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 = "
";
$build[$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 = "";
$toc[$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 = "";
//-----------------------
// 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
$path
type-tripal-toc-block\" class=\"tripal-toc-block\">$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;
}
}
}
}