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' => t("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' => t("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' => t('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' => t('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' => t('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' => t('Tools for setup of Tripal'),
'access arguments' => array('administer tripal'),
'weight' => -8
);
$items['admin/tripal/setup/chado_install'] = array(
'title' => 'Install Chado Schema',
'description' => t('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
);
$items['admin/tripal/setup/customize'] = array(
'title' => 'Customize Tripal',
'description' => t('Information on how to customize tripal'),
'page callback' => 'theme',
'page arguments' => array('tripal_core_customize'),
'access arguments' => array('administer tripal'),
'weight' => 10
);
// Jobs Management
$items['admin/tripal/tripal_jobs'] = array(
'title' => 'Jobs',
'description' => t('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' => t('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' => t('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' => t('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' => t('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_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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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' => t('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_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 $items;
}
/**
* Implements hook_permission().
*
* Set the permission types that the chado module uses. Essentially we
* want permissionis that protect creation, editing and deleting of chado
* data objects
*
* @ingroup tripal_core
*/
function tripal_core_permission() {
return array(
'install chado' => array(
'title' => t('Install Chado'),
'description' => t('Allow the user to install or upgrade a Chado database in the existing Drupal database.')
),
'administer tripal' => array(
'title' => t('Administer Tripal'),
'description' => t('Allow the user to access administrative pages of Tripal.')
),
'view dev helps' => array(
'title' => t('View Developer Hints'),
'description' => t('Tripal will provide blue shaded boxes that provide
instructions for how to customize or setup specific pages on a
site. This permission should be enabled for developers. But can
be disabled once developers are accustomed to these hints.'),
'restrict access' => TRUE,
),
'view ids' => array(
'title' => t('View Internal IDs'),
'description' => t('On content pages Tripal will typically provide
a table of information pulled from the Chado database but the
primary key IDs for that data is typically not shown. The
default Tripal templates can show the primary key ID inside of a
blue shaded table row if this permission is enabled. This can
be useful for site developers who might want these IDs when working
with the underlying database.'),
'restrict access' => TRUE,
)
);
}
/**
* Implements hook_theme().
* Registers template files/functions used by this module.
*
* @ingroup tripal_core
*/
function tripal_core_theme($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;
}
}
}
}