contrib/util/ccda_import/import_ccda.php

   1 <?php
   2
   3 /**
   4  * Import CCDA script
   5  *
   6  * Prior to use:
   7  *   1. Turn on Carecoordination modules in OpenEMR.
   8  *   2. Place ccdas in a directory.
   9  *   3. Uncomment exit at top of this script.
  10  *   4. Consider turning off the audit log (turn off both the 'Enable Audit Logging' and
  11  *      'Audit all Emergency User Queries' settings) in OpenEMR to improve performance (if audit log
  12  *      not needed).
  13  *
  14  * Use:
  15  *   1. use: php import_ccda.php <ccda-directory> <site> <openemr-directory> <development-mode>
  16  *   2. use example: php import_ccda.php /var/www/localhost/htdocs/openemr/synthea default /var/www/localhost/htdocs/openemr true
  17  *   3. use example: php import_ccda.php /var/www/localhost/htdocs/openemr/synthea default /var/www/localhost/htdocs/openemr false
  18  *   4. Note that development-mode will markedly improve performance by bypassing the import of
  19  *      the ccda document and bypassing the use of the audit_master and audit_details tables and
  20  *      will directly import the new patient data from the ccda. Note this should never be done
  21  *      on sites that already contain real data/use. This will also turn off the audit log during
  22  *      the import.
  23  *   5. Note that a log.txt file is created with log/stats of the run.
  24  *
  25  * Description of what this script automates (for unlimited number of ccda documents):
  26  *  1. import ccda document (bypassed in development-mode)
  27  *  2. import to ccda table (bypassed in development-mode)
  28  *  3. import as new patient
  29  *  4. run function to populate all the uuids via the universal service function that already exists
  30  *
  31  *
  32  * @package   OpenEMR
  33  * @link      https://www.open-emr.org
  34  * @author    Brady Miller <brady.g.miller@gmail.com>
  35  * @copyright Copyright (c) 2021 Brady Miller <brady.g.miller@gmail.com>
  36  * @license   https://github.com/openemr/openemr/blob/master/LICENSE GNU General Public License 3
  37  */
  38
  39 // comment this out when using this script (and then uncomment it again when done using script)
  40 exit;
  41
  42 if (php_sapi_name() !== 'cli' || count($argv) != 5) {
  43     echo "Only php cli can execute a command\n";
  44     echo "use: php import_ccda.php <ccda-directory> <site> <openemr-directory> <development-mode>\n";
  45     echo "example use: php import_ccda.php /var/www/localhost/htdocs/openemr/synthea default /var/www/localhost/htdocs/openemr true\n";
  46     echo "example use: php import_ccda.php /var/www/localhost/htdocs/openemr/synthea default /var/www/localhost/htdocs/openemr false\n";
  47     die;
  48 }
  49
  50 function outputMessage($message)
  51 {
  52     echo $message;
  53     file_put_contents("log.txt", $message, FILE_APPEND);
  54 }
  55
  56 // collect parameters (need to do before globals)
  57 $dir = $argv[1] . '/*';
  58 $_GET['site'] = $argv[2];
  59 $openemrPath = $argv[3];
  60 $seriousOptimizeFlag = $argv[4];
  61 if ($seriousOptimizeFlag == "true") {
  62     $seriousOptimize = true;
  63 } else {
  64     $seriousOptimize = false;
  65 }
  66
  67 $ignoreAuth = 1;
  68 require_once($openemrPath . "/interface/globals.php");
  69
  70 use OpenEMR\Common\Uuid\UuidRegistry;
  71
  72 // show parameters (need to do after globals)
  73 outputMessage("ccda directory: " . $argv[1] . "\n");
  74 outputMessage("site: " . $_SESSION['site_id'] . "\n");
  75 outputMessage("openemr path: " . $openemrPath . "\n");
  76
  77 if ($seriousOptimize) {
  78     outputMessage("development mode is on\n");
  79     // temporarily disable the audit log
  80     $auditLogSetting = sqlQueryNoLog("SELECT `gl_value` FROM `globals` WHERE `gl_name` = 'enable_auditlog'")['gl_value'] ?? 0;
  81     sqlStatementNoLog("UPDATE `globals` SET `gl_value` = 0 WHERE `gl_name` = 'enable_auditlog'");
  82     $auditLogBreakglassSetting = sqlQueryNoLog("SELECT `gl_value` FROM `globals` WHERE `gl_name` = 'gbl_force_log_breakglass'")['gl_value'] ?? 0;
  83     sqlStatementNoLog("UPDATE `globals` SET `gl_value` = 0 WHERE `gl_name` = 'gbl_force_log_breakglass'");
  84 } else {
  85     outputMessage("development mode is off\n");
  86 }
  87
  88 outputMessage("Starting patients import\n");
  89 $counter = 0;
  90 $millisecondsStart = round(microtime(true) * 1000);
  91 foreach (glob($dir) as $file) {
  92     if ($seriousOptimize) {
  93         // development-mode is on (note step 1 and step 2 are bypassed)
  94         // 3. import as new patient (note need to escape ' characters in the filename)
  95         $file = str_replace("'", "\'", $file);
  96         exec("php " . $openemrPath . "/bin/console openemr:ccda-newpatient-import --site=" . $_SESSION['site_id'] . " --document=" . $file);
  97     } else {
  98         // development mode is off
  99         //  1. import ccda document
 100         $fileContents = file_get_contents($file);
 101         $document = new Document();
 102         // TODO: collect CCDA category id instead of hardcoding 13
 103         $document->createDocument('00', 13, basename($file), 'text/xml', $fileContents);
 104         $documentId = $document->get_id();
 105         //  2. import to ccda table
 106         exec("php " . $openemrPath . "/bin/console openemr:ccda-import --site=" . $_SESSION['site_id'] . " --document_id=" . $documentId);
 107         $auditId = sqlQueryNoLog("SELECT max(`id`) as `maxid` FROM `audit_master`")['maxid'];
 108         //  3. import as new patient
 109         exec("php " . $openemrPath . "/bin/console openemr:ccda-newpatient --site=" . $_SESSION['site_id'] . " --am_id=" . $auditId . " --document_id=" . $documentId);
 110     }
 111     $counter++;
 112     $incrementCounter = 50; // echo every 50 records imported
 113     if (($counter % $incrementCounter) == 0) {
 114         $timeSec = round(((round(microtime(true) * 1000)) - $millisecondsStart) / 1000);
 115         outputMessage($counter . " patients imported (" . $timeSec . " total seconds) (" . ((isset($lasttimeSec) ? ($timeSec - $lasttimeSec) : $timeSec) / $incrementCounter) . " average seconds per patient for last " . $incrementCounter . " patients)\n");
 116         $lasttimeSec = $timeSec;
 117     }
 118 }
 119 $timeSec = round(((round(microtime(true) * 1000)) - $millisecondsStart) / 1000);
 120 echo outputMessage("Completed patients import (" . $counter . " patients) (" . $timeSec . " total seconds) (" . (($timeSec) / $counter) . " average seconds per patient)\n");
 121 //  4. run function to populate all the uuids via the universal service function that already exists
 122 echo outputMessage("Started uuid creation\n");
 123 UuidRegistry::populateAllMissingUuids(false);
 124 $timeSec = round(((round(microtime(true) * 1000)) - $millisecondsStart) / 1000);
 125 echo outputMessage("Completed uuid creation (" . $timeSec . " total seconds; " . $timeSec / 3600 . " total hours)\n");
 126
 127 if ($seriousOptimize) {
 128     // reset the audit log to the original value
 129     sqlStatementNoLog("UPDATE `globals` SET `gl_value` = ? WHERE `gl_name` = 'enable_auditlog'", [$auditLogSetting]);
 130     sqlStatementNoLog("UPDATE `globals` SET `gl_value` = ? WHERE `gl_name` = 'gbl_force_log_breakglass'", [$auditLogBreakglassSetting]);
 131 }