Tripal: Bulk Loader -Fixed some AHAH errors; added schema definitions for all natural diversity tables

theme_tripal/tripal_bulk_loader/tripal_bulk_loader_add_template_field_form.tpl.php

@@ -1,4 +1,6 @@
 
+<?php print $form['add_fields']['#prefix']; ?>
+<fieldset><legend> <?php print $form['add_fields']['#title']; ?> </legend>
 <?php
   print drupal_render($form['template_name']);
 
@@ -70,7 +72,12 @@
     }
   }
   unset($form['add_fields']);
-  
+?>
+
+</fieldset>
+</div>
+
+<?php
   //Render remaining -Needed to submit
   print drupal_render($form);
 ?>

theme_tripal/tripal_bulk_loader/tripal_bulk_loader_edit_template_field_form.tpl.php

@@ -1,4 +1,6 @@
 
+<?php print $form['edit_fields']['#prefix']; ?>
+<fieldset><legend> <?php print $form['edit_fields']['#title']; ?> </legend>
 <?php
   print drupal_render($form['template_name']);
 
@@ -70,7 +72,12 @@
     }
   }
   unset($form['edit_fields']);
-  
+?>
+
+</fieldset>
+</div>
+
+<?php
   //Render remaining -Needed to submit
   print drupal_render($form);
 ?>

tripal_bulk_loader/tripal_bulk_loader.admin.inc

@@ -644,9 +644,9 @@ function tripal_bulk_loader_edit_template_record_form (&$form_state = NULL) {
     '#type' => 'radios',
     '#title' => 'Action to take when Loading Record',
     '#options' => array(
-      'insert' => 'Insert the record if it doesn\'t already exist',
-      'select' => 'Don\'t insert this record: it\'s used to define a foreign key in another record',
-      'optional' => 'Record will only be inserted if all required data is filled in'
+      'insert' => 'INSERT: Insert the record if it doesn\'t already exist',
+      'select' => 'SELECT: Don\'t insert this record: it\'s used to define a foreign key in another record',
+      'optional' => 'OPTIONAL: Record will only be inserted if all required data is filled in'
     ),
     '#default_value' => 'insert'
   );
@@ -1957,7 +1957,7 @@ function tripal_bulk_loader_add_field_ahah () {
   
   $form_element = $form['add_fields'];
   // Remove the wrapper so we don't double it up.
-  unset($form_element['#prefix'], $form_element['#suffix']);
+  //unset($form_element['#prefix'], $form_element['#suffix']);
 
   $output = theme('status_messages');
   $output .= drupal_render($form_element);

tripal_feature/tripal_feature.api.inc

@@ -124,5 +124,37 @@ function tripal_feature_chado_featureloc_schema() {
   );
   $description['referring_tables'] = $referring_tables;
 
+  return $description;
+}
+
+/**
+ * Implements hook_chado_feature_dbxref_schema()
+ * Purpose: To add descriptions and foreign keys to default table description
+ * Note: This array will be merged with the array from all other implementations
+ *
+ * @return
+ *    Array describing the feature_dbxref table
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_feature_chado_feature_dbxref_schema() {
+  $description = array();
+
+  // Default table description in tripal_core.schema.api.inc: tripal_core_chado_feature_dbxref_schema()
+
+  $description['foreign keys']['feature'] = array(
+        'table' => 'feature',
+        'columns' => array(
+          'feature_id' => 'feature_id',
+        ),
+  );
+
+  $description['foreign keys']['dbxref'] = array(
+        'table' => 'dbxref',
+        'columns' => array(
+          'dbxref_id' => 'dbxref_id',
+        ),
+  );
+
   return $description;
 }

tripal_natural_diversity/tripal_natural_diversity.api.inc

@@ -1,5 +1,788 @@
 <?php
 
+function tripal_natural_diversity_chado_nd_experiment_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment',
+    'fields' => array(
+      'nd_experiment_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_geolocation_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_id',
+    ),
+    'foreign keys' => array(
+      'nd_geolocation' => array(
+        'table' => 'nd_geolocation',
+        'columns' => array(
+          'nd_geolocation_id' => 'nd_geolocation_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+      'nd_experiment_contact',
+      'nd_experiment_dbxref',
+      'nd_experiment_genotype',
+      'nd_experiment_phenotype',
+      'nd_experiment_project',
+      'nd_experiment_protocol',
+      'nd_experiment_pub',
+      'nd_experiment_stock',
+      'nd_experimentprop'
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_contact_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_contact',
+    'fields' => array(
+      'nd_experiment_contact_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'contact_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_contact_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'contact' => array(
+        'table' => 'contact',
+        'columns' => array(
+          'contact_id' => 'contact_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_dbxref_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_dbxref',
+    'fields' => array(
+      'nd_experiment_dbxref_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'dbxref_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_dbxref_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'dbxref' => array(
+        'table' => 'dbxref',
+        'columns' => array(
+          'dbxref_id' => 'dbxref_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_genotype_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_genotype',
+    'fields' => array(
+      'nd_experiment_genotype_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'genotype_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_genotype_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'genotype' => array(
+        'table' => 'genotype',
+        'columns' => array(
+          'genotype_id' => 'genotype_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_phenotype_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_phenotype',
+    'fields' => array(
+      'nd_experiment_phenotype_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'phenotype_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_phenotype_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'phenotype' => array(
+        'table' => 'phenotype',
+        'columns' => array(
+          'phenotype_id' => 'phenotype_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_project_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_project',
+    'fields' => array(
+      'nd_experiment_project_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'project_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_project_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'project' => array(
+        'table' => 'project',
+        'columns' => array(
+          'project_id' => 'project_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_protocol_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_protocol',
+    'fields' => array(
+      'nd_experiment_protocol_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'protocol_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_protocol_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'protocol' => array(
+        'table' => 'protocol',
+        'columns' => array(
+          'protocol_id' => 'protocol_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_pub_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_pub',
+    'fields' => array(
+      'nd_experiment_pub_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'pub_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_pub_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'pub' => array(
+        'table' => 'pub',
+        'columns' => array(
+          'pub_id' => 'pub_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_stock_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_stock',
+    'fields' => array(
+      'nd_experiment_stock_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'stock_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_stock_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'stock' => array(
+        'table' => 'stock',
+        'columns' => array(
+          'stock_id' => 'stock_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+      'nd_experiment_stock_dbxref',
+      'nd_experiment_stockprop',
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_stockprop_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_stockprop',
+    'fields' => array(
+      'nd_experiment_stockprop_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_experiment_stock_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'value' => array(
+        'type' => 'varchar',
+      ),
+      'rank' => array(
+        'type' => 'int',
+        'not null' => 1,
+        'default' => 1
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_stockprop_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment_stock' => array(
+        'table' => 'nd_experiment_stock',
+        'columns' => array(
+          'nd_experiment_stock_id' => 'nd_experiment_stock_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experiment_stock_dbxref_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experiment_stock_dbxref',
+    'fields' => array(
+      'nd_experiment_stock_dbxref_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_experiment_stock_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'dbxref_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experiment_stock_dbxref_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment_stock' => array(
+        'table' => 'nd_experiment_stock',
+        'columns' => array(
+          'nd_experiment_stock_id' => 'nd_experiment_stock_id',
+        ),
+      ),
+      'dbxref' => array(
+        'table' => 'dbxref',
+        'columns' => array(
+          'dbxref_id' => 'dbxref_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_experimentprop_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_experimentprop',
+    'fields' => array(
+      'nd_experimentprop_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_experiment_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'value' => array(
+        'type' => 'varchar',
+      ),
+      'rank' => array(
+        'type' => 'int',
+        'not null' => 1,
+        'default' => 1
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_experimentprop_id',
+    ),
+    'foreign keys' => array(
+      'nd_experiment' => array(
+        'table' => 'nd_experiment',
+        'columns' => array(
+          'nd_experiment_id' => 'nd_experiment_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_geolocation_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_reagent',
+    'fields' => array(
+      'nd_geolocation_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'description' => array(
+        'type' => 'varchar'
+      ),
+      'latitude' => array(
+        'type' => 'real',
+      ),
+      'longitude' => array(
+        'type' => 'real',
+      ),
+      'altitude' => array(
+        'type' => 'real',
+      ),
+      'geodetic_datum' => array(
+        'type' => 'varchar',
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_geolocation_id',
+    ),
+    'referring tables' => array(
+      'nd_experiment',
+      'nd_geolocationprop'
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_geolocationprop_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_geolocationprop',
+    'fields' => array(
+      'nd_geolocationprop_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_geolocation_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'value' => array(
+        'type' => 'varchar',
+      ),
+      'rank' => array(
+        'type' => 'int',
+        'not null' => 1,
+        'default' => 1
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_geolocationprop_id',
+    ),
+    'foreign keys' => array(
+      'nd_geolocation' => array(
+        'table' => 'nd_geolocation',
+        'columns' => array(
+          'nd_geolocation_id' => 'nd_geolocation_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_protocol_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => ,
+    'fields' => array(
+      'nd_protocol_id' => array(
+        'type' => 'serial',
+        'not null' => 1,
+      ),
+      'name' => array(
+        'type' => 'varchar',
+        'not null' => 1,
+      ),
+    ),
+    'primary key' => array(
+     '0' => 'nd_protocol_id',
+    ),
+    'referring tables' => array(
+      'nd_experiment_protocol',
+      'nd_protocol_reagent',
+      'nd_protocolprop'  
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_protocol_reagent_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => ,
+    'fields' => array(
+      'nd_protocol_reagent_id' => array(
+        'type' => 'serial',
+        'not null' => 1,
+      ),    
+      'nd_protocol_id' => array(
+        'type' => 'int',
+        'not null' => 1,
+      ),
+      'nd_reagent_id' => array(
+        'type' => 'int',
+        'not null' => 1,
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => 1,
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_protocol_reagent_id',   
+    ),
+    'foreign keys' => array(
+      'nd_protocol' => array(
+        'table' => 'nd_protocol',
+        'columns' => array(
+          'nd_protocol_id' => 'nd_protocol_id',
+        ),
+      ),
+      'nd_reagent' => array(
+        'table' => 'nd_reagent',
+        'columns' => array(
+          'nd_reagent_id' => 'nd_reagent_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    
+    ),
+  );
+  
+  return $description;
+}
+
+function tripal_natural_diversity_chado_nd_protocolprop_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_protocolprop',
+    'fields' => array(
+      'nd_protocolprop_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_protocol_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'value' => array(
+        'type' => 'varchar',
+      ),
+      'rank' => array(
+        'type' => 'int',
+        'not null' => 1,
+        'default' => 1
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_protocolprop_id',
+    ),
+    'foreign keys' => array(
+      'nd_protocol' => array(
+        'table' => 'nd_protocol',
+        'columns' => array(
+          'nd_protocol_id' => 'nd_protocol_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    ),
+  );
+  
+  return $description;
+}
+
 function tripal_natural_diversity_chado_nd_reagent_schema () {
   $description = array();
   
@@ -85,3 +868,54 @@ function tripal_natural_diversity_chado_nd_reagent_relationship_schema () {
   
   return $description;
 }
+
+function tripal_natural_diversity_chado_nd_reagentprop_schema () {
+  $description = array();
+  
+  $description = array(
+    'table' => 'nd_reagentprop',
+    'fields' => array(
+      'nd_reagentprop_id' => array(
+        'type' => 'serial',
+        'not null' => '1',
+      ),
+      'nd_reagent_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'type_id' => array(
+        'type' => 'int',
+        'not null' => '1',
+      ),
+      'value' => array(
+        'type' => 'varchar',
+      ),
+      'rank' => array(
+        'type' => 'int',
+        'not null' => 1,
+        'default' => 1
+      ),
+    ),
+    'primary key' => array(
+      '0' => 'nd_reagentprop_id',
+    ),
+    'foreign keys' => array(
+      'nd_reagent' => array(
+        'table' => 'nd_reagent',
+        'columns' => array(
+          'nd_reagent_id' => 'nd_reagent_id',
+        ),
+      ),
+      'cvterm' => array(
+        'table' => 'cvterm',
+        'columns' => array(
+          'type_id' => 'cvterm_id',
+        ),
+      ),
+    ),
+    'referring tables' => array(
+    ),
+  );
+  
+  return $description;
+}