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