X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=site%2Fphp%2Fjsmol.php;fp=site%2Fphp%2Fjsmol.php;h=1917b925d3f32f867994ea2af135fa7ebfed1627;hp=5871d4a58e14bbf28534e9987ec4c758ca5aff25;hb=b9b7a352eee79b7764c3b09c9d19663075061d8c;hpb=7301a2415adab88038b291fc54caeeb3a5a47a44

diff --git a/site/php/jsmol.php b/site/php/jsmol.php
index 5871d4a..1917b92 100644
--- a/site/php/jsmol.php
+++ b/site/php/jsmol.php
@@ -1,198 +1,198 @@
-<?php
-
-// jsmol.php
-// Bob Hanson hansonr@stolaf.edu 1/11/2013
-//
-// 23 Mar 2015 -- checking for missing :// in queries
-// 2 Feb 2014 -- stripped of any exec calls and image options-- this was for JSmol image option - abandoned
-// 30 Oct 2013 -- saveFile should not convert " to _
-// 30 Sep 2013 -- adjusted error handling to only report E_ERROR not E_WARNING
-// 7 Sep 2013 -- adding PHP error handling
-//
-//////// note to administrators:
-//
-// from http://us3.php.net/file_get_contents: 
-//
-// A URL can be used as a filename with this function if the fopen wrappers 
-// have been enabled. See fopen() for more details on how to specify the 
-// filename. See the Supported Protocols and Wrappers for links to information 
-// about what abilities the various wrappers have, notes on their usage, and 
-// information on any predefined variables they may provide.
-///////
-//
-// Server-side Jmol delivers:
-//   simple relay for cross-domain files
-//
-//   options:
-//
-//   call
-//         "saveFile"
-//             returns posted data in "data=" with mime type "mimetype=" to file name "filename="
-//         "getInfoFromDatabase" 
-//             returns XML data
-//             requires database="=" (RCSB REST service)
-//         "getRawDataFromDatabase"
-//               "_" 
-//                  just use $query
-//               (anything else)
-//                  use $database.$query
-//
-//   encoding
-//         ""        no encoding (default)
-//         "base64"  BASE64-encoded binary files for Chrome synchronous AJAX
-//                      prepends ";base64," to encoded output  
-//
-// simple server tests:
-//
-// http://foo.wherever/jsmol.php?call=getRawDataFromDatabase&database=_&query=http://chemapps.stolaf.edu/jmol/data/t.pdb.gz
-// http://goo.wherever/jsmol.php?call=getRawDataFromDatabase&database=_&query=http://chemapps.stolaf.edu/jmol/data/t.pdb.gz&encoding=base64
-
-
-$myerror = "";
-
-function handleError($severity, $msg, $filename, $linenum) {
-  global $myerror;
-  switch($severity) {
-  case E_ERROR:
-    $myerror = "PHP error:$severity $msg $filename $linenum";
-    break;
-  }
-  return true;
-}
-
-set_error_handler("handleError");
-
-function getValueSimple($json, $key, $default) {
- if ($json == "") {
-	$val = $_REQUEST[$key];
- } else {
- // just do a crude check for "key"..."value"  -- nothing more than that;
- // only for very simple key/value pairs; mostly because we don't have the JSON
- // module set up for our server.
-
-	list($junk,$info) = explode('"'.$key.'"', $json, 2);
-	list($junk,$val) = explode('"', $info, 3);
-	if ($val == "") {
-		$val = str_replace('"','_',$_REQUEST[$key]);
-	}
- }
- if ($val == "") {
-   $val = $default;
- }
- return $val;
-}
-
-if ($_GET['isform']=="true") {
-	$values = "";
-} else {
-	$values= file_get_contents("php://input");
-}
-$encoding = getValueSimple($values, "encoding", "");
-$call = getValueSimple($values, "call", "getRawDataFromDatabase");
-$query = getValueSimple($values, "query", "http://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True");
-$database = getValueSimple($values, "database", "_");
-
-$imagedata = "";
-$contentType = "";
-$output = "";
-$isBinary = false;
-$filename = "";
-
-if ($call == "getInfoFromDatabase") {
-  // TODO: add PDBe annotation business here
-	if ($database == '=') {
-		$restQueryUrl = "http://www.pdb.org/pdb/rest/search";
-		$restReportUrl = "http://www.pdb.org/pdb/rest/customReport";
-		$xml = "<orgPdbQuery><queryType>org.pdb.query.simple.AdvancedKeywordQuery</queryType><description>Text Search</description><keywords>$query</keywords></orgPdbQuery>";
-		$context = stream_context_create(array('http' => array(
-			'method' => 'POST',
-			'header' => 'Content-Type: application/x-www-form-urlencoded',
-			'content' => $xml))
-		);
-		$output = file_get_contents($restQueryUrl, false, $context);
-		$n = strlen($output)/5;
-		if ($n == 0) {
-			$output = "ERROR: \"$query\" not found";
-		} else {
-			if (strlen($query) == 4 && $n != 1) {
-				$QQQQ = strtoupper($query);
-				if (strpos("123456789", substr($QQQQ, 0, 1)) == 0 && strpos($output, $QQQQ) > 0) {
-					$output = "$QQQQ\n".$output.str_replace("$QQQQ\n", "",$output);
-				}		  
-			}
-			if ($n > 50) {
-				$output = substr($output, 0, 250);
-			}
-			$output = str_replace("\n",",",$output);
-			//http://www.rcsb.org/pdb/rest/customReport?pdbids=1crn,1d66,1blu,&customReportColumns=structureId,structureTitle
-			$output = $restReportUrl."?pdbids=".$output."&customReportColumns=structureId,structureTitle";
-			$output = "<result query=\"$query\" count=\"$n\">".file_get_contents($output)."</result>";
-		}
-	} else {
-	  $myerror = "jsmol.php cannot use $call with $database";
-	}
-	
-} else if ($call == "getRawDataFromDatabase") {
-	$isBinary = (strpos(".gz", $query) >= 0);
-		if ($database != "_")
-			$query = $database.$query;
-		if (strpos($query, '://') == 0) {
-      $output = "";
-    } else if (strpos($query, '?POST?') > 0) {
-			list($query,$data) = explode('?POST?', $query, 2);
-			$context = stream_context_create(array('http' => array(
-				'method' => 'POST',
-				'header' => 'Content-Type: application/x-www-form-urlencoded',
-				'content' => $data))
-			);
-			$output = file_get_contents($query, false, $context);
-		} else {
-			$output = file_get_contents($query);
-		}
-} else if ($call == "saveFile") {
-	$imagedata = $_REQUEST["data"];//getValueSimple($values, "data", ""); don't want to convert " to _ here
-	$filename = getValueSimple($values, "filename", "");
-	$contentType = getValueSimple($values, "mimetype", "application/octet-stream");
-	if ($encoding == "base64") {
-		$imagedata = base64_decode($imagedata);
-		$encoding = "";
-	}
-} else {
-	$myerror = "jsmol.php unrecognized call: $call";
-}
-
-ob_start();
-
- if ($myerror != "") {
-   $output = $myerror;
- } else { 
-   if ($imagedata != "") {
-  	$output = $imagedata;
-  	header('Content-Type: '.$contentType);
-  	if ($filename != "") {
-  	  header('Content-Description: File Transfer');
-  		header("Content-Disposition: attachment; filename=\"$filename\"");
-      header('Content-Transfer-Encoding: binary');
-      header('Expires: 0');
-      header('Cache-Control: must-revalidate');
-      header('Pragma: public');
-  	}
-   } else {
-  	header('Access-Control-Allow-Origin: *');
-  	if ($isBinary) {
-  		header('Content-Type: text/plain; charset=x-user-defined');
-  	} else {
-  		header('Content-Type: application/json');
-  	}
-   }
-   if ($encoding == "base64") {
-  	 $output = ";base64,".base64_encode($output);
-   }
- } 
- header('Last-Modified: '.date('r'));
- header('Accept-Ranges: bytes');
- header('Content-Length: '.strlen($output));
- print($output);
-ob_end_flush();
-?>
-
+<?php
+
+// jsmol.php
+// Bob Hanson hansonr@stolaf.edu 1/11/2013
+//
+// 23 Mar 2015 -- checking for missing :// in queries
+// 2 Feb 2014 -- stripped of any exec calls and image options-- this was for JSmol image option - abandoned
+// 30 Oct 2013 -- saveFile should not convert " to _
+// 30 Sep 2013 -- adjusted error handling to only report E_ERROR not E_WARNING
+// 7 Sep 2013 -- adding PHP error handling
+//
+//////// note to administrators:
+//
+// from http://us3.php.net/file_get_contents: 
+//
+// A URL can be used as a filename with this function if the fopen wrappers 
+// have been enabled. See fopen() for more details on how to specify the 
+// filename. See the Supported Protocols and Wrappers for links to information 
+// about what abilities the various wrappers have, notes on their usage, and 
+// information on any predefined variables they may provide.
+///////
+//
+// Server-side Jmol delivers:
+//   simple relay for cross-domain files
+//
+//   options:
+//
+//   call
+//         "saveFile"
+//             returns posted data in "data=" with mime type "mimetype=" to file name "filename="
+//         "getInfoFromDatabase" 
+//             returns XML data
+//             requires database="=" (RCSB REST service)
+//         "getRawDataFromDatabase"
+//               "_" 
+//                  just use $query
+//               (anything else)
+//                  use $database.$query
+//
+//   encoding
+//         ""        no encoding (default)
+//         "base64"  BASE64-encoded binary files for Chrome synchronous AJAX
+//                      prepends ";base64," to encoded output  
+//
+// simple server tests:
+//
+// http://foo.wherever/jsmol.php?call=getRawDataFromDatabase&database=_&query=http://chemapps.stolaf.edu/jmol/data/t.pdb.gz
+// http://goo.wherever/jsmol.php?call=getRawDataFromDatabase&database=_&query=http://chemapps.stolaf.edu/jmol/data/t.pdb.gz&encoding=base64
+
+
+$myerror = "";
+
+function handleError($severity, $msg, $filename, $linenum) {
+  global $myerror;
+  switch($severity) {
+  case E_ERROR:
+    $myerror = "PHP error:$severity $msg $filename $linenum";
+    break;
+  }
+  return true;
+}
+
+set_error_handler("handleError");
+
+function getValueSimple($json, $key, $default) {
+ if ($json == "") {
+	$val = $_REQUEST[$key];
+ } else {
+ // just do a crude check for "key"..."value"  -- nothing more than that;
+ // only for very simple key/value pairs; mostly because we don't have the JSON
+ // module set up for our server.
+
+	list($junk,$info) = explode('"'.$key.'"', $json, 2);
+	list($junk,$val) = explode('"', $info, 3);
+	if ($val == "") {
+		$val = str_replace('"','_',$_REQUEST[$key]);
+	}
+ }
+ if ($val == "") {
+   $val = $default;
+ }
+ return $val;
+}
+
+if ($_GET['isform']=="true") {
+	$values = "";
+} else {
+	$values= file_get_contents("php://input");
+}
+$encoding = getValueSimple($values, "encoding", "");
+$call = getValueSimple($values, "call", "getRawDataFromDatabase");
+$query = getValueSimple($values, "query", "http://cactus.nci.nih.gov/chemical/structure/ethanol/file?format=sdf&get3d=True");
+$database = getValueSimple($values, "database", "_");
+
+$imagedata = "";
+$contentType = "";
+$output = "";
+$isBinary = false;
+$filename = "";
+
+if ($call == "getInfoFromDatabase") {
+  // TODO: add PDBe annotation business here
+	if ($database == '=') {
+		$restQueryUrl = "http://www.pdb.org/pdb/rest/search";
+		$restReportUrl = "http://www.pdb.org/pdb/rest/customReport";
+		$xml = "<orgPdbQuery><queryType>org.pdb.query.simple.AdvancedKeywordQuery</queryType><description>Text Search</description><keywords>$query</keywords></orgPdbQuery>";
+		$context = stream_context_create(array('http' => array(
+			'method' => 'POST',
+			'header' => 'Content-Type: application/x-www-form-urlencoded',
+			'content' => $xml))
+		);
+		$output = file_get_contents($restQueryUrl, false, $context);
+		$n = strlen($output)/5;
+		if ($n == 0) {
+			$output = "ERROR: \"$query\" not found";
+		} else {
+			if (strlen($query) == 4 && $n != 1) {
+				$QQQQ = strtoupper($query);
+				if (strpos("123456789", substr($QQQQ, 0, 1)) == 0 && strpos($output, $QQQQ) > 0) {
+					$output = "$QQQQ\n".$output.str_replace("$QQQQ\n", "",$output);
+				}		  
+			}
+			if ($n > 50) {
+				$output = substr($output, 0, 250);
+			}
+			$output = str_replace("\n",",",$output);
+			//http://www.rcsb.org/pdb/rest/customReport?pdbids=1crn,1d66,1blu,&customReportColumns=structureId,structureTitle
+			$output = $restReportUrl."?pdbids=".$output."&customReportColumns=structureId,structureTitle";
+			$output = "<result query=\"$query\" count=\"$n\">".file_get_contents($output)."</result>";
+		}
+	} else {
+	  $myerror = "jsmol.php cannot use $call with $database";
+	}
+	
+} else if ($call == "getRawDataFromDatabase") {
+	$isBinary = (strpos(".gz", $query) >= 0);
+		if ($database != "_")
+			$query = $database.$query;
+		if (strpos($query, '://') == 0) {
+      $output = "";
+    } else if (strpos($query, '?POST?') > 0) {
+			list($query,$data) = explode('?POST?', $query, 2);
+			$context = stream_context_create(array('http' => array(
+				'method' => 'POST',
+				'header' => 'Content-Type: application/x-www-form-urlencoded',
+				'content' => $data))
+			);
+			$output = file_get_contents($query, false, $context);
+		} else {
+			$output = file_get_contents($query);
+		}
+} else if ($call == "saveFile") {
+	$imagedata = $_REQUEST["data"];//getValueSimple($values, "data", ""); don't want to convert " to _ here
+	$filename = getValueSimple($values, "filename", "");
+	$contentType = getValueSimple($values, "mimetype", "application/octet-stream");
+	if ($encoding == "base64") {
+		$imagedata = base64_decode($imagedata);
+		$encoding = "";
+	}
+} else {
+	$myerror = "jsmol.php unrecognized call: $call";
+}
+
+ob_start();
+
+ if ($myerror != "") {
+   $output = $myerror;
+ } else { 
+   if ($imagedata != "") {
+  	$output = $imagedata;
+  	header('Content-Type: '.$contentType);
+  	if ($filename != "") {
+  	  header('Content-Description: File Transfer');
+  		header("Content-Disposition: attachment; filename=\"$filename\"");
+      header('Content-Transfer-Encoding: binary');
+      header('Expires: 0');
+      header('Cache-Control: must-revalidate');
+      header('Pragma: public');
+  	}
+   } else {
+  	header('Access-Control-Allow-Origin: *');
+  	if ($isBinary) {
+  		header('Content-Type: text/plain; charset=x-user-defined');
+  	} else {
+  		header('Content-Type: application/json');
+  	}
+   }
+   if ($encoding == "base64") {
+  	 $output = ";base64,".base64_encode($output);
+   }
+ } 
+ header('Last-Modified: '.date('r'));
+ header('Accept-Ranges: bytes');
+ header('Content-Length: '.strlen($output));
+ print($output);
+ob_end_flush();
+?>
+