param $form_state
  */
 function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
-  dpm($form_state, '$form_state in validation');
   $values = $form_state['values'];
   $organism = isset($values['organism']) ? $values['organism'] : NULL;
 
@@ -218,7 +217,6 @@ function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
   //  if selected organism already exist, analysis_id is required
   //  also make sure organism+analysis does not exist
   $instances = tripal_jbrowse_mgmt_get_instances(['organism_id' => $organism]);
-  dpm($instances, '$instances after tripal_jbrowse_mgmt_get_instances([\'organism_id\' => $organism]) ');
   if (empty($values['analysis'])) {
     if (!empty($instances)){
       form_set_error(
@@ -257,7 +255,6 @@ function tripal_jbrowse_mgmt_add_form_validate($form, &$form_state) {
  */
 function tripal_jbrowse_mgmt_add_form_submit($form, &$form_state) {
   global $user;
-  dpm($form_state, '$form_state in tripal_jbrowse_mgmt_add_form_submit');
   $values = $form_state['values'];
   $organism_id = $values['organism'];
   preg_match_all('!\d+!', $values['analysis'], $match_analysis);

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_commands.inc

@@ -10,7 +10,6 @@
  */
 function tripal_jbrowse_mgmt_cmd_prepare_refseq($instance) {
   $settings = tripal_jbrowse_mgmt_get_settings();
-  dpm($settings,'$settings in tripal_jbrowse_mgmt_cmd_prepare_refseq');
   $data = $settings['data_dir'];
   $bin = $settings['bin_path'];
 

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_list.page.inc

@@ -29,6 +29,7 @@ function tripal_jbrowse_mgmt_instances_page() {
 
   $header = [
     'Organism',
+    'Analysis',
     'Submitter',
     'Description',
     'Tracks',
@@ -43,6 +44,7 @@ function tripal_jbrowse_mgmt_instances_page() {
         $instance->title,
         'admin/tripal/extension/tripal_jbrowse/management/instances/' . $instance->id
       ),
+      $instance->analysis->name,
       $instance->user->name,
       $instance->description ?: 'Not provided',
       l('Manage Tracks', 'admin/tripal/extension/tripal_jbrowse/management/instances/' . $instance->id),

tripal_jbrowse_mgmt/includes/tripal_jbrowse_mgmt_tracks.form.inc

@@ -276,7 +276,6 @@ function tripal_jbrowse_mgmt_add_track_form_validate($form, &$form_state) {
  */
 function tripal_jbrowse_mgmt_add_track_form_submit($form, &$form_state) {
   global $user;
-  dpm($form_state, '$form_state in tripal_jbrowse_mgmt_add_track_form_submit');
   $values = $form_state['values'];
 
   $file = isset($values['file_path']) ? $values['file_path'] : NULL;