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chooseAsync.php
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chooseAsync.php
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<?php
/*
Copyright 2006-2018 Felix Rudolphi and Lukas Goossen
open enventory is distributed under the terms of the GNU Affero General Public License, see COPYING for details. You can also find the license under http://www.gnu.org/licenses/agpl.txt
open enventory is a registered trademark of Felix Rudolphi and Lukas Goossen. Usage of the name "open enventory" or the logo requires prior written permission of the trademark holders.
This file is part of open enventory.
open enventory is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
open enventory is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.
You should have received a copy of the GNU Affero General Public License
along with open enventory. If not, see <http://www.gnu.org/licenses/>.
*/
/*
asynchrone Seite, wird im unsichtbaren Iframe "comm" geladen und erzeugt Javascript-Code, der Suchergebnisse für Moleküle, Gebinde, Lager oder Institutionen ausgibt. Außerdem werden GIFs für Rxnfile und Molfile bei reaction erzeugt und angezeigt, indem JS-Code auf parent zugreift.
*/
// Parameter: table, search, id, page, cached_query
require_once "lib_global_funcs.php";
require_once "lib_constants.php";
require_once "lib_db_query.php";
require_once "lib_db_manip_helper.php";
require_once "lib_molfile.php";
require_once "lib_formatting.php";
require_once "lib_form_elements_helper.php";
require_once "lib_chooseAsync.php";
$page_type="async";
$barcodeTerminal=true;
setGlobalVars();
pageHeader(true,true,false);
//~ print_r($_REQUEST);
echo "</head>
<body>".
script."
if (parent && parent!=self) {\n";
$do_not_use_inventory=($settings["do_not_use_inventory"]??false);
switch ($_REQUEST["desired_action"]??null) {
case "loadSciflectionCaptcha":
require_once "lib_http.php";
$url=SCIFLECTION_URL.
"/jsonSignup.jsp";
$response=oe_http_get($url,$default_http_options);
if ($response) {
$result=json_decode($response->getBody(), true);
$dataToSet=array("captchaText" => "");
arr_trans($dataToSet, $result, array("now","nonce","compoundSecret"), true);
echo "parent.setImgSrc(\"captcha\",".fixStr($result["captcha"]).");\n".
"parent.setControlValues(".json_encode($dataToSet).",false,false);"; // do overwrite
}
break;
case "searchAssignableEntries":
$int_name=$_REQUEST["int_name"];
$add_url= getSelfRef(array("desired_action"))."&desired_action=assignEntries&crit0=";
// buttons: add experiments & ana data, add experiments only, add ana data only?
$html="<table class=\"listtable\"><tbody>";
$_REQUEST["limit"]="20"; // for all
// projects
$_REQUEST["table"]="project";
$_REQUEST["query"]="<0>";
$_REQUEST["crit0"]="project_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
list($results,$dataArray,$sort_hints)=handleQueryRequest(1);
foreach ($results as $result) {
$html.="<tr><td><a href=".fixStr($add_url."reaction.project_id&val0=".$result["project_id"])." target=\"comm\"><img src=\"lib/project_sm.png\" border=\"0\"> ".$result["project_name"]." +</a></td></tr>";
}
unset($_REQUEST["cached_query"]);
// lab notebook entries for code+nr, title, carried out by
$_REQUEST["table"]="reaction";
$_REQUEST["query"]="<0> OR <1> OR <2> OR <3>";
$_REQUEST["crit0"]="lab_journal.lab_journal_code";
$_REQUEST["op0"]="co";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="nr_in_lab_journal";
$_REQUEST["op1"]="eq";
$_REQUEST["val1"]=getNumber($_REQUEST["search"]);
$_REQUEST["crit2"]="reaction_carried_out_by";
$_REQUEST["op2"]="ct";
$_REQUEST["val2"]=$_REQUEST["search"];
$_REQUEST["crit3"]="reaction_title";
$_REQUEST["op3"]="ct";
$_REQUEST["val3"]=$_REQUEST["search"];
list($results,$dataArray,$sort_hints)=handleQueryRequest(1);
foreach ($results as $result) {
$html.="<tr><td><a href=".fixStr($add_url."reaction.reaction_id&val0=".$result["reaction_id"])." target=\"comm\"><img src=\"lib/reaction_sm.png\" border=\"0\"> ".$result["lab_journal_code"]." ".$result["nr_in_lab_journal"]." +</a></td></tr>";
}
unset($_REQUEST["cached_query"]);
// lab notebooks
$_REQUEST["table"]="lab_journal";
$_REQUEST["query"]="<0>";
$_REQUEST["crit0"]="lab_journal.lab_journal_code";
$_REQUEST["op0"]="sw";
$_REQUEST["val0"]=$_REQUEST["search"];
list($results,$dataArray,$sort_hints)=handleQueryRequest(1);
foreach ($results as $result) {
$html.="<tr><td><a href=".fixStr($add_url."reaction.lab_journal_id&val0=".$result["lab_journal_id"])." target=\"comm\"><img src=\"lib/lab_journal_sm.png\" border=\"0\"> ".$result["lab_journal_code"]." +</a></td></tr>";
}
//var_dump($results);
$html.="</tbody></table>";
// write into parent page
echo "parent.setiHTML(".fixStr($int_name).",".fixStr($html).");";
//
break;
case "assignEntries":
// attach one or more reaction_id's or analytical_data_id's to respective subitemlist
if ($_REQUEST["val0"]) {
$_REQUEST["dbs"]="-1";
$_REQUEST["table"]="reaction";
$_REQUEST["query"]="<0>";
$_REQUEST["op0"]="eq";
list($results,$dataArray,$sort_hints)=handleQueryRequest(1);
// go through results
// var_dump($results);
$dataToSet=array("publication_reaction" => array(),"publication_analytical_data" => array());
foreach ($results as $result) {
// add reaction
$dataToSet["publication_reaction"][]=$result;
// add analytical_data
if (is_array($result["analytical_data"])) foreach ($result["analytical_data"] as $analytical_data) {
$dataToSet["publication_analytical_data"][]=$analytical_data;
}
unset($result["analytical_data"]);
}
echo "parent.setControlValues(".json_encode($dataToSet).",false,true);";
}
break;
case "loadExpFromUrl":
$url=$_REQUEST["url"];
if ($url) {
require_once "lib_http.php";
if (!isUrl($url)) {
// assume only uuid
$url=SCIFLECTION_URL."/performSearch?table=ElnReaction&UUID=".$url;
}
$parsed=parse_url($url);
if (IDENTIFIERS_ORG==$parsed["host"]) {
// get redirect URL and then append jsonRaw
$my_http_options=$default_http_options;
$my_http_options["follow_redirects"]=false;
$response=oe_http_get($url,$my_http_options);
if ($response && $response->isRedirect()) {
$url=$response->getHeader("location");
$parsed=parse_url($url);
}
}
$base_url=$parsed["scheme"]."://".$parsed["host"].ifnotempty(":",$parsed["port"]??"");
// get cookies
$response=oe_http_get($base_url,$default_http_options);
$cookies=oe_get_cookies($response);
$my_http_options=$default_http_options;
$my_http_options["cookies"]=$cookies;
$url=str_ireplace("startUseCase?useCase=performSearch&", "performSearch?", $url);
$response=oe_http_get(addParameter($url,"format=jsonRaw"),$my_http_options);
if ($response) {
$result=json_decode($response->getBody(), true)[0];
// print_r($result);
$unit_result=mysql_select_array(array("table" => "units", "dbs" => "-1"));
$dataToSet=array( "reaction_title" => makeHTMLSafe($result["reactionTitle"]),
"realization_text" => makeHTMLSafe($result["realizationText"]),
"ref_amount_unit" => makeHTMLSafe($result["refAmountUnit"]),
"ref_amount" => getHumanReadable($result["refAmount"],$result["refAmountUnit"]),
"reactants" => array(),"reagents" => array(),"products" => array(),
);
if (is_array($result["elnReactionPropertyCollection"])) foreach ($result["elnReactionPropertyCollection"] as $idx => $entry) {
$name=makeHTMLSafe($entry["name"]);
if ($name=="solventAmount") {
$name="solvent_amount";
}
$dataToSet[$name]=makeHTMLSafe($entry["strValue"]);
}
if (is_array($result["elnReactionComponentCollection"])) foreach ($result["elnReactionComponentCollection"] as $idx => $entry) {
// compute SMILES, allowing to get the connection between MOLfile and part of RXNfile
$molfile=base64_decode($entry["molfileBlob"]);
$structure=readMolfile($molfile);
$rxnComp=array(
"cas_nr" => makeHTMLSafe($entry["casNr"]),
"emp_formula" => makeHTMLSafe($entry["empFormula"]),
"mw" => floatval($entry["mw"]),
"safety_sym" => makeHTMLSafe($entry["safetySym"]),
"safety_sym_ghs" => makeHTMLSafe($entry["safetySymGhs"]),
"safety_r" => makeHTMLSafe($entry["safetyR"]),
"safety_s" => makeHTMLSafe($entry["safetyS"]),
"safety_h" => makeHTMLSafe($entry["safetyH"]),
"safety_p" => makeHTMLSafe($entry["safetyP"]),
"standard_name" => makeHTMLSafe($entry["moleculeName"]),
"density_20" => floatval($entry["density20"]),
"rc_conc_unit" => makeHTMLSafe($entry["concentrationUnit"]),
"mass_unit" => makeHTMLSafe($entry["massUnit"]),
"volume_unit" => makeHTMLSafe($entry["volumeUnit"]),
"rc_amount_unit" => makeHTMLSafe($entry["amountUnit"]),
"colour" => makeHTMLSafe($entry["color"]),
"description" => makeHTMLSafe($entry["comment"]),
"molfile_blob" => $molfile,
"smiles" => $structure["smiles"]??"",
"smiles_stereo" => $structure["smiles_stereo"]??"",
"rc_conc" => getHumanReadable($entry["concentration"],$entry["concentrationUnit"]),
"stoch_coeff" => floatval($entry["stoichCoeff"]),
"rc_amount" => getHumanReadable($entry["amount"],$entry["amountUnit"]),
"m_brutto" => getHumanReadable($entry["mass"],$entry["massUnit"]),
"volume" => getHumanReadable($entry["volume"],$entry["volumeUnit"]),
);
switch ($entry["rxnRole"]) {
case 1:
$dataToSet["reactants"][]=$rxnComp;
break;
case 2:
$dataToSet["reagents"][]=$rxnComp;
break;
case 6:
unset($rxnComp["m_brutto"]); // do not import yield
$dataToSet["products"][]=$rxnComp;
break;
}
}
echo "parent.setControlValues(".json_encode($dataToSet).",false,true);".
"parent.afterLoadRxn();"; // build new rxnfile and load data for molecules as if pasted from clipboard
// important: logout
$response=oe_http_get($base_url."/logout",$my_http_options);
}
}
break;
case "searchPk";
if ($_REQUEST["search"]!="" || $_REQUEST["cached_query"]!="") {
$int_name=$_REQUEST["int_name"];
$_REQUEST["per_page"]=async_per_page; // standardmäßig 10
if ($table=="molecule") {
$_REQUEST["per_page"]=molecules_per_async_page; // 3, sonst wird die Liste zu lang
}
switch ($table) { // form query request
case "molecule":
case "chemical_storage":
$_REQUEST["query"]="<0> OR <1>";
$_REQUEST["crit0"]="molecule_names.molecule_name";
$_REQUEST["op0"]="ca";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="cas_nr";
$_REQUEST["op1"]="ex";
$_REQUEST["val1"]=$_REQUEST["search"];
if (isEmpFormula($_REQUEST["search"])) {
$_REQUEST["crit2"]="emp_formula";
$_REQUEST["op2"]="bn";
$_REQUEST["val2"]=getEmpFormulaHill($_REQUEST["search"]);
$_REQUEST["query"].=" OR <2>";
}
break;
case "storage":
$_REQUEST["query"]="<0>";
$_REQUEST["crit0"]="storage_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
break;
case "institution":
$_REQUEST["query"]="<0>";
$_REQUEST["crit0"]="institution_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
break;
case "person":
$_REQUEST["query"]="<0> OR <1> OR <2> OR <3>";
$_REQUEST["crit0"]="last_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="first_name";
$_REQUEST["op1"]="ct";
$_REQUEST["val1"]=$_REQUEST["search"];
$_REQUEST["crit2"]="username";
$_REQUEST["op2"]="ct";
$_REQUEST["val2"]=$_REQUEST["search"];
$_REQUEST["crit3"]="nee";
$_REQUEST["op3"]="ct";
$_REQUEST["val3"]=$_REQUEST["search"];
break;
case "project":
$_REQUEST["query"]="<0>";
$_REQUEST["crit0"]="project_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
break;
case "analytics_type":
$_REQUEST["query"]="<0> OR <1>";
$_REQUEST["crit0"]="analytics_type.analytics_type_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="analytics_device.analytics_device_name";
$_REQUEST["op1"]="ct";
$_REQUEST["val1"]=$_REQUEST["search"];
break;
case "analytics_method":
$_REQUEST["query"]="<0> OR <1> OR <2>";
$_REQUEST["crit0"]="analytics_type.analytics_type_name";
$_REQUEST["op0"]="ct";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="analytics_device.analytics_device_name";
$_REQUEST["op1"]="ct";
$_REQUEST["val1"]=$_REQUEST["search"];
$_REQUEST["crit2"]="analytics_method.analytics_method_name";
$_REQUEST["op2"]="ct";
$_REQUEST["val2"]=$_REQUEST["search"];
break;
case "reaction":
$_REQUEST["query"]="<0> OR <1> OR <2> OR <3>";
$_REQUEST["crit0"]="lab_journal.lab_journal_code";
$_REQUEST["op0"]="co";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="nr_in_lab_journal";
$_REQUEST["op1"]="eq";
$_REQUEST["val1"]=getNumber($_REQUEST["search"]);
$_REQUEST["crit2"]="reaction_carried_out_by";
$_REQUEST["op2"]="ct";
$_REQUEST["val2"]=$_REQUEST["search"];
$_REQUEST["crit3"]="reaction_title";
$_REQUEST["op3"]="ct";
$_REQUEST["val3"]=$_REQUEST["search"];
break;
case "sci_journal":
$_REQUEST["dbs"]="-1"; // gives n times the same journals otherwise
$_REQUEST["query"]="<0> OR <1>";
$_REQUEST["crit0"]="sci_journal_name";
$_REQUEST["op0"]="ca";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="sci_journal_abbrev";
$_REQUEST["op1"]="ca";
$_REQUEST["val1"]=$_REQUEST["search"];
break;
case "literature":
$_REQUEST["dbs"]="-1";
$_REQUEST["query"]="<0> OR <1> OR <2> OR <3> OR <4> OR <5> OR <6> OR <9> OR <10>";
$_REQUEST["crit0"]="sci_journal.sci_journal_name";
$_REQUEST["op0"]="ca";
$_REQUEST["val0"]=$_REQUEST["search"];
$_REQUEST["crit1"]="sci_journal.sci_journal_abbrev";
$_REQUEST["op1"]="ca";
$_REQUEST["val1"]=$_REQUEST["search"];
$_REQUEST["crit2"]="literature.literature_year";
$_REQUEST["op2"]="eq";
$_REQUEST["val2"]=$_REQUEST["search"];
$_REQUEST["crit3"]="literature.literature_volume";
$_REQUEST["op3"]="eq";
$_REQUEST["val3"]=$_REQUEST["search"];
$_REQUEST["crit4"]="literature.issue";
$_REQUEST["op4"]="eq";
$_REQUEST["val4"]=$_REQUEST["search"];
$_REQUEST["crit5"]="literature.page_high";
$_REQUEST["op5"]="bt";
$_REQUEST["val5"]=$_REQUEST["search"];
$_REQUEST["crit6"]="author.literature_id";
$_REQUEST["op6"]="sq";
$_REQUEST["val6"]="<7> OR <8>";
$_REQUEST["crit7"]="author.author_last";
$_REQUEST["op7"]="co";
$_REQUEST["val7"]=$_REQUEST["search"];
$_REQUEST["crit8"]="author.author_first";
$_REQUEST["op8"]="co";
$_REQUEST["val8"]=$_REQUEST["search"];
$_REQUEST["crit9"]="literature.literature_title";
$_REQUEST["op9"]="ca";
$_REQUEST["val9"]=$_REQUEST["search"];
$_REQUEST["crit10"]="literature.keywords";
$_REQUEST["op10"]="ca";
$_REQUEST["val10"]=$_REQUEST["search"];
break;
}
if (is_numeric($_REQUEST["pk_exclude"]??null)) {
$_REQUEST["query"]="(".$_REQUEST["query"].") AND NOT <100>";
//~ $_REQUEST["crit100"]=$query[$table]["primary"];
$_REQUEST["crit100"]=getLongPrimary($table);
$_REQUEST["op100"]="eq";
$_REQUEST["val100"]=$_REQUEST["pk_exclude"];
$_REQUEST["dbs"]="-1"; // merge only with stuff from own db
}
//~ list($results,$totalCount,$page,$skip,$per_page,$cache_active)=handleQueryRequest(1);
list($results,$dataArray,$sort_hints)=handleQueryRequest(1);
$totalCount=& $dataArray["totalCount"];
$page=& $dataArray["page"];
$skip=& $dataArray["skip"];
$per_page=& $dataArray["per_page"];
$cache_active=& $dataArray["cache_active"];
echo "parent.showPkResults(".fixStr($int_name).",".$page.",".$per_page.",".$totalCount.",".fixStr($_REQUEST["cached_query"]).",".fixStr(json_encode($results)).");";
}
break;
case "transferRxnPDF":
require_once "File/Archive.php";
@File_Archive::setOption('tmpDirectory',oe_get_temp_dir());
require_once "lib_rxn_pdf.php";
require_once "lib_http.php";
$results=mysql_select_array(array(
"table" => $_REQUEST["table"],
"dbs" => $_REQUEST["db"],
"filter" => getLongPrimary($_REQUEST["table"])."=".fixNull($_REQUEST["pk"]),
"limit" => 1,
"flags" => QUERY_EDIT,
));
$pdf=new PDF_MemImage("P","mm","A4");
addReactionToPDF($pdf,$results[0]);
// create TAR archive
$tar=File_Archive::toArchive(null,File_Archive::toVariable($tar_content),"tar");
$lj_entry=$results[0]["lab_journal_code"].$results[0]["nr_in_lab_journal"];
$pdf_filename=$lj_entry.".pdf";
$pdf_content=$pdf->Output($pdf_filename,"S");
$tar->newFile($pdf_filename);
$tar->writeData($pdf_content);
$pdf_hash=hash($belab_options["hashAlgorithm"],$pdf_content);
// create mets
$date_format_sec="D M d H:i:s T Y";
$created_when=strtotime($results[0]["reaction_created_when"]);
$mets='<?xml version="1.0" encoding="utf-8" standalone="no"?>
<mets OBJID="'.$results[0]["reaction_uid"].'" xmlns="http://www.loc.gov/METS/" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.loc.gov/METS/ http://www.loc.gov/standards/mets/mets.xsd">
<metsHdr CREATEDATE="'.date("c",$created_when).'">'.
//~ 2013-06-03T11:11:32
' <agent ROLE="ARCHIVIST" TYPE="INDIVIDUAL">
<name>'.$db_user.'</name>
</agent>
<agent ROLE="ARCHIVIST" TYPE="ORGANIZATION">
<name>'.$g_settings["organisation_name"].'</name>
</agent>
<agent ROLE="CREATOR" TYPE="INDIVIDUAL">
<name>'.$results[0]["reaction_created_by"].'</name>
</agent>
</metsHdr>
<dmdSec ID="belabinformation">
<mdWrap MIMETYPE="text/xml" MDTYPE="OTHER" OTHERMDTYPE="BELAB">
<xmlData><elabid>'.$results[0]["lab_journal_id"].'</elabid>';
if ($results[0]["project_id"]) {
$mets.='<projectid>'.$results[0]["project_id"].'</projectid>';
}
$mets.='<containerid>'.$results[0]["reaction_uid"].'</containerid>
<duration>'.date($date_format_sec,strtotime("+".$belab_options["durationDays"]." days")).'</duration>'.
//~ Wed Jul 03 11:11:57 CEST 2013
'</xmlData>
</mdWrap>
</dmdSec>
<dmdSec ID="dmd_base_0">
<mdWrap MIMETYPE="text/xml" MDTYPE="DC">
<xmlData><title>'.$lj_entry.'</title>
<creator>'.$results[0]["reaction_created_by"].'</creator>
<date>'.date($date_format_sec,$created_when).'</date>'.
//~ Mon Jun 03 11:11:32 CEST 2013
'</xmlData>
</mdWrap>
</dmdSec>
<fileSec>
<fileGrp ID="base">
<file ID="base_0" CHECKSUM="'.strtoupper($pdf_hash).'" CHECKSUMTYPE="SHA-256'.
//~ $belab_options["hashAlgorithm"].
'">
<FLocat LOCTYPE="URL" xlink:type="simple" xlink:href="'.$lj_entry.'.pdf" xlink:title="simple"/>
</file>
</fileGrp>
</fileSec>
</mets>';
$tar->newFile("mets.xml");
$tar->writeData($mets);
//~ die($mets);
// send to belab
$tar->close();
$url=$belab_options["serverURL"]."/".$results[0]["lab_journal_id"];
// was it archived previously?
if ($results[0]["reaction_ext_archive_id"]) {
$url.="/".$results[0]["reaction_ext_archive_id"];
}
$request=new HTTP_Request2($url,"PUT");
oe_http_map_option($request,$default_http_options,"proxyhost","proxy");
oe_http_map_option($request,$default_http_options,"connect_timeout","connect_timeout");
oe_http_map_option($request,$default_http_options,"timeout","timeout");
$request->setHeader("user-agent",$default_http_options["useragent"]);
$request->setAuth($belab_options["username"],$belab_options["password"]);
$request->setBody($tar_content);
$response=$request->send();
//~ file_put_contents("/tmp/uof.tar",$tar_content);
// save belab ID to DB
if ($response->getStatus()==200) {
if (!$results[0]["reaction_ext_archive_id"]) {
$sql_query[]="UPDATE reaction SET reaction_ext_archive_id=".fixStr($response->getBody())." WHERE reaction.reaction_id=".fixNull($_REQUEST["pk"]).";";
$result=performQueries($sql_query,$db);
}
// show success message
echo "parent.showMessage(".fixStr(s("pdf_archive_success")).");\n";
}
else {
// show error message
echo "parent.showMessage(".fixStr(s("pdf_archive_failure").": ".$response->getReasonPhrase()).");\n";
}
break;
case "findSimilarRetentionTimes":
$retention_time_data=mysql_select_array(array(
"table" => "retention_time_structure",
"dbs" => "-1",
"filter" => "analytics_type_id=".fixNull($_REQUEST["analytics_type_id"])." AND
analytics_device_id=".fixNull($_REQUEST["analytics_device_id"])." AND
analytics_method_id=".fixNull($_REQUEST["analytics_method_id"]),
"order_obj" => array(
array("field" => "ABS(retention_time.retention_time-".fixNull($_REQUEST["retention_time"]).")", "order" => "ASC"),
),
"limit" => 5,
));
if (count($retention_time_data)) {
echo "parent.showSimilarOverlay(".fixStr($_REQUEST["id"]).",".json_encode($retention_time_data).");\n";
}
break;
case "loadReactionRef": // load data for reaction that has been set as reference, for comparison
echo getRefReaction("parent.")."
if (top.sidenav) {
var iHTML=".fixStr("<a href=\"Javascript:clearRefRxn()\"><img src=\"lib/del.png\" width=\"16\" height=\"17\" border=\"0\" style=\"float:left\"></a>".
showHidden(array("int_name" => "ref_reaction_db_id", "value" => $_REQUEST["ref_reaction_db_id"], )).
showHidden(array("int_name" => "ref_reaction_id", "value" => $_REQUEST["ref_reaction_id"], )).
s("compare_to1")." <b>")."+parent.getReactionName(parent.ref_reaction)+".fixStr("</b>".s("compare_to2")).";
top.sidenav.setiHTML(\"ref_reaction\",iHTML);
if (top.searchBottom && top.searchBottom.showControl) {
top.searchBottom.setiHTML(\"ref_reaction\",iHTML);
top.searchBottom.showControl(\"ref_reaction\",true);
}
}";
switch ($_REQUEST["type"]) {
case "list":
echo "if (!parent.compare_obj.length) { // data for comparison not loaded yet
parent.activateView();
}";
break;
}
echo "if (parent.applyComparisonList) {
parent.applyComparisonList(".fixStr($_REQUEST["type"]).");
}
";
break;
case "generateNewBESSI":
$max_bessi=mysql_select_array(array(
"table" => "max_bessi",
));
$max_bessi_no=0;
for ($a=0;$a<count($max_bessi);$a++) {
if ($max_bessi_no<$max_bessi[$a]["max_bessi"]) {
$max_bessi_no=$max_bessi[$a]["max_bessi"];
}
}
echo "parent.setInputValue(\"migrate_id_mol\",".fixStr($max_bessi_no+1).");\n";
break;
case "print_selection":
echo "parent.printSelection(".fixStr($_REQUEST["sizeJoin"]).",".fixStr($_REQUEST["additionalParameters"]).",".json_encode(getSelectionHier($_REQUEST["table"])).");\n";
break;
case "update_custom_view":
$table=$_REQUEST["table"];
if (isset($table)) {
$custom_view=array(
"visibleControls" => array(),
"visibleIds" => array(),
"hiddenControls" => array(),
"hiddenIds" => array(),
);
for ($a=0;$a<count($view_controls[$table]);$a++) {
if ($_REQUEST[ $view_controls[$table][$a] ]??false) {
//~ array_push($custom_view["visibleControls"],$a);
array_push($custom_view["visibleControls"],$view_controls[$table][$a]);
}
else {
//~ array_push($custom_view["hiddenControls"],$a);
array_push($custom_view["hiddenControls"],$view_controls[$table][$a]);
}
}
for ($a=0;$a<count($view_ids[$table]);$a++) {
if ($_REQUEST[ $view_ids[$table][$a] ]??false) {
//~ array_push($custom_view["visibleIds"],$a);
array_push($custom_view["visibleIds"],$view_ids[$table][$a]);
}
else {
//~ array_push($custom_view["hiddenIds"],$a);
array_push($custom_view["hiddenIds"],$view_ids[$table][$a]);
}
}
$settings["custom_view"][$table]=$custom_view;
saveUserSettings();
echo "parent.edit_views[\"custom_view\"]=(".json_encode($custom_view).");
parent.showCustomMenu(false);
parent.activateEditView();\n";
}
break;
case "addStandard":
$molecule_data["molecule"]=mysql_select_array(array(
"table" => "molecule_for_reaction",
"dbs" => "-1",
"filter" => "molecule.smiles_stereo=".fixStrSQLSearch(ifempty($settings["std_smiles"],stdSMILES)),
"flags" => $do_not_use_inventory ? QUERY_SIMPLE:QUERY_EDIT,
));
// generate package names
addPackageNames($molecule_data);
echo "var list_int_name=\"reagents\";
var UID=parent.SILaddLine(list_int_name);
parent.setControlDataMolecule(list_int_name,UID,\"\",undefined,".json_encode($molecule_data).");
parent.SILsetValues(list_int_name,UID,undefined,".json_encode(array("m_brutto" => ifempty($settings["m_standard"],stdmg), "mass_unit" => "mg","measured" => 1)).");
parent.updateMolSelect(list_int_name,UID,\"\",undefined);
parent.valChanged();\n";
break;
case "getRetentionTimes":
if (!empty($_REQUEST["analytics_method_id"]) && (!empty($_REQUEST["molecule_id"]) || !empty($_REQUEST["smiles_stereo"]) || !empty($_REQUEST["smiles"]) ) ) {
$smiles_stereo=explode(",",$_REQUEST["smiles_stereo"]);
$smiles=explode(",",$_REQUEST["smiles"]);
if (count($smiles_stereo)==count($smiles)) {
for ($a=0;$a<count($smiles_stereo);$a++) {
list($retention_time_data)=mysql_select_array(array(
"table" => "retention_time",
"dbs" => "-1",
"filter" => "(smiles_stereo LIKE BINARY ".fixStrSQLSearch($smiles_stereo[$a])." OR smiles LIKE BINARY ".fixStrSQLSearch($smiles[$a]).") AND
analytics_type_id=".fixNull($_REQUEST["analytics_type_id"])." AND
analytics_device_id=".fixNull($_REQUEST["analytics_device_id"])." AND
analytics_method_id=".fixNull($_REQUEST["analytics_method_id"]),
"order_obj" => array(
array("field" => "smiles_stereo LIKE BINARY ".fixStrSQLSearch($smiles_stereo[$a]), "order" => "DESC"),
array("field" => "smiles LIKE BINARY ".fixStrSQLSearch($smiles[$a]), "order" => "DESC"),
),
"limit" => 1,
));
if (!empty($retention_time_data)) {
echo "parent.procRetentionTime(".fixStr($_REQUEST["UID"]).",".fixStr($retention_time_data["smiles_stereo"]).",".fixStr($retention_time_data["smiles"]).",".fixNull($retention_time_data["retention_time"]).",".fixNull($retention_time_data["response_factor"]).");\n";
}
}
}
// suchen, was möglichst gut zu molecule_id, smiles_stereo und smiles passt
//~ $retention_time_data=mysql_select_array(array(
//~ "table" => "retention_time",
//~ "dbs" => "-1",
//~ "filter" => "molecule_id IN(".secSQL($_REQUEST["molecule_id"]).") AND analytics_method_id=".fixNull($_REQUEST["analytics_method_id"])
//~ ));
//~ echo "parent.procRetentionTimes(".fixStr($_REQUEST["UID"]).",".json_encode($retention_time_data).");\n";
}
break;
case "checkMessage":
$message_results=mysql_select_array(array(
"table" => "message_new",
"dbs" => "-1",
));
echo "parent.updateMessageCount(".fixNull(count($message_results)).");\n";
break;
case "parse_doi_txt":
if (count($_FILES["load_txt"]) && $_FILES["load_txt"]["error"]==0) { // upload
// datei öffnen
$text=@file_get_contents($_FILES["load_txt"]["tmp_name"]);
// DOIs suchen
require_once "lib_literature.php";
$dois=getDOIsFromText($text);
// in parent-form anhängen
if (count($dois)) {
echo "if (parent!=self) {
var dois=parent.\$(\"dois\");
if (dois) {
dois.value+=\"\\n".join("\\n",$dois)."\";
}
}";
}
// datei löschen
@unlink($_FILES["spzfile_file"]["tmp_name"]);
}
break;
case "add_lit_by_doi":
// split
$dois=explode("\n",$_REQUEST["dois"]);
$_REQUEST["table"]="literature";
$_REQUEST["db_id"]=-1;
$doi_not_found=array();
foreach ($dois as $doi) {
$doi=trim($doi); // keep < xyz >
//~ $doi=trim(urlencode($doi)); // keep < xyz >
if (empty($doi)) {
continue;
}
// check if doi is already in DB
$literature=getDOIResult($doi);
if (!empty($literature["literature_id"])) {
// yes: link
$_REQUEST["pk"]=$literature["literature_id"];
}
else {
// no: read and add if found
require_once "lib_literature.php";
set_time_limit(ini_get("max_execution_time"));
$literature=getDataForDOI($doi);
if (!count($literature)) {
$doi_not_found[]=$doi;
continue;
}
// check again if $doi was an URL instead of a real DOI
$literature_check=getDOIResult($literature["doi"]);
if (!empty($literature["literature_id"])) {
$_REQUEST["pk"]=$literature_check["literature_id"];
}
else {
// add, design this a bit more beautiful in the future
$oldReq=$_REQUEST;
$_REQUEST=array_merge($_REQUEST,$literature);
performEdit("literature",-1,$db);
$oldReq["pk"]=$_REQUEST["literature_id"];
$_REQUEST=$oldReq;
}
}
handleLoadDataForPk();
}
// tell about not found/recognized
if (count($doi_not_found)) {
echo "var infoWin=window.open(\"\",Number(new Date()),\"height=450,width=300,scrollbars=yes\");
infoWin.document.open();
infoWin.document.write(".fixStr("<html><head>".stylesheet."</head><body>").");
infoWin.document.write(".fixStr("<form>".s("doi_not_found").":<br/>".join("<br/>",$doi_not_found)."<br/><input type=\"submit\" value=".fixStr(s("ok"))." onClick=\"self.close();\"></form>").");
infoWin.document.write(\"</body></html>\");
infoWin.document.close();
";
}
echo "parent.showMessage(".fixStr(s("doi_complete")).");\n";
break;
case "loadDataForSearch":
$filter_obj=getFilterObject(array(
"dbs" => $_REQUEST["dbs"],
));
//~ $js_code="";
switch ($_REQUEST["list_int_name"]) {
case "item_list": // very standard situation
case "order_alternative": // very standard situation
$query_table="supplier_offer_for_accepted_order";
//~ $js_code="updateTotal(".fixStr($_REQUEST["list_int_name"]).",".fixStr($_REQUEST["UID"]).",".fixStr($_REQUEST["int_name"]).");";
break;
default:
$query_table=$_REQUEST["table"];
}
list($result)=mysql_select_array(array(
"table" => $query_table,
"dbs" => $_REQUEST["db_id"],
"filter" => $filter_obj["query_string"],
"limit" => 1,
));
if (count($result)) {
echo "parent.SILsetValues(".fixStr($_REQUEST["list_int_name"]).",".fixStr($_REQUEST["UID"]).",undefined,".json_encode($result).");\n";
}
break;
case "loadDataForPk":
// load data for primary key
handleLoadDataForPk();
break;
case "loadDataForPkSelect":
// update available options for pk_select, params: int_name,filter
/* $paramHash=array("filter" => $_REQUEST["filter"], "table" => $_REQUEST["table"], "pkName" => fixTags($_REQUEST["pkName"]), "nameField" => fixTags($_REQUEST["nameField"]), "allowNone" => fixTags($_REQUEST["allowNone"]), "noneText" => fixTags($_REQUEST["noneText"]) );
$controlData=pk_select_getList($paramHash);*/
$filter_obj=getFilterObject();
//~ echo "/*".print_r($filter_obj,true)."*/";
$controlData=mysql_select_array(array(
"table" => $_REQUEST["table"],
"filterDisabled" => $_REQUEST["filterDisabled"],
"dbs" => $_REQUEST["dbs"],
"order_obj" => getOrderObjFromKey($_REQUEST["order_by"],$baseTable),
"filter" => $filter_obj["query_string"],
"flags" => intval($_REQUEST["flags"]) | QUERY_PK_SEARCH,
));
// print_r($paramHash);
/* parent.as(\"controls\",".fixStr(json_encode($paramHash["int_names"])).",".fixStr($_REQUEST["int_name"]).",\"int_names\");
parent.as(\"controls\",".fixStr(json_encode($paramHash["texts"])).",".fixStr($_REQUEST["int_name"]).",\"texts\"); */
if (isset($_REQUEST["UID"])) { // pk_select in SIL, nicht fertigprogrammiert
echo "
parent.SILPkSelectSetControlData(".fixStr($_REQUEST["list_int_name"]).",".fixStr($_REQUEST["UID"]).",".fixStr($_REQUEST["int_name"]).",".fixStr(json_encode($controlData)).");
parent.SILPkSelectUpdated(".fixStr($_REQUEST["list_int_name"]).",".fixStr($_REQUEST["UID"]).",".fixStr($_REQUEST["int_name"]).");
";
}
else { // pk_search, complete overwrite seems ok
// funktion zur entgegennahme der daten bauen, möglichkeit zur mod schaffen
echo "
parent.as(\"controlData\",".fixStr(json_encode($controlData)).",".fixStr($_REQUEST["int_name"]).",\"data\");
parent.PkSelectUpdated(".fixStr($_REQUEST["int_name"]).");
";
}
break;
}
$emptyMolecule=array( // make sure no bogus values remain
array(
"molfile_blob" => "",
"smiles" => "",
"smiles_stereo" => "",
"mw" => "",
"emp_formula" => "",
"standard_name" => "",
"package_name" => "",
)
);
// create temp GIFs
// print_r($_REQUEST);
if (is_array($_REQUEST["molecule_UID"] ?? null)) {
$molecule_data=array();
foreach($_REQUEST["molecule_UID"] as $UID) {
$imgUID=uniqid();
// GIF generieren
$molfile=& $_REQUEST["molfile_".$UID];
if ($_REQUEST["mode_".$UID]=="rxn") {
$molecule=readRxnfile($molfile);
// identifier einfügen, nur für reaktanten
for ($a=0;$a<$molecule["reactants"];$a++) {
$molecule["identifier"][$a]=numToLett($a+1);
}
for ($a=0;$a<$molecule["products"];$a++) {
$molecule["identifier"][ $molecule["reactants"]+$a ]=$a+1;
}
//~ print_r($molecule);die();
list($_SESSION["gifFile"][$imgUID],$_SESSION["svgFile"][$imgUID])=getReactionGif($molecule,$_REQUEST["width_".$UID],$_REQUEST["height_".$UID],0,1,2,array("png","svg"));
}
else {
$molecule=readMolfile($molfile);
list($_SESSION["gifFile"][$imgUID],$_SESSION["svgFile"][$imgUID])=getMoleculeGif($molecule,$_REQUEST["width_".$UID],$_REQUEST["height_".$UID],0,1,true,array("png","svg"));
}
$_SESSION["molFile"][$imgUID]=$molfile;
if ($_REQUEST["desired_action_".$UID]=="loadData") {
switch ($_REQUEST["int_name_".$UID]) {
case "rxnfile_blob": // alles
if ($_REQUEST["invocationCommand"]=="full") {
$offset=0;
foreach (array("reactants","products") as $list_int_name) {
for ($a=0;$a<$molecule[$list_int_name];$a++) {
// UID
$molUID=uniqid();
$thisMolecule=& $molecule["molecules"][$offset+$a];
// gif
list($_SESSION["gifFile"][$molUID],$_SESSION["svgFile"][$molUID])=getMoleculeGif($thisMolecule,rc_gif_x,rc_gif_y,0,1,true,array("png","svg"));
$molfile_single=writeMolfile($thisMolecule);
$_SESSION["molFile"][$molUID]=$molfile_single;
if (!empty($thisMolecule["smiles_stereo"])) {
// data
$structure_data["molecule"]=mysql_select_array(array(
"table" => "molecule_for_reaction",
//~ "dbs" => "-1",
"filter" => "molecule.smiles_stereo LIKE BINARY ".fixStrSQLSearch(addSMILESslashes($thisMolecule["smiles_stereo"])),
"flags" => (($list_int_name!="products" && !$do_not_use_inventory) ? QUERY_EDIT:QUERY_SIMPLE),
)); // search packages as well for reactants, but not for products
// smiles LIKE BINARY ".fixStr($thisMolecule["smiles"]
if (!count($structure_data["molecule"])) {
$structure_data["molecule"][0]=array(
"molfile_blob" => addPipes($molfile_single),
"smiles" => $thisMolecule["smiles"],
"smiles_stereo" => $thisMolecule["smiles_stereo"],
"mw" => $thisMolecule["mw"],
"emp_formula" => $thisMolecule["emp_formula_string"],
);
}
addPackageNames($structure_data);
}
// update/add
echo "parent.addMolFromRxn(".fixStr($molUID).",".fixStr($list_int_name).",".$a.",".fixStr($thisMolecule["smiles_stereo"]).",".json_encode($structure_data).",".fixStr(addPipes($molfile_single)).");\n";
} // smiles
$offset+=$molecule[$list_int_name];
}
$structure_data=array();
}
// RXN schreiben und setzen (kann sich durch zusammenfassen geändert haben
echo "parent.setInputValue(".fixStr($_REQUEST["int_name_".$UID]).",".fixStr(addPipes(writeRxnfile($molecule))).");\n";
// have arrays for reactants and products SMILES for ordering and assingment of lines, all other will be done by "molfile_blob"
break;
case "reactants": // einzelnes startmat
case "products":
case "reagents":
case "copyTable":
if ($molecule["atoms"]) { // maybe polymer with no smiles
if ($molecule["smiles_stereo"]) {
// lookup molecule
$structure_data["molecule"]=mysql_select_array(array(
"table" => "molecule_for_reaction",
//~ "dbs" => "-1",
"filter" => "molecule.smiles_stereo LIKE BINARY ".fixStrSQLSearch(addSMILESslashes($molecule["smiles_stereo"])),
"flags" => (($_REQUEST["int_name_".$UID]!="products" && !$do_not_use_inventory) ? QUERY_EDIT:QUERY_SIMPLE),
)); // search packages as well for reactants, but not for products
// "molecule.smiles LIKE BINARY ".fixStrSQL($molecule["smiles"])
// if nothing found, try non-stereo SMILES
if (!count($structure_data["molecule"])) {
$structure_data["molecule"]=mysql_select_array(array(
"table" => "molecule_for_reaction",
//~ "dbs" => "-1",
"filter" => "molecule.smiles LIKE BINARY ".fixStrSQLSearch(addSMILESslashes($molecule["smiles"])),
"flags" => (($_REQUEST["int_name_".$UID]!="products" && !$do_not_use_inventory) ? QUERY_EDIT:QUERY_SIMPLE),
)); // search packages as well for reactants, but not for products
}
}
// absolutely nothing found
if (!count($structure_data["molecule"])) {
$structure_data["molecule"][0]=array(
"molfile_blob" => $molfile,
"smiles" => $molecule["smiles"],
"smiles_stereo" => $molecule["smiles_stereo"],
"mw" => $molecule["mw"],
"emp_formula" => $molecule["emp_formula_string"],
"standard_name" => "",
"package_name" => "",
);
}
// generate package_name within moleculeData
addPackageNames($structure_data);
}
else { // empty
$structure_data["molecule"]=$emptyMolecule;
}
echo "parent.setControlDataMolecule(".fixStr($_REQUEST["int_name_".$UID]).",".fixStr($UID).",".fixStr($_REQUEST["field_".$UID]).",".fixStr($_REQUEST["group_".$UID]).",".json_encode($structure_data).");
parent.updateMolSelect(".fixStr($_REQUEST["int_name_".$UID]).",".fixStr($UID).",".fixStr($_REQUEST["field_".$UID]).",".fixStr($_REQUEST["group_".$UID]).",true);\n"; // no update neccessary
break;
/* case "reagents":
//~ $structure_data=array("smiles" => $molecule["smiles"], "mw" => $molecule["mw"], "emp_formula" => $molecule["emp_formula_string"]);
if ($molecule["smiles_stereo"]) {
// lookup molecule, take only 1st result for now
$structure_data["molecule"]=mysql_select_array(array(
"table" => "molecule_for_reaction",
//~ "dbs" => "-1",
"filter" => "molecule.smiles_stereo LIKE BINARY ".fixStrSQLSearch($molecule["smiles_stereo"]),
"flags" => !$do_not_use_inventory ? QUERY_EDIT:QUERY_SIMPLE,
));
// "molecule.smiles LIKE BINARY ".fixStr($molecule["smiles"])