<?php
//
// Copyright 2009 Clemson University
//
function tripal_analysis_go_init(){
// Add style sheet
drupal_add_css(drupal_get_path('theme', 'tripal').
'/css/tripal_analysis_go.css');
drupal_add_js(drupal_get_path('theme', 'tripal').
'/js/tripal_analysis_go.js');
}
/*******************************************************************************
* Menu items are automatically added for the new node types created
* by this module to the 'Create Content' Navigation menu item. This function
* adds more menu items needed for this module.
*/
function tripal_analysis_go_menu() {
$items = array();
$items['node/%/goterms'] = array(
'title' => t('GO Analysis'),
'page callback' => 'tripal_analysis_go_organism_goterms',
'page arguments' => array(1),
'access callback' => 'tripal_analysis_go_node_has_menu',
'access arguments' => array('access chado_analysis_go content',1),
'type' => MENU_LOCAL_TASK | MENU_NORMAL_ITEM
);
$items['download_goterm_features'] = array(
'path' => 'download_goterm_features',
'title' => t('Get GO Term Features'),
'page callback' => 'tripal_analysis_go_get_goterm_features',
'page arguments' => array(1,2),
'access arguments' => array('access chado_analysis_go content'),
'type' => MENU_CALLBACK
);
$items['tripal_analysis_go_org_charts'] = array(
'path' => 'tripal_analysis_go_org_charts',
'title' => t('Analysis GO Charts'),
'page callback' => 'tripal_analysis_go_org_charts',
'page arguments' => array(1),
'access arguments' => array('access chado_analysis_go content'),
'type' => MENU_CALLBACK
);
return $items;
}
/*******************************************************************************
* Set the permission types that the chado module uses. Essentially we
* want permissionis that protect creation, editing and deleting of chado
* data objects
*/
function tripal_analysis_go_perm(){
return array(
'access chado_analysis_go content',
'create chado_analysis_go content',
'delete chado_analysis_go content',
'edit chado_analysis_go content',
);
}
/*******************************************************************************
* The following function proves access control for users trying to
* perform actions on data managed by this module
*/
function chado_analysis_go_access($op, $node, $account){
if ($op == 'create') {
return user_access('create chado_analysis_go content', $account);
}
if ($op == 'update') {
if (user_access('edit chado_analysis_go content', $account)) {
return TRUE;
}
}
if ($op == 'delete') {
if (user_access('delete chado_analysis_go content', $account)) {
return TRUE;
}
}
if ($op == 'view') {
if (user_access('access chado_analysis_go content', $account)) {
return TRUE;
}
}
return FALSE;
}
/*******************************************************************************
* Dynamic addition/removal of menu item
*/
function tripal_analysis_go_node_has_menu($type,$vid){
// check to see if this node is an organism node
$sql = 'SELECT organism_id FROM {chado_organism} WHERE vid = %d';
$result = db_query($sql, $vid);
// menu status
$box_status =variable_get("tripal_analysis_go-box-goterms","menu_off");
// if this node is not an organism or a feature node then return false
// we don't want the menu item to be shown, otherwise get the normal perms
if($org_id = db_fetch_object($result)){
if(strcmp($box_status,"menu_on")==0){
return user_access($type);
}
} else {
return FALSE;
}
}
/*******************************************************************************
* HOOK: Implementation of hook_nodeapi()
* Display library information for associated features or organisms
* This function also provides contents for indexing
*/
function tripal_analysis_go_nodeapi(&$node, $op, $teaser, $page) {
switch ($op) {
// Note that this function only adds library view to an organism/feature
// node. The view of a library node is controled by the theme *.tpl file
case 'view':
// Set the node types for showing library information
$types_to_show = variable_get('tripal_analysis_go_setting',
array('chado_feature','chado_organism'));
// Abort if this node is not one of the types we should show.
if (!in_array($node->type, $types_to_show, TRUE)) {
// Turn the menu off if it's on
$box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
if (strcmp($box_status,"menu_on")==0 && $node->type =='chado_organism'){
variable_set("tripal_analysis_go-box-goterms","menu_off");
}
break;
}
// Add library to the content item if it's not a teaser
if (!$teaser) {
// add the library to the organism/feature search indexing
if($node->build_mode == NODE_BUILD_SEARCH_INDEX){
$node->content['tripal_analysis_go_search_index'] = array(
'#value' => theme('tripal_analysis_go_search_index',$node),
'#weight' => 5,
);
} else if ($node->build_mode == NODE_BUILD_SEARCH_RESULT) {
$node->content['tripal_analysis_go_search_result'] = array(
'#value' => theme('tripal_analysis_go_search_result',$node),
'#weight' => 5,
);
} else {
// Show go terms if the organism/feature is not at teaser view
$node->content['tripal_analysis_go_node_add'] = array(
'#value' => theme('tripal_analysis_go_node_add', $node),
'#weight' => 5
);
}
}
}
}
/************************************************************************
* We need to let drupal know about our theme functions and their arguments.
* We create theme functions to allow users of the module to customize the
* look and feel of the output generated in this module
*/
function tripal_analysis_go_theme () {
return array(
'tripal_analysis_go_search_index' => array (
'arguments' => array('node'),
),
'tripal_analysis_go_search_result' => array (
'arguments' => array('node'),
),
'tripal_analysis_go_node_add' => array (
'arguments' => array('node'),
)
);
}
/************************************************************************
*/
function theme_tripal_analysis_go_search_index($node){
}
/************************************************************************
*/
function theme_tripal_analysis_go_search_result($node){
}
/************************************************************************
*/
function theme_tripal_analysis_go_node_add($node){
$content = '';
if(strcmp($node->type,'chado_feature')==0){
$content = tripal_analysis_go_feature_add($node);
}
if(strcmp($node->type,'chado_organism')==0){
$box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
if (strcmp($box_status,"menu_off")==0){
$content = tripal_analysis_go_organism_add($node);
}
}
return $content;
}
/************************************************************************
*/
function tripal_analysis_go_organism_goterms($node) {
$node = node_load($node);
return tripal_analysis_go_organism_add($node);
}
/************************************************************************
*/
function tripal_analysis_go_select_form(&$form_state = NULL,$node){
$form = array();
// find analyses that have GO terms
$sql = "
SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id
FROM {go_count_analysis} GCA
INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
WHERE organism_id = %d
ORDER BY analysis_id DESC
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$node->organism_id);
tripal_db_set_active($previous_db);
$analyses = array();
$analyses[''] = '';
while($analysis = db_fetch_object($results)){
$analyses[$analysis->analysis_id."-".$analysis->organism_id] = "$analysis->name";
}
# create the select box
$form['analysis_select'] = array(
'#title' => t('Select a GO report to view'),
'#description' => t('Any analysis with GO results related to this organism are available for viewing. For further information, see the analysis information page.'),
'#type' => 'select',
'#options' => $analyses,
'#attributes' => array (
'onchange' => 'tripal_analysis_go_org_charts(this.options[this.selectedIndex].value)'
),
);
return $form;
}
/************************************************************************
*/
function tripal_analysis_go_org_charts ($element) {
$analysis_id = preg_replace("/^(\d+)-(\d+)$/","$1",$element);
$organism_id = preg_replace("/^(\d+)-(\d+)$/","$2",$element);
$content = '';
if($analysis_id and $organism_id){
$content = "
<b>Biological Process</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_bp\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_bp\" src=\"\" border=\"0\">
<br><br><br><br>
<b>Cellular Component</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_cc\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_cc\" src=\"\" border=\"0\">
<br><br><br><br>
<b>Molecular Function</b>
<br><i>Expand the tree to browse term counts. Click a term to view term details.</i>
<div class=\"tripal_cv_tree\" id=\"tripal_analysis_go_cv_tree_".$organism_id."-".$analysis_id."_mf\"></div>
<br><br><img class=\"tripal_cv_chart\" id=\"tripal_analysis_go_cv_chart_".$organism_id."-".$analysis_id."_mf\" src=\"\" border=\"0\">
";
}
$opt = array($content);
return drupal_json($opt);
}
/************************************************************************
*/
function tripal_analysis_go_organism_add($node) {
// Show GO information in a expandable box for a organism page.
// Make sure we have $node->organism_id. In the case of creating a new
// organism, the organism_id is not created until we save. This will cause
// an error when users preview the creation without a $node->organism_id
$box_status = variable_get("tripal_analysis_go-box-goterms","menu_off");
if(strcmp($box_status,"menu_off")==0){
$content .= "
<div class=\"tripal_go_summary-info-box\">
<div class=\"tripal_expandableBox\">
<h3>Gene Ontology Summary</h3>
</div>
<div class=\"tripal_expandableBoxContent\">
";
}
// check to see if we have any analyses
$sql = "
SELECT DISTINCT A.analysis_id, A.name, GCA.organism_id
FROM {go_count_analysis} GCA
INNER JOIN Analysis A on GCA.analysis_id = A.analysis_id
WHERE organism_id = %d
ORDER BY analysis_id DESC
";
$previous_db = tripal_db_set_active('chado');
$results = db_fetch_object(db_query($sql,$node->organism_id));
tripal_db_set_active($previous_db);
if($results){
$select_analysis = drupal_get_form('tripal_analysis_go_select_form',$node);
$url = url("sites/all/themes/theme_tripal/images/ajax-loader.gif");
$content .= "
$select_analysis
<div id=\"tripal_cv_cvterm_info_box\">
<a href=\"#\" onclick=\"$('#tripal_cv_cvterm_info_box').hide()\" style=\"float: right\">Close [X]</a>
<h3>Term Information</h3>
<div id=\"tripal_cv_cvterm_info\"></div>
</div>
<div id=\"tripal_ajaxLoading\" style=\"display:none\">
<div id=\"loadingText\">Loading...</div>
<img src=\"$url\"></div><div id=\"tripal_analysis_go_org_charts\"></div>
";
} else {
$content .= "There are currently no Gene Ontology (GO) reports for this organism\n";
}
if(user_access('access administrative pages')){
$link = url("tripal_toggle_box_menu/tripal_analysis_go/goterms/$node->nid");
if(strcmp($box_status,"menu_off")==0){
$content .= "<br><a href=\"$link\">Show on menu</a>";
} else {
$content .= "<br><a href=\"$link\">Remove from menu</a>";
}
}
if(strcmp($box_status,"menu_off")==0){
$content .= "</div></div>";
}
return $content;
}
/************************************************************************
*
*/
function tripal_analysis_go_cv_chart($chart_id){
// The CV module will create the JSON array necessary for buillding a
// pie chart using jgChart and Google Charts. We have to pass to it
// a table that contains count information, tell it which column
// contains the cvterm_id and provide a filter for getting the
// results we want from the table.
$organism_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$chart_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$chart_id);
$type = preg_replace("/^tripal_analysis_go_cv_chart_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$chart_id);
$sql = "SELECT * FROM {Analysis} WHERE analysis_id = %d";
$previous_db = tripal_db_set_active('chado'); // use chado database
$analysis = db_fetch_object(db_query($sql,$analysis_id));
tripal_db_set_active($previous_db); // now use drupal database
if(strcmp($type,'mf')==0){
$class = 'molecular_function';
$title = "Number of Molecular Function Terms From $analysis->name Analysis";
}
if(strcmp($type,'cc')==0){
$class = 'cellular_component';
$title = "Number of Cellular Component Terms From $analysis->name Analysis";
}
if(strcmp($type,'bp')==0){
$class = 'biological_process';
$title = "Number of Biological Process Terms From $analysis->name Analysis";
}
$options = array(
count_mview => 'go_count_analysis',
cvterm_id_column => 'cvterm_id',
count_column => 'feature_count',
filter => "
CNT.organism_id = $organism_id AND
CNT.analysis_id = $analysis_id AND
CNT.cvterm_id IN (
SELECT CVTR.subject_id
FROM {CVTerm_relationship} CVTR
INNER JOIN CVTerm CVT on CVTR.object_id = CVT.cvterm_id
INNER JOIN CV on CVT.cv_id = CV.cv_id
WHERE CVT.name = '$class' AND
CV.name = '$class'
)
",
type => 'p',
size => '680x230',
title => $title,
);
return $options;
}
/************************************************************************
*
*/
function tripal_analysis_go_cv_tree($tree_id){
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$type = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$3",$tree_id);
if(strcmp($type,'mf')==0){
$class = 'molecular_function';
}
if(strcmp($type,'cc')==0){
$class = 'cellular_component';
}
if(strcmp($type,'bp')==0){
$class = 'biological_process';
}
$options = array(
cv_id => tripal_cv_get_cv_id($class),
count_mview => 'go_count_analysis',
cvterm_id_column => 'cvterm_id',
count_column => 'feature_count',
filter => "CNT.organism_id = $organism_id AND CNT.analysis_id = $analysis_id",
label => 'Features',
);
return $options;
}
/************************************************************************
*/
function tripal_analysis_go_cvterm_add($cvterm_id,$tree_id){
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$sql = "
SELECT DBX.accession
FROM {cvterm} CVT
INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
WHERE cvterm_id = %d
";
$previous_db = tripal_db_set_active('chado');
$xref = db_fetch_object(db_query($sql,$cvterm_id));
tripal_db_set_active($previous_db);
$link = url("download_goterm_features/$cvterm_id/$tree_id");
$options = array(
'Download sequences' => "<a href=\"$link\">GO_".$xref->accession.".fasta</a>",
);
return $options;
}
/************************************************************************
*/
function tripal_analysis_go_get_goterm_features($cvterm_id,$tree_id){
// get hte accession number for this cvterm and use it in naming the download
$sql = "
SELECT DBX.accession
FROM {cvterm} CVT
INNER JOIN dbxref DBX on DBX.dbxref_id = CVT.dbxref_id
WHERE cvterm_id = %d
";
$previous_db = tripal_db_set_active('chado');
$xref = db_fetch_object(db_query($sql,$cvterm_id));
tripal_db_set_active($previous_db);
drupal_set_header('Content-Type: text');
drupal_set_header('Content-Disposition: attachment; filename="GO_'.$xref->accession.'.fasta"');
$organism_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$1",$tree_id);
$analysis_id = preg_replace("/^tripal_analysis_go_cv_tree_(\d+)-(\d+)_(bp|cc|mf)$/","$2",$tree_id);
$sql = "
SELECT DISTINCT F.name,F.residues,F.feature_id
FROM {cvtermpath} CVTP
INNER JOIN CVTerm CVT1 on CVTP.subject_id = CVT1.cvterm_id
INNER JOIN CVTerm CVT2 on CVTP.object_id = CVT2.cvterm_id
INNER JOIN AnalysisFeatureProp AFP on AFP.type_id = CVTP.subject_id
INNER JOIN AnalysisFeature AF on AF.analysisfeature_id = AFP.analysisfeature_id
INNER JOIN Feature F on AF.feature_id = F.feature_id
WHERE CVTP.object_id = %d and F.organism_id = %d and AF.analysis_id = %d
ORDER BY F.name
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$cvterm_id,$organism_id,$analysis_id);
tripal_db_set_active($previous_db);
while($feature = db_fetch_object($results)){
// get the go term information for each sequence
$sql = "
SELECT CVT.name,DBX.accession
FROM {Feature_CVTerm} FCVT
INNER JOIN CVTerm CVT on FCVT.cvterm_id = CVT.cvterm_id
INNER JOIN DBXref DBX on CVT.dbxref_id = DBX.dbxref_id
WHERE FCVT.feature_id = %d
";
$previous_db = tripal_db_set_active('chado');
$terms = db_query($sql,$feature->feature_id);
tripal_db_set_active($previous_db);
$desc = '[';
while($term = db_fetch_object($terms)){
$desc .= "GO:$term->accession $term->name; ";
}
$desc = chop($desc);
$desc = chop($desc,';');
$desc .= ']';
print tripal_feature_return_fasta($feature, $desc);
}
return;
}
/************************************************************************
*/
function tripal_analysis_go_feature_add($node) {
$content = "";
$sql = "
SELECT DISTINCT FCVT.feature_id,DBX.accession,CVT.name as goterm,
CVT.cvterm_id as go_id, CV.name as cvname
FROM {Feature_Cvterm} FCVT
INNER JOIN Cvterm CVT ON CVT.cvterm_ID = FCVT.cvterm_ID
INNER JOIN CV ON CV.cv_id = CVT.cv_id
INNER JOIN dbxref DBX ON DBX.dbxref_id = CVT.dbxref_id
WHERE
(CV.name = 'biological_process' OR
CV.name = 'cellular_component' OR
CV.name = 'molecular_function') AND
FCVT.feature_id = %d
ORDER BY CV.name, CVT.name
";
$previous_db = tripal_db_set_active('chado');
$results = db_query($sql,$node->feature->feature_id);
tripal_db_set_active($previous_db);
$term = db_fetch_object($results); // retrive the first result
if ($term) {
$content .= "<div id=\"tripal_go_box\" class=\"tripal_go-info-box\">";
$content .= "<div class=\"tripal_expandableBox\">".
"<h3>GO terms assigned to this feature</h3>".
"</div>";
$content .= "<div class=\"tripal_expandableBoxContent\">";
$content .= "<table class=\"feature-go-terms\">";
$content .= " <tr>";
$content .= " <th class=\"dbfieldname\">Accession</th>";
$content .= " <th class=\"dbfieldname\">Category</th>";
$content .= " <th class=\"dbfieldname\">Term</th>";
$content .= " </tr>";
do {
$content .= "<tr>";
$content .= " <td>GO:$term->accession</td>";
$content .= " <td>$term->cvname</td>";
$content .= " <td>$term->goterm</td>";
$content .= "</tr>";
} while($term = db_fetch_object($results));
$content .= "</table>";
$content .= "</div></div>";
}
return $content;
}
/*******************************************************************************
* Tripal GO administrative setting form. This function is called by
* tripal_analysis module which asks for an admin form to show on the page
*/
function tripal_analysis_go_get_settings() {
// Get an array of node types with internal names as keys
$options = node_get_types('names');
// Add 'chado_feature' to allowed content types for showing unigene results
$allowedoptions ['chado_feature'] = "Show GO terms on feature pages";
$allowedoptions ['chado_organism'] = "Show GO analysis on organism pages";
$form['description'] = array(
'#type' => 'item',
'#value' => t("This option allows user to display the Gene Ontology (GO) ".
"information. For features, this would include all GO terms assigned to a feature ".
"and for organisms this would be statistical pie charts of GO terms for a organism. Check the box to ".
"enable the display of GO information. Uncheck to disable."),
'#weight' => 0,
);
$form['tripal_analysis_go_setting'] = array(
'#type' => 'checkboxes',
'#options' => $allowedoptions,
'#default_value'=>variable_get('tripal_analysis_go_setting',array('chado_feature', 'chado_organism')),
);
$settings->form = $form;
$settings->title = "Tripal GO";
return $settings;
}