tripal/tripal_analysis_go/tripal_analysis_go.module

<?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;
}