|
|
@@ -1342,6 +1342,41 @@ function tripal_feature_load_organism_feature_counts($organism){
|
|
|
if(strcmp($show_counts,'show_feature_summary')!=0){
|
|
|
return array ('enabled' => false );
|
|
|
}
|
|
|
+
|
|
|
+
|
|
|
+ $args = array();
|
|
|
+ $names = array();
|
|
|
+ $order = array();
|
|
|
+
|
|
|
+ // build the where clause for the SQL statement if we have a custom term list
|
|
|
+ // we'll also keep track of the names the admin provided (if any) and the
|
|
|
+ // order that the terms should appear.
|
|
|
+ $is_custom = 0;
|
|
|
+ $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', ''));
|
|
|
+ $where = '';
|
|
|
+ if($temp){
|
|
|
+ $is_custom = 1;
|
|
|
+ $temp = explode("\n",$temp);
|
|
|
+ foreach ($temp as $key => $value){
|
|
|
+ // separate the key value pairs
|
|
|
+ $temp2 = explode("=",$value);
|
|
|
+ $feature_type = rtrim($temp2[0]);
|
|
|
+ $args[] = $feature_type;
|
|
|
+ $order[] = $feature_type;
|
|
|
+ // if a new name is provided then use that otherwise just
|
|
|
+ // use the feature type
|
|
|
+ if(count($temp2) == 2){
|
|
|
+ $names[] = rtrim($temp2[1]);
|
|
|
+ } else {
|
|
|
+ $names[] = $feature_type;
|
|
|
+ }
|
|
|
+ $where .= "OFC.feature_type = '%s' OR \n";
|
|
|
+ }
|
|
|
+ if($where){
|
|
|
+ $where = substr($where,0,-5); # remove OR from the end
|
|
|
+ $where = "($where) AND";
|
|
|
+ }
|
|
|
+ }
|
|
|
|
|
|
// get the feature counts. This is dependent on a materialized view
|
|
|
// installed with the organism module
|
|
|
@@ -1349,19 +1384,32 @@ function tripal_feature_load_organism_feature_counts($organism){
|
|
|
SELECT OFC.num_features,OFC.feature_type,CVT.definition
|
|
|
FROM {organism_feature_count} OFC
|
|
|
INNER JOIN {cvterm} CVT on OFC.cvterm_id = CVT.cvterm_id
|
|
|
- WHERE organism_id = %d
|
|
|
+ WHERE $where organism_id = %d
|
|
|
ORDER BY num_features desc
|
|
|
";
|
|
|
+ $args[] = $organism->organism_id;
|
|
|
$previous_db = tripal_db_set_active('chado'); // use chado database
|
|
|
- $org_features = db_query($sql,$organism->organism_id);
|
|
|
+ $org_features = db_query($sql,$args);
|
|
|
tripal_db_set_active($previous_db); // now use drupal database
|
|
|
-
|
|
|
- $i=0;
|
|
|
+
|
|
|
+ // iterate through the types
|
|
|
$types = array();
|
|
|
while($type = db_fetch_object($org_features)){
|
|
|
- $types[$i++] = $type;
|
|
|
+ $types[$type->feature_type] = $type;
|
|
|
+ // if we don't have an order this means we didn't go through the loop
|
|
|
+ // above to set the names, so do that now
|
|
|
+ if(!$is_custom){
|
|
|
+ $names[] = $type->feature_type;
|
|
|
+ $order[] = $type->feature_type;
|
|
|
+ }
|
|
|
}
|
|
|
- return array ( 'types' => $types, 'enabled' => true );
|
|
|
+
|
|
|
+ # now reorder the types
|
|
|
+ $ordered_types = array();
|
|
|
+ foreach ($order as $type){
|
|
|
+ $ordered_types[] = $types[$type];
|
|
|
+ }
|
|
|
+ return array ( 'types' => $ordered_types, 'names' => $names, 'enabled' => true );
|
|
|
}
|
|
|
/**
|
|
|
*
|
|
|
@@ -1822,20 +1870,37 @@ function tripal_feature_preprocess_tripal_analysis_feature_browser(&$variables){
|
|
|
*/
|
|
|
function tripal_feature_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.
|
|
|
- $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$chart_id);
|
|
|
- $options = array(
|
|
|
+ // we only want the chart to show feature types setup by the admin
|
|
|
+ $temp = rtrim(variable_get('tripal_feature_summary_report_mapping', ''));
|
|
|
+ $where = '';
|
|
|
+ if($temp){
|
|
|
+ $temp = explode("\n",$temp);
|
|
|
+ foreach ($temp as $key => $value){
|
|
|
+ $temp2 = explode("=",$value);
|
|
|
+ $feature_type = rtrim($temp2[0]);
|
|
|
+ $where .= "CNT.feature_type = '$feature_type' OR \n";
|
|
|
+ }
|
|
|
+ if($where){
|
|
|
+ $where = substr($where,0,-5); # remove OR from the end
|
|
|
+ $where = "($where) AND";
|
|
|
+ }
|
|
|
+ }
|
|
|
+
|
|
|
+ $organism_id = preg_replace("/^tripal_feature_cv_chart_(\d+)$/","$1",$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.
|
|
|
+ $options = array(
|
|
|
count_mview => 'organism_feature_count',
|
|
|
cvterm_id_column => 'cvterm_id',
|
|
|
count_column => 'num_features',
|
|
|
size => '550x200',
|
|
|
- filter => "CNT.organism_id = $organism_id",
|
|
|
- );
|
|
|
- return $options;
|
|
|
+ filter => "$where CNT.organism_id = $organism_id",
|
|
|
+ );
|
|
|
+ return $options;
|
|
|
}
|
|
|
|
|
|
/**
|
Stephen Ficklin