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-<?php
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-
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-/**
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- * @file
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- * This file should contain all Drupal hooks for interacting with nodes.
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- *
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- */
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-
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-/**
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- * Implementation of hook_node_info().
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- *
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- * This hook provides information to Drupal about any node types that are being
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- * created by this module. If your module does not create any node types then
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- * this function is not required.
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- *
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- * @ingroup tripal_example
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- */
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-function tripal_example_node_info() {
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- $nodes = array();
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-
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- // EXPLANATION: this array describes all of the node types that are created
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- // by this module. For many Tripal modules (e.g. tripal_example, tripal_stock,
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- // tripal_library, tripal_pub, etc.) new node types are created. It is
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- // customary to name all new node types that interact with data in Chado
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- // with a 'chado_' prefix.
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-
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- $nodes['chado_example'] = array(
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- 'name' => t('Example'),
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- 'base' => 'chado_example',
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- 'description' => t('A record from the fake chado example table'),
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- 'has_title' => TRUE,
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- 'locked' => TRUE,
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- // EXPLANATION: This section of the node type array specifies how Tripal
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- // will sync the node types with data in Chado. When Drupal creates a node
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- // it has no way of coordinating which node belongs to which record in
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- // Chado. Therefore, Tripal maintains tables in the Drupal schema that maps
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- // Drupal nodes to records in Chado. Syncing is the process of creating
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- // Drupal nodes and linking them to the appropriate record.
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- 'chado_node_api' => array(
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- // the base table name (e.g. example, example, contact)
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- 'base_table' => 'example',
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- // the node type hook prefix
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- 'hook_prefix' => 'chado_example',
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- 'record_type_title' => array(
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- // how to refer to the record
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- 'singular' => t('Example'),
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- // how to refer to the record in plurals
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- 'plural' => t('Examples')
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- ),
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- 'sync_filters' => array(
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- 'type_id' => TRUE, // if the record has a type_id set to TRUE
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- 'organism_id' => TRUE // if the record has an organism_id set to TRUE
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- ),
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- )
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- );
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-
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- return $nodes;
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-}
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-
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-/**
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- * Implement hook_access(). This hook provides instructions to Drupal for which
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- * users can access the custom content types created in the function above. The
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- * available permissions are set in the chado_example_permissions() hook in the
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- * tripal_example.module file. This hook is not needed if no node types were
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- * defined in the hook_node_info() hook.
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- *
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- * @return
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- * This function should return null if it does not specifically deny access.
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- * This allows for other mechanisms to to deny or reject access. If the return
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- * value is TRUE then access is granted regardless of any other rules that might
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- * be implemented by other modules.
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- */
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-function tripal_example_node_access($node, $op, $account) {
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- $node_type = $node;
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- if (is_object($node)) {
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- $node_type = $node->type;
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- }
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- // EXPLANATION: in the tripal_example_permissions() function we created the
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- // permission types that are used here to check for access permissions to the
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- // 'chado_exmaple' node type.
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- if($node_type == 'chado_example') {
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- if ($op == 'create') {
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- if (!user_access('create chado_example content', $account)) {
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- return NODE_ACCESS_DENY;
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- }
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- return NODE_ACCESS_ALLOW;
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- }
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- if ($op == 'update') {
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- if (!user_access('edit chado_example content', $account)) {
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- return NODE_ACCESS_DENY;
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- }
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- }
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- if ($op == 'delete') {
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- if (!user_access('delete chado_example content', $account)) {
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- return NODE_ACCESS_DENY;
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- }
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- }
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- if ($op == 'view') {
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- if (!user_access('access chado_example content', $account)) {
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- return NODE_ACCESS_DENY;
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- }
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- }
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- }
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- return NODE_ACCESS_IGNORE;
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-}
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-
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-/**
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- * Implementation of hook_form()
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- *
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- * Creates the form for editing or inserting a record
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- *
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- * @ingroup tripal_example
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- */
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-function chado_example_form($node, &$form_state) {
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-
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- // EXPLANATION: This function should construct a form array that is used by
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- // Drupal to construct a form for inserting or editing our new node type.
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- // See this page for information about the Form API:
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- // https://api.drupal.org/api/drupal/includes!form.inc/group/form_api/7
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- //
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- // The code below is laid out in the following order
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- // 1) Set default values
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- // 2) Add form elements used by this node type
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- // 3) Use the Tripal API to add form elements for properties,
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- // dbxref's and relationships
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- //
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- // For the example code below we assume that the fake 'example' table only has
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- // a uniquename, organism_id, type_id and example_id.
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-
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- $form = array();
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-
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- // Default values can come in the following ways:
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- //
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- // 1) as elements of the $node object. This occurs when editing an existing
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- // example
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- // 2) in the $form_state['values'] array which occurs on a failed validation
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- // or ajax callbacks from non submit form elements
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- // 3) in the $form_state['input'[ array which occurs on ajax callbacks from
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- // submit form elements and the form is being rebuilt
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- //
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- // set form field defaults
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-
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-
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- // SET FORM DEFAULTS
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- //---------------------------------------------
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- $example = null; // holds the example object record
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- $example_id = null; // when editing an example record we'll have an example_id
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-
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- // initialize the defaults for the form fields
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- $uniquename = '';
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- $example_type = '';
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- $organism_id = '';
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- $description = '';
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-
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- // if we are editing an existing node then the 'example' record from Chado
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- // is already part of the node, so we set the defaults from that object
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- if (property_exists($node, 'example')) {
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- $example = $node->example;
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- $example_id = $example->example_id;
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- $uniquename = $example->uniquename;
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- $description = $example->description;
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- $organism_id = $example->organism_id;
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-
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- // keep track of the example id
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- $form['example_id'] = array(
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- '#type' => 'value',
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- '#value' => $example_id,
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- );
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- }
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- // if we are re constructing the form from a failed validation or ajax
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- // callback then use the $form_state['values'] values
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- if (array_key_exists('values', $form_state)) {
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- $uniquename = $form_state['values']['uniquename'];
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- $example_type = $form_state['values']['example_type'];
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- $description = $form_state['values']['description'];
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- $organism_id = $form_state['values']['organism_id'];
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- }
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- // if we are re building the form from after submission (from ajax call) then
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- // the values are in the $form_state['input'] array
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- if (array_key_exists('input', $form_state) and !empty($form_state['input'])) {
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- $uniquename = $form_state['input']['uniquename'];
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- $example_type = $form_state['input']['example_type'];
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- $organism_id = $form_state['input']['organism_id'];
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- }
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-
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-
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- // FORM ELEMENTS
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- //---------------------------------------------
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- $form['uniquename'] = array(
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- '#type' => 'textfield',
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- '#title' => t('Unique Name'),
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- '#required' => TRUE,
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- '#default_value' => $uniquename,
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- '#description' => t('Enter a unique name for this example. This name must be unique.'),
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- '#maxlength' => 255
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- );
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-
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- // for the type_id we want to use the default vocabulary so that this field
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- // can have auto-complete functionality
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- $type_cv = tripal_get_default_cv('example', 'type_id');
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- $cv_id = $type_cv->cv_id;
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- $form['example_type'] = array(
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- '#title' => t('Example Type'),
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- '#type' => 'textfield',
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- '#description' => t("Choose the example type (e.g. Test Type)."),
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- '#required' => TRUE,
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- '#default_value' => $example_type,
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- '#autocomplete_path' => "admin/tripal/vocab/cvterm/auto_name/$cv_id",
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- );
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-
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- // add a select box of organisms
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- $organisms = tripal_get_organism_select_options();
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- $form['organism_id'] = array(
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- '#title' => t('Organism'),
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- '#type' => t('select'),
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- '#description' => t("Choose the organism with which this example is associated"),
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- '#required' => TRUE,
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- '#default_value' => $organism_id,
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- '#options' => $organisms,
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- );
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-
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- $form['description'] = array(
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- '#type' => 'text_format',
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- '#title' => t('Description'),
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- '#required' => TRUE,
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- '#default_value' => $description,
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- '#description' => t('Enter a description for this example.'),
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- );
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-
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- // PROPERTIES FORM
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- //---------------------------------------------
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- // If there is a exampleprop table and you want to allow users to add/remove
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- // entries from it through your node form then add this section to your own
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- // node form
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- $prop_cv = tripal_get_default_cv('exampleprop', 'type_id');
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- $cv_id = $prop_cv ? $prop_cv->cv_id : NULL;
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- $details = array(
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- // the name of the prop table
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- 'property_table' => 'exampleprop',
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- // the value of example_id for this record
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- 'chado_id' => $example_id,
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- // the cv.cv_id of the cv governing exampleprop.type_id
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- 'cv_id' => $cv_id
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- );
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- // Adds the form elements to your current form
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- chado_add_node_form_properties($form, $form_state, $details);
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-
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- // ADDITIONAL DBXREFS FORM
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- //---------------------------------------------
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- // If there is a example_dbxref table and you want to allow users to
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- // add/remove entries from it through your node form then add this section to
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- // your own node form
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- $details = array(
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- // the name of the _dbxref table
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- 'linking_table' => 'example_dbxref',
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- // the name of the key in your base chado table
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- 'base_foreign_key' => 'example_id',
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- // the value of example_id for this record
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- 'base_key_value' => $example_id
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- );
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- // Adds the form elements to your current form
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- chado_add_node_form_dbxrefs($form, $form_state, $details);
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-
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- // RELATIONSHIPS FORM
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- //---------------------------------------------
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- // If there is a example_relationship table and you want to allow users to
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- // add/remove entries from it through your node form then add this section to
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- // your own node form
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- $rels_cv = tripal_get_default_cv('example_relationship', 'type_id');
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- $cv_id = $rels_cv ? $rels_cv->cv_id : NULL;
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- $details = array(
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- // the name of the _relationship table
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- 'relationship_table' => 'example_relationship',
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- // the name of your chado base table
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- 'base_table' => 'example',
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- // the name of the key in your base chado table
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- 'base_foreign_key' => 'example_id',
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- // the value of example_id for this record
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- 'base_key_value' => $example_id,
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- // the human-readable name of your node type
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- 'nodetype' => 'example',
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- // the cv.cv_id of the cv governing example_relationship.type_id
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- 'cv_id' => $cv_id
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- );
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- // Adds the form elements to your current form
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- chado_add_node_form_relationships($form, $form_state, $details);
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-
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- // return the form
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- return $form;
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-}
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-
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-/**
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- * Implementation of hook_validate
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- *
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- * This function validates a form prior to insert or update. If an error is
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- * detected, it sets the error using form_set_error() which takes the user back
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- * to the form to make corrections.
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- *
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- * This validation is being used for three activities:
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- * CASE A: Update a node that exists in both Drupal and Chado
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- * CASE B: Synchronizing a node from Chado to Drupal
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- * CASE C: Inserting a new node that exists in neither Drupal nor Chado
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- *
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- * @param $node
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- *
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- *
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- * @ingroup tripal_example
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- */
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-function chado_example_validate($node, $form, &$form_state) {
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-
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- // We only want to validate when the node is saved.
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- // Since this validate can be called on AJAX and Deletion of the node
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- // we need to make this check to ensure queries are not executed
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- // without the proper values.
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- if(property_exists($node, "op") and $node->op != 'Save') {
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- return;
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- }
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-
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- // we are syncing if we do not have a node ID but we do have a example_id. We
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- // don't need to validate during syncing so just skip it.
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- if (!property_exists($node, 'nid') and property_exists($node, 'example_id') and $node->example_id != 0) {
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- return;
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- }
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-
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- // be sure to always trim text fields
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- $node->uniquename = property_exists($node, 'uniquename') ? trim($node->uniquename) : '';
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-
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- // Validating for an update. If the 'nid' property is present in the node then
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- // this is an update and validation can be different for updates
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- if (property_exists($node, 'nid')) {
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-
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- // make sure the example type is an allowed term
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- $type_cv = tripal_get_default_cv('example', 'type_id');
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- $type = tripal_get_cvterm(array(
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- 'name' => $node->example_type,
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- 'cv_id' => $type_cv->cv_id,
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- ));
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- if (!$type) {
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- form_set_error('example_type', t("The example type is not a valid name from the Sequence Ontology."));
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- }
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-
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- // TODO: also we should check that the unique constraint is not invalidated
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- // by changing either the type_id, organism_id or uniquename.
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- }
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- // Validating for an insert
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- else {
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- // make sure the example type is an allowed term
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- $type_cv = tripal_get_default_cv('example', 'type_id');
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- $type = tripal_get_cvterm(array(
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- 'name' => $node->example_type,
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- 'cv_id' => $type_cv->cv_id,
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- ));
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- if (!$type) {
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- form_set_error('example_type', t("The example type is not a valid name from the Sequence Ontology."));
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- }
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-
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- // TODO: also we should check that the unique constraint doesn't already exist
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- }
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-}
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-
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-/**
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- * Implementation of hook_insert(). This function is called after the node is
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- * inserted into the database. We need it so that we can insert appropriate
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- * fields as provided by the user into the database. And so that we can link the
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- * new Drupal node to the data in Chado via the chado_example linking table. We
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- * can get to this function also during "syncing".
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- * With syncing, however, the data already exists in Chado and we do not want
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- * to try to re-add it. But we do need to add an entry to the chado_example
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- * table to link the Drupal node with the data in the 'example' table of Chado.
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- *
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- * This function is not required if the hook_node_info() does not define
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- * any custom node types.
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- *
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- * @ingroup tripal_example
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- */
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-function chado_example_insert($node) {
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-
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- $example_id = '';
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-
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- // if there is an example_id in the $node object then this must be a sync so
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- // we can skip adding the example as it is already there, although we do need
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- // to proceed with insertion into the chado/drupal linking table.
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- if (!property_exists($node, 'example_id')) {
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-
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- // be sure to always trim text fields
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- $node->uniquename = trim($node->uniquename);
|
|
|
- $node->description = trim($node->description['value']);
|
|
|
-
|
|
|
- // get the example type record
|
|
|
- $type_cv = tripal_get_default_cv('example', 'type_id');
|
|
|
- $type = tripal_get_cvterm(array(
|
|
|
- 'name' => $node->example_type,
|
|
|
- 'cv_id' => $type_cv->cv_id,
|
|
|
- ));
|
|
|
-
|
|
|
- // perform the insert using the chado_insert_record function();
|
|
|
- $values = array(
|
|
|
- 'uniquename' => $node->uniquename,
|
|
|
- 'description' => $node->description,
|
|
|
- 'type_id' => $type->cvterm_id,
|
|
|
- 'organism_id' => $node->organism_id,
|
|
|
- );
|
|
|
- $example = chado_insert_record('example', $values);
|
|
|
- if (!$example) {
|
|
|
- drupal_set_message(t('Unable to add example.'), 'warning');
|
|
|
- tripal_report_error('tripal_example', TRIPAL_WARNING, 'Insert example: Unable to create example where values: %values',
|
|
|
- array('%values' => print_r($values, TRUE)));
|
|
|
- return;
|
|
|
- }
|
|
|
-
|
|
|
- // get the example_id for linking Drupal node with Chado data
|
|
|
- $example_id = $example['example_id'];
|
|
|
-
|
|
|
- // Only add to other Chado tables if the base record was inserted properly
|
|
|
- if ($example_id > 0) {
|
|
|
-
|
|
|
- // If you implemented the properties form in chado_example_form then you
|
|
|
- // need to handle inserting these properties into your Chado prop table.
|
|
|
- $details = array(
|
|
|
- // the name of the prop table
|
|
|
- 'property_table' => 'exampleprop',
|
|
|
- // the name of your Chado base table
|
|
|
- 'base_table' => 'example',
|
|
|
- // the name of the key in your base table
|
|
|
- 'foreignkey_name' => 'example_id',
|
|
|
- // the value of the example_id key
|
|
|
- 'foreignkey_value' => $example_id
|
|
|
- );
|
|
|
- chado_update_node_form_properties($node, $details);
|
|
|
-
|
|
|
- // If you implemented the dbxrefs form in chado_example_form then you need
|
|
|
- // to handle inserting these database references into your Chado _dbxref
|
|
|
- // table.
|
|
|
- $details = array(
|
|
|
- // the name of your _dbxref table
|
|
|
- 'linking_table' => 'example_dbxref',
|
|
|
- // the name of the key in your base table
|
|
|
- 'foreignkey_name' => 'example_id',
|
|
|
- // the value of the example_id key
|
|
|
- 'foreignkey_value' => $example_id
|
|
|
- );
|
|
|
- chado_update_node_form_dbxrefs($node, $details);
|
|
|
-
|
|
|
- // If you implemented the relationships form in chado_example_form then
|
|
|
- // you need to handle inserting these relationships into your Chado
|
|
|
- // _relationship table.
|
|
|
- $details = array(
|
|
|
- // name of the _relationship table
|
|
|
- 'relationship_table' => 'example_relationship',
|
|
|
- // value of the example_id key
|
|
|
- 'foreignkey_value' => $example_id
|
|
|
- );
|
|
|
- chado_update_node_form_relationships($node, $details);
|
|
|
- }
|
|
|
- }
|
|
|
- else {
|
|
|
- // the node has an example_id so get it for linking Drupal node with Chado
|
|
|
- // data
|
|
|
- $example_id = $node->example_id;
|
|
|
- }
|
|
|
-
|
|
|
- // Make sure the entry for this example doesn't already exist in the
|
|
|
- // chado_example table if it doesn't exist then we want to add it.
|
|
|
- $check_org_id = chado_get_id_from_nid('example', $node->nid);
|
|
|
- if (!$check_org_id) {
|
|
|
- $record = new stdClass();
|
|
|
- $record->nid = $node->nid;
|
|
|
- $record->vid = $node->vid;
|
|
|
- $record->example_id = $example_id;
|
|
|
- drupal_write_record('chado_example', $record);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implementation of hook_update(). This function runs after the node has been
|
|
|
- * inserted into the Drupal schema and allows us to update the record in Chado.
|
|
|
- *
|
|
|
- * This function is not required if the hook_node_info() does not define any
|
|
|
- * custom node types.
|
|
|
- *
|
|
|
- * @ingroup tripal_example
|
|
|
- */
|
|
|
-function chado_example_update($node) {
|
|
|
- // be sure to always trim text fields
|
|
|
- $node->uniquename = trim($node->uniquename);
|
|
|
- $node->description = trim($node->description['value']);
|
|
|
-
|
|
|
- // use the chado_update_record() function to update the record
|
|
|
- $match = array(
|
|
|
- 'example_id' => $example_id,
|
|
|
- );
|
|
|
- $values = array(
|
|
|
- 'uniquename' => $node->uniquename,
|
|
|
- );
|
|
|
- $options = array('return_record' => TRUE);
|
|
|
- $status = chado_update_record('example', $match, $values, $options);
|
|
|
-
|
|
|
- if (!$status) {
|
|
|
- drupal_set_message(t('Unable to update example.'), 'warning');
|
|
|
- tripal_report_error('tripal_example', TRIPAL_WARNING, 'Update example: Unable to update example where values: %values',
|
|
|
- array('%values' => print_r($values, TRUE)));
|
|
|
- }
|
|
|
-
|
|
|
- // If you implemented the properties form in chado_example_form then you need
|
|
|
- // to handle updating these properties into your Chado prop table.
|
|
|
- $details = array(
|
|
|
- 'property_table' => 'exampleprop', // the name of the prop table
|
|
|
- 'base_table' => 'example', // the name of your Chado base table
|
|
|
- 'foreignkey_name' => 'example_id', // the name of the key in your base table
|
|
|
- 'foreignkey_value' => $example_id // the value of the example_id key
|
|
|
- );
|
|
|
- chado_update_node_form_properties($node, $details);
|
|
|
-
|
|
|
- // If you implemented the dbxrefs form in chado_example_form then you need to
|
|
|
- // handle updating these database references into your Chado _dbxref table.
|
|
|
- $details = array(
|
|
|
- 'linking_table' => 'example_dbxref', // the name of your _dbxref table
|
|
|
- 'foreignkey_name' => 'example_id', // the name of the key in your base table
|
|
|
- 'foreignkey_value' => $example_id // the value of the example_id key
|
|
|
- );
|
|
|
- chado_update_node_form_dbxrefs($node, $details);
|
|
|
-
|
|
|
- // If you implemented the relationships form in chado_example_form then you
|
|
|
- // need to handle updating these relationships into your Chado _relationship
|
|
|
- // table.
|
|
|
- $details = array(
|
|
|
- // name of the _relationship table
|
|
|
- 'relationship_table' => 'example_relationship',
|
|
|
- // value of the example_id key
|
|
|
- 'foreignkey_value' => $example_id
|
|
|
- );
|
|
|
- chado_update_node_form_relationships($node, $details);
|
|
|
-
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implementation of hook_delete(). This function runs after the node has been
|
|
|
- * deleted from the Drupal schema and allows us to delete the corresponding
|
|
|
- * record in Chado.
|
|
|
- *
|
|
|
- * This function is not required if the hook_node_info() does not define any
|
|
|
- * custom node types.
|
|
|
- *
|
|
|
- * @ingroup tripal_example
|
|
|
- */
|
|
|
-function chado_example_delete($node) {
|
|
|
-
|
|
|
- // get the example id from the node
|
|
|
- $example_id = chado_get_id_from_nid('example', $node->nid);
|
|
|
-
|
|
|
- // if we don't have a example id for this node then this isn't a node of type
|
|
|
- // chado_example or the entry in the chado_example table was lost.
|
|
|
- if (!$example_id) {
|
|
|
- return;
|
|
|
- }
|
|
|
-
|
|
|
- // remove the entry in the chado_exapmle table linking the deleted
|
|
|
- // Drupal node with the data in Chado
|
|
|
- $sql_del = "DELETE FROM {chado_example} WHERE nid = :nid AND vid = :vid";
|
|
|
- db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid));
|
|
|
-
|
|
|
- // Remove data from example tables of Chado database. This will
|
|
|
- // cause a cascade delete and remove all data in referencing tables
|
|
|
- // for this example
|
|
|
- chado_query("DELETE FROM {example} WHERE example_id = :example_id", array(':example_id' => $example_id));
|
|
|
-
|
|
|
- // inform the user that the data was deleted
|
|
|
- drupal_set_message(t("The example and all associated data were removed from Chado"));
|
|
|
-
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implementation of hook_load(). This function is necessary to load into the
|
|
|
- * $node object the fields of the table form Chado. For example for the example
|
|
|
- * table, the chado_example_load() function adds in a example object which
|
|
|
- * contains all of the fields and sub objects for data in tables with foreign
|
|
|
- * key relationships.
|
|
|
- *
|
|
|
- * This function is not required if the hook_node_info() does not define any
|
|
|
- * custom node types.
|
|
|
- *
|
|
|
- * @ingroup tripal_example
|
|
|
- */
|
|
|
-function chado_example_load($nodes) {
|
|
|
-
|
|
|
- // EXPLANATION: when displaying or node or accessing the node in a template
|
|
|
- // we need the data from Chado. This function finds the record in Chado that
|
|
|
- // this node belongs to and adds the record.
|
|
|
-
|
|
|
- // there may be multiple nodes that get passed in so we have to iterate
|
|
|
- // through them all
|
|
|
- foreach ($nodes as $nid => $node) {
|
|
|
- // find the example and add in the details
|
|
|
- $example_id = chado_get_id_from_nid('example', $nid);
|
|
|
-
|
|
|
- // if the nid does not have a matching record then skip this node.
|
|
|
- // this can happen with orphaned nodes.
|
|
|
- if (!$example_id) {
|
|
|
- continue;
|
|
|
- }
|
|
|
-
|
|
|
- // build the example variable by using the chado_generate_var() function
|
|
|
- $values = array('example_id' => $example_id);
|
|
|
- $example = chado_generate_var('example', $values);
|
|
|
-
|
|
|
- // for fields in the table that are of type 'text' you may want to include
|
|
|
- // those by default, the chado_generate_var does not include text fields as
|
|
|
- // they may be very large and including a large text field can slow the page
|
|
|
- // load.
|
|
|
- // If you know a text field will never be large and it is important for the
|
|
|
- // other functions that will see the node to have access to a field you can
|
|
|
- // include it here using the chado_expand_var() function. In most
|
|
|
- // cases it is probably best to let the end-user decide if text fields
|
|
|
- // should be included by using this function in the templates.
|
|
|
- $example = chado_expand_var($example, 'field', 'example.description');
|
|
|
-
|
|
|
- // add the new example object to this node.
|
|
|
- $nodes[$nid]->example = $example;
|
|
|
-
|
|
|
- // If your module is using the Chado Node: Title & Path API to allow custom
|
|
|
- // titles for your node type. Every time you want the title of the node, you
|
|
|
- // need to use the following API function:
|
|
|
- $node->title = chado_get_node_title($node);
|
|
|
-
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implementation of hook_node_presave().
|
|
|
- *
|
|
|
- * Performs actions on a node object prior to it being saved
|
|
|
- *
|
|
|
- * @ingroup tripal_example
|
|
|
- */
|
|
|
-function tripal_example_node_presave($node) {
|
|
|
-
|
|
|
- // EXPLANATION: This node is useful for making changes to the node prior to it
|
|
|
- // being saved to the database.
|
|
|
- // One useful case for this is to set the title of a node using values
|
|
|
- // supplied by the user.
|
|
|
- //
|
|
|
- // This function is not required. You probably won't need it if you don't
|
|
|
- // define a custom node type in the hook_node_info() function. But it is node
|
|
|
- // type agnostic, so you can use this function to change the contents of any
|
|
|
- // node regardless of it's type.
|
|
|
-
|
|
|
- // set the node title
|
|
|
- switch ($node->type) {
|
|
|
- // This step is for setting the title for the Drupal node. This title is
|
|
|
- // permanent and thus is created to be unique. Title changes provided by
|
|
|
- // tokens are generated on the fly dynamically, but the node title seen in
|
|
|
- // the content listing needs to be set here. Do not call the
|
|
|
- // chado_get_node_title() function here to set the title as the node object
|
|
|
- // isn't properly filled out and the function will fail.
|
|
|
- case 'chado_example':
|
|
|
- // for a form submission the 'uniquename' field will be set,
|
|
|
- // for a sync, we must pull from the example object
|
|
|
- if (property_exists($node, 'uniquename')) {
|
|
|
- // set the title
|
|
|
- $node->title = $node->uniquename;
|
|
|
- }
|
|
|
- else if (property_exists($node, 'example')) {
|
|
|
- $node->title = $node->example->uniquename;
|
|
|
- }
|
|
|
- break;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implementation of hook node_insert().
|
|
|
- *
|
|
|
- * Performs actions after any node has been inserted.
|
|
|
- *
|
|
|
- * @ingroup tripal_example
|
|
|
- */
|
|
|
-function tripal_example_node_insert($node) {
|
|
|
-
|
|
|
- // EXPLANATION: This function is used after any a node is inserted into the
|
|
|
- // database. It is different from the hook_insert() function above in that it
|
|
|
- // is called after any node is saved, regardless of it's type. This function
|
|
|
- // is useful for making changes to the database after a node is inserted.
|
|
|
- // An example comes from the tripal_feature module where the URL alias of a
|
|
|
- // node cannot be set in the hook_insert() function. Therefore the
|
|
|
- // tripal_feature module uses this function to set the URL path of a newly
|
|
|
- // inserted example node.
|
|
|
- //
|
|
|
- // This function is not required. You probably won't need it if you don't
|
|
|
- // define a custom node type in the hook_node_info() function. But it is node
|
|
|
- // type agnostic, so you can use this function to do any activity after insert
|
|
|
- // of any node.
|
|
|
-
|
|
|
- // the Example code below will set the URL path after inserting. We do it here
|
|
|
- // because we do not know the example_id in the pre-save and cannot do it in
|
|
|
- // the hook_insert()
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_example':
|
|
|
-
|
|
|
- // find the example and add in the details
|
|
|
- $example_id = chado_get_id_from_nid('example', $nid);
|
|
|
-
|
|
|
- // build the example variable by using the chado_generate_var() function
|
|
|
- $values = array('example_id' => $example_id);
|
|
|
- $example = chado_generate_var('example', $values);
|
|
|
- $node->example = $example;
|
|
|
-
|
|
|
-
|
|
|
- // EXPLANATION: You can allow the site admin to customize the
|
|
|
- // title and URL of your node. The 'Chado Node: Title & Path API'
|
|
|
- // contains two functions that can be called to generate the title and
|
|
|
- // URL based a schema provided by the site admin. These functions are
|
|
|
- // named chado_get_node_title() and chado_set_node_url(). These
|
|
|
- // functions use a string of tokens to build the URL and titles and the
|
|
|
- // site admin has the ability to set these tokens. There are
|
|
|
- // form elements made available in the tripal_example_admin() function
|
|
|
- // that allow the admin to set these tokens. The default token string
|
|
|
- // is provided to Tripal using two hook functions, and are found below.
|
|
|
- // These are: chado_exmaple_chado_node_default_title() and
|
|
|
- // chado_example_chdo_node_default_url().
|
|
|
-
|
|
|
- // Set the Title and URL for this node.
|
|
|
- $example->title = chado_get_node_title($node);
|
|
|
- chado_set_node_url($node);
|
|
|
- break;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implementation of hook node_update().
|
|
|
- *
|
|
|
- * Performs actions after any node has been updated.
|
|
|
- *
|
|
|
- */
|
|
|
-function tripal_example_node_update($node) {
|
|
|
-
|
|
|
- // EXPLANATION: This function is used after any a node is updated in the
|
|
|
- // database. It is different from the hook_update() function above in that it
|
|
|
- // is called after any node is updated, regardless of it's type.
|
|
|
- // An example comes from the tripal_feature module where the URL alias of a
|
|
|
- // node cannot be set in the hook_update() function. Therefore the
|
|
|
- // tripal_feature module uses this function to reset the URL path of an
|
|
|
- // updated feature node.
|
|
|
- //
|
|
|
- // This function is not required. You probably won't need it if you don't
|
|
|
- // define a custom node type in the hook_node_info() function. But it is node
|
|
|
- // type agnostic, so you can use this function to do any activity after insert
|
|
|
- // of a node.
|
|
|
-
|
|
|
- // add items to other nodes, build index and search results
|
|
|
- switch ($node->type) {
|
|
|
- case 'chado_example':
|
|
|
-
|
|
|
- // If your module is using the Chado Node: Title & Path API to allow
|
|
|
- // custom titles for your node type. Every time you want the title of the
|
|
|
- // node, you need to use the following API function:
|
|
|
- $example->title = chado_get_node_title($node);
|
|
|
-
|
|
|
- // set the URL for this example page
|
|
|
- // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc
|
|
|
- // file in the function tripal_feature_node_insert for an example of how
|
|
|
- // that module sets the URL. It uses a configuration file to allow the
|
|
|
- // user to dynamically build a URL schema and then uses that schema to
|
|
|
- // generate a URL string.
|
|
|
- break;
|
|
|
- }
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-}
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-/**
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- * Implementation of hook_node_view().
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- *
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- * @ingroup tripal_example
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- */
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-function tripal_example_node_view($node, $view_mode, $langcode) {
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-
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- // EXPLANATION: This function defines the content "blocks" that appear when
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- // the node is displayed. It is node type agnostic so we can add content to
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- // any node type. So, we use this function to add the content from all of our
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- // theme templates onto our new node type. We will also use this function to
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- // add content to other node types.
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-
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- switch ($node->type) {
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- case 'chado_example':
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- // there are different ways a node can be viewed. Primarily Tripal
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- // supports full page view and teaser view.
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- if ($view_mode == 'full') {
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-
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- // If you want to use the default Tripal node template then you need to
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- // tell Tripal to generate the Table of Contents. This is done by
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- // setting the following to TRUE. If your content type follows the
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- // chado_<base table> convention then this is the default. In this case
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- // if you don't want to use the default template then you need to set
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- // the following to FALSE.
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- $node->content['#tripal_generic_node_template'] = TRUE;
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-
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- // There is always a base template. This is the template that is first
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- // shown when the example node type is first displayed.
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- // If you are using the default Tripal node template, then you should
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- // also set two additional items in each array: tripal_toc_id and
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- // tripal_toc_title. The tripal_tock_id should be a single unique
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- // world that is used to reference the template. This ID is used for
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- // constructing URLs for the content. The tripal_toc_title contains
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- // the title that should appear in the table of contents for this
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- // content. You should only set the '#weight' element for the base
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- // template (or Overview) to ensure that it appears at the top of the
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- // list. Otherwise items are sorted alphabetically.
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- $node->content['tripal_example_base'] = array(
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- '#theme' => 'tripal_example_base',
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- '#node' => $node,
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- '#tripal_toc_id' => 'base',
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- '#tripal_toc_title' => 'Overview',
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- '#weight' => -100,
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- );
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- // we can add other templates as well for properties, publications,
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- // dbxrefs, etc...
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- $node->content['tripal_example_properties'] = array(
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- '#theme' => 'tripal_example_properties',
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- '#node' => $node,
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- '#tripal_toc_id' => 'properties',
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- '#tripal_toc_title' => 'Properties',
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- );
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- $node->content['tripal_example_references'] = array(
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- '#theme' => 'tripal_example_references',
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- '#node' => $node,
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- '#tripal_toc_id' => 'references',
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- '#tripal_toc_title' => 'Cross References',
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- );
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- $node->content['tripal_example_relationships'] = array(
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- '#theme' => 'tripal_example_relationships',
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- '#node' => $node,
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- '#tripal_toc_id' => 'relationships',
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- '#tripal_toc_title' => 'Relationships',
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- );
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-
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- // Note: if you create a template that you do not want a user to know
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- // where it is (discourage editing of it), you can add the following
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- // key: '#tripal_template_show' => FALSE. If this key/value is set the
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- // administrator message that Tripal provides indicating where the
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- // template is housed will not be shown.
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- }
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- // set the content for the teaser view
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- if ($view_mode == 'teaser') {
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- // The teaser is also a required template
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- $node->content['tripal_example_teaser'] = array(
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- '#theme' => 'tripal_example_teaser',
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- '#node' => $node,
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- );
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- }
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- break;
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- // you can add custom content to any node type by adding content to the node
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- // in the same way as above.
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- case 'chado_organism':
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- if ($view_mode == 'full') {
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- $node->content['tripal_organism_examples'] = array(
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- '#theme' => 'tripal_organism_examples',
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- '#node' => $node,
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- '#tripal_toc_id' => 'examples',
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- '#tripal_toc_title' => 'Examples',
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- );
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- }
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- break;
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- // ... etc
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- }
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-}
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-
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-
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-/**
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|
- * Implements [content_type]_chado_node_default_title_format().
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|
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- *
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|
|
- * Defines a default title format for the Chado Node API to set the titles on
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|
|
- * Chado example nodes based on chado fields.
|
|
|
- */
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|
|
-function chado_example_chado_node_default_title_format() {
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|
- return '[example.name], [example.uniquename] ([example.type_id>cvterm.name]) [example.organism_id>organism.genus] [example.organism_id>organism.species]';
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-}
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-
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|
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-/**
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|
|
- * Implements hook_chado_node_default_url_format().
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|
|
- *
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|
|
- * Designates a default URL format for example nodes.
|
|
|
- */
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|
|
-function chado_example_chado_node_default_url_format() {
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|
|
- return '/example/[example.organism_id>organism.genus]/[example.organism_id>organism.species]/[example.type_id>cvterm.name]/[example.uniquename]';
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|
|
-}
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Stephen Ficklin