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standard_tables_capture.inc
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<?php
/**
* This library contains functions that implement the database load processing
* of external database files into LIBREEHR
*
* Copyright (C) 2011 Phyaura, LLC <[email protected]>
*
* LICENSE: This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
* This program 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 General Public License for more details.
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://opensource.org/licenses/gpl-license.php>;.
*
* @package LibreEHR
* @author Rohit Kumar <[email protected]>
* @author (Mac) Kevin McAloon <[email protected]>
* @author Brady Miller <[email protected]>
* @link http://librehealth.io
*/
// Function to copy a package to temp
// $type (RXNORM, SNOMED etc.)
function temp_copy($filename,$type) {
if(!file_exists($filename)) {
return false;
}
if(!file_exists($GLOBALS['temporary_files_dir']."/".$type)) {
if(!mkdir($GLOBALS['temporary_files_dir']."/".$type, 0777, true)) {
return false;
}
}
if(copy($filename,$GLOBALS['temporary_files_dir']."/".$type."/".basename($filename))) {
return true;
}
else {
return false;
}
}
// Function to unarchive a package
// $type (RXNORM, SNOMED etc.)
function temp_unarchive($filename,$type) {
$filename = $GLOBALS['temporary_files_dir']."/".$type."/".basename($filename);
if(!file_exists($filename)) {
return false;
}
else {
// let's uzip the file
// use checksums to determine the "version"
//
$zip = new ZipArchive;
if ($zip->open($filename) === TRUE) {
if (!($zip->extractTo($GLOBALS['temporary_files_dir']."/".$type))) {
return false;
}
$zip->close();
return true;
}
else {
return false;
}
}
}
// Function to import the RXNORM tables
// $is_windows_flag - pass the IS_WINDOWS constant
function rxnorm_import($is_windows_flag) {
// set paths
$dirScripts = $GLOBALS['temporary_files_dir']."/RXNORM/scripts/mysql";
$dir = $GLOBALS['temporary_files_dir']."/RXNORM/rrf";
$dir=str_replace('\\','/',$dir);
$rx_info = array();
$rx_info['rxnatomarchive'] = array('title' => "Archive Data", 'dir' => "$dir", 'origin' => "RXNATOMARCHIVE.RRF", 'filename' => "RXNATOMARCHIVE.RRF", 'table' => "rxnatomarchive", 'required' => 0);
$rx_info['rxnconso'] = array('title' => "Concept Names and Sources", 'dir' => "$dir", 'origin' => "RXNCONSO.RRF", 'filename' => "RXNCONSO.RRF", 'table' => "rxnconso", 'required' => 1);
$rx_info['rxncui'] = array('title' => "Retired RXCUI Data", 'dir' => "$dir", 'origin' => "RXNCUI.RRF", 'filename' => "RXNCUI.RRF", 'table' => "rxncui", 'required' => 1);
$rx_info['rxncuichanges'] = array('title' => "Concept Changes", 'dir' => "$dir", 'origin' => "RXNCUICHANGES.RRF", 'filename' => "RXNCUICHANGES.RRF", 'table' => "rxncuichanges", 'required' => 1);
$rx_info['rxndoc'] = array('title' => "Documentation for Abbreviated Values", 'dir' => "$dir", 'origin' => "RXNDOC.RRF", 'filename' => "RXNDOC.RRF", 'table' => "rxndoc", 'required' => 1);
$rx_info['rxnrel'] = array('title' => "Relationships", 'dir' => "$dir", 'origin' => "RXNREL.RRF", 'filename' => "RXNREL.RRF", 'table' => "rxnrel", 'required' => 1);
$rx_info['rxnsab'] = array('title' => "Source Information", 'dir' => "$dir", 'origin' => "RXNSAB.RRF", 'filename' => "RXNSAB.RRF", 'table' => "rxnsab", 'required' => 0);
$rx_info['rxnsat'] = array('title' => "Simple Concept and Atom Attributes", 'dir' => "$dir", 'origin' => "RXNSAT.RRF", 'filename' => "RXNSAT.RRF", 'table' => "rxnsat", 'required' => 0);
$rx_info['rxnsty'] = array('title' => "Semantic Types ", 'dir' => "$dir", 'origin' => "RXNSTY.RRF", 'filename' => "RXNSTY.RRF", 'table' => "rxnsty", 'required' => 1);
// load scripts
$file_load = file_get_contents($dirScripts.'/Table_scripts_mysql_rxn.sql', true);
if ($is_windows_flag) {
$data_load = file_get_contents($dirScripts.'/Load_scripts_mysql_rxn_win.sql', true);
}
else {
$data_load = file_get_contents($dirScripts.'/Load_scripts_mysql_rxn_unix.sql', true);
}
$indexes_load = file_get_contents($dirScripts.'/Indexes_mysql_rxn.sql', true);
//
// Creating the structure for table and applying indexes
//
$file_array=explode(";",$file_load);
foreach($file_array as $val){
if(trim($val)!='')
{
sqlStatement($val);
}
}
$indexes_array=explode(";",$indexes_load);
foreach($indexes_array as $val1){
if(trim($val1)!='')
{
sqlStatement($val1);
}
}
$data=explode(";",$data_load);
foreach($data as $val)
{
foreach($rx_info as $key => $value)
{
$file_name= $value['origin'];
$replacement=$dir."/".$file_name;
$pattern='/'.$file_name.'/';
if(strpos($val,$file_name) !== false) {
$val1 = str_replace($file_name,$replacement,$val);
if(trim($val1)!='') {
sqlStatement($val1);
}
}
}
}
return true;
}
// Function to import SNOMED tables
function snomed_import($us_extension=FALSE) {
// set up array
$table_array_for_snomed=array(
"sct_concepts_drop"=>"DROP TABLE IF EXISTS `sct_concepts`",
"sct_concepts_structure"=>"CREATE TABLE IF NOT EXISTS `sct_concepts` (
`ConceptId` bigint(20) NOT NULL,
`ConceptStatus` int(11) NOT NULL,
`FullySpecifiedName` varchar(255) NOT NULL,
`CTV3ID` varchar(5) NOT NULL,
`SNOMEDID` varchar(8) NOT NULL,
`IsPrimitive` tinyint(1) NOT NULL,
PRIMARY KEY (`ConceptId`)
) ENGINE=MyISAM",
"sct_descriptions_drop"=>"DROP TABLE IF EXISTS `sct_descriptions`",
"sct_descriptions_structure"=>"CREATE TABLE IF NOT EXISTS `sct_descriptions` (
`DescriptionId` bigint(20) NOT NULL,
`DescriptionStatus` int(11) NOT NULL,
`ConceptId` bigint(20) NOT NULL,
`Term` varchar(255) NOT NULL,
`InitialCapitalStatus` tinyint(1) NOT NULL,
`DescriptionType` int(11) NOT NULL,
`LanguageCode` varchar(8) NOT NULL,
PRIMARY KEY (`DescriptionId`)
) ENGINE=MyISAM",
"sct_relationships_drop"=>"DROP TABLE IF EXISTS `sct_relationships`",
"sct_relationships_structure"=>"CREATE TABLE IF NOT EXISTS `sct_relationships` (
`RelationshipId` bigint(20) NOT NULL,
`ConceptId1` bigint(20) NOT NULL,
`RelationshipType` bigint(20) NOT NULL,
`ConceptId2` bigint(20) NOT NULL,
`CharacteristicType` int(11) NOT NULL,
`Refinability` int(11) NOT NULL,
`RelationshipGroup` int(11) NOT NULL,
PRIMARY KEY (`RelationshipId`)
) ENGINE=MyISAM"
);
// set up paths
$dir_snomed = $GLOBALS['temporary_files_dir']."/SNOMED/";
$sub_path="Terminology/Content/";
$dir=$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 (!$us_extension) {
foreach($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."".$filename."/RF1Release/".$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,"Concepts") !== false){
$new_str=str_replace($array_replace,array($file_replace,"sct_concepts"),$load_script);
}
if(strpos($filename1,"Descriptions") !== false){
$new_str=str_replace($array_replace,array($file_replace,"sct_descriptions"),$load_script);
}
if(strpos($filename1,"Relationships") !== false){
$new_str=str_replace($array_replace,array($file_replace,"sct_relationships"),$load_script);
}
if($new_str!=''){
sqlStatement($new_str);
}
}
}
}
closedir($handle1);
}
}
closedir($handle);
}
return true;
}
// Function to import ICD tables $type differentiates ICD 9, 10 and eventually 11 (circa 2018 :-) etc.
//
function icd_import($type) {
// 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 == 'ICD10') {
$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 " . $incoming[$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 == 'ICD10') {
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");
}
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, $file_checksum) );
return true;
}
else if ($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;
}
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;
}
}
?>