<?php
/*******************************************************************************
 *
 * LEIDEN OPEN VARIATION DATABASE (LOVD)
 *
 * Created     : 2006-10-12
 * Modified    : 2011-01-20
 * For LOVD    : 2.0-30
 *
 * Access      : Submitters and up.
 * Purpose     : Submit new variant and patient data.
 *
 * Copyright   : 2004-2011 Leiden University Medical Center; http://www.LUMC.nl/
 * Programmers : Ing. Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
 *               Ir. Gerard C.P. Schaafsma <G.C.P.Schaafsma@LUMC.nl>
 * Last edited : Ing. Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
 *
 *
 * This file is part of LOVD.
 *
 * LOVD 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.
 *
 * LOVD 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 LOVD; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 *************/

define('ROOT_PATH', './');
require ROOT_PATH . 'inc-init.php';

if (HAS_AUTH) {
    // If authorized, check for updates.
    require ROOT_PATH . 'inc-upgrade.php';
}

if (!GENE_COUNT) {
    // No gene? No submission, then.
    require ROOT_PATH . 'inc-top.php';
    lovd_showInfoTable('There are no configured genes yet.', 'stop');
    require ROOT_PATH . 'inc-bot.php';
    exit;
}

// Require valid user.
lovd_requireAUTH();





if (empty($_GET['action'])) {
    // 2010-01-19; 2.0-25; Add page that presents the visitor with a set of questions, to help users so that they know where to go.
    require ROOT_PATH . 'inc-top.php';

    // Curators can use all functions, submitters can submit new data but can only edit data if $_CONF['my_submissions'] is turned on.
    $bEditable = (HAS_SUBS? $_CONF['my_submissions'] : true);

    if (!$bEditable) {
        lovd_showInfoTable('Please note that due to configuration settings, submitters are currently not allowed to make changes to previously submitted data; please contact the curator of this database if you need to modify data you have previously submitted to this database.', 'info');
    }

    // 2010-01-19; 2.0-25; We need the Javascript to control showing/hiding the information table contents.
    lovd_includeJS(ROOT_PATH . 'inc-js-toggle-visibility.js');

    print('      <H3>Update an existing patient record</H3>' . "\n\n" .
          '      <TABLE border="0" cellpadding="0" cellspacing="2" width="950" class="data">' . "\n");
    if ($bEditable) {
        // Print this option only when the 'My Submissions' option in the System settings was enabled, or when the user is curator or higher
        print('        <TR style="cursor : pointer; cursor : hand;" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';" onclick="lovd_toggleVisibility(\'update_patient\');">' . "\n" .
              '          <TH><H5>Update patient &amp; phenotype data &raquo;&raquo;</H5></TH></TR>' . "\n" .
              '        <TR id="update_patient" style="display : none;">' . "\n" .
              '          <TD>' . "\n" .
              '            To update patient and/or phenotype data, you first need to locate the patient in the database. If you know the patient\'s internal ID or the laboratory\'s patient ID, please fill in the value in the text field below and press the "Next &raquo;" button.' . "\n" .
              '            <FORM action="' . $_SERVER['PHP_SELF'] . '" method="get">' . "\n" .
              '              <INPUT type="hidden" name="action" value="patient_update">' . "\n" .
              '              <INPUT type="text" name="patientid" value="">' . "\n" .
              '              <INPUT type="submit" value="Next &raquo;">' . "\n" .
              '            </FORM><BR>' . "\n" .
              '            If you don\'t know the patient\'s IDs, you need to find the patient in the database by searching the database contents based on information that you know about the patient or the variants found in the patient. Click the "Search the patient &raquo;" button below to go to the database search table. On the top of the page the currently selected gene is displayed; make sure it\'s a gene in which you are sure the patient has a variant reported. You can change to a different gene database by using the green "switch gene database" icon on the top of the screen next to the name of the currently selected gene database. Use the search fields above the data table to search for the patient you are looking for, and click the entry you want to edit. Now you should see the patient\'s detailed view including the variants reported. Below the patient data table, click the link "Edit patient" to edit the patient entry.<BR>' . "\n" .
              '            <BUTTON onclick="window.location.href=\'' . ROOT_PATH . 'variants.php?action=search_all' . lovd_showSID(true, true) . '\';" class="S11">Search the patient &raquo;</BUTTON><BR>');
        // 2010-09-28; 2.0-29; Added text about submitters variants list (only visible for submitters)
        if (HAS_SUBS) {
            print('<BR>You might also want to try <A href="submitters_variants.php?submitterid=' . $_AUTH['submitterid'] . '&amp;all_genes">your submissions list</A> to find the patient you\'re looking for.<BR>');
        }
        print('         </TD></TR>' . "\n" .
              '        <TR style="cursor : pointer; cursor : hand;" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';" onclick="lovd_toggleVisibility(\'update_variant\');">' . "\n" .
              '          <TH><H5>Update variant data &raquo;&raquo;</H5></TH></TR>' . "\n" .
              '        <TR id="update_variant" style="display:none;">' . "\n" .
              '          <TD>' . "\n" .
              '            To update variant data, you need to find the variant in the database by searching the database contents based on information that you know about the variants. Click the "Search the variant &raquo;" button below, and make sure the correct gene is mentioned on the top of the page. You can change to a different gene database by using the green "switch gene database" icon on the top of the screen next to the name of the currently selected gene database. Use the search fields above the data table to search for the variant you are looking for, and click the entry you want to edit. Now you should see the detailed view with the patient information at the top of the page with the found variants below it, showing variant you selected in detail. Below the variant data table, click the link "Edit variant" to edit the variant entry.<BR>' . "\n" .
              '            <BUTTON onclick="window.location.href=\'' . ROOT_PATH . 'variants.php?action=search_all' . lovd_showSID(true, true) . '\';" class="S11">Search the variant &raquo;</BUTTON></TD></TR>' . "\n");
    }
    print('        <TR style="cursor : pointer; cursor : hand;" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';" onclick="lovd_toggleVisibility(\'add_variant\');">' . "\n" .
          '          <TH><H5>Add new variant to existing patient &raquo;&raquo;</H5></TH></TR>' . "\n" .
          '        <TR id="add_variant" style="display : none;">' . "\n" .
          '          <TD>' . "\n" .
          '            To add a new variant to an existing patient, you first need to locate the patient in the database. If you know the patient\'s internal ID or the laboratory\'s patient ID, please fill in the value in the text field below and press the "Next &raquo;" button.' . "\n" .
          '            <FORM action="' . $_SERVER['PHP_SELF'] . '" method="get">' . "\n" .
          '              <INPUT type="hidden" name="action" value="patient_add_variant">' . "\n" .
          '              <INPUT type="text" name="patientid" value="">' . "\n" .
          '              <INPUT type="submit" value="Next &raquo;">' . "\n" .
          '            </FORM><BR>' . "\n" .
          '            If you don\'t know the patient\'s IDs, you need to find the patient in the database by searching the database contents based on information that you know about the patient or the variants found in the patient. Click the "Search the patient &raquo;" button below to go to the database search table. On the top of the page the currently selected gene is displayed; make sure it\'s a gene in which you are sure the patient has a variant reported. You can change to a different gene database by using the green "switch gene database" icon on the top of the screen next to the name of the currently selected gene database. Use the search fields above the data table to search for the patient you are looking for, and click the entry you want to edit. Now you should see the patient\'s detailed view including the variants reported. Below the patient data table, click the link "Add new variant to patient" to add a new variant.<BR>' . "\n" .
          '            <BUTTON onclick="window.location.href=\'' . ROOT_PATH . 'variants.php?action=search_all' . lovd_showSID(true, true) . '\';" class="S11">Search the patient &raquo;</BUTTON>');
    // 2010-09-28; 2.0-29; Added text about submitters variants list (only visible for submitters)
    if (HAS_SUBS) {
        print('<BR>You might also want to try <A href="submitters_variants.php?submitterid=' . $_AUTH['submitterid'] . '&amp;all_genes">your submissions list</A> to find the patient you\'re looking for.<BR>');
    }
    print('       </TD></TR>' . "\n" .
          '      </TABLE>' . "\n\n" .
          '      <BR>' . "\n\n" .
          '      <H3>Add a new patient</H3>' . "\n\n" .
          '      <TABLE border="0" cellpadding="0" cellspacing="2" width="950" class="data">' . "\n" .
          '        <TR style="cursor : pointer; cursor : hand;" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';" onclick="lovd_toggleVisibility(\'add_patient\');">' . "\n" .
          '          <TH><H5>Add new patient and variant data &raquo;&raquo;</H5></TH></TR>' . "\n" .
          '        <TR id="add_patient" style="display : none;">' . "\n" .
          '          <TD>' . "\n" .
          '            To add new patient data, you also need to submit at least one variant that has been found in the patient. Click the "Next &raquo;" button to start the submission process.' . "\n" .
          '            <FORM action="' . $_SERVER['PHP_SELF'] . '" method="get">' . "\n" .
          '              <INPUT type="hidden" name="action" value="submit">' . "\n" .
          '              <INPUT type="hidden" name="hide" value="exist_pat">' . "\n" .
          '              <INPUT type="submit" value="Next &raquo;">' . "\n" .
          '            </FORM>' . '</TD></TR>' . "\n" .
          '     </TABLE>' . "\n\n");

    require ROOT_PATH . 'inc-bot.php';
    exit;





} elseif (in_array($_GET['action'], array('patient_update', 'patient_add_variant')) && !empty($_GET['patientid'])) {
    // Find patients, based on their internal patientid, or the lab's patient ID (Patient/Patient_ID).
    $sQ = 'SELECT p.patientid, p.* FROM ' . TABLE_PATIENTS . ' AS p WHERE (p.patientid = "' . $_GET['patientid'] . '" OR p.`Patient/Patient_ID` = "' . $_GET['patientid'] . '")';
    if (HAS_SUBS) {
        $sQ .= ' AND p.submitterid = "' . $_AUTH['submitterid'] . '"';
    }
    $qPatients = mysql_query($sQ);
    $nResults = mysql_num_rows($qPatients);
    if (!$nResults) {
        // No patients were found.
        require ROOT_PATH . 'inc-top.php';
        lovd_showInfoTable('Could not find this patient in the system or you are not the owner of this patient!', 'stop');
        require ROOT_PATH . 'inc-bot.php';
        exit;
    }    
    
    if ($nResults == 1) {
        list($nPatientid) = mysql_fetch_row($qPatients);
        if ($_GET['action'] == 'patient_add_variant') {
            // Coming from "Add new variant to existing patient".
            header('Location: ' . PROTOCOL . $_SERVER['HTTP_HOST'] . $_SERVER['PHP_SELF'] . '?action=submit&add_pat=' . $nPatientid . lovd_showSID(true));
        } else {
            // Coming from "Update patient & phenotype data".
            header('Location: ' . PROTOCOL . $_SERVER['HTTP_HOST'] . rtrim(dirname($_SERVER['PHP_SELF']), '/') . '/submit_patients.php?action=edit&edit=' . $nPatientid . lovd_showSID(true));
        }
        exit;
    }

    // $nResults > 1: User has to choose a patient, show them in a table.
    require ROOT_PATH . 'inc-top.php';
    lovd_printHeader('submit', 'Submit new sequence variant');

    require ROOT_PATH . 'inc-lib-list.php';
    require ROOT_PATH . 'class/currdb.php';
    $_CURRDB = new CurrDB();
    $_CURRDB->hideColsByTable('Patient');
    define('IS_CURATOR', (HAS_SUBS || $_AUTH['level'] >= LEVEL_MANAGER));
    $_CURRDB->hideCols('public', IS_CURATOR);

    lovd_showInfoTable('Multiple patient entries found that match this patient ID. Please select which patient you wish to ' . ($_GET['action'] == 'patient_update'? 'edit' : 'add a new variant to') . ' by clicking on a row.', 'question');

    // Array which will make up the table (header and data).
    $aTable = $_CURRDB->buildTable('list');

    // Total width.
    $nTotalWidth = 2;
    foreach ($aTable as $aCol) {
        $nTotalWidth += $aCol[1] + 8;
    }

    // Stretch table up, to respect column widths.
    print('      <IMG src="' . ROOT_PATH . 'gfx/trans.png" alt="" width="' . $nTotalWidth . '" height="1"><BR>' . "\n\n");

    // Table.
    print('      <TABLE border="0" cellpadding="0" cellspacing="1" class="data">' . "\n" .
          '        <TR>');

    // Table header
    foreach ($aTable as $sField => $aCol) {
        print("\n" . '          <TH' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . $aCol[0] . '</TH>');
    }
    print('</TR>');
    
    // Print the rows with the patients.
    while ($zData = mysql_fetch_assoc($qPatients)) {
        print("\n" .
              '        <TR valign="top" style="cursor : pointer; cursor : hand;" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';" onclick="window.location.href = \'' . ($_GET['action'] == 'patient_update'? ROOT_PATH . 'submit_patients.php?action=edit&amp;edit=' : $_SERVER['PHP_SELF'] . '?action=submit&amp;add_pat=') . $zData['patientid'] . lovd_showSID(true) . '\';">');

        // Parse and build Custom Links.
        lovd_buildLinks($zData);

        // Transform select lists' values.
        $_CURRDB->transformSelectValues($zData);

        // print patient data in table
        foreach ($aTable as $sField => $aCol) {
            print("\n" .
                  '          <TD' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . (!$zData[$sField]? '-' : $zData[$sField]) . '</TD>');
        }
        print('</TR>');
    }
    print('</TABLE><BR>' . "\n");
    require ROOT_PATH . 'inc-bot.php';
    exit;





} elseif ($_GET['action'] == 'submit') {
    // View all / search variants in this gene.
    if (!empty($_GET['add_pat'])) {
        // Unset a previously set $_SESSION['submit_pat'].
        $_SESSION['submit_pat'] = array();
    }

    // Require form functions.
    require ROOT_PATH . 'inc-lib-form.php';
    require ROOT_PATH . 'inc-top.php';
    lovd_printHeader('submit', 'Submit new sequence variant');

    // 2008-08-06; 2.0-10; Prevent any type of attack through $_GET['gene'] and $_POST['gene'] by verifying it exists.
    if (!empty($_GET['gene']) && !in_array($_GET['gene'], lovd_getGeneList())) {
        unset($_GET['gene']);
    }
    if (!empty($_POST['gene']) && !in_array($_POST['gene'], lovd_getGeneList())) {
        unset($_POST['gene']);
    }

    // 2007-08-17; 2.0-beta-07; We want to click a link, and add the patient info right away. So we need $_POST['patientid'].
    if (!empty($_GET['add_pat']) && empty($_GET['add']) && empty($_POST['patientid']) && empty($_SESSION['submit_pat'])) {
        $_POST['patientid'] = $_GET['add_pat'];
        $_GET['add'] = 'pat';
    }

    // Delete entries?
    if (!empty($_GET['delete']) && !empty($_GET['gene']) && preg_match('/^(pat|var)([0-9]{1,})?$/', $_GET['delete'], $aRegs)) {
        list(, $sList) = $aRegs;
        if ($sList == 'var') {
            $nDel = (int) $aRegs[2];
        }
        if ($sList == 'var' && isset($nDel) && !empty($_SESSION['submit_muts'][$_GET['gene']][$nDel])) {
            unset($_SESSION['submit_muts'][$_GET['gene']][$nDel]);
        } elseif ($sList == 'pat' && !empty($_SESSION['submit_pat'])) {
            unset($_SESSION['submit_pat']);
            unset($_SESSION['submit_patid']);
        }

        $_POST['gene'] = $_GET['gene'];
    }

    if (empty($_POST['gene'])) {
        // Select gene?

        if (GENE_COUNT == 1) {
            // Never mind, we've only got one.
            list($_POST['gene']) = lovd_getGeneList();

        } else {
            $_POST['gene'] = $_SESSION['currdb'];

            // Table.
            print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . (!empty($_GET['add'])? '&amp;add=' . $_GET['add'] : '') . (!empty($_GET['hide'])? '&amp;hide=' . $_GET['hide'] : '') . '" method="post">' . "\n" .
                  (!empty($_POST['patientid'])? '        <INPUT type="hidden" name="patientid" value="' . $_POST['patientid'] . '">' . "\n" : '') .
                  '        <TABLE border="0" cellpadding="0" cellspacing="1" width="600">');

            // Get gene list.
            // 2010-03-12; 2.0-25; This will make this query very complicated, but it will also shorten the gene names quite properly.
            $qGenes = mysql_query('SELECT symbol, CONCAT(SUBSTRING(CONCAT(symbol, " (", gene), 1, 50), SUBSTRING("...)", (((LENGTH(CONCAT(symbol, gene))<49)+1)*3)-2)) AS gene FROM ' . TABLE_DBS . ' ORDER BY symbol');

            $aForm = array(
                            array('POST', '', '', '40%', '60%'),
                            array('Submit new sequence variation for:', 'select', 'gene', 1, $qGenes, false, false, false),
                            'skip',
                            array('', 'submit', 'Select gene database'),
                          );
            $_MODULES->processForm('SubmitGeneSelect', $aForm);
            lovd_viewForm($aForm);
            print('</TABLE></FORM>' . "\n\n");

            require ROOT_PATH . 'inc-bot.php';
            exit;
        }
    }





    // Whether or not a user can submit non-public data.
    if (lovd_isCurator($_POST['gene'])) {
        define('IS_CURATOR', true);
    } else {
        define('IS_CURATOR', false);
    }

    // Set some vars.
    require ROOT_PATH . 'class/currdb.php';
    $_CURRDB = new CurrDB(true, $_POST['gene']);
    $_CURRDB->hideCols('public_form', IS_CURATOR);

    if (!isset($_SESSION['submit_muts']) || !is_array($_SESSION['submit_muts'])) {
        $_SESSION['submit_muts'] = array($_POST['gene'] => array());
    } elseif (!isset($_SESSION['submit_muts'][$_POST['gene']]) || !is_array($_SESSION['submit_muts'][$_POST['gene']])) {
        $_SESSION['submit_muts'][$_POST['gene']] = array();
    }

    if (!isset($_SESSION['submit_pat']) || !is_array($_SESSION['submit_pat'])) {
        $_SESSION['submit_pat'] = array();
    }
    if (!isset($_GET['add'])) {
        $_GET['add'] = '';
    }





    // Step 2: Add patient data.
    if ($_GET['add'] == 'pat' && empty($_SESSION['submit_pat'])) {
        // Add patient data.

        // 2007-08-09; 2.0-beta-07; Added option for curators and up (and submitters
        // owning the patient) to submit variants to an existing patient.
        if (!empty($_POST['patientid'])) {
            // Patient ID sent; we're importing everything.
            $zData = @mysql_fetch_assoc(mysql_query('SELECT p.* FROM ' . TABLE_PATIENTS . ' AS p WHERE p.patientid = "' . $_POST['patientid'] . '"'));

            if (!$zData || (!HAS_AUTH && $zData['submitterid'] != $_SUBS['submitterid'])) {
                // Wrong ID, apparently.
                if (!$zData) {
                    lovd_showInfoTable('Could not find this patient in the system!', 'stop');
                } else {
                    // This is a submitter, and he/she does not own this patient.
                    // The issue is, the system can't even store who added the variants if we would allow this.
                    lovd_showInfoTable('This patient has not been submitted by you!', 'stop');
                }
                print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
                      '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
                      '        <INPUT type="submit" value="Continue &raquo;">' . "\n" .
                      '      </FORM>' . "\n\n" .
                      '      <SCRIPT type="text/javascript">' . "\n" .
                      '        <!--' . "\n" .
                      '        setTimeout("document.forms[0].submit()", 3000);' . "\n" .
                      '        // -->' . "\n" .
                      '      </SCRIPT>' . "\n\n");

                require ROOT_PATH . 'inc-bot.php';
                exit;
            }

            // $zData comes from the database, and is therefore not quoted.
            lovd_magicQuote($zData);

            // Mark as being taken from the database.
            $_SESSION['submit_patid'] = $zData['patientid'];
            // Load data into $_POST.
            $aCols = $_CURRDB->getColList('Patient');
            // 2008-10-02; 2.0-13; SubmitterID is now sent by patient form.
            $aCols[] = 'submitterid';
            foreach ($aCols as $sCol) {
                $_POST[$sCol] = $zData[$sCol];
            }
            $_CURRDB->transformSelectValues($_POST, true);
            // Make it look like the form has been sent. This has a downside; if a check returns
            // an error, the user gets the form back, and has to make changes, which will not be
            // put in the database, but will appear in the confirmation email.
            $_GET['sent'] = '';
        }

        if (isset($_GET['sent'])) {
            lovd_errorClean();

            // Mandatory fields.
            $_CURRDB->checkMandatory('Patient');

            // Field lengths.
            $_CURRDB->checkInputLength();

            // Field types.
            $_CURRDB->checkInputType();

            // Regular expressions.
            $_CURRDB->checkInputRegExp();

            // 2006-12-07; 2.0-alpha-02
            // XSS attack prevention. Simply deny input of HTML, PHP other stuff blocked by strip_tags().
            lovd_checkXSS();

            if (!lovd_error()) {
                // Insert into $_SESSION and return to the submission overview page.
                $aCols = $_CURRDB->getColList('Patient');
                // 2008-10-02; 2.0-13; SubmitterID is now sent by patient form.
                $aCols[] = 'submitterid';
                if (!HAS_AUTH) {
                    $_POST['submitterid'] = $_AUTH['submitterid'];
                }

                // Build session array.
                $aSession = array();
                foreach ($aCols as $sCol) {
                    // 2007-12-21; 2.0-02; Reset to empty value to prevent notices + warnings about non-existent indexes.
                    if (!isset($_POST[$sCol])) {
                        // Multiple select list without selected value.
                        $_POST[$sCol] = '';
                    }
                    if (is_array($_POST[$sCol])) {
                        $_POST[$sCol] = implode(';', $_POST[$sCol]);
                    }
                    $aSession[$sCol] = $_POST[$sCol];
                }
                $_SESSION['submit_pat'] = $aSession;

                // Thank the user...
                print('      Successfully added patient data to your submission!<BR><BR>' . "\n\n");
                
                print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
                      '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
                      '        <INPUT type="submit" value="Continue &raquo;">' . "\n" .
                      '      </FORM>' . "\n\n" .
                      '      <SCRIPT type="text/javascript">' . "\n" .
                      '        <!--' . "\n" .
                      '        setTimeout("document.forms[0].submit()", ' . (empty($_POST['patientid'])? 1000 : 0) . ');' . "\n" .
                      '        // -->' . "\n" .
                      '      </SCRIPT>' . "\n\n");

                require ROOT_PATH . 'inc-bot.php';
                exit;

            } else {
                // Errors, so the whole lot returns to the form.
                lovd_magicUnquoteAll();
            }

        } else {
            // Default values.

            // 2009-02-16; 2.0-16; Introducing default values.
            if (empty($_POST['patientid'])) {
                // But only for NEW patients!
                $_CURRDB->initDefaultValues('Patient');
            }
        }



        if (!isset($_GET['sent'])) {
            print('      To add patient data to your submission, please fill out the form below.<BR>' . "\n" .
                  '      <BR>' . "\n\n");
        }

        lovd_showInfoTable('All fields, unless specified otherwise, are required to be filled in.', 'information');

        lovd_errorPrint();

        // Table.
        print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;add=' . $_GET['add'] . '&amp;sent=true" method="post">' . "\n" .
              '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
              '        <TABLE border="0" cellpadding="0" cellspacing="1" width="950">');

        // Array which will make up the form table.
        $aForm = array_merge(
                             array(
                                    array('POST', '', '', '40%', '60%'),
                                    array('', 'print', '<B>Add patient data to the ' . $_POST['gene'] . ' database</B>'),
                                  ),
                             $_CURRDB->buildFormTable('Patient'));

        // 2008-10-02; 2.0-13; Allow curator to set submitter.
        if (IS_CURATOR) {
            $qSubmitters = mysql_query('SELECT s.submitterid, CONCAT(c.country, " / ", s.city, " - ", s.firstname, " ", s.lastname, " (#", s.submitterid, ")") AS name FROM ' . TABLE_SUBS . ' AS s LEFT JOIN ' . TABLE_COUNTRIES . ' AS c ON (s.country = c.code) WHERE s.deleted = 0 ORDER BY name');
            $aForm = array_merge($aForm,
                                 array(
                                        'skip',
                                        array('Submitter', 'select', 'submitterid', 1, $qSubmitters, '-- None --', false, false),
                                      ));
        }

        $aForm = array_merge($aForm,
                             array(
                                    'skip',
                                    // 2007-08-08; 2.0-beta-07; Added "cancel" button.
                                    array('', 'print', '<INPUT type="submit" value="Add patient data">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<INPUT type="submit" value="Cancel" onclick="document.forms[1].submit(); return false;" style="border : 1px solid #FF4422;">'),
                                  ));
        $_MODULES->processForm('SubmitPatientData', $aForm);
        lovd_viewForm($aForm);

        print('</TABLE></FORM>' . "\n\n");

        // This form is merely to support the "Cancel" button. Because we need a $_POST value in the next page.
        print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
              '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
              '      </FORM>' . "\n\n");

        require ROOT_PATH . 'inc-bot.php';
        exit;
    }





    // Step 3: Add variant data.
    if ($_GET['add'] == 'var') {
        // Add variant data.

        // 2007-08-30; 2.0-beta-08; Added option to add a variant to the
        // submission process, which is already in the database.
        if (!empty($_POST['variant_name'])) {
            // Variant name sent; we're importing everything (well, this is just the first one we happen to find).
            $zData = mysql_fetch_assoc(mysql_query('SELECT v.* FROM ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants AS v WHERE v.`' . $_CURRDB->getMutationCol() . '` = "' . $_POST['variant_name'] . '"'));

            if (!$zData) {
                // Wrong ID, apparently.
                lovd_showInfoTable('Could not find this variant in the system!', 'stop');
                print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
                      '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
                      '        <INPUT type="submit" value="Continue &raquo;">' . "\n" .
                      '      </FORM>' . "\n\n" .
                      '      <SCRIPT type="text/javascript">' . "\n" .
                      '        <!--' . "\n" .
                      '        setTimeout("document.forms[0].submit()", 3000);' . "\n" .
                      '        // -->' . "\n" .
                      '      </SCRIPT>' . "\n\n");

                require ROOT_PATH . 'inc-bot.php';
                exit;
            }

            // We will not mark this as being taken from the database... at the
            // end, LOVD checks if the variant exists already anyway.

            // Load data into $_POST.
            $aCols = $_CURRDB->getColList('Variant');
            foreach ($aCols as $sCol) {
                $_POST[$sCol] = $zData[$sCol];
            }
            $_CURRDB->transformSelectValues($_POST, true);
        }

        if (isset($_GET['sent'])) {
            lovd_errorClean();

            // 2008-04-24; 2.0-06; Check Variant/DBID field to make sure it's consistent with the variant.
            // Submitters don't see this DBID column. Possibly, this LOVD has been configured to hide it anyway. So:
            $_CURRDBtmp = new CurrDB(true, $_POST['gene']);
            if ($_CURRDBtmp->colExists('Variant/DBID')) {
                $sMutationCol = $_CURRDB->getMutationCol();
                if (!empty($_POST[$sMutationCol])) {
                    // 2008-05-19; 2.0-07; Some modifications here to apply new function that checks if
                    // the given ID matches the given variant and predict the ID only when left empty.
                    if (empty($_POST['Variant/DBID'])) {
                        // Submitters who don't have this field AND curators who left this field open.
                        $sIDGenerated = lovd_fetchDBID($_POST['gene'], $_POST[$sMutationCol], $sMutationCol);
                        // 2008-10-13; 2.0-13; If this ID is a new ID, and this ID also exists in the submission for a different variant, increment by one.
                        list($n) = @mysql_fetch_row(mysql_query('SELECT COUNT(*) FROM `' . TABLEPREFIX . '_' . mysql_real_escape_string($_POST['gene']) . '_variants` WHERE `Variant/DBID` LIKE "' . $sIDGenerated . '%"'));
                        if (!$n) {
                            // This is a new ID, make sure it does not exist in this submission for a different variant.
                            while (true) {
                                foreach ($_SESSION['submit_muts'][$_POST['gene']] as $aSession) {
                                    if (substr($aSession['Variant/DBID'], 0, strlen($sIDGenerated)) == $sIDGenerated && str_replace(array('(', ')', '?'), '', $_POST[$sMutationCol]) != str_replace(array('(', ')', '?'), '', $aSession[$sMutationCol])) {
                                        // Exists already and this is not the same variant!
                                        $sIDGenerated ++; // I know this looks weird, but it works.
                                        continue 2;
                                    }
                                }
                                break;
                            }
                        }
                        $_POST['Variant/DBID'] = $sIDGenerated;
                    } else {
                        // 2008-10-13; 2.0-13; The DBID check allowed invalid DBID values if the DBID field contained more than just the ID.
                        // $sSymb = substr($_POST['gene'], 0, strpos($_POST['gene'] . '_', '_'));
                        // $sDBID = substr($_POST['Variant/DBID'], 0, strlen($sSymb) + 6);
                        // 2010-05-17; 2.0-27; Select the first so-called word of the Variant/DBID field, not select the first 6 chars after the gene symbol.
                        // We're assuming here that the start of the DBID field will always be the ID, like the column's default RegExp forces.
                        preg_match('/^(\w+)\b/', $_POST['Variant/DBID'], $aMatches);
                        $sDBID = $aMatches[1];
                        if (!lovd_checkDBID($_POST['gene'], $_POST[$sMutationCol], $sMutationCol, $sDBID)) {
                            lovd_errorAdd('The given variant ID "' . strip_tags($sDBID) . '" does not match the variant "' . strip_tags($_POST[$sMutationCol]) . '".');
                        } elseif (count($_SESSION['submit_muts'][$_POST['gene']])) {
                            // 2008-10-13; 2.0-13; Check given ID against submission, also.
                            foreach ($_SESSION['submit_muts'][$_POST['gene']] as $aSession) {
                                if (substr($aSession['Variant/DBID'], 0, strlen($sDBID)) == $sDBID && str_replace(array('(', ')', '?'), '', $_POST[$sMutationCol]) != str_replace(array('(', ')', '?'), '', $aSession[$sMutationCol])) {
                                    // Exists already and this is not the same variant!
                                    lovd_errorAdd('The given variant ID "' . strip_tags($sDBID) . '" does not match the variant "' . strip_tags($_POST[$sMutationCol]) . '".');
                                }
                            }
                        }
                    }
                }
            }
            unset($_CURRDBtmp);

            // Mandatory fields.
            $_CURRDB->checkMandatory('Variant');

            // Field lengths.
            $_CURRDB->checkInputLength();

            // Field types.
            $_CURRDB->checkInputType();

            // Regular expressions.
            $_CURRDB->checkInputRegExp();

            // 2006-12-07; 2.0-alpha-02
            // XSS attack prevention. Simply deny input of HTML, PHP other stuff blocked by strip_tags().
            lovd_checkXSS();

            // 2008-10-10; 2.0-13; Deny this entry, if the exact combination is already present in the database, or the submission. Otherwise, an SQL error would show up.
            // Step 1: Check current submission for the same variant.
            if (!lovd_error() && count($_SESSION['submit_muts'][$_POST['gene']])) {
                // Check submission for other variant that is actually equal.
                $aCols = $_CURRDB->getColList('Variant');
                // Compare session array.
                foreach ($_SESSION['submit_muts'][$_POST['gene']] as $aSession) {
                    $bEqual = true;
                    foreach ($aCols as $sCol) {
                        if (!isset($_POST[$sCol])) {
                            // Multiple select list without selected value.
                            $_POST[$sCol] = '';
                        }
                        if (is_array($_POST[$sCol])) {
                            // Multiple select list.
                            if (implode(';', $_POST[$sCol]) != $aSession[$sCol]) {
                                $bEqual = false;
                            }
                        } elseif ($_POST[$sCol] != $aSession[$sCol]) {
                            $bEqual = false;
                        }
                    }
                    if ($bEqual && $_POST['allele'] == $aSession['allele']) {
                        // This is bad... we should not allow this!
                        lovd_errorAdd('An entry in your submission exactly like this already exists! Are you sure you don\'t want a different value for the \'Variant allele\' field?');
                    }
                }
            }

            // Step 2: Check database for the same variant, only if an existing patient has been selected.
            if (!lovd_error() && !empty($_SESSION['submit_patid'])) {
                // Determine if mutation already exists in database. If so, check allele value and throw error if necessary.
                $aCols = $_CURRDB->getColList('Variant');
                $sQ = 'SELECT variantid FROM ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants WHERE ';
                foreach ($aCols as $key => $sCol) {
                    if (!isset($_POST[$sCol])) {
                        // Multiple select list without selected value.
                        $_POST[$sCol] = '';
                    }
                    if (is_array($_POST[$sCol])) {
                        // Multiple select list.
                        $sQ .= (!$key? '' : ' AND ') . '`' . $sCol . '` = "' . implode(';', $_POST[$sCol]) . '"';
                    } else {
                        $sQ .= (!$key? '' : ' AND ') . '`' . $sCol . '` = "' . $_POST[$sCol] . '"';
                    }
                }

                // Store IDs that match.
                $aIDs = array();
                $qIDs = mysql_query($sQ);
                while (list($nID) = mysql_fetch_row($qIDs)) {
                    $aIDs[] = $nID;
                }

                // Now, find if these ID's exist with the same patient and the same allele data. If so, throw a warning.
                // 2010-04-12; 2.0-26; Of course, this means that you actually need to include the patientid in the query!!! (stupid mistake)
                list($n) = mysql_fetch_row(mysql_query('SELECT COUNT(*) FROM ' . TABLE_PAT2VAR . ' WHERE symbol = "' . $_POST['gene'] . '" AND (variantid = "' . implode('" OR variantid = "', $aIDs) . '") AND patientid = "' . $_SESSION['submit_patid'] . '" AND allele = "' . $_POST['allele'] . '"'));
                if ($n) {
                    // This is bad... we should not allow this!
                    lovd_errorAdd('An entry in the database exactly like this already exists! Are you sure you don\'t want a different value for the \'Variant allele\' field?');
                }
            }

            if (!lovd_error()) {
                // Insert into $_SESSION and return to the submission overview page.
                $aCols = $_CURRDB->getColList('Variant');

                // 2008-04-24; 2.0-06; Include auto generated Variant/DBID field for submitters.
                if (array_search('Variant/DBID', $aCols) === false && !empty($_POST['Variant/DBID'])) {
                    // Variant/DBID was hidden, but value is filled in.
                    $aCols[] = 'Variant/DBID';
                }

                while (true) {
                    // Loop to process possible homozygous mutation ($_POST['allele'] == 3).

                    // Build session array.
                    $aSession = array('allele' => ($_POST['allele'] == 3? 10 : $_POST['allele']));
                    foreach ($aCols as $sCol) {
                        // 2007-12-21; 2.0-02; Reset to empty value to prevent notices + warnings about non-existent indexes.
                        if (!isset($_POST[$sCol])) {
                            // Multiple select list without selected value.
                            $_POST[$sCol] = '';
                        }
                        // 2007-12-21; 2.0-02; Multiple select lists need to be stored properly, such as is done in the patient data processing.
                        if (is_array($_POST[$sCol])) {
                            $_POST[$sCol] = implode(';', $_POST[$sCol]);
                        }
                        $aSession[$sCol] = $_POST[$sCol];
                    }

                    // Define variant status.
                    if (IS_CURATOR) {
                        $aSession['status'] = $_POST['status'];
                    } else {
                        $aSession['status'] = STATUS_NEW;
                    }

                    // Variant pathogenicity.
                    if (HAS_AUTH) {
                        // Curator and up.
                        $aSession['pathogenic'] = $_POST['pathogenic_reported'] . $_POST['pathogenic_concluded'];
                    } else {
                        // Submitter...
                        if (!array_key_exists($_POST['pathogenic_reported'], $_SETT['var_pathogenic'])) {
                            $aSession['pathogenic'] = 55;
                        } else {
                            $aSession['pathogenic'] = $_POST['pathogenic_reported'] . '5';
                        }
                    }

                    // The check if variant already exists is done when finalizing.
                    $_SESSION['submit_muts'][$_POST['gene']][] = $aSession;

                    // End loop, or continue?
                    if ($_POST['allele'] == 3) {
                        $_POST['allele'] = 20;
                    } else {
                        break;
                    }
                }

                // Thank the user...
                print('      Successfully added variant data to your submission!<BR><BR>' . "\n\n");

                print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
                      '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
                      '        <INPUT type="submit" value="Continue &raquo;">' . "\n" .
                      '      </FORM>' . "\n\n" .
                      '      <SCRIPT type="text/javascript">' . "\n" .
                      '        <!--' . "\n" .
                      '        setTimeout("document.forms[0].submit()", ' . (empty($_POST['variantid'])? 1000 : 0) . ');' . "\n" .
                      '        // -->' . "\n" .
                      '      </SCRIPT>' . "\n\n");

                require ROOT_PATH . 'inc-bot.php';
                exit;

            } else {
                // Errors, so the whole lot returns to the form.
                lovd_magicUnquoteAll();
            }

        } else {
            // Default values.
            $_POST['pathogenic_reported'] = 5;
            $_POST['pathogenic_concluded'] = 5;

            // 2009-02-16; 2.0-16; Introducing default values.
            if (empty($_POST['variant_name'])) {
                // But only for NEW variants!
                $_CURRDB->initDefaultValues('Variant');
            }
        }



        if (!isset($_GET['sent'])) {
            print('      To add sequence variant data to your submission, please fill out the form below.<BR>' . "\n" .
                  '      <BR>' . "\n\n");
        }

        lovd_showInfoTable('All fields, unless specified otherwise, are required to be filled in.', 'information');

        lovd_errorPrint();

        // Table.
        print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;add=' . $_GET['add'] . '&amp;sent=true" method="post">' . "\n" .
              '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
              '        <TABLE border="0" cellpadding="0" cellspacing="1" width="950">');

        // 2009-12-09; 2.0-24; Added link to either the coding DNA reference sequence or the mRNA sequence at NCBI, depending on their availability.
        list($sRefType, $sURL, $smRNA) = @mysql_fetch_row(mysql_query('SELECT refseq, refseq_url, refseq_mrna FROM ' . TABLE_DBS . ' WHERE symbol = "' . $_POST['gene'] . '"'));
        $sLinkText = '';
        if ($sURL) {
            $sLinkText = 'To check your numbering, please check the <A href="' . $sURL .'" target="_blank">' . ($sRefType == 'c' ? 'coding' : 'genomic') . ' DNA reference sequence</A> used in the ' . $_POST['gene'] . ' database.';
        } elseif ($_SETT['currdb']['refseq_mrna']) {
            $sLinkText = 'To check your numbering, please check the <A href="' . lovd_getExternalSource('genbank', $smRNA, true) . '" target="_blank">' . $smRNA . ' mRNA reference sequence</A>.';
        }
        $_CURRDB->aColList['Variant/DNA']['description_form'] .= ($_CURRDB->aColList['Variant/DNA']['description_form'] && $sLinkText? '<BR>' : '') . $sLinkText;

        // Array which will make up the form table.
        $aForm = array_merge(
                             array(
                                    array('POST', '', '', '40%', '60%'),
                                    array('', 'print', '<B>Add sequence variant data to the ' . $_POST['gene'] . ' database</B>'),
                                    array('Variant allele', 'select', 'allele', 1, $_SETT['var_allele'], false, false, false),
                                    // 2010-05-03; 2.0-26; Hopefully this helps people, when they submit a homozygous variant just once or try twice with Allele = Unknown, which doesn't work.
                                    array('', 'print', '<SPAN class="form_note">If you wish to report an homozygous variant, please select "Both (homozygous)" here. LOVD will then duplicate this variant automatically.</SPAN>'),
                                  ),
                             $_CURRDB->buildFormTable('Variant'));
        // 2007-12-06; 2.0-02; Ooops... submitters never had the option to report the pathogenicity.
        $aForm = array_merge($aForm,
                             array(
                                    'skip',
                                    array('Pathogenicity (reported)', 'select', 'pathogenic_reported', 1, $_SETT['var_pathogenic'], false, false, false),
                                  ));

        if (IS_CURATOR) {
            // Authorized user logged in; provide status control.
            $aForm = array_merge($aForm,
                                 array(
                                        array('Pathogenicity (concluded)', 'select', 'pathogenic_concluded', 1, $_SETT['var_pathogenic'], false, false, false),
                                        array('Variant status', 'select', 'status', 1, $_SETT['var_status'], false, false, false),
                                      ));
        }

        $aForm = array_merge($aForm,
                             array(
                                    'skip',
                                    // 2007-08-08; 2.0-beta-07; Added "cancel" button.
                                    array('', 'print', '<INPUT type="submit" value="Add new variant">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<INPUT type="submit" value="Cancel" onclick="document.forms[1].submit(); return false;" style="border : 1px solid #FF4422;">'),
                                  ));

        $_MODULES->processForm('SubmitVariantData', $aForm);
        lovd_viewForm($aForm);

        print('</TABLE></FORM>' . "\n\n");

        // This form is merely to support the "Cancel" button. Because we need a $_POST value in the next page.
        print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '" method="post">' . "\n" .
              '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
              '      </FORM>' . "\n\n");

        require ROOT_PATH . 'inc-bot.php';
        exit;
    }





    // Step 4: Show options / overview.
    require ROOT_PATH . 'inc-lib-list.php';
    lovd_showInfoTable('Please note that your submission is only stored <I>after</I> you click the button "Finalize submission".', 'warning');
    if (!IS_CURATOR) {
        print('      On submission, your data will be collected and stored in the database. You will immediately receive a confirmation email and the curator(s) of the specified gene will be notified that a new submission has taken place. Your submission will appear online when the curator agrees with your findings.<BR><BR>' . "\n\n");
    }



    // Do we have some patient data already?
    print('      <HR>' . "\n" .
          '      <B>Patient data</B><BR>' . "\n");
    if (empty($_SESSION['submit_pat'])) {
        $nPat = 0;
        print('      <BR>' . "\n" .
              '      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;add=pat" method="post">' . "\n" .
              '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
              '        <INPUT type="hidden" name="patientid" value="">' . "\n" .
              '        <INPUT type="submit" value="Add new patient data &raquo;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;');
        if (!isset($_GET['hide'])) {
            print('<INPUT type="submit" value="Use an existing patient &raquo;" onclick="var patid = window.prompt(\'Please insert the internal Patient ID reference number\', \'\'); if (patid) { document.forms[0].patientid.value = patid; } else { return false; }">');
        }
        print("\n" .
              '      </FORM>' . "\n");
        // 2010-03-10; 2.0-25; Not having submitted patient data yet has become a fatal error.
        require ROOT_PATH . 'inc-bot.php';
        exit;

    } else {
        // Show patient data list.
        $nPat = count($_SESSION['submit_pat']);

        // Array which will make up the table (header and data).
        $aTable = $_CURRDB->buildTable('list');

        // Remove columns not for variants.
        $aCols = $_CURRDB->getColList('Patient');
        foreach ($aTable as $sCol => $aCol) {
            if (!in_array($sCol, $aCols)) {
                unset($aTable[$sCol]);
            }
        }

        // Add Del column.
        $aTable['del'] = array('&nbsp;', '14', 'valign="middle" align="center"');

        // Total width.
        $nTotalWidth = 2;
        foreach ($aTable as $aCol) {
            $nTotalWidth += $aCol[1] + 8;
        }

        // Stretch table up, to respect column widths.
        print('      <IMG src="' . ROOT_PATH . 'gfx/trans.png" alt="" width="' . $nTotalWidth . '" height="1"><BR>' . "\n\n");

        // Table.
        print('      <TABLE border="0" cellpadding="0" cellspacing="1" class="data">' . "\n" .
              '        <TR>');

        foreach ($aTable as $sField => $aCol) {
            print("\n" . '          <TH' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . $aCol[0] . '</TH>');
        }
        print('</TR>');

        $zData = $_SESSION['submit_pat'];
        print("\n" .
              '        <TR valign="top" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';">');

        // $zData is taken from a form, and is therefore still quoted.
        lovd_magicUnquote($zData);

        $zData['del'] = '<A href="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;gene=' . $_POST['gene'] . '&amp;delete=pat" onclick="if (!confirm(\'Are you sure to remove this data from your submission?\')) { return false; } return true;"><IMG src="gfx/mark_0.png" alt="Delete" title="Delete" width="11" height="11" border="0"></A>';

        // Parse and build Custom Links.
        lovd_buildLinks($zData);

        // Transform select lists' values.
        $_CURRDB->transformSelectValues($zData);

        // 2008-10-02; 2.0-13; Allow curator to set submitter.
        if ($_CURRDB->colExists('Patient/Reference') && $zData['submitterid']) {
            list($sReference) = mysql_fetch_row(mysql_query('SELECT reference FROM ' . TABLE_SUBS . ' WHERE submitterid = "' . $zData['submitterid'] . '"'));
            if ($sReference) {
                $zData['Patient/Reference'] .= (!empty($zData['Patient/Reference'])? ', ' : '') . '<A href="#" onclick="lovd_openWindow(\'' . ROOT_PATH . 'submitters.php?action=view&amp;view=' . $zData['submitterid'] . lovd_showSID(true, true) . '\', \'SubmitterView\', 400, 175, event.screenX - 50, event.screenY - 50); return false;">' . $sReference . '</A>';
            }
        }

        foreach ($aTable as $sField => $aCol) {
            print("\n" . '          <TD' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . (!$zData[$sField]? '-' : $zData[$sField]) . '</TD>');
        }
        print('</TR>');
        print('</TABLE><BR>' . "\n");
    }

    print('      <HR> ' . "\n" .
          '      <BR><BR>' . "\n\n");



    // Do we have some mutation data already?
    print('      <HR>' . "\n" .
          '      <B>Sequence variant data</B><BR>' . "\n");
    if (!count($_SESSION['submit_muts'][$_POST['gene']])) {
        $nMuts = 0;
        print('      <BR>' . "\n");

    } else {
        // Show mutation list.
        $nMuts = count($_SESSION['submit_muts'][$_POST['gene']]);
        print('      <SPAN class="S11">' . $nMuts . ' entr' . ($nMuts == 1? 'y' : 'ies') . '</SPAN><BR>' . "\n");

        // Array which will make up the table (header and data).
        $aTable = $_CURRDB->buildTable('list');

        // Remove columns not for variants.
        $aCols = $_CURRDB->getColList('Variant');
        foreach ($aTable as $sCol => $aCol) {
            if (!in_array($sCol, $aCols)) {
                unset($aTable[$sCol]);
            }
        }

        // Add columns.
        $aTable = array_merge(
                 array(
                        'pathogenic_' => array('Path.', 40),
                        'allele' => array('Allele', '120'),
                      ),
                 $aTable,
                 array(
                        'status' => array('Status', '60'),
                        'del' => array('&nbsp;', '14', 'valign="middle" align="center"'),
                      ));

        // Total width.
        $nTotalWidth = 2;
        foreach ($aTable as $aCol) {
            $nTotalWidth += $aCol[1] + 8;
        }

        // Stretch table up, to respect column widths.
        print('      <IMG src="' . ROOT_PATH . 'gfx/trans.png" alt="" width="' . $nTotalWidth . '" height="1"><BR>' . "\n\n");

        // Table.
        print('      <TABLE border="0" cellpadding="0" cellspacing="1" class="data">' . "\n" .
              '        <TR>');

        foreach ($aTable as $sField => $aCol) {
            print("\n" . '          <TH' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . $aCol[0] . '</TH>');
        }
        print('</TR>');

        foreach ($_SESSION['submit_muts'][$_POST['gene']] as $nVar => $zData) {
            print("\n" .
                  '        <TR valign="top" onmouseover="this.className = \'hover\';" onmouseout="this.className = \'\';">');

            // $zData is taken from a form, and is therefore still quoted.
            lovd_magicUnquote($zData);

            $zData['pathogenic_'] = $_SETT['var_pathogenic_short'][$zData['pathogenic']];
            $zData['allele']      = $_SETT['var_allele'][$zData['allele']];
            $nVar                 = str_pad($nVar, 2, '0', STR_PAD_LEFT);
            $zData['del']         = '<A href="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;gene=' . $_POST['gene'] . '&amp;delete=var' . $nVar . '" onclick="if (!confirm(\'Are you sure to remove this data from your submission?\')) { return false; } return true;"><IMG src="gfx/mark_0.png" alt="Delete" title="Delete" width="11" height="11" border="0"></A>';
            $zData['status']      = $_SETT['var_status'][$zData['status']];

            // Parse and build Custom Links.
            lovd_buildLinks($zData);

            // Transform select lists' values.
            $_CURRDB->transformSelectValues($zData);

            foreach ($aTable as $sField => $aCol) {
                print("\n" . '          <TD' . (!empty($aCol[2])? ' ' . $aCol[2] : '') . (is_numeric($aCol[1])? ' width="' . $aCol[1] . '"' : '') . '>' . (!$zData[$sField]? '-' : $zData[$sField]) . '</TD>');
            }
            print('</TR>');
        }
        print('</TABLE><BR>' . "\n");
    }

    // 2010-12-02; 2.0-30; Added focus() to make sure the popup window does not stay hidden when it was already opened.
    print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;add=var" id="variant_form" method="post">' . "\n" .
          '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
          '        <INPUT type="hidden" name="variant_name" value="">' . "\n" .
          '        <INPUT type="submit" value="Add ' . (count($_SESSION['submit_muts'][$_POST['gene']])? 'more variants' : 'a new variant') . ' &raquo;">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<INPUT type="submit" value="Use an existing variant &raquo;" onclick="SearchVar=lovd_openWindow(\'' . $_SERVER['PHP_SELF'] . '?action=search_var&amp;gene=' . $_POST['gene'] . lovd_showSID(true, true) . '\', \'SearchVar\', 400, 175); SearchVar.focus(); return false;">' . "\n" .
          '      </FORM>' . "\n" .
          '      <HR> ' . "\n" .
          '      <BR><BR>' . "\n\n");



    // Finalize submission.
    // 2009-06-09; 2.0-19; If finalize button is clicked before both variant and patient data are submitted you will get an error message.
    print('      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=finalize" method="post">' . "\n" .
          '        <INPUT type="hidden" name="gene" value="' . $_POST['gene'] . '">' . "\n" .
          '        <INPUT type="submit" value="Finalize submission" style="font-weight : bold;');
    if (!($nMuts && $nPat)) {
        $sMessage = 'Unable to process an incomplete submission!\n';
        if ($nMuts && !$nPat) {
            $sMessage .= 'Please also provide patient data - without patient data';
        } elseif (!$nMuts && $nPat) {
            $sMessage .= 'Please also provide variant data - without variant data';
        } else {
            $sMessage .= 'You have not entered any information yet - without patient or variant data';
        }
        $sMessage .= ' we cannot process your submission.';
        print(' color : #AAAAAA;" onclick="alert(\'' . $sMessage . '\'); return false;"');
    }
    print('">' . "\n" .
          '      </FORM>' . "\n");

    require ROOT_PATH . 'inc-bot.php';
    exit;





} elseif ($_GET['action'] == 'finalize' && !empty($_POST['gene']) && in_array($_POST['gene'], lovd_getGeneList()) && !empty($_SESSION['submit_muts'][$_POST['gene']]) && !empty($_SESSION['submit_pat'])) {
    // Put all the stuff in the database.

    // Require form functions - just for lovd_sort() and lovd_wrapText();
    require ROOT_PATH . 'inc-lib-form.php';

    // Finalize submission; put in database and mail people.
    require ROOT_PATH . 'inc-top.php';
    require ROOT_PATH . 'class/currdb.php';
    $_CURRDB = new CurrDB(true, $_POST['gene']);
    $_CURRDB->hideCols('public_form', lovd_isCurator($_POST['gene']));
    lovd_printHeader('submit', 'Submit new sequence variant');

    // If using transactional tables; begin transaction.
    if ($_INI['database']['engine'] == 'InnoDB') {
        // FIXME; It's better to use 'START TRANSACTION', but that's only available from 4.0.11.
        //   This works from the introduction of InnoDB in 3.23.
        @mysql_query('BEGIN WORK');
    }



    // Step 1: Add patient to database.
    if (empty($_SESSION['submit_patid'])) {
        $sQ = 'INSERT INTO ' . TABLE_PATIENTS . ' (';
        $aColsToCopy = $_CURRDB->getColList('Patient');
        // 2008-10-02; 2.0-13; SubmitterID is now sent by patient form.
        $aColsToCopy[] = 'submitterid';
        $aCol = array();
        foreach ($aColsToCopy as $sCol) {
            if (isset($_SESSION['submit_pat'][$sCol])) {
                $sQ .= (substr($sQ, -1) == '('? '' : ', ') . '`' . $sCol . '`';
                $aCol[] = $_SESSION['submit_pat'][$sCol];
            }
        }
        $sQ .= ', created_by, created_date) VALUES (';

        // FIXME; reference should include the submitter stuff, as indicated by him.
        foreach ($aCol as $key => $val) {
            $sQ .= ($key? ', ' : '') . '"' . $val . '"';
        }
        // 2008-10-02; 2.0-13; SubmitterID is now sent by patient form.
        // "0" (created_by) means submitter; "ID" means user.
        $sQ .= ', "' . (HAS_AUTH? $_AUTH['userid'] : '0') . '", NOW())';

        $q = mysql_query($sQ);
        if (!$q) {
            lovd_dbFout('SubmitNew_A', $sQ, mysql_error());
        }
    
        // Remember patient id.
        $nPatientID = str_pad(mysql_insert_id(), 7, '0', STR_PAD_LEFT);

    } else {
        // Patient ID was stored, therefore we're not inserting into the database.
        $nPatientID = $_SESSION['submit_patid'];
    }



    // Step 2: Add variants + links to database.
    $aColsToCopy = $_CURRDB->getColList('Variant');
    $aVariantIDs = array();
    // 2008-10-09; 2.0-13; Use this separate array because we don't want to loose existing variants when things to wrong.
    $aVariantsAdded = array();
    $nMinStatus  = STATUS_NEW; // Determine the min status for the submission email.

    $sMutationCol = $_CURRDB->getMutationCol();
    if ($sMutationCol && in_array($sMutationCol, array('Variant/DNA', 'Variant/RNA'))) {
        // Find mutation column, include sort column in list.
        $aColsToCopy[] = 'sort';
    }

    foreach ($_SESSION['submit_muts'][$_POST['gene']] as $nMut => $aMut) {
        // Determine sort code if sort column is in the list.
        if (in_array('sort', $aColsToCopy)) {
            // 2009-06-12; 2.0-19; Added exon column for better search results.
            // A bit crude; we're not checking if Variant/Exon exists, we just suppress a possible notice.
            $aMut['sort'] = @lovd_sort($aMut[$sMutationCol], $aMut['Variant/Exon']);
        }

        // 2008-04-24; 2.0-06; Include auto generated Variant/DBID field for submitters.
        if (array_search('Variant/DBID', $aColsToCopy) === false && !empty($aMut['Variant/DBID'])) {
            // Variant/DBID was hidden, but value is filled in.
            $aColsToCopy[] = 'Variant/DBID';
        }

        // Determine if mutation already exists in database. If so, insert link only.
        $sQ = 'SELECT variantid FROM ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants WHERE ';
        foreach ($aColsToCopy as $key => $sCol) {
            if (isset($aMut[$sCol])) {
                $sQ .= (!$key? '' : ' AND ') . '`' . $sCol . '` = "' . $aMut[$sCol] . '"';
            }
        }
        $sQ .= ' ORDER BY variantid LIMIT 1';
        list($nVariantID) = @mysql_fetch_row(mysql_query($sQ));
        if (!$nVariantID) {
            // Not found!
            $sQ = 'INSERT INTO ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants (';
            $nMut = str_pad($nMut + 1, 2, '0', STR_PAD_LEFT); // 01, 02, 03, 04 ...
            $aCol = array();
            foreach ($aColsToCopy as $sCol) {
                if (isset($aMut[$sCol])) {
                    $sQ .= (substr($sQ, -1) == '('? '' : ', ') . '`' . $sCol . '`';
                    $aCol[] = $aMut[$sCol];
                }
            }
            $sQ .= ') VALUES (';

            foreach ($aCol as $key => $val) {
                $sQ .= ($key? ', ' : '') . '"' . $val . '"';
            }
            $sQ .= ')';

            $q = mysql_query($sQ);
            if (!$q) {
                // Save the mysql_error before it disappears.
                $sError = mysql_error();

                if ($_INI['database']['engine'] == 'InnoDB') {
                    @mysql_query('ROLLBACK');
                } else {
                    if (empty($_SESSION['submit_patid'])) {
                        @mysql_query('DELETE FROM ' . TABLE_PATIENTS . ' WHERE patientid = "' . $nPatientID . '"');
                    }
                    // 2008-10-09; 2.0-13; Use this separate array because we don't want to loose existing variants when things to wrong.
                    if (count($aVariantsAdded)) {
                        @mysql_query('DELETE FROM ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants WHERE variantid = "' . implode('" OR variantid = "', $aVariantsAdded) . '"');
                    }
                    // 2008-10-09; 2.0-13; Nor do we want to loose the Pat2Var values...
                    if (empty($_SESSION['submit_patid'])) {
                        @mysql_query('DELETE FROM ' . TABLE_PAT2VAR . ' WHERE patientid = "' . $nPatientID . '"');
                    }
                }
                lovd_dbFout('SubmitNew_B' . $nMut, $sQ, $sError);
            }

            // Remember variant id.
            $nVariantID = str_pad(mysql_insert_id(), 7, '0', STR_PAD_LEFT);
            $aVariantsAdded[] = $nVariantID;
        }



        // Store variant id.
        $aVariantIDs[] = $nVariantID;

        // FIXME; 0 (created_by) means, not a user. How do we do this with submitters?
        $sQ = 'INSERT INTO ' . TABLE_PAT2VAR . ' VALUES ("' . $nPatientID . '", "' . $aMut['allele'] . '", "' . $_POST['gene'] . '", "' . $nVariantID . '", "' . $aMut['pathogenic'] . '", "' . $aMut['status'] . '", "' . (HAS_AUTH? $_AUTH['userid'] : 0) . '", NOW(), NULL, NULL)';
        $q = mysql_query($sQ);
        if (!$q) {
            // Save the mysql_error before it disappears.
            $sError = mysql_error();

            if ($_INI['database']['engine'] == 'InnoDB') {
                @mysql_query('ROLLBACK');
            } else {
                if (empty($_SESSION['submit_patid'])) {
                    @mysql_query('DELETE FROM ' . TABLE_PATIENTS . ' WHERE patientid = "' . $nPatientID . '"');
                }
                // 2008-10-09; 2.0-13; Use this separate array because we don't want to loose existing variants when things to wrong.
                if (count($aVariantsAdded)) {
                    @mysql_query('DELETE FROM ' . TABLEPREFIX . '_' . $_POST['gene'] . '_variants WHERE variantid = "' . implode('" OR variantid = "', $aVariantsAdded) . '"');
                }
                // 2008-10-09; 2.0-13; Nor do we want to loose the Pat2Var values...
                if (empty($_SESSION['submit_patid'])) {
                    @mysql_query('DELETE FROM ' . TABLE_PAT2VAR . ' WHERE patientid = "' . $nPatientID . '"');
                }
            }
            lovd_dbFout('SubmitNew_C' . $nMut, $sQ, $sError);
        }

        // Store status, so we can see if curator even needs to publish anything from this submission.
        if ($nMinStatus > $aMut['status']) {
            $nMinStatus = $aMut['status'];
        }
    }

    // If we don't do this, we haven't got anything in the DB... duh!
    if ($_INI['database']['engine'] == 'InnoDB') {
        // Could this actually fail?!!??
        @mysql_query('COMMIT');
    }

    // 2007-12-05; 2.0-02; Fixed bug #20 - Gene's "Last update" field not updated.
    if (lovd_isCurator($_POST['gene'])) {
        // We assume here that curators and up will probably submit entries as public and therefore 'change' the way the database looks like for the public.
        lovd_setUpdatedDate($_POST['gene']);
    }

    // Submission completed successfully!
    // 2009-11-25; 2.0-23; Reset mapping counter.
    $_SESSION['mapping']['time_complete'] = 0;

    // Write to log...
    lovd_writeLog('MySQL:Event', 'SubmitNew', $_AUTH['username'] . ' (' . mysql_real_escape_string($_AUTH['name']) . ') successfully created new submission for ' . $_POST['gene'] . ' (Patient #' . $nPatientID . '; Mutation' . (count($aVariantIDs) == 1? '' : 's') . ' #' . implode(', #', $aVariantIDs) . ')');



    // Step 3: Mail curators and submitter.
    // Grab email adresses of addressees, to prevent double emails.
    $aEmails = array();

    // Find me the curator of this gene...
    $qCurators = mysql_query('SELECT u.name, u.email FROM ' . TABLE_CURATES . ' AS c, ' . TABLE_USERS . ' AS u WHERE c.userid = u.userid AND c.symbol = "' . $_POST['gene'] . '" ORDER BY u.level DESC, u.name');
    $nCurators = mysql_num_rows($qCurators);
    $sCurators = '';
    while ($r = mysql_fetch_row($qCurators)) {
        // If email hasn't been added before, add it.
        if (!in_array($r[1], $aEmails)) {
            // 2009-02-27; 2.0-16; Sending emails on Windows requires removal of names from the email addresses.
            $sCurators .= ($sCurators? ', ' : '') . (ON_WINDOWS? '' : '"' . $r[0] . '" ') . '<' . $r[1] . '>';
            $aEmails[] = $r[1];
        }
    }

    // 2009-02-27; 2.0-16; Sending emails on Windows requires removal of names from the email addresses.
    $sSubmitter = (ON_WINDOWS? '' : '"' . $_AUTH['name'] . '" ') . '<' . str_replace(array("\r\n", "\r", "\n"), '>, <', trim($_AUTH['email'])) . '>';

    $sBody = 'LOVD ' . $_SETT['system']['version'] . ' @ ' . $_CONF['location_name'] . ' for ' . $_POST['gene'] . "\n" .
             'To Curator' . ($nCurators == 1? ' ' : 's') . '  : ' . str_replace('"', '', $sCurators) . "\n" .
             'CC Submitter : ' . str_replace('"', '', $sSubmitter) . "\n\n" .
             'Dear Curator' . ($nCurators == 1? '' : 's') . ',' . "\n\n" .
             $_AUTH['name'] . ' has submitted an addition to the ' . $_POST['gene'] . ' database.' . "\n" .
             ($nMinStatus <  STATUS_MARKED? 'This submission won\'t be viewable to the public until you as curator agree with the additions. ' : '') .
             'Below is a copy of the submission.' . "\n\n";
    // 2009-04-06; 2.0-17; Add the location of the new entry, so that the curator can just click the link.
    if ($_CONF['location_url']) {
        $sBody .= 'To view the new entry, click this link (you may need to log in first):' . "\n" .
                  $_CONF['location_url'] . 'variants.php?select_db=' . $_POST['gene'] . '&action=view&view=' . $nPatientID . "\n\n";
    }
    $sBody .= 'Regards,' . "\n" .
              '    LOVD system at ' . $_CONF['location_name'] . "\n\n";

    // Submitter information.
    $sBody .= str_repeat('-', 80) . "\n" .
              '  SUBMITTER DETAILS' . "\n" .
              str_repeat('-', 80) . "\n";

    // Array containing the fields.
    $aMail =
             array(
                    'submitterid' => 'Submitter ID',
                    'userid' => 'User ID',
                    'name' => 'Name',
                    'institute' => 'Institute',
                    'department' => 'Department',
                    'address' => 'Address',
                    'city' => 'City',
                    'country_' => 'Country',
                    'email' => 'Email address',
                    'telephone' => 'Telephone',
                  );

    // Remove unnecessary columns.
    if (HAS_AUTH) {
        unset($aMail['submitterid'], $aMail['department'], $aMail['address'], $aMail['city'], $aMail['country_'], $aMail['telephone']);
    } else {
        unset($aMail['userid']);
    }

    // Fetching country name.
    if (!HAS_AUTH) {
        list($_AUTH['country_']) = mysql_fetch_row(mysql_query('SELECT country FROM ' . TABLE_COUNTRIES . ' WHERE code = "' . $_AUTH['country'] . '"'));
    }

    // Padding to...
    $lPad = 0;
    foreach ($aMail as $val) {
        $l = strlen($val);
        if ($l > $lPad) {
            $lPad = $l;
        }
    }

    foreach ($aMail as $key => $val) {
        $sBody .= str_pad($val, $lPad) . ' : ' . str_replace("\n", "\n" . str_repeat(' ', $lPad + 3), lovd_wrapText($_AUTH[$key], 80 - $lPad - 3)) . "\n";
    }
    $sBody .= str_repeat('-', 80) . "\n\n";

    // Variant information.
    $sBody .= str_repeat('-', 80) . "\n" .
              '  VARIANT DETAILS' . "\n" .
              str_repeat('-', 80) . "\n";

    // Array containing the fields.
    $aMail = $_CURRDB->buildTable('detail');

    // Remove columns not for variants.
    $aCols = $_CURRDB->getColList('Variant');
    foreach ($aMail as $sCol => $aCol) {
        if (!in_array($sCol, $aCols)) {
            unset($aMail[$sCol]);
        }
    }

    // Add columns.
    $aMail = array_merge(
             array(
                    'pathogenic' => 'Pathogenic',
                    'allele' => 'Allele',
                  ),
             $aMail,
             array(
                    'status' => 'Status',
                  ));

    // Padding to...
    $lPad = 0;
    foreach ($aMail as $val) {
        $l = strlen($val);
        if ($l > $lPad) {
            $lPad = $l;
        }
    }

    // Loop the variant data.
    foreach ($_SESSION['submit_muts'][$_POST['gene']] as $nVar => $zData) {
        // Good practice when mailing and printing.
        lovd_magicUnquote($zData);

        $zData['pathogenic'] = $_SETT['var_pathogenic'][$zData['pathogenic']{0}] . (HAS_AUTH? ' (reported) / ' . $_SETT['var_pathogenic'][$zData['pathogenic']{1}] . ' (concluded)' : '');
        $zData['allele']     = $_SETT['var_allele'][$zData['allele']];
        $zData['status']     = $_SETT['var_status'][$zData['status']];

        // Transform select lists' values.
        $_CURRDB->transformSelectValues($zData);

        foreach ($aMail as $key => $val) {
            $sBody .= str_pad($val, $lPad) . ' : ' . str_replace("\n", "\n" . str_repeat(' ', $lPad + 3), lovd_wrapText($zData[$key], 80 - $lPad - 3)) . "\n";
        }
        $sBody .= str_repeat('-', 80) . "\n";
    }
    $sBody .= "\n";

    // Patient information.
    $sBody .= str_repeat('-', 80) . "\n" .
              '  PATIENT DETAILS' . (empty($_SESSION['submit_patid'])? '' : ' (Addition to existing patient)') . "\n" .
              str_repeat('-', 80) . "\n";

    // Array containing the fields.
    $aMail = $_CURRDB->buildTable('detail');

    // Remove columns not for variants.
    $aCols = $_CURRDB->getColList('Patient');
    foreach ($aMail as $sCol => $aCol) {
        if (!in_array($sCol, $aCols)) {
            unset($aMail[$sCol]);
        }
    }

    // Padding to...
    $lPad = 0;
    foreach ($aMail as $val) {
        $l = strlen($val);
        if ($l > $lPad) {
            $lPad = $l;
        }
    }

    // Loop the variant data.
    $zData = $_SESSION['submit_pat'];

    // Good practice when mailing and printing.
    lovd_magicUnquote($zData);

    // Transform select lists' values.
    $_CURRDB->transformSelectValues($zData);

    foreach ($aMail as $key => $val) {
        $sBody .= str_pad($val, $lPad) . ' : ' . str_replace("\n", "\n" . str_repeat(' ', $lPad + 3), lovd_wrapText($zData[$key], 80 - $lPad - 3)) . "\n";
    }
    $sBody .= str_repeat('-', 80) . "\n";

    // Set proper subject.
    $sSubject = 'LOVD submission (' . $_POST['gene'] . ')';

    // Send mail.
    $bMail = @mail($sCurators,
                   $sSubject,
                   lovd_wrapText($sBody),
                   $_SETT['headers'] . $sEol .
                   'Reply-To: ' . $sSubmitter .
                   (HAS_AUTH && in_array($_AUTH['email'], $aEmails)? '' : $sEol . 'Cc: ' . $sSubmitter));
    if (HAS_AUTH) {
        $aEmails[] = $_AUTH['email'];
    }



    // Step 4: Possibly, mail the database admin if he's not the submitter or the curator(s).
    if ($bMail) {
        if ($_CONF['send_fwd'] && !in_array($_SETT['admin']['email'], $aEmails)) {
            // Sent mail to curator(s), send copy to database administrator.
            $sBody = 'Dear ' . $_SETT['admin']['name'] . ",\n\n" .
                     'As requested, a copy of the message I\'ve just sent.' . "\n\n" .
                     str_repeat('-', 30) . ' Forwarded  Message ' . str_repeat('-', 30) . "\n\n" .
                     rtrim($sBody) . "\n\n" .
                     str_repeat('-', 27) . ' End of Forwarded Message ' . str_repeat('-', 27) . "\n";

            // Send mail.
            // 2009-02-27; 2.0-16; Sending emails on Windows requires removal of names from the email addresses.
            $bMail = @mail((ON_WINDOWS? '' : '"' . $_SETT['admin']['name'] . '" ') . '<' . $_SETT['admin']['email'] . '>',
                           'Fw: ' . $sSubject,
                           lovd_wrapText($sBody),
                           $_SETT['headers'] . $sEol .
                           'Reply-To: ' . $sSubmitter);

            if (!$bMail) {
                // Couldn't sent confirmation to admin...
                lovd_writeLog('MySQL:Error', 'EmailNotify', $_SERVER['PHP_SELF'] . ' returned SubmitNewNotifyAdmin error for submitter ' . $_AUTH['username'] . ' (' . mysql_real_escape_string($_AUTH['name']) . ')');
            }
        }

        // Thank the user...
        print('      Thank you, ' . $_AUTH['name'] . '. Your submission was successful!<BR>' . "\n" .
              '      The curator' . ($nCurators == 1? '' : 's') . ' of the ' . $_POST['gene'] . ' database ha' . ($nCurators == 1? 's' : 've') . ' been sent an email containing your submission. A copy has been sent to you.<BR><BR>' . "\n\n");

    } else {
        // Couldn't sent confirmation...
        lovd_writeLog('MySQL:Error', 'EmailNotify', $_SERVER['PHP_SELF'] . ' returned SubmitNewNotify error for submitter ' . $_AUTH['username'] . ' (' . mysql_real_escape_string($_AUTH['name']) . ')');

        print('      Thank you, ' . $_AUTH['name'] . '. Your submission was successful!<BR>' . "\n" .
              '      <B>Due to an unknown error, no email regarding the submission could be sent to the curator' . ($nCurators == 1? '' : 's') . ' of the ' . $_POST['gene'] . ' database. Your submission has successfully been added to the database.</B><BR><BR>' . "\n\n");
    }

    // 2009-06-11; 2.0-19; Authorized users: jump back to the patient.
    if (HAS_AUTH) {
        print('      <SCRIPT type="text/javascript">' . "\n" .
              '        <!--' . "\n" .
              '        setTimeout("window.location.href = \'' . PROTOCOL . $_SERVER['HTTP_HOST'] . rtrim(dirname($_SERVER['PHP_SELF'])) . '/variants.php' . '?select_db=' . $_POST['gene'] . '&action=view&view=' . $nPatientID . '\'", ' . ($bMail? 2000 : 5000) . ');' . "\n" .
              '        // -->' . "\n" .
              '      </SCRIPT>' . "\n\n");
    }

    // Now that we're done, we must clean the $_SESSION vars.
    $_SESSION['submit_pat'] = array();
    unset($_SESSION['submit_patid']);
    $_SESSION['submit_muts'][$_POST['gene']] = array();

    require ROOT_PATH . 'inc-bot.php';
    exit;





} elseif ($_GET['action'] == 'search_var' && !empty($_GET['gene']) && in_array($_GET['gene'], lovd_getGeneList())) {
    // Search for mutation, and send it's ID to the form so that the data can be loaded.

    require ROOT_PATH . 'inc-top-clean.php';

    // Fetch mutation names.
    require ROOT_PATH . 'class/currdb.php';
    $_CURRDB = new CurrDB(true, $_GET['gene']);
    $sMutationCol = $_CURRDB->getMutationCol();
    $aMuts = array();
    // In case this doesn't run: big deal! It's just a service to the user, that's all.
    $qMuts = @mysql_query('SELECT DISTINCT `' . $sMutationCol . '` FROM ' . TABLEPREFIX . '_' . $_GET['gene'] . '_variants ORDER BY ' . ($_CURRDB->colExists('Variant/Exon')? '`Variant/Exon`, ' : '') . 'sort');
    while ($r = @mysql_fetch_row($qMuts)) {
        $aMuts[] = $r[0];
    }
    $sMuts = '["' . implode('",' . "\n" . '                "', $aMuts) . '"];';

    // Show form and all.
    lovd_includeJS('inc-js-autocomplete.js');

    print("\n" .
          '      <TABLE border="0" cellpadding="0" cellspacing="0" width="100%"><TR><TD>' . "\n" .
          '      Please insert the mutation name below.<BR><BR>' . "\n\n" .
          '      <FORM action="' . $_SERVER['PHP_SELF'] . '?action=' . $_GET['action'] . '&amp;gene=' . $_GET['gene'] . '" method="post" onsubmit="opener.document.forms[\'variant_form\'][\'variant_name\'].value = this[\'variant_name\'].value; opener.document.forms[\'variant_form\'].submit(); self.close();">' . "\n" .
          '        <INPUT type="text" name="variant_name" size="30" value="" id="variant_name"><BR>' . "\n" .
          '        <INPUT type="submit" value="Cancel" onclick="self.close(); return false;" style="border : 1px solid #FF4422;">' . "\n" .
          '        <INPUT type="submit" value="Review variant data &raquo;">' . "\n" .
          '      </FORM>' . "\n");
    print('      </TD></TR></TABLE>' . "\n\n");

    // 2007-12-14; 2.0-02; Fixing feature non-functional in IE.
    // Normally, we would just print it out here, but that doesn't work in IE. So we're going to dump it in inc-bot-clean.php.
    $sBotClean = '      <SCRIPT type="text/javascript">' . "\n" .
                 '        <!--' . "\n" .
                 '        data = ' . $sMuts . "\n\n" .
                 '        AutoComplete_Create("variant_name", data, 5);' . "\n" .
                 '        // -->' . "\n" .
                 '      </SCRIPT>' . "\n\n";

    require ROOT_PATH . 'inc-bot-clean.php';
    exit;





} else {
    // Default action:
    header('Location: ' . PROTOCOL . $_SERVER['HTTP_HOST'] . $_SERVER['PHP_SELF'] . lovd_showSID());
    exit;
}
?>
