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   $s = preg_replace('/[^0-9]/', '', $s);
  61   if (empty($s)) return '0000-00-00 00:00:00';
  62   $ret = substr($s, 0, 4) . '-' . substr($s, 4, 2) . '-' . substr($s, 6, 2);
  63   if (strlen($s) > 8) $ret .= ' ' . substr($s, 8, 2) . ':' . substr($s, 10, 2) . ':';
  64   if (strlen($s) > 12) {
  65     $ret .= substr($s, 12, 2);
  66   } else {
  67     $ret .= '00';
  68   }
  69   return $ret;
  70 }
  71
  72 function rhl7Abnormal($s) {
  73   if ($s == ''  ) return 'no';
  74   if ($s == 'A' ) return 'yes';
  75   if ($s == 'H' ) return 'high';
  76   if ($s == 'L' ) return 'low';
  77   if ($s == 'HH') return 'vhigh';
  78   if ($s == 'LL') return 'vlow';
  79   return rhl7Text($s);
  80 }
  81
  82 function rhl7ReportStatus($s) {
  83   if ($s == 'F') return 'final';
  84   if ($s == 'P') return 'prelim';
  85   if ($s == 'C') return 'correct';
  86   return rhl7Text($s);
  87 }
  88
  89 /**
  90  * Convert a lower case file extension to a MIME type.
  91  * The extension comes from OBX[5][0] which is itself a huge assumption that
  92  * the HL7 2.3 standard does not help with. Don't be surprised when we have to
  93  * adapt to conventions of various other labs.
  94  *
  95  * @param  string  $fileext  The lower case extension.
  96  * @return string            MIME type.
  97  */
  98 function rhl7MimeType($fileext) {
  99   if ($fileext == 'pdf') return 'application/pdf';
 100   if ($fileext == 'doc') return 'application/msword';
 101   if ($fileext == 'rtf') return 'application/rtf';
 102   if ($fileext == 'txt') return 'text/plain';
 103   if ($fileext == 'zip') return 'application/zip';
 104   return 'application/octet-stream';
 105 }
 106
 107 /**
 108  * Extract encapsulated document data according to its encoding type.
 109  *
 110  * @param  string  $enctype  Encoding type from OBX[5][3].
 111  * @param  string  &$src     Encoded data  from OBX[5][4].
 112  * @return string            Decoded data, or FALSE if error.
 113  */
 114 function rhl7DecodeData($enctype, &$src) {
 115   if ($enctype == 'Base64') return base64_decode($src);
 116   if ($enctype == 'A'     ) return rhl7Text($src);
 117   if ($enctype == 'Hex') {
 118     $data = '';
 119     for ($i = 0; $i < strlen($src) - 1; $i += 2) {
 120       $data .= chr(hexdec($src[$i] . $src[$i+1]));
 121     }
 122     return $data;
 123   }
 124   return FALSE;
 125 }
 126
 127 /**
 128  * Parse and save.
 129  *
 130  * @param  string  &$pprow   A row from the procedure_providers table.
 131  * @param  string  &$hl7     The input HL7 text.
 132  * @return string            Error text, or empty if no errors.
 133  */
 134 function receive_hl7_results(&$hl7) {
 135   if (substr($hl7, 0, 3) != 'MSH') {
 136     return xl('Input does not begin with a MSH segment');
 137   }
 138
 139   // End-of-line delimiter for text in procedure_result.comments
 140   $commentdelim = "\n";
 141
 142   $today = time();
 143
 144   $in_message_id = '';
 145   $in_ssn = '';
 146   $in_dob = '';
 147   $in_lname = '';
 148   $in_fname = '';
 149   $in_orderid = 0;
 150   $in_procedure_code = '';
 151   $in_report_status = '';
 152   $in_encounter = 0;
 153
 154   $porow = false;
 155   $pcrow = false;
 156   $procedure_report_id = 0;
 157   $arep = array(); // holding area for OBR and its NTE data
 158   $ares = array(); // holding area for OBX and its NTE data
 159   $code_seq_array = array(); // tracks sequence numbers of order codes
 160
 161   // This is so we know where we are if a segment like NTE that can appear in
 162   // different places is encountered.
 163   $context = '';
 164
 165   // Delimiters
 166   $d0 = "\r";
 167   $d1 = substr($hl7, 3, 1); // typically |
 168   $d2 = substr($hl7, 4, 1); // typically ^
 169   $d3 = substr($hl7, 5, 1); // typically ~
 170
 171   // We'll need the document category ID for any embedded documents.
 172   $catrow = sqlQuery("SELECT id FROM categories WHERE name = ?",
 173     array($GLOBALS['lab_results_category_name']));
 174   if (empty($catrow['id'])) {
 175     return xl('Document category for lab results does not exist') .
 176       ': ' . $GLOBALS['lab_results_category_name'];
 177   }
 178   $results_category_id = $catrow['id'];
 179
 180   $segs = explode($d0, $hl7);
 181
 182   foreach ($segs as $seg) {
 183     if (empty($seg)) continue;
 184
 185     $a = explode($d1, $seg);
 186
 187     if ($a[0] == 'MSH') {
 188       $context = $a[0];
 189       if ($a[8] != 'ORU^R01') {
 190         return xl('Message type') . " '${a[8]}' " . xl('does not seem valid');
 191       }
 192       $in_message_id = $a[9];
 193     }
 194
 195     else if ($a[0] == 'PID') {
 196       $context = $a[0];
 197       rhl7FlushResult($ares);
 198       // Next line will do something only if there was a report with no results.
 199       rhl7FlushReport($arep);
 200       $in_ssn = $a[4];
 201       $in_dob = $a[7]; // yyyymmdd format
 202       $tmp = explode($d2, $a[5]);
 203       $in_lname = $tmp[0];
 204       $in_fname = $tmp[1];
 205     }
 206
 207     else if ($a[0] == 'PV1') {
 208       // Save placer encounter number if present.
 209       if (!empty($a[19])) {
 210         $tmp = explode($d2, $a[19]);
 211         $in_encounter = intval($tmp[0]);
 212       }
 213     }
 214
 215     else if ($a[0] == 'ORC') {
 216       $context = $a[0];
 217       rhl7FlushResult($ares);
 218       // Next line will do something only if there was a report with no results.
 219       rhl7FlushReport($arep);
 220       $porow = false;
 221       $pcrow = false;
 222       if ($a[2]) $in_orderid = intval($a[2]);
 223     }
 224
 225     else if ($a[0] == 'NTE' && $context == 'ORC') {
 226       // TBD? Is this ever used?
 227     }
 228
 229     else if ($a[0] == 'OBR') {
 230       $context = $a[0];
 231       rhl7FlushResult($ares);
 232       // Next line will do something only if there was a report with no results.
 233       rhl7FlushReport($arep);
 234       $procedure_report_id = 0;
 235       if ($a[2]) $in_orderid = intval($a[2]);
 236       $tmp = explode($d2, $a[4]);
 237       $in_procedure_code = $tmp[0];
 238       $in_procedure_name = $tmp[1];
 239       $in_report_status = rhl7ReportStatus($a[25]);
 240       if (empty($porow)) {
 241         $porow = sqlQuery("SELECT * FROM procedure_order WHERE " .
 242           "procedure_order_id = ?", array($in_orderid));
 243         // The order must already exist. Currently we do not handle electronic
 244         // results returned for manual orders.
 245         if (empty($porow)) {
 246           return xl('Procedure order') . " '$in_orderid' " . xl('was not found');
 247         }
 248         if ($in_encounter) {
 249           if ($porow['encounter_id'] != $in_encounter) {
 250             return xl('Encounter ID') .
 251               " '" . $porow['encounter_id'] . "' " .
 252               xl('for OBR placer order number') .
 253               " '$in_orderid' " .
 254               xl('does not match the PV1 encounter number') .
 255               " '$in_encounter'";
 256           }
 257         }
 258         else {
 259           // They did not return an encounter number to verify, so more checking
 260           // might be done here to make sure the patient seems to match.
 261         }
 262         $code_seq_array = array();
 263       }
 264       // Find the order line item (procedure code) that matches this result.
 265       // If there is more than one, then we select the one whose sequence number
 266       // is next after the last sequence number encountered for this procedure
 267       // code; this assumes that result OBRs are returned in the same sequence
 268       // as the corresponding OBRs in the order.
 269       if (!isset($code_seq_array[$in_procedure_code])) {
 270         $code_seq_array[$in_procedure_code] = 0;
 271       }
 272       $pcquery = "SELECT pc.* FROM procedure_order_code AS pc " .
 273         "WHERE pc.procedure_order_id = ? AND pc.procedure_code = ? " .
 274         "ORDER BY (procedure_order_seq <= ?), procedure_order_seq LIMIT 1";
 275       $pcrow = sqlQuery($pcquery, array($in_orderid, $in_procedure_code,
 276         $code_seq_array['$in_procedure_code']));
 277       if (empty($pcrow)) {
 278         // There is no matching procedure in the order, so it must have been
 279         // added after the original order was sent, either as a manual request
 280         // from the physician or as a "reflex" from the lab.
 281         // procedure_source = '2' indicates this.
 282         sqlInsert("INSERT INTO procedure_order_code SET " .
 283           "procedure_order_id = ?, " .
 284           "procedure_code = ?, " .
 285           "procedure_name = ?, " .
 286           "procedure_source = '2'",
 287           array($in_orderid, $in_procedure_code, $in_procedure_name));
 288         $pcrow = sqlQuery($pcquery, array($in_orderid, $in_procedure_code));
 289       }
 290       $code_seq_array[$in_procedure_code] = 0 + $pcrow['procedure_order_seq'];
 291       $arep = array();
 292       $arep['procedure_order_id'] = $in_orderid;
 293       $arep['procedure_order_seq'] = $pcrow['procedure_order_seq'];
 294       $arep['date_collected'] = rhl7DateTime($a[7]);
 295       $arep['date_report'] = substr(rhl7DateTime($a[22]), 0, 10);
 296       $arep['report_status'] = $in_report_status;
 297       $arep['report_notes'] = '';
 298     }
 299
 300     else if ($a[0] == 'NTE' && $context == 'OBR') {
 301       $arep['report_notes'] .= rhl7Text($a[3]) . "\n";
 302     }
 303
 304     else if ($a[0] == 'OBX') {
 305       $context = $a[0];
 306       rhl7FlushResult($ares);
 307       if (!$procedure_report_id) {
 308         $procedure_report_id = rhl7FlushReport($arep);
 309       }
 310       $ares = array();
 311       $ares['procedure_report_id'] = $procedure_report_id;
 312       $ares['result_data_type'] = substr($a[2], 0, 1); // N, S, F or E
 313       $ares['comments'] = $commentdelim;
 314       if ($a[2] == 'ED') {
 315         // This is the case of results as an embedded document. We will create
 316         // a normal patient document in the assigned category for lab results.
 317         $tmp = explode($d2, $a[5]);
 318         $fileext = strtolower($tmp[0]);
 319         $filename = date("Ymd_His") . '.' . $fileext;
 320         $data = rhl7DecodeData($tmp[3], $tmp[4]);
 321         if ($data === FALSE) return xl('Invalid encapsulated data encoding type') . ': ' . $tmp[3];
 322         $d = new Document();
 323         $rc = $d->createDocument($porow['patient_id'], $results_category_id,
 324           $filename, rhl7MimeType($fileext), $data);
 325         if ($rc) return $rc; // This would be error message text.
 326         $ares['document_id'] = $d->get_id();
 327       }
 328       else if (strlen($a[5]) > 200) {
 329         // OBX-5 can be a very long string of text with "~" as line separators.
 330         // The first line of comments is reserved for such things.
 331         $ares['result_data_type'] = 'L';
 332         $ares['result'] = '';
 333         $ares['comments'] = rhl7Text($a[5]) . $commentdelim;
 334       }
 335       else {
 336         $ares['result'] = rhl7Text($a[5]);
 337       }
 338       $tmp = explode($d2, $a[3]);
 339       $ares['result_code'] = rhl7Text($tmp[0]);
 340       $ares['result_text'] = rhl7Text($tmp[1]);
 341       $ares['date'] = rhl7DateTime($a[14]);
 342       $ares['facility'] = rhl7Text($a[15]);
 343       $ares['units'] = rhl7Text($a[6]);
 344       $ares['range'] = rhl7Text($a[7]);
 345       $ares['abnormal'] = rhl7Abnormal($a[8]); // values are lab dependent
 346       $ares['result_status'] = rhl7ReportStatus($a[11]);
 347     }
 348
 349     else if ($a[0] == 'ZEF') {
 350       // ZEF segment is treated like an OBX with an embedded Base64-encoded PDF.
 351       $context = 'OBX';
 352       rhl7FlushResult($ares);
 353       if (!$procedure_report_id) {
 354         $procedure_report_id = rhl7FlushReport($arep);
 355       }
 356       $ares = array();
 357       $ares['procedure_report_id'] = $procedure_report_id;
 358       $ares['result_data_type'] = 'E';
 359       $ares['comments'] = $commentdelim;
 360       //
 361       $fileext = 'pdf';
 362       $filename = date("Ymd_His") . '.' . $fileext;
 363       $data = rhl7DecodeData('Base64', $a[2]);
 364       if ($data === FALSE) return xl('ZEF segment internal error');
 365       $d = new Document();
 366       $rc = $d->createDocument($porow['patient_id'], $results_category_id,
 367         $filename, rhl7MimeType($fileext), $data);
 368       if ($rc) return $rc; // This would be error message text.
 369       $ares['document_id'] = $d->get_id();
 370       //
 371       $ares['date'] = $arep['date_report'];
 372     }
 373
 374     else if ($a[0] == 'NTE' && $context == 'OBX') {
 375       $ares['comments'] .= rhl7Text($a[3]) . $commentdelim;
 376     }
 377
 378     // Add code here for any other segment types that may be present.
 379
 380     else {
 381       return xl('Segment name') . " '${a[0]}' " . xl('is misplaced or unknown');
 382     }
 383   }
 384
 385   rhl7FlushResult($ares);
 386   // Next line will do something only if there was a report with no results.
 387   rhl7FlushReport($arep);
 388   return '';
 389 }
 390
 391 /**
 392  * Poll all eligible labs for new results and store them in the database.
 393  *
 394  * @param  array   &$messages  Receives messages of interest.
 395  * @return string  Error text, or empty if no errors.
 396  */
 397 function poll_hl7_results(&$messages) {
 398   global $srcdir;
 399
 400   $messages = array();
 401   $filecount = 0;
 402   $badcount = 0;
 403
 404   $ppres = sqlStatement("SELECT * FROM procedure_providers ORDER BY name");
 405
 406   while ($pprow = sqlFetchArray($ppres)) {
 407     $protocol = $pprow['protocol'];
 408     $remote_host = $pprow['remote_host'];
 409     $hl7 = '';
 410
 411     if ($protocol == 'SFTP') {
 412       $remote_port = 22;
 413       // Hostname may have ":port" appended to specify a nonstandard port number.
 414       if ($i = strrpos($remote_host, ':')) {
 415         $remote_port = 0 + substr($remote_host, $i + 1);
 416         $remote_host = substr($remote_host, 0, $i);
 417       }
 418       ini_set('include_path', ini_get('include_path') . PATH_SEPARATOR . "$srcdir/phpseclib");
 419       require_once("$srcdir/phpseclib/Net/SFTP.php");
 420       // Compute the target path name.
 421       $pathname = '.';
 422       if ($pprow['results_path']) $pathname = $pprow['results_path'] . '/' . $pathname;
 423       // Connect to the server and enumerate files to process.
 424       $sftp = new Net_SFTP($remote_host, $remote_port);
 425       if (!$sftp->login($pprow['login'], $pprow['password'])) {
 426         return xl('Login to remote host') . " '$remote_host' " . xl('failed');
 427       }
 428       $files = $sftp->nlist($pathname);
 429       foreach ($files as $file) {
 430         if (substr($file, 0, 1) == '.') continue;
 431         ++$filecount;
 432         $hl7 = $sftp->get("$pathname/$file");
 433         // Archive the results file.
 434         $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
 435         if (!file_exists($prpath)) mkdir($prpath);
 436         $prpath .= '/' . $pprow['ppid'];
 437         if (!file_exists($prpath)) mkdir($prpath);
 438         $fh = fopen("$prpath/$file", 'w');
 439         if ($fh) {
 440           fwrite($fh, $hl7);
 441           fclose($fh);
 442         }
 443         else {
 444           $messages[] = xl('File') . " '$file' " . xl('cannot be archived, ignored');
 445           ++$badcount;
 446           continue;
 447         }
 448         // Now delete it from its ftp directory.
 449         if (!$sftp->delete("$pathname/$file")) {
 450           $messages[] = xl('File') . " '$file' " . xl('cannot be deleted, ignored');
 451           ++$badcount;
 452           continue;
 453         }
 454         // Parse and process its contents.
 455         $msg = receive_hl7_results($hl7);
 456         if ($msg) {
 457           $tmp = xl('Error processing file') . " '$file': " . $msg;
 458           $messages[] = $tmp;
 459           newEvent("lab-results-error", $_SESSION['authUser'], $_SESSION['authProvider'], 0, $tmp);
 460           ++$badcount;
 461           continue;
 462         }
 463         $messages[] = xl('New file') . " '$file' " . xl('processed successfully');
 464       }
 465     }
 466
 467     // TBD: Insert "else if ($protocol == '???') {...}" to support other protocols.
 468
 469   }
 470
 471   if ($badcount) return "$badcount " . xl('error(s) encountered from new results');
 472
 473   return '';
 474 }
 475 ?>