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803 lines
38 KiB
803 lines
38 KiB
2 years ago
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<?php
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/**
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* This library contains functions that implement the database load processing
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* of external database files into openEMR
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*
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* @package OpenEMR
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* @link https://www.open-emr.org
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* @author Rohit Kumar <pandit.rohit@netsity.com>
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* @author (Mac) Kevin McAloon <mcaloon@patienthealthcareanalytics.com>
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* @author Brady Miller <brady.g.miller@gmail.com>
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* @author Roberto Vasquez <robertogagliotta@gmail.com>
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* @author Stephen Waite <stephen.waite@cmsvt.com>
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* @copyright Copyright (c) 2011 Phyaura, LLC <info@phyaura.com>
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* @copyright Copyright (c) 2019 Brady Miller <brady.g.miller@gmail.com>
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* @copyright Copyright (c) 2019 Stephen Waite <stephen.waite@cmsvt.com>
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* @license https://github.com/openemr/openemr/blob/master/LICENSE GNU General Public License 3
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*/
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use OpenEMR\Events\Codes\CodeTypeInstalledEvent;
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// Function to copy a package to temp
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// $type (RXNORM, SNOMED etc.)
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function temp_copy($filename, $type)
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{
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if (!file_exists($filename)) {
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return false;
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}
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if (!file_exists($GLOBALS['temporary_files_dir'] . "/" . $type)) {
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if (!mkdir($GLOBALS['temporary_files_dir'] . "/" . $type, 0777, true)) {
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return false;
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}
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}
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if (copy($filename, $GLOBALS['temporary_files_dir'] . "/" . $type . "/" . basename($filename))) {
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return true;
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} else {
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return false;
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}
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}
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// Function to unarchive a package
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// $type (RXNORM, SNOMED etc.)
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function temp_unarchive($filename, $type)
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{
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$filename = $GLOBALS['temporary_files_dir'] . "/" . $type . "/" . basename($filename);
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if (!file_exists($filename)) {
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return false;
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} elseif ($type == "ICD10") {
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// copy zip file contents to /tmp/ICD10 due to CMS zip file
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$zip = new ZipArchive();
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$path = $GLOBALS['temporary_files_dir'] . "/" . $type;
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if ($zip->open($filename) === true) {
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for ($i = 0; $i < $zip->numFiles; $i++) {
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$sub_dir_filename = $zip->getNameIndex($i);
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$fileinfo = pathinfo($sub_dir_filename);
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if (!(copy("zip://" . $filename . "#" . $sub_dir_filename, "$path/" . $fileinfo['basename']))) {
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return false;
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}
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}
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$zip->close();
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return true;
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} else {
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return false;
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}
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} else {
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// unzip the file
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$zip = new ZipArchive();
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if ($zip->open($filename) === true) {
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if (!($zip->extractTo($GLOBALS['temporary_files_dir'] . "/" . $type))) {
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return false;
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}
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$zip->close();
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return true;
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}
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}
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}
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// Function to import the RXNORM tables
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// $is_windows_flag - pass the IS_WINDOWS constant
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function rxnorm_import($is_windows_flag)
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{
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// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
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// or any manual processing that needs to occur.
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if (!empty($GLOBALS['kernel'])) {
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$codeTypeInstalledEvent = new CodeTypeInstalledEvent('RXNORM', ['is_windows_flag' => $is_windows_flag]);
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$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_PRE);
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}
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// set paths
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$dirScripts = $GLOBALS['temporary_files_dir'] . "/RXNORM/scripts/mysql";
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$dir = $GLOBALS['temporary_files_dir'] . "/RXNORM/rrf";
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$dir = str_replace('\\', '/', $dir);
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$rx_info = array();
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$rx_info['rxnatomarchive'] = array('title' => "Archive Data", 'dir' => "$dir", 'origin' => "RXNATOMARCHIVE.RRF", 'filename' => "RXNATOMARCHIVE.RRF", 'table' => "rxnatomarchive", 'required' => 0);
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$rx_info['rxnconso'] = array('title' => "Concept Names and Sources", 'dir' => "$dir", 'origin' => "RXNCONSO.RRF", 'filename' => "RXNCONSO.RRF", 'table' => "rxnconso", 'required' => 1);
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$rx_info['rxncui'] = array('title' => "Retired RXCUI Data", 'dir' => "$dir", 'origin' => "RXNCUI.RRF", 'filename' => "RXNCUI.RRF", 'table' => "rxncui", 'required' => 1);
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$rx_info['rxncuichanges'] = array('title' => "Concept Changes", 'dir' => "$dir", 'origin' => "RXNCUICHANGES.RRF", 'filename' => "RXNCUICHANGES.RRF", 'table' => "rxncuichanges", 'required' => 1);
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$rx_info['rxndoc'] = array('title' => "Documentation for Abbreviated Values", 'dir' => "$dir", 'origin' => "RXNDOC.RRF", 'filename' => "RXNDOC.RRF", 'table' => "rxndoc", 'required' => 1);
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$rx_info['rxnrel'] = array('title' => "Relationships", 'dir' => "$dir", 'origin' => "RXNREL.RRF", 'filename' => "RXNREL.RRF", 'table' => "rxnrel", 'required' => 1);
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$rx_info['rxnsab'] = array('title' => "Source Information", 'dir' => "$dir", 'origin' => "RXNSAB.RRF", 'filename' => "RXNSAB.RRF", 'table' => "rxnsab", 'required' => 0);
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$rx_info['rxnsat'] = array('title' => "Simple Concept and Atom Attributes", 'dir' => "$dir", 'origin' => "RXNSAT.RRF", 'filename' => "RXNSAT.RRF", 'table' => "rxnsat", 'required' => 0);
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$rx_info['rxnsty'] = array('title' => "Semantic Types ", 'dir' => "$dir", 'origin' => "RXNSTY.RRF", 'filename' => "RXNSTY.RRF", 'table' => "rxnsty", 'required' => 1);
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// load scripts
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$file_load = file_get_contents($dirScripts . '/Table_scripts_mysql_rxn.sql', true);
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if ($is_windows_flag) {
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$data_load = file_get_contents($dirScripts . '/Load_scripts_mysql_rxn_win.sql', true);
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} else {
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$data_load = file_get_contents($dirScripts . '/Load_scripts_mysql_rxn_unix.sql', true);
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}
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$indexes_load = file_get_contents($dirScripts . '/Indexes_mysql_rxn.sql', true);
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//
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// Creating the structure for table and applying indexes
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//
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$file_array = explode(";", $file_load);
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foreach ($file_array as $val) {
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if (trim($val) != '') {
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sqlStatementNoLog($val);
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}
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}
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$indexes_array = explode(";", $indexes_load);
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foreach ($indexes_array as $val1) {
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if (trim($val1) != '') {
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sqlStatementNoLog($val1);
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}
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}
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// Settings to drastically speed up import with InnoDB
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sqlStatementNoLog("SET autocommit=0");
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sqlStatementNoLog("START TRANSACTION");
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$data = explode(";", $data_load);
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foreach ($data as $val) {
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foreach ($rx_info as $key => $value) {
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$file_name = $value['origin'];
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$replacement = $dir . "/" . $file_name;
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$pattern = '/' . $file_name . '/';
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if (strpos($val, $file_name) !== false) {
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$val1 = str_replace($file_name, $replacement, $val);
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if (trim($val1) != '') {
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sqlStatementNoLog($val1);
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}
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}
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}
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}
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// Settings to drastically speed up import with InnoDB
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sqlStatementNoLog("COMMIT");
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sqlStatementNoLog("SET autocommit=1");
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// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
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// or any manual processing that needs to occur.
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if (!empty($GLOBALS['kernel'])) {
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$codeTypeInstalledEvent = new CodeTypeInstalledEvent('RXNORM', ['is_windows_flag' => $is_windows_flag]);
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$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
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}
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return true;
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}
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// Function to import SNOMED tables
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function snomed_import($us_extension = false)
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{
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// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
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// or any manual processing that needs to occur.
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if (!empty($GLOBALS['kernel'])) {
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$codeTypeInstalledEvent = new CodeTypeInstalledEvent('SNOMED', ['us_extension' => $us_extension]);
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$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
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}
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// set up array
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$table_array_for_snomed = array(
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"sct_concepts_drop" => "DROP TABLE IF EXISTS `sct_concepts`",
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"sct_concepts_structure" => "CREATE TABLE IF NOT EXISTS `sct_concepts` (
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`ConceptId` bigint(20) NOT NULL,
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`ConceptStatus` int(11) NOT NULL,
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`FullySpecifiedName` varchar(255) NOT NULL,
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`CTV3ID` varchar(5) NOT NULL,
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`SNOMEDID` varchar(8) NOT NULL,
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`IsPrimitive` tinyint(1) NOT NULL,
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PRIMARY KEY (`ConceptId`)
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) ENGINE=InnoDB",
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"sct_descriptions_drop" => "DROP TABLE IF EXISTS `sct_descriptions`",
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"sct_descriptions_structure" => "CREATE TABLE IF NOT EXISTS `sct_descriptions` (
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`DescriptionId` bigint(20) NOT NULL,
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`DescriptionStatus` int(11) NOT NULL,
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`ConceptId` bigint(20) NOT NULL,
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`Term` varchar(255) NOT NULL,
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`InitialCapitalStatus` tinyint(1) NOT NULL,
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`DescriptionType` int(11) NOT NULL,
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`LanguageCode` varchar(8) NOT NULL,
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PRIMARY KEY (`DescriptionId`),
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KEY `idx_concept_id` (`ConceptId`)
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) ENGINE=InnoDB",
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"sct_relationships_drop" => "DROP TABLE IF EXISTS `sct_relationships`",
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"sct_relationships_structure" => "CREATE TABLE IF NOT EXISTS `sct_relationships` (
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`RelationshipId` bigint(20) NOT NULL,
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`ConceptId1` bigint(20) NOT NULL,
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`RelationshipType` bigint(20) NOT NULL,
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`ConceptId2` bigint(20) NOT NULL,
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`CharacteristicType` int(11) NOT NULL,
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`Refinability` int(11) NOT NULL,
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`RelationshipGroup` int(11) NOT NULL,
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PRIMARY KEY (`RelationshipId`)
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) ENGINE=InnoDB"
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);
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// set up paths
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$dir_snomed = $GLOBALS['temporary_files_dir'] . "/SNOMED/";
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$sub_path = "Terminology/Content/";
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$dir = $dir_snomed;
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$dir = str_replace('\\', '/', $dir);
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// executing the create statement for tables, these are defined in snomed_capture.inc file
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// this is skipped if the US extension is being added
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if (!$us_extension) {
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foreach ($table_array_for_snomed as $val) {
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if (trim($val) != '') {
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sqlStatement($val);
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}
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}
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}
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// reading the SNOMED directory and identifying the files to import and replacing the variables by originals values.
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if (is_dir($dir) && $handle = opendir($dir)) {
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while (false !== ($filename = readdir($handle))) {
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if ($filename != "." && $filename != ".." && !strpos($filename, "zip")) {
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$path = $dir . "" . $filename . "/" . $sub_path;
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if (!(is_dir($path))) {
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$path = $dir . "" . $filename . "/RF1Release/" . $sub_path;
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}
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if (is_dir($path) && $handle1 = opendir($path)) {
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while (false !== ($filename1 = readdir($handle1))) {
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$load_script = "Load data local infile '#FILENAME#' into table #TABLE# fields terminated by '\\t' ESCAPED BY '' lines terminated by '\\n' ignore 1 lines ";
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$array_replace = array("#FILENAME#","#TABLE#");
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if ($filename1 != "." && $filename1 != "..") {
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$file_replace = $path . $filename1;
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if (strpos($filename1, "Concepts") !== false) {
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$new_str = str_replace($array_replace, array($file_replace,"sct_concepts"), $load_script);
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}
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if (strpos($filename1, "Descriptions") !== false) {
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$new_str = str_replace($array_replace, array($file_replace,"sct_descriptions"), $load_script);
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}
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if (strpos($filename1, "Relationships") !== false) {
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$new_str = str_replace($array_replace, array($file_replace,"sct_relationships"), $load_script);
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}
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if ($new_str != '') {
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sqlStatement($new_str);
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}
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}
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}
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}
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closedir($handle1);
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}
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}
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closedir($handle);
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}
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// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
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// or any manual processing that needs to occur.
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if (!empty($GLOBALS['kernel'])) {
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$codeTypeInstalledEvent = new CodeTypeInstalledEvent('SNOMED', ['us_extension' => $us_extension]);
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$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
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}
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return true;
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}
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function drop_old_sct()
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{
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$array_to_truncate = array(
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"sct_concepts_drop" => "DROP TABLE IF EXISTS `sct_concepts`",
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"sct_descriptions_drop" => "DROP TABLE IF EXISTS `sct_descriptions`",
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"sct_relationships_drop" => "DROP TABLE IF EXISTS `sct_relationships`"
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);
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foreach ($array_to_truncate as $val) {
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if (trim($val) != '') {
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sqlStatement($val);
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}
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}
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}
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function drop_old_sct2()
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{
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$array_to_truncate = array(
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"sct2_concept_drop" => "DROP TABLE IF EXISTS `sct2_concept`",
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"sct2_description_drop" => "DROP TABLE IF EXISTS `sct2_description`",
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"sct2_identifier_drop" => "DROP TABLE IF EXISTS `sct2_identifier`",
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"sct2_relationship_drop" => "DROP TABLE IF EXISTS `sct2_relationship`",
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"sct2_statedrelationship_drop" => "DROP TABLE IF EXISTS `sct2_statedrelationship`",
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"sct2_textdefinition_drop" => "DROP TABLE IF EXISTS `sct2_textdefinition`"
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);
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foreach ($array_to_truncate as $val) {
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if (trim($val) != '') {
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sqlStatement($val);
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}
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}
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}
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function chg_ct_external_torf1()
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{
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sqlStatement("UPDATE code_types SET ct_external = 2 WHERE ct_key = 'SNOMED'");
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sqlStatement("UPDATE code_types SET ct_external = 7 WHERE ct_key = 'SNOMED-CT'");
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|
|
sqlStatement("UPDATE code_types SET ct_external = 9 WHERE ct_key = 'SNOMED-PR'");
|
||
|
|
}
|
||
|
|
|
||
|
|
function chg_ct_external_torf2()
|
||
|
|
{
|
||
|
|
sqlStatement("UPDATE code_types SET ct_external = 10 WHERE ct_key = 'SNOMED'");
|
||
|
|
sqlStatement("UPDATE code_types SET ct_external = 11 WHERE ct_key = 'SNOMED-CT'");
|
||
|
|
sqlStatement("UPDATE code_types SET ct_external = 12 WHERE ct_key = 'SNOMED-PR'");
|
||
|
|
}
|
||
|
|
|
||
|
|
function snomedRF2_import()
|
||
|
|
{
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('SNOMED', []);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_PRE);
|
||
|
|
}
|
||
|
|
|
||
|
|
// set up array
|
||
|
|
$table_array_for_snomed = array(
|
||
|
|
"sct2_concept_drop" => "DROP TABLE IF EXISTS `sct2_concept`",
|
||
|
|
"sct2_concept_structure" => "CREATE TABLE IF NOT EXISTS `sct2_concept` (
|
||
|
|
`id` bigint(20) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` int(11) NOT NULL,
|
||
|
|
`moduleId` bigint(20) NOT NULL,
|
||
|
|
`definitionStatusId` bigint(25) NOT NULL,
|
||
|
|
PRIMARY KEY (`id`)
|
||
|
|
) ENGINE=InnoDB",
|
||
|
|
"sct2_description_drop" => "DROP TABLE IF EXISTS `sct2_description`",
|
||
|
|
"sct2_description_structure" => "CREATE TABLE IF NOT EXISTS `sct2_description` (
|
||
|
|
`id` bigint(20) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` bigint(11) NOT NULL,
|
||
|
|
`moduleId` bigint(25) NOT NULL,
|
||
|
|
`conceptId` bigint(20) NOT NULL,
|
||
|
|
`languageCode` varchar(8) NOT NULL,
|
||
|
|
`typeId` bigint(25) NOT NULL,
|
||
|
|
`term` varchar(255) NOT NULL,
|
||
|
|
`caseSignificanceId` bigint(25) NOT NULL,
|
||
|
|
PRIMARY KEY (`id`, `active`, `conceptId`),
|
||
|
|
KEY `idx_concept_id` (`conceptId`)
|
||
|
|
) ENGINE=InnoDB",
|
||
|
|
"sct2_identifier_drop" => "DROP TABLE IF EXISTS `sct2_identifier`",
|
||
|
|
"sct2_identifier_structure" => "CREATE TABLE IF NOT EXISTS `sct2_identifier` (
|
||
|
|
`identifierSchemeId` bigint(25) NOT NULL,
|
||
|
|
`alternateIdentifier` bigint(25) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` int(11) NOT NULL,
|
||
|
|
`moduleId` bigint(25) NOT NULL,
|
||
|
|
`referencedComponentId` bigint(25) NOT NULL,
|
||
|
|
PRIMARY KEY (`identifierSchemeId`)
|
||
|
|
) ENGINE=InnoDB",
|
||
|
|
"sct2_relationship_drop" => "DROP TABLE IF EXISTS `sct2_relationship`",
|
||
|
|
"sct2_relationship_structure" => "CREATE TABLE IF NOT EXISTS `sct2_relationship` (
|
||
|
|
`id` bigint(20) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` int(11) NOT NULL,
|
||
|
|
`moduleId` bigint(25) NOT NULL,
|
||
|
|
`sourceId` bigint(20) NOT NULL,
|
||
|
|
`destinationId` bigint(20) NOT NULL,
|
||
|
|
`typeId` bigint(25) NOT NULL,
|
||
|
|
`characteristicTypeId` bigint(25) NOT NULL,
|
||
|
|
`modifierId` bigint(25) NOT NULL,
|
||
|
|
PRIMARY KEY (`id`)
|
||
|
|
) ENGINE=InnoDB",
|
||
|
|
"sct2_statedrelationship_drop" => "DROP TABLE IF EXISTS `sct2_statedrelationship`",
|
||
|
|
"sct2_statedrelationship_structure" => "CREATE TABLE IF NOT EXISTS `sct2_statedrelationship` (
|
||
|
|
`id` bigint(20) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` int(11) NOT NULL,
|
||
|
|
`moduleId` bigint(25) NOT NULL,
|
||
|
|
`sourceId` bigint(20) NOT NULL,
|
||
|
|
`destinationId` bigint(20) NOT NULL,
|
||
|
|
`relationshipGroup` int(11) NOT NULL,
|
||
|
|
`typeId` bigint(25) NOT NULL,
|
||
|
|
PRIMARY KEY (`id`)
|
||
|
|
) ENGINE=InnoDB",
|
||
|
|
"sct2_textdefinition_drop" => "DROP TABLE IF EXISTS `sct2_textdefinition`",
|
||
|
|
"sct2_textdefinition_structure" => "CREATE TABLE IF NOT EXISTS `sct2_textdefinition` (
|
||
|
|
`id` bigint(20) NOT NULL,
|
||
|
|
`effectiveTime` date NOT NULL,
|
||
|
|
`active` int(11) NOT NULL,
|
||
|
|
`moduleId` bigint(25) NOT NULL,
|
||
|
|
`conceptId` bigint(20) NOT NULL,
|
||
|
|
`languageCode` varchar(8) NOT NULL,
|
||
|
|
`typeId` bigint(25) NOT NULL,
|
||
|
|
`term` varchar(655) NOT NULL,
|
||
|
|
PRIMARY KEY (`id`)
|
||
|
|
) ENGINE=InnoDB"
|
||
|
|
);
|
||
|
|
|
||
|
|
// set up paths
|
||
|
|
$dir_snomed = $GLOBALS['temporary_files_dir'] . "/SNOMED/";
|
||
|
|
// $sub_path="Terminology/Content/";
|
||
|
|
$sub_path = "Full/Terminology/";
|
||
|
|
$dir = $dir_snomed;
|
||
|
|
$dir = str_replace('\\', '/', $dir);
|
||
|
|
|
||
|
|
// executing the create statement for tables, these are defined in snomed_capture.inc file
|
||
|
|
// this is skipped if the US extension is being added
|
||
|
|
//if (!$us_extension) {
|
||
|
|
//var_dump($us_extension);
|
||
|
|
foreach ($table_array_for_snomed as $val) {
|
||
|
|
if (trim($val) != '') {
|
||
|
|
sqlStatement($val);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
//}
|
||
|
|
|
||
|
|
// reading the SNOMED directory and identifying the files to import and replacing the variables by originals values.
|
||
|
|
if (is_dir($dir) && $handle = opendir($dir)) {
|
||
|
|
while (false !== ($filename = readdir($handle))) {
|
||
|
|
if ($filename != "." && $filename != ".." && !strpos($filename, "zip")) {
|
||
|
|
$path = $dir . "" . $filename . "/" . $sub_path;
|
||
|
|
if (!(is_dir($path))) {
|
||
|
|
$path = $dir . "" . $filename . "/RF2Release/" . $sub_path;
|
||
|
|
}
|
||
|
|
if (is_dir($path) && $handle1 = opendir($path)) {
|
||
|
|
while (false !== ($filename1 = readdir($handle1))) {
|
||
|
|
$load_script = "Load data local infile '#FILENAME#' into table #TABLE# fields terminated by '\\t' ESCAPED BY '' lines terminated by '\\n' ignore 1 lines ";
|
||
|
|
$array_replace = array("#FILENAME#","#TABLE#");
|
||
|
|
if ($filename1 != "." && $filename1 != "..") {
|
||
|
|
$file_replace = $path . $filename1;
|
||
|
|
if (strpos($filename1, "Concept") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_concept"), $load_script);
|
||
|
|
}
|
||
|
|
if (strpos($filename1, "Description") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_description"), $load_script);
|
||
|
|
}
|
||
|
|
if (strpos($filename1, "Identifier") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_identifier"), $load_script);
|
||
|
|
}
|
||
|
|
if (strpos($filename1, "Relationship") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_relationship"), $load_script);
|
||
|
|
}
|
||
|
|
if (strpos($filename1, "StatedRelationship") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_statedrelationship"), $load_script);
|
||
|
|
}
|
||
|
|
if (strpos($filename1, "TextDefinition") !== false) {
|
||
|
|
$new_str = str_replace($array_replace, array($file_replace,"sct2_textdefinition"), $load_script);
|
||
|
|
}
|
||
|
|
if ($new_str != '') {
|
||
|
|
sqlStatement($new_str);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
closedir($handle1);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
closedir($handle);
|
||
|
|
}
|
||
|
|
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('SNOMED', []);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
|
||
|
|
}
|
||
|
|
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
// Function to import ICD tables $type differentiates ICD 9, 10 and eventually 11 (circa 2018 :-) etc.
|
||
|
|
//
|
||
|
|
function icd_import($type)
|
||
|
|
{
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('ICD', ['type' => $type]);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_PRE);
|
||
|
|
}
|
||
|
|
|
||
|
|
// set up paths
|
||
|
|
$dir_icd = $GLOBALS['temporary_files_dir'] . "/" . $type . "/";
|
||
|
|
$dir = str_replace('\\', '/', $dir_icd);
|
||
|
|
$db_load = '';
|
||
|
|
$db_update = '';
|
||
|
|
|
||
|
|
// the incoming array is a metadata array containing keys that substr match to the incoming filename
|
||
|
|
// followed by the field name, position and length of each fixed length text record in the incoming
|
||
|
|
// flat files. There are separate definitions for ICD 9 and 10 based on the type passed in
|
||
|
|
$incoming = array();
|
||
|
|
if ($type == 'ICD9') {
|
||
|
|
$incoming['SHORT_DX'] = array('#TABLENAME#' => "icd9_dx_code",
|
||
|
|
'#FLD1#' => "dx_code", '#POS1#' => 1, '#LEN1#' => 5,
|
||
|
|
'#FLD2#' => "short_desc", '#POS2#' => 7, '#LEN2#' => 60);
|
||
|
|
$incoming['SHORT_SG'] = array('#TABLENAME#' => "icd9_sg_code",
|
||
|
|
'#FLD1#' => "sg_code", '#POS1#' => 1, '#LEN1#' => 4,
|
||
|
|
'#FLD2#' => "short_desc", '#POS2#' => 6, '#LEN2#' => 60);
|
||
|
|
$incoming['LONG_SG'] = array('#TABLENAME#' => "icd9_sg_long_code",
|
||
|
|
'#FLD1#' => "sg_code", '#POS1#' => 1, '#LEN1#' => 4,
|
||
|
|
'#FLD2#' => "long_desc", '#POS2#' => 6, '#LEN2#' => 300);
|
||
|
|
$incoming['LONG_DX'] = array('#TABLENAME#' => "icd9_dx_long_code",
|
||
|
|
'#FLD1#' => "dx_code", '#POS1#' => 1, '#LEN1#' => 5,
|
||
|
|
'#FLD2#' => "long_desc", '#POS2#' => 7, '#LEN2#' => 300);
|
||
|
|
} else {
|
||
|
|
$incoming['icd10pcs_order_'] = array('#TABLENAME#' => "icd10_pcs_order_code",
|
||
|
|
'#FLD1#' => "pcs_code", '#POS1#' => 7, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "valid_for_coding", '#POS2#' => 15, '#LEN2#' => 1,
|
||
|
|
'#FLD3#' => "short_desc", '#POS3#' => 17, '#LEN3#' => 60,
|
||
|
|
'#FLD4#' => "long_desc", '#POS4#' => 78, '#LEN4#' => 300);
|
||
|
|
$incoming['icd10cm_order_'] = array('#TABLENAME#' => "icd10_dx_order_code",
|
||
|
|
'#FLD1#' => "dx_code", '#POS1#' => 7, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "valid_for_coding", '#POS2#' => 15, '#LEN2#' => 1,
|
||
|
|
'#FLD3#' => "short_desc", '#POS3#' => 17, '#LEN3#' => 60,
|
||
|
|
'#FLD4#' => "long_desc", '#POS4#' => 78, '#LEN4#' => 300);
|
||
|
|
$incoming['reimb_map_pr_'] = array('#TABLENAME#' => "icd10_reimbr_pcs_9_10",
|
||
|
|
'#FLD1#' => "code", '#POS1#' => 1, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "code_cnt", '#POS2#' => 9, '#LEN2#' => 1,
|
||
|
|
'#FLD3#' => "ICD9_01", '#POS3#' => 11, '#LEN3#' => 5,
|
||
|
|
'#FLD4#' => "ICD9_02", '#POS4#' => 17, '#LEN4#' => 5,
|
||
|
|
'#FLD5#' => "ICD9_03", '#POS5#' => 23, '#LEN5#' => 5,
|
||
|
|
'#FLD6#' => "ICD9_04", '#POS6#' => 29, '#LEN6#' => 5,
|
||
|
|
'#FLD7#' => "ICD9_05", '#POS7#' => 35, '#LEN7#' => 5,
|
||
|
|
'#FLD8#' => "ICD9_06", '#POS8#' => 41, '#LEN8#' => 5);
|
||
|
|
$incoming['reimb_map_dx_'] = array('#TABLENAME#' => "icd10_reimbr_dx_9_10",
|
||
|
|
'#FLD1#' => "code", '#POS1#' => 1, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "code_cnt", '#POS2#' => 9, '#LEN2#' => 1,
|
||
|
|
'#FLD3#' => "ICD9_01", '#POS3#' => 11, '#LEN3#' => 5,
|
||
|
|
'#FLD4#' => "ICD9_02", '#POS4#' => 17, '#LEN4#' => 5,
|
||
|
|
'#FLD5#' => "ICD9_03", '#POS5#' => 23, '#LEN5#' => 5,
|
||
|
|
'#FLD6#' => "ICD9_04", '#POS6#' => 29, '#LEN6#' => 5,
|
||
|
|
'#FLD7#' => "ICD9_05", '#POS7#' => 35, '#LEN7#' => 5,
|
||
|
|
'#FLD8#' => "ICD9_06", '#POS8#' => 41, '#LEN8#' => 5);
|
||
|
|
$incoming['I10gem'] = array('#TABLENAME#' => "icd10_gem_dx_10_9",
|
||
|
|
'#FLD1#' => "dx_icd10_source", '#POS1#' => 1, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "dx_icd9_target", '#POS2#' => 9, '#LEN2#' => 5,
|
||
|
|
'#FLD3#' => "flags", '#POS3#' => 15, '#LEN3#' => 5);
|
||
|
|
$incoming['I9gem'] = array('#TABLENAME#' => "icd10_gem_dx_9_10",
|
||
|
|
'#FLD1#' => "dx_icd9_source", '#POS1#' => 1, '#LEN1#' => 5,
|
||
|
|
'#FLD2#' => "dx_icd10_target", '#POS2#' => 7, '#LEN2#' => 7,
|
||
|
|
'#FLD3#' => "flags", '#POS3#' => 15, '#LEN3#' => 5);
|
||
|
|
$incoming['gem_pcsi9'] = array('#TABLENAME#' => "icd10_gem_pcs_10_9",
|
||
|
|
'#FLD1#' => "pcs_icd10_source", '#POS1#' => 1, '#LEN1#' => 7,
|
||
|
|
'#FLD2#' => "pcs_icd9_target", '#POS2#' => 9, '#LEN2#' => 5,
|
||
|
|
'#FLD3#' => "flags", '#POS3#' => 15, '#LEN3#' => 5);
|
||
|
|
$incoming['gem_i9pcs'] = array('#TABLENAME#' => "icd10_gem_pcs_9_10",
|
||
|
|
'#FLD1#' => "pcs_icd9_source", '#POS1#' => 1, '#LEN1#' => 5,
|
||
|
|
'#FLD2#' => "pcs_icd10_target", '#POS2#' => 7, '#LEN2#' => 7,
|
||
|
|
'#FLD3#' => "flags", '#POS3#' => 15, '#LEN3#' => 5);
|
||
|
|
}
|
||
|
|
|
||
|
|
// set up the start of the load script to be appended from the incoming array defined above where incoming
|
||
|
|
// file matches
|
||
|
|
$db_load = "LOAD DATA LOCAL INFILE '#INFILE#' INTO TABLE #TABLENAME# FIELDS TERMINATED BY '\0' (@var) SET revision = 0, ";
|
||
|
|
$col_template = "#FLD# = trim(Substring(@var, #POS#, #LEN#))";
|
||
|
|
|
||
|
|
// load all data and set active revision
|
||
|
|
if (is_dir($dir) && $handle = opendir($dir)) {
|
||
|
|
while (false !== ($filename = readdir($handle))) {
|
||
|
|
// bypass unwanted entries
|
||
|
|
if (!stripos($filename, ".txt") || stripos($filename, "diff") || stripos($filename, "addenda")) {
|
||
|
|
continue;
|
||
|
|
}
|
||
|
|
|
||
|
|
// reset the sql load command and susbtitute the filename
|
||
|
|
$run_sql = $db_load;
|
||
|
|
$run_sql = str_replace("#INFILE#", $dir . $filename, $run_sql);
|
||
|
|
$keys = array_keys($incoming);
|
||
|
|
while ($this_key = array_pop($keys)) {
|
||
|
|
if (stripos($filename, $this_key) !== false) {
|
||
|
|
// now substitute the tablename
|
||
|
|
$run_sql = str_replace("#TABLENAME#", $incoming[$this_key]['#TABLENAME#'], $run_sql);
|
||
|
|
|
||
|
|
// the range defines the maximum number of fields contained
|
||
|
|
// in any of the incoming files
|
||
|
|
foreach (range(1, 8) as $field) {
|
||
|
|
$fld = "#FLD" . $field . "#";
|
||
|
|
$nxtfld = "#FLD" . ($field + 1) . "#";
|
||
|
|
$pos = "#POS" . $field . "#";
|
||
|
|
$len = "#LEN" . $field . "#";
|
||
|
|
|
||
|
|
// concat this fields template in the sql string
|
||
|
|
$run_sql .= $col_template;
|
||
|
|
$run_sql = str_replace("#FLD#", $incoming[$this_key][$fld], $run_sql);
|
||
|
|
$run_sql = str_replace("#POS#", $incoming[$this_key][$pos], $run_sql);
|
||
|
|
$run_sql = str_replace("#LEN#", $incoming[$this_key][$len], $run_sql);
|
||
|
|
// at the end of this table's field list
|
||
|
|
if (!array_key_exists($nxtfld, $incoming[$this_key])) {
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
|
||
|
|
$run_sql .= ",";
|
||
|
|
}
|
||
|
|
|
||
|
|
sqlStatement($run_sql);
|
||
|
|
|
||
|
|
// now update the revision for this load
|
||
|
|
$res = sqlStatement("SELECT max(revision) rev FROM " . escape_table_name($incoming[$this_key]['#TABLENAME#']));
|
||
|
|
$row = sqlFetchArray($res);
|
||
|
|
$next_rev = $row['rev'] + 1;
|
||
|
|
$run_sql = "UPDATE " . $incoming[$this_key]['#TABLENAME#'] . " SET active = 0";
|
||
|
|
sqlQuery($run_sql);
|
||
|
|
$run_sql = "UPDATE " . $incoming[$this_key]['#TABLENAME#'] . " SET active = 1, revision = ? WHERE revision = 0";
|
||
|
|
sqlQuery($run_sql, array($next_rev));
|
||
|
|
break;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
closedir($handle);
|
||
|
|
} else {
|
||
|
|
echo htmlspecialchars(xl('ERROR: No ICD import directory.'), ENT_NOQUOTES) . "<br />";
|
||
|
|
return;
|
||
|
|
}
|
||
|
|
|
||
|
|
// now update the tables where necessary
|
||
|
|
if ($type == 'ICD9') {
|
||
|
|
sqlStatement("update `icd9_dx_code` SET formatted_dx_code = dx_code");
|
||
|
|
sqlStatement("update `icd9_dx_code` SET formatted_dx_code = concat(concat(left(dx_code, 3), '.'), substr(dx_code, 4)) WHERE dx_code RLIKE '^[V0-9]{1}.*' AND LENGTH(dx_code) > 3");
|
||
|
|
sqlStatement("update `icd9_dx_code` SET formatted_dx_code = concat(concat(left(dx_code, 4), '.'), substr(dx_code, 5)) WHERE dx_code RLIKE '^[E]{1}.*' AND LENGTH(dx_code) > 4");
|
||
|
|
sqlStatement("update `icd9_sg_code` SET formatted_sg_code = concat(concat(left(sg_code, 2), '.'), substr(sg_code, 3))");
|
||
|
|
sqlStatement("update `icd9_dx_code` A, `icd9_dx_long_code` B set A.long_desc = B.long_desc where A.dx_code = B.dx_code and A.active = 1 and A.long_desc is NULL");
|
||
|
|
sqlStatement("update `icd9_sg_code` A, `icd9_sg_long_code` B set A.long_desc = B.long_desc where A.sg_code = B.sg_code and A.active = 1 and A.long_desc is NULL");
|
||
|
|
} else { // ICD 10
|
||
|
|
sqlStatement("update `icd10_dx_order_code` SET formatted_dx_code = dx_code");
|
||
|
|
sqlStatement("update `icd10_dx_order_code` SET formatted_dx_code = concat(concat(left(dx_code, 3), '.'), substr(dx_code, 4)) WHERE LENGTH(dx_code) > 3");
|
||
|
|
}
|
||
|
|
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('ICD', ['type' => $type]);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
|
||
|
|
}
|
||
|
|
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
function valueset_import($type)
|
||
|
|
{
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('CQM_VALUESET', ['type' => $type]);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_PRE);
|
||
|
|
}
|
||
|
|
|
||
|
|
$dir_valueset = $GLOBALS['temporary_files_dir'] . "/" . $type . "/";
|
||
|
|
$dir = str_replace('\\', '/', $dir_valueset);
|
||
|
|
|
||
|
|
// Settings to drastically speed up import with InnoDB
|
||
|
|
sqlStatementNoLog("SET autocommit=0");
|
||
|
|
sqlStatementNoLog("START TRANSACTION");
|
||
|
|
if (is_dir($dir) && $handle = opendir($dir)) {
|
||
|
|
while (false !== ($filename = readdir($handle))) {
|
||
|
|
if (stripos($filename, ".xml")) {
|
||
|
|
$abs_path = $dir . $filename;
|
||
|
|
$xml = simplexml_load_file($abs_path, null, null, 'ns0', true);
|
||
|
|
foreach ($xml->DescribedValueSet as $vset) {
|
||
|
|
$vset_attr = $vset->attributes();
|
||
|
|
$nqf = $vset->xpath('ns0:Group[@displayName="NQF Number"]/ns0:Keyword');
|
||
|
|
foreach ($vset->ConceptList as $cp) {
|
||
|
|
foreach ($nqf as $nqf_code) {
|
||
|
|
foreach ($cp->Concept as $con) {
|
||
|
|
$con_attr = $con->attributes();
|
||
|
|
sqlStatementNoLog(
|
||
|
|
"INSERT INTO valueset values(?,?,?,?,?,?,?) on DUPLICATE KEY UPDATE
|
||
|
|
code_system = values(code_system),
|
||
|
|
description = values(description),
|
||
|
|
valueset_name = values(valueset_name)",
|
||
|
|
array(
|
||
|
|
$nqf_code,
|
||
|
|
$con_attr->code,
|
||
|
|
$con_attr->codeSystem,
|
||
|
|
$con_attr->codeSystemName,
|
||
|
|
$vset_attr->ID,
|
||
|
|
$con_attr->displayName,
|
||
|
|
$vset_attr->displayName
|
||
|
|
)
|
||
|
|
);
|
||
|
|
sqlStatementNoLog(
|
||
|
|
"INSERT INTO valueset_oid values(?,?,?,?,?,?,?) on DUPLICATE KEY UPDATE
|
||
|
|
code_system = values(code_system),
|
||
|
|
description = values(description),
|
||
|
|
valueset_name = values(valueset_name)",
|
||
|
|
array(
|
||
|
|
$nqf_code,
|
||
|
|
$vset_attr->ID,
|
||
|
|
$con_attr->codeSystem,
|
||
|
|
'OID',
|
||
|
|
$vset_attr->ID,
|
||
|
|
$vset_attr->displayName,
|
||
|
|
$vset_attr->displayName
|
||
|
|
)
|
||
|
|
);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
sqlStatementNoLog("UPDATE valueset set code_type='SNOMED CT' where code_type='SNOMEDCT'");
|
||
|
|
sqlStatementNoLog("UPDATE valueset set code_type='ICD9' where code_type='ICD9CM'");
|
||
|
|
sqlStatementNoLog("UPDATE valueset set code_type='ICD10' where code_type='ICD10CM'");
|
||
|
|
}
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
// Settings to drastically speed up import with InnoDB
|
||
|
|
sqlStatementNoLog("COMMIT");
|
||
|
|
sqlStatementNoLog("SET autocommit=1");
|
||
|
|
|
||
|
|
// let's fire off an event so people can listen if needed and handle any module upgrading, version checks,
|
||
|
|
// or any manual processing that needs to occur.
|
||
|
|
if (!empty($GLOBALS['kernel'])) {
|
||
|
|
$codeTypeInstalledEvent = new CodeTypeInstalledEvent('CQM_VALUESET', ['type' => $type]);
|
||
|
|
$GLOBALS['kernel']->getEventDispatcher()->dispatch($codeTypeInstalledEvent, CodeTypeInstalledEvent::EVENT_INSTALLED_POST);
|
||
|
|
}
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
// Function to clean up temp files
|
||
|
|
// $type (RXNORM etc.)
|
||
|
|
function temp_dir_cleanup($type)
|
||
|
|
{
|
||
|
|
if (is_dir($GLOBALS['temporary_files_dir'] . "/" . $type)) {
|
||
|
|
rmdir_recursive($GLOBALS['temporary_files_dir'] . "/" . $type);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
|
||
|
|
// Function to update version tracker table if successful
|
||
|
|
// $type (RXNORM etc.)
|
||
|
|
function update_tracker_table($type, $revision, $version, $file_checksum)
|
||
|
|
{
|
||
|
|
if ($type == 'RXNORM') {
|
||
|
|
sqlStatement("INSERT INTO `standardized_tables_track` (`imported_date`,`name`,`revision_date`, `revision_version`, `file_checksum`) VALUES (NOW(),'RXNORM',?,?,?)", array($revision, $version, $file_checksum));
|
||
|
|
return true;
|
||
|
|
} elseif ($type == 'SNOMED') {
|
||
|
|
sqlStatement("INSERT INTO `standardized_tables_track` (`imported_date`,`name`,`revision_date`, `revision_version`, `file_checksum`) VALUES (NOW(),'SNOMED',?,?,?)", array($revision, $version, $file_checksum));
|
||
|
|
return true;
|
||
|
|
} elseif ($type == 'ICD9') {
|
||
|
|
sqlStatement("INSERT INTO `standardized_tables_track` (`imported_date`,`name`,`revision_date`, `revision_version`, `file_checksum`) VALUES (NOW(),'ICD9',?,?,?)", array($revision, $version, $file_checksum));
|
||
|
|
return true;
|
||
|
|
} elseif ($type == 'CQM_VALUESET') {
|
||
|
|
sqlStatement("INSERT INTO `standardized_tables_track` (`imported_date`,`name`,`revision_date`, `revision_version`, `file_checksum`) VALUES (NOW(),'CQM_VALUESET',?,?,?)", array($revision, $version, $file_checksum));
|
||
|
|
return true;
|
||
|
|
} else { // $type == 'ICD10')
|
||
|
|
sqlStatement("INSERT INTO `standardized_tables_track` (`imported_date`,`name`,`revision_date`, `revision_version`, `file_checksum`) VALUES (NOW(),'ICD10',?,?,?)", array($revision, $version, $file_checksum));
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
|
||
|
|
// Function to delete an entire directory
|
||
|
|
function rmdir_recursive($dir)
|
||
|
|
{
|
||
|
|
$files = scandir($dir);
|
||
|
|
array_shift($files); // remove '.' from array
|
||
|
|
array_shift($files); // remove '..' from array
|
||
|
|
|
||
|
|
foreach ($files as $file) {
|
||
|
|
$file = $dir . '/' . $file;
|
||
|
|
if (is_dir($file)) {
|
||
|
|
rmdir_recursive($file);
|
||
|
|
continue;
|
||
|
|
}
|
||
|
|
|
||
|
|
unlink($file);
|
||
|
|
}
|
||
|
|
|
||
|
|
rmdir($dir);
|
||
|
|
}
|
||
|
|
|
||
|
|
// function to cleanup temp, copy and unarchive the zip file
|
||
|
|
function handle_zip_file($mode, $file)
|
||
|
|
{
|
||
|
|
// 1. copy the file to temp directory
|
||
|
|
if (!temp_copy($file, $mode)) {
|
||
|
|
echo htmlspecialchars(xl('ERROR: Unable to copy the file.'), ENT_NOQUOTES) . "<br />";
|
||
|
|
temp_dir_cleanup($mode);
|
||
|
|
exit;
|
||
|
|
}
|
||
|
|
// 2. unarchive the file
|
||
|
|
if (!temp_unarchive($file, $mode)) {
|
||
|
|
echo htmlspecialchars(xl('ERROR: Unable to extract the file.'), ENT_NOQUOTES) . "<br />";
|
||
|
|
temp_dir_cleanup($mode);
|
||
|
|
exit;
|
||
|
|
}
|
||
|
|
}
|