interface/orders/receive_hl7_results.inc.php

   1 <?php
   2 /**
   3 * Functions to support parsing and saving hl7 results.
   4 *
   5 * Copyright (C) 2013 Rod Roark <rod@sunsetsystems.com>
   6 *
   7 * LICENSE: This program is free software; you can redistribute it and/or
   8 * modify it under the terms of the GNU General Public License
   9 * as published by the Free Software Foundation; either version 2
  10 * of the License, or (at your option) any later version.
  11 * This program is distributed in the hope that it will be useful,
  12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  14 * GNU General Public License for more details.
  15 * You should have received a copy of the GNU General Public License
  16 * along with this program.  If not, see <http://opensource.org/licenses/gpl-license.php>.
  17 *
  18 * @package   OpenEMR
  19 * @author    Rod Roark <rod@sunsetsystems.com>
  20 */
  21
  22 function rhl7InsertRow(&$arr, $tablename) {
  23   if (empty($arr)) return;
  24
  25   // echo "<!-- ";   // debugging
  26   // print_r($arr);
  27   // echo " -->\n";
  28
  29   $query = "INSERT INTO $tablename SET";
  30   $binds = array();
  31   $sep = '';
  32   foreach ($arr as $key => $value) {
  33     $query .= "$sep `$key` = ?";
  34     $sep = ',';
  35     $binds[] = $value;
  36   }
  37   $arr = array();
  38   return sqlInsert($query, $binds);
  39 }
  40
  41 function rhl7FlushResult(&$ares) {
  42   return rhl7InsertRow($ares, 'procedure_result');
  43 }
  44
  45 function rhl7FlushReport(&$arep) {
  46   return rhl7InsertRow($arep, 'procedure_report');
  47 }
  48
  49 function rhl7Text($s) {
  50   $s = str_replace('\\S\\'  ,'^' , $s);
  51   $s = str_replace('\\F\\'  ,'|' , $s);
  52   $s = str_replace('\\R\\'  ,'~' , $s);
  53   $s = str_replace('\\T\\'  ,'&' , $s);
  54   $s = str_replace('\\X0d\\',"\r", $s);
  55   $s = str_replace('\\E\\'  ,'\\', $s);
  56   return $s;
  57 }
  58
  59 function rhl7DateTime($s) {
  60   if (empty($s)) return '0000-00-00 00:00:00';
  61   $ret = substr($s, 0, 4) . '-' . substr($s, 4, 2) . '-' . substr($s, 6, 2);
  62   if (strlen($s) > 8) $ret .= ' ' . substr($s, 8, 2) . ':' . substr($s, 10, 2) . ':';
  63   if (strlen($s) > 12) {
  64     $ret .= substr($s, 12, 2);
  65   } else {
  66     $ret .= '00';
  67   }
  68   return $ret;
  69 }
  70
  71 function rhl7Abnormal($s) {
  72   if ($s == ''  ) return 'no';
  73   if ($s == 'A' ) return 'yes';
  74   if ($s == 'H' ) return 'high';
  75   if ($s == 'L' ) return 'low';
  76   if ($s == 'HH') return 'vhigh';
  77   if ($s == 'LL') return 'vlow';
  78   return rhl7Text($s);
  79 }
  80
  81 function rhl7ReportStatus($s) {
  82   if ($s == 'F') return 'final';
  83   if ($s == 'P') return 'prelim';
  84   if ($s == 'C') return 'correct';
  85   return rhl7Text($s);
  86 }
  87
  88 /**
  89  * Parse and save.
  90  *
  91  * @param  string  &$pprow   A row from the procedure_providers table.
  92  * @param  string  &$hl7     The input HL7 text.
  93  * @return string            Error text, or empty if no errors.
  94  */
  95 function receive_hl7_results(&$hl7) {
  96   if (substr($hl7, 0, 3) != 'MSH') {
  97     return xl('Input does not begin with a MSH segment');
  98   }
  99
 100   // End-of-line delimiter for text in procedure_result.comments
 101   $commentdelim = "\n";
 102
 103   $today = time();
 104
 105   $in_message_id = '';
 106   $in_ssn = '';
 107   $in_dob = '';
 108   $in_lname = '';
 109   $in_fname = '';
 110   $in_orderid = 0;
 111   $in_procedure_code = '';
 112   $in_report_status = '';
 113   $in_encounter = 0;
 114
 115   $porow = false;
 116   $pcrow = false;
 117   $procedure_report_id = 0;
 118   $arep = array(); // holding area for OBR and its NTE data
 119   $ares = array(); // holding area for OBX and its NTE data
 120
 121   // This is so we know where we are if a segment like NTE that can appear in
 122   // different places is encountered.
 123   $context = '';
 124
 125   // Delimiters
 126   $d0 = "\r";
 127   $d1 = substr($hl7, 3, 1); // typically |
 128   $d2 = substr($hl7, 4, 1); // typically ^
 129   $d3 = substr($hl7, 5, 1); // typically ~
 130
 131   $segs = explode($d0, $hl7);
 132
 133   foreach ($segs as $seg) {
 134     if (empty($seg)) continue;
 135
 136     $a = explode($d1, $seg);
 137
 138     if ($a[0] == 'MSH') {
 139       $context = $a[0];
 140       if ($a[8] != 'ORU^R01') {
 141         return xl('Message type') . " '${a[8]}' " . xl('does not seem valid');
 142       }
 143       $in_message_id = $a[9];
 144     }
 145
 146     else if ($a[0] == 'PID') {
 147       $context = $a[0];
 148       rhl7FlushResult($ares);
 149       // Next line will do something only if there was a report with no results.
 150       rhl7FlushReport($arep);
 151       $in_ssn = $a[4];
 152       $in_dob = $a[7]; // yyyymmdd format
 153       $tmp = explode($d2, $a[5]);
 154       $in_lname = $tmp[0];
 155       $in_fname = $tmp[1];
 156     }
 157
 158     else if ($a[0] == 'PV1') {
 159       // Save placer encounter number if present.
 160       if (!empty($a[19])) {
 161         $tmp = explode($d2, $a[19]);
 162         $in_encounter = intval($tmp[0]);
 163       }
 164     }
 165
 166     else if ($a[0] == 'ORC') {
 167       $context = $a[0];
 168       rhl7FlushResult($ares);
 169       // Next line will do something only if there was a report with no results.
 170       rhl7FlushReport($arep);
 171       $porow = false;
 172       $pcrow = false;
 173       if ($a[2]) $in_orderid = intval($a[2]);
 174     }
 175
 176     else if ($a[0] == 'NTE' && $context == 'ORC') {
 177       // TBD? Is this ever used?
 178     }
 179
 180     else if ($a[0] == 'OBR') {
 181       $context = $a[0];
 182       rhl7FlushResult($ares);
 183       // Next line will do something only if there was a report with no results.
 184       rhl7FlushReport($arep);
 185       $procedure_report_id = 0;
 186       if ($a[2]) $in_orderid = intval($a[2]);
 187       $tmp = explode($d2, $a[4]);
 188       $in_procedure_code = $tmp[0];
 189       $in_procedure_name = $tmp[1];
 190       $in_report_status = rhl7ReportStatus($a[25]);
 191       if (empty($porow)) {
 192         $porow = sqlQuery("SELECT * FROM procedure_order WHERE " .
 193           "procedure_order_id = ?", array($in_orderid));
 194         // The order must already exist. Currently we do not handle electronic
 195         // results returned for manual orders.
 196         if (empty($porow)) {
 197           return xl('Procedure order') . " '$in_orderid' " . xl('was not found');
 198         }
 199         if ($in_encounter) {
 200           if ($porow['encounter_id'] != $in_encounter) {
 201             return xl('Encounter ID') .
 202               " '" . $porow['encounter_id'] . "' " .
 203               xl('for OBR placer order number') .
 204               " '$in_orderid' " .
 205               xl('does not match the PV1 encounter number') .
 206               " '$in_encounter'";
 207           }
 208         }
 209         else {
 210           // They did not return an encounter number to verify, so more checking
 211           // might be done here to make sure the patient seems to match.
 212         }
 213       }
 214       // Find the order line item (procedure code) that matches this result.
 215       $pcquery = "SELECT pc.* FROM procedure_order_code AS pc " .
 216         "WHERE pc.procedure_order_id = ? AND pc.procedure_code = ? " .
 217         "ORDER BY procedure_order_seq LIMIT 1";
 218       $pcrow = sqlQuery($pcquery, array($in_orderid, $in_procedure_code));
 219       if (empty($pcrow)) {
 220         // There is no matching procedure in the order, so it must have been
 221         // added after the original order was sent, either as a manual request
 222         // from the physician or as a "reflex" from the lab.
 223         // procedure_source = '2' indicates this.
 224         sqlInsert("INSERT INTO procedure_order_code SET " .
 225           "procedure_order_id = ?, " .
 226           "procedure_code = ?, " .
 227           "procedure_name = ?, " .
 228           "procedure_source = '2'",
 229           array($in_orderid, $in_procedure_code, $in_procedure_name));
 230         $pcrow = sqlQuery($pcquery, array($in_orderid, $in_procedure_code));
 231       }
 232       $arep = array();
 233       $arep['procedure_order_id'] = $in_orderid;
 234       $arep['procedure_order_seq'] = $pcrow['procedure_order_seq'];
 235       $arep['date_collected'] = rhl7DateTime($a[7]);
 236       $arep['date_report'] = substr(rhl7DateTime($a[22]), 0, 10);
 237       $arep['report_status'] = $in_report_status;
 238       $arep['report_notes'] = '';
 239     }
 240
 241     else if ($a[0] == 'NTE' && $context == 'OBR') {
 242       $arep['report_notes'] .= rhl7Text($a[3]) . "\n";
 243     }
 244
 245     else if ($a[0] == 'OBX') {
 246       $context = $a[0];
 247       rhl7FlushResult($ares);
 248       if (!$procedure_report_id) {
 249         $procedure_report_id = rhl7FlushReport($arep);
 250       }
 251       $ares = array();
 252       $ares['procedure_report_id'] = $procedure_report_id;
 253       // OBX-5 can be a very long string of text with "~" as line separators.
 254       // The first line of comments is reserved for such things.
 255       if (strlen($a[5]) > 200) {
 256         $ares['result_data_type'] = 'L';
 257         $ares['result'] = '';
 258         $ares['comments'] = rhl7Text($a[5]) . $commentdelim;
 259       }
 260       else {
 261         $ares['result_data_type'] = substr($a[2], 0, 1); // N, S or F
 262         $ares['result'] = rhl7Text($a[5]);
 263         $ares['comments'] = $commentdelim;
 264       }
 265       $tmp = explode($d2, $a[3]);
 266       $ares['result_code'] = rhl7Text($tmp[0]);
 267       $ares['result_text'] = rhl7Text($tmp[1]);
 268       $ares['date'] = rhl7DateTime($a[14]);
 269       $ares['facility'] = rhl7Text($a[15]);
 270       $ares['units'] = rhl7Text($a[6]);
 271       $ares['range'] = rhl7Text($a[7]);
 272       $ares['abnormal'] = rhl7Abnormal($a[8]); // values are lab dependent
 273       $ares['result_status'] = rhl7ReportStatus($a[11]);
 274     }
 275
 276     else if ($a[0] == 'NTE' && $context == 'OBX') {
 277       $ares['comments'] .= rhl7Text($a[3]) . $commentdelim;
 278     }
 279
 280     // Add code here for any other segment types that may be present.
 281
 282     else {
 283       return xl('Segment name') . " '${a[0]}' " . xl('is misplaced or unknown');
 284     }
 285   }
 286
 287   rhl7FlushResult($ares);
 288   // Next line will do something only if there was a report with no results.
 289   rhl7FlushReport($arep);
 290   return '';
 291 }
 292
 293 /**
 294  * Poll all eligible labs for new results and store them in the database.
 295  *
 296  * @param  array   &$messages  Receives messages of interest.
 297  * @return string  Error text, or empty if no errors.
 298  */
 299 function poll_hl7_results(&$messages) {
 300   global $srcdir;
 301
 302   $messages = array();
 303   $filecount = 0;
 304   $badcount = 0;
 305
 306   $ppres = sqlStatement("SELECT * FROM procedure_providers ORDER BY name");
 307
 308   while ($pprow = sqlFetchArray($ppres)) {
 309     $protocol = $pprow['protocol'];
 310     $remote_host = $pprow['remote_host'];
 311     $hl7 = '';
 312
 313     if ($protocol == 'SFTP') {
 314       ini_set('include_path', ini_get('include_path') . PATH_SEPARATOR . "$srcdir/phpseclib");
 315       require_once("$srcdir/phpseclib/Net/SFTP.php");
 316       // Compute the target path name.
 317       $pathname = '.';
 318       if ($pprow['results_path']) $pathname = $pprow['results_path'] . '/' . $pathname;
 319       // Connect to the server and enumerate files to process.
 320       $sftp = new Net_SFTP($remote_host);
 321       if (!$sftp->login($pprow['login'], $pprow['password'])) {
 322         return xl('Login to remote host') . " '$remote_host' " . xl('failed');
 323       }
 324       $files = $sftp->nlist($pathname);
 325       foreach ($files as $file) {
 326         if (substr($file, 0, 1) == '.') continue;
 327         ++$filecount;
 328         $hl7 = $sftp->get("$pathname/$file");
 329         // Archive the results file.
 330         $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
 331         if (!file_exists($prpath)) mkdir($prpath);
 332         $prpath .= '/' . $pprow['ppid'];
 333         if (!file_exists($prpath)) mkdir($prpath);
 334         $fh = fopen("$prpath/$file", 'w');
 335         if ($fh) {
 336           fwrite($fh, $hl7);
 337           fclose($fh);
 338         }
 339         else {
 340           $messages[] = xl('File') . " '$file' " . xl('cannot be archived, ignored');
 341           ++$badcount;
 342           continue;
 343         }
 344         // Now delete it from its ftp directory.
 345         if (!$sftp->delete("$pathname/$file")) {
 346           $messages[] = xl('File') . " '$file' " . xl('cannot be deleted, ignored');
 347           ++$badcount;
 348           continue;
 349         }
 350         // Parse and process its contents.
 351         $msg = receive_hl7_results($hl7);
 352         if ($msg) {
 353           $messages[] = xl('Error processing file') . " '$file':" . $msg;
 354           ++$badcount;
 355           continue;
 356         }
 357         $messages[] = xl('New file') . " '$file' " . xl('processed successfully');
 358       }
 359     }
 360
 361     // TBD: Insert "else if ($protocol == '???') {...}" to support other protocols.
 362
 363   }
 364
 365   if ($badcount) return "$badcount " . xl('error(s) encountered from new results');
 366
 367   return '';
 368 }
 369 ?>