array( 'name' => t('Contact (Tripal v2 legacy)'), 'base' => 'chado_contact', 'description' => t('A contact from the Chado database'), 'has_title' => TRUE, 'locked' => TRUE, 'chado_node_api' => array( 'base_table' => 'contact', 'hook_prefix' => 'chado_contact', 'record_type_title' => array( 'singular' => t('Contact'), 'plural' => t('Contacts') ), 'sync_filters' => array( 'type_id' => FALSE, 'organism_id' => FALSE ), ) ), ); } /** * Implementation of hook_form(). * * @parm $node * The node that is created when the database is initialized * * @parm $form_state * The state of the form, that has the user entered information that is neccessary for, setting * up the database tables for the contact * * @return $form * The information that was enterd allong with * * @ingroup tripal_legacy_contact */ function chado_contact_form(&$node, $form_state) { $form = array(); // Default values can come in the following ways: // // 1) as elements of the $node object. This occurs when editing an existing contact // 2) in the $form_state['values'] array which occurs on a failed validation or // ajax callbacks from non submit form elements // 3) in the $form_state['input'[ array which occurs on ajax callbacks from submit // form elements and the form is being rebuilt // // set form field defaults $contact_id = null; $type_id = 0; $contactname = ''; $description = ''; // if we are editing an existing node then the contact is already part of the node if (property_exists($node, 'contact')) { $contact = $node->contact; $contact_id = $contact->contact_id; // get form defaults $type_id = $contact->type_id->cvterm_id; $contactname = $contact->name; // get the contact default values. When this module was first created // the contact description was incorrectly stored in the $node->body field. // It is better to store it in the Chado tables. However, the 'description' // field of the contact table is only 255 characters. So, we are going // to follow the same as the contact module and store the description in // the contactprop table and leave the contact.description field blank. // however, for backwards compatibitily, we check to see if the description // is in the $node->body field. If it is we'll use that. When the node is // edited the text will be moved out of the body and into the contactprop // table where it should belong. $description = ''; if (property_exists($node, 'body')) { $description = $node->body; } else { $description = $contact->description; } if (!$description) { $contactprop = chado_get_property( array('table' => 'contact', 'id' => $contact->contact_id), array('type_name' => 'contact_description', 'cv_name' => 'tripal_contact') ); $description = (isset($contactprop->value)) ? $contactprop->value : ''; } // set the contact_id in the form $form['contact_id'] = array( '#type' => 'value', '#value' => $contact->contact_id, ); } // if we are re constructing the form from a failed validation or ajax callback // then use the $form_state['values'] values if (array_key_exists('values', $form_state)) { $type_id = $form_state['values']['type_id']; $contactname = $form_state['values']['contactname']; $description = $form_state['values']['description']; } // if we are re building the form from after submission (from ajax call) then // the values are in the $form_state['input'] array if (array_key_exists('input', $form_state) and !empty($form_state['input'])) { $type_id = $form_state['input']['type_id']; $contactname = $form_state['input']['contactname']; $description = $form_state['input']['description']; } // get the contact type $type_cv = tripal_get_default_cv('contact', 'type_id'); if ($type_cv->name == 'tripal_contact') { // get the contact types. If the default is the 'tripal_contact' vocabulary, // then we want terms that are part of the tripal_contact // vocabulary and are children of the term 'Contact Type', so we need // to join on the cvtermpath table and select those with a distance of 1 $sql = " SELECT CVTS.cvterm_id, CVTS.name FROM {cvtermpath} CVTP INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id INNER JOIN {cv} CV ON CVTO.cv_id = CV.cv_id WHERE CV.name = 'tripal_contact' AND CVTO.name = 'Contact Type' AND CVTP.pathdistance = 1 ORDER BY CVTS.name ASC "; $results = chado_query($sql); while ($contact_type = $results->fetchObject()) { $contact_types[$contact_type->cvterm_id] = $contact_type->name; if (strcmp($contact_type->name, "Person") == 0 and !$type_id) { $type_id = $contact_type->cvterm_id; } } } else { $contact_types = tripal_get_cvterm_default_select_options('contact', 'type_id', 'contact types'); } $form['type_id'] = array( '#type' => 'select', '#title' => t('Contact Type'), '#options' => $contact_types, '#required' => TRUE, '#default_value' => $type_id, ); $form['contactname']= array( '#type' => 'textfield', '#title' => t('Contact Name'), '#description' => t('Enter the name of this contact'), '#required' => TRUE, '#default_value' => $contactname, '#maxlength' => 255, ); $form['description']= array( '#type' => 'text_format', '#title' => t('Contact Description'), '#description' => t('A brief description of the contact'), '#required' => TRUE, '#default_value' => $description, ); // Properties Form // ---------------------------------- $prop_cv = tripal_get_default_cv('contactprop', 'type_id'); $cv_id = $prop_cv ? $prop_cv->cv_id : NULL; $select_options = array(); // the Tripal contact vocabulary is heirarchical so if that vocab is default we // want to use the subset of terms not under the type 'Contact Type' for our // properties list. if($prop_cv->name == 'tripal_contact') { // Need to pass in our own select_options since we use cvtermpath to filter ours $select_options[] = 'Select a Property'; $sql = " SELECT CVTS.cvterm_id, CVTS.name FROM {cvtermpath} CVTP INNER JOIN {cvterm} CVTS ON CVTP.subject_id = CVTS.cvterm_id INNER JOIN {cvterm} CVTO ON CVTP.object_id = CVTO.cvterm_id INNER JOIN {cv} CV ON CVTO.cv_id = CV.cv_id WHERE CV.name = 'tripal_contact' AND NOT CVTO.name = 'Contact Type' ORDER BY CVTS.name ASC"; $prop_types = chado_query($sql); while ($prop = $prop_types->fetchObject()) { // add all properties except the Citation. That property is set via the uniquename field if ($prop->name != 'Citation') { if (!isset($select_options[$prop->cvterm_id])) { $select_options[$prop->cvterm_id] = $prop->name; } } } } $details = array( 'property_table' => 'contactprop', 'chado_id' => $contact_id, 'cv_id' => $cv_id, 'select_options' => $select_options, ); chado_add_node_form_properties($form, $form_state, $details); // RELATIONSHIPS FORM //--------------------------------------------- $relationship_cv = tripal_get_default_cv('contact_relationship', 'type_id'); $cv_id = $relationship_cv ? $relationship_cv->cv_id : NULL; $details = array( 'relationship_table' => 'contact_relationship', // the name of the _relationship table 'base_table' => 'contact', // the name of your chado base table 'base_foreign_key' => 'contact_id', // the name of the key in your base chado table 'base_key_value' => $contact_id, // the value of example_id for this record 'nodetype' => 'contact', // the human-readable name of your node type 'cv_id' => $cv_id, // the cv.cv_id of the cv governing contact_relationship.type_id 'base_name_field' => 'name', // the base table field you want to be used as the name ); // Adds the form elements to your current form chado_add_node_form_relationships($form, $form_state, $details); return $form; } /** * Implements hook_validate(). * Validates submission of form when adding or updating a contact node. * * @ingroup tripal_legacy_contact */ function chado_contact_validate($node, $form, &$form_state) { // We only want to validate when the node is saved. // Since this validate can be called on AJAX and Deletion of the node // we need to make this check to ensure queries are not executed // without the proper values. if(property_exists($node, "op") and $node->op != 'Save') { return; } // we are syncing if we do not have a node ID but we do have a contact_id. We don't // need to validate during syncing so just skip it. if (!property_exists($node, 'nid') and property_exists($node, 'contact_id') and $node->contact_id != 0) { return; } // remove surrounding white-space on submitted values $node->contactname = property_exists($node, 'contactname') ? trim($node->contactname) : ''; // Validating for an update if (!is_null($node->nid)) { // get the existing node $values = array('contact_id' => $node->contact_id); $result = chado_select_record('contact', array('*'), $values); $contact = $result[0]; // if the name has changed make sure it doesn't conflict with an existing name if ($contact->name != $node->contactname) { $values = array('name' => $node->contactname); $result = chado_select_record('contact', array('contact_id'), $values); if ($result and count($result) > 0) { form_set_error('contactname', 'Cannot update the contact with this contact name. A contact with this name already exists.'); return; } } } // Validating for an insert else { // The unique constraint for the chado contact table is: name $values = array( 'name' => $node->contactname, ); $contact = chado_select_record('contact', array('contact_id'), $values); if ($contact and count($contact) > 0) { form_set_error('contactname', 'Cannot add the contact with this name. A contact with these values already exists.'); return; } } } /** * Implements hook_access(). * * This hook allows node modules to limit access to the node types they define. * * @param $node * The node on which the operation is to be performed, or, if it does not yet exist, the * type of node to be created * * @param $op * The operation to be performed * * @param $account * A user object representing the user for whom the operation is to be performed * * @return * If the permission for the specified operation is not set then return FALSE. If the * permission is set then return NULL as this allows other modules to disable * access. The only exception is when the $op == 'create'. We will always * return TRUE if the permission is set. * * @ingroup tripal_legacy_contact */ function tripal_contact_node_access($node, $op, $account ) { $node_type = $node; if (is_object($node)) { $node_type = $node->type; } if($node_type == 'chado_contact') { if ($op == 'create') { if (!user_access('create chado_contact content', $account)) { return NODE_ACCESS_DENY; } return NODE_ACCESS_ALLOW; } if ($op == 'update') { if (!user_access('edit chado_contact content', $account)) { return NODE_ACCESS_DENY; } } if ($op == 'delete') { if (!user_access('delete chado_contact content', $account)) { return NODE_ACCESS_DENY; } } if ($op == 'view') { if (!user_access('access chado_contact content', $account)) { return NODE_ACCESS_DENY; } } } return NODE_ACCESS_IGNORE; } /** * Implements of hook_insert(). * * This function inserts user entered information pertaining to the contact instance into the * 'contactauthor', 'contactprop', 'chado_contact', 'contact' talble of the database. * * @parm $node * Then node which contains the information stored within the node-ID * * @ingroup tripal_legacy_contact */ function chado_contact_insert($node) { $contact_id = ''; // if there is a contact_id in the $node object then this must be a sync so // we can skip adding the contact as it is already there, although // we do need to proceed with insertion into the chado/drupal linking table. if (!property_exists($node, 'contact_id')) { // remove surrounding white-space on submitted values $node->contactname = trim($node->contactname); $node->description = trim($node->description['value']); // insert and then get the newly inserted contact record $values = array( 'name' => $node->contactname, 'description' => '', 'type_id' => $node->type_id, ); $contact = chado_insert_record('contact', $values); if (!$contact) { drupal_set_message(t('Unable to add contact.', 'warning')); tripal_report_error('tripal_contact', TRIPAL_ERROR, 'Insert contact: Unable to create contact where values: %values', array('%values' => print_r($values, TRUE))); return; } $contact_id = $contact['contact_id']; // Add the description property $properties = chado_retrieve_node_form_properties($node); $contact_descrip_id = tripal_get_cvterm(array( 'name' => 'contact_description', 'cv_id' => array('name' => 'tripal_contact') )); $properties[$contact_descrip_id->cvterm_id][0] = $node->description; // * Properties Form * $details = array( 'property_table' => 'contactprop', 'base_table' => 'contact', 'foreignkey_name' => 'contact_id', 'foreignkey_value' => $contact_id ); chado_update_node_form_properties($node, $details, $properties); // * Relationships Form * $details = array( 'relationship_table' => 'contact_relationship', // name of the _relationship table 'foreignkey_value' => $contact_id // value of the contact_id key ); chado_update_node_form_relationships($node, $details); } else { $contact_id = $node->contact_id; } // Make sure the entry for this contact doesn't already exist in the // chado_contact table if it doesn't exist then we want to add it. $check_org_id = chado_get_id_from_nid('contact', $node->nid); if (!$check_org_id) { $record = new stdClass(); $record->nid = $node->nid; $record->vid = $node->vid; $record->contact_id = $contact_id; drupal_write_record('chado_contact', $record); } return TRUE; } /** * Implements hook_update * * The purpose of the function is to allow the module to take action when an * edited node is being updated. It updates any name changes to the database * tables that were created upon registering a contact. * As well, the database will be changed, so the user changed information will * be saved to the database. * * @param $node * The node being updated * * @ingroup tripal_legacy_contact */ function chado_contact_update($node) { // remove surrounding white-space on submitted values $node->contactname = trim($node->contactname); $node->description = trim($node->description['value']); $contact_id = chado_get_id_from_nid('contact', $node->nid) ; // update the contact record $match = array( 'contact_id' => $contact_id, ); $values = array( 'name' => $node->contactname, 'description' => '', 'type_id' => $node->type_id ); $status = chado_update_record('contact', $match, $values); if (!$status) { drupal_set_message("Error updating contact", "error"); tripal_report_error('tripal_contact', TRIPAL_ERROR, "Error updating contact", array()); return; } // Add the description property $properties = chado_retrieve_node_form_properties($node); $contact_descrip_id = tripal_get_cvterm(array( 'name' => 'contact_description', 'cv_id' => array('name' => 'tripal_contact') )); $properties[$contact_descrip_id->cvterm_id][0] = $node->description; // now add in the properties by first removing any the contact // already has and adding the ones we have $details = array( 'property_table' => 'contactprop', 'base_table' => 'contact', 'foreignkey_name' => 'contact_id', 'foreignkey_value' => $contact_id ); chado_update_node_form_properties($node, $details, $properties); // * Relationships Form * $details = array( 'relationship_table' => 'contact_relationship', // name of the _relationship table 'foreignkey_value' => $contact_id // value of the contact_id key ); chado_update_node_form_relationships($node, $details); } /** * Implements hook_load(). * * @param $node * The node that is to be accessed from the database * * @return $node * The node with the information to be loaded into the database * * @ingroup tripal_legacy_contact */ function chado_contact_load($nodes) { foreach ($nodes as $nid => $node) { // find the contact and add in the details $contact_id = chado_get_id_from_nid('contact', $nid); // if the nid does not have a matching record then skip this node. // this can happen with orphaned nodes. if (!$contact_id) { continue; } // get the contact $values = array('contact_id' => $contact_id); $contact = chado_generate_var('contact', $values); // get the contact description from the contactprop table and replace // the contact.description field with this one (we don't use the contact.description // field because it is only 255 characters (too small)). $values = array( 'contact_id' => $contact->contact_id, 'type_id' => array( 'name' => 'contact_description', ), ); $options = array( 'return_array' => 1, 'include_fk' => array('type_id' => 1), ); $description = chado_generate_var('contactprop', $values, $options); if (count($description) == 1) { $description = chado_expand_var($description, 'field', 'contactprop.value'); $contact->description = $description[0]->value; } $nodes[$nid]->contact = $contact; // Now get the title $node->title = chado_get_node_title($node); } } /** * Implements hook_delete(). * * This function takes a node and if the delete button has been chosen by the user, the contact * and it's details will be removed.Following,given the node-ID, the instance will be deleted from * the 'chado_contact' table. * * @parm $node * Then node which contains the information stored within the node-ID * * @ingroup tripal_legacy_contact */ function chado_contact_delete(&$node) { $contact_id = chado_get_id_from_nid('contact', $node->nid); // if we don't have a contact id for this node then this isn't a node of // type chado_contact or the entry in the chado_contact table was lost. if (!$contact_id) { return; } // Remove data from {chado_contact}, {node} and {node_revisions} tables of // drupal database $sql_del = "DELETE FROM {chado_contact} WHERE nid = :nid AND vid = :vid"; db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid)); $sql_del = "DELETE FROM {node_revision} WHERE nid = :nid AND vid = :vid"; db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid)); $sql_del = "DELETE FROM {node} WHERE nid = :nid AND vid = :vid"; db_query($sql_del, array(':nid' => $node->nid, ':vid' => $node->vid)); // Remove data from contact and contactprop tables of chado database as well chado_query("DELETE FROM {contactprop} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id)); chado_query("DELETE FROM {contact} WHERE contact_id = :contact_id", array(':contact_id' => $contact_id)); } /** * Implements hook_node_view(). * * @ingroup tripal_legacy_contact */ function tripal_contact_node_view($node, $view_mode, $langcode) { switch ($node->type) { case 'chado_contact': // Show feature browser and counts if ($view_mode == 'full') { $node->content['tripal_contact_base'] = array( '#theme' => 'tripal_contact_base', '#node' => $node, '#tripal_toc_id' => 'base', '#tripal_toc_title' => 'Overview', '#weight' => -100, ); $node->content['tripal_contact_properties'] = array( '#theme' => 'tripal_contact_properties', '#node' => $node, '#tripal_toc_id' => 'properties', '#tripal_toc_title' => 'Properties', ); if (module_exists('tripal_pub')) { $node->content['tripal_contact_publications'] = array( '#theme' => 'tripal_contact_publications', '#node' => $node, '#tripal_toc_id' => 'publications', '#tripal_toc_title' => 'Publications', ); } $node->content['tripal_contact_relationships'] = array( '#theme' => 'tripal_contact_relationships', '#node' => $node, '#tripal_toc_id' => 'relationships', '#tripal_toc_title' => 'Relationships', ); } if ($view_mode == 'teaser') { $node->content['tripal_contact_teaser'] = array( '#theme' => 'tripal_contact_teaser', '#node' => $node, ); } break; } } /** * Implements hook_node_presave(). * * @ingroup tripal_legacy_contact */ function tripal_contact_node_presave($node) { switch ($node->type) { case 'chado_contact': // for a form submission the 'contactname' field will be set, // for a sync, we must pull from the contact object if (property_exists($node, 'contactname')) { // set the title $node->title = $node->contactname; } else if (property_exists($node, 'contact')) { $node->title = $node->contact->name; } break; } } /** * Implements hook_node_insert(). * Acts on all content types. * * @ingroup tripal_legacy_contact */ function tripal_contact_node_insert($node) { switch ($node->type) { case 'chado_contact': // find the contact and add in the details $contact_id = chado_get_id_from_nid('contact', $node->nid); // get the contact $values = array('contact_id' => $contact_id); $contact = chado_generate_var('contact', $values); $node->contact = $contact; // Now get the title $node->title = chado_get_node_title($node); // Now use the API to set the path. chado_set_node_url($node); break; } } /** * Implements hook_node_update(). * Acts on all content types. * * @ingroup tripal_legacy_contact */ function tripal_contact_node_update($node) { switch ($node->type) { case 'chado_contact': // Set the title $node->title = chado_get_node_title($node); // Now use the API to set the path. chado_set_node_url($node); break; } } /** * Implements [content_type]_chado_node_default_title_format(). * * Defines a default title format for the Chado Node API to set the titles on * Chado contact nodes based on chado fields. */ function chado_contact_chado_node_default_title_format() { return '[contact.name]'; } /** * Implements hook_chado_node_default_url_format(). * * Designates a default URL format for contact nodes. */ function chado_contact_chado_node_default_url_format() { return '/contact/[contact.name]'; } /** * Implements [content_type]_chado_node_sync_select_query(). * * Adds a where clause to the query to exclude the NULL contact. */ function chado_contact_chado_node_sync_select_query($query) { $query['where_clauses']['title'][] = 'contact.name <> :contact_name_null1'; $query['where_clauses']['title'][] = 'contact.name <> :contact_name_null2'; $query['where_args']['title'][':contact_name_null1'] = 'null'; $query['where_args']['title'][':contact_name_null2'] = 'NULL'; return $query; }