fetchObject(); if (!$tripal_cv) { $results = chado_query( "INSERT INTO {cv} (name,definition) " . "VALUES ('tripal', 'Terms used by Tripal for modules to manage data such as that stored in property tables like featureprop, analysisprop, etc')" ); } // if the Tripal db is missing then add it $results = chado_query("SELECT * FROM {db} WHERE name = 'tripal'"); $tripal_db = $results->fetchObject(); if (!$tripal_db) { $results = chado_query( "INSERT INTO {db} (name,description) " . "VALUES ('tripal', 'Used as a database placeholder for tripal defined objects such as tripal cvterms')" ); } } // add some variables for all javasript to use for building URLs $theme_dir = drupal_get_path('theme', 'tripal'); $clean_urls = variable_get('clean_url', 0); drupal_add_js( " var baseurl = '$base_url'; var themedir = '$theme_dir'; var isClean = $clean_urls;", 'inline', 'header'); // make sure the date time settings are the way Tripal will insert them // otherwise PostgreSQL version that may have a different datestyle setting // will fail when inserting or updating a date column in a table. db_query("SET DATESTYLE TO :style", array(':style' => 'MDY')); // If we want AHAH elements on the node forms (e.g. chado_pub form) then we need to include // the node.pages file. Otherwise this error message is given: // // warning: call_user_func_array() expects parameter 1 to be a valid callback, // function 'node_form' not found or invalid function name // in /var/www/includes/form.inc on line 382. module_load_include('inc', 'node', 'node.pages'); } /** * Implements hook_menu(). * Defines all menu items needed by Tripal Core * * @ingroup tripal_core */ function tripal_core_menu() { $items = array(); // Triapl setting groups $items['admin/tripal'] = array( 'title' => 'Tripal', 'description' => "Manage the behavior or Tripal and its various modules.", 'weight' => -8, 'page callback' => 'system_admin_menu_block_page', 'access arguments' => array('administer tripal'), 'file' => 'system.admin.inc', 'file path' => drupal_get_path('module', 'system'), ); $items['admin/tripal/schema'] = array( 'title' => 'Chado Schema', 'description' => "Tools to extend the chado schema through custom tables & materialized views.", 'weight' => -2, 'access arguments' => array('administer tripal'), ); $items['admin/tripal/chado'] = array( 'title' => 'Chado Modules', 'description' => 'Configuration for specific chado data types such as Vocabularies, Features, etc.', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => -6 ); $items['admin/tripal/loaders'] = array( 'title' => 'Chado Data Loaders', 'description' => 'Tools facilitating loading data into the chado database. Includes a generic tab-delimited loader (Bulk Loader).', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => -4 ); $items['admin/tripal/extension'] = array( 'title' => 'Extension Modules', 'description' => 'Configuration for Tripal extension modules.', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => 0 ); // Tripal Setup $items['admin/tripal/setup'] = array( 'title' => 'Setup Tripal', 'description' => 'Tools for initial setup of Tripal', 'access arguments' => array('administer tripal'), 'weight' => -8 ); $items['admin/tripal/setup/customize'] = array( 'title' => 'Customize Tripal', 'description' => 'Information on how to customize tripal', 'page callback' => 'theme', 'page arguments' => array('tripal_core_customize'), 'access arguments' => array('administer tripal'), 'weight' => 10 ); $items['admin/tripal/setup/chado_install'] = array( 'title' => 'Install Chado Schema', 'description' => 'Installs the Chado database tables, views, etc., inside the current Drupal database', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_core_chado_load_form'), 'access arguments' => array('install chado'), 'type' => MENU_NORMAL_ITEM, 'weight' => -10 ); // Jobs Management $items['admin/tripal/tripal_jobs'] = array( 'title' => 'Jobs', 'description' => 'Jobs managed by Tripal', 'page callback' => 'tripal_jobs_admin_view', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => -10 ); $items['admin/tripal/tripal_jobs/help'] = array( 'title' => 'Help', 'description' => 'Help for the tripal job management system', 'page callback' => 'theme', 'page arguments' => array('tripal_core_job_help'), 'access arguments' => array('administer tripal'), 'type' => MENU_LOCAL_TASK, 'weight' => 10 ); $items['admin/tripal/tripal_jobs/cancel/%'] = array( 'title' => 'Jobs', 'description' => 'Cancel a pending job', 'page callback' => 'tripal_cancel_job', 'page arguments' => array(4), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/tripal_jobs/rerun/%'] = array( 'title' => 'Jobs', 'description' => 'Re-run an existing job.', 'page callback' => 'tripal_rerun_job', 'page arguments' => array(4), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/tripal_jobs/view/%'] = array( 'title' => 'Jobs Details', 'description' => 'View job details.', 'page callback' => 'tripal_jobs_view', 'page arguments' => array(4), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/tripal_jobs/views/jobs/enable'] = array( 'title' => 'Enable Jobs Administrative View', 'page callback' => 'tripal_views_admin_enable_view', 'page arguments' => array('tripal_core_admin_jobs', 'admin/tripal/tripal_jobs'), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); // Materialized Views $items['admin/tripal/schema/mviews'] = array( 'title' => 'Materialized Views', 'description' => 'Materialized views are used to improve speed of large or complex queries.', 'page callback' => 'tripal_mview_admin_view', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => -10 ); $items['admin/tripal/schema/mviews/help'] = array( 'title' => 'Help', 'description' => 'Help for the materialized views management system', 'page callback' => 'theme', 'page arguments' => array('tripal_core_mviews_help'), 'access arguments' => array('administer tripal'), 'type' => MENU_LOCAL_TASK, 'weight' => 10 ); $items['admin/tripal/schema/mviews/report/%'] = array( 'title' => 'Materialized View', 'description' => 'Materialized views are used to improve speed of large or complex queries. These are database views as compared to Drupal views.', 'page callback' => 'tripal_mview_report', 'page arguments' => array(5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/mviews/new'] = array( 'title' => 'Create Materialized View', 'description' => 'Create a new materialized view.', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_mviews_form'), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/mviews/edit/%'] = array( 'title' => 'Edit Materialized View', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_mviews_form', 5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/mviews/update/%'] = array( 'title' => 'Create Materialized View', 'description' => 'Materialized views are used to improve speed of large or complex queries.', 'page callback' => 'tripal_mviews_add_populate_job', 'page arguments' => array(5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/mviews/delete/%'] = array( 'title' => 'Create Materialized View', 'description' => 'Materialized views are used to improve speed of large or complex queries.', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_mviews_delete_form', 5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); // Custom Tables $items['admin/tripal/schema/custom_tables'] = array( 'title' => 'Custom Tables', 'description' => 'Creation of custom tables that are added to Chado database.', 'page callback' => 'tripal_custom_table_admin_view', 'access arguments' => array('administer tripal'), 'type' => MENU_NORMAL_ITEM, 'weight' => -10 ); $items['admin/tripal/schema/custom_tables/help'] = array( 'title' => 'Help', 'description' => 'Help for the tripal job management system', 'page callback' => 'theme', 'page arguments' => array('tripal_core_job_help'), 'access arguments' => array('administer tripal'), 'type' => MENU_LOCAL_TASK, 'weight' => 10 ); $items['admin/tripal/schema/custom_tables/view/%'] = array( 'title' => 'Custom Tables', 'description' => 'Custom tables are added to Chado.', 'page callback' => 'tripal_custom_table_view', 'page arguments' => array(5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/custom_tables/new'] = array( 'title' => 'Create Custom Table', 'description' => 'An interface for creating your own custom tables.', 'page callback' => 'tripal_custom_table_new_page', 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/custom_tables/edit/%'] = array( 'title' => 'Edit Custom Table', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_custom_tables_form', 5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/custom_tables/delete/%'] = array( 'title' => 'Create Custom Table', 'description' => 'Custom tables are added to Chado.', 'page callback' => 'drupal_get_form', 'page arguments' => array('tripal_custom_tables_delete_form', 5), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); $items['admin/tripal/schema/custom_tables/views/tables/enable'] = array( 'title' => 'Enable Custom Tables Administrative View', 'page callback' => 'tripal_views_admin_enable_view', 'page arguments' => array('tripal_core_admin_custom_table', 'admin/tripal/schema/custom_tables'), 'access arguments' => array('administer tripal'), 'type' => MENU_CALLBACK, ); // Relationshi API autocomplete callback $items['tripal_ajax/relationship_nodeform/%/%/name_to_id'] = array( 'page callback' => 'chado_add_node_form_relationships_name_to_id_callback', 'page arguments' => array(2,3), 'access arguments' => array('access content'), 'type' => MENU_CALLBACK ); return $items; } /** * Implements hook_permission(). * * Set the permission types that the chado module uses. Essentially we * want permissionis that protect creation, editing and deleting of chado * data objects * * @ingroup tripal_core */ function tripal_core_permission() { return array( 'install chado' => array( 'title' => t('Install Chado'), 'description' => t('Allow the user to install or upgrade a Chado database in the existing Drupal database.') ), 'administer tripal' => array( 'title' => t('Administer Tripal'), 'description' => t('Allow the user to access administrative pages of Tripal.') ), ); } /** * Implements hook_theme(). * Registers template files/functions used by this module. * * @ingroup tripal_core */ function tripal_core_theme($existing, $type, $theme, $path) { return array( 'tripal_core_customize' => array( 'arguments' => array('job_id' => NULL), 'template' => 'tripal_core_customize', 'path' => "$path/theme/templates" ), 'theme_file_upload_combo' => array( 'render element' => 'element', ), 'theme_sequence_combo' => array( 'render element' => 'element', ), 'tripal_core_jobs_help' => array( 'template' => 'tripal_core_jobs_help', 'variables' => array(NULL), 'path' => "$path/theme/templates" ), 'tripal_core_customtables_help' => array( 'template' => 'tripal_core_customtables_help', 'variables' => array(NULL), 'path' => "$path/theme/templates" ), // Chado Node API Themes // -------------------------------- // Properties Node Form 'chado_node_properties_form_table' => array( 'function' => 'theme_chado_add_node_form_properties', 'render element' => 'element', ), // Additional Dbxrefs Nore Form 'chado_node_additional_dbxrefs_form_table' => array( 'function' => 'theme_chado_add_node_form_dbxrefs_table', 'render element' => 'element', ), // Relationships Nore Form 'chado_node_relationships_form_table' => array( 'function' => 'theme_chado_add_node_form_relationships_table', 'render element' => 'element', ), // Admin messages theme // -------------------------------- 'tripal_admin_message' => array( 'function' => 'theme_tripal_admin_message', 'variables' => array('message' => NULL), ) ); } /** * Implements hook_job_describe_args(). * Describes the arguements for the tripal_populate_mview job to allow for greater * readability in the jobs details pages. * * @param $callback * The callback of the current tripal job (this is the function that will be executed * when tripal_launch_jobs.php is run. * @param $args * An array of arguments passed in when the job was registered. * * @return * A more readable $args array * * @ingroup tripal_core */ function tripal_core_job_describe_args($callback, $args) { $new_args = array(); if ($callback == 'tripal_populate_mview') { // get this mview details $sql = "SELECT * FROM {tripal_mviews} WHERE mview_id = :mview_id "; $results = db_query($sql, array(':mview_id' => $args[0])); $mview = $results->fetchObject(); $new_args['View Name'] = $mview->name; } elseif ($callback == 'tripal_core_install_chado') { $new_args['Action'] = $args[0]; } return $new_args; } /** * this is just a wrapper for backwards compatibility with a naming mistake. * it can go away in the future as it only is useful for jobs created by v0.3b * * @todo remove this function */ function tripal_core_load_gff3($gff_file, $organism_id, $analysis_id, $add_only = 0, $update = 0, $refresh = 0, $remove = 0, $job = NULL) { tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id, $add_only, $update, $refresh, $remove, $job); } /** * Implements hook_coder_ignore(). * Defines the path to the file (tripal_core.coder_ignores.txt) where ignore rules for coder are stored */ function tripal_core_coder_ignore() { return array( 'path' => drupal_get_path('module', 'tripal_core'), 'line prefix' => drupal_get_path('module', 'tripal_core'), ); } /** * Implements hook_views_api() * Purpose: Essentially this hook tells drupal that there is views support for * for this module which then includes tripal_db.views.inc where all the * views integration code is * * @ingroup tripal_organism */ function tripal_core_views_api() { return array( 'api' => 3.0, ); } /** * After the node is built, we want to add instructions to each * content section letting the administrator know which template * they can customize * * @param unknown $build */ function tripal_core_node_view_alter(&$build) { global $theme; // if this is not a full node view, we do not want to alter if ($build['#view_mode'] != 'full' OR !array_key_exists('#tripal_generic_node_template', $build)) { return; } $node_type = $build["#node"]->type; $nid = $build["#node"]->nid; $cache = cache_get("theme_registry:$theme", 'cache'); $node = $build['#node']; $toc = array(); $toc_html = ''; // if we are looking at a Tripal node template then we want to // make some changes to each block of content so that we can associate // a table of contents and add administrator and curator messages if ($build['#tripal_generic_node_template'] == TRUE) { // iterate through all the elements of the $build array and for those // that are wanting to provide content for this node $markup = array(); foreach ($build as $key => $value) { // skip the body element as the Tripal node types do not use it if ($key == 'body') { continue; } // examine elements without a '#' prefix as these should be adding // contents to the page. Skip the table of contents and links as those // will be placed elsewhere if (preg_match('/^#/', $key) or $key == 'tripal_toc' or $key == 'links') { continue; } //kook to see if the title, position and visibilty of this element has // custom settings. First check if the node is customized then check // if the node type. $override_title = ''; $override_weight = ''; $override_hide = 0; $toc_item_overrides = db_select('tripal_toc', 'tc') ->fields('tc', array('toc_item_id', 'title', 'weight', 'hide')) ->condition('node_type', $node_type) ->condition('key', $key) ->condition('nid', $nid) ->execute() ->fetchObject(); if ($toc_item_overrides) { $override_title = $toc_item_overrides->title; $override_weight = $toc_item_overrides->weight; $override_hide = $toc_item_overrides->hide; } else { // get the override title, weight for the general case $toc_item_overrides = db_select('tripal_toc', 'tc') ->fields('tc', array('toc_item_id', 'title', 'weight', 'hide')) ->condition('node_type', $node_type) ->condition('key', $key) ->isNull('nid') ->execute() ->fetchObject(); if ($toc_item_overrides) { $override_title = $toc_item_overrides->title; $override_weight = $toc_item_overrides->weight; $override_hide = $toc_item_overrides->hide; } } // if the element should be hiddent then unset this key the build // array continue to the next one if ($override_hide == 1) { unset($build[$key]); continue; } // for backwards compatibility we will handle the content type fields // named 'field_resource_blocks', 'field_resource_titles', and 'field_resource_links' // these fields can be added on the Drupal content types page and were // specifically recoginzed by Tripal v1.1. if ($key == "field_resource_links") { // links should just appear on the sidebar as is and not open up a panel foreach (element_children($build[$key]) as $index) { $element = $build[$key][$index]; $weight = 0; $parts = explode("|", $element['#markup']); if (count($parts) == 2) { $toc[$weight][$parts[0]] = "
" . l($parts[0], $parts[1], array('attributes' => array('target' => '_blank'))) . "
"; } else { $toc[$weight][$parts[0]] = "
" . $element['#markup'] . "
"; } // remove this link from the build array as we've moved it to appear in the TOC unset($build[$key]); } continue; } if ($key == "field_resource_titles") { // ignore these, we will use them in the field_resource_blocks if // statement below continue; } if ($key == "field_resource_blocks") { foreach (element_children($build[$key]) as $index) { // get the block details and the title $weight = 0; $markup = $build[$key][$index]["#markup"]; $toc_item_id = "resource-$index"; $toc_item_title = $build["field_resource_titles"][$index]["#markup"]; $updated_markup = "
$toc_item_title
$markup
"; $build[$toc_item_id]['#markup'] = $updated_markup; $build[$toc_item_id]['#weight'] = $weight; $build[$toc_item_id]['#toc_handled'] = TRUE; // add the entry to the TOC $toc_item_link = "
$toc_item_title
"; $toc[$weight][$toc_item_title] = $toc_item_link; } // remove the key from the build array. We have have replaced it unset($build[$key]); unset($build["field_resource_titles"]); continue; } // skip any keys we may have already handled. This is the case for // the field_resource_blocks where we removed the old CCK fields // and added new ones. We don't want these new ones to be processed // again by the code below. if (array_key_exists('#toc_handled', $build[$key]) and $build[$key]['#toc_handled'] == TRUE) { continue; } // for all other fields we will handle in the following way //----------------------- // INITIALIZE THE CONTENT VARIABLES //----------------------- $toc_item_title = $key; $toc_item_id = $key; $toc_item_link = ''; // get the title for the table of contents. Tripal templates should // have a '#tripal_toc_title' element in the build array if (array_key_exists('#tripal_toc_title', $build[$key])) { $toc_item_title = $build[$key]['#tripal_toc_title']; } // other elements in the $build array may just have a '#title' element, if (array_key_exists('#title', $build[$key])) { $toc_item_title = $build[$key]['#title']; } $toc_item_title = ucwords($toc_item_title); // now override the title if a value is set in the tripal_toc table $toc_item_title = $override_title ? $override_title : $toc_item_title; if (array_key_exists('#tripal_toc_id', $build[$key])) { $toc_item_id = $build[$key]['#tripal_toc_id']; } $toc_item_link = "
$toc_item_title
"; //----------------------- // GET THE MARKUP FOR EACH ELEMENT //----------------------- $markup = ''; // find the markup. Some fields will have a '#markup' and others, such // as CCK elements may have a set of '#markup' elements organized by // numerical keys. if (array_key_exists('#markup', $build[$key]) and trim($build[$key]['#markup'])) { $markup = $build[$key]['#markup']; } // For backwards copmatibility we should support the '#value' element as well. elseif (array_key_exists('#value', $build[$key]) and trim($build[$key]['#value'])) { $markup = $build[$key]['#markup']; } // if we have no '#markup' field then this element has not yet // been rendered. Let's render it and substitute that for markup if (!$markup) { $markup = trim(render($build[$key])); $build[$key] = array( '#markup' => $markup, ); } // if we still don't have markup then skip this one if (!$markup) { continue; } //----------------------- // FIND THE TEMPLATE PATH //----------------------- // get the template path so we can put it in an admin message box $path = ''; if (!array_key_exists('#tripal_template_show', $build[$key]) or $build[$key]['#tripal_template_show'] == TRUE) { if ($cache and array_key_exists($key, $cache->data) and array_key_exists('path', $cache->data[$key])) { $path = $cache->data[$key]['path'] . '/' . $key . '.tpl.php'; $path = tripal_set_message("Administrators, you can customize the way the content above is presented. Tripal provides a template file for each block of content. To customize, copy the template file to your site's default theme, edit then " . l('clear the Drupal cache', 'admin/config/development/performance', array('attributes' => array('target' => '_blank'))) . ". Currently, the content above is provided by this template:

$path", TRIPAL_INFO, array('return_html' => 1) ); } } //----------------------- // SET THE WEIGHTS FOR THE TOC ELEMENTS //----------------------- // set the weight of the TOC item and add it to our $toc array // for building of the TOC below $weight = 0; if (array_key_exists('#weight', $build[$key])) { $weight = $build[$key]['#weight']; } // override the weight if it's set in the tripal_toc table $weight = $override_weight ? $override_weight : $weight; $toc[$weight][$toc_item_title] = $toc_item_link; //----------------------- // CREATE THE DATA BLOCK //----------------------- // add a surrounding
box around the content $updated_markup = "
$toc_item_title
$markup $path
"; $build[$key]['#markup'] = $updated_markup; $build[$key]['#weight'] = $weight; } // end foreach ($build as $key => $value) { } // end if ($build['#tripal_generic_node_template'] == TRUE) { //----------------------- // BUILD THE TABLE OF CONTENTS LINKS //----------------------- // first sort the links numerically by their weight ksort($toc, SORT_NUMERIC); $toc_html = ''; foreach ($toc as $weight => $links) { // for links in the same weight, sort them alphabetically ksort($links); foreach ($links as $toc_item_title => $toc_item_link) { $toc_html .= $toc_item_link; } } $build['tripal_toc']['#markup'] = "
type-tripal-toc-block\" class=\"tripal-toc-block\">$toc_html
"; } /** * * @ingroup tripal_core */ function tripal_core_node_view($node, $view_mode, $langcode) { // if this node type is a chado-based node (i.e. Tripal node) // the we want to add a table of contents to it's content list // this table of contents will be an empty if (preg_match('/^chado_/', $node->type)) { // Show feature browser and counts if ($view_mode == 'full') { if (!isset($node->content['#tripal_generic_node_template'])) { $node->content['#tripal_generic_node_template'] = TRUE; } } } }