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updateToolDevTest.php
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updateToolDevTest.php
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<?php
require __DIR__."/../../config/bootstrap.php";
redirectOutside();
$debug=0;
if ($debug){
print "</br>RAW ARGUMENTS ARE<br/>";
var_dump($_REQUEST['arguments']);
print "<br/>";
print "</br>RAW INPUT_FILES ARE<br/>";
var_dump($_REQUEST['input_files']);
print "<br/>";
print "</br>RAW INPUT_FILES_PUBLIC ARE<br/>";
var_dump($_REQUEST['input_files_public_dir']);
print "<br/>";
print "</br>METADATA<br/>";
var_dump($_REQUEST['metadata']);
print "<br/>";
foreach ($_REQUEST as $k=>$v){
if ($k!="arguments" && $k!="input_files" && $k!="input_files_public_dir" && $k!="fn"){
print "<br/><br/>REQUEST[$k]</br>";
var_dump($v);
}
}
}
//
// Get tool.
$tooldev = getToolDev_fromId($_REQUEST['toolid'],1);
$tool_io = $tooldev['step1']["tool_io"];
if (empty($tool_io)){
$_SESSION['errorData']['Error'][]="Given tool 'id' (".$_REQUEST['toolid'].") has not definitions for input and output. Please, set a new one! <a href=\"admin/updateToolDevSpec.php?id=".$_REQUEST['toolid']."\">Update I/O definition again</a>";
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Start RegisterTool process to generate test files
if (!isset($_REQUEST['execution']) ){
$_SESSION['errorData']['Internal'][]="Error creating test data for tool '".$_REQUEST['toolid']."'. 'execution' not received";
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
if (!isset($_REQUEST['tool_lib']) ){
$_REQUEST['tool_lib']=0;
}
$submitTool = new RegisterTool($tool_io,$_REQUEST['execution'],$_REQUEST['tool_executable'],$_REQUEST['tool_lib']);
if ($debug){
print "<br/>NEW TOOL SUBMIT:</br>";
var_dump($submitTool);
}
//
// Check input file requirements
if (!isset($_REQUEST['input_files'])){
$_SESSION['errorData']['Error'][]="Tool is not receiving input files. Please, select them from your workspace table.";
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Get input_files medatada (TODO with associated_files)
$files = Array(); // distinct file Objs to stage in
$filesId = Array();
foreach($_REQUEST['input_files'] as $input_file){
if (is_array($input_file)){
$filesId = array_merge($filesId,$input_file);
}else{
if ($input_file)
array_push($filesId,$input_file);
}
}
$filesId=array_unique($filesId);
$r = $submitTool->setMetadata_fromTool($_REQUEST['input_files'],$_REQUEST['metadata']);
$files = $submitTool->metadata;
if ($debug){
print "<br/></br>TOTAL number of FILES given as params : ".count($filesId);
print "<br/></br>TOTAL number of FILES (including associated) : ".count(array_keys($files))."</br>";
//print "<br/></br>METADATA for given files is :<br/>"; var_dump($submitTool->metadata);
}
//
// Get input_files medatada (from input_files_public_dir)
if (count($_REQUEST['input_files_public_dir'])){
$r = $submitTool->setMetadata_fromTool($_REQUEST['input_files_public_dir'],$_REQUEST['metadata'],true);
if ($debug){
print "<br/></br>METADATA PUBLIC for given files is :<br/>"; var_dump($submitTool->metadata_pub);
}
}
// Set Arguments
if (!$_REQUEST['arguments']){
$_REQUEST['arguments']=array();
}
$submitTool->setArguments($_REQUEST['arguments']);
//
// Check InputFiles
$r = $submitTool->setInput_files($_REQUEST['input_files']);
if ($debug){
print "<br/>TOOL Input_files are (R=$r):</br>";
var_dump($submitTool->input_files);
}
if ($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Check InputFiles (from input_files_public_dir)
if (count($_REQUEST['input_files_public_dir'])){
$r = $submitTool->setInput_files($_REQUEST['input_files_public_dir'],true);
if ($debug){
print "<br/><br/>TOOL Public Input_files are (R=$r):</br>";
var_dump($submitTool->input_files_pub);
}
if ($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
}
//
// Creating Config files
$r = $submitTool->setConfiguration_files();#$_REQUEST['execution'],$_REQUEST['project']);
if ($debug){
echo "<br/></br>Configuration Files are <br/>";
var_dump($r);
}
if($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Creating Metadata files
$r = $submitTool->setMetadata_files();
if ($debug){
echo "<br/></br>Metadata Files are. <br/>";
var_dump($r);
}
if($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Creating Bash Test files
$r = $submitTool->setBash_files($_REQUEST['workflowtype']);
if ($debug){
echo "<br/></br>Test Files are. <br/>";
var_dump($r);
}
if($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Creating TAR file with configuration files + metadata files + bash files
$r = $submitTool->tar_test_files();
if ($debug){
echo "<br/></br>TAR Files returns: <br/>";
var_dump($r);
}
if($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
//
// Register generated test files
$r = $submitTool->save_test_files();
if ($debug){
echo "<br/></br>Save te4st files returns:<br/>";
var_dump($r);
}
if($r == "0"){
if ($debug){ exit(0);}
?><script type="text/javascript">window.history.go(-1);</script><?php
exit(0);
}
// Save REQUEST data to allow edit/update form data
//
$r = $submitTool->save_form_data("step1",$_REQUEST);
if (!isset($_SESSION['errorData']['Error'])){
$_SESSION['errorData']['Info'][]="Test files successfully generated! </br>";
}
if ($debug){
print "<br/>#############################<br/>";
var_dump($_SESSION['errorData']);
unset($_SESSION['errorData']);
print "<br/>#############################<br/>";
exit(0);
}
redirect($GLOBALS['BASEURL'].'admin/myNewTools.php');
?>