Removed tripal_api module

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

@@ -1,417 +0,0 @@
-<?php
-
-/**
- * @file
- * Wrappers for functions created for Tripal 2 whose names were changed before release
- */
-
-/**
- * This function is a wrapper for adding fields to an existing form for managing properties.
- * Many of the chado tables have a corresponding 'prop' table (e.g. analysisprop, contactprop,
- * organismprop, etc) and those prop tables all have the same schema.  Use this function
- * to add all the necessary components to a form for allowing the user to add/edit properties to
- * a given record.  To retreive properties in hook_insert or hook_update of a node form use
- * use the function tripal_core_properties_form_retreive().
- *
- * @param $form
- *   The Drupal form array into which the properties elements will be added
- * @param $form_state
- *   The corresponding form_state array for the form
- * @param $prop_table
- *   The name of the property table (e.g. anlaysisprop, contactprop)
- * @param $id_field
- *   The name of the ID field in the property table (e.g. analysis_id, contact_id)
- * @param $cv_name
- *   The name of the controlled vocabulary that these properties are derived from
- * @param $available_props
- *   An array of properties to inclde in the properties drop down.  This array should
- *   have cvterm_id's as the key and the cvterm name as the value
- * @param $id
- *   The current base table ID.  For example, if the property table is analysisprop then the
- *   value should be that of the analysis_id.  If the property table is contactprop then the
- *   value should be that of the contact_id.  This is the record from which currently assigned
- *   properties will be retrieved.
- * @param $exclude
- *   An optional array of cvterms to exclude when retreiving terms already saved in the database.
- *   Use this array when properties are present but should be handled elsewhere.
- *   For example, for contacts, the description field is stored as a property because
- *   the actual field is only 255 characters. The 'contact_description' therefore should
- *   not be shown in the list of properties, even if present, because it is handled by
- *   a different form element.
- * @param $include
- *   An optional array of terms to pre-populate in the form.  This argument can be used to
- *   add a default set of pre-populated properties regardless if they exist in the database
- *   or not.  The array should be of the following form:
- *     array(
- *       array('cvterm' => $obj1, 'value' => $val1),
- *       array('cvterm' => $obj2, 'value' => $val2),
- *       ... etc
- *     );
- *   The 'cvterm' key should have as a value an object with these properties: 'name', 'cvterm_id', 'definition'.
- * @param $instructions
- *   An optional additional set of instructions for the form properties.
- * @param $fset_title
- *   A title for the property field set.  The default is 'Additional Details'.
- * @ingroup tripal_properties_api
- */
-function tripal_core_properties_form(&$form, &$form_state, $prop_table, $id_field, $cv_name,
-    $available_props, $id = NULL, $exclude = array(), $include = array(), $instructions = '',
-    $fset_title = 'Additional Details') {
-
-    // $available_props is now created by the form based on the cv
-    // $exclude and $include are not yet supported
-
-    $details = array(
-    'property_table' => $prop_table,
-    'base_foreign_key' => $id_field,
-    'base_key_value' => $id,
-    'cv_name' => $cv_name,
-    'fieldset_title' => $fset_title,
-    'additional_instructions' => $instructions
-  );
-  tripal_api_chado_node_properties_form($form, $form_state, $details);
-
-}
-
-/**
- * This function is used in a hook_insert, hook_update for a node form
- * when the properties form has been added to the form.  It retrieves all of the properties
- * and returns them in an array of the format:
- *
- *   $properties[<property name>][<rank>] = <value>
- *
- * This array can then be used for inserting or updating properties using the API call
- * tripal_hook_insert_property()
- *
- * @param $node
- * @param $cvname
- *   The name of the controlled vocabulary that the properties belong to
- *
- * @return
- *   A properties array
- *
- * @ingroup tripal_properties_api
- */
-function tripal_core_properties_form_retreive($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.properties.inc

@@ -1,637 +0,0 @@
-<?php
-
-/**
- * @file
- * API to manage the chado prop 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 chado properties form elements, you first need to prepare the arguments
-    // for the function call.
-
-    $details = array(
-      'property_table' => 'example_property',      // the name of the table linking additional properties to this node
-      'base_foreign_key' => 'example_id',          // key to link to the chado content created by this node
-      'base_key_value' => $example_id,             // the value of the above key
-      'cv_name' => 'example_prop_cv',              // the name of the cv governing the _prop.type_id
-      'fieldset_title' => 'Additional References', // the non-translated title for this fieldset
-      'additional_instructions' => ''              // a non-stranslated string providing additional instructions
-    );
-
-    // Finally, and add the additional form elements to the form
-    tripal_api_chado_node_properties_form($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 properties
-      // Existing _property links will be cleared and then re-added
-      tripal_api_chado_node_properties_form_update_properties(
-        $node,                // the node object passed in via hook_insert()
-        'example_property',   // the name of the _property linking table
-        'example',            // the name of the base chado table for the node
-        '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 properties
-      // Existing _property links will be cleared and then re-added
-      tripal_api_chado_node_properties_form_update_properties(
-        $node,                // the node object passed in via hook_insert()
-        'example_property',   // the name of the _property linking table
-        'example',            // the name of the base chado table for the node
-        '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
- * Properties Form to be added to node forms
- */
-
-/**
- * Provides a form for adding to BASEprop table
- *
- * @param $form
- *   The Drupal form array into which the property form elements will be added
- * @param $form_state
- *   The corresponding form_state array for the form
- * @param $details
- *   An array defining details needed by this form. Required Keys are:
- *     - property_table: the name of the property linking table (ie: featureprop)
- *     - base_foreign_key: the name of the foreign key linking this table to the non-property table (ie: feature_id)
- *     - base_key_value: the value of the base_foreign_key for the current form (ie: 999 if the feature_id=999)
- *   Require ONE of the following:
- *     The controlled vocabulary governing the property types
- *       -cv_id: the unique key from the cv table
- *       -cv_name: the cv.name field uniquely identifying the controlled vocab
- *   Optional keys include:
- *     - fieldset_title: the non-translated title for this fieldset
- *     - additional_instructions: a non-translated string providing additional instructions
- */
-function tripal_api_chado_node_properties_form(&$form, &$form_state, $details) {
-
-  // Set Defaults for optional fields
-  $details['fieldset_title'] = 'Properties';
-  $details['additional_instructions'] = '';
-
-  // Get Property Types for the Select List
-  if (isset($details['cv_name'])) {
-    $property_options = array();
-    $property_options[] = 'Select a Property';
-    $sql = "
-      SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
-      FROM  {cvterm} CVT
-        INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
-      WHERE
-        CV.name = :cv_name AND
-        NOT CVT.is_obsolete = 1
-      ORDER BY CVT.name ASC
-    ";
-    $prop_types = chado_query($sql, array(':cv_name' => $details['cv_name']));
-    while ($prop = $prop_types->fetchObject()) {
-      $property_options[$prop->cvterm_id] = $prop->name;
-    }
-  } elseif (isset($details['cv_id'])) {
-    $property_options = array();
-    $property_options[] = 'Select a Property';
-    $sql = "
-      SELECT DISTINCT CVT.cvterm_id, CVT.name, CVT.definition
-      FROM  {cvterm} CVT
-        INNER JOIN {cv} CV ON CVT.cv_id = CV.cv_id
-      WHERE
-        CV.cv_id = :cv_id AND
-        NOT CVT.is_obsolete = 1
-      ORDER BY CVT.name ASC
-    ";
-    $prop_types = chado_query($sql, array(':cv_id' => $details['cv_id']));
-    while ($prop = $prop_types->fetchObject()) {
-      $property_options[$prop->cvterm_id] = $prop->name;
-    }
-  }
-
-  // the fieldset of the property elements
-  $form['properties'] = array(
-    '#type' => 'fieldset',
-    '#title' => t($details['fieldset_title']),
-    '#description' => t('You may add additional properties by selecting a property type
-      from the dropdown and adding text. You may add as many properties as desired by
-      clicking the add button on the right. To remove a property, click the remove button.
-      To add additional properties to the drop down. ' . $details['additional_instructions']),
-    '#prefix' => "<div id='properties-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']['property_table'] heading.
-  $form['properties']['property_table'] = array(
-    '#type' => 'markup',
-    '#tree' => TRUE,
-    '#prefix' => '<div id="tripal-generic-edit-properties-table">',
-    '#suffix' => '</div>',
-    '#theme' => 'tripal_api_chado_node_properties_form_table'
-  );
-
-  // Add defaults into form_state to be used elsewhere
-  $form['properties']['property_table']['details'] = array(
-    '#type' => 'hidden',
-    '#value' => serialize($details)
-  );
-
-  /* Properties can come to us in two ways:
-   *
-   * 1) In the form state in the $form_state['chado_properties']. 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 properties 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 $form_state['chado_properties']
-   *    entry.
-   */
-  if (isset($form_state['chado_properties'])) {
-    $existing_properties = $form_state['chado_properties'];
-  }
-  else {
-    if (isset($details['cv_name'])) {
-      $existing_properties = chado_query(
-        "SELECT CVT.cvterm_id, CVT.name as type_name, CVT.definition, PP.value, PP.rank
-        FROM {" . $details['property_table'] . "} PP
-        INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
-        INNER JOIN {cv} CV      ON CVT.cv_id     = CV.cv_id
-        WHERE
-        PP." . $details['base_foreign_key'] . " = :base_key_value AND
-        CV.name = '" .$details['cv_name']. "'
-        ORDER BY CVT.name, PP.rank",
-         array(':base_key_value' => $details['base_key_value'])
-      );
-    } elseif (isset($details['cv_id'])) {
-      $existing_properties = chado_query(
-        "SELECT PP.".$details['property_table']."_id property_id, CVT.cvterm_id as type_id, CVT.name as type_name, CVT.definition, PP.value, PP.rank
-        FROM {" . $details['property_table'] . "} PP
-        INNER JOIN {cvterm} CVT ON CVT.cvterm_id = PP.type_id
-        INNER JOIN {cv} CV      ON CVT.cv_id     = CV.cv_id
-        WHERE
-        PP." . $details['base_foreign_key'] . " = :base_key_value AND
-        CV.cv_id = '" .$details['cv_id']. "'
-        ORDER BY CVT.name, PP.rank",
-         array(':base_key_value' => $details['base_key_value'])
-      );
-    }
-  }
-
-  /* The format of the $existing_properties array is either:
-   *
-   * From the chado_properties array:
-   * $form_state['chado_properties'] = array(
-   *   '[type_id]-[rank]' => array(
-   *     'type_id' => [the cvterm.cvterm_id value]
-   *     'type_name' => [the cvterm.name value]
-   *     'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
-   *     'value' => [the BASEprop.value value],
-   *     'rank' => [the BASEprop.rank value],
-   *   ),
-   * );
-   *
-   * OR
-   * Populated from the database:
-   * $existing_property = array(
-   *   0 => array(
-   *     'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
-   *     'type_id' => [the cvterm.cvterm_id value]
-   *     'type_name' => [the cvterm.name value]
-   *     'value' => [the BASEprop.value value],
-   *     'rank' => [the BASEprop.rank value],
-   *   ),
-   * );
-   *
-   * NOTE: The main difference is the key
-   *
-   * Loop on the array elements of the $existing_properties array and add
-   * an element to the form for each one.
-   */
-  foreach ($existing_properties as $property) {
-
-    $form['properties']['property_table'][$property->type_id]['#type'] = 'markup';
-    $form['properties']['property_table'][$property->type_id]['#value'] = '';
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['#type'] = 'markup';
-    $form['properties']['property_table'][$property->type_id][$property->rank]['#value'] = '';
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['prop_type_id'] = array(
-      '#type' => 'hidden',
-      '#value' => $property->type_id
-    );
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['prop_value'] = array(
-      '#type' => 'hidden',
-      '#value' => $property->value
-    );
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['property_id'] = array(
-      '#type' => 'hidden',
-      '#value' => $property->property_id
-    );
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['type'] = array(
-      '#type' => 'markup',
-      '#markup' => $property->type_name
-    );
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['value'] = array(
-      '#type' => 'markup',
-      '#markup' => $property->value
-    );
-
-    $form['properties']['property_table'][$property->type_id][$property->rank]['rank'] = array(
-      '#type' => 'markup',
-      '#markup' => $property->rank
-    );
-    // remove button
-    $form['properties']['property_table'][$property->type_id][$property->rank]['property_action'] = array(
-      '#type' => 'submit',
-      '#value' => t('Remove'),
-      '#name' => "property_remove-".$property->type_id.'-'.$property->rank,
-      '#ajax' => array(
-        'callback' => "tripal_api_chado_node_properties_form_ajax_update",
-        'wrapper' => 'tripal-generic-edit-properties-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
-      // property fields and in the submit we remove the indicated property
-      // from the chado_properties array. In order to keep validate errors
-      // from the node form validate and Drupal required errors for non-property fields
-      // preventing the user from removing properties we set the #limit_validation_errors below
-      '#validate' => array('tripal_api_chado_node_properties_form_remove_button_validate'),
-      '#submit' => array('tripal_api_chado_node_properties_form_remove_button_submit'),
-      // Limit the validation of the form upon clicking this button to the property_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('property_table')  // Validate all fields within $form_state['values']['property_table']
-      )
-    );
-  }
-
-  // Form elements for adding a new property
-  //---------------------------------------------
-  $form['properties']['property_table']['new'] = array(
-    '#type' => 'markup',
-    '#prefix' => '<span class="addtl-properties-add-new-property">',
-    '#suffix' => '</span>'
-  );
-
-  $form['properties']['property_table']['new']['type'] = array(
-    '#type' => 'select',
-    '#options' => $property_options, // Set at top of form
-  );
-
-  $form['properties']['property_table']['new']['value'] = array(
-    '#type' => 'textfield',
-  );
-
-  // add button
-  $form['properties']['property_table']['new']['property_action'] = array(
-    '#type' => 'submit',
-    '#value' => t('Add'),
-    '#name' => "property-add",
-    '#ajax' => array(
-      'callback' => "tripal_api_chado_node_properties_form_ajax_update",
-      'wrapper' => 'tripal-generic-edit-properties-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 property fields and in the submit we add them to the chado_properties
-    // array. In order to keep validate errors from the node form validate and Drupal
-    // required errors for non-property fields preventing the user from adding properties we
-    // set the #limit_validation_errors below
-    '#validate' => array('tripal_api_chado_node_properties_form_add_button_validate'),
-    '#submit' => array('tripal_api_chado_node_properties_form_add_button_submit'),
-    // Limit the validation of the form upon clicking this button to the property_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('property_table')  // Validate all fields within $form_state['values']['property_table']
-    )
-  );
-
-}
-
-/**
- * Validate the user input for creating a new property
- * Called by the add button in tripal_api_chado_node_properties_form
- */
-function tripal_api_chado_node_properties_form_add_button_validate($form, &$form_state) {
-
-  // Ensure the type_id is supplied & Valid
-  $cvterm = tripal_core_chado_select(
-    'cvterm',
-    array('cvterm_id', 'name'),
-    array('cvterm_id' => $form_state['values']['property_table']['new']['type'])
-  );
-  if (!isset($cvterm[0])) {
-    form_set_error('property_table][new][cvterm', 'Please select a property type before attempting to add a new property.');
-  }
-  else {
-    $form_state['values']['property_table']['new']['type_name'] = $cvterm[0]->name;
-  }
-
-  // Ensure value is supplied
-  if (empty($form_state['values']['property_table']['new']['value'])) {
-    form_set_error('property_table][new][value','You must enter the property value before attempting to add a new property.');
-  }
-}
-
-/**
- * Called by the add button in tripal_api_chado_node_properties_form
- *
- * Create an array of properties in the form state. This array will then be
- * used to rebuild the form in subsequent builds
- */
-function tripal_api_chado_node_properties_form_add_button_submit(&$form, &$form_state) {
-
-  $details = unserialize($form_state['values']['property_table']['details']);
-
-  // if the chado_additional_properties array is not set then this is the first time modifying the
-  // property table. this means we need to include all the properties from the db
-  if (!isset($form_state['chado_properties'])) {
-    tripal_api_chado_node_properties_form_create_property_formstate_array($form, $form_state);
-  }
-
-  // get details for the new property
-  $property = array(
-    'type_id' => $form_state['values']['property_table']['new']['type'],
-    'type_name' => $form_state['values']['property_table']['new']['type_name'],
-    'property_id' => NULL,
-    'value' => $form_state['values']['property_table']['new']['value'],
-    'rank' => '0',
-  );
-
-  // get max rank
-  $rank = tripal_core_get_max_chado_rank(
-    $details['property_table'],
-    array(
-      $details['base_foreign_key'] => $details['base_key_value'],
-      'type_id' => $property['type_id']
-    )
-  );
-  $property['rank'] = strval($rank + 1);
-
-  $key = $property['type_id'] . '-' . $property['rank'];
-  $form_state['chado_properties'][$key] = (object) $property;
-
-  $form_state['rebuild'] = TRUE;
-}
-
-/**
- * There is no user input for the remove buttons so there is no need to validate
- * However, both a submit & validate need to be specified so this is just a placeholder
- *
- * Called by the many remove buttons in tripal_api_chado_node_properties_form
- */
-function tripal_api_chado_node_properties_form_remove_button_validate($form, $form_state) {
-  // No Validation needed for remove
-}
-
-/**
- * Remove the correct property from the form
- * Called by the many remove buttons in tripal_api_chado_node_properties_form
- */
-function tripal_api_chado_node_properties_form_remove_button_submit(&$form, &$form_state) {
-
-  // if the chado_properties array is not set then this is the first time modifying the
-  // property table. this means we need to include all the properties from the db
-  if (!isset($form_state['chado_properties'])) {
-    tripal_api_chado_node_properties_form_create_property_formstate_array($form, $form_state);
-  }
-
-  // remove the specified property from the form property table
-  if(preg_match('/property_remove-([^-]+-[^-]+)/',$form_state['triggering_element']['#name'],$match)) {
-    $key = $match[1];
-    if (array_key_exists($key, $form_state['chado_properties'])) {
-      unset($form_state['chado_properties'][$key]);
-    }
-  }
-
-  $form_state['rebuild'] = TRUE;
-}
-
-/**
- * Ajax function which returns the section of the form to be re-rendered
- */
-function tripal_api_chado_node_properties_form_ajax_update($form, $form_state) {
-  return $form['properties']['property_table'];
-}
-
-/**
- * Creates an array in form_state containing the existing properties. 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_properties'] array
- *
- * $form_state['chado_properties'] = array(
- *   '[type_id]-[rank]' => array(
- *     'type_id' => [the cvterm.cvterm_id value]
- *     'type_name' => [the cvterm.name value]
- *     'property_id' => [the property.property_id value, or NULL if it doesn't yet exist],
- *     'value' => [the BASEprop.value value],
- *     'rank' => [the BASEprop.rank value],
- *   ),
- * );
- */
-function tripal_api_chado_node_properties_form_create_property_formstate_array($form, &$form_state) {
-
-  $form_state['chado_properties'] = array();
-
-  foreach (element_children($form['properties']['property_table']) as $type_id) {
-    if ($type_id != 'new') {
-      foreach (element_children($form['properties']['property_table'][$type_id]) as $rank) {
-          $element = $form['properties']['property_table'][$type_id][$rank];
-          $property = array(
-            'type_id' => $element['type_id']['#value'],
-            'type_name' => $element['type']['#markup'],
-            'property_id' => $element['property_id']['#value'],
-            'value' => $element['value']['#markup'],
-            'rank' => $element['rank']['#markup']
-          );
-          $key = $property['type_id'] . '-' . $property['rank'];
-          $form_state['chado_properties'][$key] = (object) $property;
-      }
-    }
-  }
-}
-
-/**
- * Function to theme the add/remove properties form into a table
- */
-function theme_tripal_api_chado_node_properties_form_table($variables) {
-  $element = $variables['element'];
-
-  $header = array(
-    'type' => t('Type'),
-    'value' => t('Value'),
-    'rank' => t('Rank'),
-    'property_action' => t('Actions'),
-  );
-
-  $rows = array();
-  foreach (element_children($element) as $type_id) {
-    if ($type_id == 'new') {
-      $row = array();
-
-        $row['data'] = array();
-        foreach ($header as $fieldname => $title) {
-          $row['data'][] = drupal_render($element[$type_id][$fieldname]);
-        }
-        $rows[] = $row;
-    }
-    else {
-      foreach (element_children($element[$type_id]) as $version) {
-        $row = array();
-
-        $row['data'] = array();
-        foreach ($header as $fieldname => $title) {
-          $row['data'][] = drupal_render($element[$type_id][$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 chado node properties form has been added to the form.  It retrieves all of the properties
- * and returns them in an array of the format:
- *
- *   $dbxefs[<type_id>][<rank>] = <value>
- *
- * This array can then be used for inserting or updating properties
- *
- * @param $node
- *
- * @return
- *   A property array
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_chado_node_properties_form_retreive($node) {
-  $properties = array();
-  foreach ($node->property_table as $type_id => $elements) {
-    if ($type_id != 'new' AND $type_id != 'details') {
-      foreach ($elements as $rank => $element) {
-        $properties[$type_id][$rank] = $element['prop_value'];
-      }
-    }
-  }
-
-  return $properties;
-}
-
-/**
- * This function is used in hook_insert or hook_update and handles inserting of any new
- * properties
- *
- * @param $node
- *    The node passed into hook_insert & hook_update
- * @param $details
- *   - property_table: the name of the _property linking table (ie: feature_property)
- *   - base_table: the name of the base table (ie: feature)
- *   - foreignkey_name: the name of the foreign key used to link to the node content (ie: feature_id)
- *   - foreignkey_value: the value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
- */
-function tripal_api_chado_node_properties_form_update_properties($node, $details) {
-
-  // First remove existing property links
-  tripal_core_chado_delete($details['property_table'], array($details['foreignkey_name'] => $details['foreignkey_value']));
-
-  // Add back in property links and insert properties as needed
-  $properties = tripal_api_chado_node_properties_form_retreive($node);
-  foreach ($properties as $type_id => $ranks) {
-    foreach ($ranks as $rank => $value) {
-
-      $success = tripal_core_chado_insert(
-        $details['property_table'],
-        array(
-          $details['foreignkey_name'] => $details['foreignkey_value'],
-          'type_id' => $type_id,
-          'value' => $value,
-          'rank' => $rank
-        )
-      );
-
-      if (!$success) {
-        watchdog(
-          'tripal_' . $details['base_table'],
-          $details['base_table'] . ' Insert: Unable to insert property type_id %cvterm with value %value.',
-          array('%cvterm' => $type_id, '%value' => $value),
-          WATCHDOG_ERROR
-        );
-      }
-
-    }
-  }
-}

tripal_api/chado_node_api/tripal_api.chado_node.references.inc

@@ -1,597 +0,0 @@
-<?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

@@ -1,720 +0,0 @@
-<?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

@@ -1,335 +0,0 @@
-<?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 $cv_name
- *   The name of the cv that the above cvterm is part of
- *
- * @return
- *   An array in the same format as that generated by the function
- *   tripal_core_generate_chado_var().  If only one record is returned it
- *   is a single object.  If more than one record is returned then it is an array
- *   of objects
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_get_property($basetable, $record_id, $property, $cv_name) {
-  // get the foreign key for this property table
-  $table_desc = tripal_core_get_chado_table_schema($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
-    ),
-  );
-  $results = tripal_core_generate_chado_var($basetable . 'prop', $values);
-  if ($results) {
-    $results = tripal_core_expand_chado_vars($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 $update_if_present
- *   A boolean indicating whether an existing record should be updated. If the
- *   property already exists and this value is not specified or is zero then
- *   a new property will be added with the next largest rank.
- *
- * @return
- *   Return True on Insert/Update and False otherwise
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_insert_property($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
-  $props = tripal_api_get_property($basetable, $record_id, $property, $cv_name);
-  if (!is_array($props) and $props) {
-    $props = array($props);
-  }
-
-  $rank = 0;
-  if (count($props) > 0) {
-    if ($update_if_present) {
-      return tripal_api_update_property($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_core_chado_select('cvterm', array('cvterm_id'), $values, $options);
-  if (!$term or count($term) == 0) {
-    watchdog('tripal_core', "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
-  $table_desc = tripal_core_get_chado_table_schema($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();
-  $result = tripal_core_chado_insert($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_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
- * $property and then it is updated with the supplied value
- *
- * @return
- *   Return True on Update/Insert and False otherwise
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_update_property($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
-  $prop = tripal_api_get_property($basetable, $record_id, $property, $cv_name);
-  if (count($prop)==0) {
-    if ($insert_if_missing) {
-      return tripal_api_insert_property($basetable, $record_id, $property, $cv_name, $value);
-    }
-    else {
-      return FALSE;
-    }
-  }
-
-  // get the foreign key for this property table
-  $table_desc = tripal_core_get_chado_table_schema($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' => $value,
-  );
-
-  return tripal_core_chado_update($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 $value
- *   The value of the property to be inserted (can be empty)
- *
- * @return
- *   Return True on Update/Insert and False otherwise
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_update_property_by_id($basetable, $record_id, $property,
-$cv_name, $value) {
-
-  // get the primary key for this property table
-  $table_desc = tripal_core_get_chado_table_schema($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' => $value,
-  );
-
-  return tripal_core_chado_update($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 $property
- *
- * @return
- *   Return True on Delete and False otherwise
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_delete_property($basetable, $record_id, $property, $cv_name) {
-
-  // get the foreign key for this property table
-  $table_desc = tripal_core_get_chado_table_schema($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' => $property,
-    ),
-  );
-
-  return tripal_core_chado_delete($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 $record_id
- *   The primary key of the basetable to delete a property for. This should be in integer.
- *
- * @return
- *   Return True on Delete and False otherwise
- *
- * @ingroup tripal_properties_api
- */
-function tripal_api_delete_property_by_id($basetable, $record_id) {
-
-  // get the foreign key for this property table
-  $table_desc = tripal_core_get_chado_table_schema($basetable . 'prop');
-  $pkcol = $table_desc['primary key'][0];
-
-  // construct the array that will match the exact record to update
-  $match = array(
-    $pkcol => $record_id,
-  );
-
-  return tripal_core_chado_delete($basetable . 'prop', $match);
-}

tripal_api/tripal_api.info

@@ -1,7 +0,0 @@
-name = Tripal API
-description = Contains general API functionality useful to a number of Tripal modules.
-core = 7.x
-project = tripal_api
-package = Tripal
-version = 7.x-2.0-beta1
-configure = admin/tripal

tripal_api/tripal_api.module

@@ -1,46 +0,0 @@
-<?php
-
-/**
- *
- */
-
-// 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';
-
-/**
- * Implements hook_theme().
- * Registers template files/functions used by this module.
- *
- * @ingroup tripal_core
- *
-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',
-    ),
-  );
-}
-*/