Added warning messages when namespace conflicts occur with fields (i.e. the same term is used multiple times

tripal/api/tripal.entities.api.inc

@@ -628,6 +628,8 @@ function tripal_get_content_type($bundle_name) {
  *
  * @param $bundle_name
  *   The name of the bundle to refresh (e.g. bio_data_4).
+ * @param $term
+ *   The term object for the bundle.
  *
  * @return
  *   The array of field instance names that were added.
@@ -635,38 +637,34 @@ function tripal_get_content_type($bundle_name) {
  * @ingroup tripal_entities_api
  */
 function tripal_create_bundle_fields($bundle, $term) {
-
   $added = array();
 
   // Allow modules to add fields to the new bundle.
   $modules = module_implements('bundle_fields_info');
-  $info = array();
+  $field_info = array();
   foreach ($modules as $module) {
     $function = $module . '_bundle_fields_info';
     $temp = $function('TripalEntity', $bundle);
     if (is_array($temp)) {
       // TODO: it would be good to check this array to make sure it follows
       // protocol.  It would help identify potential errors.
-      $info = array_merge($info, $temp);
+      $field_info = array_merge($field_info, $temp);
     }
   }
 
   // Allow modules to alter which fields should be attached to content
   // types they create.
-  drupal_alter('bundle_fields_info', $info, $bundle, $term);
+  drupal_alter('bundle_fields_info', $field_info, $bundle, $term);
 
   // Iterate through all of the fields and create them.
-  foreach ($info as $field_name => $details) {
+  foreach ($field_info as $field_name => $details) {
     $field_type = $details['type'];
 
-    // TODO: make sure the field term exits. If not then
-    // skip it.
-
     // If the field already exists then skip it.
     $field = field_info_field($details['field_name']);
     if ($field) {
       continue;
-    }
+    }    
 
     // Create the field.
     $field = field_create_field($details);
@@ -678,35 +676,99 @@ function tripal_create_bundle_fields($bundle, $term) {
 
   // Allow modules to add instances to the new bundle.
   $modules = module_implements('bundle_instances_info');
-  $info = array();
+  $instance_info = array();
   foreach ($modules as $module) {
     $function = $module . '_bundle_instances_info';
     $temp = $function('TripalEntity', $bundle);
     if (is_array($temp)) {
       // TODO: it would be good to check this array to make sure it follows
       // protocol.  It would help identify potential errors.
-      $info = array_merge($info, $temp);
+      $instance_info = array_merge($instance_info, $temp);
     }
   }
 
   // Allow modules to alter which fields should be attached to content
   // types they create.
-  drupal_alter('bundle_instances_info', $info, $bundle, $term);
-
+  drupal_alter('bundle_instances_info', $instance_info, $bundle, $term);
+  
+  // Get the list of existing instances
+  $existing_instances = field_info_instances('TripalEntity', $bundle->name);
+  
   // Iterate through all of the field instances and create them.
-  foreach ($info as $field_name => $details) {
+  foreach ($instance_info as $instance_name => $details) {
+    
+    // Make sure the instance has a term. If not, report it and skip the field.
+    if (!array_key_exists('term_vocabulary', $details['settings'])) {
+      tripal_report_error('tripal_fields', TRIPAL_WARNING,
+        'The field instance, !field, is missing the "term_vocabulary" setting. The field instance cannot be added. Please check the field settings.',
+        ['!field' => $instance_name], ['drupal_set_message' => TRUE]);
+        continue;
+    }
+    if (!array_key_exists('term_accession', $details['settings'])) {
+      tripal_report_error('tripal_fields', TRIPAL_WARNING,
+        'The field instance, !field, is missing the "term_accession" setting. The field instance cannot be added. Please check the field settings.',
+        ['!field' => $instance_name], ['drupal_set_message' => TRUE]);
+        continue;}
+    
+    // Make sure the term exists. If not, skip the field instance and 
+    // report an error.
+    $field_term_id = $details['settings']['term_vocabulary'] . ':' . $details['settings']['term_accession'];    
+    $field_term = tripal_get_term_details($details['settings']['term_vocabulary'], $details['settings']['term_accession']);
+    if (!$field_term) {
+      tripal_report_error('tripal_fields', TRIPAL_WARNING, 
+        'The term, !term, for the field, !field, does not exist in the database. The  ' .
+        'field instance cannot be added. Please make sure the term is correct and add it if necessary.',
+        ['!term' => $field_term_id,
+          '!field' => $instance_name],
+        ['drupal_set_message' => TRUE]);
+      continue;
+    }
+    
+    // Make sure the term is not used for any other existing field instance.
+    $skip = TRUE;
+    foreach ($existing_instances as $existing_name => $existing_instance) {
+      // If this instance term is the same as this exsiting term and the 
+      // instance name is not the same then we have a problem.
+      $existing_term_id = $existing_instance['settings']['term_vocabulary'] . ':' . $existing_instance['settings']['term_accession'];
+      $existing_field = field_info_field($existing_name);
+      if ($existing_term_id == $field_term_id and $instance_name != $existing_name) {
+        tripal_report_error('tripal_fields', TRIPAL_WARNING,
+          'The field, !field, uses a term, !term, that is already in use on this content type. The ' .
+          'field instance cannot be added.',
+          ['!term' => $existing_term_id,
+            '!field' => $instance_name],
+          ['drupal_set_message' => TRUE]);
+        $skip = TRUE;
+      }
+      
+      // If the instance term is the same as this exsting term but the storage
+      // types are different then we have a problem.
+      $existing_storage = $existing_field['storage']['type'];
+      $this_field_storage = $field_info[$details['field_name']]['storage']['type'];
+      if ($existing_term_id == $field_term_id and $existing_storage != $this_field_storage) {
+        tripal_report_error('tripal_fields', TRIPAL_WARNING,
+          'The field, !field, provided by the storage type, !type, uses a term, !term, that is already in use on this content type and provided by another storage backend. The ' .
+          'field instance cannot be added.  Perhaps, consider a different term and adjust the data in the database.',
+          ['!term' => $existing_term_id,
+           '!type' => $this_field_storage,
+           '!field' => $instance_name],
+          ['drupal_set_message' => TRUE]);
+        $skip = TRUE;
+      }
+    }
+    if ($skip) {
+      continue;
+    }
 
     // If the field is already attached to this bundle then skip it.
-    $field = field_info_field($details['field_name']);
-    if ($field and array_key_exists('bundles', $field) and
-        array_key_exists('TripalEntity', $field['bundles']) and
-        in_array($bundle->name, $field['bundles']['TripalEntity'])) {
+    if (array_key_exists($instance_name, $existing_instances)) {
       continue;
     }
 
     // Create the field instance.
     $instance = field_create_instance($details);
-    $added[] = $field_name;
+    $existing_instances[$instance_name] = $instance;
+    $added[] = $instance_name;
   }
   return $added;
 }

tripal/api/tripal.notice.api.inc

@@ -58,6 +58,8 @@ define('TRIPAL_DEBUG',7);
  *   An array of options. Some available options include:
  *     - print: prints the error message to the terminal screen. Useful when
  *       display is the command-line
+ *     - drupal_set_message: set to TRUE to call drupal_set_message with the 
+ *       same error.
  *
  * @ingroup tripal_notify_api
  */
@@ -113,7 +115,7 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
     watchdog($type, $message, $variables, $severity);
   }
   catch (Exception $e) {
-    print "CRITICAL (TRIPAL): Unable to register error message with watchdog: " . $e->getMessage(). "\n.";
+    print "CRITICAL (TRIPAL): Unable to add error message with watchdog: " . $e->getMessage(). "\n.";
     $options['print'] = TRUE;
   }
 
@@ -129,6 +131,19 @@ function tripal_report_error($type, $severity, $message, $variables = array(), $
   if (isset($options['print'])) {
     print $severity_string . ' (' . strtoupper($type) . '): ' . $print_message . "\n";
   }
+  
+  if (isset($options['drupal_set_message'])) {
+    if (in_array($severity, [TRIPAL_CRITICAL, TRIPAL_ERROR])) {
+      $status = 'error';
+    }
+    elseif ($severity == TRIPAL_WARNING) {
+      $status = 'warning';
+    }
+    else {
+      $status = 'status';
+    }
+    drupal_set_message($print_message, $status);
+  }
 
   // Print to the Tripal error log but only if the severity is not info.
   if (($severity != TRIPAL_INFO)) {

tripal/includes/tripal.fields.inc

@@ -271,10 +271,12 @@ function tripal_form_field_ui_field_overview_form_alter(&$form, &$form_state, $f
       $term = $instance['settings']['term_vocabulary'] . ':' . $instance['settings']['term_accession'];
       if (array_key_exists($term, $used_terms)) {
         $used_terms[$term][] = $field_name;
-        drupal_set_message(t('The term !term is in use by multiple fields: !fields. 
-          This is not allowed. Every field must have a different controlled vocabulary term. 
-          Please correct the term assignments.', 
-          array('!term' => $term, '!fields' => implode(', ', $used_terms[$term]))), 'error');
+        tripal_report_error('tripal_fields', TRIPAL_WARNING,
+          'The term !term is in use by multiple fields: !fields. ' .
+          'This is not allowed. Every field must have a different controlled vocabulary term. ' . 
+          'Please correct the term assignments.',
+          ['!term' => $term, '!fields' => implode(', ', $used_terms[$term])], 
+          ['drupal_set_message' => TRUE]);
       }
       $used_terms[$term][] = $field_name;
     }
@@ -734,6 +736,19 @@ function tripal_field_instance_settings_form_alter_validate($form, &$form_state)
         }
       }
     }
+    
+    // Make sure this term is not already used.    
+    $bundle_name = $form_state['values']['instance']['bundle'];
+    $existing_instances = field_info_instances('TripalEntity', $bundle_name);
+    $field_term_id = $form_state['values']['instance']['settings']['term_vocabulary'] . ':' . $form_state['values']['instance']['settings']['term_accession'];
+    $field_name = $form_state['values']['instance']['field_name'];  
+    foreach ($existing_instances as $existing_name => $existing_instance) {
+      $existing_term_id = $existing_instance['settings']['term_vocabulary'] . ':' . $existing_instance['settings']['term_accession'];
+      if ($existing_term_id == $field_term_id and $field_name != $existing_name) {       
+        form_set_error('term-', t('The term, !term, is already in use on this content type.  A term can only be used once per content type. Please choose a different term.',
+          ['!term' => $field_term_id]));
+      }
+    }
 
     if ($num_selected > 1) {
       form_set_error('term-', 'Please select only one term

tripal_chado/includes/tripal_chado.fields.inc

@@ -532,6 +532,17 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
           'type' => 'field_chado_storage',
         ),
       );
+      $field_name = 'efo__array_design';
+      $field_type = 'efo__array_design';
+      $info[$field_name] = array(
+        'field_name' => $field_name,
+        'type' => $field_type,
+        'cardinality' => 1,
+        'locked' => FALSE,
+        'storage' => array(
+          'type' => 'field_chado_storage',
+        ),
+      );
     }
   
   // For the pub_id field in the base table.
@@ -554,7 +565,6 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
       ),
     );
   } 
-
 }
 
 /**
@@ -702,8 +712,24 @@ function tripal_chado_bundle_fields_info_linker(&$info, $details, $entity_type,
       }
 
       $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
-      $field_name = substr($field_name, 0, 32);
+
+      // The field name can only be 32 chars, but if our name is longer we need
+      // to add some random chars to ensure we don't have naming conflicts 
+      // with other terms (e.g. mitochondrial_genetic_code and 
+      // mitochondrial_genetic_code_name)
+      if (strlen($field_name) >= 32) {
+        $field_name = substr($field_name, 0, 20) . '_' . $term->cvterm_id;
+      }
       $field_type = 'chado_linker__prop';
+      
+      // Don't try to add a property that uses the same term as another field.
+      if (array_key_exists($field_name, $info)) {
+        tripal_report_error('chado_fields', TRIPAL_WARNING, 
+          'A field of type !type already exists, yet a property wants to use the same term. The property cannot be added.',
+         ['!type' => $field_name],
+         ['drupal_set_message' => TRUE]);
+        continue;
+      }
       $info[$field_name] = array(
         'field_name' => $field_name,
         'type' => $field_type,
@@ -832,7 +858,6 @@ function tripal_chado_bundle_instances_info($entity_type, $bundle) {
   tripal_chado_bundle_instances_info_base($info, $entity_type, $bundle, $details);
   tripal_chado_bundle_instances_info_custom($info, $entity_type, $bundle, $details);
   tripal_chado_bundle_instances_info_linker($info, $entity_type, $bundle, $details);
-
   return $info;
 
 }
@@ -1016,11 +1041,11 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
     }
     if ($base_info['label'] == 'Timeaccessioned') {
       $base_info['label'] = 'Time Accessioned';
-      $base_info['description'] = 'Please enter the time that this record was first added to the database.';
+      $base_info['description'] = 'The time that this record was first added to the database.';
     }
     if ($base_info['label'] == 'Timelastmodified') {
       $base_info['label'] = 'Time Last Modified';
-      $base_info['description'] = 'Please enter the time that this record was last modified. The default is the current time.';
+      $base_info['description'] = 'The time that this record was last modified. The default is the current time.';
     }
 
     // Sometimes the boolean fields are listed as integer.  We need to
@@ -1178,6 +1203,8 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
       if ($column_name == 'name') {
         $base_info['widget']['type'] = 'text_textfield';
         $base_info['settings']['text_processing'] = '0';
+        $base_info['required'] = TRUE;
+        $base_info['description'] = 'A unique name for this assay..';
       }
       if ($column_name == 'protcol_id') {
         $base_info['label'] = 'Protocol';
@@ -1186,20 +1213,24 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
         $base_info['label'] = 'Array Batch Identifier';
         $base_info['widget']['type'] = 'text_textfield';
         $base_info['settings']['text_processing'] = '0';
+        $base_info['description'] = 'A unique identifier for the array batch.';
       }
       if ($column_name == 'operator_id') {
         $base_info['label'] = 'Operator';
+        $base_info['description'] = 'The individual who performed the assay.';
       }
       if ($column_name == 'arrayidentifier') {
         $base_info['label'] = 'Array Identifier';
         $base_info['widget']['type'] = 'text_textfield';
         $base_info['settings']['text_processing'] = '0';
+        $base_info['description'] = 'A unique alternate identifier for the array.';
       }
       if ($column_name == 'arraydesign_id') {
         $base_info['label'] = 'Array Design';
       }
       if ($column_name == 'assaydate') {
         $base_info['label'] = 'Assay Date';
+        $base_info['description'] = 'The date the assay was performed';
       }
     }
     //
@@ -1287,6 +1318,9 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'base_table' => $table_name,
         'vocabulary' => $default_vocab,
         'parent_term' => $parent_term,
+        'term_vocabulary' => 'schema',
+        'term_name' => 'additionalType',
+        'term_accession' => 'additionalType',
       ),
       'widget' => array(
         'type' => 'schema__additional_type_widget',
@@ -1527,6 +1561,10 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
   // BASE DBXREF
   if (array_key_exists('dbxref_id', $schema['fields'])) {
     $field_name = 'data__accession';
+    $required = FALSE;
+    if ($table == 'phylotree') {
+      $required = TRUE;
+    }
     $info[$field_name] = array(
       'field_name' => $field_name,
       'entity_type' => $entity_type,
@@ -1534,7 +1572,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
       'label' => 'Accession',
       'description' => 'This field specifies the unique stable accession (ID) for
         this record. It requires that this site have a database entry.',
-      'required' => FALSE,
+      'required' => $required,
       'settings' => array(
         'auto_attach' => TRUE,
         'chado_table' => $table_name,
@@ -1772,6 +1810,9 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'chado_table' => 'organism',
         'chado_column' => 'type_id',
         'base_table' => 'organism',
+        'term_vocabulary' => 'TAXRANK',
+        'term_name' => 'infraspecific_taxon',
+        'term_accession' => '0000046',
       ),
       'widget' => array(
         'type' => 'taxrank__infraspecific_taxon_widget',
@@ -1973,6 +2014,9 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'chado_table' => $table_name,
         'chado_column' => 'pub_id',
         'base_table' => $table_name,
+        'term_accession' => 'publication',
+        'term_vocabulary' => 'schema',
+        'term_name' => 'publication',
       ),
       'widget' => array(
         'type' => 'schema__publication_widget',
@@ -2027,7 +2071,80 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
+    
+    $field_name = 'efo__array_design';
+    $info[$field_name] =  array(
+      'field_name' => $field_name,
+      'entity_type' => $entity_type,
+      'bundle' => $bundle->name,
+      'label' => 'Array design',
+      'description' => 'An instrument design which describes the design of the array.',
+      'required' => TRUE,
+      'settings' => array(
+        'auto_attach' => TRUE,
+        'chado_table' => 'assay',
+        'chado_column' => 'arraydesign_id',
+        'base_table' => 'assay',
+        'term_vocabulary' => 'EFO',
+        'term_name' => 'array design',
+        'term_accession' => '0000269',
+        
+      ),
+      'widget' => array(
+        'type' => 'efo__array_design_widget',
+        'settings' => array(
+          'display_label' => 1,
+        ),
+      ),
+      'display' => array(
+        'default' => array(
+          'label' => 'inline',
+          'type' => 'efo__array_design_formatter',
+          'settings' => array(),
+        ),
+      ),
+    );
   } 
+  // Analysis Id
+  if (array_key_exists('analysis_id', $schema['fields'])) {
+    $field_name = 'operation__analysis';
+    $is_required = FALSE;
+    if (array_key_exists('not null', $schema['fields']['analysis_id']) and
+        $schema['fields']['analysis_id']['not null']) {
+      $is_required = TRUE;
+    }
+    $info[$field_name] =  array(
+      'field_name' => $field_name,
+      'entity_type' => $entity_type,
+      'bundle' => $bundle->name,
+      'label' => 'Analysis',
+      'description' => 'Application of analytical methods to existing data of a specific type.',
+      'required' => $is_required,
+      'settings' => array(
+        'auto_attach' => TRUE,
+        'chado_table' => $table_name,
+        'chado_column' => 'analysis_id',
+        'base_table' => $table_name,
+        'term_vocabulary' => 'operation',
+        'term_name' => 'Analysis',
+        'term_accession' => '2945',
+        
+      ),
+      'widget' => array(
+        'type' => 'operation__analysis_widget',
+        'settings' => array(
+          'display_label' => 0,
+        ),
+      ),
+      'display' => array(
+        'default' => array(
+          'label' => 'inline',
+          'type' => 'operation__analysis_formatter',
+          'settings' => array(),
+        ),
+      ),
+    );
+  }
 }
 
 /**
@@ -2095,6 +2212,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
         'chado_table' => $dbxref_table,
         'chado_column' => $pkey,
         'base_table' => $table_name,
+        'term_vocabulary' => 'SBO',
+        'term_name' => 'Database Cross Reference',
+        'term_accession' => '0000554',
       ),
       'widget' => array(
         'type' => 'sbo__database_cross_reference_widget',
@@ -2377,7 +2497,13 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
          }
 
          $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
-         $field_name = substr($field_name, 0, 32);
+         // The field name can only be 32 chars, but if our name is longer we need
+         // to add some random chars to ensure we don't have naming conflicts
+         // with other terms (e.g. mitochondrial_genetic_code and
+         // mitochondrial_genetic_code_name)
+         if (strlen($field_name) >= 32) {
+           $field_name = substr($field_name, 0, 20) . '_' . $term->cvterm_id;
+         }
          $info[$field_name] = array(
            'field_name' => $field_name,
            'entity_type' => $entity_type,
@@ -2448,6 +2574,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
         'chado_table' => $term_table,
         'chado_column' => $pkey,
         'base_table' => $table_name,
+        'term_vocabulary' => 'SIO',
+        'term_name' => 'annotation',
+        'term_accession' => '001166',
       ),
       'widget' => array(
         'type' => 'sio__annotation_widget',
@@ -2483,6 +2612,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
         'chado_table' => $pub_table,
         'chado_column' => $pkey,
         'base_table' => $table_name,
+        'term_accession' => 'publication',
+        'term_vocabulary' => 'schema',
+        'term_name' => 'publication',
       ),
       'widget' => array(
         'type' => 'schema__publication_widget',
@@ -2555,6 +2687,9 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
         'chado_table' => $rel_table,
         'chado_column' => $pkey,
         'base_table' => $table_name,
+        'term_vocabulary' => 'SBO',
+        'term_name' => 'Relationship',
+        'term_accession' => '0000374',
       ),
       'widget' => array(
         'type' => 'sbo__relationship_widget',