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prepareSampleMetadata.php
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prepareSampleMetadata.php
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<?php
/*
* IN PROGRESS
*
* Given a directory file id, lists the metadata of each of the child files/directories
* following the format of the sample_metadata files.
* No recursive.
*
*/
require "phplib/genlibraries.php";
/*
* IMPORTANT:
* - execute with sudo to be able to 'rm' www-data data : sudo php applib/cleanUsersData.php
* - make sure that mongo 'userscol'(phplib/db.inc.php) and 'shared' global are in agreement (dev/prod)
*
*/
// params
array_shift($argv);
$parentId = $argv[0];
$metadata_rfn = ($argv[1]?$argv[1]:getcwd()."/sample_metadata.json");
if (!isset($parentId)){
fwrite(STDERR, "\nUSAGE: applib/prepareSampleMetadata.php [FILE_ID]\n FILE_ID: parent directory of the files/dirs whose metadata is to written\n\n");
exit(0);
}
// disk
$GLOBALS['shared'] = "/orozco/services/MuG/"; // MuGdev/";
$GLOBALS['dataDir'] = $GLOBALS['shared']."MuG_userdata/";
// db
$GLOBALS['dbname_VRE'] = "MuGVRE_irb";
require "phplib/db.inc.php";
// identification
$u = checkUserIDExists("MuGUSER59e5ead574743");
if (!$u){
fwrite(STDERR, "Admin user with ID=MuGUSER59e5ead574743 do not exists in ".$GLOBALS['dbname_VRE'].". Change it in this script!");
exit(0);
}
if (!isset($_SESSION['User'])){
$_SESSION['User'] = $u;
}
////////////////////////////////////
function fromVREfile_toMUGfile($file) {
$mugfile = array();
$compressions = $GLOBALS['compressions'];
//path -> file_path
if (isset($file['path'])){
if (preg_match('/'.$GLOBALS['AppPrefix'].'[^\/]*\/[^\/]*\/(.*)$/', $file['path'],$m)){
$mugfile['file_path'] = $m[1];
}else{
$mugfile['file_path'] = $file['path'];
}
}else{
$mugfile['file_path'] = "";
}
// type -> type
if (isset($file['type'])){
$mugfile['type'] = $file['type'];
}else{
$mugfile['type'] = "file";
}
if ($mugfile['type'] != "dir" ){
// format -> file_type
if (isset($file['data_type'])){
$mugfile['file_type'] = $file['format'];
}else{
$mugfile['file_type'] = "";
}
// data_type -> data_type
if (isset($file['data_type'])){
$mugfile['data_type'] = $file['data_type'];
}else{
$mugfile['data_type'] = "";
}
// taxon_id -> taxon_id
if (isset($file['taxon_id'])){
$mugfile['taxon_id'] = (int)($file['taxon_id']);
}else{
$mugfile['taxon_id'] = 0;
}
}
// input_files -> source_id
if (isset($file['input_files'])){
if (basename($mugfile['file_path']) == "uploads" || dirname($mugfile['file_path']) == "uploads" ){
$mugfile['source_id'] = array(0);
}else{
if (!is_array($file['input_files'])){
$file['input_files'] = array($file['input_files']);
}
$mugfile['source_id']=array();
foreach ($file['input_files'] as $fn){
$f = getAttr_fromGSFileId($fn,"path",1);
if (preg_match('/'.$GLOBALS['AppPrefix'].'[^\/]*\/[^\/]*\/(.*)$/', $f,$m)){
array_push($mugfile['source_id'],$m[1]);
}else{
array_push($mugfile['source_id'],$f);
}
}
}
}else{
$mugfile['source_id'] = array(0);
}
unset($file['_id']);
unset($file['type']);
unset($file['path']);
unset($file['format']);
unset($file['taxon_id']);
unset($file['data_type']);
unset($file['owner']);
unset($file['mtime']);
unset($file['atime']);
unset($file['size']);
unset($file['project']);
unset($file['tracktype']);
unset($file['input_files']);
unset($file['owner']);
unset($file['parentDir']);
unset($file['associated_id']);
unset($file['validated']);
// other -> meta_data
$mugfile['meta_data'] = $file;
// compressed -> compressed
if (isset($mugfile['file_path'])){
$ext = pathinfo($mugfile['file_path'], PATHINFO_EXTENSION);
$ext = preg_replace('/_\d+$/',"",$ext);
$ext = strtolower($ext);
if (in_array($ext,array_keys($compressions))){
$mugfile['meta_data']['compressed'] = $compressions[$ext];
}else{
if (isset($mugfile['meta_data']['compressed'])){unset($mugfile['meta_data']['compressed']);}
}
}
// meta submission_file -> submission_file path
if (isset($mugfile['meta_data']['submission_file'])){
if (preg_match('/'.$GLOBALS['AppPrefix'].'[^\/]*\/__PROJ[^\/]*\/(.*)$/', $mugfile['meta_data']['submission_file'],$m)){
if (! preg_match('/\.tmp/',$m[1])){
$mugfile['meta_data']['submission_file'] = $m[1];
}else{
unset($mugfile['meta_data']['submission_file']);
}
}
}
// meta log_file -> log_file path
if (isset($mugfile['meta_data']['log_file'])){
if (preg_match('/'.$GLOBALS['AppPrefix'].'[^\/]*\/__PROJ[^\/]*\/(.*)$/', $mugfile['meta_data']['log_file'],$m)){
if (! preg_match('/\.tmp/',$m[1])){
$mugfile['meta_data']['log_file'] = $m[1];
}else{
unset($mugfile['meta_data']['log_file']);
}
}
}
// meta files -> []
if (isset($mugfile['meta_data']['files'])){
$mugfile['meta_data']['files'] = array();
}
// expiration -> -1
if (isset($mugfile['meta_data']['expiration'])){
$mugfile['meta_data']['expiration'] = -1;
}
// refGenome -> assembly
if (isset($mugfile['meta_data']['refGenome'])){
$mugfile['meta_data']['assembly'] = $mugfile['meta_data']['refGenome'];
unset($mugfile['meta_data']['refGenome']);
}
// associated_files -> associated_files path
if (isset($mugfile['meta_data']['associated_files'])){
$arr_t=array();
foreach ($mugfile['meta_data']['associated_files'] as $fn){
$f = getAttr_fromGSFileId($fn,"path",1);
if (preg_match('/'.$GLOBALS['AppPrefix'].'[^\/]*\/__PROJ[^\/]*\/(.*)$/', $f,$m)){
array_push($arr_t,$m[1]);
}
}
$mugfile['meta_data']['associated_files']=$arr_t;
}
return $mugfile;
}
///////////////////////////////////////////////
// get files from given parentId
print ">> Parent ID: $parentId\n";
$filesId = getAttr_fromGSFileId($parentId,"files",1);
if (!$filesId){
fwrite(STDERR, "Given parent ID has no files");
$file = getGSFile_fromId($parentId,"",1);
var_dump($file);
exit(0);
}
// get file info from DB
print "\nBuilding files list\n";
$files = array();
foreach ($filesId as $fnId){
$file = getGSFile_fromId($fnId,"",1);
if (!$file){
$_SESSION['errorData']['Error'][]="Input file $fnId does not belong to current user or has been not properly registered. Stopping execution";
next;
}
$associated_files = getAssociatedFiles_fromId($fnId);
foreach ($associated_files as $assocId){
$assocFile = getGSFile_fromId($assocId,"",1);
if (!$assocFile){
$_SESSION['errorData']['Error'][]="File associated to ".basename($file['path'])." ($assocId) does not belong to current user or has been not properly registered. Stopping execution";
next;
}
if (!isset($files[$assocFile['_id']])){
$files[$assocFile['_id']]=$assocFile;
print "-- ".$assocFile['_id']." : ".basename($assocFile['path'])."(associated file)\n";
}
}
if (!isset($files[$file['_id']])){
print "-- $fnId : ".basename($file['path'])."\n";
$files[$file['_id']]=$file;
}
}
// add input_files metadata
print "\nCreting metadata obj for each file\n";
$fileMuGs=Array();
foreach ($files as $fnId => $file){
print "-- $fnId converting...\n";
// convert metadata to DMP format
$fileMuG = fromVREfile_toMUGfile($file);
if (!$fileMuG){
$_SESSION['errorData']['Error'][]="Cannot create MuG file for $fnId";
continue;
}
array_push($fileMuGs,$fileMuG);
if (isset($file['files'])){
print " AFTERWARDS RUN: applib/prepareSampleMetadata.php $fnId ".basename($file['path'])."_sample_metadata.json\n";
}
}
// write JSON
print "\nWritting metadata objs into file\n";
try{
$F = fopen($metadata_rfn,"w");
if (!$F) {
throw new Exception('Failed to create metadata file for tool execution'.$metadata_rfn);
}
}
catch (Exception $e){
$_SESSION['errorData']['Internal Error'][]= $e->getMessage();
exit(0);
}
fwrite($F, json_encode($fileMuGs,JSON_PRETTY_PRINT | JSON_UNESCAPED_SLASHES));
fclose($F);
print "$metadata_rfn written\n\n";
// print errors
if (isset($_SESSION['errorData'])){
print "\nERRORDATA:\n";
var_dump($_SESSION['errorData']);
$_SESSION['errorData']=array();
}