Added documentation and re-organized the install file for easier reading (moved schema defn. to the bottom, each in their own function for easy documentation.

tripal_entities/tripal_entities.install

@@ -4,306 +4,186 @@
  * Install for a tripal data entity - creates the base table for our entity.
  */
 
+/**
+ * Implements hook_install().
+ */
 function tripal_entities_install() {
 
-  // add any custom tables. For this case we will add an 'file' table to the
-  // chado schema
-  tripal_entities_add_custom_tables();
-
-
+  // Create a number of Chado custom tables to keep track of vocabularies and terms
+  // that are available for use with entities.
+  // @TODO: Ask Stephen why these are chado instead of drupal tables...
+  chado_create_custom_table(
+    'tripal_vocabulary', 
+    tripal_entities_tripal_vocabulary_schema(), 
+    TRUE
+  );
+  chado_create_custom_table(
+    'tripal_vocabulary_usage', 
+    tripal_entities_tripal_vocabulary_usage_schema(), 
+    TRUE
+  );
+  chado_create_custom_table(
+    'tripal_term', 
+    tripal_entities_tripal_term_schema(), 
+    TRUE
+  );
+  chado_create_custom_table(
+    'tripal_term_usage', 
+    tripal_entities_tripal_term_usage_schema(), 
+    TRUE
+  );
+  chado_create_custom_table(
+    'tripal_term_relationship', 
+    tripal_entities_tripal_term_relationship_schema(), 
+    TRUE
+  );
 }
 
-
 /**
- *
+ * Implements hook_schema().
  */
-function tripal_entities_add_custom_tables() {
-  tripal_entities_add_tripal_vocabulary_table();
-  tripal_entities_add_tripal_vocabulary_usage_table();
-  tripal_entities_add_tripal_term_table();
-  tripal_entities_add_tripal_term_usage_table();
-  tripal_entities_add_tripal_term_relationship_table();
-}
+function tripal_entities_schema() {
 
-/**The current Entity Example (Genes) requires the Sequence Ontology.                                     [warning]
+  // Biological Data
+  $schema['tripal_entity'] = tripal_entities_tripal_entity_schema();
 
- *
- */
-function tripal_entities_add_tripal_vocabulary_table() {
-  $schema = array (
-    'table' => 'tripal_vocabulary',
-    'fields' => array (
-      'vocabulary_id' => array(
+  // Biological Data Types
+  $schema['tripal_bundle'] = tripal_entities_tripal_bundle_schema();
+
+  // Links Biological Data Entities to the chado "base" table the data is stored in.
+  $schema['chado_entity'] = tripal_entities_chado_entity_schema();
+
+  // @TODO: Move these tables into the tripal_fields_layout module.
+  $schema['tripal_panels'] = array(
+    'description' => 'The list of panels into which fields can be placed.',
+    'fields' => array(
+      'panel_id' => array(
+        'description' => 'The primary identifier for this table.',
         'type' => 'serial',
-        'not null' => TRUE
+        'unsigned' => TRUE,
+        'not null' => TRUE,
       ),
-      'cv_id' => array (
+      'bundle_id' => array(
+        'description' => 'A bundle ID from the tripal_bundle table.',
         'type' => 'int',
-        'not null' => TRUE
+        'not null' => TRUE,
       ),
-      'db_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
+      'name' => array(
+        'description' => 'The computer readable name for the panel. This name must only have alphanumerical characters and underscores and must not begin with a number. ',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE,
+        'default' => '',
       ),
-      'publish' => array (
-        'type' => 'int',
+      'label' => array(
+        'description' => 'A human readable name for panel. This name will be shown to users in the sidebar menu.',
+        'type' => 'varchar',
+        'length' => 128,
         'not null' => TRUE,
+        'default' => '',
+      ),
+      'settings' => array(
+        'description' => 'Contains a serialized array tripal_fields_layoutof settings for the panel.',
+        'type' => 'text',
+        'not null' => FALSE,
+      ),
+      'weight' => array(
+        'type' => 'int',
+        'not null' => FALSE,
         'default' => 0
       ),
     ),
-    'primary key' => array (
-      0 => 'vocabulary_id'
+    'indexes' => array(
+      'bundle_id' => array('bundle_id'),
     ),
-    'foreign keys' => array (
-      'cv' => array (
-        'table' => 'cv',
-        'columns' => array (
-          'cv_id' => 'cv_id'
-        )
-      ),
-      'db' => array (
-        'table' => 'db',
-        'columns' => array (
-          'db_id' => 'db_id'
-        )
-      ),
+    'unique keys' => array(
+      'bundle_panel' => array('bundle_id', 'name'),
     ),
-    'unique keys' => array (
-      'tripal_vocabulary_cvdb' => array (
-        'cv_id', 'db_id'
+    'foreign keys' => array(
+      'tripal_bundle' => array(
+        'table' => 'tripal_bundle',
+        'columns' => array(
+          'bundle_id' => 'id',
+        ),
       ),
     ),
-    'indexes' => array(
-      'tripal_vocabulary_cv_id' => array('cv_id'),
-      'tripal_vocabulary_db_id' => array('db_id'),
-    )
+    'primary key' => array('panel_id'),
   );
-  chado_create_custom_table('tripal_vocabulary', $schema, TRUE);
-}
-/**
- *
- */
-function tripal_entities_add_tripal_term_table() {
-  $schema = array (
-    'table' => 'tripal_term',
-    'fields' => array (
-      'term_id' => array(
+  $schema['tripal_panel_fields'] = array(
+    'description' => 'The list of panels into which fields can be placed.',
+    'fields' => array(
+      'panel_field_id' => array(
+        'description' => 'The primary identifier for this table.',
         'type' => 'serial',
-        'not null' => TRUE
-      ),
-      'vocabulary_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
+        'unsigned' => TRUE,
+        'not null' => TRUE,
       ),
-      'cvterm_id' => array (
+      'panel_id' => array(
+        'description' => 'The primary identifier for this table.',
         'type' => 'int',
-        'not null' => TRUE
+        'not null' => TRUE,
       ),
-      'publish' => array (
+      'field_id' => array(
+        'description' => 'A bundle ID from the tripal_bundle table.',
         'type' => 'int',
         'not null' => TRUE,
-        'default' => 0
-      ),
-    ),
-    'primary key' => array (
-      0 => 'term_id'
-    ),
-    'foreign keys' => array (
-      'cvterm' => array (
-        'table' => 'cvterm',
-        'columns' => array (
-          'cvterm_id' => 'cvterm_id'
-        )
-      ),
-      'tripal_vocabulary' => array (
-        'table' => 'tripal_vocabulary',
-        'columns' => array (
-          'vocabulary_id' => 'vocabulary_id'
-        )
-      ),
-    ),
-    'unique keys' => array (
-      'tripal_term_unq' => array (
-        'vocabulary_id', 'cvterm_id'
       ),
     ),
     'indexes' => array(
-      'tripal_term_vocabulary_id' => array('vocabulary_id'),
-      'tripal_term_cvterm_id' => array('cvterm_id'),
-    ),
-  );
-  chado_create_custom_table('tripal_term', $schema, TRUE);
-}
-/**
- *
- */
-function tripal_entities_add_tripal_vocabulary_usage_table(){
-  $schema = array (
-    'table' => 'tripal_vocabulary_usage',
-    'fields' => array (
-      'vocabulary_usage_id' => array(
-        'type' => 'serial',
-        'not null' => TRUE
-      ),
-      'vocabulary_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
-      ),
-      'data_table' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
-      'type_table' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
-      'field' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
+      'panel_id' => array('panel_id'),
+      'field_id' => array('field_id'),
     ),
-    'primary key' => array (
-      0 => 'vocabulary_usage_id'
+    'unique keys' => array(
+      'panel_field' => array('panel_id', 'field_id'),
     ),
-    'foreign keys' => array (
-      'tripal_vocabulary' => array (
-        'table' => 'tripal_vocabulary',
-        'columns' => array (
-          'vocabulary_id' => 'vocabulary_id'
+    'foreign keys' => array(
+      'tripal_panel' => array(
+        'table' => 'tripal_panel',
+        'columns' => array(
+          'panel_id' => 'panel_id',
         ),
       ),
-    ),
-    'unique keys' => array (
-      'tripal_vocabulary_ridbase' => array (
-        'vocabulary_id', 'data_table'
+      'field_config' => array(
+        'table' => 'field_config',
+        'columns' => array(
+          'field_id' => 'id',
+        ),
       ),
     ),
-    'indexes' => array(
-      'tripal_vocabulary_vocabulary_id' => array('vocabulary_id'),
-      'tripal_vocabulary_data_table' => array('data_table'),
-      'tripal_vocabulary_type_table' => array('type_table'),
-    ),
+    'primary key' => array('panel_field_id'),
   );
-  chado_create_custom_table('tripal_vocabulary_usage', $schema, TRUE);
+  
+  return $schema;
 }
+
 /**
+ * Implements hook_uninstall().
  *
+ * At uninstall time we'll notify field.module that the entity was deleted
+ * so that attached fields can be cleaned up.
  */
-function tripal_entities_add_tripal_term_usage_table(){
-  $schema = array (
-    'table' => 'tripal_term_usage',
-    'fields' => array (
-      'term_usage_id' => array(
-        'type' => 'serial',
-        'not null' => TRUE
-      ),
-      'term_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
-      ),
-      'data_table' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
-      'type_table' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
-      'field' => array (
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => TRUE
-      ),
-    ),
-    'primary key' => array (
-      0 => 'term_usage_id'
-    ),
-    'foreign keys' => array (
-      'tripal_term' => array (
-        'table' => 'tripal_term',
-        'columns' => array (
-          'term_id' => 'term_id'
-        ),
-      ),
-    ),
-    'unique keys' => array (
-      'tripal_term_usage_ridbase' => array (
-        'term_id', 'type_table', 'field'
-      ),
-    ),
-    'indexes' => array(
-      'tripal_term_usage_term_id' => array('term_id'),
-    ),
-  );
-  chado_create_custom_table('tripal_term_usage', $schema, TRUE);
+function tripal_entities_uninstall() {
+  $terms = chado_generate_var('tripal_term', array('publish' => 1), array('return_array' => 1));
+  foreach ($terms as $term) {
+    $bundle_id = $term->cvterm_id->dbxref_id->db_id->name . '_' . $term->cvterm_id->dbxref_id->accession;
+    field_attach_delete_bundle('BioData', $bundle_id);
+  }
 }
+
 /**
- *
+ * @section
+ * Schema Definitions.
  */
-function tripal_entities_add_tripal_term_relationship_table(){
-  $schema = array (
-    'table' => 'tripal_term_relationship',
-    'fields' => array (
-      'relationship_id' => array(
-        'type' => 'serial',
-        'not null' => TRUE
-      ),
-      'subject_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
-      ),
-      'type_id' => array (
-        'type' => 'int',
-        'not null' => TRUE
-      ),
-      'object_id' => array (
-        'type' => 'int',
-        'not null' => FALSE
-      ),
-      'fieldname' => array(
-        'type' => 'varchar',
-        'length' => 128,
-        'not null' => FALSE,
-      )
-    ),
-    'primary key' => array (
-      0 => 'relationship_id'
-    ),
-    'foreign keys' => array (
-      'tripal_term' => array (
-        'table' => 'tripal_term',
-        'columns' => array (
-          'subject_id' => 'term_id',
-          'object_id'  => 'term_id',
-        ),
-      ),
-    ),
-    'unique keys' => array (
-      'tripal_term_relationship_unq' => array (
-        'subject_id', 'type_id', 'object_id'
-      ),
-    ),
-    'indexes' => array(
-      'tripal_term_relationship_subject_id' => array('subject_id'),
-      'tripal_term_relationship_object_id' => array('object_id'),
-      'tripal_term_relationship_type_id' => array('type_id'),
-    ),
-  );
-  chado_create_custom_table('tripal_term_relationship', $schema, TRUE);
-}
+
 /**
- * Implements hook_schema().
+ * The base table for Biological Data Entities.
  *
- * @ingroup entity_example
+ * This contains the actual data. For example, if you have a 5 genes and 10 mRNA then
+ * this table will have 15 records and include both genes and mRNA's.
  */
-function tripal_entities_schema() {
+function tripal_entities_tripal_entity_schema() {
 
-  $schema['tripal_entity'] = array(
+  $schema = array(
     'description' => 'The base table for Tripal Vocabulary-based entities.',
     'fields' => array(
       'id' => array(
@@ -373,8 +253,18 @@ function tripal_entities_schema() {
     ),
     'primary key' => array('id'),
   );
+  return $schema;
+}
 
-  $schema['tripal_bundle'] = array(
+/**
+ * The base table for Biological Data Type Entites.
+ * This table contains a list of Biological Data Types. 
+ * For the example above (5 genes and 10 mRNAs), there would only be two records in 
+ * this table one for "gene" and another for "mRNA".
+ */
+function tripal_entities_tripal_bundle_schema() {
+
+  $schema = array(
     'description' => 'Stores information about defined tripal data types.',
     'fields' => array(
       'id' => array(
@@ -410,185 +300,397 @@ function tripal_entities_schema() {
         'size' => 'tiny',
         'description' => 'The weight of this tripal data type in relation to others.',
       ),
-      'data' => array(
-        'type' => 'text',
-        'not null' => FALSE,
-        'size' => 'big',
-        'serialize' => TRUE,
-        'description' => 'A serialized array of additional data related to this tripal data type.',
+      'data' => array(
+        'type' => 'text',
+        'not null' => FALSE,
+        'size' => 'big',
+        'serialize' => TRUE,
+        'description' => 'A serialized array of additional data related to this tripal data type.',
+      ),
+    ) + entity_exportable_schema_fields(),
+    'primary key' => array('id'),
+    'unique keys' => array(
+      'bundle' => array('bundle'),
+    ),
+  );
+  return $schema;
+}
+
+/**
+ * Links Biological Data Entities to the chado "base" table the data is stored in.
+ * This is where we would specify that a particular gene maps to the record in the
+ * chado.feature table with a feature_id=2432;
+ */
+function tripal_entities_chado_entity_schema() {
+
+  $schema = array(
+    'description' => 'The linker table that associates an enitity from the public.tripal_entity table with a "base" record in Chado',
+    'fields' => array(
+      'chado_entity_id' => array(
+        'description' => 'The primary identifier for this table.',
+        'type' => 'serial',
+        'unsigned' => TRUE,
+        'not null' => TRUE,
+      ),
+      'entity_id' => array(
+        'description' => 'The unique entity id.',
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'record_id' => array(
+        'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
+        'type' => 'int',
+        'not null' => TRUE,
+      ),
+      'data_table' => array(
+        'description' => 'Indicates the table in Chado that this term services (e.g. feature, stock, library, etc.)',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'type_table' => array(
+        'description' => 'Sometimes the record in the data table doesn’t have a field that specifies  the record type.  For example, an analysis type is stored in the analysisprop table.  If the data_table does have a type field then this value will be the same as the data_table.',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE,
+        'default' => '',
+      ),
+      'field' => array(
+        'description' => 'The name of the field in the typetable that contains the cvterm record.',
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => FALSE,
+        'default' => ''
+      ),
+    ),
+    'indexes' => array(
+      'record_id' => array('record_id'),
+      'entity_id' => array('entity_id'),
+      'data_table' => array('data_table'),
+    ),
+    'unique keys' => array(
+      'record' => array('data_table', 'record_id'),
+      'entity_id' => array('entity_id'),
+    ),
+    'primary key' => array('chado_entity_id'),
+  );
+  return $schema;
+}
+
+/**
+ * A list of published vocabularies.
+ *
+ * Usage: This table will be used by the Entity type admin page that lets the site admin 
+ *   specify which vocabularies should be used as entity types.  This table will only be 
+ *   populated with vocabularies that are actually used within the Chado database.  This 
+ *   table will also be used by web services to provide a list of all of the entity types 
+ *   that are available for access.
+ */
+function tripal_entities_tripal_vocabulary_schema() {
+
+  $schema = array (
+    'table' => 'tripal_vocabulary',
+    'fields' => array (
+      'vocabulary_id' => array(
+        'type' => 'serial',
+        'not null' => TRUE
+      ),
+      'cv_id' => array (
+        'type' => 'int',
+        'not null' => TRUE
+      ),
+      'db_id' => array (
+        'type' => 'int',
+        'not null' => TRUE
+      ),
+      'publish' => array (
+        'type' => 'int',
+        'not null' => TRUE,
+        'default' => 0
+      ),
+    ),
+    'primary key' => array (
+      0 => 'vocabulary_id'
+    ),
+    'foreign keys' => array (
+      'cv' => array (
+        'table' => 'cv',
+        'columns' => array (
+          'cv_id' => 'cv_id'
+        )
+      ),
+      'db' => array (
+        'table' => 'db',
+        'columns' => array (
+          'db_id' => 'db_id'
+        )
+      ),
+    ),
+    'unique keys' => array (
+      'tripal_vocabulary_cvdb' => array (
+        'cv_id', 'db_id'
+      ),
+    ),
+    'indexes' => array(
+      'tripal_vocabulary_cv_id' => array('cv_id'),
+      'tripal_vocabulary_db_id' => array('db_id'),
+    )
+  );
+  return $schema;
+}
+
+/**
+ * A list of published terms.
+ *
+ * Usage: This table is used by web services to provide a list of all of the bundles 
+ *   (i.e. vocabulary terms) that have data in the site.   It is also used by the Entity 
+ *   administrative pages to allow the site admin to specify which terms should be 
+ *   publishable (i.e. used as bundles).
+ */
+function tripal_entities_tripal_term_schema() {
+
+  $schema = array (
+    'table' => 'tripal_term',
+    'fields' => array (
+      'term_id' => array(
+        'type' => 'serial',
+        'not null' => TRUE
+      ),
+      'vocabulary_id' => array (
+        'type' => 'int',
+        'not null' => TRUE
+      ),
+      'cvterm_id' => array (
+        'type' => 'int',
+        'not null' => TRUE
+      ),
+      'publish' => array (
+        'type' => 'int',
+        'not null' => TRUE,
+        'default' => 0
+      ),
+    ),
+    'primary key' => array (
+      0 => 'term_id'
+    ),
+    'foreign keys' => array (
+      'cvterm' => array (
+        'table' => 'cvterm',
+        'columns' => array (
+          'cvterm_id' => 'cvterm_id'
+        )
+      ),
+      'tripal_vocabulary' => array (
+        'table' => 'tripal_vocabulary',
+        'columns' => array (
+          'vocabulary_id' => 'vocabulary_id'
+        )
+      ),
+    ),
+    'unique keys' => array (
+      'tripal_term_unq' => array (
+        'vocabulary_id', 'cvterm_id'
       ),
-    ) + entity_exportable_schema_fields(),
-    'primary key' => array('id'),
-    'unique keys' => array(
-      'bundle' => array('bundle'),
+    ),
+    'indexes' => array(
+      'tripal_term_vocabulary_id' => array('vocabulary_id'),
+      'tripal_term_cvterm_id' => array('cvterm_id'),
     ),
   );
+  return $schema;
+}
 
-  $schema['chado_entity'] = array(
-    'description' => 'The linker table that associates an enitity from the public.tripal_entity table with a "base" record in Chado',
-    'fields' => array(
-      'chado_entity_id' => array(
-        'description' => 'The primary identifier for this table.',
+/**
+ * 
+ *
+ * Specifies the source table in Chado where this entity will pull data.  Because 
+ * vocabularies can be used in multiple tables there could be many entries here for each 
+ * vocabulary.
+ *
+ * Usage: This table is used by web services when querying for all of the records of a 
+ * given type.  Web services must know where to look for records of a given term.
+ */
+function tripal_entities_tripal_vocabulary_usage_schema(){
+
+  $schema = array (
+    'table' => 'tripal_vocabulary_usage',
+    'fields' => array (
+      'vocabulary_usage_id' => array(
         'type' => 'serial',
-        'unsigned' => TRUE,
-        'not null' => TRUE,
-      ),
-      'entity_id' => array(
-        'description' => 'The unique entity id.',
-        'type' => 'int',
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'record_id' => array(
-        'description' => 'The unique numerical identifier for the record that this entity is associated with (e.g. feature_id, stock_id, library_id, etc.).',
+      'vocabulary_id' => array (
         'type' => 'int',
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'data_table' => array(
-        'description' => 'Indicates the table in Chado that this term services (e.g. feature, stock, library, etc.)',
+      'data_table' => array (
         'type' => 'varchar',
         'length' => 128,
-        'not null' => TRUE,
-        'default' => '',
+        'not null' => TRUE
       ),
-      'type_table' => array(
-        'description' => 'Sometimes the record in the data table doesn’t have a field that specifies  the record type.  For example, an analysis type is stored in the analysisprop table.  If the data_table does have a type field then this value will be the same as the data_table.',
+      'type_table' => array (
         'type' => 'varchar',
         'length' => 128,
-        'not null' => TRUE,
-        'default' => '',
+        'not null' => TRUE
       ),
-      'field' => array(
-        'description' => 'The name of the field in the typetable that contains the cvterm record.',
+      'field' => array (
         'type' => 'varchar',
         'length' => 128,
-        'not null' => FALSE,
-        'default' => ''
+        'not null' => TRUE
       ),
     ),
-    'indexes' => array(
-      'record_id' => array('record_id'),
-      'entity_id' => array('entity_id'),
-      'data_table' => array('data_table'),
+    'primary key' => array (
+      0 => 'vocabulary_usage_id'
     ),
-    'unique keys' => array(
-      'record' => array('data_table', 'record_id'),
-      'entity_id' => array('entity_id'),
+    'foreign keys' => array (
+      'tripal_vocabulary' => array (
+        'table' => 'tripal_vocabulary',
+        'columns' => array (
+          'vocabulary_id' => 'vocabulary_id'
+        ),
+      ),
+    ),
+    'unique keys' => array (
+      'tripal_vocabulary_ridbase' => array (
+        'vocabulary_id', 'data_table'
+      ),
+    ),
+    'indexes' => array(
+      'tripal_vocabulary_vocabulary_id' => array('vocabulary_id'),
+      'tripal_vocabulary_data_table' => array('data_table'),
+      'tripal_vocabulary_type_table' => array('type_table'),
     ),
-    'primary key' => array('chado_entity_id'),
   );
+  return $schema;
+}
 
-  $schema['tripal_panels'] = array(
-    'description' => 'The list of panels into which fields can be placed.',
-    'fields' => array(
-      'panel_id' => array(
-        'description' => 'The primary identifier for this table.',
+/**
+ *
+ *
+ * Specifies the source table in Chado where this bundle will pull data.  Because terms 
+ * can be used in multiple tables there could be many entries here for each term. 
+ * 
+ * Note: this table contains the list of tables where a particular cvterm is used, 
+ * whereas, the tripal_entity_type_source just provides a list of where cvterms from a 
+ * particular vocabulary might be found.
+ */
+function tripal_entities_tripal_term_usage_schema() {
+
+  $schema = array (
+    'table' => 'tripal_term_usage',
+    'fields' => array (
+      'term_usage_id' => array(
         'type' => 'serial',
-        'unsigned' => TRUE,
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'bundle_id' => array(
-        'description' => 'A bundle ID from the tripal_bundle table.',
+      'term_id' => array (
         'type' => 'int',
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'name' => array(
-        'description' => 'The computer readable name for the panel. This name must only have alphanumerical characters and underscores and must not begin with a number. ',
+      'data_table' => array (
         'type' => 'varchar',
         'length' => 128,
-        'not null' => TRUE,
-        'default' => '',
+        'not null' => TRUE
       ),
-      'label' => array(
-        'description' => 'A human readable name for panel. This name will be shown to users in the sidebar menu.',
+      'type_table' => array (
         'type' => 'varchar',
         'length' => 128,
-        'not null' => TRUE,
-        'default' => '',
-      ),
-      'settings' => array(
-        'description' => 'Contains a serialized array tripal_fields_layoutof settings for the panel.',
-        'type' => 'text',
-        'not null' => FALSE,
+        'not null' => TRUE
       ),
-      'weight' => array(
-        'type' => 'int',
-        'not null' => FALSE,
-        'default' => 0
+      'field' => array (
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => TRUE
       ),
     ),
-    'indexes' => array(
-      'bundle_id' => array('bundle_id'),
-    ),
-    'unique keys' => array(
-      'bundle_panel' => array('bundle_id', 'name'),
+    'primary key' => array (
+      0 => 'term_usage_id'
     ),
-    'foreign keys' => array(
-      'tripal_bundle' => array(
-        'table' => 'tripal_bundle',
-        'columns' => array(
-          'bundle_id' => 'id',
+    'foreign keys' => array (
+      'tripal_term' => array (
+        'table' => 'tripal_term',
+        'columns' => array (
+          'term_id' => 'term_id'
         ),
       ),
     ),
-    'primary key' => array('panel_id'),
+    'unique keys' => array (
+      'tripal_term_usage_ridbase' => array (
+        'term_id', 'type_table', 'field'
+      ),
+    ),
+    'indexes' => array(
+      'tripal_term_usage_term_id' => array('term_id'),
+    ),
   );
+  return $schema;
+}
 
-  $schema['tripal_panel_fields'] = array(
-    'description' => 'The list of panels into which fields can be placed.',
-    'fields' => array(
-      'panel_field_id' => array(
-        'description' => 'The primary identifier for this table.',
+/**
+ *
+ *
+ * Specifies the predicates used for the semantic web for all properties of a bundle.
+ *
+ * Usage: When fields are added to an entity then there must be some “relationship” term 
+ * (i.e. predicate) that indicates the meaning of the relationship.  This predicate must 
+ * itself be a cvterm from a vocabulary.  For all fields that are automatically added to 
+ * bundles by tripal there should be a record here.  The site admin should be able to 
+ * change these if desired, but there should be some sort of default set by Tripal 
+ * itself.  This will require that all fields for all tables in Chado have some default 
+ * predicate value.  Also, relationship between two different bundles (whether published 
+ * or not) should also have a relationship predicate.  See the section in the 
+ * specification for how default predicates are set.
+ */
+function tripal_entities_tripal_term_relationship_schema() {
+
+  $schema = array (
+    'table' => 'tripal_term_relationship',
+    'fields' => array (
+      'relationship_id' => array(
         'type' => 'serial',
-        'unsigned' => TRUE,
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'panel_id' => array(
-        'description' => 'The primary identifier for this table.',
+      'subject_id' => array (
         'type' => 'int',
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
-      'field_id' => array(
-        'description' => 'A bundle ID from the tripal_bundle table.',
+      'type_id' => array (
         'type' => 'int',
-        'not null' => TRUE,
+        'not null' => TRUE
       ),
+      'object_id' => array (
+        'type' => 'int',
+        'not null' => FALSE
+      ),
+      'fieldname' => array(
+        'type' => 'varchar',
+        'length' => 128,
+        'not null' => FALSE,
+      )
     ),
-    'indexes' => array(
-      'panel_id' => array('panel_id'),
-      'field_id' => array('field_id'),
-    ),
-    'unique keys' => array(
-      'panel_field' => array('panel_id', 'field_id'),
+    'primary key' => array (
+      0 => 'relationship_id'
     ),
-    'foreign keys' => array(
-      'tripal_panel' => array(
-        'table' => 'tripal_panel',
-        'columns' => array(
-          'panel_id' => 'panel_id',
+    'foreign keys' => array (
+      'tripal_term' => array (
+        'table' => 'tripal_term',
+        'columns' => array (
+          'subject_id' => 'term_id',
+          'object_id'  => 'term_id',
         ),
       ),
-      'field_config' => array(
-        'table' => 'field_config',
-        'columns' => array(
-          'field_id' => 'id',
-        ),
+    ),
+    'unique keys' => array (
+      'tripal_term_relationship_unq' => array (
+        'subject_id', 'type_id', 'object_id'
       ),
     ),
-    'primary key' => array('panel_field_id'),
+    'indexes' => array(
+      'tripal_term_relationship_subject_id' => array('subject_id'),
+      'tripal_term_relationship_object_id' => array('object_id'),
+      'tripal_term_relationship_type_id' => array('type_id'),
+    ),
   );
   return $schema;
 }
-/**
- * Implements hook_uninstall().
- *
- * At uninstall time we'll notify field.module that the entity was deleted
- * so that attached fields can be cleaned up.
- */
-function tripal_entities_uninstall() {
-  $terms = chado_generate_var('tripal_term', array('publish' => 1), array('return_array' => 1));
-  foreach ($terms as $term) {
-    $bundle_id = $term->cvterm_id->dbxref_id->db_id->name . '_' . $term->cvterm_id->dbxref_id->accession;
-    field_attach_delete_bundle('BioData', $bundle_id);
-  }
-}
-

tripal_entities/tripal_entities.module

@@ -60,6 +60,7 @@ function tripal_entities_menu() {
 
 /**
  * Implements hook_admin_paths().
+ * Define administrative paths.
  */
 function tripal_entities_admin_paths() {
   if (variable_get('node_admin_theme')) {
@@ -72,11 +73,14 @@ function tripal_entities_admin_paths() {
     return $paths;
   }
 }
+
 /**
  * Implements hook_menu_local_tasks_alter().
+ * Used to add action links to pages.
  */
 function tripal_entities_menu_local_tasks_alter(&$data, $router_item, $root_path) {
-  // Add action link to 'BioData/add' on 'admin/content/BioData' page.
+
+  // Add an "Add Biological Data" action link to the Admin > Content > Biological Data page.
   if ($root_path == 'admin/content/BioData') {
     $item = menu_get_item('BioData/add');
     if ($item['access']) {
@@ -89,8 +93,15 @@ function tripal_entities_menu_local_tasks_alter(&$data, $router_item, $root_path
 }
 
 /**
+ * Implements hook_shortcut_default_set().
+ * Modify the shortcut menu to include Biological data links.
+ *
+ * @param object $account
+ *   The user account whose default shortcut set will be returned. If not provided, the 
+ *   function will return the currently logged-in user's default shortcut set.
  *
- * @param unknown $account
+ * @return
+ *   An object representing the default shortcut set.
  */
 function tripal_entities_shortcut_default_set($account) {
   $sets = shortcut_sets();
@@ -142,6 +153,7 @@ function tripal_entities_shortcut_default_set($account) {
  * Implements hook_permission().
  */
 function tripal_entities_permission() {
+
   // We set up permisssions to manage entity types, manage all entities and the
   // permissions for each individual entity
   $permissions = array(
@@ -154,6 +166,7 @@ function tripal_entities_permission() {
       'description' => t('Edit and delete all tripal data'),
     ),
   );
+  
   return $permissions;
 }