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@@ -9,7 +9,7 @@
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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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+ * 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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@@ -30,22 +30,26 @@ function tripal_example_node_info() {
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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 will sync the node
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- // types with data in Chado. When Drupal creates a node it has no way of
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- // coordinating which node belongs to which record in Chado. Therefore,
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- // Tripal maintains tables in the Drupal schema that maps Drupal nodes
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- // to recrords in Chado. Syncing is the process of creating Drupal nodes
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- // and linking them to the appropriate record.
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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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- 'base_table' => 'example', // the base table name (e.g. example, example, contact)
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- 'hook_prefix' => 'chado_example',// the node type hook prefix
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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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- 'singular' => t('Example'), // how to refer to the record
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- 'plural' => t('Examples') // how to refer to the record in plurals
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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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+ '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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@@ -54,28 +58,26 @@ function tripal_example_node_info() {
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}
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/**
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- * Implement hook_access(). This hook provides instructions to
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- * drupal for which users can access the custom content types
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- * created in the function above. The available permissions
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- * are set in the chado_example_permissions() hook in the
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- * tripal_example.module file. This hook is not needed
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- * if no node types were defined in the hook_node_info() hook.
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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 specificially
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- * deny access. This allows for other mechanisms to to deny
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- * or reject access. If the return value is TRUE then access
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- * is granted regardless of any other rules that might be implemented
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- * by other modules.
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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 chado_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 = $node->type;
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}
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- // EXPLANATION: in the tripal_example_permissions() function we
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- // created the permission types that are used here to check for
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- // access permissions to the 'chado_exmaple' node type.
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+ // EXPLANATION: in the tripal_example_permissions() function we created the
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+ // permission types that are used here to check for access permissions to the
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+ // 'chado_exmaple' node type.
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if($node_type == 'chado_example') {
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if ($op == 'create') {
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if (!user_access('create chado_example content', $account)) {
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@@ -111,37 +113,38 @@ function chado_example_node_access($node, $op, $account) {
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*/
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function chado_example_form($node, &$form_state) {
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- // EXPLANATION: This function should construct a form array that is used
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- // by Drupal to contruct a form for inserting or editing our new node type.
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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 elemetns for properties,
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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
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- // only has a uniquename, organism_id, type_id and example_id.
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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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$form = array();
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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 example
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- // 2) in the $form_state['values'] array which occurs on a failed validation or
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- // ajax callbacks from non submit form elements
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- // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit
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- // form elements and the form is being rebuilt
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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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// 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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+ $example = null; // holds the example object record
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+ $example_id = null; // when editing an example record we'll have an example_id
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// initialize the defaults for the form fields
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$uniquename = '';
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@@ -164,8 +167,8 @@ function chado_example_form($node, &$form_state) {
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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 callback
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- // then use the $form_state['values'] values
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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 = $form_state['values']['example_type'];
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@@ -188,12 +191,12 @@ function chado_example_form($node, &$form_state) {
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'#title' => t('Unique Name'),
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'#required' => TRUE,
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'#default_value' => $uniquename,
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- '#description' => t('Enter a unique name for this example. This name must be unique.'),
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+ '#description' => t('Enter a unique name for this example. This name must be unique.'),
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'#maxlength' => 255
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);
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- // for the type_id we want to use the default vocabulary so that this
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- // field can have autocomplete functionality
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+ // for the type_id we want to use the default vocabulary so that this field
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+ // can have auto-complete functionality
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$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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@@ -226,43 +229,58 @@ function chado_example_form($node, &$form_state) {
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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 entries
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- // from it through your node form then add this section to your own node form
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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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- 'property_table' => 'exampleprop', // the name of the prop table
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- 'chado_id' => $example_id, // the value of example_id for this record
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- 'cv_id' => $cv_id // the cv.cv_id of the cv governing exampleprop.type_id
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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, $details);
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// ADDITIONAL DBXREFS FORM
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//---------------------------------------------
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- // If there is a example_dbxref table and you want to allow users to add/remove entries
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- // from it through your node form then add this section to your own node form
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+ // If there is a example_dbxref table and you want to allow users to
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+ // add/remove entries from it through your node form then add this section to
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+ // your own node form
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$details = array(
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- 'linking_table' => 'example_dbxref', // the name of the _dbxref table
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- 'base_foreign_key' => 'example_id', // the name of the key in your base chado table
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- 'base_key_value' => $example_id // the value of example_id for this record
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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, $details);
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// RELATIONSHIPS FORM
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//---------------------------------------------
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- // If there is a example_relationship table and you want to allow users to add/remove entries
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- // from it through your node form then add this section to your own node form
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+ // If there is a example_relationship table and you want to allow users to
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+ // add/remove entries from it through your node form then add this section to
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+ // your own node form
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$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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- 'relationship_table' => 'example_relationship', // the name of the _relationship table
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- 'base_table' => 'example', // the name of your chado base table
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- 'base_foreign_key' => 'example_id', // the name of the key in your base chado table
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- 'base_key_value' => $example_id, // the value of example_id for this record
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- 'nodetype' => 'example', // the human-readable name of your node type
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- 'cv_id' => $cv_id // the cv.cv_id of the cv governing example_relationship.type_id
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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, $details);
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@@ -274,14 +292,14 @@ function chado_example_form($node, &$form_state) {
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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
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- * is detected, it sets the error using form_set_error() which takes the
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- * user back to the form to make corrections.
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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 niether drupal nor chado
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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 $node
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*
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@@ -294,19 +312,19 @@ function chado_example_validate($node, $form, &$form_state) {
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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($node->op != 'Save') {
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+ if(property_exists($node, "op") and $node->op != 'Save') {
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return;
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}
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- // we are syncing if we do not have a node ID but we do have a example_id. We don't
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- // need to validate during syncing so just skip it.
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- if (is_null($node->nid) and property_exists($node, 'example_id') and $node->example_id != 0) {
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+ // we are syncing if we do not have a node ID but we do have a example_id. We
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+ // don't need to validate during syncing so just skip it.
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+ if (!property_exists($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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// be sure to always trim text fields
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- $node->uniquename = trim($node->uniquename);
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- $node->description = trim($node->description);
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+ $node->uniquename = property_exists($node, 'uniquename') ? trim($node->uniquename) : '';
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+ $node->description = property_exists($node, 'description') ? trim($node->description) : '';
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// Validating for an update. If the 'nid' property is present in the node then
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// this is an update and validation can be different for updates
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@@ -322,8 +340,8 @@ function chado_example_validate($node, $form, &$form_state) {
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form_set_error('feature_type', t("The feature type is not a valid name from the Sequence Ontology."));
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}
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- // TODO: also we should check that the unique constraint is not invalidated by
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- // changing either the type_id, organism_id or uniquename.
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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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@@ -342,14 +360,14 @@ function chado_example_validate($node, $form, &$form_state) {
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}
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/**
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- * Implementation of hook_insert(). This function is called after the
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- * node is inserted into the database. We need it so that we can insert
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- * appropriate fields as provided by the user into the database. And so that
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- * we can link the new Drupal node to the data in Chado via the chado_example
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- * linking table. We 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 table
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- * to link the Drupal node with the data in the 'example' table of Chado.
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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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@@ -357,22 +375,25 @@ function chado_example_validate($node, $form, &$form_state) {
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* @ingroup tripal_example
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*/
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function chado_example_insert($node) {
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- // be sure to always trim text fields
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- $node->uniquename = trim($node->uniquename);
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- $node->description = trim($node->description);
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- // get the example type record
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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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+ $example_id = '';
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// if there is an example_id in the $node object then this must be a sync so
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- // we can skip adding the example as it is already there, although
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- // we do need to proceed with the rest of the insert
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+ // we can skip adding the example as it is already there, although we do need
|
|
|
+ // to proceed with insertion into the chado/drupal linking table.
|
|
|
if (!property_exists($node, 'example_id')) {
|
|
|
|
|
|
+ // be sure to always trim text fields
|
|
|
+ $node->uniquename = trim($node->uniquename);
|
|
|
+ $node->description = trim($node->description);
|
|
|
+
|
|
|
+ // 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' => $node->uniquename,
|
|
|
@@ -391,39 +412,51 @@ function chado_example_insert($node) {
|
|
|
// get the example_id for linking Drupal node with Chado data
|
|
|
$example_id = $example['example_id'];
|
|
|
|
|
|
- // Only add to other chado tables if the base record was inserted properly
|
|
|
+ // Only add to other Chado tables if the base record was inserted properly
|
|
|
if ($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.
|
|
|
+ // 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(
|
|
|
- '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
|
|
|
+ // 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.
|
|
|
+ // 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(
|
|
|
- '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
|
|
|
+ // 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.
|
|
|
+ // 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(
|
|
|
- 'relationship_table' => 'example_relationship', // name of the _relationship table
|
|
|
- 'foreignkey_value' => $example_id // value of the example_id key
|
|
|
+ // 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
|
|
|
+ // the node has an example_id so get it for linking Drupal node with Chado
|
|
|
+ // data
|
|
|
$example_id = $node->example_id;
|
|
|
}
|
|
|
|
|
|
@@ -440,12 +473,11 @@ function chado_example_insert($node) {
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- * 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.
|
|
|
+ * 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.
|
|
|
+ * This function is not required if the hook_node_info() does not define any
|
|
|
+ * custom node types.
|
|
|
*
|
|
|
* @ingroup tripal_example
|
|
|
*/
|
|
|
@@ -470,41 +502,44 @@ function chado_example_update($node) {
|
|
|
array('%values' => print_r($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.
|
|
|
+ // 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
|
|
|
+ '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.
|
|
|
+ // 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
|
|
|
+ '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.
|
|
|
+ // 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(
|
|
|
- 'relationship_table' => 'example_relationship', // name of the _relationship table
|
|
|
- 'foreignkey_value' => $example_id // value of the example_id key
|
|
|
+ // 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, $details);
|
|
|
|
|
|
}
|
|
|
/**
|
|
|
- * Implementation of hook_delete(). This function runs after the
|
|
|
- * node has been deleted from the Drupal schema and allows us to
|
|
|
- * delete the corresponding recrod in Chado.
|
|
|
+ * Implementation of hook_delete(). This function runs after the node has been
|
|
|
+ * deleted from the Drupal schema and allows us to delete the corresponding
|
|
|
+ * record in Chado.
|
|
|
*
|
|
|
- * This function is not required if the hook_node_info() does not define
|
|
|
- * any custom node types.
|
|
|
+ * This function is not required if the hook_node_info() does not define any
|
|
|
+ * custom node types.
|
|
|
*
|
|
|
* @ingroup tripal_example
|
|
|
*/
|
|
|
@@ -513,18 +548,18 @@ function chado_example_delete($node) {
|
|
|
// get the example id from the node
|
|
|
$example_id = chado_get_id_from_nid('example', $node->nid);
|
|
|
|
|
|
- // if we don't have a example id for this node then this isn't a node of
|
|
|
- // type chado_example or the entry in the chado_example table was lost.
|
|
|
+ // if we don't have a example id for this node then this isn't a node of type
|
|
|
+ // chado_example or the entry in the chado_example table was lost.
|
|
|
if (!$example_id) {
|
|
|
return;
|
|
|
}
|
|
|
|
|
|
// remove the entry in the chado_exapmle table linking the deleted
|
|
|
- // Drupal node with the data in chado
|
|
|
+ // 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
|
|
|
+ // 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' => $example_id));
|
|
|
@@ -535,25 +570,25 @@ function chado_example_delete($node) {
|
|
|
}
|
|
|
|
|
|
/**
|
|
|
- * 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.
|
|
|
+ * Implementation of hook_load(). This function is necessary to load into the
|
|
|
+ * $node object the fields of the table form Chado. For example for the example
|
|
|
+ * table, the chado_example_load() function adds in a example object which
|
|
|
+ * contains all of the fields and sub objects for data in tables with foreign
|
|
|
+ * key relationships.
|
|
|
*
|
|
|
- * This function is not required if the hook_node_info() does not define
|
|
|
- * any custom node types.
|
|
|
+ * This function is not required if the hook_node_info() does not define any
|
|
|
+ * custom node types.
|
|
|
*
|
|
|
* @ingroup tripal_example
|
|
|
*/
|
|
|
function chado_example_load($nodes) {
|
|
|
|
|
|
// EXPLANATION: when displaying or node or accessing the node in a template
|
|
|
- // we need the data from Chado. This fucntion finds the record in Chado that
|
|
|
+ // 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
|
|
|
+ // 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', $nid);
|
|
|
@@ -568,20 +603,21 @@ function chado_example_load($nodes) {
|
|
|
$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.
|
|
|
+ // 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.
|
|
|
+ // 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');
|
|
|
|
|
|
|
|
|
- // 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:
|
|
|
+ // 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);
|
|
|
|
|
|
// add the new example object to this node.
|
|
|
@@ -598,24 +634,24 @@ function chado_example_load($nodes) {
|
|
|
*/
|
|
|
function tripal_example_node_presave($node) {
|
|
|
|
|
|
- // EXPLANATION: This node is useful for
|
|
|
- // making changes to the node prior to it being saved to the database.
|
|
|
+ // 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.
|
|
|
+ // 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 ($node->type) {
|
|
|
- // This step is for setting the title for the Drupal node. This title
|
|
|
- // is permanent and thus is created to be unique. Title changes provided
|
|
|
- // by tokens are generated on the fly dynamically, but the node title
|
|
|
- // seen in the content listing needs to be set here. Do not call
|
|
|
- // the chado_get_node_title() function here to set the title as the node
|
|
|
- // object isn't properly filled out and the function will fail.
|
|
|
+ // This step is for setting the title for the Drupal node. This title is
|
|
|
+ // permanent and thus is created to be unique. Title changes provided by
|
|
|
+ // tokens are generated on the fly dynamically, but the node title seen in
|
|
|
+ // the content listing needs to be set here. Do not call the
|
|
|
+ // chado_get_node_title() function here to set the title as the node object
|
|
|
+ // isn't properly filled out and the function will fail.
|
|
|
case 'chado_example':
|
|
|
// for a form submission the 'uniquename' field will be set,
|
|
|
// for a sync, we must pull from the example object
|
|
|
@@ -639,24 +675,23 @@ function tripal_example_node_presave($node) {
|
|
|
*/
|
|
|
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, regardlesss 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.
|
|
|
+ // 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 presave and cannot do
|
|
|
- // it in the hook_insert()
|
|
|
+ // 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':
|
|
|
|
|
|
@@ -668,17 +703,17 @@ function tripal_example_node_insert($node) {
|
|
|
$example = chado_generate_var('example', $values);
|
|
|
$node->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:
|
|
|
+ // 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
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- // to dynmically build a URL schema and then uses that schema to generate
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- // a URL string.
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+ // see the code in the tripal_feature/includes/tripal_feature.chado_node.inc
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+ // file in the function tripal_feature_node_insert for an example of how
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+ // that module sets the URL. It uses a configuration file to allow the
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+ // user to dynamically build a URL schema and then uses that schema to
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+ // generate a URL string.
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break;
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}
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}
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@@ -691,35 +726,34 @@ function tripal_example_node_insert($node) {
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*/
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function tripal_example_node_update($node) {
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- // EXPLANATION: This function is used
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- // after any a node is updated in the database. It is different
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- // from the hook_update() function above in that it is called after
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- // any node is updated, regardlesss of it's type.
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- // An example comes from the tripal_feature module where the URL alias
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- // of a node cannot be set in the hook_update() function. Therefore
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- // the tripal_feature module uses this function to reset the url path
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- // of an updated feature node.
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+ // EXPLANATION: This function is used after any a node is updated in the
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+ // database. It is different from the hook_update() function above in that it
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+ // is called after any node is updated, regardless of it's type.
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+ // An example comes from the tripal_feature module where the URL alias of a
|
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+ // node cannot be set in the hook_update() function. Therefore the
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+ // tripal_feature module uses this function to reset the URL path of an
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+ // updated feature node.
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//
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- // This function is not required. You probably won't need it if you
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- // don't define a custom node type in the hook_node_info() function. But
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- // it is node type agnostic, so you can use this function to do any
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- // activity after insert of a node.
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+ // This function is not required. You probably won't need it if you don't
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|
+ // define a custom node type in the hook_node_info() function. But it is node
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+ // type agnostic, so you can use this function to do any activity after insert
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+ // of a node.
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// add items to other nodes, build index and search results
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switch ($node->type) {
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|
case 'chado_example':
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- // If your module is using the Chado Node: Title & Path API to allow custom titles
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|
- // for your node type. Every time you want the title of the node, you need to use the
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|
- // following API function:
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|
+ // 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:
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|
|
$example->title = chado_get_node_title($node);
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|
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|
|
// 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 dynmically build a URL schema and then uses that schema to generate
|
|
|
- // a URL string.
|
|
|
+ // 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;
|
|
|
}
|
|
|
}
|
|
|
@@ -730,11 +764,11 @@ function tripal_example_node_update($node) {
|
|
|
*/
|
|
|
function tripal_example_node_view($node, $view_mode, $langcode) {
|
|
|
|
|
|
- // EXPLANATION: This function defines the content "blocks" that appear
|
|
|
- // when thhe node is displayed. It is node type agnostic so we can add
|
|
|
- // content to any node type. So, we use this function to add the content
|
|
|
- // from all of our theme templates onto our new node type. We will also
|
|
|
- // use this function to add content to other node types.
|
|
|
+ // EXPLANATION: This function defines the content "blocks" that appear when
|
|
|
+ // the node is displayed. It is node type agnostic so we can add content to
|
|
|
+ // any node type. So, we use this function to add the content from all of our
|
|
|
+ // theme templates onto our new node type. We will also use this function to
|
|
|
+ // add content to other node types.
|
|
|
|
|
|
switch ($node->type) {
|
|
|
case 'chado_example':
|
|
|
@@ -742,24 +776,25 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
|
|
|
// supports full page view and teaser view.
|
|
|
if ($view_mode == 'full') {
|
|
|
|
|
|
- // If you want to use the default Tripal node template then you need to tell
|
|
|
- // tripal to generate the Table of Contents. This is done by setting the following
|
|
|
- // to TRUE. If your content type follows the chado_<base table> convention
|
|
|
- // then this is the default. In this case if you don't want to use the default
|
|
|
- // template then you need to set the following to FALSE.
|
|
|
+ // If you want to use the default Tripal node template then you need to
|
|
|
+ // tell Tripal to generate the Table of Contents. This is done by
|
|
|
+ // setting the following to TRUE. If your content type follows the
|
|
|
+ // chado_<base table> convention then this is the default. In this case
|
|
|
+ // if you don't want to use the default template then you need to set
|
|
|
+ // the following to FALSE.
|
|
|
$node->content['#tripal_generic_node_template'] = TRUE;
|
|
|
|
|
|
- // There is always a base template. This is the template that
|
|
|
- // is first shown when the example node type is first displayed.
|
|
|
- // if you are using the default Tripal node template, then you should
|
|
|
+ // There is always a base template. This is the template that is first
|
|
|
+ // shown when the example node type is first displayed.
|
|
|
+ // If you are using the default Tripal node template, then you should
|
|
|
// also set two additional items in each array: tripal_toc_id and
|
|
|
- // tripal_toc_title. The tripal_tock_id should be a single unqiue
|
|
|
+ // tripal_toc_title. The tripal_tock_id should be a single unique
|
|
|
// world that is used to reference the template. This ID is used for
|
|
|
- // constructing URLs for the content. The tripal_toc_title contains
|
|
|
+ // constructing URLs for the content. The tripal_toc_title contains
|
|
|
// the title that should appear in the table of contents for this
|
|
|
- // content. You should only set the '#weight' element for the
|
|
|
- // base template (or Overview) to ensure that it appears at the top of
|
|
|
- // the list. Otherwise items are sorted alphabetically.
|
|
|
+ // content. You should only set the '#weight' element for the base
|
|
|
+ // template (or Overview) to ensure that it appears at the top of the
|
|
|
+ // list. Otherwise items are sorted alphabetically.
|
|
|
$node->content['tripal_example_base'] = array(
|
|
|
'#theme' => 'tripal_example_base',
|
|
|
'#node' => $node,
|
|
|
@@ -788,11 +823,11 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
|
|
|
'#tripal_toc_title' => 'Relationships',
|
|
|
);
|
|
|
|
|
|
- // Note: if you create a template that you do not want a user to
|
|
|
- // know where it is (discourage editing of it), you can add the following
|
|
|
- // key: '#tripal_template_show' => FALSE. If this key/value is set
|
|
|
- // the the administrator message that Tripal provides indicating
|
|
|
- // where the template is housed will not be shown.
|
|
|
+ // Note: if you create a template that you do not want a user to know
|
|
|
+ // where it is (discourage editing of it), you can add the following
|
|
|
+ // key: '#tripal_template_show' => FALSE. If this key/value is set the
|
|
|
+ // administrator message that Tripal provides indicating where the
|
|
|
+ // template is housed will not be shown.
|
|
|
}
|
|
|
// set the content for the teaser view
|
|
|
if ($view_mode == 'teaser') {
|
|
|
@@ -803,8 +838,8 @@ function tripal_example_node_view($node, $view_mode, $langcode) {
|
|
|
);
|
|
|
}
|
|
|
break;
|
|
|
- // you can add custom content to any node type by adding
|
|
|
- // content to the node in the same way as above.
|
|
|
+ // you can add custom content to any node type by adding content to the node
|
|
|
+ // in the same way as above.
|
|
|
case 'chado_organism':
|
|
|
if ($view_mode == 'full') {
|
|
|
$node->content['tripal_organism_examples'] = array(
|
Lacey Sanderson