Fixed issue with adding properties to cvterm-based content type

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -1612,17 +1612,17 @@ function tripal_chado_field_storage_bundle_mapping_form_add_cvterm(&$form,
       within the cvterm table?',
     '#options' => array(
       'cv' => 'All records that belong to a single controlled vocabulary?',
-      'parent' => 'All child records of the specified term?'
+      //  SPF: Commenting out until we can write the code to deal with
+      //  using a parent term to indicate child elements that belong to the
+      //  content type.
+      // 'parent' => 'All child records of the specified term?'
     ),
     '#description' => t('Records in the cvterm table are often not used for content
         types. The records in the cvterm table are meant to be vocabulary terms.
-        However, there are times when records in the cvterm table can be
+        However, there are times when records in the cvterm table may be
         used for a content type. One example is for trait "pages" that
-        use phenotype values stored in the phenotype table.  Because records in
-        the cvterm table are vocabulary terms they do not have "types" so the
-        only ways to distinguish them are 1) to use the controlled vocabulary to
-        distinguish the records or 2) to use all children records of the
-        selected term.  Please select the appropriate value for this case.'),
+        use phenotype values stored in the phenotype table. The vocabulary that
+        contains the "trait" terms should then be provided.'),
     '#default_value' => $default['use_cvterm'],
   );
   if ($default['use_cvterm'] == 'cv') {

tripal_chado/includes/tripal_chado.fields.inc

@@ -227,10 +227,10 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
   $schema = chado_get_schema($table_name);
 
   // Add the additional_type field to all tables with a type_id that is not used
-  // as the type column nor has a $base_type_id (i.e. the content type uses a 
+  // as the type column nor has a $base_type_id (i.e. the content type uses a
   // prop or linker table to resolve the type).
-  if (array_key_exists('type_id', $schema['fields']) and 'type_id' != $type_column and 
-      !$base_type_id and $table_name != 'organism') {    
+  if (array_key_exists('type_id', $schema['fields']) and 'type_id' != $type_column and
+      !$base_type_id and $table_name != 'organism') {
 
     $field_name = 'schema__additional_type';
     $field_type = 'schema__additional_type';
@@ -244,7 +244,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
       ),
     );
   }
-  
+
   // BASE ARRAYDESIGN TABLE
   if ($table_name == 'arraydesign') {
     $field_name = 'ncit__technology_platform';
@@ -258,7 +258,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
         'type' => 'field_chado_storage',
       ),
     );
-    
+
     $field_name = 'efo__substrate_type';
     $field_type = 'schema__additional_type';
     $info[$field_name] = array(
@@ -511,7 +511,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
   }
 
   // Protocol.
-  if ($table_name != 'protocol' and 
+  if ($table_name != 'protocol' and
       array_key_exists('protocol_id', $schema['fields'])) {
     $field_name = 'sep__protocol';
     $field_type = 'sep__protocol';
@@ -525,7 +525,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
       ),
     );
   }
-  
+
   // Assay operator.
   if ($table_name == 'assay') {
       $field_name = 'assay__operator_id';
@@ -551,15 +551,15 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
         ),
       );
     }
-  
+
   // For the pub_id field in the base table.
   $schema = chado_get_schema($table_name);
   if (array_key_exists('pub_id', $schema['fields']) and $table_name != 'pub') {
-    
+
     // Remove the schema__publication added by the
     // tripal_chado_bunde_instnaces_info_base function.
     unset($info['schema__publication']);
-    
+
     $field_name = 'schema__publication_single';
     $field_type = 'schema__publication';
     $info[$field_name] = array(
@@ -571,7 +571,7 @@ function tripal_chado_bundle_fields_info_custom(&$info, $details, $entity_type,
         'type' => 'field_chado_storage',
       ),
     );
-  } 
+  }
 
   // Analysis Id
   if (array_key_exists('analysis_id', $schema['fields']) and $table_name != 'analysis') {
@@ -717,24 +717,24 @@ function tripal_chado_bundle_fields_info_linker(&$info, $details, $entity_type,
   // PROPERTIES
   $prop_table = $table_name . 'prop';
   if (chado_table_exists($prop_table)) {
-    
-    $props = tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id);
+
+    $props = tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id, $type_value);
     foreach ($props as $term) {
-          
+
       $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
 
       // 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 
+      // 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, 
+        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' => $field_name],
          ['drupal_set_message' => TRUE]);
@@ -1250,7 +1250,7 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
     // ARRAYDESIGN TABLE
     //
     if ($table_name == 'arraydesign') {
-      if ($column_name == 'name' or $column_name == 'version' or 
+      if ($column_name == 'name' or $column_name == 'version' or
           $column_name == 'array_dimensions' or $column_name == 'element_dimensions') {
         $base_info['widget']['type'] = 'text_textfield';
         $base_info['settings']['text_processing'] = '0';
@@ -1264,7 +1264,7 @@ function tripal_chado_bundle_instances_info_base(&$info, $entity_type, $bundle,
       if ($column_name == 'manufacturer_id') {
         $base_info['label'] = 'Manufacturer';
       }
-      
+
     }
 
     $info[$field_name] = $base_info;
@@ -1287,14 +1287,14 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
   $type_column = $details['chado_type_column'];
   $cvterm_id  = $details['chado_cvterm_id'];
   $type_value = $details['chado_type_value'];
-  $base_type_id = $details['chado_base_type_id'];  
+  $base_type_id = $details['chado_base_type_id'];
   $schema = chado_get_schema($table_name);
 
   // Add the additional_type field to all tables with a type_id that is not used
   // as the type column nor has a $base_type_id (i.e. the content type uses a
   // prop or linker table to resolve the type).
   if (array_key_exists('type_id', $schema['fields']) and 'type_id' != $type_column and
-      !$base_type_id and $table_name != 'organism') { 
+      !$base_type_id and $table_name != 'organism') {
     $field_name = 'schema__additional_type';
     $is_required = FALSE;
     if (array_key_exists('not null', $schema['fields']['type_id']) and
@@ -1354,7 +1354,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
       ),
     );
   }
-  
+
   if ($table_name == 'arraydesign') {
     $field_name = 'ncit__technology_platform';
     $default_vocab = '';
@@ -1392,7 +1392,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
-    
+
     $field_name = 'efo__substrate_type';
     $default_vocab = '';
     $parent_term = '';
@@ -2051,15 +2051,15 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
-  } 
+  }
   // pub_id field in table.
   $schema = chado_get_schema($table_name);
   if (array_key_exists('pub_id', $schema['fields']) and $table_name != 'pub') {
-    
-    // Remove the schema__publication added by the 
+
+    // Remove the schema__publication added by the
     // tripal_chado_bunde_instnaces_info_base function.
     unset($info['schema__publication']);
-      
+
     $field_name = 'schema__publication_single';
     $info[$field_name] =  array(
       'field_name' => $field_name,
@@ -2091,13 +2091,13 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
-  } 
-  
-  if ($table_name == 'assay') {      
+  }
+
+  if ($table_name == 'assay') {
     // Remove the ncit__operator added by the
     // tripal_chado_bunde_instnaces_info_base function.
     unset($info['ncit__operator']);
-    
+
     $field_name = 'assay__operator_id';
     $info[$field_name] =  array(
       'field_name' => $field_name,
@@ -2114,7 +2114,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'term_vocabulary' => 'NCIT',
         'term_name' => 'Operator',
         'term_accession' => 'C48036',
-        
+
       ),
       'widget' => array(
         'type' => 'local__contact_widget',
@@ -2130,7 +2130,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
-    
+
     $field_name = 'efo__array_design';
     $info[$field_name] =  array(
       'field_name' => $field_name,
@@ -2147,7 +2147,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'term_vocabulary' => 'EFO',
         'term_name' => 'array design',
         'term_accession' => '0000269',
-        
+
       ),
       'widget' => array(
         'type' => 'efo__array_design_widget',
@@ -2163,7 +2163,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         ),
       ),
     );
-  } 
+  }
   // Analysis Id
   if (array_key_exists('analysis_id', $schema['fields']) and $table_name != 'analysis') {
     $field_name = 'operation__analysis';
@@ -2187,7 +2187,7 @@ function tripal_chado_bundle_instances_info_custom(&$info, $entity_type, $bundle
         'term_vocabulary' => 'operation',
         'term_name' => 'Analysis',
         'term_accession' => '2945',
-        
+
       ),
       'widget' => array(
         'type' => 'operation__analysis_widget',
@@ -2489,11 +2489,11 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
   $prop_table = $table_name . 'prop';
   if (chado_table_exists($prop_table)) {
 
-    $props = tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id);
-    foreach ($props as $term) {     
+    $props = tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id, $type_value);
+    foreach ($props as $term) {
 
        $field_name = strtolower(preg_replace('/[^\w]/','_', $term->dbxref_id->db_id->name . '__' . $term->name));
-       
+
        // The field name can only be 32 chars, but if our name is longer we need
        // to add some random chars to ensure we don't have naming conflicts
        // with other terms (e.g. mitochondrial_genetic_code and
@@ -2708,7 +2708,7 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
       ),
     );
   }
-
+  return;
   // SYNONYMS
   $syn_table = $table_name . '_synonym';
   if (chado_table_exists($syn_table)) {
@@ -2751,7 +2751,7 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
 
 /**
  * Used to find all of the properties for a given table.
- *  
+ *
  * @param $table_name
  *   The name of the base table.
  * @param unknown $prop_table
@@ -2760,33 +2760,46 @@ function tripal_chado_bundle_instances_info_linker(&$info, $entity_type, $bundle
  *   The name of the table that contains the type specifier.
  * @param $type_column
  *   The name of the column that contains the type specifier.
- *   
+ *
  * @return
  *   An array of cvterm objects for the properties to be added as fields.
  */
-function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id) {
-  
+function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_table, $type_column, $cvterm_id, $type_value) {
+
   $tschema = chado_get_schema($table_name);
   $schema = chado_get_schema($prop_table);
   $tpkey = $tschema['primary key'][0];
   $pkey = $schema['primary key'][0];
-  
+
   $props = NULL;
-  
+
   // Property tables can be a bit tricky because not all property types
   // in the prop table are appropriate for each type of data.  Also som
   // bundle types are resolved via a property.  So, we have to distinguish
   // between these two cases.
   $sql = '';
   $args = array();
-  
-  // First, is this the case where all of the records in the table are
+
+  // First, If this is the case where the base table is 'cvterm' then we are wanting
+  // to get properties from the cvterm table using the cv_id as the
+  // differentiator.
+  if ($prop_table == 'cvtermprop') {
+    $sql = "
+        SELECT DISTINCT P.type_id
+        FROM {" . db_escape_table($prop_table) . "} P
+          INNER JOIN {" . db_escape_table($table_name) . "} T on T.$tpkey = P.$tpkey
+        WHERE T.cv_id = :cv_id
+      ";
+    $args[':cv_id'] = $type_value;
+    $props = chado_query($sql, $args);
+  }
+  // Second, is this the case where all of the records in the table are
   // of this type?  If so, then all properties apply
-  if (!$type_column) {
+  else if (!$type_column) {
     $sql = 'SELECT DISTINCT type_id FROM {' . db_escape_table($prop_table) . '}';
     $props = chado_query($sql, $args);
   }
-  // Second, if this is the case where a content type is uniquely identified
+  // Third, if this is the case where a content type is uniquely identified
   // by a type_id value in the base table, then only properties associated
   // with that type ID should be used.
   else if ($type_column and !$type_table) {
@@ -2799,7 +2812,7 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
     $args[':cvterm_id'] = $cvterm_id;
     $props = chado_query($sql, $args);
   }
-  // Third, if this is the case where a content type is uniquely identified
+  // Fourth, if this is the case where a content type is uniquely identified
   // via a term/value pair in the prop table.
   else if ($type_column and $type_table == $prop_table and !empty($type_value)) {
     $sql = "
@@ -2814,7 +2827,7 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
     $args[':prop_value'] = $type_value;
     $props = chado_query($sql, $args);
   }
-  // Fourth, if this is the case where the content type is uinquely identifed
+  // Fifth, if this is the case where the content type is uniquely identified
   // via another table (e.g. cvterm linking table) and not this prop table.
   else if ($type_column and $type_table != $prop_table and empty($type_value)) {
     $sql = "
@@ -2830,7 +2843,7 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
   if (!$props) {
     return [];
   }
-  
+
   // Iterate through all of the properties and do some final checks to see
   // which ones should be added.
   $prop_arr = [];
@@ -2840,8 +2853,8 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
   while ($prop = $props->fetchObject()) {
     $term = chado_generate_var('cvterm', array('cvterm_id' => $prop->type_id));
     $term = chado_expand_var($term, 'field', 'cvterm.definition');
-    
-   
+
+
     // The tripal_analysis_KEGG, tripal_analysis_blast, and
     // tripal_analysis_interpro modules store results in the analysisprop
     // table which is probably not the best place, but we don't want to
@@ -2851,7 +2864,7 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
          $term->dbxref_id->db_id->name == 'tripal')) {
       continue;
     }
-    
+
     // The Tripal publication importer adds properties to publications that
     // are also represented in the table fields.  We want editing of pub
     // related fields to always go back to the pub table, so we do not
@@ -2870,7 +2883,7 @@ function tripal_chado_bundle_get_properties($table_name, $prop_table, $type_tabl
         continue;
       }
     }
-    
+
     // Add the term to our list!
     $prop_arr[] = $term;
   }