interface/orders/receive_hl7_results.inc.php

   1 <?php
   2 /**
   3 * Functions to support parsing and saving hl7 results.
   4 *
   5 * Copyright (C) 2013-2014 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 $rhl7_return = array();
  23 $rhl7_segnum = 0;
  24
  25 function rhl7LogMsg($msg, $fatal=true) {
  26   // global $rhl7_return, $rhl7_segnum;
  27   $rhl7_return['mssgs'][] = $msg;
  28   if ($fatal) {
  29     $rhl7_return['fatal'] = true;
  30     newEvent("lab-results-error", $_SESSION['authUser'], $_SESSION['authProvider'], 0, $msg);
  31   }
  32   return $rhl7_return;
  33 }
  34
  35 function rhl7InsertRow(&$arr, $tablename) {
  36   if (empty($arr)) return;
  37
  38   // echo "<!-- ";   // debugging
  39   // print_r($arr);
  40   // echo " -->\n";
  41
  42   $query = "INSERT INTO $tablename SET";
  43   $binds = array();
  44   $sep = '';
  45   foreach ($arr as $key => $value) {
  46     $query .= "$sep `$key` = ?";
  47     $sep = ',';
  48     $binds[] = $value;
  49   }
  50   $arr = array();
  51   return sqlInsert($query, $binds);
  52 }
  53
  54 function rhl7FlushResult(&$ares) {
  55   return rhl7InsertRow($ares, 'procedure_result');
  56 }
  57
  58 function rhl7FlushReport(&$arep) {
  59   return rhl7InsertRow($arep, 'procedure_report');
  60 }
  61
  62 function rhl7Text($s) {
  63   $s = str_replace('\\S\\'  ,'^' , $s);
  64   $s = str_replace('\\F\\'  ,'|' , $s);
  65   $s = str_replace('\\R\\'  ,'~' , $s);
  66   $s = str_replace('\\T\\'  ,'&' , $s);
  67   $s = str_replace('\\X0d\\',"\r", $s);
  68   $s = str_replace('\\E\\'  ,'\\', $s);
  69   return $s;
  70 }
  71
  72 function rhl7DateTime($s) {
  73   $s = preg_replace('/[^0-9]/', '', $s);
  74   if (empty($s)) return '0000-00-00 00:00:00';
  75   $ret = substr($s, 0, 4) . '-' . substr($s, 4, 2) . '-' . substr($s, 6, 2);
  76   if (strlen($s) > 8) $ret .= ' ' . substr($s, 8, 2) . ':' . substr($s, 10, 2) . ':';
  77   if (strlen($s) > 12) {
  78     $ret .= substr($s, 12, 2);
  79   } else {
  80     $ret .= '00';
  81   }
  82   return $ret;
  83 }
  84
  85 function rhl7Date($s) {
  86   return substr(rhl7DateTime($s), 0, 10);
  87 }
  88
  89 function rhl7Abnormal($s) {
  90   if ($s == ''  ) return 'no';
  91   if ($s == 'N' ) return 'no';
  92   if ($s == 'A' ) return 'yes';
  93   if ($s == 'H' ) return 'high';
  94   if ($s == 'L' ) return 'low';
  95   if ($s == 'HH') return 'vhigh';
  96   if ($s == 'LL') return 'vlow';
  97   return rhl7Text($s);
  98 }
  99
 100 function rhl7ReportStatus($s) {
 101   if ($s == 'F') return 'final';
 102   if ($s == 'P') return 'prelim';
 103   if ($s == 'C') return 'correct';
 104   return rhl7Text($s);
 105 }
 106
 107 /**
 108  * Convert a lower case file extension to a MIME type.
 109  * The extension comes from OBX[5][0] which is itself a huge assumption that
 110  * the HL7 2.3 standard does not help with. Don't be surprised when we have to
 111  * adapt to conventions of various other labs.
 112  *
 113  * @param  string  $fileext  The lower case extension.
 114  * @return string            MIME type.
 115  */
 116 function rhl7MimeType($fileext) {
 117   if ($fileext == 'pdf') return 'application/pdf';
 118   if ($fileext == 'doc') return 'application/msword';
 119   if ($fileext == 'rtf') return 'application/rtf';
 120   if ($fileext == 'txt') return 'text/plain';
 121   if ($fileext == 'zip') return 'application/zip';
 122   return 'application/octet-stream';
 123 }
 124
 125 /**
 126  * Extract encapsulated document data according to its encoding type.
 127  *
 128  * @param  string  $enctype  Encoding type from OBX[5][3].
 129  * @param  string  &$src     Encoded data  from OBX[5][4].
 130  * @return string            Decoded data, or FALSE if error.
 131  */
 132 function rhl7DecodeData($enctype, &$src) {
 133   if ($enctype == 'Base64') return base64_decode($src);
 134   if ($enctype == 'A'     ) return rhl7Text($src);
 135   if ($enctype == 'Hex') {
 136     $data = '';
 137     for ($i = 0; $i < strlen($src) - 1; $i += 2) {
 138       $data .= chr(hexdec($src[$i] . $src[$i+1]));
 139     }
 140     return $data;
 141   }
 142   return FALSE;
 143 }
 144
 145 /**
 146  * Look for a patient matching the given data.
 147  * Return values are:
 148  *  >0  Definite match, this is the pid.
 149  *   0  No patient is close to a match.
 150  *  -1  It's not clear if there is a match.
 151  */
 152 function match_patient($in_ss, $in_fname, $in_lname, $in_dob) {
 153   $patient_id = 0;
 154   $tmp = sqlQuery("SELECT pid FROM patient_data WHERE " .
 155     "((ss IS NULL OR ss = '' OR '' = ?) AND " .
 156     "fname IS NOT NULL AND fname != '' AND fname = ? AND " .
 157     "lname IS NOT NULL AND lname != '' AND lname = ? AND " .
 158     "DOB IS NOT NULL AND DOB = ?) OR " .
 159     "(ss IS NOT NULL AND ss != '' AND ss = ? AND (" .
 160     "fname IS NOT NULL AND fname != '' AND fname = ? OR " .
 161     "lname IS NOT NULL AND lname != '' AND lname = ? OR " .
 162     "DOB IS NOT NULL AND DOB = ?)) " .
 163     "ORDER BY ss DESC, pid DESC LIMIT 1",
 164     array($in_ss, $in_fname, $in_lname, $in_dob, $in_ss, $in_fname, $in_lname, $in_dob));
 165   if (!empty($tmp['pid'])) {
 166     // Got a match.
 167     $patient_id = intval($tmp['pid']);
 168   }
 169   else {
 170     // No match good enough, figure out if there's enough ambiguity to ask the user.
 171     $tmp = sqlQuery("SELECT pid FROM patient_data WHERE " .
 172       "(ss IS NOT NULL AND ss != '' AND ss = ?) OR " .
 173       "(fname IS NOT NULL AND fname != '' AND fname = ? AND " .
 174       "lname IS NOT NULL AND lname != '' AND lname = ?) OR " .
 175       "(DOB IS NOT NULL AND DOB = ?) " .
 176       "LIMIT 1",
 177       array($in_ss, $in_fname, $in_lname, $in_dob));
 178     if (!empty($tmp['pid'])) {
 179       $patient_id = -1;
 180     }
 181   }
 182   return $patient_id;
 183 }
 184
 185 /**
 186  * Create a patient using whatever patient_data attributes are provided.
 187  */
 188 function create_skeleton_patient($patient_data) {
 189   $employer_data = array();
 190   $tmp = sqlQuery("SELECT MAX(pid)+1 AS pid FROM patient_data");
 191   $ptid = empty($tmp['pid']) ? 1 : intval($tmp['pid']);
 192   if (!isset($patient_data['pubpid'])) $patient_data['pubpid'] = $ptid;
 193   updatePatientData($ptid, $patient_data, true);
 194   updateEmployerData($ptid, $employer_data, true);
 195   newHistoryData($ptid);
 196   return $ptid;
 197 }
 198
 199 /**
 200  * Parse and save.
 201  *
 202  * @param  string  &$hl7      The input HL7 text.
 203  * @param  char    $direction B=Bidirectional, R=Results-only
 204  * @param  book    $dryrun    True = do not update anything, just report errors
 205  * @return array              Array of errors and match requests, if any.
 206  */
 207 function receive_hl7_results(&$hl7, $lab_id=0, $direction='B', $dryrun=false, $matchresp=NULL) {
 208   // This will hold returned error messages and related variables.
 209   $rhl7_return = array();
 210   $rhl7_return['mssgs'] = array();
 211   $rhl7_return['match'] = array();
 212   $rhl7_segnum = 0;
 213
 214   if (substr($hl7, 0, 3) != 'MSH') {
 215     return rhl7LogMsg(xl('Input does not begin with a MSH segment'), true);
 216   }
 217
 218   // End-of-line delimiter for text in procedure_result.comments
 219   $commentdelim = "\n";
 220
 221   $today = time();
 222
 223   $in_message_id = '';
 224   $in_ssn = '';
 225   $in_dob = '';
 226   $in_lname = '';
 227   $in_fname = '';
 228   $in_orderid = 0;
 229   $in_procedure_code = '';
 230   $in_report_status = '';
 231   $in_encounter = 0;
 232   $patient_id = 0; // for results-only patient matching logic
 233
 234   $porow = false;
 235   $pcrow = false;
 236   $procedure_report_id = 0;
 237   $arep = array(); // holding area for OBR and its NTE data
 238   $ares = array(); // holding area for OBX and its NTE data
 239   $code_seq_array = array(); // tracks sequence numbers of order codes
 240   $results_category_id = 0;  // document category ID for lab results
 241
 242   // This is so we know where we are if a segment like NTE that can appear in
 243   // different places is encountered.
 244   $context = '';
 245
 246   // Delimiters
 247   $d0 = "\r";
 248   $d1 = substr($hl7, 3, 1); // typically |
 249   $d2 = substr($hl7, 4, 1); // typically ^
 250   $d3 = substr($hl7, 5, 1); // typically ~
 251
 252   // We'll need the document category ID for any embedded documents.
 253   $catrow = sqlQuery("SELECT id FROM categories WHERE name = ?",
 254     array($GLOBALS['lab_results_category_name']));
 255   if (empty($catrow['id'])) {
 256     return rhl7LogMsg(xl('Document category for lab results does not exist') .
 257       ': ' . $GLOBALS['lab_results_category_name'], true);
 258   }
 259   else {
 260     $results_category_id = $catrow['id'];
 261   }
 262
 263   $segs = explode($d0, $hl7);
 264
 265   foreach ($segs as $seg) {
 266     if (empty($seg)) continue;
 267
 268     // echo "<!-- $dryrun $seg -->\n"; // debugging
 269
 270     ++$rhl7_segnum;
 271     $a = explode($d1, $seg);
 272
 273     if ($a[0] == 'MSH') {
 274       $context = $a[0];
 275       if ($a[8] != 'ORU^R01') {
 276         return rhl7LogMsg(xl('MSH.8 message type is not valid') . ": '" . $a[8] . "'", true);
 277       }
 278       $in_message_id = $a[9];
 279     }
 280
 281     else if ($a[0] == 'PID') {
 282       $context = $a[0];
 283       if (!$dryrun) rhl7FlushResult($ares);
 284       $ares = array();
 285       // Next line will do something only if there was a report with no results.
 286       if (!$dryrun) rhl7FlushReport($arep);
 287       $arep = array();
 288       $porow = false;
 289       $pcrow = false;
 290       $in_orderid = 0;
 291       $in_ssn = preg_replace('/[^0-9]/', '', $a[4]);
 292       $in_dob = rhl7Date($a[7]);
 293       $tmp = explode($d2, $a[5]);
 294       $in_lname = rhl7Text($tmp[0]);
 295       $in_fname = rhl7Text($tmp[1]);
 296       $patient_id = 0;
 297       if ($direction == 'R') {
 298         $patient_id = match_patient($in_ss, $in_fname, $in_lname, $in_dob);
 299         if ($patient_id == -1) {
 300           // Indeterminate, check if the user has specified the patient.
 301           if (isset($matchresp[$rhl7_segnum]) /* && $matchresp[$rhl7_segnum] !== '' */) {
 302             // This will be an existing pid, or 0 to specify creating a patient.
 303             $patient_id = intval($matchresp[$rhl7_segnum]);
 304           }
 305           else {
 306             // Nope, ask the user to do so.
 307             $rhl7_return['match'][$rhl7_segnum] = array('ss' => $in_ss,
 308               'fname' => $in_fname, 'lname' => $in_lname, 'DOB' => $in_dob);
 309           }
 310         }
 311         if ($patient_id == 0 && !$dryrun) {
 312           // We must create the patient.
 313           $patient_id = create_skeleton_patient(array(
 314             'fname' => $in_fname,
 315             'lname' => $in_lname,
 316             'DOB'   => $in_dob,
 317             'ss'    => $in_ssn,
 318           ));
 319         }
 320         if ($patient_id == -1) $patient_id = 0;
 321       } // end results-only logic
 322     }
 323
 324     else if ($a[0] == 'PV1') {
 325       // Save placer encounter number if present.
 326       if ($direction != 'R' && !empty($a[19])) {
 327         $tmp = explode($d2, $a[19]);
 328         $in_encounter = intval($tmp[0]);
 329       }
 330     }
 331
 332     else if ($a[0] == 'ORC') {
 333       $context = $a[0];
 334       if (!$dryrun) rhl7FlushResult($ares);
 335       $ares = array();
 336       // Next line will do something only if there was a report with no results.
 337       if (!$dryrun) rhl7FlushReport($arep);
 338       $arep = array();
 339       $porow = false;
 340       $pcrow = false;
 341       if ($direction != 'R' && $a[2]) $in_orderid = intval($a[2]);
 342     }
 343
 344     else if ($a[0] == 'NTE' && $context == 'ORC') {
 345       // Is this ever used?
 346     }
 347
 348     else if ($a[0] == 'OBR') {
 349       $context = $a[0];
 350       if (!$dryrun) rhl7FlushResult($ares);
 351       $ares = array();
 352       // Next line will do something only if there was a report with no results.
 353       if (!$dryrun) rhl7FlushReport($arep);
 354       $arep = array();
 355       $procedure_report_id = 0;
 356       if ($direction != 'R' && $a[2]) {
 357         $in_orderid = intval($a[2]);
 358         $porow = false;
 359         $pcrow = false;
 360       }
 361       $tmp = explode($d2, $a[4]);
 362       $in_procedure_code = $tmp[0];
 363       $in_procedure_name = $tmp[1];
 364       $in_report_status = rhl7ReportStatus($a[25]);
 365       //
 366       if ($direction == 'R') {
 367         // $in_orderid will be 0 here.
 368         // Save their order ID to procedure_order.control_id.
 369         // That column will need to change from bigint to varchar.
 370         // Look for an existing order using that plus lab_id.
 371         // Ordering provider is OBR.16 (NPI^Last^First).
 372         // Might not need to create a dummy encounter.
 373         // Need also provider_id (probably), patient_id, date_ordered, lab_id.
 374         // We have observation date/time in OBR.7.
 375         // We have report date/time in OBR.22.
 376         // We do not have an order date.
 377
 378         $external_order_id = empty($a[2]) ? $a[3] : $a[2];
 379         $porow = false;
 380         if ($external_order_id) {
 381           $porow = sqlQuery("SELECT * FROM procedure_order " .
 382             "WHERE lab_id = ? AND control_id = ? " .
 383             "ORDER BY procedure_order_id DESC LIMIT 1",
 384             array($lab_id, $external_order_id));
 385         }
 386         if (!empty($porow)) {
 387           $in_orderid = intval($porow['procedure_order_id']);
 388         }
 389         else {
 390           // Create order.
 391           // Need to identify the ordering provider and, if possible, a recent encounter.
 392           $datetime_report = rhl7DateTime($a[22]);
 393           $date_report = substr($datetime_report, 0, 10) . ' 00:00:00';
 394           $encounter_id = 0;
 395           $provider_id = 0;
 396           // Look for the most recent encounter within 30 days of the report date.
 397           $encrow = sqlQuery("SELECT encounter FROM form_encounter WHERE " .
 398             "pid = ? AND date <= ? AND DATE_ADD(date, INTERVAL 30 DAY) > ? " .
 399             "ORDER BY date DESC, encounter DESC LIMIT 1",
 400             array($patient_id, $date_report, $date_report));
 401           if (!empty($encrow)) {
 402             $encounter_id = intval($encrow['encounter']);
 403             $provider_id = intval($encrow['provider_id']);
 404           }
 405           if (!$provider_id) {
 406             // Attempt ordering provider matching by name or NPI.
 407             $op_lname = $op_fname = '';
 408             $tmp = explode($d2, $a[16]);
 409             $op_npi = preg_replace('/[^0-9]/', '', $tmp[0]);
 410             if (!empty($tmp[1])) $op_lname = $tmp[1];
 411             if (!empty($tmp[2])) $op_fname = $tmp[2];
 412             if ($op_npi || ($op_fname && $op_lname)) {
 413               if ($op_npi) {
 414                 if ($op_fname && $op_lname) {
 415                   $where = "(npi IS NOT NULL AND npi = ?) OR ((npi IS NULL OR npi = ?) AND lname = ? AND fname = ?)";
 416                   $qarr = array($op_npi, '', $op_lname, $op_fname);
 417                 }
 418                 else {
 419                   $where = "npi IS NOT NULL AND npi = ?";
 420                   $qarr = array($op_npi);
 421                 }
 422               }
 423               else {
 424                 $where = "lname = ? AND fname = ?";
 425                 $qarr = array($op_lname, $op_fname);
 426               }
 427             }
 428             $oprow = sqlQuery("SELECT id FROM users WHERE $where " .
 429               "ORDER BY active DESC, authorized DESC, username DESC, id LIMIT 1",
 430               $qarr);
 431             if (!empty($oprow)) $provider_id = intval($oprow['id']);
 432           }
 433           if (!$dryrun) {
 434             // Now create the procedure order.
 435             $in_orderid = sqlInsert("INSERT INTO procedure_order SET " .
 436               "date_ordered   = ?, " .
 437               "provider_id    = ?, " .
 438               "lab_id         = ?, " .
 439               "date_collected = ?, " .
 440               "date_transmitted = ?, " .
 441               "patient_id     = ?, " .
 442               "encounter_id   = ?, " .
 443               "control_id     = ?",
 444               array($datetime_report, $provider_id, $lab_id, rhl7DateTime($a[22]),
 445               rhl7DateTime($a[7]), $patient_id, $encounter_id, $external_order_id));
 446             // If an encounter was identified then link the order to it.
 447             if ($encounter_id && $in_orderid) {
 448               addForm($encounter_id, "Procedure Order", $in_orderid, "procedure_order", $patient_id);
 449             }
 450           }
 451         } // end no $porow
 452       } // end results-only
 453       if (empty($porow)) {
 454         $porow = sqlQuery("SELECT * FROM procedure_order WHERE " .
 455           "procedure_order_id = ?", array($in_orderid));
 456         // The order must already exist. Currently we do not handle electronic
 457         // results returned for manual orders.
 458         if (empty($porow) && !($dryrun && $direction == 'R')) {
 459           return rhl7LogMsg(xl('Procedure order not found') . ": $in_orderid", true);
 460         }
 461         if ($in_encounter) {
 462           if ($direction != 'R' && $porow['encounter_id'] != $in_encounter) {
 463             return rhl7LogMsg(xl('Encounter ID') .
 464               " '" . $porow['encounter_id'] . "' " .
 465               xl('for OBR placer order number') .
 466               " '$in_orderid' " .
 467               xl('does not match the PV1 encounter number') .
 468               " '$in_encounter'");
 469           }
 470         }
 471         else {
 472           // They did not return an encounter number to verify, so more checking
 473           // might be done here to make sure the patient seems to match.
 474         }
 475         // Save the lab's control ID if there is one.
 476         $tmp = explode($d2, $a[3]);
 477         $control_id = $tmp[0];
 478         if ($control_id && empty($porow['control_id'])) {
 479           sqlStatement("UPDATE procedure_order SET control_id = ? WHERE " .
 480             "procedure_order_id = ?", array($control_id, $in_orderid));
 481         }
 482         $code_seq_array = array();
 483       }
 484       // Find the order line item (procedure code) that matches this result.
 485       // If there is more than one, then we select the one whose sequence number
 486       // is next after the last sequence number encountered for this procedure
 487       // code; this assumes that result OBRs are returned in the same sequence
 488       // as the corresponding OBRs in the order.
 489       if (!isset($code_seq_array[$in_procedure_code])) {
 490         $code_seq_array[$in_procedure_code] = 0;
 491       }
 492       $pcquery = "SELECT pc.* FROM procedure_order_code AS pc " .
 493         "WHERE pc.procedure_order_id = ? AND pc.procedure_code = ? " .
 494         "ORDER BY (procedure_order_seq <= ?), procedure_order_seq LIMIT 1";
 495       $pcqueryargs = array($in_orderid, $in_procedure_code, $code_seq_array[$in_procedure_code]);
 496       $pcrow = sqlQuery($pcquery, $pcqueryargs);
 497       if (empty($pcrow)) {
 498         // There is no matching procedure in the order, so it must have been
 499         // added after the original order was sent, either as a manual request
 500         // from the physician or as a "reflex" from the lab.
 501         // procedure_source = '2' indicates this.
 502         if (!$dryrun) {
 503           sqlInsert("INSERT INTO procedure_order_code SET " .
 504             "procedure_order_id = ?, " .
 505             "procedure_code = ?, " .
 506             "procedure_name = ?, " .
 507             "procedure_source = '2'",
 508             array($in_orderid, $in_procedure_code, $in_procedure_name));
 509           $pcrow = sqlQuery($pcquery, $pcqueryargs);
 510         }
 511         else {
 512           // Dry run, make a dummy procedure_order_code row.
 513           $pcrow = array(
 514             'procedure_order_id' => $in_orderid,
 515             'procedure_order_seq' => 0, // TBD?
 516           );
 517         }
 518       }
 519       $code_seq_array[$in_procedure_code] = 0 + $pcrow['procedure_order_seq'];
 520       $arep = array();
 521       $arep['procedure_order_id'] = $in_orderid;
 522       $arep['procedure_order_seq'] = $pcrow['procedure_order_seq'];
 523       $arep['date_collected'] = rhl7DateTime($a[7]);
 524       $arep['date_report'] = rhl7Date($a[22]);
 525       $arep['report_status'] = $in_report_status;
 526       $arep['report_notes'] = '';
 527     }
 528
 529     else if ($a[0] == 'NTE' && $context == 'OBR') {
 530       $arep['report_notes'] .= rhl7Text($a[3]) . "\n";
 531     }
 532
 533     else if ($a[0] == 'OBX') {
 534       $context = $a[0];
 535       if (!$dryrun) rhl7FlushResult($ares);
 536       $ares = array();
 537       if (!$procedure_report_id) {
 538         if (!$dryrun) $procedure_report_id = rhl7FlushReport($arep);
 539         $arep = array();
 540       }
 541       $ares['procedure_report_id'] = $procedure_report_id;
 542       $ares['result_data_type'] = substr($a[2], 0, 1); // N, S, F or E
 543       $ares['comments'] = $commentdelim;
 544       if ($a[2] == 'ED') {
 545         // This is the case of results as an embedded document. We will create
 546         // a normal patient document in the assigned category for lab results.
 547         $tmp = explode($d2, $a[5]);
 548         $fileext = strtolower($tmp[0]);
 549         $filename = date("Ymd_His") . '.' . $fileext;
 550         $data = rhl7DecodeData($tmp[3], $tmp[4]);
 551         if ($data === FALSE) {
 552           return rhl7LogMsg(xl('Invalid encapsulated data encoding type') . ': ' . $tmp[3]);
 553         }
 554         if (!$dryrun) {
 555           $d = new Document();
 556           $rc = $d->createDocument($porow['patient_id'], $results_category_id, // TBD: Make sure not 0
 557             $filename, rhl7MimeType($fileext), $data);
 558           if ($rc) return rhl7LogMsg($rc);
 559           $ares['document_id'] = $d->get_id();
 560         }
 561       }
 562       else if (strlen($a[5]) > 200) {
 563         // OBX-5 can be a very long string of text with "~" as line separators.
 564         // The first line of comments is reserved for such things.
 565         $ares['result_data_type'] = 'L';
 566         $ares['result'] = '';
 567         $ares['comments'] = rhl7Text($a[5]) . $commentdelim;
 568       }
 569       else {
 570         $ares['result'] = rhl7Text($a[5]);
 571       }
 572       $tmp = explode($d2, $a[3]);
 573       $ares['result_code'] = rhl7Text($tmp[0]);
 574       $ares['result_text'] = rhl7Text($tmp[1]);
 575       $ares['date'] = rhl7DateTime($a[14]);
 576       $ares['facility'] = rhl7Text($a[15]);
 577       $ares['units'] = rhl7Text($a[6]);
 578       $ares['range'] = rhl7Text($a[7]);
 579       $ares['abnormal'] = rhl7Abnormal($a[8]); // values are lab dependent
 580       $ares['result_status'] = rhl7ReportStatus($a[11]);
 581     }
 582
 583     else if ($a[0] == 'ZEF') {
 584       // ZEF segment is treated like an OBX with an embedded Base64-encoded PDF.
 585       $context = 'OBX';
 586       if (!$dryrun) rhl7FlushResult($ares);
 587       $ares = array();
 588       if (!$procedure_report_id) {
 589         if (!$dryrun) $procedure_report_id = rhl7FlushReport($arep);
 590         $arep = array();
 591       }
 592       $ares['procedure_report_id'] = $procedure_report_id;
 593       $ares['result_data_type'] = 'E';
 594       $ares['comments'] = $commentdelim;
 595       //
 596       $fileext = 'pdf';
 597       $filename = date("Ymd_His") . '.' . $fileext;
 598       $data = rhl7DecodeData('Base64', $a[2]);
 599       if ($data === FALSE) return rhl7LogMsg(xl('ZEF segment internal error'));
 600       if (!$dryrun) {
 601         $d = new Document();
 602         $rc = $d->createDocument($porow['patient_id'], $results_category_id, // TBD: Make sure not 0
 603           $filename, rhl7MimeType($fileext), $data);
 604         if ($rc) return rhl7LogMsg($rc);
 605         $ares['document_id'] = $d->get_id();
 606       }
 607       $ares['date'] = $arep['date_report'];
 608     }
 609
 610     else if ($a[0] == 'NTE' && $context == 'OBX') {
 611       $ares['comments'] .= rhl7Text($a[3]) . $commentdelim;
 612     }
 613
 614     // Add code here for any other segment types that may be present.
 615
 616     else {
 617       return rhl7LogMsg(xl('Segment name') . " '${a[0]}' " . xl('is misplaced or unknown'));
 618     }
 619   }
 620
 621   if (!$dryrun) rhl7FlushResult($ares);
 622   // Next line will do something only if there was a report with no results.
 623   if (!$dryrun) rhl7FlushReport($arep);
 624   return $rhl7_return;
 625 }
 626
 627 /**
 628  * Poll all eligible labs for new results and store them in the database.
 629  *
 630  * @param  array   &$info  Conveys information to and from the caller:
 631  * FROM THE CALLER:
 632  * $info["$ppid/$filename"]['delete'] = a non-empty value if file deletion is requested.
 633  * $info["$ppid/$filename"]['select'] = array of patient matching responses where key is segment
 634  *   number and value is selected pid for this patient, or 0 to create the patient.
 635  * TO THE CALLER:
 636  * $info["$ppid/$filename"]['mssgs'] = array of messages from this function.
 637  * $info["$ppid/$filename"]['match'] = array of patient matching requests where key is
 638  *   (PID) segment number and value is an associative array of patient attributes from the hl7 file:
 639  *   ss, fname, lname, DOB.
 640  *
 641  * @return string  Error text, or empty if no errors.
 642  */
 643 function poll_hl7_results(&$info) {
 644   global $srcdir;
 645
 646   // echo "<!-- post: "; print_r($_POST); echo " -->\n"; // debugging
 647   // echo "<!-- in:   "; print_r($info); echo " -->\n"; // debugging
 648
 649   $filecount = 0;
 650   $badcount = 0;
 651
 652   $ppres = sqlStatement("SELECT * FROM procedure_providers ORDER BY name");
 653
 654   while ($pprow = sqlFetchArray($ppres)) {
 655     $ppid        = $pprow['ppid'];
 656     $protocol    = $pprow['protocol'];
 657     $remote_host = $pprow['remote_host'];
 658     $hl7 = '';
 659
 660     if ($protocol == 'SFTP') {
 661       $remote_port = 22;
 662       // Hostname may have ":port" appended to specify a nonstandard port number.
 663       if ($i = strrpos($remote_host, ':')) {
 664         $remote_port = 0 + substr($remote_host, $i + 1);
 665         $remote_host = substr($remote_host, 0, $i);
 666       }
 667       ini_set('include_path', ini_get('include_path') . PATH_SEPARATOR . "$srcdir/phpseclib");
 668       require_once("$srcdir/phpseclib/Net/SFTP.php");
 669       // Compute the target path name.
 670       $pathname = '.';
 671       if ($pprow['results_path']) $pathname = $pprow['results_path'] . '/' . $pathname;
 672       // Connect to the server and enumerate files to process.
 673       $sftp = new Net_SFTP($remote_host, $remote_port);
 674       if (!$sftp->login($pprow['login'], $pprow['password'])) {
 675         return xl('Login to remote host') . " '$remote_host' " . xl('failed');
 676       }
 677       $files = $sftp->nlist($pathname);
 678       foreach ($files as $file) {
 679         if (substr($file, 0, 1) == '.') continue;
 680         ++$filecount;
 681         if (!isset($info["$ppid/$file"])) $info["$ppid/$file"] = array();
 682         // Ensure that archive directory exists.
 683         $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
 684         if (!file_exists($prpath)) mkdir($prpath);
 685         $prpath .= '/' . $pprow['ppid'];
 686         if (!file_exists($prpath)) mkdir($prpath);
 687         // Get file contents.
 688         $hl7 = $sftp->get("$pathname/$file");
 689         // If user requested reject and delete, do that.
 690         if (!empty($info["$ppid/$file"]['delete'])) {
 691           $fh = fopen("$prpath/$file.rejected", 'w');
 692           if ($fh) {
 693             fwrite($fh, $hl7);
 694             fclose($fh);
 695           }
 696           else {
 697             return xl('Cannot create file') . ' "' . "$prpath/$file.rejected" . '"';
 698           }
 699           if (!$sftp->delete("$pathname/$file")) {
 700             return xl('Cannot delete (from SFTP server) file') . ' "' . "$pathname/$file" . '"';
 701           }
 702           continue;
 703         }
 704         // Do a dry run of its contents and check for errors and match requests.
 705         $tmp = receive_hl7_results($hl7, $ppid, $pprow['direction'], true, $info["$ppid/$file"]['select']);
 706         $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
 707         $info["$ppid/$file"]['match'] = $tmp['match'];
 708         if (!empty($tmp['fatal']) || !empty($tmp['match'])) {
 709           // There are errors or matching requests so skip this file.
 710           continue;
 711         }
 712         // Now the money shot - not a dry run.
 713         $tmp = receive_hl7_results($hl7, $ppid, $pprow['direction'], false, $info["$ppid/$file"]['select']);
 714         $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
 715         $info["$ppid/$file"]['match'] = $tmp['match'];
 716         if (empty($tmp['fatal']) && empty($tmp['match'])) {
 717           // It worked, archive and delete the file.
 718           $fh = fopen("$prpath/$file", 'w');
 719           if ($fh) {
 720             fwrite($fh, $hl7);
 721             fclose($fh);
 722           }
 723           else {
 724             return xl('Cannot create file') . ' "' . "$prpath/$file" . '"';
 725           }
 726           if (!$sftp->delete("$pathname/$file")) {
 727             return xl('Cannot delete (from SFTP server) file') . ' "' . "$pathname/$file" . '"';
 728           }
 729         }
 730       } // end of this file
 731     } // end SFTP
 732
 733     else if ($protocol == 'FS') {
 734       // Filesystem directory containing results files.
 735       $pathname = $pprow['results_path'];
 736       if (!($dh = opendir($pathname))) {
 737         return xl('Unable to access directory') . " '$pathname'";
 738       }
 739       // Sort by filename just because.
 740       $files = array();
 741       while (false !== ($file = readdir($dh))) {
 742         if (substr($file, 0, 1) == '.') continue;
 743         $files[$file] = $file;
 744       }
 745       closedir($dh);
 746       ksort($files);
 747       // For each file...
 748       foreach ($files as $file) {
 749         ++$filecount;
 750         if (!isset($info["$ppid/$file"])) $info["$ppid/$file"] = array();
 751         // Ensure that archive directory exists.
 752         $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
 753         if (!file_exists($prpath)) mkdir($prpath);
 754         $prpath .= '/' . $pprow['ppid'];
 755         if (!file_exists($prpath)) mkdir($prpath);
 756         // Get file contents.
 757         $hl7 = file_get_contents("$pathname/$file");
 758         // If user requested reject and delete, do that.
 759         if (!empty($info["$ppid/$file"]['delete'])) {
 760           $fh = fopen("$prpath/$file.rejected", 'w');
 761           if ($fh) {
 762             fwrite($fh, $hl7);
 763             fclose($fh);
 764           }
 765           else {
 766             return xl('Cannot create file') . ' "' . "$prpath/$file.rejected" . '"';
 767           }
 768           if (!unlink("$pathname/$file")) {
 769             return xl('Cannot delete file') . ' "' . "$pathname/$file" . '"';
 770           }
 771           continue;
 772         }
 773         // Do a dry run of its contents and check for errors and match requests.
 774         $tmp = receive_hl7_results($hl7, $ppid, $pprow['direction'], true, $info["$ppid/$file"]['select']);
 775         $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
 776         $info["$ppid/$file"]['match'] = $tmp['match'];
 777         if (!empty($tmp['fatal']) || !empty($tmp['match'])) {
 778           // There are errors or matching requests so skip this file.
 779           continue;
 780         }
 781         // Now the money shot - not a dry run.
 782         $tmp = receive_hl7_results($hl7, $ppid, $pprow['direction'], false, $info["$ppid/$file"]['select']);
 783         $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
 784         $info["$ppid/$file"]['match'] = $tmp['match'];
 785         if (empty($tmp['fatal']) && empty($tmp['match'])) {
 786           // It worked, archive and delete the file.
 787           $fh = fopen("$prpath/$file", 'w');
 788           if ($fh) {
 789             fwrite($fh, $hl7);
 790             fclose($fh);
 791           }
 792           else {
 793             return xl('Cannot create file') . ' "' . "$prpath/$file" . '"';
 794           }
 795           if (!unlink("$pathname/$file")) {
 796             return xl('Cannot delete file') . ' "' . "$pathname/$file" . '"';
 797           }
 798         }
 799       } // end of this file
 800     } // end FS protocol
 801
 802     // TBD: Insert "else if ($protocol == '???') {...}" to support other protocols.
 803
 804   } // end procedure provider
 805
 806   // echo "<!-- out: "; print_r($info); echo " -->\n"; // debugging
 807
 808   return '';
 809 }
 810 // PHP end tag omitted intentionally.
 811