Highway to PSR2

[openemr.git] / interface / orders / receive_hl7_results.inc.php

<?php
/**
* Functions to support parsing and saving hl7 results.
*
* Copyright (C) 2013-2016 Rod Roark <rod@sunsetsystems.com>
*
* 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   OpenEMR
* @author    Rod Roark <rod@sunsetsystems.com>
*
* 07-2015: Ensoftek: Edited for MU2 170.314(b)(5)(A)
*/

require_once("$srcdir/forms.inc");

$rhl7_return = array();

function rhl7LogMsg($msg, $fatal = true)
{
    global $rhl7_return;
    if ($fatal) {
        $rhl7_return['mssgs'][] = '*' . $msg;
        $rhl7_return['fatal'] = true;
        newEvent("lab-results-error", $_SESSION['authUser'], $_SESSION['authProvider'], 0, $msg);
    } else {
        $rhl7_return['mssgs'][] = '>' . $msg;
    }

    return $rhl7_return;
}

function rhl7InsertRow(&$arr, $tablename)
{
    if (empty($arr)) {
        return;
    }

  // echo "<!-- ";   // debugging
  // print_r($arr);
  // echo " -->\n";

    $query = "INSERT INTO $tablename SET";
    $binds = array();
    $sep = '';
    foreach ($arr as $key => $value) {
        $query .= "$sep `$key` = ?";
        $sep = ',';
        $binds[] = $value;
    }

    $arr = array();
    return sqlInsert($query, $binds);
}

// Write all of the accumulated reports and their results.
function rhl7FlushMain(&$amain, $commentdelim = "\n")
{
    foreach ($amain as $arr) {
        $procedure_report_id = rhl7InsertRow($arr['rep'], 'procedure_report');
        foreach ($arr['res'] as $ares) {
            $ares['procedure_report_id'] = $procedure_report_id;
            // obxkey was used to identify parent results but is not stored.
            unset($ares['obxkey']);
            // If TX result is not over 10 characters, move it from comments to result field.
            if ($ares['result'] === '' && $ares['result_data_type'] == 'L') {
                $i = strpos($ares['comments'], $commentdelim);
                if ($i && $i <= 10) {
                    $ares['result'  ] = substr($ares['comments'], 0, $i);
                    $ares['comments'] = substr($ares['comments'], $i);
                }
            }

            rhl7InsertRow($ares, 'procedure_result');
        }
    }
}

// Write the MDM document if appropriate.
//
function rhl7FlushMDM($patient_id, $mdm_docname, $mdm_datetime, $mdm_text, $mdm_category_id, $provider)
{
    if ($patient_id) {
        if (!empty($mdm_docname)) {
            $mdm_docname .= '_';
        }

        $mdm_docname .= preg_replace('/[^0-9]/', '', $mdm_datetime);
        $filename = $mdm_docname . '.txt';
        $d = new Document();
        $rc = $d->createDocument($patient_id, $mdm_category_id, $filename, 'text/plain', $mdm_text);
        if (!$rc) {
            rhl7LogMsg(xl('Document created') . ": $filename", false);
            if ($provider) {
                $d->postPatientNote($provider, $mdm_category_id, xl('Electronic document received'));
                rhl7LogMsg(xl('Notification sent to') . ": $provider", false);
            } else {
                rhl7LogMsg(xl('No provider was matched'), false);
            }
        }

        return $rc;
    }

    return '';
}

function rhl7Text($s, $allow_newlines = false)
{
    $s = str_replace('\\S\\', '^', $s);
    $s = str_replace('\\F\\', '|', $s);
    $s = str_replace('\\R\\', '~', $s);
    $s = str_replace('\\T\\', '&', $s);
    $s = str_replace('\\X0d\\', "\r", $s);
    $s = str_replace('\\E\\', '\\', $s);
    if ($allow_newlines) {
        $s = str_replace('\\.br\\', "\n", $s);
    } else {
        $s = str_replace('\\.br\\', '~', $s);
    }

    return $s;
}

function rhl7DateTime($s)
{
  // Remove UTC offset if present.
    if (preg_match('/^([0-9.]+)[+-]/', $s, $tmp)) {
        $s = $tmp[1];
    }

    $s = preg_replace('/[^0-9]/', '', $s);
    if (empty($s)) {
        return '0000-00-00 00:00:00';
    }

    $ret = substr($s, 0, 4) . '-' . substr($s, 4, 2) . '-' . substr($s, 6, 2);
    if (strlen($s) > 8) {
        $ret .= ' ' . substr($s, 8, 2) . ':' . substr($s, 10, 2) . ':';
        if (strlen($s) > 12) {
            $ret .= substr($s, 12, 2);
        } else {
            $ret .= '00';
        }
    }

    return $ret;
}

function rhl7DateTimeZone($s)
{
  // UTC offset if present always begins with "+" or "-".
    if (preg_match('/^[0-9.]+([+-].*)$/', $s, $tmp)) {
        return trim($tmp[1]);
    }

    return '';
}

function rhl7Date($s)
{
    return substr(rhl7DateTime($s), 0, 10);
}

function rhl7Abnormal($s)
{
    if ($s == '') {
        return 'no';
    }

    if ($s == 'N') {
        return 'no';
    }

    if ($s == 'A') {
        return 'yes';
    }

    if ($s == 'H') {
        return 'high';
    }

    if ($s == 'L') {
        return 'low';
    }

    if ($s == 'HH') {
        return 'vhigh';
    }

    if ($s == 'LL') {
        return 'vlow';
    }

    return rhl7Text($s);
}

function rhl7ReportStatus($s)
{
    if ($s == 'F') {
        return 'final';
    }

    if ($s == 'P') {
        return 'prelim';
    }

    if ($s == 'C') {
        return 'correct';
    }

    if ($s == 'X') {
        return 'error';
    }

    return rhl7Text($s);
}

/**
 * Convert a lower case file extension to a MIME type.
 * The extension comes from OBX[5][0] which is itself a huge assumption that
 * the HL7 2.3 standard does not help with. Don't be surprised when we have to
 * adapt to conventions of various other labs.
 *
 * @param  string  $fileext  The lower case extension.
 * @return string            MIME type.
 */
function rhl7MimeType($fileext)
{
    if ($fileext == 'pdf') {
        return 'application/pdf';
    }

    if ($fileext == 'doc') {
        return 'application/msword';
    }

    if ($fileext == 'rtf') {
        return 'application/rtf';
    }

    if ($fileext == 'txt') {
        return 'text/plain';
    }

    if ($fileext == 'zip') {
        return 'application/zip';
    }

    return 'application/octet-stream';
}

/**
 * Extract encapsulated document data according to its encoding type.
 *
 * @param  string  $enctype  Encoding type from OBX[5][3].
 * @param  string  &$src     Encoded data  from OBX[5][4].
 * @return string            Decoded data, or FALSE if error.
 */
function rhl7DecodeData($enctype, &$src)
{
    if ($enctype == 'Base64') {
        return base64_decode($src);
    }

    if ($enctype == 'A') {
        return rhl7Text($src);
    }

    if ($enctype == 'Hex') {
        $data = '';
        for ($i = 0; $i < strlen($src) - 1; $i += 2) {
            $data .= chr(hexdec($src[$i] . $src[$i+1]));
        }

        return $data;
    }

    return false;
}

function rhl7CWE($s, $componentdelimiter)
{
    $out = '';
    if ($s === '') {
        return $out;
    }

    $arr = explode($componentdelimiter, $s);
    if (!empty($arr[8])) {
        $out = $arr[8];
    } else {
        $out = $arr[0];
        if (isset($arr[1])) {
            $out .= " (" . $arr[1] . ")";
        }
    }

    return $out;
}

/**
 * Parse the SPM segment and get the specimen display name and update the table.
 *
 * @param  string  $specimen  Encoding type from SPM.
 */
function rhl7UpdateReportWithSpecimen(&$amain, $specimen, $d2)
{
    $specimen_display = '';

  // SPM4: Specimen Type: Example: 119297000^BLD^SCT^BldSpc^Blood^99USA^^^Blood Specimen
    $specimen_display = rhl7CWE($specimen[4], $d2);

    $tmpnotes = xl('Specimen type') . ': ' . $specimen_display;
    $tmp = rhl7CWE($specimen[21], $d2);
    if ($tmp) {
        $tmpnotes .= '; ' . xl('Rejected') . ': ' . $tmp;
    }

    $tmp = rhl7CWE($specimen[24], $d2);
    if ($tmp) {
        $tmpnotes .= '; ' . xl('Condition') . ': ' . $tmp;
    }

    $alast = count($amain) - 1;
    $amain[$alast]['rep']['specimen_num'] = $specimen_display;
    $amain[$alast]['rep']['report_notes'] .= rhl7Text($tmpnotes) . "\n";
}

/**
 * Get the Performing Lab Details from the OBX segment. Mandatory for MU2.
 *
 * @param  string  $obx23  Encoding type from OBX23.
 * @param  string  $obx23  Encoding type from OBX24.
 * @param  string  $obx23  Encoding type from OBX25.
 * @param  string  $obx23  New line character.
 */
function getPerformingOrganizationDetails($obx23, $obx24, $obx25, $componentdelimiter, $commentdelim)
{
    $s = null;

    if (!empty($obx23) || !empty($obx24) || !empty($obx25)) {
        // Organization Name
        // OBX23 Example: "Century Hospital^^^^^NIST-AA-1&2.16.840.1.113883.3.72.5.30.1&ISO^XX^^^987"
        $obx23_segs = explode($componentdelimiter, $obx23);
        if (!empty($obx23_segs[0])) {
            $s .= $obx23_segs[0] . $commentdelim;
        }

        // Medical Director
        // OBX25 Example: "2343242^Knowsalot^Phil^J.^III^Dr.^^^NIST-AA-1&2.16.840.1.113883.3.72.5.30.1&ISO^L^^^DNSPM"
        //             Dr. Phil Knowsalot J. III
        if (!empty($obx25)) {
            $obx25_segs = explode($componentdelimiter, $obx25);
            $s .= "$obx25_segs[5] $obx25_segs[2] $obx25_segs[1] $obx25_segs[3] $obx25_segs[4]" . $commentdelim;
        }

        // Organization Address
        // OBX24 Example: "2070 Test Park^^Los Angeles^CA^90067^USA^B^^06037"
        if (!empty($obx24)) {
            $obx24_segs = explode($componentdelimiter, $obx24);
            //$s .= "$obx24_segs[0] $obx24_segs[1], $obx24_segs[2], $obx24_segs[3], $obx24_segs[4], $obx24_segs[5]" . $commentdelim;
            $s .= "$obx24_segs[0]$commentdelim$obx24_segs[2], $obx24_segs[3] $obx24_segs[4]$commentdelim$obx24_segs[5]$commentdelim";
            if (!empty($obx24_segs[8])) {
                $s .= "County/Parish Code: $obx24_segs[8]$commentdelim";
            }
        }
    }

    return $s;
}

/**
 * Look for a patient matching the given data.
 * Return values are:
 *  >0  Definite match, this is the pid.
 *   0  No patient is close to a match.
 *  -1  It's not clear if there is a match.
 */
function match_patient($ptarr)
{
    $in_ss = str_replace('-', '', $ptarr['ss']);
    $in_fname = $ptarr['fname'];
    $in_lname = $ptarr['lname'];
    $in_dob = $ptarr['DOB'];
    $patient_id = 0;
    $res = sqlStatement(
        "SELECT pid FROM patient_data WHERE " .
        "((ss IS NULL OR ss = '' OR '' = ?) AND " .
        "fname IS NOT NULL AND fname != '' AND fname = ? AND " .
        "lname IS NOT NULL AND lname != '' AND lname = ? AND " .
        "DOB IS NOT NULL AND DOB = ?) OR " .
        "(ss IS NOT NULL AND ss != '' AND REPLACE(ss, '-', '') = ? AND (" .
        "fname IS NOT NULL AND fname != '' AND fname = ? OR " .
        "lname IS NOT NULL AND lname != '' AND lname = ? OR " .
        "DOB IS NOT NULL AND DOB = ?)) " .
        "ORDER BY ss DESC, pid DESC LIMIT 2",
        array($in_ss, $in_fname, $in_lname, $in_dob, $in_ss, $in_fname, $in_lname, $in_dob)
    );
    if (sqlNumRows($res) > 1) {
        // Multiple matches, so ambiguous.
        $patient_id = -1;
    } else if (sqlNumRows($res) == 1) {
        // Got exactly one match, so use it.
        $tmp = sqlFetchArray($res);
        $patient_id = intval($tmp['pid']);
    } else {
        // No match good enough, figure out if there's enough ambiguity to ask the user.
        $tmp = sqlQuery(
            "SELECT pid FROM patient_data WHERE " .
            "(ss IS NOT NULL AND ss != '' AND REPLACE(ss, '-', '') = ?) OR " .
            "(fname IS NOT NULL AND fname != '' AND fname = ? AND " .
            "lname IS NOT NULL AND lname != '' AND lname = ?) OR " .
            "(DOB IS NOT NULL AND DOB = ?) " .
            "LIMIT 1",
            array($in_ss, $in_fname, $in_lname, $in_dob)
        );
        if (!empty($tmp['pid'])) {
              $patient_id = -1;
        }
    }

    return $patient_id;
}

/**
 * Look for a local provider matching the given XCN field from some segment.
 *
 * @param  array  $arr  array(NPI, lastname, firstname) identifying a provider.
 * @return mixed        Array(id, username), or FALSE if no match.
 */
function match_provider($arr)
{
    if (empty($arr)) {
        return false;
    }

    $op_lname = $op_fname = '';
    $op_npi = preg_replace('/[^0-9]/', '', $arr[0]);
    if (!empty($arr[1])) {
        $op_lname = $arr[1];
    }

    if (!empty($arr[2])) {
        $op_fname = $arr[2];
    }

    if ($op_npi || ($op_fname && $op_lname)) {
        if ($op_npi) {
            if ($op_fname && $op_lname) {
                $where = "((npi IS NOT NULL AND npi = ?) OR ((npi IS NULL OR npi = ?) AND lname = ? AND fname = ?))";
                $qarr = array($op_npi, '', $op_lname, $op_fname);
            } else {
                $where = "npi IS NOT NULL AND npi = ?";
                $qarr = array($op_npi);
            }
        } else {
            $where = "lname = ? AND fname = ?";
            $qarr = array($op_lname, $op_fname);
        }

        $oprow = sqlQuery(
            "SELECT id, username FROM users WHERE " .
            "username IS NOT NULL AND username != '' AND $where " .
            "ORDER BY active DESC, authorized DESC, username, id LIMIT 1",
            $qarr
        );
        if (!empty($oprow)) {
            return $oprow;
        }
    }

    return false;
}

/**
 * Create a patient using whatever patient_data attributes are provided.
 */
function create_skeleton_patient($patient_data)
{
    $employer_data = array();
    $tmp = sqlQuery("SELECT MAX(pid)+1 AS pid FROM patient_data");
    $ptid = empty($tmp['pid']) ? 1 : intval($tmp['pid']);
    if (!isset($patient_data['pubpid'])) {
        $patient_data['pubpid'] = $ptid;
    }

    updatePatientData($ptid, $patient_data, true);
    updateEmployerData($ptid, $employer_data, true);
    newHistoryData($ptid);
    return $ptid;
}

/**
 * Parse and save.
 *
 * @param  string  &$hl7      The input HL7 text
 * @param  string  &$matchreq Array of shared patient matching requests
 * @param  int     $lab_id    Lab ID
 * @param  char    $direction B=Bidirectional, R=Results-only
 * @param  bool    $dryrun    True = do not update anything, just report errors
 * @param  array   $matchresp Array of responses to match requests; key is relative segment number,
 *                            value is an existing pid or 0 to specify creating a patient
 * @return array              Array of errors and match requests, if any
 */
function receive_hl7_results(&$hl7, &$matchreq, $lab_id = 0, $direction = 'B', $dryrun = false, $matchresp = null)
{
    global $rhl7_return;

  // This will hold returned error messages and related variables.
    $rhl7_return = array();
    $rhl7_return['mssgs'] = array();
    $rhl7_return['needmatch'] = false; // indicates if this file is pending a match request

    $rhl7_segnum = 0;

    if (substr($hl7, 0, 3) != 'MSH') {
        return rhl7LogMsg(xl('Input does not begin with a MSH segment'), true);
    }

  // This array holds everything to be written to the database.
  // We save and postpone these writes in case of errors while processing the message,
  // so we can look up data from parent results when child results are encountered,
  // and for other logic simplification.
  // Each element of this array is another array containing the following possible keys:
  // 'rep' - row of data to write to procedure_report
  // 'res' - array of rows to write to procedure_result for this procedure_report
  // 'fid' - unique lab-provided identifier for this report
  //
    $amain = array();

  // End-of-line delimiter for text in procedure_result.comments and other multi-line notes.
    $commentdelim = "\n";

  // Ensoftek: Different labs seem to send different EOLs. Edit HL7 input to a character we know.
    $hl7 = (string)str_replace(array("\r\n", "\r", "\n"), "\r", $hl7);

    $today = time();

    $in_message_id = '';
    $in_ssn = '';
    $in_dob = '';
    $in_lname = '';
    $in_fname = '';
    $in_orderid = 0;
    $in_procedure_code = '';
    $in_report_status = '';
    $in_encounter = 0;
    $patient_id = 0; // for results-only patient matching logic
    $porow = false;
    $pcrow = false;
    $oprow = false;

    $code_seq_array = array(); // tracks sequence numbers of order codes
    $results_category_id = 0;  // document category ID for lab results

  // This is so we know where we are if a segment like NTE that can appear in
  // different places is encountered.
    $context = '';

  // This will be "ORU" or "MDM".
    $msgtype = '';

  // Stuff collected for MDM documents.
    $mdm_datetime = '';
    $mdm_docname = '';
    $mdm_text = '';

  // Delimiters
    $d0 = "\r";
    $d1 = substr($hl7, 3, 1); // typically |
    $d2 = substr($hl7, 4, 1); // typically ^
    $d3 = substr($hl7, 5, 1); // typically ~
    $d4 = substr($hl7, 6, 1); // typically \
    $d5 = substr($hl7, 7, 1); // typically &

  // We'll need the document category IDs for any embedded documents.
    $catrow = sqlQuery(
        "SELECT id FROM categories WHERE name = ?",
        array($GLOBALS['lab_results_category_name'])
    );
    if (empty($catrow['id'])) {
        return rhl7LogMsg(xl('Document category for lab results does not exist') .
        ': ' . $GLOBALS['lab_results_category_name'], true);
    } else {
        $results_category_id = $catrow['id'];
        $mdm_category_id = $results_category_id;
        $catrow = sqlQuery(
            "SELECT id FROM categories WHERE name = ?",
            array($GLOBALS['gbl_mdm_category_name'])
        );
        if (!empty($catrow['id'])) {
            $mdm_category_id = $catrow['id'];
        }
    }

    $segs = explode($d0, $hl7);

    foreach ($segs as $seg) {
        if (empty($seg)) {
            continue;
        }

        // echo "<!-- $dryrun $seg -->\n"; // debugging

        ++$rhl7_segnum;
        $a = explode($d1, $seg);

        if ($a[0] == 'MSH') {
            if (!$dryrun) {
                rhl7FlushMain($amain, $commentdelim);
            }

            $amain = array();

            if ('MDM' == $msgtype && !$dryrun) {
                $rc = rhl7FlushMDM(
                    $patient_id,
                    $mdm_docname,
                    $mdm_datetime,
                    $mdm_text,
                    $mdm_category_id,
                    $oprow ? $oprow['username'] : 0
                );
                if ($rc) {
                    return rhl7LogMsg($rc);
                }

                $patient_id = 0;
            }

            $context = $a[0];
            // Ensoftek: Could come is as 'ORU^R01^ORU_R01'. Handle all cases when 'ORU^R01' is seen.
            if (strstr($a[8], "ORU^R01")) {
                $msgtype = 'ORU';
            } else if ($a[8] == 'MDM^T02' || $a[8] == 'MDM^T04' || $a[8] == 'MDM^T08') {
                $msgtype = 'MDM';
                $mdm_datetime = '';
                $mdm_docname = '';
                $mdm_text = '';
            } else {
                return rhl7LogMsg(xl('MSH.8 message type is not supported') . ": '" . $a[8] . "'", true);
            }

            $in_message_id = $a[9];
        } else if ($a[0] == 'PID') {
            $context = $a[0];

            if ('MDM' == $msgtype && !$dryrun) {
                $rc = rhl7FlushMDM(
                    $patient_id,
                    $mdm_docname,
                    $mdm_datetime,
                    $mdm_text,
                    $mdm_category_id,
                    $oprow ? $oprow['username'] : 0
                );
                if ($rc) {
                    return rhl7LogMsg($rc);
                }
            }

            $porow = false;
            $pcrow = false;
            $oprow = false;
            $in_orderid = 0;
            $in_ssn = preg_replace('/[^0-9]/', '', $a[4]);
            $in_dob = rhl7Date($a[7]);
            $tmp = explode($d2, $a[5]);
            $in_lname = rhl7Text($tmp[0]);
            $in_fname = rhl7Text($tmp[1]);
            $in_mname = rhl7Text($tmp[2]);
            $patient_id = 0;
            // Patient matching is needed for a results-only interface or MDM message type.
            if ('R' == $direction || 'MDM' == $msgtype) {
                $ptarr = array('ss' => strtoupper($in_ss), 'fname' => strtoupper($in_fname),
                'lname' => strtoupper($in_lname), 'mname' => strtoupper($in_mname),
                'DOB' => strtoupper($in_dob));
                $patient_id = match_patient($ptarr);
                if ($patient_id == -1) {
                        // Result is indeterminate.
                        // Make a stringified form of $ptarr to use as a key.
                        $ptstring = serialize($ptarr);
                        // Check if the user has specified the patient.
                    if (isset($matchresp[$ptstring])) {
                        // This will be an existing pid, or 0 to specify creating a patient.
                        $patient_id = intval($matchresp[$ptstring]);
                    } else {
                        if ($dryrun) {
                            // Nope, ask the user to match.
                            $matchreq[$ptstring] = true;
                            $rhl7_return['needmatch'] = true;
                        } else {
                            // Should not happen, but it would be bad to abort now.  Create the patient.
                            $patient_id = 0;
                            rhl7LogMsg(xl('Unexpected non-match, creating new patient for segment') .
                              ' ' . $rhl7_segnum, false);
                        }
                    }
                }

                if ($patient_id == 0 && !$dryrun) {
                          // We must create the patient.
                          $patient_id = create_skeleton_patient($ptarr);
                }

                if ($patient_id == -1) {
                    $patient_id = 0;
                }
            } // end results-only/MDM logic
        } else if ('PD1' == $a[0]) {
            // TBD: Save primary care provider name ($a[4]) somewhere?
        } else if ('PV1' == $a[0]) {
            if ('ORU' == $msgtype) {
                // Save placer encounter number if present.
                if ($direction != 'R' && !empty($a[19])) {
                    $tmp = explode($d2, $a[19]);
                    $in_encounter = intval($tmp[0]);
                }
            } else if ('MDM' == $msgtype) {
                // For documents we want the ordering provider.
                // Try Referring Provider first.
                $oprow = match_provider(explode($d2, $a[8]));
                // If no match, try Other Provider.
                if (empty($oprow)) {
                    $oprow = match_provider(explode($d2, $a[52]));
                }
            }
        } else if ('ORC' == $a[0] && 'ORU' == $msgtype) {
            $context = $a[0];
            $arep = array();
            $porow = false;
            $pcrow = false;
            if ($direction != 'R' && $a[2]) {
                $in_orderid = intval($a[2]);
            }
        } else if ('TXA' == $a[0] && 'MDM' == $msgtype) {
            $context = $a[0];
            $mdm_datetime = rhl7DateTime($a[4]);
            $mdm_docname = rhl7Text($a[12]);
        } else if ($a[0] == 'NTE' && ($context == 'ORC' || $context == 'TXA')) {
            // Is this ever used?
        } else if ('OBR' == $a[0] && 'ORU' == $msgtype) {
            $context = $a[0];
            $arep = array();
            if ($direction != 'R' && $a[2]) {
                $in_orderid = intval($a[2]);
                $porow = false;
                $pcrow = false;
            }

            $tmp = explode($d2, $a[4]);
            $in_procedure_code = $tmp[0];
            $in_procedure_name = $tmp[1];
            $in_report_status = rhl7ReportStatus($a[25]);

            // Filler identifier is supposed to be unique for each incoming report.
            $in_filler_id = $a[3];
            // Child results will have these pointers to their parent.
            $in_parent_obrkey = '';
            $in_parent_obxkey = '';
            $parent_arep = false; // parent report, if any
            $parent_ares = false; // parent result, if any
            if (!empty($a[29])) {
                // This is a child so there should be a parent.
                $tmp = explode($d2, $a[29]);
                $in_parent_obrkey = str_replace($d5, $d2, $tmp[1]);
                $tmp = explode($d2, $a[26]);
                $in_parent_obxkey = str_replace($d5, $d2, $tmp[0]) . $d1 . $tmp[1];
                // Look for the parent report.
                foreach ($amain as $arr) {
                    if (isset($arr['fid']) && $arr['fid'] == $in_parent_obrkey) {
                        $parent_arep = $arr['rep'];
                        // Now look for the parent result within that report.
                        foreach ($arr['res'] as $tmpres) {
                            if (isset($tmpres['obxkey']) && $tmpres['obxkey'] == $in_parent_obxkey) {
                                $parent_ares = $tmpres;
                                break;
                            }
                        }

                        break;
                    }
                }
            }

            if ($parent_arep) {
                $in_orderid = $parent_arep['procedure_order_id'];
            }

            if ($direction == 'R') {
                // Save their order ID to procedure_order.control_id.
                // Look for an existing order using that plus lab_id.
                // Ordering provider is OBR.16 (NPI^Last^First).
                // Might not need to create a dummy encounter.
                // Need also provider_id (probably), patient_id, date_ordered, lab_id.
                // We have observation date/time in OBR.7.
                // We have report date/time in OBR.22.
                // We do not have an order date.

                $external_order_id = empty($a[2]) ? $a[3] : $a[2];
                $porow = false;

                if (!$in_orderid && $external_order_id) {
                    $porow = sqlQuery(
                        "SELECT * FROM procedure_order " .
                        "WHERE lab_id = ? AND control_id = ? " .
                        "ORDER BY procedure_order_id DESC LIMIT 1",
                        array($lab_id, $external_order_id)
                    );
                }

                if (!empty($porow)) {
                    $in_orderid = intval($porow['procedure_order_id']);
                }

                if (!$in_orderid) {
                    // Create order.
                    // Need to identify the ordering provider and, if possible, a recent encounter.
                    $datetime_report = rhl7DateTime($a[22]);
                    $date_report = substr($datetime_report, 0, 10) . ' 00:00:00';
                    $encounter_id = 0;
                    $provider_id = 0;
                    // Look for the most recent encounter within 30 days of the report date.
                    $encrow = sqlQuery(
                        "SELECT encounter FROM form_encounter WHERE " .
                        "pid = ? AND date <= ? AND DATE_ADD(date, INTERVAL 30 DAY) > ? " .
                        "ORDER BY date DESC, encounter DESC LIMIT 1",
                        array($patient_id, $date_report, $date_report)
                    );
                    if (!empty($encrow)) {
                              $encounter_id = intval($encrow['encounter']);
                              $provider_id = intval($encrow['provider_id']);
                    }

                    if (!$provider_id) {
                              // Attempt ordering provider matching by name or NPI.
                              $oprow = match_provider(explode($d2, $a[16]));
                        if (!empty($oprow)) {
                            $provider_id = intval($oprow['id']);
                        }
                    }

                    if (!$dryrun) {
                              // Now create the procedure order.
                              $in_orderid = sqlInsert(
                                  "INSERT INTO procedure_order SET " .
                                  "date_ordered   = ?, " .
                                  "provider_id    = ?, " .
                                  "lab_id         = ?, " .
                                  "date_collected = ?, " .
                                  "date_transmitted = ?, " .
                                  "patient_id     = ?, " .
                                  "encounter_id   = ?, " .
                                  "control_id     = ?",
                                  array($datetime_report, $provider_id, $lab_id, rhl7DateTime($a[22]),
                                  rhl7DateTime($a[7]),
                                  $patient_id,
                                  $encounter_id,
                                  $external_order_id)
                              );
                              // If an encounter was identified then link the order to it.
                        if ($encounter_id && $in_orderid) {
                                              addForm($encounter_id, "Procedure Order", $in_orderid, "procedure_order", $patient_id);
                        }
                    }
                } // end no $porow
            } // end results-only
            if (empty($porow)) {
                $porow = sqlQuery("SELECT * FROM procedure_order WHERE " .
                "procedure_order_id = ?", array($in_orderid));
                // The order must already exist. Currently we do not handle electronic
                // results returned for manual orders.
                if (empty($porow) && !($dryrun && $direction == 'R')) {
                        return rhl7LogMsg(xl('Procedure order not found') . ": $in_orderid", true);
                }

                if ($in_encounter) {
                    if ($direction != 'R' && $porow['encounter_id'] != $in_encounter) {
                        return rhl7LogMsg(xl('Encounter ID') .
                          " '" . $porow['encounter_id'] . "' " .
                          xl('for OBR placer order number') .
                          " '$in_orderid' " .
                          xl('does not match the PV1 encounter number') .
                          " '$in_encounter'");
                    }
                } else {
                          // They did not return an encounter number to verify, so more checking
                          // might be done here to make sure the patient seems to match.
                }

                // Save the lab's control ID if there is one.
                $tmp = explode($d2, $a[3]);
                $control_id = $tmp[0];
                if ($control_id && empty($porow['control_id'])) {
                          sqlStatement("UPDATE procedure_order SET control_id = ? WHERE " .
                            "procedure_order_id = ?", array($control_id, $in_orderid));
                }

                $code_seq_array = array();
            }

            // Find the order line item (procedure code) that matches this result.
            // If there is more than one, then we select the one whose sequence number
            // is next after the last sequence number encountered for this procedure
            // code; this assumes that result OBRs are returned in the same sequence
            // as the corresponding OBRs in the order.
            if (!isset($code_seq_array[$in_procedure_code])) {
                $code_seq_array[$in_procedure_code] = 0;
            }

            $pcquery = "SELECT pc.* FROM procedure_order_code AS pc " .
            "WHERE pc.procedure_order_id = ? AND pc.procedure_code = ? " .
            "ORDER BY (procedure_order_seq <= ?), procedure_order_seq LIMIT 1";
            $pcqueryargs = array($in_orderid, $in_procedure_code, $code_seq_array[$in_procedure_code]);
            $pcrow = sqlQuery($pcquery, $pcqueryargs);
            if (empty($pcrow)) {
                // There is no matching procedure in the order, so it must have been
                // added after the original order was sent, either as a manual request
                // from the physician or as a "reflex" from the lab.
                // procedure_source = '2' indicates this.
                if (!$dryrun) {
                    sqlBeginTrans();
                    $procedure_order_seq = sqlQuery("SELECT IFNULL(MAX(procedure_order_seq),0) + 1 AS increment FROM procedure_order_code WHERE procedure_order_id = ? ", array($in_orderid));
                    sqlInsert(
                        "INSERT INTO procedure_order_code SET " .
                        "procedure_order_id = ?, " .
                        "procedure_order_seq = ?, " .
                        "procedure_code = ?, " .
                        "procedure_name = ?, " .
                        "procedure_source = '2'",
                        array($in_orderid, $procedure_order_seq['increment'], $in_procedure_code, $in_procedure_name)
                    );
                    $pcrow = sqlQuery($pcquery, $pcqueryargs);
                    sqlCommitTrans();
                } else {
                    // Dry run, make a dummy procedure_order_code row.
                    $pcrow = array(
                    'procedure_order_id' => $in_orderid,
                    'procedure_order_seq' => 0, // TBD?
                    );
                }
            }

            $code_seq_array[$in_procedure_code] = 0 + $pcrow['procedure_order_seq'];
            $arep = array();
            $arep['procedure_order_id'] = $in_orderid;
            $arep['procedure_order_seq'] = $pcrow['procedure_order_seq'];
            $arep['date_collected'] = rhl7DateTime($a[7]);
            $arep['date_collected_tz'] = rhl7DateTimeZone($a[7]);
            $arep['date_report'] = rhl7DateTime($a[22]);
            $arep['date_report_tz'] = rhl7DateTimeZone($a[22]);
            $arep['report_status'] = $in_report_status;
            $arep['report_notes'] = '';
            $arep['specimen_num'] = '';

            // If this is a child report, add some info from the parent.
            if (!empty($parent_ares)) {
                $arep['report_notes'] .= xl('This is a child of result') . ' ' .
                $parent_ares['result_code'] . ' ' . xl('with value') . ' "' .
                $parent_ares['result'] . '".' . "\n";
            }

            if (!empty($parent_arep)) {
                $arep['report_notes'] .= $parent_arep['report_notes'];
                $arep['specimen_num']  = $parent_arep['specimen_num'];
            }

            // Create the main array entry for this report and its results.
            $i = count($amain);
            $amain[$i] = array();
            $amain[$i]['rep'] = $arep;
            $amain[$i]['fid'] = $in_filler_id;
            $amain[$i]['res'] = array();
        } else if ($a[0] == 'NTE' && $context == 'OBR') {
            // Append this note to those for the most recent report.
            $amain[count($amain)-1]['rep']['report_notes'] .= rhl7Text($a[3], true) . "\n";
        } else if ('OBX' == $a[0] && 'ORU' == $msgtype) {
            $tmp = explode($d2, $a[3]);
            $result_code = rhl7Text($tmp[0]);
            $result_text = rhl7Text($tmp[1]);
            // If this is a text result that duplicates the previous result except
            // for its value, then treat it as an extension of that result's value.
            $i = count($amain) - 1;
            $j = count($amain[$i]['res']) - 1;
            if ($j >= 0 && $context == 'OBX' && $a[2] == 'TX'
            && $amain[$i]['res'][$j]['result_data_type'] == 'L'
            && $amain[$i]['res'][$j]['result_code'     ] == $result_code
            && $amain[$i]['res'][$j]['date'            ] == rhl7DateTime($a[14])
            && $amain[$i]['res'][$j]['facility'        ] == rhl7Text($a[15])
            && $amain[$i]['res'][$j]['abnormal'        ] == rhl7Abnormal($a[8])
            && $amain[$i]['res'][$j]['result_status'   ] == rhl7ReportStatus($a[11])
            ) {
                $amain[$i]['res'][$j]['comments'] =
                substr($amain[$i]['res'][$j]['comments'], 0, strlen($amain[$i]['res'][$j]['comments']) - 1) .
                '~' . rhl7Text($a[5]) . $commentdelim;
                continue;
            }

            $context = $a[0];
            $ares = array();
            $ares['result_data_type'] = substr($a[2], 0, 1); // N, S, F or E
            $ares['comments'] = $commentdelim;
            if ($a[2] == 'ED') {
                // This is the case of results as an embedded document. We will create
                // a normal patient document in the assigned category for lab results.
                $tmp = explode($d2, $a[5]);
                $fileext = strtolower($tmp[0]);
                $filename = date("Ymd_His") . '.' . $fileext;
                $data = rhl7DecodeData($tmp[3], $tmp[4]);
                if ($data === false) {
                    return rhl7LogMsg(xl('Invalid encapsulated data encoding type') . ': ' . $tmp[3]);
                }

                if (!$dryrun) {
                    $d = new Document();
                    $rc = $d->createDocument(
                        $porow['patient_id'],
                        $results_category_id, // TBD: Make sure not 0
                        $filename,
                        rhl7MimeType($fileext),
                        $data
                    );
                    if ($rc) {
                        return rhl7LogMsg($rc);
                    }

                    $ares['document_id'] = $d->get_id();
                }
            } else if ($a[2] == 'CWE') {
                $ares['result'] = rhl7CWE($a[5], $d2);
            } else if ($a[2] == 'SN') {
                $ares['result'] = trim(str_replace($d2, ' ', $a[5]));
            } else if ($a[2] == 'TX' || strlen($a[5]) > 200) {
                // OBX-5 can be a very long string of text with "~" as line separators.
                // The first line of comments is reserved for such things.
                $ares['result_data_type'] = 'L';
                $ares['result'] = '';
                $ares['comments'] = rhl7Text($a[5]) . $commentdelim;
            } else {
                $ares['result'] = rhl7Text($a[5]);
            }

            $ares['result_code'  ] = $result_code;
            $ares['result_text'  ] = $result_text;
            $ares['date'         ] = rhl7DateTime($a[14]);
            $ares['facility'     ] = rhl7Text($a[15]);
            // Ensoftek: Units may have mutiple segments(as seen in MU2 samples), parse and take just first segment.
            $tmp = explode($d2, $a[6]);
            $ares['units'] = rhl7Text($tmp[0]);
            $ares['range'        ] = rhl7Text($a[7]);
            $ares['abnormal'     ] = rhl7Abnormal($a[8]); // values are lab dependent
            $ares['result_status'] = rhl7ReportStatus($a[11]);

            // Ensoftek: Performing Organization Details. Goes into "Pending Review/Patient Results--->Notes--->Facility" section.
            $performingOrganization = getPerformingOrganizationDetails($a[23], $a[24], $a[25], $d2, $commentdelim);
            if (!empty($performingOrganization)) {
                $ares['facility'] .= $performingOrganization . $commentdelim;
            }

            /****
          // Probably need a better way to report this, if it matters.
          if (!empty($a[19])) {
            $ares['comments'] .= xl('Analyzed') . ' ' . rhl7DateTime($a[19]) . '.' . $commentdelim;
          }
            ****/

            // obxkey is to allow matching this as a parent result.
            $ares['obxkey'] = $a[3] . $d1 . $a[4];

            // Append this result to those for the most recent report.
            // Note the 'procedure_report_id' item is not yet present.
            $amain[count($amain)-1]['res'][] = $ares;
        } else if ('OBX' == $a[0] && 'MDM' == $msgtype) {
            $context = $a[0];
            if ($a[2] == 'TX') {
                if ($mdm_text !== '') {
                    $mdm_text .= "\r\n";
                }

                $mdm_text .= rhl7Text($a[5]);
            } else {
                return rhl7LogMsg(xl('Unsupported MDM OBX result type') . ': ' . $a[2]);
            }
        } else if ('ZEF' == $a[0] && 'ORU' == $msgtype) {
            // ZEF segment is treated like an OBX with an embedded Base64-encoded PDF.
            $context = 'OBX';
            $ares = array();
            $ares['result_data_type'] = 'E';
            $ares['comments'] = $commentdelim;
            //
            $fileext = 'pdf';
            $filename = date("Ymd_His") . '.' . $fileext;
            $data = rhl7DecodeData('Base64', $a[2]);
            if ($data === false) {
                return rhl7LogMsg(xl('ZEF segment internal error'));
            }

            if (!$dryrun) {
                $d = new Document();
                $rc = $d->createDocument(
                    $porow['patient_id'],
                    $results_category_id, // TBD: Make sure not 0
                    $filename,
                    rhl7MimeType($fileext),
                    $data
                );
                if ($rc) {
                    return rhl7LogMsg($rc);
                }

                $ares['document_id'] = $d->get_id();
            }

            $ares['date'] = $arep['date_report']; // $arep is left over from the OBR logic.
            // Append this result to those for the most recent report.
            // Note the 'procedure_report_id' item is not yet present.
            $amain[count($amain)-1]['res'][] = $ares;
        } else if ('NTE' == $a[0] && 'OBX' == $context && 'ORU' == $msgtype) {
            // Append this note to the most recent result item's comments.
            $alast = count($amain) - 1;
            $rlast = count($amain[$alast]['res']) - 1;
            $amain[$alast]['res'][$rlast]['comments'] .= rhl7Text($a[3], true) . $commentdelim;
        } // Ensoftek: Get data from SPM segment for specimen.
        // SPM segment always occurs after the OBX segment.
        else if ('SPM' == $a[0] && 'ORU' == $msgtype) {
            rhl7UpdateReportWithSpecimen($amain, $a, $d2);
        } // Add code here for any other segment types that may be present.

        // Ensoftek: Get data from SPM segment for specimen. Comes in with MU2 samples, but can be ignored.
        else if ('TQ1' == $a[0] && 'ORU' == $msgtype) {
            // Ignore and do nothing.
        } else {
            return rhl7LogMsg(xl('Segment name') . " '${a[0]}' " . xl('is misplaced or unknown'));
        }
    }

  // Write all reports and their results to the database.
  // This will do nothing if a dry run or MDM message type.
    if ('ORU' == $msgtype && !$dryrun) {
        rhl7FlushMain($amain, $commentdelim);
    }

    if ('MDM' == $msgtype && !$dryrun) {
        // Write documents.
        $rc = rhl7FlushMDM(
            $patient_id,
            $mdm_docname,
            $mdm_datetime,
            $mdm_text,
            $mdm_category_id,
            $oprow ? $oprow['username'] : 0
        );
        if ($rc) {
            return rhl7LogMsg($rc);
        }
    }

    return $rhl7_return;
}

/**
 * Poll all eligible labs for new results and store them in the database.
 *
 * @param  array   &$info  Conveys information to and from the caller:
 * FROM THE CALLER:
 * $info["$ppid/$filename"]['delete'] = a non-empty value if file deletion is requested.
 * $info['select'] = array of patient matching responses where key is serialized patient
 *   attributes and value is selected pid for this patient, or 0 to create the patient.
 * TO THE CALLER:
 * $info["$ppid/$filename"]['mssgs'] = array of messages from this function.
 * $info['match'] = array of patient matching requests where key is serialized patient
 *   attributes (ss, fname, lname, DOB) and value is TRUE (irrelevant).
 *
 * @return string  Error text, or empty if no errors.
 */
function poll_hl7_results(&$info)
{
    global $srcdir;

  // echo "<!-- post: "; print_r($_POST); echo " -->\n"; // debugging
  // echo "<!-- in:   "; print_r($info); echo " -->\n"; // debugging

    $filecount = 0;
    $badcount = 0;

    if (!isset($info['match' ])) {
        $info['match' ] = array(); // match requests
    }

    if (!isset($info['select'])) {
        $info['select'] = array(); // match request responses
    }

    $ppres = sqlStatement("SELECT * FROM procedure_providers ORDER BY name");

    while ($pprow = sqlFetchArray($ppres)) {
        $ppid        = $pprow['ppid'];
        $protocol    = $pprow['protocol'];
        $remote_host = $pprow['remote_host'];
        $hl7 = '';

        if ($protocol == 'SFTP') {
            $remote_port = 22;
            // Hostname may have ":port" appended to specify a nonstandard port number.
            if ($i = strrpos($remote_host, ':')) {
                $remote_port = 0 + substr($remote_host, $i + 1);
                $remote_host = substr($remote_host, 0, $i);
            }

            // Compute the target path name.
            $pathname = '.';
            if ($pprow['results_path']) {
                $pathname = $pprow['results_path'] . '/' . $pathname;
            }

            // Connect to the server and enumerate files to process.
            $sftp = new \phpseclib\Net\SFTP($remote_host, $remote_port);
            if (!$sftp->login($pprow['login'], $pprow['password'])) {
                return xl('Login to remote host') . " '$remote_host' " . xl('failed');
            }

            $files = $sftp->nlist($pathname);
            foreach ($files as $file) {
                if (substr($file, 0, 1) == '.') {
                    continue;
                }

                ++$filecount;
                if (!isset($info["$ppid/$file"])) {
                    $info["$ppid/$file"] = array();
                }

                // Ensure that archive directory exists.
                $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
                if (!file_exists($prpath)) {
                    mkdir($prpath);
                }

                $prpath .= '/' . $pprow['ppid'];
                if (!file_exists($prpath)) {
                    mkdir($prpath);
                }

                // Get file contents.
                $hl7 = $sftp->get("$pathname/$file");
                // If user requested reject and delete, do that.
                if (!empty($info["$ppid/$file"]['delete'])) {
                    $fh = fopen("$prpath/$file.rejected", 'w');
                    if ($fh) {
                        fwrite($fh, $hl7);
                        fclose($fh);
                    } else {
                        return xl('Cannot create file') . ' "' . "$prpath/$file.rejected" . '"';
                    }

                    if (!$sftp->delete("$pathname/$file")) {
                        return xl('Cannot delete (from SFTP server) file') . ' "' . "$pathname/$file" . '"';
                    }

                    continue;
                }

                // Do a dry run of its contents and check for errors and match requests.
                $tmp = receive_hl7_results($hl7, $info['match'], $ppid, $pprow['direction'], true, $info['select']);
                $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
                // $info["$ppid/$file"]['match'] = $tmp['match'];
                if (!empty($tmp['fatal']) || !empty($tmp['needmatch'])) {
                    // There are errors or matching requests so skip this file.
                    continue;
                }

                // Now the money shot - not a dry run.
                $tmp = receive_hl7_results($hl7, $info['match'], $ppid, $pprow['direction'], false, $info['select']);
                $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
                // $info["$ppid/$file"]['match'] = $tmp['match'];
                if (empty($tmp['fatal']) && empty($tmp['needmatch'])) {
                    // It worked, archive and delete the file.
                    $fh = fopen("$prpath/$file", 'w');
                    if ($fh) {
                        fwrite($fh, $hl7);
                        fclose($fh);
                    } else {
                        return xl('Cannot create file') . ' "' . "$prpath/$file" . '"';
                    }

                    if (!$sftp->delete("$pathname/$file")) {
                        return xl('Cannot delete (from SFTP server) file') . ' "' . "$pathname/$file" . '"';
                    }
                }
            } // end of this file
        } // end SFTP

        else if ($protocol == 'FS') {
            // Filesystem directory containing results files.
            $pathname = $pprow['results_path'];
            if (!($dh = opendir($pathname))) {
                return xl('Unable to access directory') . " '$pathname'";
            }

            // Sort by filename just because.
            $files = array();
            while (false !== ($file = readdir($dh))) {
                if (substr($file, 0, 1) == '.') {
                    continue;
                }

                $files[$file] = $file;
            }

            closedir($dh);
            ksort($files);
            // For each file...
            foreach ($files as $file) {
                ++$filecount;
                if (!isset($info["$ppid/$file"])) {
                    $info["$ppid/$file"] = array();
                }

                // Ensure that archive directory exists.
                $prpath = $GLOBALS['OE_SITE_DIR'] . "/procedure_results";
                if (!file_exists($prpath)) {
                    mkdir($prpath);
                }

                $prpath .= '/' . $pprow['ppid'];
                if (!file_exists($prpath)) {
                    mkdir($prpath);
                }

                // Get file contents.
                $hl7 = file_get_contents("$pathname/$file");
                // If user requested reject and delete, do that.
                if (!empty($info["$ppid/$file"]['delete'])) {
                    $fh = fopen("$prpath/$file.rejected", 'w');
                    if ($fh) {
                        fwrite($fh, $hl7);
                        fclose($fh);
                    } else {
                        return xl('Cannot create file') . ' "' . "$prpath/$file.rejected" . '"';
                    }

                    if (!unlink("$pathname/$file")) {
                        return xl('Cannot delete file') . ' "' . "$pathname/$file" . '"';
                    }

                    continue;
                }

                // Do a dry run of its contents and check for errors and match requests.
                $tmp = receive_hl7_results($hl7, $info['match'], $ppid, $pprow['direction'], true, $info['select']);
                $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
                // $info["$ppid/$file"]['match'] = $tmp['match'];
                if (!empty($tmp['fatal']) || !empty($tmp['needmatch'])) {
                    // There are errors or matching requests so skip this file.
                    continue;
                }

                // Now the money shot - not a dry run.
                $tmp = receive_hl7_results($hl7, $info['match'], $ppid, $pprow['direction'], false, $info['select']);
                $info["$ppid/$file"]['mssgs'] = $tmp['mssgs'];
                // $info["$ppid/$file"]['match'] = $tmp['match'];
                if (empty($tmp['fatal']) && empty($tmp['needmatch'])) {
                    // It worked, archive and delete the file.
                    $fh = fopen("$prpath/$file", 'w');
                    if ($fh) {
                        fwrite($fh, $hl7);
                        fclose($fh);
                    } else {
                        return xl('Cannot create file') . ' "' . "$prpath/$file" . '"';
                    }

                    if (!unlink("$pathname/$file")) {
                        return xl('Cannot delete file') . ' "' . "$pathname/$file" . '"';
                    }
                }
            } // end of this file
        } // end FS protocol

        // TBD: Insert "else if ($protocol == '???') {...}" to support other protocols.
    } // end procedure provider

  // echo "<!-- out: "; print_r($info); echo " -->\n"; // debugging

    return '';
}
// PHP end tag omitted intentionally.