--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plugins/debug_logger/runlog/runlog.php	Thu Jan 04 15:50:29 2018 -0500
@@ -0,0 +1,233 @@
+<?php
+
+/**
+ * runlog
+ *
+ * @author Ziba Scott <ziba@umich.edu>
+ */
+class runlog {
+
+    private $start_time   = FALSE;
+    private $parent_stack = array();
+    private $file_handles = array();
+    private $indent       = 0;
+    private $run_log      = array();
+
+    public $print_to_console = FALSE;
+    public $threshold        = 0;
+    public $tag_count        = array();
+    public $timestamp        = "d-M-Y H:i:s O";
+    public $max_line_size    = 150;
+
+    function runlog()
+    {
+        $this->start_time = microtime(true);
+    }
+
+    public function start($name, $tag = false)
+    {
+        $this->run_log[] = array(
+                'type'    => 'start',
+                'tag'     => $tag,
+                'index'   => count($this->run_log),
+                'value'   => $name,
+                'time'    => microtime(true),
+                'parents' => $this->parent_stack,
+                'ended'   => false,
+        );
+
+        $this->parent_stack[] = $name;
+
+        $this->print_to_console("start: ".$name, $tag, 'start');
+        $this->print_to_file("start: ".$name, $tag, 'start');
+        $this->indent++;
+    }
+
+    public function end()
+    {
+        $name = array_pop($this->parent_stack);
+        foreach ($this->run_log as $k => $entry) {
+            if ($entry['value'] == $name && $entry['type'] == 'start' && !$entry['ended']) {
+                $lastk = $k;
+            }
+        }
+
+        $start = $this->run_log[$lastk]['time'];
+        $this->run_log[$lastk]['duration'] = microtime(true) - $start;
+        $this->run_log[$lastk]['ended'] = true;
+        $this->run_log[] = array(
+                'type'     => 'end',
+                'tag'      =>  $this->run_log[$lastk]['tag'],
+                'index'    => $lastk,
+                'value'    => $name,
+                'time'     => microtime(true),
+                'duration' => microtime(true) - $start,
+                'parents'  => $this->parent_stack,
+        );
+
+        $this->indent--;
+        if ($this->run_log[$lastk]['duration'] >= $this->threshold) {
+            $tag_report = "";
+            foreach ($this->tag_count as $tag => $count){
+                $tag_report .= "$tag: $count, ";
+            }
+            if (!empty($tag_report)) {
+//                $tag_report = "\n$tag_report\n";
+            }
+            $end_txt = sprintf("end: $name - %0.4f seconds $tag_report", $this->run_log[$lastk]['duration']);
+            $this->print_to_console($end_txt, $this->run_log[$lastk]['tag'], 'end');
+            $this->print_to_file($end_txt,  $this->run_log[$lastk]['tag'], 'end');
+        }
+    }
+
+    public function increase_tag_count($tag)
+    {
+        if (!isset($this->tag_count[$tag])) {
+            $this->tag_count[$tag] = 0;
+        }
+
+        $this->tag_count[$tag]++;
+    }
+
+    public function get_text()
+    {
+        $text = "";
+        foreach ($this->run_log as $entry){
+            $text .= str_repeat("   ",count($entry['parents']));
+            if ($entry['tag'] != 'text'){
+                $text .= $entry['tag'].': ';
+            }
+            $text .= $entry['value'];
+
+            if ($entry['tag'] == 'end') {
+                $text .= sprintf(" - %0.4f seconds", $entry['duration']);
+            }
+
+            $text .= "\n";
+        }
+
+        return $text;
+    }
+
+    public function set_file($filename, $tag = 'master')
+    {
+        if (!isset($this->file_handle[$tag])) {
+            $this->file_handles[$tag] = fopen($filename, 'a');
+            if (!$this->file_handles[$tag]) {
+                trigger_error('Could not open file for writing: '.$filename);
+            }
+        }
+    }
+
+    public function note($msg, $tag = false)
+    {
+        if ($tag) {
+            $this->increase_tag_count($tag);
+        }
+        if (is_array($msg)) {
+            $msg = '<pre>' . print_r($msg, true) . '</pre>';
+        }
+        $this->debug_messages[] = $msg;
+        $this->run_log[] = array(
+                'type'    => 'note',
+                'tag'     => $tag ?: 'text',
+                'value'   => htmlentities($msg),
+                'time'    => microtime(true),
+                'parents' => $this->parent_stack,
+        );
+
+        $this->print_to_file($msg, $tag);
+        $this->print_to_console($msg, $tag);
+    }
+
+    public function print_to_file($msg, $tag = false, $type = false)
+    {
+        if (!$tag) {
+            $file_handle_tag = 'master';
+        }
+        else{
+            $file_handle_tag = $tag;
+        }
+
+        if ($file_handle_tag != 'master' && isset($this->file_handles[$file_handle_tag])) {
+            $buffer = $this->get_indent();
+            $buffer .= "$msg\n";
+            if (!empty($this->timestamp)) {
+                $buffer = sprintf("[%s] %s",date($this->timestamp, time()), $buffer);
+            }
+            fwrite($this->file_handles[$file_handle_tag], wordwrap($buffer, $this->max_line_size, "\n     "));
+        }
+
+        if (isset($this->file_handles['master']) && $this->file_handles['master']) {
+            $buffer = $this->get_indent();
+            if ($tag) {
+                $buffer .= "$tag: ";
+            }
+            $msg = str_replace("\n","",$msg);
+            $buffer .= "$msg";
+            if (!empty($this->timestamp)) {
+                $buffer = sprintf("[%s] %s",date($this->timestamp, time()), $buffer);
+            }
+            if(strlen($buffer) > $this->max_line_size){
+                $buffer = substr($buffer,0,$this->max_line_size - 3) . "...";
+            }
+            fwrite($this->file_handles['master'], $buffer."\n");
+        }
+    }
+
+    public function print_to_console($msg, $tag = false)
+    {
+        if ($this->print_to_console) {
+            if (is_array($this->print_to_console)) {
+                if (in_array($tag, $this->print_to_console)) {
+                    echo $this->get_indent();
+                    if ($tag) {
+                        echo "$tag: ";
+                    }
+                    echo "$msg\n";
+                }
+            }
+            else {
+                echo $this->get_indent();
+                if ($tag) {
+                    echo "$tag: ";
+                }
+                echo "$msg\n";
+            }
+        }
+    }
+
+    public function print_totals()
+    {
+        $totals = array();
+        foreach ($this->run_log as $entry) {
+            if ($entry['type'] == 'start' && $entry['ended']) {
+                $totals[$entry['value']]['duration'] += $entry['duration'];
+                $totals[$entry['value']]['count'] += 1;
+            }
+        }
+
+        if ($this->file_handle) {
+            foreach ($totals as $name => $details) {
+                fwrite($this->file_handle,$name.": ".number_format($details['duration'],4)."sec,  ".$details['count']." calls \n");
+            }
+        }
+    }
+
+    private function get_indent()
+    {
+        $buf = "";
+        for ($i = 0; $i < $this->indent; $i++) {
+            $buf .= "  ";
+        }
+        return $buf;
+    }
+
+
+    function  __destruct()
+    {
+        foreach ($this->file_handles as $handle) {
+            fclose($handle);
+        }
+    }
+}