split workflow in 3 pieces

mchenry · Oct 4, 2012 · 6608a48 · 6608a48
1 parent 4013d2e
commit 6608a48
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Showing 8 changed files with 802 additions and 92 deletions.
diff --git a/web/finished.php b/web/finished.php
@@ -55,11 +55,19 @@
 }
 
 $logs="";
-$logs .= createOption("workflow.Rout");
+foreach(scandir($folder . DIRECTORY_SEPARATOR) as $file) {
+	if (preg_match("/^workflow_stage.*\.Rout$/", $file) === 1) {
+		$logs .= createOption($file);
+	}
+}
 
 $outputs  = "";
 $outputs .= "<option>pecan.xml</option>";
-$outputs .= "<option>workflow.R</option>";
+foreach(scandir($folder . DIRECTORY_SEPARATOR) as $file) {
+	if (preg_match("/^workflow_stage.*\.R$/", $file) === 1) {
+		$outputs .= createOption($file);
+	}
+}
 
 # check the run output folder
 foreach(scandir("$folder/run") as $file) {

diff --git a/web/running_stage1.php b/web/running_stage1.php
@@ -0,0 +1,291 @@
+<?php
+/**
+ * Copyright (c) 2012 University of Illinois, NCSA.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the 
+ * University of Illinois/NCSA Open Source License
+ * which accompanies this distribution, and is available at
+ * http://opensource.ncsa.illinois.edu/license.html
+ */
+# offline mode?
+if (isset($_REQUEST['offline'])) {
+	$offline=true;
+} else {
+	$offline=false;
+}
+
+// runid
+if (!isset($_REQUEST['workflowid'])) {
+  die("Need a workflowid.");
+}
+$workflowid=$_REQUEST['workflowid'];
+
+// database parameters
+require("dbinfo.php");
+$connection=open_database();
+
+// get run information
+$query = "SELECT site_id, model_id, model_type, hostname, folder FROM workflows WHERE workflows.id=$workflowid";
+$result = mysql_query($query);
+if (!$result) {
+	die('Invalid query: ' . mysql_error());
+}
+$workflow = mysql_fetch_assoc($result);
+$folder = $workflow['folder'];
+
+// check result
+$status=file($folder . DIRECTORY_SEPARATOR . "STATUS");
+if ($status === FALSE) {
+	$status = array();
+}
+
+// check the global status
+switch(checkStatus("CONFIG")) {
+	case 0:
+		$nextenabled="disabled=\"disabled\"";
+				header( "refresh:5" );
+		break;		
+	case 1:
+		$nextenabled="disabled=\"disabled\"";
+				chdir($folder);
+		pclose(popen('R_LIBS_USER="/home/kooper/lib/R" R CMD BATCH workflow_stage2.R &', 'r'));
+		if ($offline) {
+			header( "Location: running_stage2.php?workflowid=$workflowid&offline=offline");
+		} else {
+			header( "Location: running_stage2.php?workflowid=$workflowid");
+		}
+		break;
+	case 2:
+		$nextenabled="";
+		if ($offline) {
+			header( "Location: finished.php?workflowid=$workflowid&offline=offline");
+		} else {
+			header( "Location: finished.php?workflowid=$workflowid");
+		}
+		mysql_query("UPDATE workflows SET finished_at=NOW() WHERE id=${workflowid} AND finished_at IS NULL");
+		break;
+}
+
+?>
+<!DOCTYPE html>
+<html>
+<head>
+<title>PEcAn Running</title>
+<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=no" />
+<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
+<link rel="stylesheet" type="text/css" href="sites.css" />
+<script type="text/javascript" src="jquery-1.7.2.min.js"></script>
+<script type="text/javascript">
+	window.onresize = resize;
+	window.onload = resize;
+
+	function resize() {
+    	$("#stylized").height($(window).height() - 5);
+    	$("#output").height($(window).height() - 1);
+    	$("#output").width($(window).width() - $('#stylized').width() - 5);
+
+    	$('#log').scrollTop($('#log')[0].scrollHeight);
+	}
+
+	function prevStep() {
+		$("#formprev").submit();
+	}
+
+	function nextStep() {
+		$("#formnext").submit();
+	}
+</script>
+</head>
+<body>
+<div id="wrap">
+	<div id="stylized">
+		<h1>Job is running</h1>
+		<p>Job is currently executing, please wait.</p>
+
+		<form id="formprev" method="POST" action="selectdata.php">
+<?php if ($offline) { ?>
+			<input name="offline" type="hidden" value="offline">
+<?php } ?>
+				<input type="hidden" name="siteid" value="<?=$workflow['site_id']?>" />
+		<input type="hidden" name="modelid" value="<?=$workflow['model_id']?>" />
+		<input type="hidden" name="modeltype" value="<?=$workflow['model_type']?>" />
+		<input type="hidden" name="hostname" value="<?=$workflow['hostname']?>" />
+		</form>
+
+		<form id="formemail" method="POST" action="sendemail.php">
+		<input type="hidden" name="workflowid" value="<?=$workflowid?>" />
+		</form>
+
+		<form id="formnext" method="POST" action="finished.php">
+<?php if ($offline) { ?>
+			<input name="offline" type="hidden" value="offline">
+<?php } ?>
+		<input type="hidden" name="workflowid" value="<?=$workflowid?>" />
+		<span id="error" class="small">&nbsp;</span>
+		<input id="prev" type="button" value="Prev" onclick="prevStep();" />
+		<input id="next" type="button" value="Next" onclick="nextStep();" <?=$nextenabled?>/>		
+		<div class="spacer"></div>
+		</form>
+	</div>
+	<div id="output">
+	<h2>Execution Status</h2>
+	<table border=1>
+		<tr>
+			<th>Stage Name</th>
+			<th>Start Time</th>
+			<th>End Time</th>
+			<th>Status</th>
+		</tr>
+		<tr>
+			<th>setup</th>
+			<td><?=startTime("SETUP");?></td>
+			<td><?=endTime("SETUP");?></td>
+			<td><?=status("SETUP");?></td>
+		</tr>
+		<tr>
+			<th>fia2ed</th>
+			<td><?=startTime("FIA2ED");?></td>
+			<td><?=endTime("FIA2ED");?></td>
+			<td><?=status("FIA2ED");?></td>
+		</tr>
+		<tr>
+			<th>query.trait</th>
+			<td><?=startTime("TRAIT");?></td>
+			<td><?=endTime("TRAIT");?></td>
+			<td><?=status("TRAIT");?></td>
+		</tr>
+		<tr>
+			<th>meta.analysis</th>
+			<td><?=startTime("META");?></td>
+			<td><?=endTime("META");?></td>
+			<td><?=status("META");?></td>
+		</tr>
+		<tr>
+			<th>write.config</th>
+			<td><?=startTime("CONFIG");?></td>
+			<td><?=endTime("CONFIG");?></td>
+			<td><?=status("CONFIG");?></td>
+		</tr>
+		<tr>
+			<th>model</th>
+			<td><?=startTime("MODEL");?></td>
+			<td><?=endTime("MODEL");?></td>
+			<td><?=status("MODEL");?></td>
+		</tr>
+				<tr>
+			<th>output.conversion</th>
+			<td><?=startTime("OUTPUT");?></td>
+			<td><?=endTime("OUTPUT");?></td>
+			<td><?=status("OUTPUT");?></td>
+		</tr>
+				<tr>
+			<th>finished</th>
+			<td><?=startTime("FINISHED");?></td>
+			<td><?=endTime("FINISHED");?></td>
+			<td><?=status("FINISHED");?></td>
+		</tr>
+	</table>
+	<hr/>
+ 	<h2>Output from PEcAn</h2>
+ 	<textarea id="log" cols="80" rows="10" readonly="readonly">
+<?php
+  	foreach(scandir($folder . DIRECTORY_SEPARATOR) as $file) {
+  		if (preg_match("/^workflow_stage.*\.Rout$/", $file) === 1) {
+  			parselog($folder . DIRECTORY_SEPARATOR . $file);
+  		}
+	}
+?>
+ 	</textarea>
+	</div>
+</div>
+</body>
+</html>
+
+<?php 
+close_database($connection);
+
+function checkStatus($token) {
+  	global $status;
+	foreach ($status as $line) {
+		$data = explode("\t", $line);
+		if ((count($data) >= 4) && ($data[3] == 'ERROR')) {
+			return 2;
+		}
+	}
+
+	if (endTime($token) != "") {
+		return 1;
+	}
+
+	return 0;
+}
+
+function startTime($token) {
+  global $status;
+  foreach ($status as $line) {
+    $data = explode("\t", $line);
+    if ($data[0] == $token) {
+      return $data[1];
+    }
+  }
+  return "";
+}
+
+function endTime($token) {
+  global $status;
+  foreach ($status as $line) {
+    $data = explode("\t", $line);
+    if ($data[0] == $token && count($data) >= 3) {
+      return $data[2];
+    }
+  }
+  return "";
+}
+
+function status($token) {
+  global $folder;
+  global $status;
+
+  foreach ($status as $line) {
+    $data = explode("\t", $line);
+    if ($data[0] == $token) {
+      if (count($data) >= 4) {
+        return $data[3];
+      }
+      if ($token == "MODEL") {
+        return exec("tail -20 `ls -1rt $folder/run/*.log` |  grep 'Simulating:' | tail -1 | sed 's/^.*Simulating:[ ]*//' | awk '{print $1}'");
+      }
+      return "Running";
+    }
+  }
+  return "Waiting";
+}
+
+function parselog($filename)
+{
+	// Open the file
+	$f = fopen($filename, "rb");
+	if ($f === false) {
+		return "file does not exist.";
+	}
+
+	// read the file line by line
+	$check = false;
+	while (($buffer = fgets($f, 4096)) !== false) {
+		if ($check && ($buffer[0]==" ")) {
+			print($buffer);
+		} else if (stristr($buffer, "error") !== false) {
+			print($buffer);
+			$check = true;
+		} else if (stristr($buffer, "warn") !== false) {
+			print($buffer);
+			$check = true;
+		} else {
+			$check = false;
+		}
+	}
+
+	// Close file and return
+	fclose($f);
+}
+?>