array( 'name' => t('Project (Tripal v2 legacy)'), 'base' => 'chado_project', 'description' => t('A project from the Chado database'), 'has_title' => TRUE, 'locked' => TRUE, 'chado_node_api' => array( 'base_table' => 'project', 'hook_prefix' => 'chado_project', 'record_type_title' => array( 'singular' => t('Project'), 'plural' => t('Projects') ), 'sync_filters' => array( 'type_id' => FALSE, 'organism_id' => FALSE ), ), ), ); } /** * Implementation of hook_form(). * * This form takes the Project Title information and description from the user. * * @parm $node * The initialized node * * @parm $form_state * The state of the form, that has the user entered information that is neccessary for adding * information to the project * * @return $form * An array as described by the Drupal Form API * * * @ingroup tripal_legacy_project */ function chado_project_form(&$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 project // 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 $project_id = null; $title = ''; $description = ''; // if we are editing an existing node then the project is already part of the node if (property_exists($node, 'project')) { $project = $node->project; // get the project default values. When this module was first created // the project 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 project table is only 255 characters. So, we are going // to follow the same as the project module and store the description in // the projectprop table and leave the project.description field blank. // however, for backwards compatibitily, we check to see if the description // is in the $node->body field. If it is we'll use that. When the node is // edited the text will be moved out of the body and into the projectprop // table where it should belong. if (property_exists($node, 'body')) { $description = $node->body; } else { $description = $project->description; } if (!$description) { $projectprop = chado_get_property( array('table' => 'project', 'id' => $project->project_id), array('type_name' => 'Project Description', 'cv_name' =>'project_property') ); $description = $projectprop->value; } $title = $project->name; $project_id = $project->project_id; // keep track of the project id if we have. If we do have one then // this is an update as opposed to an insert. $form['project_id'] = array( '#type' => 'value', '#value' => $project_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)) { $title = $form_state['values']['title']; $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'])) { $title = $form_state['input']['title']; $description = $form_state['input']['description']; } $form['title']= array( '#type' => 'textfield', '#title' => t('Project Title'), '#description' => t('Please enter the title for this project. This appears at the top of the project page.'), '#required' => TRUE, '#default_value' => $node->title, ); $form['description']= array( '#type' => 'text_format', '#title' => t('Project Description'), '#description' => t('A brief description of the project'), '#required' => TRUE, '#default_value' => $description, ); // Properties Form // ---------------------------------- $select_options = array(); $prop_cv = tripal_get_default_cv('projectprop', 'type_id'); $cv_id = $prop_cv ? $prop_cv->cv_id : NULL; if ($prop_cv = 'project_property') { // if this is the project_property CV then // we want to exclude the project description from being loaded as a stored property // because we want to use the property to replace the project.description field as it is // only 255 characters which isn't large enough. We don't want the user to set it // as a property even though it will be stored as a property. $cv_result = chado_select_record('cv',array('cv_id'),array('name' => 'project_property')); $cv_id = $cv_result[0]->cv_id; $select_options = tripal_get_cvterm_select_options($cv_id); $descrip_id = array_search('Project Description', $select_options); unset($select_options[$descrip_id]); } $instructions = t('To add properties to the drop down list, you must ' . l("add terms to the project_property vocabulary", "admin/tripal/vocab/cvterm/add") . "."); $details = array( 'property_table' => 'projectprop', 'chado_id' => $project_id, 'cv_id' => $cv_id, 'additional_instructions' => $instructions, 'select_options' => $select_options ); chado_add_node_form_properties($form, $form_state, $details); // RELATIONSHIPS FORM //--------------------------------------------- $relationship_cv = tripal_get_default_cv('project_relationship', 'type_id'); $cv_id = $relationship_cv ? $relationship_cv->cv_id : NULL; $details = array( 'relationship_table' => 'project_relationship', // the name of the _relationship table 'base_table' => 'project', // the name of your chado base table 'base_foreign_key' => 'project_id', // the name of the key in your base chado table 'base_key_value' => $project_id, // the value of example_id for this record 'nodetype' => 'project', // the human-readable name of your node type 'cv_id' => $cv_id, // the cv.cv_id of the cv governing example_relationship.type_id 'base_name_field' => 'name', // the base table field you want to be used as the name 'subject_field_name' => 'subject_project_id', 'object_field_name' => 'object_project_id' ); // Adds the form elements to your current form chado_add_node_form_relationships($form, $form_state, $details); return $form; } /** * Implements hook_validate(). * Validates submission of form when adding or updating a project node * * @ingroup tripal_legacy_project */ function chado_project_validate($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 $node->op != 'Save') { return; } // we are syncing if we do not have a node ID but we do have a project_id. We don't // need to validate during syncing so just skip it. if (!property_exists($node, 'nid') and property_exists($node, 'project_id') and $node->project_id != 0) { return; } // trim white space from text fields $node->title = property_exists($node, 'title') ? trim($node->title) : ''; $project = 0; // check to make sure the name on the project is unique // before we try to insert into chado. if (property_exists($node, 'project_id')) { $sql = "SELECT * FROM {project} WHERE name = :name AND NOT project_id = :project_id"; $project = chado_query($sql, array(':name' => $node->title, ':project_id' => $node->project_id))->fetchObject(); } else { $sql = "SELECT * FROM {project} WHERE name = :name"; $project = chado_query($sql, array(':name' => $node->title))->fetchObject(); } if ($project) { form_set_error('title', t('The unique project name already exists. Please choose another')); } } /** * Implementation of hook_insert(). * * @parm $node * Then node that has the information stored within, accessed given the nid * * @ingroup tripal_legacy_project */ function chado_project_insert($node) { $project_id = ''; // if there is an project_id in the $node object then this must be a sync so // we can skip adding the project as it is already there, although // we do need to proceed with insertion into the chado/drupal linking table. if (!property_exists($node, 'project_id')) { $node->title = trim($node->title); $node->description = trim($node->description['value']); $values = array( 'name' => $node->title, 'description' => '', ); $project = chado_insert_record('project', $values); if (!$project) { drupal_set_message(t('Unable to add project.', 'warning')); watchdog('tripal_project', 'Insert project: Unable to create project where values:%values', array('%values' => print_r($values, TRUE)), WATCHDOG_ERROR); return; } $project_id = $project['project_id']; // * Properties Form * // Add the description property $properties = chado_retrieve_node_form_properties($node); $descrip_id = tripal_get_cvterm(array( 'name' => 'Project Description', 'cv_id' => array('name' => 'project_property') )); $properties[$descrip_id->cvterm_id][0] = $node->description; $details = array( 'property_table' => 'projectprop', 'base_table' => 'project', 'foreignkey_name' => 'project_id', 'foreignkey_value' => $project_id ); chado_update_node_form_properties($node, $details, $properties); // * Relationships Form * $details = array( 'relationship_table' => 'project_relationship', // name of the _relationship table 'foreignkey_value' => $project_id // value of the example_id key ); chado_update_node_form_relationships($node, $details); } else { $project_id = $node->project_id; } // Make sure the entry for this project doesn't already exist in the // chado_project table if it doesn't exist then we want to add it. $check_org_id = chado_get_id_from_nid('project', $node->nid); if (!$check_org_id) { $record = new stdClass(); $record->nid = $node->nid; $record->vid = $node->vid; $record->project_id = $project_id; drupal_write_record('chado_project', $record); } } /** * Implementation of hook_delete(). * * @param $node * The node which is to be deleted, only chado project and chado_project need to be dealt with * since the drupal node is deleted automagically * * @ingroup tripal_legacy_project */ function chado_project_delete($node) { $project_id = chado_get_id_from_nid('project', $node->nid); // if we don't have a project id for this node then this isn't a node of // type chado_project or the entry in the chado_project table was lost. if (!$project_id) { return; } // Remove data from {chado_project}, {node} and {node_revisions} tables of // drupal database $sql_del = "DELETE FROM {chado_project} WHERE nid = :nid AND vid = :vid"; db_query($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 project and projectprop tables of chado database as well chado_query("DELETE FROM {projectprop} WHERE project_id = :project_id", array(':project_id' => $project_id)); chado_query("DELETE FROM {project} WHERE project_id = :project_id", array(':project_id' => $project_id)); } /** * Implements hook_update(). * * @param $node * The node which is to have its containing information updated when the user modifies information * pertaining to the specific project * * @ingroup tripal_legacy_project */ function chado_project_update($node) { $node->title = trim($node->title); $node->description = trim($node->description['value']); // update the project and the description $project_id = chado_get_id_from_nid('project', $node->nid) ; $match = array('project_id' => $project_id); $values = array( 'name' => $node->title, 'description' => '', ); $status = chado_update_record('project', $match, $values); if (!$status) { drupal_set_message(t('Unable to update project.', 'warning')); watchdog('tripal_project', 'Update project: Unable to update project where values: %values', array('%values' => print_r($values, TRUE)), WATCHDOG_ERROR); } // * Properties Form * // Add the description property $properties = chado_retrieve_node_form_properties($node); $descrip_id = tripal_get_cvterm(array( 'name' => 'Project Description', 'cv_id' => array('name' => 'project_property') )); $properties[$descrip_id->cvterm_id][0] = $node->description; $details = array( 'property_table' => 'projectprop', 'base_table' => 'project', 'foreignkey_name' => 'project_id', 'foreignkey_value' => $project_id ); chado_update_node_form_properties($node, $details, $properties); // * Relationships Form * $details = array( 'relationship_table' => 'project_relationship', // name of the _relationship table 'foreignkey_value' => $project_id // value of the example_id key ); chado_update_node_form_relationships($node, $details); } /** * Implementation of hook_load(). * * @param $node * The node that is to have its containing information loaded * * @ingroup tripal_legacy_project */ function chado_project_load($nodes) { foreach ($nodes as $nid => $node) { // get the feature details from chado $project_id = chado_get_id_from_nid('project', $node->nid); // if the nid does not have a matching record then skip this node. // this can happen with orphaned nodes. if (!$project_id) { continue; } $values = array('project_id' => $project_id); $project = chado_generate_var('project', $values); $nodes[$nid]->project = $project; // Now get the title $node->title = chado_get_node_title($node); } } /** * Implement hook_node_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 $op == 'create'. We will always * return TRUE if the permission is set. * * @ingroup tripal_legacy_project */ function tripal_project_node_access($node, $op, $account) { $node_type = $node; if (is_object($node)) { $node_type = $node->type; } if($node_type == 'chado_project') { if ($op == 'create') { if (!user_access('create chado_project content', $account)) { return NODE_ACCESS_DENY; } return NODE_ACCESS_ALLOW; } if ($op == 'update') { if (!user_access('edit chado_project content', $account)) { return NODE_ACCESS_DENY; } } if ($op == 'delete') { if (!user_access('delete chado_project content', $account)) { return NODE_ACCESS_DENY; } } if ($op == 'view') { if (!user_access('access chado_project content', $account)) { return NODE_ACCESS_DENY; } } return NODE_ACCESS_IGNORE; } } /** * Implements hook_node_view(). * * @ingroup tripal_legacy_project */ function tripal_project_node_view($node, $view_mode, $langcode) { switch ($node->type) { case 'chado_project': // Show feature browser and counts if ($view_mode == 'full') { $node->content['tripal_project_base'] = array( '#theme' => 'tripal_project_base', '#node' => $node, '#tripal_toc_id' => 'base', '#tripal_toc_title' => 'Overview', '#weight' => -100, ); $node->content['tripal_project_contact'] = array( '#theme' => 'tripal_project_contact', '#node' => $node, '#tripal_toc_id' => 'contacts', '#tripal_toc_title' => 'Contacts', ); $node->content['tripal_project_properties'] = array( '#theme' => 'tripal_project_properties', '#node' => $node, '#tripal_toc_id' => 'properties', '#tripal_toc_title' => 'Properties', ); $node->content['tripal_project_publications'] = array( '#theme' => 'tripal_project_publications', '#node' => $node, '#tripal_toc_id' => 'publications', '#tripal_toc_title' => 'Publications', ); $node->content['tripal_project_relationships'] = array( '#theme' => 'tripal_project_relationships', '#node' => $node, '#tripal_toc_id' => 'relationships', '#tripal_toc_title' => 'Relationships', ); } if ($view_mode == 'teaser') { $node->content['tripal_project_teaser'] = array( '#theme' => 'tripal_project_teaser', '#node' => $node, ); } break; } } /** * Implements hook_node_insert(). * Acts on all content types. * * @ingroup tripal_legacy_project */ function tripal_project_node_insert($node) { // set the URL path after inserting. We do it here because we do not // know the project_id in the presave switch ($node->type) { case 'chado_project': // We still don't have a fully loaded node object in this hook. Therefore, // we need to simulate one so that the right values are available for // the URL to be determined. $project_id = chado_get_id_from_nid('project', $node->nid); $node->project = chado_generate_var('project', array('project_id' => $project_id)); // Now get the title. $node->title = chado_get_node_title($node); // Now use the API to set the path. chado_set_node_url($node); break; } } /** * Implements hook_node_update(). * Acts on all content types. * * @ingroup tripal_legacy_project */ function tripal_project_node_update($node) { // add items to other nodes, build index and search results switch ($node->type) { case 'chado_project': // 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 [content_type]_chado_node_default_title_format(). * * Defines a default title format for the Chado Node API to set the titles on * Chado project nodes based on chado fields. */ function chado_project_chado_node_default_title_format() { return '[project.name]'; } /** * Implements hook_chado_node_default_url_format(). * * Designates a default URL format for project nodes. */ function chado_project_chado_node_default_url_format() { return '/project/[project.project_id]'; }