Added a very simple GAF 2.0 loader for loading GO terms (specifically for Blast2GO)

theme_tripal/tripal_feature/tripal_feature_go_terms.tpl.php

@@ -4,7 +4,7 @@ $terms = $feature->tripal_analysis_go->terms;
 ?>
 <div id="tripal_feature-go_terms-box" class="tripal_feature-info-box tripal-info-box">
   <div class="tripal_feature-info-box-title tripal-info-box-title">GO Assignments</div>
-  <div class="tripal_feature-info-box-desc tripal-info-box-desc">The feature '<?php print $feature->featurename ?>' is annotated with the following GO terms. Hover your mouse over the term name for a popup description.</div>
+  <div class="tripal_feature-info-box-desc tripal-info-box-desc">This <?php print $feature->type_id->name ?> is annotated with the following GO terms.</div>
   <?php if(count($terms) > 0){ ?>
   <table id="tripal_feature-go_terms-table" class="tripal_feature-table tripal-table tripal-table-horz">
     <tr>

tripal_analysis_blast/parse_blast_XML.inc

@@ -165,10 +165,11 @@ function tripal_analysis_blast_parseXML($analysis_id, $blastdb, $blastfile,
 	// Get cvterm_id for 'analysis_blast_output_iteration_hits' which is required
 	// for inserting into the analysisfeatureprop table
 	$previous_db = tripal_db_set_active('chado'); // use chado database
-	$sql = "SELECT CVT.cvterm_id FROM {cvterm} CVT ".
-       "INNER JOIN cv ON cv.cv_id = CVT.cv_id ".
-       "WHERE CVT.name = 'analysis_blast_output_iteration_hits' ".
-       "AND CV.name = 'tripal'";
+	$sql = "SELECT CVT.cvterm_id ".
+          "FROM {cvterm} CVT ".
+          "   INNER JOIN {cv} ON cv.cv_id = CVT.cv_id ".
+          "WHERE CVT.name = 'analysis_blast_output_iteration_hits' ".
+          "   AND CV.name = 'tripal'";
 	$type_id = db_result(db_query($sql));
 
 	// Load the XML file.

tripal_analysis_go/gaf_loader.inc

@@ -0,0 +1,403 @@
+<?php
+
+function tripal_analysis_go_gaf_load_form (){
+
+   $form['notice']= array(
+      '#type' => 'item',
+      '#value' => t('Note: currently, the GAF loader only uses column 2 (Object ID) and 5 (GO ID) 
+          from the GAF file, and simply imports GO terms for the features. 
+          Further support for this file format will be provided later.'),
+   );
+
+   $form['gaf_file']= array(
+      '#type'          => 'textfield',
+      '#title'         => t('GAF File'),
+      '#description'   => t('Please enter the full system path for the GAF file, or a path within the Drupal
+                             installation (e.g. /sites/default/files/xyz.txt).  The path must be accessible to the
+                             server on which this Drupal instance is running.'),
+      '#required' => TRUE,
+   );
+   // get the list of organisms
+   $sql = "SELECT * FROM {organism} ORDER BY genus, species";
+   $previous_db = tripal_db_set_active('chado');  // use chado database
+   $org_rset = db_query($sql);
+   tripal_db_set_active($previous_db);  // now use drupal database
+   $organisms = array();
+   $organisms[''] = '';
+   while($organism = db_fetch_object($org_rset)){
+      $organisms[$organism->organism_id] = "$organism->genus $organism->species ($organism->common_name)";
+   }
+   $form['type']= array(
+      '#type' => 'textfield',
+      '#title' => t('Sequence Type'),
+      '#required' => TRUE,
+      '#description' => t('Please enter the Sequence Ontology term that describes the sequences in the GAF file.'),
+   );
+   $form['organism_id'] = array (
+     '#title'       => t('Organism'),
+     '#type'        => t('select'),
+     '#description' => t("Choose the organism to which these sequences are associated "),
+     '#required'    => TRUE,
+     '#options'     => $organisms,
+   );
+   $form['import_options'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Import Options'),
+      '#collapsed' => TRUE
+   );
+   $form['import_options']['add_only']= array(
+      '#type' => 'checkbox',
+      '#title' => t('Add GO terms'),
+      '#required' => FALSE,
+      '#description' => t('GO terms in the GAF file will be added to each feature.'),
+   );
+//   $form['import_options']['replace']= array(
+//      '#type' => 'checkbox',
+//      '#title' => t('Replace GO terms'),
+//      '#required' => FALSE,
+//      '#description' => t('All GO terms for features in the GAF file will be replaced with terms in the GAF file.'),
+//   );
+   $form['import_options']['remove']= array(
+      '#type' => 'checkbox',
+      '#title' => t('Delete GO terms'),
+      '#required' => FALSE,
+      '#description' => t('GO terms for features in the GAF file will be removed. Other terms will remain.'),
+   );
+
+   $form['analysis'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Analysis Used to Derive GO terms'),
+      '#collapsed' => TRUE
+   ); 
+
+   // get the list of organisms
+   $sql = "SELECT * FROM {analysis} ORDER BY name";
+   $previous_db = tripal_db_set_active('chado');  // use chado database
+   $org_rset = db_query($sql);
+   tripal_db_set_active($previous_db);  // now use drupal database
+   $analyses = array();
+   $analyses[''] = '';
+   while($analysis = db_fetch_object($org_rset)){
+      $analyses[$analysis->analysis_id] = "$analysis->name ($analysis->program $analysis->programversion, $analysis->sourcename)";
+   }
+   $form['analysis']['analysis_id'] = array (
+     '#title'       => t('Analysis'),
+     '#type'        => t('select'),
+     '#description' => t("Choose the analysis that defines how the GO annotations in the GAF file were created. "),
+     '#required'    => TRUE,
+     '#options'     => $analyses,
+   );
+
+
+  // Advanced Options
+   $form['advanced'] = array(
+      '#type' => 'fieldset',
+      '#title' => t('Advanced Options'),
+      '#collapsed' => TRUE
+   );
+   $form['advanced']['re_help']= array(
+      '#type' => 'item',
+      '#value' => t('A regular expression is an advanced method for extracting information from a string of text.  
+                     By default, this loader will use the first word in the second column of the GAF file 
+                     as the uniquename for the sequences.  If this is not desired, you may use the following regular 
+                     expressions to define the location of the name or unique name within the text of column 2.'),
+   );
+
+   $form['advanced']['re_name']= array(
+      '#type' => 'textfield',
+      '#title' => t('Regular expression for the name'),
+      '#required' => FALSE,
+      '#description' => t('Enter the regular expression that will extract the feature name. For example, for text with a name and uniquename separated by a bar \'|\' (>seqname|uniquename), the regular expression would be, "^(.*?)\|.*$".  the name must be unique for this organism and sequence type.' ),
+   );   
+
+   $form['advanced']['re_uname']= array(
+      '#type' => 'textfield',
+      '#title' => t('Regular expression for the unique name'),
+      '#required' => FALSE,
+      '#description' => t('Enter the regular expression that will extract the unique feature name.  For example, for text with a name and uniquename separated by a bar \'|\' (>seqname|uniquename), the regular expression would be, "^.*?\|(.*)$".  the name must be unique for this organism and sequence type.' ),
+   );   
+
+   $form['button'] = array(
+      '#type' => 'submit',
+      '#value' => t('Import GAF file'),
+   );
+   return $form;
+}
+/**
+ *
+ *
+ * @ingroup gff3_loader
+ */
+function tripal_analysis_go_gaf_load_form_validate ($form, &$form_state){
+
+   $gaf_file = $form_state['values']['gaf_file'];
+   $organism_id = $form_state['values']['organism_id'];
+   $add_only = $form_state['values']['add_only'];
+   $remove   = $form_state['values']['remove'];
+   $replace  = $form_state['values']['replace'];
+   $analysis_id = $form_state['values']['analysis_id'];
+   $type      = trim($form_state['values']['type']);
+   $re_name      = trim($form_state['values']['re_name']);
+   $re_uname     = trim($form_state['values']['re_uname']);
+
+
+   // check to see if the file is located local to Drupal
+   $dfile = $_SERVER['DOCUMENT_ROOT'] . base_path() . $gaf_file; 
+   if(!file_exists($dfile)){
+      // if not local to Drupal, the file must be someplace else, just use
+      // the full path provided
+      $dfile = $gaf_file;
+   }
+   if(!file_exists($dfile)){
+      form_set_error('gff_file',t("Cannot find the file on the system. Check that the file exists or that the web server has permissions to read the file."));
+   }
+
+   if (($add_only and ($remove or $replace)) or 
+       ($replace and ($add_only or $remove)) or
+       ($remove and ($replace or $add_only))){
+       form_set_error('add_only',t("Please select only one checkbox from the import options section"));
+   }
+
+   if($re_name and $re_uname){
+     form_set_error('re_name',t("Please provide a regular expression for the name or the unique name only, not both."));
+   }
+
+   // check to make sure the types exists
+   $cvtermsql = "SELECT CVT.cvterm_id
+                 FROM {cvterm} CVT
+                    INNER JOIN {cv} CV on CVT.cv_id = CV.cv_id
+                    LEFT JOIN {cvtermsynonym} CVTS on CVTS.cvterm_id = CVT.cvterm_id
+                 WHERE cv.name = '%s' and (CVT.name = '%s' or CVTS.synonym = '%s')";
+   $cvterm = db_fetch_object(db_query($cvtermsql,'sequence',$type,$type));
+   if(!$cvterm){
+      form_set_error('type',t("The Sequence Ontology (SO) term selected for the sequence type is not available in the database. Please check spelling or select another."));
+   }
+   if($rel_type){
+      $cvterm = db_fetch_object(db_query($cvtermsql,'sequence',$parent_type,$parent_type));
+      if(!$cvterm){
+         form_set_error('parent_type',t("The Sequence Ontology (SO) term selected for the parent relationship is not available in the database. Please check spelling or select another."));
+      }
+   }
+}
+
+/**
+ *
+ * @ingroup gff3_loader
+ */
+function tripal_analysis_go_gaf_load_form_submit ($form, &$form_state){
+   global $user;
+
+   $gaf_file = $form_state['values']['gaf_file'];
+   $organism_id = $form_state['values']['organism_id'];
+   $add_only = $form_state['values']['add_only'];
+   $remove   = $form_state['values']['remove'];
+   $replace  = $form_state['values']['replace'];
+   $analysis_id = $form_state['values']['analysis_id'];
+   $type      = trim($form_state['values']['type']);
+   $re_name      = trim($form_state['values']['re_name']);
+   $re_uname     = trim($form_state['values']['re_uname']);
+
+
+   $args = array($gaf_file,$organism_id,$analysis_id,$add_only,$replace,$remove,$re_name,$re_uname,$type);
+   if($add_only){
+     $type = 'add GO terms';
+   }
+   if($replace){
+     $type = 'replace and add GO terms';
+   }
+   if($remove){
+     $type = 'remove GO terms';
+   }
+   tripal_add_job("Import GAF 2.0 file $gaf_file and $type",'tripal_analysis_go',
+      'tripal_analysis_go_load_gaf',$args,$user->uid);
+
+   return '';
+}
+
+/**
+ *
+ *
+ * @ingroup gff3_loader
+ */
+function tripal_analysis_go_load_gaf($gaf_file, $organism_id,$analysis_id,$add_only =0, 
+   $replace = 0, $remove = 0, $re_name, $re_uname, $type, $job = NULL)
+{
+   print "Opening GAF file $gaf_file\n";
+
+    
+   $lines = file($gaf_file,FILE_SKIP_EMPTY_LINES);
+   $i = 0;
+
+   $name = '';
+   $residues = '';
+   $num_lines = sizeof($lines);
+   $interval = intval($num_lines * 0.01);
+   if($interval == 0){
+      $interval = 1;
+   }
+
+   foreach ($lines as $line_num => $line) {
+      $i++;  // update the line count     
+
+      // skip comments
+      if(preg_match('/^\!/',$line)){
+         continue; 
+      }
+
+      // update the job status every 1% features
+      if($job and $i % $interval == 0){
+         tripal_job_set_progress($job,intval(($i/$num_lines)*100));
+      }
+
+      // split the line into it's columns
+      $cols = explode("\t",$line);
+      if(sizeof($cols) < 15){
+         print "ERROR: improper number of columns on line $i\n";
+         print_r($cols);
+         return '';
+      }
+      $db        = $cols[0];
+      $object    = $cols[1];
+      $symbol    = $cols[2];
+      $qualifier = $cols[3];
+      $go_id     = $cols[4];
+      $dbxref    = $cols[5];
+      $ecode     = $cols[6];
+      $with      = $cols[7];
+      $aspect    = $cols[8];
+      $obj_name  = $cols[9];
+      $obj_syn   = $cols[10];
+      $obj_type  = $cols[11];
+      $taxon     = $cols[12];
+      $date      = $cols[13];
+      $assigned  = $cols[14];
+      $exten     = $cols[15];
+      $product   = $cols[16];
+
+      // get the name or uniquename for the feature
+      $uname = $object;
+      $name = '';
+      if($re_name){
+         if(!preg_match("/$re_name/",$object,$matches)){
+            print "Regular expression for the feature name finds nothing\n";
+         } else {
+            $name = trim($matches[1]);
+         }
+      } else {
+         preg_match("/^\s*(.*?)[\s\|].*$/",$object,$matches);
+         $name = trim($matches[1]);
+      }
+      if($re_uname){
+         if(!preg_match("/$re_uname/",$object,$matches)){
+            print "Regular expression for the feature unique name finds nothing\n";
+         } else {
+            $uname = trim($matches[1]);
+         }
+      }
+
+      // get the feature
+      $values = array(
+         'type_id' => array(
+            'cv_id' => array(
+               'name' => 'sequence'
+            ),
+            'name' => $type,
+         ),
+         'organism_id' => $organism_id,
+      );
+      if($name){
+        $values['name'] = $name;
+      } 
+      if($uname){
+        $values['uniquename'] = $uname;
+      } 
+      $feature = tripal_core_chado_select('feature',array('*'),$values);
+
+      // add the GO term to the feature
+      tripal_analysis_go_load_gaff_go_term($feature[0],$go_id,$remove);
+   }
+   return 1;
+}
+/**
+*
+*/
+function tripal_analysis_go_load_gaff_go_term($feature,$dbxref,$remove){
+
+   // get the database name from the reference.  If it doesn't exist then create one.
+   $ref = explode(":",$dbxref);
+   $dbname = $ref[0];
+   $accession = $ref[1];
+
+   // first look for the database name 
+   $db = tripal_core_chado_select('db',array('db_id'),array('name' => "DB:$dbname"));  
+   if(sizeof($db) == 0){
+      $db = tripal_core_chado_select('db',array('db_id'),array('name' => "$dbname"));      
+   }        
+   if(sizeof($db) == 0){
+      print "ERROR: Database, $dbname is missing for reference: $dbname:$accession\n";
+      return 0;
+   } 
+   $db = $db[0];
+    
+   // now check to see if the accession exists
+   $dbxref = tripal_core_chado_select('dbxref',array('dbxref_id'),array(
+      'accession' => $accession,'db_id' => $db->db_id));
+   if(sizeof($dbxref) == 0){
+      print "ERROR: Accession, $accession is missing for reference: $dbname:$accession\n";
+      return 0;
+   }
+   $dbxref = $dbxref[0];
+
+   // now check to see if the cvterm exists
+   $cvterm = tripal_core_chado_select('cvterm',array('cvterm_id'),array(
+      'dbxref_id' => $dbxref->dbxref_id));
+   // if it doesn't exist in the cvterm table, look for an alternate id
+   if(sizeof($cvterm) == 0){
+      $cvterm = tripal_core_chado_select('cvterm_dbxref',array('cvterm_id'),array(
+         'dbxref_id' => $dbxref->dbxref_id));
+   }
+   if(sizeof($cvterm) == 0){
+      print "ERROR: CVTerm is missing for reference: $dbname:$accession\n";
+      return 0;
+   }
+   $cvterm = $cvterm[0];
+   
+
+   // check to see if this feature cvterm already exists
+   $fcvt = tripal_core_chado_select('feature_cvterm',array('feature_cvterm_id'),
+      array('cvterm_id' => $cvterm->cvterm_id,'feature_id' => $feature->feature_id));
+
+   // now associate this feature with the cvterm if it doesn't already exist
+   if(sizeof($fcvt)==0){
+      $values = array(
+         'feature_id' => $feature->feature_id,
+         'cvterm_id' => $cvterm->cvterm_id,
+         'pub_id' => array(
+            'uniquename' => 'null',
+         ),
+      );
+      $ret = tripal_core_chado_insert('feature_cvterm',$values);
+
+      if($ret){
+         print "   Added ontology term $dbname:$accession to feature $feature->uniquename\n";
+      } else {
+         print "ERROR: failed to insert ontology term: $dbname:$accession\n";
+         return 0;
+      }
+   } else {
+      if($remove){
+         $status = tripal_core_chado_delete('feature_cvterm',
+            array('cvterm_id' => $cvterm->cvterm_id,
+                 'feature_id' => $feature->feature_id));
+         if(!$status){
+            print "ERROR: Failed to delete ontology term $dbname:$accession from feature $feature->uniquename\n";
+         } else {
+            print "   Deleted ontology term $dbname:$accession from feature $feature->uniquename\n";
+         }
+      } else {
+         print "   Ontology term already associated to feature $feature->uniquename, skipping $dbname:$accession\n";
+      }
+   }
+
+   return 1;
+}

tripal_analysis_go/tripal_analysis_go.module

@@ -1,5 +1,7 @@
 <?php
 
+require_once "gaf_loader.inc";
+
 function tripal_analysis_go_init(){
    // Add style sheet
    drupal_add_css(drupal_get_path('theme', 'tripal').'/css/tripal_analysis_go.css');
@@ -31,10 +33,44 @@ function tripal_analysis_go_menu() {
       'access arguments' => array('access chado_analysis_go content'),
       'type' => MENU_CALLBACK
    );
-
+   $items['admin/tripal/tripal_analysis_go'] = array(
+     'title' => 'Gene Ontology',
+     'description' => 'Administrative tools for managing Gene Ontology data.',
+     'page callback' => 'tripal_analysis_go_module_description_page',
+     'access arguments' => array('administer site configuration'),
+     'type' => MENU_NORMAL_ITEM,
+   );
+   $items['admin/tripal/tripal_analysis_go/gaf_load'] = array(
+     'title' => t('Import GO terms with GAF file'),
+     'description' => t("Import GO terms into Chado using the Gene Ontology's GAF 2.0 file format"),
+     'page callback' => 'drupal_get_form',
+     'page arguments' => array('tripal_analysis_go_gaf_load_form'),
+     'access arguments' => array('access administration pages'),
+     'type' => MENU_NORMAL_ITEM,
+   );
 
    return $items;
 }
+/*************************************************************************
+ * Purpose: Provide Guidance to new Tripal Admin
+ *
+ * @return HTML Formatted text
+ */
+function tripal_analysis_go_module_description_page() {
+  $text = '';
+  
+  $text .= '<h3>Description:</h3>';
+  $text .= '<p>TODO: Basic Description of this module including mention/link to the chado module</p>';
+
+  $text .= '<h3>Post Installation Instructions:</h3>';
+  $text .= '<p>TODO: Describe any post installation intructions here. You shouldalways include setting user permissions.</p>';
+  
+  
+  $text .= '<h3>Features of this Module:</h3>';
+  $text .= '<p>TODO: Discuss the Features of this module including links. Some features to consider are creating content, details pages/node content, editing/deleteing, basic listings and vies integration. See admin/tripal/tripal_stock for an example.</p>';
+  
+  return $text;
+}
 /*******************************************************************************
  * Set the permission types that the chado module uses.  Essentially we
  * want permissionis that protect creation, editing and deleting of chado
@@ -510,3 +546,42 @@ function tripal_analysis_go_get_settings() {
    $settings->title = "Tripal GO";
    return $settings;
 }
+/**
+ *
+ *
+ * @ingroup tripal_feature
+ */
+function tripal_analysis_go_job_describe_args($callback,$args){
+
+   $new_args = array();
+   if($callback == 'tripal_analysis_go_load_gaf'){
+      
+      $new_args['GAF 2.0 file'] = $args[0];
+
+      $organism = tripal_core_chado_select('organism',array('genus','species'),array('organism_id' => $args[1]));
+      $new_args['Organism'] = $organism[0]->genus." ". $organism[0]->species;
+      $new_args['Sequence Type'] = $args[8];
+
+      // add in the analysis 
+      if($args[2]){
+         $analysis = tripal_core_chado_select('analysis',array('name'),array('analysis_id' => $args[2]));
+      }
+      $new_args['Analysis'] = $analysis[0]->name;
+
+      if($args[3]){
+        $new_args['Function to perform'] = 'Add GO terms';
+      }
+      if($args[4]){
+        $new_args['Function to perform'] = 'Replace GO terms';
+      }
+      if($args[5]){
+        $new_args['Function to perform'] = 'Delete GO terms';
+      }
+
+      $new_args['Regular expression for the feature name'] = $args[6];
+      $new_args['Regular expression for the feature unique name'] = $args[7];
+
+
+   }
+   return $new_args;
+}

tripal_feature/gff_loader.php

@@ -23,7 +23,7 @@ function tripal_core_gff3_load_form (){
       '#type'          => 'textfield',
       '#title'         => t('GFF3 File'),
       '#description'   => t('Please enter the full system path for the GFF file, or a path within the Drupal
-                             installation (e.g. /sites/default/files/xyz.obo).  The path must be accessible to the
+                             installation (e.g. /sites/default/files/xyz.gff).  The path must be accessible to the
                              server on which this Drupal instance is running.'),
       '#required' => TRUE,
       '#weight'        => 1