Merge branch '7.x-2.x' of git.drupal.org:sandbox/spficklin/1337878 into 7.x-2.x

tripal_api/DEPRECATED/tripal-2.0_pre-release.inc

@@ -93,6 +93,325 @@ function tripal_core_properties_form(&$form, &$form_state, $prop_table, $id_fiel
  * @ingroup tripal_properties_api
  */
 function tripal_core_properties_form_retreive($node, $cv_name) {
-
   return tripal_api_chado_node_properties_form_retreive($node);
+}
+
+/**
+ * Retrieve a property for a given base table record
+ *
+ * @param $basetable
+ *   The base table for which the property should be retrieved. Thus to retrieve a property
+ *   for a feature the basetable=feature and property is retrieved from featureprop
+ * @param $record_id
+ *   The foriegn key field of the base table. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of properties to be retrieved
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ *
+ * @return
+ *   An array in the same format as that generated by the function
+ *   tripal_core_generate_chado_var().  If only one record is returned it
+ *   is a single object.  If more than one record is returned then it is an array
+ *   of objects
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_get_property($basetable, $record_id, $property, $cv_name) {
+  return tripal_api_chado_get_property($basetable, $record_id, $property, $cv_name);
+}
+
+/**
+ * Insert a property for a given base table.  By default if the property already
+ * exists a new property is added with the next available rank.  If
+ * $update_if_present argument is specified then the record will be updated if it
+ * exists rather than adding a new property.
+ *
+ * @param $basetable
+ *   The base table for which the property should be inserted. Thus to insert a property
+ *   for a feature the basetable=feature and property is inserted into featureprop
+ * @param $record_id
+ *   The foriegn key value of the base table. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of properties to be inserted
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ * @param $update_if_present
+ *   A boolean indicating whether an existing record should be updated. If the
+ *   property already exists and this value is not specified or is zero then
+ *   a new property will be added with the next largest rank.
+ *
+ * @return
+ *   Return True on Insert/Update and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_insert_property($basetable, $record_id, $property,
+$cv_name, $value, $update_if_present = 0) {
+
+  return tripal_api_chado_insert_property($basetable, $record_id, $property,
+$cv_name, $value, $update_if_present);
+}
+
+/**
+ * Update a property for a given base table record and property name.  This
+ * function should be used only if one record of the property will be present.
+ * If the property name can have multiple entries (with increasing rank) then
+ * use the function named tripal_core_update_property_by_id
+ *
+ * @param $basetable
+ *   The base table for which the property should be updated. The property table
+ *   is constructed using  a combination of the base table name and the suffix
+ *   'prop' (e.g. basetable = feature then property tabie is featureprop).
+ * @param $record_id
+ *   The foreign key of the basetable to update a property for. This should be in integer.
+ *   For example, if the basetable is 'feature' then the $record_id should be the feature_id
+ * @param $property
+ *   The cvterm name of property to be updated
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ * @param $insert_if_missing
+ *   A boolean indicating whether a record should be inserted if one doesn't exist to update
+ *
+ * Note: The property to be updated is select via the unique combination of $record_id and
+ * $property and then it is updated with the supplied value
+ *
+ * @return
+ *   Return True on Update/Insert and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_update_property($basetable, $record_id, $property,
+$cv_name, $value, $insert_if_missing = 0) {
+
+  return tripal_api_chado_update_property($basetable, $record_id, $property,
+$cv_name, $value, $insert_if_missing);
+}
+
+/**
+ * Update a property for a given base table record.  This function should be
+ * used if multiple records of the same property will be present. Also, use this
+ * function to change the property name of an existing property.
+ *
+ * @param $basetable
+ *   The base table for which the property should be updated. The property table
+ *   is constructed using  a combination of the base table name and the suffix
+ *   'prop' (e.g. basetable = feature then property tabie is featureprop).
+ * @param $record_id
+ *   The primary key of the base table. This should be in integer.
+ *   For example, if the basetable is 'feature' then the $record_id should be the featureprop_id
+ * @param $property
+ *   The cvterm name of property to be updated
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ *
+ * @return
+ *   Return True on Update/Insert and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_update_property_by_id($basetable, $record_id, $property,
+$cv_name, $value) {
+
+  return tripal_api_chado_update_property_by_id($basetable, $record_id, $property,
+$cv_name, $value);
+}
+
+/**
+ * Deletes a property for a given base table record using the property name
+ *
+ * @param $basetable
+ *   The base table for which the property should be deleted. Thus to deleted a property
+ *   for a feature the basetable=feature and property is deleted from featureprop
+ * @param $record_id
+ *   The primary key of the basetable to delete a property for. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of property to be deleted
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ *
+ * Note: The property to be deleted is select via the unique combination of $record_id and $property
+ *
+ * @return
+ *   Return True on Delete and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_delete_property($basetable, $record_id, $property, $cv_name) {
+  return tripal_api_chado_delete_property($basetable, $record_id, $property, $cv_name);
+}
+
+/**
+ * Deletes a property using the property ID
+ *
+ * @param $basetable
+ *   The base table for which the property should be deleted. Thus to deleted a property
+ *   for a feature the basetable=feature and property is deleted from featureprop
+ * @param $record_id
+ *   The primary key of the basetable to delete a property for. This should be in integer.
+ *
+ * @return
+ *   Return True on Delete and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_core_delete_property_by_id($basetable, $record_id) {
+  return tripal_api_chado_delete_property_by_id($basetable, $record_id);
+}
+
+
+/**
+ * @section Database References API
+ */
+
+/**
+ * Provides a form for adding to BASE_dbxref and dbxref tables
+ *
+ * @param $form
+ *   The Drupal form array into which the dbxref elements will be added
+ * @param $form_state
+ *   The corresponding form_state array for the form
+ * @param $details
+ *   An array defining details needed by this form. Required Keys are:
+ *     - linking_table: the name of the dbxref linking table (ie: feature_dbxref)
+ *     - base_foreign_key: the name of the foreign key linking this table to the non-dbxref table (ie: feature_id)
+ *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
+ *   Optional keys include:
+ *     - fieldset_title: the non-translated title for this fieldset
+ *     - additional_instructions: a non-translated string providing additional instructions
+ */
+function tripal_core_additional_dbxrefs_form(&$form, &$form_state, $details) {
+  tripal_api_chado_node_additional_dbxrefs_form($form, $form_state, $details);
+}
+
+/**
+ * Function to theme the add/remove dbxrefs form into a table
+ */
+function theme_tripal_core_additional_dbxrefs_form_table($variables) {
+  return theme_tripal_api_chado_node_additional_dbxrefs_form_table($variables);
+}
+
+/**
+ * This function is used in a hook_insert, hook_update for a node form
+ * when the additional_dbxrefs form has been added to the form.  It retrieves all of the dbxrefs
+ * and returns them in an array of the format:
+ *
+ *   $dbxefs[<db_id>][<version>][<dbxref_id>] = <accession>
+ *
+ * This array can then be used for inserting or updating dbxrefs using the API call
+ * tripal_hook_insert_dbxref()
+ *
+ * @param $node
+ *
+ * @return
+ *   A dbxref array
+ *
+ * @ingroup tripal_databaserefernce_api
+ */
+function tripal_core_additional_dbxrefs_form_retreive($node) {
+  return tripal_api_chado_node_additional_dbxrefs_form_retreive($node);
+}
+
+/**
+ * This function is used in hook_insert or hook_update and handles inserting of any new
+ * dbxrefs and creation of links between those dbxrefs and node content
+ *
+ * @param $node
+ *    The node passed into hook_insert & hook_update
+ * @param $linking_table
+ *    The name of the _dbxref linking table (ie: feature_dbxref)
+ * @param $foreignkey_name
+ *    The name of the foreign key used to link to the node content (ie: feature_id)
+ * @param $foreignkey_value
+ *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ */
+function tripal_core_additional_dbxrefs_form_update_dbxrefs($node, $linking_table, $foreignkey_name, $foreignkey_value) {
+  tripal_api_chado_node_additional_dbxrefs_form_update_dbxrefs($node, $linking_table, $foreignkey_name, $foreignkey_value);
+}
+
+/**
+ * @section Relationships API
+ */
+
+/**
+ * Provides a form for adding to BASE_relationship and relationship tables
+ *
+ * @param $form
+ *   The Drupal form array into which the relationship elements will be added
+ * @param $form_state
+ *   The corresponding form_state array for the form
+ * @param $details
+ *   An array defining details needed by this form. Required Keys are:
+ *     - relationship_table: the name of the relationship table (ie: feature_relationship)
+ *     - base_table: the name of the base table (ie: feature)
+ *     - base_foreign_key: the name of the foreign key linking this table to the non-relationship table (ie: feature_id)
+ *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
+ *     - nodetype: the non-translated singular title of this node type
+ *   One of the following:
+ *     - cv_id: the id of the ontology to supply terms for the type dropdown
+ *     - cv_name: the name of the ontology to supply terms for the type dropdown
+ *   Optional keys include:
+ *     - fieldset_title: the non-translated title for this fieldset
+ *     - additional_instructions: a non-translated string providing additional instructions
+ *     - nodetype_plural: the non-translated plural title of this node type
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_core_relationships_form(&$form, &$form_state, $details) {
+  tripal_api_chado_node_relationships_form($form, $form_state, $details);
+}
+
+/**
+ * Function to theme the add/remove relationships form into a table
+ *
+ * @ingroup tripal_relationships_api
+ */
+function theme_tripal_core_relationships_form_table($variables) {
+  return theme_tripal_api_chado_node_relationships_form_table($variables);
+}
+
+/**
+ * This function is used in a hook_insert, hook_update for a node form
+ * when the relationships form has been added to the form.  It retrieves all of the relationships
+ * and returns them in an array of the format:
+ *
+ *   $relationships[<type_id>][<rank>] = array(
+ *         'subject_id' => <subject_id>,
+ *         'object_id'  => <object_id>,
+ *   );
+ *
+ * This array can then be used for inserting or updating relationships manually
+ *
+ * @param $node
+ *
+ * @return
+ *   A relationship array
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_core_relationships_form_retreive($node) {
+  tripal_api_chado_node_relationships_form_retreive($node);
+}
+
+/**
+ * This function is used in hook_insert or hook_update and handles inserting of
+ * relationships between the current nodetype and other memebers of the same nodetype
+ *
+ * @param $node
+ *    The node passed into hook_insert & hook_update
+ * @param $relationship_table
+ *    The name of the _relationship linking table (ie: feature_relationship)
+ * @param $current_id
+ *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_core_relationships_form_update_relationships($node, $relationship_table, $current_id) {
+  tripal_api_chado_node_relationships_form_update_relationships($node, $relationship_table, $current_id);
 }

tripal_api/chado_node_api/tripal_api.chado_node.references.inc

@@ -0,0 +1,597 @@
+<?php
+
+/**
+ * @file
+ * API to manage the chado _dbxref table for various Tripal Node Types
+ *
+ * How To Use:
+ * @code
+
+  function chado_example_form($form, $form_state) {
+
+    // Default values for form elements can come in the following ways:
+    //
+    // 1) as elements of the $node object.  This occurs when editing an existing node
+    // 2) in the $form_state['values'] array which occurs on a failed validation or
+    //    ajax callbacks when the ajax call originates from non-submit fields other
+    //    than button
+    // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
+    //    form elements (e.g. buttons) and the form is being rebuilt but has not yet
+    //    been validated
+    //
+    // The reference elements added by this function do use AJAX calls from buttons,
+    // therefore, it is important to check for form values in the $form_state['values']
+    // for case #2 above, and in the $form_state['input'] for case #3.
+    // See the chado analysis node form for an example.
+
+
+    // Next, add in all the form array definition particular to your node type
+
+    // To add in the additional database reference form elements, you first need to prepare the arguments
+    // for the function call.
+
+    $details = array(
+      'linking_table' => 'example_dbxref',         // the name of the table linking additional dbxrefs to this node
+      'base_foreign_key' => 'example_id',          // key to link to the chado content created by this node
+      'base_key_value' => $example_id,             // the value of the above key
+      'fieldset_title' => 'Additional References', // the non-translated title for this fieldset
+      'additional_instructions' => ''              // a non-stranslated string providing additional instructions
+    );
+
+    // Finally, and add the additional form elements to the form
+    tripal_api_chado_node_additional_dbxrefs_form($form, $form_state, $details);
+
+    return $form;
+  }
+
+  function chado_example_insert($node) {
+
+    // if there is an example_id in the $node object then this must be a sync so
+    // we can skip adding the chado_example as it is already there, although
+    // we do need to proceed with the rest of the insert
+    if (!property_exists($node, 'example_id')) {
+
+      // Add record to chado example table
+
+      // Add to any other tables needed
+
+      // Add all additional database references
+      // This function will create new database references as needed and select existing ones.
+      // Existing _dbxref links will be cleared and then re-added
+      tripal_api_chado_node_additional_dbxrefs_form_update_dbxrefs(
+        $node,              // the node object passed in via hook_insert()
+        'example_dbxref',   // the name of the _dbxref linking table
+        'example_id',       // key to link to the chado content created by this node
+        $node->example_id   // value of the above key
+      );
+    }
+
+    // Add record to chado_example linking example_id to new node
+
+  }
+
+  function chado_example_update($node) {
+
+
+      // Update record in chado example table
+
+      // Update any other tables needed
+
+      // Update all additional database references
+      // This function will create new database references as needed and select existing ones.
+      // Existing _dbxref links will be cleared and then re-added
+      tripal_api_chado_node_additional_dbxrefs_form_update_dbxrefs(
+        $node,              // the node object passed in via hook_insert()
+        'example_dbxref',   // the name of the _dbxref linking table
+        'example_id',       // key to link to the chado content created by this node
+        $node->example_id   // value of the above key
+      );
+
+    // Don't need to update chado_example linking table since niether example_id or nid can be changed in update
+
+  }
+
+ * @endcode
+ */
+
+/**
+ * @section
+ * Additional Database References Form to be added to node forms
+ */
+
+/**
+ * Provides a form for adding to BASE_dbxref and dbxref tables
+ *
+ * @param $form
+ *   The Drupal form array into which the dbxref elements will be added
+ * @param $form_state
+ *   The corresponding form_state array for the form
+ * @param $details
+ *   An array defining details needed by this form. Required Keys are:
+ *     - linking_table: the name of the dbxref linking table (ie: feature_dbxref)
+ *     - base_foreign_key: the name of the foreign key linking this table to the non-dbxref table (ie: feature_id)
+ *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
+ *   Optional keys include:
+ *     - fieldset_title: the non-translated title for this fieldset
+ *     - additional_instructions: a non-translated string providing additional instructions
+ */
+function tripal_api_chado_node_additional_dbxrefs_form(&$form, &$form_state, $details) {
+
+  // Set Defaults for optional fields
+  $details['fieldset_title'] = 'Additional Database References';
+  $details['additional_instructions'] = '';
+
+  // the fieldset of the dbxref elements
+  $form['addtl_dbxrefs'] = array(
+    '#type' => 'fieldset',
+    '#title' => t($details['fieldset_title']),
+    '#description' => t('You may add additional database references by
+      selecting a database reference type from the dropdown and adding text.  You may add
+      as many database references as desired by clicking the add button on the right.  To
+      remove a database reference, click the remove button. ' . $details['additional_instructions']),
+    '#prefix' => "<div id='addtl-dbxrefs-fieldset'>",
+    '#suffix' => '</div>'
+  );
+
+  // this form element is a tree, so that we don't puke all of the values into then node variable
+  // it is set as a tree, and keeps them in the $form_state['values']['dbxref_table'] heading.
+  $form['addtl_dbxrefs']['dbxref_table'] = array(
+    '#type' => 'markup',
+    '#tree' => TRUE,
+    '#prefix' => '<div id="tripal-generic-edit-addtl_dbxrefs-table">',
+    '#suffix' => '</div>',
+    '#theme' => 'tripal_api_chado_node_additional_dbxrefs_form_table'
+  );
+
+  /* DBxrefs can come to us in two ways:
+   *
+   * 1) In the form state in the $form_state['chado_additional_dbxrefs']. Data is in this field
+   *    when an AJAX call updates the form state or a validation error.
+   *
+   * 2) Directly from the database if the record already has dbxref's associated.  This
+   *    data is only used the first time the form is loaded. On AJAX calls or validation
+   *    errors the fields on the form are populated from the $form_state['chado_additional_dbxrefs']
+   *    entry.
+   */
+  if (isset($form_state['chado_additional_dbxrefs'])) {
+    $existing_dbxrefs = $form_state['chado_additional_dbxrefs'];
+  }
+  else {
+    $existing_dbxrefs = chado_query(
+      "SELECT dbxref.dbxref_id, db.name as db_name, db.db_id as db_id, dbxref.accession as accession, dbxref.description as description, dbxref.version
+        FROM {dbxref} dbxref
+        LEFT JOIN {db} db ON db.db_id = dbxref.db_id
+        LEFT JOIN {".$details['linking_table']."} linking_table ON linking_table.dbxref_id = dbxref.dbxref_id
+       WHERE linking_table.".$details['base_foreign_key']."= :base_key_value
+       ORDER BY db.name ASC, dbxref.version ASC",
+       array(':base_key_value' => $details['base_key_value'])
+    );
+  }
+
+  /* The format of the $existing_dbxref's array is either:
+   *
+   * From the chado_additional_dbxrefs array:
+   * $form_state['chado_additional_dbxrefs'] = array(
+   *   '[db_id]-[version]' => array(
+   *     'db_id' => [the db.db_id value]
+   *     'db_name' => [the db.name value]
+   *     'dbxref_id' => [the dbxref.dbxref_id value, or NULL if it doesn't yet exists],
+   *     'version' => [the dbxref.version value],
+   *     'accession' => [the dbxref.accession value],
+   *   ),
+   * );
+   *
+   * OR
+   * Populated from the database:
+   * $existing_dbxref = array(
+   *   0 => array(
+   *     'dbxref_id' => [the dbxref.dbxref_id value],
+   *     'db_name' => [the db.name value],
+   *     'db_id' => [the db.db_id value],
+   *     'accession' => [the dbxref.accession value],
+   *     'description' => [the dbxref.description value],
+   *     'version' => [the dbxref.versiion value],
+   *   ),
+   * );
+   *
+   * NOTE: The main difference is the key
+   *
+   * Loop on the array elements of the $existing_dbxrefs array and add
+   * an element to the form for each one.
+   */
+  foreach ($existing_dbxrefs as $dbxref) {
+
+    // Since the version is part of the key, when it is '' we need to use something
+    // in the key to indicate this case. Otherwise, you wouldn't be able to select
+    // those elements from the array (ie: $form['addtl_dbxrefs']['dbxref_table'][9999]['']
+    // doesn't work as expected whereas $form['addtl_dbxrefs']['dbxref_table'][9999][NONE]
+    // is much better)
+    $version = (!empty($dbxref->version)) ? $dbxref->version : 'NONE';
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id] = array(
+      '#type' => 'markup',
+      '#value' => ''
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version] = array(
+      '#type' => 'markup',
+      '#value' => ''
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['db_id'] = array(
+      '#type' => 'hidden',
+      '#value' => $dbxref->db_id
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['accession'] = array(
+      '#type' => 'hidden',
+      '#value' => $dbxref->accession
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['dbxref_id'] = array(
+      '#type' => 'hidden',
+      '#value' => $dbxref->dbxref_id
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['db'] = array(
+      '#type' => 'markup',
+      '#markup' => $dbxref->db_name
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['dbxref_version'] = array(
+      '#type' => 'markup',
+      '#markup' => $dbxref->version
+    );
+
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['dbxref_accession'] = array(
+      '#type' => 'markup',
+      '#markup' => $dbxref->accession
+    );
+    // remove button
+    $form['addtl_dbxrefs']['dbxref_table'][$dbxref->db_id][$version]['dbxref_action'] = array(
+      '#type' => 'submit',
+      '#value' => t('Remove'),
+      '#name' => "dbxref_remove-".$dbxref->db_id.'-'.$version,
+      '#ajax' => array(
+        'callback' => "tripal_api_chado_node_additional_dbxrefs_form_ajax_update",
+        'wrapper' => 'tripal-generic-edit-addtl_dbxrefs-table',
+        'effect'   => 'fade',
+        'method'   => 'replace',
+        'prevent'  => 'click'
+      ),
+      // When this button is clicked, the form will be validated and submitted.
+      // Therefore, we set custom submit and validate functions to override the
+      // default node form submit.  In the validate function we validate only the
+      // additional dbxref fields and in the submit we remove the indicated dbxref
+      // from the chado_additional_dbxrefs array. In order to keep validate errors
+      // from the node form validate and Drupal required errors for non-dbxref fields
+      // preventing the user from removing dbxrefs we set the #limit_validation_errors below
+      '#validate' => array('tripal_api_chado_node_additional_dbxrefs_form_remove_button_validate'),
+      '#submit' => array('tripal_api_chado_node_additional_dbxrefs_form_remove_button_submit'),
+      // Limit the validation of the form upon clicking this button to the dbxref_table tree
+      // No other fields will be validated (ie: no fields from the main form or any other api
+      // added form).
+      '#limit_validation_errors' => array(
+        array('dbxref_table')  // Validate all fields within $form_state['values']['dbxref_table']
+      )
+    );
+  }
+
+  // Form elements for adding a new dbxref
+  //---------------------------------------------
+  $form['addtl_dbxrefs']['dbxref_table']['new'] = array(
+    '#type' => 'markup',
+    '#prefix' => '<span class="addtl-dbxrefs-add-new-dbxref">',
+    '#suffix' => '</span>'
+  );
+
+  // add in the existing databases
+  $db_options = array(0 => 'Select a Database');
+  $select = tripal_core_chado_select('db', array('db_id','name'), array(), array('order_by' => array('name' => 'ASC')));
+  foreach($select as $db) {
+    $db_options[$db->db_id] = $db->name;
+  }
+  $form['addtl_dbxrefs']['dbxref_table']['new']['db'] = array(
+    '#type' => 'select',
+    '#options' => $db_options,
+  );
+
+  $form['addtl_dbxrefs']['dbxref_table']['new']['dbxref_accession'] = array(
+    '#type' => 'textfield',
+  );
+
+  $form['addtl_dbxrefs']['dbxref_table']['new']['dbxref_version'] = array(
+    '#type' => 'textfield',
+  );
+
+  // add button
+  $form['addtl_dbxrefs']['dbxref_table']['new']['dbxref_action'] = array(
+    '#type' => 'submit',
+    '#value' => t('Add'),
+    '#name' => "dbxref-add",
+    '#ajax' => array(
+      'callback' => "tripal_api_chado_node_additional_dbxrefs_form_ajax_update",
+      'wrapper' => 'tripal-generic-edit-addtl_dbxrefs-table',
+      'effect'   => 'fade',
+      'method'   => 'replace',
+      'prevent'  => 'click'
+    ),
+    // When this button is clicked, the form will be validated and submitted.
+    // Therefore, we set custom submit and validate functions to override the
+    // default node form submit.  In the validate function we validate only the
+    // additional dbxref fields and in the submit we add them to the chado_additional_dbxrefs
+    // array. In order to keep validate errors from the node form validate and Drupal
+    // required errors for non-dbxref fields preventing the user from adding dbxrefs we
+    // set the #limit_validation_errors below
+    '#validate' => array('tripal_api_chado_node_additional_dbxrefs_form_add_button_validate'),
+    '#submit' => array('tripal_api_chado_node_additional_dbxrefs_form_add_button_submit'),
+    // Limit the validation of the form upon clicking this button to the dbxref_table tree
+    // No other fields will be validated (ie: no fields from the main form or any other api
+    // added form).
+    '#limit_validation_errors' => array(
+      array('dbxref_table')  // Validate all fields within $form_state['values']['dbxref_table']
+    )
+  );
+
+}
+
+/**
+ * Validate the user input for creating a new dbxref
+ * Called by the add button in tripal_api_chado_node_additional_dbxrefs_form
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_add_button_validate($form, &$form_state) {
+
+  // Ensure the db_id is supplied & Valid
+  $db = tripal_core_chado_select(
+    'db',
+    array('db_id', 'name'),
+    array('db_id' => $form_state['values']['dbxref_table']['new']['db'])
+  );
+  if (!isset($db[0])) {
+    form_set_error('dbxref_table][new][db', 'Please select a database before attempting to add a new database reference.');
+  }
+  else {
+    $form_state['values']['dbxref_table']['new']['db_name'] = $db[0]->name;
+  }
+
+  // Ensure accession is supplied
+  if (empty($form_state['values']['dbxref_table']['new']['dbxref_accession'])) {
+    form_set_error('dbxref_table][new][dbxref_accession','You must enter the accession before attempting to add a new database reference.');
+  }
+}
+
+/**
+ * Called by the add button in tripal_api_chado_node_additional_dbxrefs_form
+ *
+ * Create an array of additional dbxrefs in the form state. This array will then be
+ * used to rebuild the form in subsequent builds
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_add_button_submit(&$form, &$form_state) {
+
+  // if the chado_additional_dbxrefs array is not set then this is the first time modifying the
+  // dbxref table. this means we need to include all the dbxrefs from the db
+  if (!isset($form_state['chado_additional_dbxrefs'])) {
+    tripal_api_chado_node_additional_dbxrefs_form_create_dbxref_formstate_array($form, $form_state);
+  }
+
+  // get details for the new dbxref
+  $dbxref = array(
+    'db_id' => $form_state['values']['dbxref_table']['new']['db'],
+    'db_name' => $form_state['values']['dbxref_table']['new']['db_name'],
+    'dbxref_id' => NULL,
+    'version' => $form_state['values']['dbxref_table']['new']['dbxref_version'],
+    'accession' => $form_state['values']['dbxref_table']['new']['dbxref_accession'],
+  );
+  $version = (!empty($dbxref['version'])) ? $dbxref['version'] : 'NONE';
+  $key = $dbxref['db_id'] . '-' . $version;
+  $form_state['chado_additional_dbxrefs'][$key] = (object) $dbxref;
+
+  $form_state['rebuild'] = TRUE;
+}
+
+/**
+ * There is no user input for the remove buttons so there is no need to validate
+ * However, both a submit & validate need to be specified so this is just a placeholder
+ *
+ * Called by the many remove buttons in tripal_api_chado_node_additional_dbxrefs_form
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_remove_button_validate($form, $form_state) {
+  // No Validation needed for remove
+}
+
+/**
+ * Remove the correct dbxref from the form
+ * Called by the many remove buttons in tripal_api_chado_node_additional_dbxrefs_form
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_remove_button_submit(&$form, &$form_state) {
+
+  // if the chado_additional_dbxrefs array is not set then this is the first time modifying the
+  // dbxref table. this means we need to include all the dbxrefs from the db
+  if (!isset($form_state['chado_additional_dbxrefs'])) {
+    tripal_api_chado_node_additional_dbxrefs_form_create_dbxref_formstate_array($form, $form_state);
+  }
+
+  // remove the specified dbxref from the form dbxref table
+  if(preg_match('/dbxref_remove-([^-]+-[^-]+)/',$form_state['triggering_element']['#name'],$match)) {
+    $key = $match[1];
+    if (array_key_exists($key, $form_state['chado_additional_dbxrefs'])) {
+      unset($form_state['chado_additional_dbxrefs'][$key]);
+    }
+  }
+
+  $form_state['rebuild'] = TRUE;
+}
+
+/**
+ * Ajax function which returns the section of the form to be re-rendered
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_ajax_update($form, $form_state) {
+  return $form['addtl_dbxrefs']['dbxref_table'];
+}
+
+/**
+ * Creates an array in form_state containing the existing addtl_dbxrefs. This array is
+ * then modified by the add/remove buttons and used as a source for rebuilding the form.
+ * This function get's called at each button (add and remove) button submits the first
+ * time one of the button's is clicked to instantiates the $form_state['chado_additional_dbxrefs'] array
+ *
+ * $form_state['chado_additional_dbxrefs'] = array(
+ *   '[db_id]-[version]' => array(
+ *     'db_id' => [the db.db_id value]
+ *     'db_name' => [the db.name value]
+ *     'dbxref_id' => [the dbxref.dbxref_id value, or NULL if it doesn't yet exists],
+ *     'version' => [the dbxref.version value],
+ *     'accession' => [the dbxref.accession value],
+ *   ),
+ * );
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_create_dbxref_formstate_array($form, &$form_state) {
+
+  $form_state['chado_additional_dbxrefs'] = array();
+
+  foreach (element_children($form['addtl_dbxrefs']['dbxref_table']) as $db_id) {
+    if ($db_id != 'new') {
+      foreach (element_children($form['addtl_dbxrefs']['dbxref_table'][$db_id]) as $version) {
+          $element = $form['addtl_dbxrefs']['dbxref_table'][$db_id][$version];
+          $dbxref = array(
+            'db_id' => $element['db_id']['#value'],
+            'db_name' => $element['db']['#markup'],
+            'dbxref_id' => $element['dbxref_id']['#value'],
+            'version' => $element['dbxref_version']['#markup'],
+            'accession' => $element['dbxref_accession']['#markup'],
+          );
+          $version = (!empty($dbxref['version'])) ? $dbxref['version'] : 'NONE';
+          $key = $dbxref['db_id'] . '-' . $version;
+          $form_state['chado_additional_dbxrefs'][$key] = (object) $dbxref;
+      }
+    }
+  }
+}
+
+/**
+ * Function to theme the add/remove dbxrefs form into a table
+ */
+function theme_tripal_api_chado_node_additional_dbxrefs_form_table($variables) {
+  $element = $variables['element'];
+
+  $header = array(
+    'db' => t('Database'),
+    'dbxref_accession' => t('Accession'),
+    'dbxref_version' => t('Version'),
+    'dbxref_action' => t('Actions'),
+  );
+
+  $rows = array();
+  foreach (element_children($element) as $db_id) {
+    if ($db_id == 'new') {
+      $row = array();
+
+        $row['data'] = array();
+        foreach ($header as $fieldname => $title) {
+          $row['data'][] = drupal_render($element[$db_id][$fieldname]);
+        }
+        $rows[] = $row;
+    }
+    else {
+      foreach (element_children($element[$db_id]) as $version) {
+        $row = array();
+
+        $row['data'] = array();
+        foreach ($header as $fieldname => $title) {
+          $row['data'][] = drupal_render($element[$db_id][$version][$fieldname]);
+        }
+        $rows[] = $row;
+      }
+    }
+  }
+
+  return theme('table', array(
+    'header' => $header,
+    'rows' => $rows
+  ));
+}
+
+/**
+ * This function is used in a hook_insert, hook_update for a node form
+ * when the additional_dbxrefs form has been added to the form.  It retrieves all of the dbxrefs
+ * and returns them in an array of the format:
+ *
+ *   $dbxefs[<db_id>][<version>][<dbxref_id>] = <accession>
+ *
+ * This array can then be used for inserting or updating dbxrefs using the API call
+ * tripal_hook_insert_dbxref()
+ *
+ * @param $node
+ *
+ * @return
+ *   A dbxref array
+ *
+ * @ingroup tripal_databaserefernce_api
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_retreive($node) {
+  $dbxrefs = array();
+  foreach ($node->dbxref_table as $db_id => $elements) {
+    if ($db_id != 'new') {
+      foreach ($elements as $version => $dbxref) {
+        $dbxref_id = (!empty($dbxref['dbxref_id'])) ? $dbxref['dbxref_id'] : 'NONE';
+        $dbxrefs[$db_id][$version][$dbxref_id] = $dbxref['accession'];
+      }
+    }
+  }
+
+  return $dbxrefs;
+}
+
+/**
+ * This function is used in hook_insert or hook_update and handles inserting of any new
+ * dbxrefs and creation of links between those dbxrefs and node content
+ *
+ * @param $node
+ *    The node passed into hook_insert & hook_update
+ * @param $linking_table
+ *    The name of the _dbxref linking table (ie: feature_dbxref)
+ * @param $foreignkey_name
+ *    The name of the foreign key used to link to the node content (ie: feature_id)
+ * @param $foreignkey_value
+ *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ */
+function tripal_api_chado_node_additional_dbxrefs_form_update_dbxrefs($node, $linking_table, $foreignkey_name, $foreignkey_value) {
+
+  // First remove existing dbxref links
+  tripal_core_chado_delete($linking_table, array($foreignkey_name => $foreignkey_value));
+
+  // Add back in dbxref links and insert dbxrefs as needed
+  $dbxrefs = tripal_api_chado_node_additional_dbxrefs_form_retreive($node);
+  foreach ($dbxrefs as $db_id => $versions) {
+    foreach ($versions as $version => $elements) {
+      foreach ($elements as $dbxref_id => $accession) {
+        // If there is no dbxref then we have to create that first
+        if ($dbxref_id == 'NONE') {
+          $version = ($version == 'NONE') ? '' : $version;
+          $success = tripal_db_add_dbxref(
+            $db_id,
+            $accession,
+            $version,
+            NULL
+          );
+          if ($success) {
+            $dbxref_id = $success->dbxref_id;
+          }
+          else {
+            $dbxref_id = FALSE;
+          }
+        }
+
+        // add _dbxref linker
+        if ($dbxref_id) {
+          $success_link = tripal_db_add_dbxref_link(
+            $linking_table,
+            $dbxref_id,
+            $foreignkey_name,
+            $foreignkey_value
+          );
+        }
+      }
+    }
+  }
+}

tripal_api/chado_node_api/tripal_api.chado_node.relationships.inc

@@ -0,0 +1,720 @@
+<?php
+
+/**
+ * @file
+ * API to manage the chado _relationship table for various Tripal Node Types
+ *
+ * How To Use:
+ * @code
+
+  function chado_example_form($form, $form_state) {
+
+    // Default values for form elements can come in the following ways:
+    //
+    // 1) as elements of the $node object.  This occurs when editing an existing node
+    // 2) in the $form_state['values'] array which occurs on a failed validation or
+    //    ajax callbacks when the ajax call originates from non-submit fields other
+    //    than button
+    // 3) in the $form_state['input'] array which occurs on ajax callbacks from submit
+    //    form elements (e.g. buttons) and the form is being rebuilt but has not yet
+    //    been validated
+    //
+    // The reference elements added by this function do use AJAX calls from buttons,
+    // therefore, it is important to check for form values in the $form_state['values']
+    // for case #2 above, and in the $form_state['input'] for case #3.
+    // See the chado analysis node form for an example.
+
+
+    // Next, add in all the form array definition particular to your node type
+
+    // To add in the relationship form elements, you first need to prepare the arguments
+    // for the function call.
+
+    $details = array(
+      'relationship_table' => 'example_relationship',    // the name of the table linking additional dbxrefs to this node
+      'base_table' => 'example',                         // the name of the chado table this node links to
+      'base_foreign_key' => 'example_id',                // key to link to the chado content created by this node
+      'base_key_value' => $example_id,                   // the value of the above key
+      'fieldset_title' => 'Relationships',               // the non-translated title for this fieldset
+      'additional_instructions' => ''                    // a non-stranslated string providing additional instructions
+    );
+
+    // Finally, and add the additional form elements to the form
+    tripal_api_chado_node_relationships_form($form, $form_state, $details);
+
+    return $form;
+  }
+
+  function chado_example_insert($node) {
+
+    // if there is an example_id in the $node object then this must be a sync so
+    // we can skip adding the chado_example as it is already there, although
+    // we do need to proceed with the rest of the insert
+    if (!property_exists($node, 'example_id')) {
+
+      // Add record to chado example table
+
+      // Add to any other tables needed
+
+      // Add all relationships
+      // Existing _relationship links with the current example as either the subject_id
+      // or object_id will be cleared and then re-added
+      tripal_api_chado_node_relationships_form_update_relationships(
+        $node,
+        'example_relationship',
+        $node->example_id
+      );
+    }
+
+    // Add record to chado_example linking example_id to new node
+
+  }
+
+  function chado_example_update($node) {
+
+
+      // Update record in chado example table
+
+      // Update any other tables needed
+
+      // Update all additional database references
+      // Existing _relationship links with the current example as either the subject_id
+      // or object_id will be cleared and then re-added
+      tripal_api_chado_node_relationships_form_update_relationships(
+        $node,
+        'example_relationship',
+        $node->example_id
+      );
+
+    // Don't need to update chado_example linking table since niether example_id or nid can be changed in update
+
+  }
+
+ * @endcode
+ */
+
+/**
+ * Provides a form for adding to BASE_relationship and relationship tables
+ *
+ * @param $form
+ *   The Drupal form array into which the relationship elements will be added
+ * @param $form_state
+ *   The corresponding form_state array for the form
+ * @param $details
+ *   An array defining details needed by this form. Required Keys are:
+ *     - relationship_table: the name of the relationship table (ie: feature_relationship)
+ *     - base_table: the name of the base table (ie: feature)
+ *     - base_foreign_key: the name of the foreign key linking this table to the non-relationship table (ie: feature_id)
+ *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
+ *     - nodetype: the non-translated singular title of this node type
+ *   One of the following:
+ *     - cv_id: the id of the ontology to supply terms for the type dropdown
+ *     - cv_name: the name of the ontology to supply terms for the type dropdown
+ *   Optional keys include:
+ *     - fieldset_title: the non-translated title for this fieldset
+ *     - additional_instructions: a non-translated string providing additional instructions
+ *     - nodetype_plural: the non-translated plural title of this node type
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form(&$form, &$form_state, $details) {
+
+  $form_state['rebuild'] = TRUE;
+
+  // Set Defaults for optional fields
+  $details['fieldset_title'] = (isset($details['fieldset_title'])) ? $details['fieldset_title'] : 'Relationships';
+  $details['additional_instructions'] = (isset($details['additional_instructions'])) ? $details['additional_instructions'] : '';
+  $details['nodetype_plural']  = (isset($details['nodetype_plural'])) ? $details['nodetype_plural'] : $details['nodetype'] . 's';
+
+  // Add defaults into form_state to be used elsewhere
+  $form['rel_details'] = array(
+    '#type' => 'hidden',
+    '#value' => serialize($details)
+  );
+
+  // Get relationship type options
+  if (isset($details['cv_id'])) {
+    $query = "SELECT cvterm_id, name FROM {cvterm} cvterm WHERE cv_id = :cv_id";
+    $result = chado_query($query, array(':cv_id' => $details['cv_id']));
+  } elseif (isset($details['cv_name'])) {
+    $query = "SELECT cvterm_id, name FROM {cvterm} cvterm WHERE cv_id IN (SELECT cv_id FROM cv WHERE name = :cv_name)";
+    $result = chado_query($query, array(':cv_name' => $details['cv_name']));
+  }
+  $type_options = array(0 => 'Select a Type');
+  foreach ($result as $cvterm) {
+    $type_options[ $cvterm->cvterm_id ] = $cvterm->name;
+  }
+
+  $form['relationships'] = array(
+    '#type' => 'fieldset',
+    '#title' => t($details['fieldset_title']),
+    '#description' => t('You may add relationships between this %nodetype and other
+      %nodetype_plural by entering the details below.  You may add
+      as many relationships as desired by clicking the add button on the right.  To
+      remove a relationship, click the remove button. ' . $details['additional_instructions'],
+      array('%nodetype' => $details['nodetype'], '%nodetype_plural' => $details['nodetype_plural'])),
+    '#prefix' => "<div id='relationships-fieldset'>",
+    '#suffix' => '</div>'
+  );
+
+  // this form element is a tree, so that we don't puke all of the values into then node variable
+  // it is set as a tree, and keeps them in the $form_state['values']['relationship_table'] heading.
+  $form['relationships']['relationship_table'] = array(
+    '#type' => 'markup',
+    '#tree' => TRUE,
+    '#prefix' => '<div id="tripal-generic-edit-relationships-table">',
+    '#suffix' => '</div>',
+    '#theme' => 'tripal_api_chado_node_relationships_form_table'
+  );
+
+  // Add relationships already attached to the node
+  //---------------------------------------------
+  /* Relationships can come to us in two ways:
+   *
+   * 1) In the form state in the $form_state['chado_relationships']. Data is in this field
+   *    when an AJAX call updates the form state or a validation error.
+   *
+   * 2) Directly from the database if the record already has _relationships associated.  This
+   *    data is only used the first time the form is loaded. On AJAX calls or validation
+   *    errors the fields on the form are populated from the $form_state['chado_relationships']
+   *    entry.
+   */
+  if (isset($form_state['chado_relationships'])) {
+    $existing_rels = $form_state['chado_relationships'];
+  }
+  else {
+    $existing_rels = chado_query(
+      "SELECT rel.*, base1.uniquename as object_name, base2.uniquename as subject_name, cvterm.name as type_name
+        FROM {".$details['relationship_table']."} rel
+        LEFT JOIN {".$details['base_table']."} base1 ON base1.".$details['base_foreign_key']." = rel.object_id
+        LEFT JOIN {".$details['base_table']."} base2 ON base2.".$details['base_foreign_key']." = rel.subject_id
+        LEFT JOIN {cvterm} cvterm ON cvterm.cvterm_id = rel.type_id
+        WHERE rel.object_id = :base_key_value OR rel.subject_id = :base_key_value",
+        array(':base_key_value' => $details['base_key_value'])
+    );
+  }
+
+  /* The format of the $existing_rels' array is either:
+   *
+   * From the chado_relationships array:
+   * $form_state['chado_relationships'] = array(
+   *   '[type_id]-[rank]' => array(
+   *     'object_id' => [the _relationship.object_id value],
+   *     'object_name' => [the base_table.uniquename value linked on base_foreign_key=object_id],
+   *     'subject_id' => [the _relationship.subject_id value],
+   *     'subject_name' => [the base_table.uniquename value linked on base_foreign_key=subject_id],
+   *     'type_id' => [the _relationship.type_id value],
+   *     'type_name' => [the cvterm.name value linked on type_id],
+   *     'rank' => [the _relationship.rank value],
+   *   ),
+   * );
+   *
+   * OR
+   * Populated from the database:
+   * $existing_rels = array(
+   *   0 => array(
+   *     'relationship_id' => [the _relationship.relationship_id value],
+   *     'object_id' => [the _relationship.object_id value],
+   *     'object_name' => [the base_table.uniquename value linked on base_foreign_key=object_id],
+   *     'subject_id' => [the _relationship.subject_id value],
+   *     'subject_name' => [the base_table.uniquename value linked on base_foreign_key=subject_id],
+   *     'type_id' => [the _relationship.type_id value],
+   *     'type_name' => [the cvterm.name value linked on type_id],
+   *     'rank' => [the _relationship.rank value],
+   *   ),
+   * );
+   *
+   * NOTE: The main difference is the key
+   *
+   * Loop on the array elements of the $existing_rels array and add
+   * an element to the form for each one.
+   */
+  foreach ($existing_rels as $relationship) {
+
+    $form['relationships']['relationship_table'][$relationship->type_id]['#type'] = 'markup';
+    $form['relationships']['relationship_table'][$relationship->type_id]['#type'] = '';
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['#type'] = 'markup';
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['#value'] = '';
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['object_id'] = array(
+      '#type' => 'hidden',
+      '#value' => $relationship->object_id
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['subject_id'] = array(
+      '#type' => 'hidden',
+      '#value' => $relationship->subject_id
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['type_id'] = array(
+      '#type' => 'hidden',
+      '#value' => $relationship->type_id
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['object_name'] = array(
+      '#type' => 'markup',
+      '#markup' => $relationship->object_name
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['type_name'] = array(
+      '#type' => 'markup',
+      '#markup' => $relationship->type_name
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['subject_name'] = array(
+      '#type' => 'markup',
+      '#markup' => $relationship->subject_name
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['rank'] = array(
+      '#type' => 'markup',
+      '#markup' => $relationship->rank
+    );
+
+    $form['relationships']['relationship_table'][$relationship->type_id][$relationship->rank]['rel_action'] = array(
+      '#type' => 'submit',
+      '#value' => t('Remove'),
+      '#name' => "rel_remove-".$relationship->type_id.'-'.$relationship->rank,
+      '#ajax' => array(
+        'callback' => 'tripal_api_chado_node_relationships_form_ajax_update',
+        'wrapper' => 'tripal-generic-edit-relationships-table',
+        'effect'   => 'fade',
+        'method'   => 'replace',
+        'prevent'  => 'click'
+      ),
+      // When this button is clicked, the form will be validated and submitted.
+      // Therefore, we set custom submit and validate functions to override the
+      // default node form submit.  In the validate function we validate only the
+      // relationship fields and in the submit we remove the indicated relationship
+      // from the chado_relationships array. In order to keep validate errors
+      // from the node form validate and Drupal required errors for non-relationship fields
+      // preventing the user from removing relationships we set the #limit_validation_errors below
+      '#validate' => array('tripal_api_chado_node_relationships_form_remove_button_validate'),
+      '#submit' => array('tripal_api_chado_node_relationships_form_remove_button_submit'),
+      // Limit the validation of the form upon clicking this button to the relationship_table tree
+      // No other fields will be validated (ie: no fields from the main form or any other api
+      // added form).
+      '#limit_validation_errors' => array(
+        array('relationship_table')  // Validate all fields within $form_state['values']['relationship_table']
+      )
+    );
+  }
+
+  $form['relationships']['relationship_table']['new']['object_name'] = array(
+    '#type' => 'textfield',
+  );
+
+  $form['relationships']['relationship_table']['new']['object_is_current'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Current '.$details['nodetype']),
+  );
+
+  $form['relationships']['relationship_table']['new']['type_name'] = array(
+    '#type' => 'select',
+    '#options' => $type_options,
+  );
+
+  $form['relationships']['relationship_table']['new']['subject_name'] = array(
+    '#type' => 'textfield',
+  );
+
+  $form['relationships']['relationship_table']['new']['subject_is_current'] = array(
+    '#type' => 'checkbox',
+    '#title' => t('Current '.$details['nodetype']),
+  );
+
+  $form['relationships']['relationship_table']['new']['rank'] = array(
+    '#type' => 'markup',
+    '#markup' => ''
+  );
+
+  $form['relationships']['relationship_table']['new']['rel_action'] = array(
+    '#type' => 'submit',
+    '#value' => t('Add'),
+    '#name' => 'rel_add',
+    '#ajax' => array(
+      'callback' => 'tripal_api_chado_node_relationships_form_ajax_update',
+      'wrapper' => 'tripal-generic-edit-relationships-table',
+      'effect'   => 'fade',
+      'method'   => 'replace',
+      'prevent'  => 'click'
+    ),
+    // When this button is clicked, the form will be validated and submitted.
+    // Therefore, we set custom submit and validate functions to override the
+    // default node form submit.  In the validate function we validate only the
+    // relationship fields and in the submit we add them to the chado_relationships
+    // array. In order to keep validate errors from the node form validate and Drupal
+    // required errors for non-relationship fields preventing the user from adding relationships we
+    // set the #limit_validation_errors below
+    '#validate' => array('tripal_api_chado_node_relationships_form_add_button_validate'),
+    '#submit' => array('tripal_api_chado_node_relationships_form_add_button_submit'),
+    // Limit the validation of the form upon clicking this button to the relationship_table tree
+    // No other fields will be validated (ie: no fields from the main form or any other api
+    // added form).
+    '#limit_validation_errors' => array(
+      array('relationship_table')  // Validate all fields within $form_state['values']['relationship_table']
+    )
+  );
+
+}
+
+/**
+ * Validate the user input for creating a new relationship
+ * Called by the add button in tripal_api_chado_node_relationships_form
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_add_button_validate($form, &$form_state) {
+
+  $details = unserialize($form_state['values']['rel_details']);
+
+  // At least one of the participants must be the current node
+  if (!($form_state['values']['relationship_table']['new']['subject_is_current'] OR $form_state['values']['relationship_table']['new']['object_is_current'])) {
+    // If the checkbox isn't set then check to see if either has the same uniquename as the node
+    if ($form_state['values']['relationship_table']['new']['subject_name'] == $form_state['values']['uniquename']) {
+      $form_state['values']['relationship_table']['new']['subject_is_current'] = 1;
+      form_set_error('subject_is_current', 'To set the current '.$details['nodetype'].', select the
+        checkbox. You entered the unique name of the current '.$details['nodetype'].' as the subject,
+        is this what you meant to do?');
+    }
+    elseif ($form_state['values']['relationship_table']['new']['subject_name'] == $form_state['values']['uniquename']) {
+      $form_state['values']['relationship_table']['new']['object_is_current'] = 1;
+      form_set_error('subject_is_current', 'To set the current '.$details['nodetype'].', select the
+        checkbox. You entered the unique name of the current '.$details['nodetype'].' as the subject,
+        is this what you meant to do?');
+    }
+    else {
+      form_set_error('object_is_current', 'At least one member of the relationship must be
+        the current '.$details['nodetype'].'. This is specified by checking the "Current '.$details['nodetype'].'"
+        checkbox for either the subject or object.');
+    }
+  }
+
+  // The non-current uniquename must be exist in the base table (subject)
+  if (!($form_state['values']['relationship_table']['new']['subject_is_current'])) {
+    $result = tripal_core_chado_select(
+      $details['base_table'],
+      array($details['base_foreign_key']),
+      array('uniquename' => $form_state['values']['relationship_table']['new']['subject_name'])
+    );
+    if (!isset($result[0])) {
+      form_set_error('subject_name', 'The subject must be the unique name of an
+        existing '.$details['nodetype'].' unless the "Current '.$details['nodetype'].'" checkbox is selected');
+    }
+    else {
+      $form_state['values']['relationship_table']['new']['subject_id'] = $result[0]->{$details['base_foreign_key']};
+    }
+  }
+
+  // The non-current uniquename must exist in the base table (object)
+  if (!($form_state['values']['relationship_table']['new']['object_is_current'])) {
+    $result = tripal_core_chado_select(
+      $details['base_table'],
+      array($details['base_foreign_key']),
+      array('uniquename' => $form_state['values']['relationship_table']['new']['object_name'])
+    );
+    if (!isset($result[0])) {
+      form_set_error('object_name', 'The object must be the unique name of an
+        existing '.$details['nodetype'].' unless the "Current '.$details['nodetype'].'" checkbox is selected');
+    }
+    else {
+      $form_state['values']['relationship_table']['new']['object_id'] = $result[0]->{$details['base_foreign_key']};
+    }
+  }
+
+  // The type must be a valid cvterm
+  if ($form_state['values']['relationship_table']['new']['type_name']) {
+    $form_state['values']['relationship_table']['new']['type_id'] = $form_state['values']['relationship_table']['new']['type_name'];
+    $result = tripal_core_chado_select(
+      'cvterm',
+      array('name'),
+      array('cvterm_id' => $form_state['values']['relationship_table']['new']['type_id'])
+    );
+    if (!isset($result[0])) {
+      form_set_error('type_id', 'The select type is not a valid controlled vocabulary term.');
+    }
+    else {
+      $form_state['values']['relationship_table']['new']['type_name'] = $result[0]->name;
+    }
+  }
+  else {
+    form_set_error('type_id', 'Please select a type of relationship');
+  }
+}
+
+/**
+ * Called by the add button in tripal_api_chado_node_relationships_form
+ *
+ * Create an array of additional relationships in the form state. This array will then be
+ * used to rebuild the form in subsequent builds
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_add_button_submit(&$form, &$form_state) {
+
+  $details = unserialize($form_state['values']['rel_details']);
+
+  // if the chado_relationships array is not set then this is the first time modifying the
+  // relationship table. this means we need to include all the relationships from the db
+  if (!isset($form_state['chado_relationships'])) {
+    tripal_api_chado_node_relationships_form_create_relationship_formstate_array($form, $form_state);
+  }
+
+  // get details for the new relationship
+  if ($form_state['values']['relationship_table']['new']['subject_is_current']) {
+
+    $relationship = array(
+      'type_id' => $form_state['values']['relationship_table']['new']['type_id'],
+      'object_id' => $form_state['values']['relationship_table']['new']['object_id'],
+      'subject_id' => $form_state['values'][ $details['base_foreign_key'] ],
+      'type_name' => $form_state['values']['relationship_table']['new']['type_name'],
+      'object_name' => $form_state['values']['relationship_table']['new']['object_name'],
+      'subject_name' => $form_state['values']['uniquename'],
+      'rank' => '0'
+    );
+  }
+  else {
+    $relationship = array(
+      'type_id' => $form_state['values']['relationship_table']['new']['type_id'],
+      'object_id' => $form_state['values'][ $details['base_foreign_key'] ],
+      'subject_id' => $form_state['values']['relationship_table']['new']['subject_id'],
+      'type_name' => $form_state['values']['relationship_table']['new']['type_name'],
+      'object_name' => $form_state['values']['uniquename'],
+      'subject_name' => $form_state['values']['relationship_table']['new']['subject_name'],
+      'rank' => '0'
+    );
+  }
+
+  // get max rank
+  $rank = tripal_core_get_max_chado_rank(
+    $details['relationship_table'],
+    array(
+      'subject_id' => $relationship['subject_id'],
+      'type_id' => $relationship['type_id'],
+      'object_id' => $relationship['object_id'],
+    )
+  );
+  $relationship['rank'] = strval($rank + 1);
+
+  $key = $relationship['type_id'] . '-' . $relationship['rank'];
+  $form_state['chado_relationships'][$key] = (object) $relationship;
+
+  $form_state['rebuild'] = TRUE;
+}
+
+/**
+ * There is no user input for the remove buttons so there is no need to validate
+ * However, both a submit & validate need to be specified so this is just a placeholder
+ *
+ * Called by the many remove buttons in tripal_api_chado_node_relationships_form
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_remove_button_validate($form, $form_state) {
+  // No Validation needed for remove
+}
+
+/**
+ * Remove the correct relationship from the form
+ * Called by the many remove buttons in tripal_api_chado_node_relationships_form
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_remove_button_submit(&$form, &$form_state) {
+
+  // if the chado_relationships array is not set then this is the first time modifying the
+  // relationship table. this means we need to include all the relationships from the db
+  if (!isset($form_state['chado_relationships'])) {
+    tripal_api_chado_node_relationships_form_create_relationship_formstate_array($form, $form_state);
+  }
+
+  // @TODO: Test that this actually works
+
+  // remove the specified relationship from the form relationship table
+  if(preg_match('/rel_remove-([^-]+-[^-]+)/',$form_state['triggering_element']['#name'],$match)) {
+    $key = $match[1];
+    if (array_key_exists($key, $form_state['chado_relationships'])) {
+      unset($form_state['chado_relationships'][$key]);
+    }
+  }
+
+  $form_state['rebuild'] = TRUE;
+}
+
+/**
+ * Ajax function which returns the section of the form to be re-rendered
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_ajax_update($form, $form_state) {
+  return $form['relationships']['relationship_table'];
+}
+
+/**
+ * Creates an array in form_state containing the existing relationships. This array is
+ * then modified by the add/remove buttons and used as a source for rebuilding the form.
+ *
+ * $form_state['chado_relationships'] = array(
+ *   '[type_id]-[rank]' => array(
+ *     'object_id' => [the _relationship.object_id value],
+ *     'object_name' => [the base_table.uniquename value linked on base_foreign_key=object_id],
+ *     'subject_id' => [the _relationship.subject_id value],
+ *     'subject_name' => [the base_table.uniquename value linked on base_foreign_key=subject_id],
+ *     'type_id' => [the _relationship.type_id value],
+ *     'type_name' => [the cvterm.name value linked on type_id],
+ *     'rank' => [the _relationship.rank value],
+ *   ),
+ * );
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_create_relationship_formstate_array($form, &$form_state) {
+
+  $form_state['chado_relationships'] = array();
+
+  foreach (element_children($form['relationships']['relationship_table']) as $type_id) {
+    if ($type_id != 'new') {
+      foreach (element_children($form['relationships']['relationship_table'][$type_id]) as $rank) {
+          $element = $form['relationships']['relationship_table'][$type_id][$rank];
+          $rel = array(
+            'type_id' => $element['type_id']['#value'],
+            'object_id' => $element['object_id']['#value'],
+            'subject_id' => $element['subject_id']['#value'],
+            'type_name' => $element['type_name']['#markup'],
+            'object_name' => $element['object_name']['#markup'],
+            'subject_name' => $element['subject_name']['#markup'],
+            'rank' => $element['rank']['#markup']
+          );
+          $key = $rel['type_id'] . '-' . $rel['rank'];
+          $form_state['chado_relationships'][$key] = (object) $rel;
+      }
+    }
+  }
+}
+
+/**
+ * Function to theme the add/remove relationships form into a table
+ *
+ * @ingroup tripal_relationships_api
+ */
+function theme_tripal_api_chado_node_relationships_form_table($variables) {
+  $element = $variables['element'];
+
+  $header = array(
+    'object_name' => t('Object Unique Name'),
+    'type_name' => t('Type'),
+    'subject_name' => t('Subject Unique Name'),
+    'rank' => t('Rank'),
+    'rel_action' => t('Action')
+  );
+
+  $rows = array();
+  foreach (element_children($element) as $type_id) {
+    if ($type_id == 'new') {
+      $row = array();
+
+        $row['data'] = array();
+        foreach ($header as $fieldname => $title) {
+          if ($fieldname == 'subject_name') {
+            $row['data'][] = drupal_render($element[$type_id][$fieldname]) . drupal_render($element[$type_id]['subject_is_current']);
+          }
+          elseif ($fieldname == 'object_name') {
+            $row['data'][] = drupal_render($element[$type_id][$fieldname]) . drupal_render($element[$type_id]['object_is_current']);
+          }
+          else {
+            $row['data'][] = drupal_render($element[$type_id][$fieldname]);
+          }
+        }
+        $rows[] = $row;
+    }
+    else {
+      foreach (element_children($element[$type_id]) as $rank) {
+        $row = array();
+
+        $row['data'] = array();
+        foreach ($header as $fieldname => $title) {
+          $row['data'][] = drupal_render($element[$type_id][$rank][$fieldname]);
+        }
+        $rows[] = $row;
+      }
+    }
+  }
+
+  return theme('table', array(
+    'header' => $header,
+    'rows' => $rows
+  ));
+}
+
+/**
+ * This function is used in a hook_insert, hook_update for a node form
+ * when the relationships form has been added to the form.  It retrieves all of the relationships
+ * and returns them in an array of the format:
+ *
+ *   $relationships[<type_id>][<rank>] = array(
+ *         'subject_id' => <subject_id>,
+ *         'object_id'  => <object_id>,
+ *   );
+ *
+ * This array can then be used for inserting or updating relationships manually
+ *
+ * @param $node
+ *
+ * @return
+ *   A relationship array
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_retreive($node) {
+  $rels = array();
+  foreach ($node->rel_table as $type_id => $elements) {
+    if ($type_id != 'new') {
+      foreach ($elements as $rank => $relationships) {
+        $rels[$type_id][$rank]['subject_id'] = $relationships['subject_id'];
+        $rels[$type_id][$rank]['object_id'] = $relationships['object_id'];
+      }
+    }
+  }
+
+  return $rels;
+}
+
+/**
+ * This function is used in hook_insert or hook_update and handles inserting of
+ * relationships between the current nodetype and other memebers of the same nodetype
+ *
+ * @param $node
+ *    The node passed into hook_insert & hook_update
+ * @param $relationship_table
+ *    The name of the _relationship linking table (ie: feature_relationship)
+ * @param $current_id
+ *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ *
+ * @ingroup tripal_relationships_api
+ */
+function tripal_api_chado_node_relationships_form_update_relationships($node, $relationship_table, $current_id) {
+
+  // First remove existing relationships links
+  tripal_core_chado_delete($relationship_table, array('subject_id' => $current_id));
+  tripal_core_chado_delete($relationship_table, array('object_id' => $current_id));
+
+  // Add back in dbxref links and insert dbxrefs as needed
+  $relationships = tripal_api_chado_node_relationships_form_retreive($node);
+  foreach ($relationships as $type_id => $ranks) {
+    foreach ($ranks as $rank => $element) {
+
+      // add relationship
+      $success_link = tripal_core_chado_insert(
+        $relationship_table,
+        array(
+          'subject_id' => $element['subject_id'],
+          'type_id' => $type_id,
+          'object_id' => $element['object_id'],
+          'rank' => $rank
+        )
+      );
+
+    }
+  }
+}

tripal_api/chado_query_api/tripal_api.chado_query.manage_properties.inc

@@ -0,0 +1,335 @@
+<?php
+
+/**
+ * @file
+ * Functions to insert/update delete records in any prop table
+ */
+
+/**
+ * Retrieve a property for a given base table record
+ *
+ * @param $basetable
+ *   The base table for which the property should be retrieved. Thus to retrieve a property
+ *   for a feature the basetable=feature and property is retrieved from featureprop
+ * @param $record_id
+ *   The foriegn key field of the base table. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of properties to be retrieved
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ *
+ * @return
+ *   An array in the same format as that generated by the function
+ *   tripal_api_chado_generate_chado_var().  If only one record is returned it
+ *   is a single object.  If more than one record is returned then it is an array
+ *   of objects
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_get_property($basetable, $record_id, $property, $cv_name) {
+  // get the foreign key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
+
+  // construct the array of values to be selected
+  $values = array(
+    $fkcol => $record_id,
+    'type_id' => array(
+      'cv_id' => array(
+        'name' => $cv_name,
+      ),
+      'name' => $property,
+      'is_obsolete' => 0
+    ),
+  );
+  $results = tripal_api_chado_generate_chado_var($basetable . 'prop', $values);
+  if ($results) {
+    $results = tripal_api_chado_expand_chado_vars($results, 'field', $basetable . 'prop.value');
+  }
+
+  return $results;
+}
+
+/**
+ * Insert a property for a given base table.  By default if the property already
+ * exists a new property is added with the next available rank.  If
+ * $update_if_present argument is specified then the record will be updated if it
+ * exists rather than adding a new property.
+ *
+ * @param $basetable
+ *   The base table for which the property should be inserted. Thus to insert a property
+ *   for a feature the basetable=feature and property is inserted into featureprop
+ * @param $record_id
+ *   The foriegn key value of the base table. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of properties to be inserted
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ * @param $update_if_present
+ *   A boolean indicating whether an existing record should be updated. If the
+ *   property already exists and this value is not specified or is zero then
+ *   a new property will be added with the next largest rank.
+ *
+ * @return
+ *   Return True on Insert/Update and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_insert_property($basetable, $record_id, $property,
+$cv_name, $value, $update_if_present = 0) {
+
+  // first see if the property already exists, if the user want's to update
+  // then we can do that, but otherwise we want to increment the rank and
+  // insert
+  $props = tripal_api_chado_get_property($basetable, $record_id, $property, $cv_name);
+  if (!is_array($props) and $props) {
+    $props = array($props);
+  }
+
+  $rank = 0;
+  if (count($props) > 0) {
+    if ($update_if_present) {
+      return tripal_api_chado_update_property($basetable, $record_id, $property, $cv_name, $value);
+    }
+    else {
+      // iterate through the properties returned and check to see if the
+      // property with this value already exists if not, get the largest rank
+      // and insert the same property but with this new value
+      foreach ($props as $p) {
+        if ($p->rank > $rank) {
+          $rank = $p->rank;
+        }
+        if (strcmp($p->value, $value) == 0) {
+          return TRUE;
+        }
+      }
+      // now add 1 to the rank
+      $rank++;
+    }
+  }
+
+  // make sure the cvterm exists.  Otherwise we'll get an error with
+  // prepared statements not matching
+  $values = array(
+    'cv_id' => array(
+      'name' => $cv_name,
+    ),
+    'name' => $property,
+  );
+
+  $options = array();
+  $term = tripal_api_chado_chado_select('cvterm', array('cvterm_id'), $values, $options);
+  if (!$term or count($term) == 0) {
+    watchdog('tripal_api_chado', "Cannot find property '%prop_name' in vocabulary '%cvname'.",
+    array('%prop_name' => $property, '%cvname' => $cv_name), WATCHDOG_ERROR);
+    return FALSE;
+  }
+
+  // get the foreign key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
+
+  // construct the array of values to be inserted
+  $values = array(
+    $fkcol => $record_id,
+    'type_id' => array(
+      'cv_id' => array(
+        'name' => $cv_name,
+      ),
+      'name' => $property,
+    ),
+    'value' => $value,
+    'rank' => $rank,
+  );
+
+  $options = array();
+  $result = tripal_api_chado_chado_insert($basetable . 'prop', $values, $options);
+  return $result;
+}
+
+/**
+ * Update a property for a given base table record and property name.  This
+ * function should be used only if one record of the property will be present.
+ * If the property name can have multiple entries (with increasing rank) then
+ * use the function named tripal_api_chado_update_property_by_id
+ *
+ * @param $basetable
+ *   The base table for which the property should be updated. The property table
+ *   is constructed using  a combination of the base table name and the suffix
+ *   'prop' (e.g. basetable = feature then property tabie is featureprop).
+ * @param $record_id
+ *   The foreign key of the basetable to update a property for. This should be in integer.
+ *   For example, if the basetable is 'feature' then the $record_id should be the feature_id
+ * @param $property
+ *   The cvterm name of property to be updated
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ * @param $insert_if_missing
+ *   A boolean indicating whether a record should be inserted if one doesn't exist to update
+ *
+ * Note: The property to be updated is select via the unique combination of $record_id and
+ * $property and then it is updated with the supplied value
+ *
+ * @return
+ *   Return True on Update/Insert and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_update_property($basetable, $record_id, $property,
+$cv_name, $value, $insert_if_missing = 0) {
+
+  // first see if the property is missing (we can't update a missing property
+  $prop = tripal_api_chado_get_property($basetable, $record_id, $property, $cv_name);
+  if (count($prop)==0) {
+    if ($insert_if_missing) {
+      return tripal_api_chado_insert_property($basetable, $record_id, $property, $cv_name, $value);
+    }
+    else {
+      return FALSE;
+    }
+  }
+
+  // get the foreign key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
+
+  // construct the array that will match the exact record to update
+  $match = array(
+    $fkcol => $record_id,
+    'type_id' => array(
+      'cv_id' => array(
+        'name' => $cv_name,
+      ),
+      'name' => $property,
+    ),
+  );
+
+  // construct the array of values to be updated
+  $values = array(
+    'value' => $value,
+  );
+
+  return tripal_api_chado_chado_update($basetable . 'prop', $match, $values);
+}
+
+/**
+ * Update a property for a given base table record.  This function should be
+ * used if multiple records of the same property will be present. Also, use this
+ * function to change the property name of an existing property.
+ *
+ * @param $basetable
+ *   The base table for which the property should be updated. The property table
+ *   is constructed using  a combination of the base table name and the suffix
+ *   'prop' (e.g. basetable = feature then property tabie is featureprop).
+ * @param $record_id
+ *   The primary key of the base table. This should be in integer.
+ *   For example, if the basetable is 'feature' then the $record_id should be the featureprop_id
+ * @param $property
+ *   The cvterm name of property to be updated
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ * @param $value
+ *   The value of the property to be inserted (can be empty)
+ *
+ * @return
+ *   Return True on Update/Insert and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_update_property_by_id($basetable, $record_id, $property,
+$cv_name, $value) {
+
+  // get the primary key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $pkcol = $table_desc['primary key'][0];
+
+  // construct the array that will match the exact record to update
+  $match = array(
+    $pkcol => $record_id,
+  );
+
+  // construct the array of values to be updated
+  $values = array(
+    'type_id' => array(
+      'cv_id' => array(
+        'name' => $cv_name,
+      ),
+      'name' => $property,
+    ),
+    'value' => $value,
+  );
+
+  return tripal_api_chado_chado_update($basetable . 'prop', $match, $values);
+}
+
+/**
+ * Deletes a property for a given base table record using the property name
+ *
+ * @param $basetable
+ *   The base table for which the property should be deleted. Thus to deleted a property
+ *   for a feature the basetable=feature and property is deleted from featureprop
+ * @param $record_id
+ *   The primary key of the basetable to delete a property for. This should be in integer.
+ * @param $property
+ *   The cvterm name describing the type of property to be deleted
+ * @param $cv_name
+ *   The name of the cv that the above cvterm is part of
+ *
+ * Note: The property to be deleted is select via the unique combination of $record_id and $property
+ *
+ * @return
+ *   Return True on Delete and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_delete_property($basetable, $record_id, $property, $cv_name) {
+
+  // get the foreign key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $fkcol = key($table_desc['foreign keys'][$basetable]['columns']);
+
+  // construct the array that will match the exact record to update
+  $match = array(
+    $fkcol => $record_id,
+    'type_id' => array(
+      'cv_id' => array(
+        'name' => $cv_name,
+      ),
+      'name' => $property,
+    ),
+  );
+
+  return tripal_api_chado_chado_delete($basetable . 'prop', $match);
+}
+
+/**
+ * Deletes a property using the property ID
+ *
+ * @param $basetable
+ *   The base table for which the property should be deleted. Thus to deleted a property
+ *   for a feature the basetable=feature and property is deleted from featureprop
+ * @param $record_id
+ *   The primary key of the basetable to delete a property for. This should be in integer.
+ *
+ * @return
+ *   Return True on Delete and False otherwise
+ *
+ * @ingroup tripal_properties_api
+ */
+function tripal_api_chado_delete_property_by_id($basetable, $record_id) {
+
+  // get the foreign key for this property table
+  $table_desc = tripal_api_chado_get_chado_table_schema($basetable . 'prop');
+  $pkcol = $table_desc['primary key'][0];
+
+  // construct the array that will match the exact record to update
+  $match = array(
+    $pkcol => $record_id,
+  );
+
+  return tripal_api_chado_chado_delete($basetable . 'prop', $match);
+}

tripal_api/tripal_api.module

@@ -4,7 +4,13 @@
  *
  */
 
+// Chado Query API: Functions to query (select/insert/update/delete) from chado
+require_once 'chado_query_api/tripal_api.chado_query.manage_properties.inc';
+
+// Chado Node API: Functions to help standardize creating nodes for chado tables
 require_once 'chado_node_api/tripal_api.chado_node.properties.inc';
+require_once 'chado_node_api/tripal_api.chado_node.references.inc';
+require_once 'chado_node_api/tripal_api.chado_node.relationships.inc';
 
 // DEPRECATED Function Wrappers
 require_once 'DEPRECATED/tripal-2.0_pre-release.inc';
@@ -17,9 +23,23 @@ require_once 'DEPRECATED/tripal-2.0_pre-release.inc';
  */
 function tripal_api_theme($existing, $type, $theme, $path) {
   return array(
+
+    // Chado Node API Themes
+    // --------------------------------
+    // Properties Node Form
     'tripal_api_chado_node_properties_form_table' => array(
       'function' => 'theme_tripal_api_chado_node_properties_form_table',
       'render element' => 'element',
     ),
+    // Additional Dbxrefs node form
+    'tripal_api_chado_node_additional_dbxrefs_form_table' => array(
+      'function' => 'theme_tripal_api_chado_node_additional_dbxrefs_form_table',
+      'render element' => 'element',
+    ),
+    // Relationships node form
+    'tripal_api_chado_node_relationships_form_table' => array(
+      'function' => 'theme_tripal_api_chado_node_relationships_form_table',
+      'render element' => 'element',
+    ),
   );
 }

tripal_core/tripal_core.module

@@ -42,9 +42,9 @@ require_once "api/tripal_core_chado_nodes.api.inc";
 require_once "api/tripal_core_custom_tables.api.inc";
 require_once "api/tripal_core_jobs.api.inc";
 require_once "api/tripal_core_mviews.api.inc";
-require_once "api/tripal_core.properties.api.inc";
-require_once "api/tripal_core.database_references.api.inc";
-require_once "api/tripal_core.relationships.api.inc";
+//require_once "api/tripal_core.properties.api.inc";
+//require_once "api/tripal_core.database_references.api.inc";
+//require_once "api/tripal_core.relationships.api.inc";
 
 require_once "includes/jobs.inc";
 require_once "includes/mviews.inc";