<?php
/*******************************************************************************
 *
 * LEIDEN OPEN VARIATION DATABASE (LOVD)
 *
 * Created     : 2011-02-21
 * Modified    : 2016-06-17
 * For LOVD    : 3.0-16
 *
 * Copyright   : 2004-2016 Leiden University Medical Center; http://www.LUMC.nl/
 * Programmers : Ing. Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
 *               Jerry Hoogenboom <J.Hoogenboom@LUMC.nl>
 *               Ing. Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
 *               Msc. Daan Asscheman <D.Asscheman@LUMC.nl>
 *               M. Kroon <m.kroon@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 3 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, see <http://www.gnu.org/licenses/>.
 *
 *************/

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

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

// Require any user level.
lovd_requireAUTH(LEVEL_SUBMITTER);

function lovd_prepareSubmitData ($sDataType, $aData) {
    // Prepares the data for presentation in the mail to the users.
    global $_AUTH, $_DB, $_SETT;

    switch ($sDataType) {
        case 'individual':
            $aData['panel_'] = ($aData['panel_size'] <= 1? 'No' : 'Yes');
            break;
        case 'variant':
            if (!empty($aData['aTranscripts'])) {
                foreach ($aData['aTranscripts'] as $nTranscriptID) {
                    $aData[$nTranscriptID . '_effect_reported'] = $_SETT['var_effect'][$aData[$nTranscriptID . '_effectid']{0}];
                    $aData[$nTranscriptID . '_effect_concluded'] = $_SETT['var_effect'][$aData[$nTranscriptID . '_effectid']{1}];
                }
            }
            $aData['effect_reported'] = $_SETT['var_effect'][$aData['effectid']{0}];
            $aData['effect_concluded'] = $_SETT['var_effect'][$aData['effectid']{1}];
            break;
    }

    if (isset($aData['statusid'])) {
        $aData['statusid_'] = $_SETT['data_status'][$aData['statusid']];
    }
    if (!empty($aData['edited_by'])) {
        if ($aData['edited_by'] == $_AUTH['id']) {
            $aData['edited_by'] = $_AUTH['name'];
        } else {
            $aData['edited_by'] = $_DB->query('SELECT name FROM ' . TABLE_USERS . ' WHERE id = ?', array($aData['edited_by']))->fetchColumn();
        }
    }

    return $aData;
}




if (PATH_COUNT == 1 && !ACTION) {
    // URL: /submit
    // Submission process

    // 2012-07-10; 3.0-beta-07; Submitters are no longer allowed to add variants without individual data.
    if (!lovd_isAuthorized('gene', $_AUTH['curates'], false)) {
        header('Location: ' . lovd_getInstallURL() . 'individuals?create');
        exit;
    }

    define('PAGE_TITLE', 'Submit new information to this database');
    $_T->printHeader();
    $_T->printTitle();
    require ROOT_PATH . 'inc-lib-form.php';
    print('      Do you have any information available regarding an individual or a group of individuals?<BR><BR>' . "\n\n");

    $aOptionsList = array();
    $aOptionsList['options'][0]['onclick'] = 'individuals?create';
    $aOptionsList['options'][0]['option_text'] = '<B>Yes, I want to submit information on individuals</B>, such as phenotype or variant screening information';
    $aOptionsList['options'][1]['onclick'] = 'javascript:if(confirm(\'Please reconsider to submit individual data as well, as it makes the data you submit much more valuable!\nDo you want to continue anyway?\')){window.location.href=\'' . lovd_getInstallURL() . 'variants?create\';}';
    $aOptionsList['options'][1]['option_text'] = '<B>No, I will only submit summary variant data</B>';

    print(lovd_buildOptionTable($aOptionsList));

    $_T->printFooter();
    exit;
}





if (PATH_COUNT == 3 && $_PE[1] == 'individual' && ctype_digit($_PE[2]) && !ACTION) {
    // URL: /submit/individual/00000001
    // Individual submission
    global $_DB, $_AUTH;

    define('LOG_EVENT', 'SubmitIndividual');

    lovd_requireAUTH(LEVEL_SUBMITTER);

    $nID = sprintf('%08d', $_PE[2]);

    $zData = $_DB->query('SELECT * FROM ' . TABLE_INDIVIDUALS . ' WHERE id = ?', array($nID))->fetchAssoc();
    if (!isset($_AUTH['saved_work']['submissions']['individual'][$nID])) {
        define('PAGE_TITLE', 'Submit');
        $_T->printHeader();
        $_T->printTitle();
        lovd_showInfoTable('No such ID!', 'stop');
        $_T->printFooter();
        exit;
    }
    if (!isset($_SESSION['work']['submits']['individual'])) {
        $_SESSION['work']['submits']['individual'] = array();
    }
    while (count($_SESSION['work']['submits']['individual']) >= 10) {
        unset($_SESSION['work']['submits']['individual'][min(array_keys($_SESSION['work']['submits']['individual']))]);
    }
    $aSubmit = $_SESSION['work']['submits']['individual'][$nID] = $_AUTH['saved_work']['submissions']['individual'][$nID];

    $zData['diseases'] = $_DB->query('SELECT diseaseid FROM ' . TABLE_IND2DIS . ' WHERE individualid = ?', array($nID))->fetchAllColumn();
    if (count($zData['diseases'])) {
        $zDiseases = $_DB->query('SELECT id, name, symbol FROM ' . TABLE_DISEASES . ' WHERE id IN (?' . str_repeat(', ?', count($zData['diseases']) - 1) . ')', $zData['diseases'])->fetchAllAssoc();
        $aDiseases = array();
        foreach ($zDiseases as $a) {
            $aDiseases[$a['id']] = array('name' => $a['name'], 'symbol' => $a['symbol']);
        }
    }
    $bVariants = false;
    if (!empty($aSubmit['variants'])) {
        $bVariants = true;
    } elseif (!empty($aSubmit['confirmedVariants'])) {
        foreach ($aSubmit['confirmedVariants'] as $nVariants) {
            $bVariants = true;
            break;
        }
    } elseif (!empty($aSubmit['uploads'])) {
        foreach ($aSubmit['uploads'] as $aUpload) {
            if ($aUpload['num_variants'] >= 1) {
                $bVariants = true;
                break;
            }
        }
    }
    if (!empty($aSubmit['screenings'])) {
        $nScreeningsWithoutVariants = $_DB->query('SELECT COUNT(s.id) FROM ' . TABLE_SCREENINGS . ' AS s LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s.id = s2v.screeningid) WHERE s.variants_found = 1 AND s2v.variantid IS NULL AND s.id IN (?' . str_repeat(', ?', count($aSubmit['screenings']) - 1) . ')', $aSubmit['screenings'])->fetchColumn();
        if ($nScreeningsWithoutVariants) {
            $bVariants = false;
        }
    }

    $bScreenings = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_SCREENINGS . ' WHERE individualid = ?', array($nID))->fetchColumn();

    define('PAGE_TITLE', 'Submission of individual #' . $nID);

    $_T->printHeader();
    $_T->printTitle();
    require ROOT_PATH . 'inc-lib-form.php';
    print('      What would you like to do?<BR><BR>' . "\n\n");

    $sPersons = ($zData['panel_size'] > 1? 'this group of individuals' : 'this individual');
    $sScreeningsViewListID = 'Screenings_Submission_' . $nID;
    $sPhenotypesViewListID = 'Phenotypes_Submission_' . $nID . '_';

    $aOptionsList = array();
    //$aOptionsList['options'][0]['onclick'] = 'individuals/' . $nID . '?edit';
    //$aOptionsList['options'][0]['option_text'] = '<B>I want to edit ' . $sPersons . '</B>';

    if (count($zData['diseases'])) {
        $nDiseases = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_SHARED_COLS . ' WHERE diseaseid IN (?' . str_repeat(', ?', count($zData['diseases']) - 1) . ') GROUP BY diseaseid', $zData['diseases'])->fetchColumn();
        $sMessage = 'The disease' . (count($zData['diseases']) > 1? 's' : '') . ' added to ' . $sPersons . ' do' . (count($zData['diseases']) > 1? '' : 'es') . ' not have phenotype columns enabled yet.';
    } else {
        $nDiseases = 0;
        $sMessage = 'No diseases were selected for ' . $sPersons . '.\nThe phenotype information that can be submitted depends on the selected diseases.';
    }
    if (!$nDiseases) {
        $aOptionsList['options'][1]['disabled'] = true;
        $aOptionsList['options'][1]['onclick'] = 'javascript:alert(\'' . $sMessage . '\')';
    } else {
        $aOptionsList['options'][1]['onclick'] = 'phenotypes?create&amp;target=' . $nID;
    }
    $aOptionsList['options'][1]['option_text'] = '<B>I want to add phenotype information to ' . $sPersons . '</B>';

    //if (empty($aSubmit['phenotypes'])) {
    //    $aOptionsList['options'][2]['disabled'] = true;
    //    $aOptionsList['options'][2]['onclick'] = 'javascript:alert(\'No phenotypes are added yet to ' . $sPersons . '!\')';
    //} else {
    //    $aOptionsList['options'][2]['onclick'] = 'javascript:$(\'#container_screenings\').hide(); $(\'#container_phenotypes\').toggle(); var aDiseases = [\'' . implode('\', \'', $zData['diseases']) . '\']; for (i in aDiseases) { lovd_stretchInputs(\'' . $sPhenotypesViewListID . '\' + aDiseases[i]); }';
    //}
    //$aOptionsList['options'][2]['option_text'] = '<B>I want to edit a previously added phenotype entry</B>';
    $aOptionsList['options'][3]['onclick'] = 'screenings?create&amp;target=' . $nID;
    $aOptionsList['options'][3]['option_text'] = '<B>I want to add a variant screening to ' . $sPersons . '</B>';

    //if (empty($aSubmit['screenings'])) {
    //    $aOptionsList['options'][4]['disabled'] = true;
    //    $aOptionsList['options'][4]['onclick'] = 'javascript:alert(\'No variant screenings are added yet to ' . $sPersons . '!\')';
    //} else {
    //    $aOptionsList['options'][4]['onclick'] = 'javascript:$(\'#container_phenotypes\').hide(); $(\'#container_screenings\').toggle(); lovd_stretchInputs(\'' . $sScreeningsViewListID . '\');';
    //}
    //$aOptionsList['options'][4]['option_text'] = '<B>I want to manage a previously added variant screening</B>';

    if ($bScreenings) {
        $aOptionsList['options'][4]['option_text'] = '<B>I want to add a variant to ' . $sPersons . '</B>';
        $aOptionsList['options'][4]['onclick'] = 'submit/individual/' . $nID . '/screenings';
    }

    if (!$bVariants) {
        $aOptionsList['options'][5]['disabled'] = true;
        $aOptionsList['options'][5]['onclick']  = 'javascript:alert(\'You cannot finish your submission, because ' . (!empty($nScreeningsWithoutVariants)? 'not all screenings added to ' . $sPersons . ' have variants yet!' : 'no variants have been added to ' . $sPersons . ' yet!') . '\')';
    } else {
        $aOptionsList['options'][5]['onclick'] = 'submit/finish/individual/' . $nID;
    }
    $aOptionsList['options'][5]['option_text'] = '<B>I want to finish this submission</B>';

    print(lovd_buildOptionTable($aOptionsList));

    /*require ROOT_PATH . 'class/object_screenings.php';
    $_GET['page_size'] = 10;
    $_DATA['screening'] = new LOVD_Screening();
    $_DATA['screening']->setRowLink($sScreeningsViewListID, 'submit/screening/' . $_DATA['screening']->sRowID);
    $_GET['search_individualid'] = $nID;
    $_GET['search_screeningid'] = (isset($aSubmit['screenings'])? implode('|', $aSubmit['screenings']) : 0);
    print('      <DIV id="container_screenings"><BR>' . "\n"); // Extra div is to prevent "No entries in the database yet!" error to show up if there are no genes in the database yet.
    lovd_showInfoTable('Please select a screening you would like to manage', 'information');
    $_DATA['screening']->viewList($sScreeningsViewListID, array('individualid', 'created_date', 'edited_date', 'owned_by_'), true, true);
    unset($_GET['search_screeningid']);

    $_DATA['phenotype'] = array();
    require ROOT_PATH . 'class/object_phenotypes.php';
    $_GET['search_id_'] = (isset($aSubmit['phenotypes'])? implode('|', $aSubmit['phenotypes']) : 0);
    print('      </DIV>' . "\n" .
          '      <DIV id="container_phenotypes"><BR>' . "\n"); // Extra div is to prevent "No entries in the database yet!" error to show up if there are no genes in the database yet.
    lovd_showInfoTable('Please select a phenotype you would like to edit', 'information');
    foreach($zData['diseases'] as $nDisease) {
        $_GET['search_diseaseid'] = $nDisease;
        $_DATA['phenotype'][$nDisease] = new LOVD_Phenotype($nDisease);
        $_DATA['phenotype'][$nDisease]->setSortDefault('phenotypeid');
        print('<B>' . $aDiseases[$nDisease]['name'] . ' (<A href="diseases/' . $nDisease . '">' . $aDiseases[$nDisease]['symbol'] . '</A>)</B>');
        $_DATA['phenotype'][$nDisease]->setRowLink($sPhenotypesViewListID . $nDisease, 'phenotypes/' . $_DATA['phenotype'][$nDisease]->sRowID . '?edit');
        $_DATA['phenotype'][$nDisease]->viewList($sPhenotypesViewListID . $nDisease, array('id_', 'individualid', 'diseaseid'), true, true);
    }
    print('      </DIV>' . "\n" .
          '      <SCRIPT type="text/javascript">' . "\n" .
          '        $("#container_screenings").hide();' . "\n" .
          '        $("#container_phenotypes").hide();' . "\n" .
          '      </SCRIPT>' . "\n");*/

    $_T->printFooter();
    exit;
}





if (PATH_COUNT == 4 && $_PE[1] == 'individual' && ctype_digit($_PE[2]) && $_PE[3] == 'screenings' && !ACTION) {
    // URL: /submit/individual/00000001/screenings
    // Let submitter select screening to add variant to.

    $nID = sprintf('%08d', $_PE[2]);
    define('PAGE_TITLE', 'Select screening to add variant to');
    $_T->printHeader();
    $_T->printTitle();

    $bExists = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_INDIVIDUALS . ' WHERE id = ?', array($nID))->fetchColumn();
    if (!$bExists || !isset($_AUTH['saved_work']['submissions']['individual'][$nID])) {
        lovd_showInfoTable('No such ID!', 'stop');
        $_T->printFooter();
        exit;
    }

    require ROOT_PATH . 'class/object_screenings.php';
    $_DATA = new LOVD_Screening();
    $_GET['search_individualid'] = $nID;
    $_GET['page_size'] = '10';
    $_DATA->setRowLink('Screenings_submissions', 'variants?create&target=' . $_DATA->sRowID);
    $_DATA->viewList('Screenings_submissions', array('individualid', 'owned_by_', 'created_date'), false, false);

    $_T->printFooter();
    exit;
}





if (PATH_COUNT == 3 && $_PE[1] == 'screening' && ctype_digit($_PE[2]) && !ACTION) {
    // URL: /submit/screening/00000001
    // Screening submission
    global $_DB, $_AUTH;

    define('LOG_EVENT', 'SubmitScreening');

    lovd_requireAUTH(LEVEL_SUBMITTER);

    $nID = sprintf('%010d', $_PE[2]);

    $zData = $_DB->query('SELECT * FROM ' . TABLE_SCREENINGS . ' WHERE id = ? AND created_by = ?', array($nID, $_AUTH['id']))->fetchAssoc();
    if (empty($zData)) {
        define('PAGE_TITLE', 'Submit');
        $_T->printHeader();
        $_T->printTitle();
        lovd_showInfoTable('No such ID!', 'stop');
        $_T->printFooter();
        exit;
    }
    if (isset($_AUTH['saved_work']['submissions']['screening'][$nID])) {
        if (!isset($_SESSION['work']['submits']['screening'])) {
            $_SESSION['work']['submits']['screening'] = array();
        }
        while (count($_SESSION['work']['submits']['screening']) >= 10) {
            unset($_SESSION['work']['submits']['screening'][min(array_keys($_SESSION['work']['submits']['screening']))]);
        }
        $aSubmit = $_SESSION['work']['submits']['screening'][$nID] = $_AUTH['saved_work']['submissions']['screening'][$nID];
        $sSubmitType = 'screening';
    } elseif (isset($_AUTH['saved_work']['submissions']['individual'][$zData['individualid']]['screenings']) && in_array($nID, $_AUTH['saved_work']['submissions']['individual'][$zData['individualid']]['screenings'])) {
        if (!isset($_SESSION['work']['submits']['individual'])) {
            $_SESSION['work']['submits']['individual'] = array();
        }
        while (count($_SESSION['work']['submits']['individual']) >= 10) {
            unset($_SESSION['work']['submits']['individual'][min(array_keys($_SESSION['work']['submits']['individual']))]);
        }
        $aSubmit = $_SESSION['work']['submits']['individual'][$zData['individualid']] = $_AUTH['saved_work']['submissions']['individual'][$zData['individualid']];
        $sSubmitType = 'individual';
    } else {
        define('PAGE_TITLE', 'Submit');
        $_T->printHeader();
        $_T->printTitle();
        lovd_showInfoTable('No such ID!', 'stop');
        $_T->printFooter();
        exit;
    }

    lovd_isAuthorized('screening', $nID);
    lovd_requireAUTH(LEVEL_OWNER);

    $zData['variants'] = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_SCR2VAR . ' WHERE screeningid = ?', array($nID))->fetchColumn();

    define('PAGE_TITLE', 'Submission of screening #' . $nID);

    $_T->printHeader();
    $_T->printTitle();
    require ROOT_PATH . 'inc-lib-form.php';
    print('      What would you like to do?<BR><BR>' . "\n\n");

    $sViewListID = 'VOG_VOT_Submission_' . $nID;

    $aOptionsList = array();
    //$aOptionsList['options'][0]['onclick'] = 'screenings/' . $nID . '?edit';
    //$aOptionsList['options'][0]['option_text'] = '<B>I want to edit this variant screening entry</B>';

    if (!$zData['variants_found']) {
        $aOptionsList['options'][1]['disabled'] = true;
        $aOptionsList['options'][1]['onclick'] = 'javascript:alert(\'You cannot add variants to this screening, because the checkbox &quot;Have variants been found?&quot;\nhas been unchecked for this screening!\')';
    } else {
        $aOptionsList['options'][1]['onclick'] = 'variants?create&amp;target=' . $nID;
    }
    $aOptionsList['options'][1]['option_text'] = '<B>I want to add a variant to this screening</B>';

    //if (!$zData['variants']) {
    //    $aOptionsList['options'][2]['disabled'] = true;
    //    $aOptionsList['options'][2]['onclick'] = 'javascript:alert(\'No variants are added yet to this screening!\')';
    //} else {
    //    $aOptionsList['options'][2]['onclick'] = 'javascript:$(\'#container\').toggle(); lovd_stretchInputs(\'' . $sViewListID . '\');';
    //}
    //$aOptionsList['options'][2]['option_text'] = '<B>I want edit a previously added variant entry</B>';

    if ($sSubmitType == 'screening' && $zData['variants_found'] && !$zData['variants']) {
        $aOptionsList['options'][3]['disabled'] = true;
        $aOptionsList['options'][3]['onclick'] = 'javascript:alert(\'You cannot finish your submission, because no variants were added to this screening!\')';
        $aOptionsList['options'][3]['option_text'] = '<B>I want to finish this submission</B>';
    } elseif ($sSubmitType == 'individual') {
        $aOptionsList['options'][3]['onclick'] = 'javascript:if(window.confirm(\'Are you sure you are done with submitting the variants found with this screening?\')){document.location.href=\'submit/individual/' . $zData['individualid'] . '\';}';
        $aOptionsList['options'][3]['type'] = 'l';
        $aOptionsList['options'][3]['option_text'] = '<B>Back to the individual</B>';
        if ($zData['variants_found'] && $zData['variants']) {
            // If at least one variant has already been submitted, then we can finish as well from here.
            $aOptionsList['options'][4]['onclick'] = 'submit/finish/individual/' . $zData['individualid'];
            $aOptionsList['options'][4]['option_text'] = '<B>I want to finish this submission</B>';
        }
    } else {
        $aOptionsList['options'][3]['onclick'] = 'submit/finish/screening/' . $nID;
        $aOptionsList['options'][3]['option_text'] = '<B>I want to finish this submission</B>';
    }

    print(lovd_buildOptionTable($aOptionsList));

    /*require ROOT_PATH . 'class/object_genome_variants.php';
    $_GET['page_size'] = 10;
    $_DATA = new LOVD_GenomeVariant();
    $_DATA->setRowLink($sViewListID, 'variants/' . $_DATA->sRowID . '?edit&submission=' . $nID);
    $_GET['search_screeningids'] = $nID;
    $_GET['search_created_by'] = $_AUTH['id'];
    print('      <DIV id="container"><BR>' . "\n"); // Extra div is to prevent "No entries in the database yet!" error to show up if there are no genes in the database yet.
    lovd_showInfoTable('Please select a variant you would like to edit', 'information');
    $_DATA->viewList($sViewListID, array('id_', 'owned_by_', 'status'), true);
    print('      </DIV>' . "\n" .
          '      <SCRIPT type="text/javascript">' . "\n" .
          '        $("#container").hide();' . "\n" .
          '      </SCRIPT>' . "\n");*/

    $_T->printFooter();
    exit;
}





if (PATH_COUNT == 3 && $_PE[1] == 'review' && ctype_digit($_PE[2]) && !ACTION) {
    // URL: /submit/review
    // Review your unfinished submission
    exit;
    define('LOG_EVENT', 'SubmitScreening');

    lovd_requireAUTH(LEVEL_SUBMITTER);

    $nID = sprintf('%010d', $_PE[2]);

    $zData = $_DB->query('SELECT * FROM ' . TABLE_SCREENINGS . ' WHERE id = ? AND created_by = ?', array($nID, $_AUTH['id']))->fetchAssoc();
    if (empty($zData)) {
        define('PAGE_TITLE', 'Submit');
        $_T->printHeader();
        $_T->printTitle();
        lovd_showInfoTable('No such ID!', 'stop');
        $_T->printFooter();
        exit;
    }
    exit;
}





if (PATH_COUNT == 4 && $_PE[1] == 'finish' && in_array($_PE[2], array('individual', 'screening', 'variant', 'phenotype', 'upload', 'confirmedVariants')) && ctype_digit($_PE[3])) {
    // URL: /submit/finish/(variant|individual|screening|phenotype|upload|confirmedVariants)/00000001
    // URL: /submit/finish/(variant|individual|screening|phenotype)/00000001?edit
    // Finalize the submission and mail the apropriate users.

    if (ACTION == 'edit' && in_array($_PE[2], array('upload', 'confirmedVariants'))) {
        exit;
    }

    // Try to find the genes and or diseases associated with the submission.
    switch ($_PE[2]) {
        case 'individual':
            $sURI = 'individuals/';
            $sTitle = 'an individual';
            $nID = sprintf('%08d', $_PE[3]);
            $zData = $_DB->query('SELECT i.id, GROUP_CONCAT(DISTINCT t.geneid SEPARATOR ";") AS geneids, GROUP_CONCAT(DISTINCT i2d.diseaseid SEPARATOR ";") AS diseaseids FROM ' . TABLE_INDIVIDUALS . ' AS i LEFT OUTER JOIN ' . TABLE_IND2DIS . ' AS i2d ON (i.id = i2d.individualid) LEFT OUTER JOIN ' . TABLE_SCREENINGS . ' AS s ON (i.id = s.individualid) LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s.id = s2v.screeningid) LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (s2v.variantid = vot.id) LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE i.id = ? AND i.' . (ACTION != 'edit'? 'created' : 'edited') . '_by = ? GROUP BY i.id ORDER BY t.geneid ASC', array($nID, $_AUTH['id']))->fetchAssoc();
            lovd_isAuthorized('individual', $nID);
            break;
        case 'confirmedVariants':
            $sURI = 'screenings/';
            $sTitle = 'confirmed variants';
            $nID = sprintf('%010d', $_PE[3]);
            $aConfirmedVariants = $_SESSION['work']['submits']['confirmedVariants'][$nID];
            $zData = $_DB->query('SELECT DISTINCT t.geneid FROM ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE vot.id IN (?' . str_repeat(', ?', count($aConfirmedVariants) - 1) . ') ORDER BY t.geneid ASC', $aConfirmedVariants)->fetchAllColumn();
            $zData = array('geneids' => implode(';', $zData));
            lovd_isAuthorized('screening', $nID);
            break;
        case 'screening':
            $sURI = 'screenings/';
            $sTitle = 'a screening';
            $nID = sprintf('%010d', $_PE[3]);
            $zData = $_DB->query('SELECT s.id, GROUP_CONCAT(DISTINCT t.geneid SEPARATOR ";") AS geneids FROM ' . TABLE_SCREENINGS . ' AS s LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s.id = s2v.screeningid) LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (s2v.variantid = vot.id) LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE s.id = ? AND s.' . (ACTION != 'edit'? 'created' : 'edited') . '_by = ? GROUP BY s.id ORDER BY t.geneid ASC', array($nID, $_AUTH['id']))->fetchAssoc();
            lovd_isAuthorized('screening', $nID);
            break;
        case 'variant':
            $sURI = 'variants/';
            $sTitle = 'a variant';
            $nID = sprintf('%010d', $_PE[3]);
            $zData = $_DB->query('SELECT v.id, GROUP_CONCAT(DISTINCT t.geneid SEPARATOR ";") AS geneids FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (v.id = vot.id) LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE v.id = ? AND v.' . (ACTION != 'edit'? 'created' : 'edited') . '_by = ? GROUP BY v.id ORDER BY t.geneid ASC', array($nID, $_AUTH['id']))->fetchAssoc();
            lovd_isAuthorized('variant', $nID);
            break;
        case 'phenotype':
            $sURI = 'phenotypes/';
            $sTitle = 'a phenotype';
            $nID = sprintf('%010d', $_PE[3]);
            $zData = $_DB->query('SELECT p.id, GROUP_CONCAT(DISTINCT t.geneid SEPARATOR ";") AS geneids, GROUP_CONCAT(DISTINCT p.diseaseid SEPARATOR ";") AS diseaseids FROM ' . TABLE_PHENOTYPES . ' AS p LEFT OUTER JOIN ' . TABLE_SCREENINGS . ' AS s USING (individualid) LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s.id = s2v.screeningid) LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (s2v.variantid = vot.id) LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE p.id = ? AND p.' . (ACTION != 'edit'? 'created' : 'edited') . '_by = ? GROUP BY p.id ORDER BY t.geneid ASC', array($nID, $_AUTH['id']))->fetchAssoc();
            lovd_isAuthorized('phenotype', $nID);
            break;
        case 'upload':
            $sURI = 'variants/upload/';
            $sTitle = 'an upload';
            $nID = sprintf('%015d', $_PE[3]);
            // Setting zData to a valid, non-empty array, yet without any data because there is none.
            $zData = array('geneids' => '', 'diseaseids' => '');
            break;
    }
    $aGenes = (!empty($zData['geneids'])? explode(';', $zData['geneids']) : array());
    $aDiseases = (!empty($zData['diseaseids'])? explode(';', $zData['diseaseids']) : array());
    if (!$zData || (!isset($_SESSION['work']['submits'][$_PE[2]][$nID]) && !isset($_SESSION['work']['edits'][$_PE[2]][$nID]))) {
        exit;
    }

    // Making sure we can always refer to the same variables so that it doesn't matter how we enter this submission.
    $aSubmit = array();
    if (ACTION != 'edit') {
        if (in_array($_PE[2], array('individual', 'screening'))) {
            $aSubmit = $_SESSION['work']['submits'][$_PE[2]][$nID];
        }
        if ($_PE[2] == 'upload') {
            $aSubmit['uploads'][$nID] = $_SESSION['work']['submits']['upload'][$nID];
        } elseif ($_PE[2] == 'confirmedVariants') {
            $aSubmit['confirmedVariants'][$nID] = $_SESSION['work']['submits']['confirmedVariants'][$nID];
        } elseif ($_PE[2] != 'individual') {
            $aSubmit[$_PE[2] . 's'] = array($nID);
        }

        $_DB->beginTransaction();
        if ($_AUTH['level'] == LEVEL_OWNER) {
            // If the user is not a curator or a higher, then the status will be set from "In Progress" to "Pending".
            if (!empty($aSubmit['variants'])) {
                $q = $_DB->query('UPDATE ' . TABLE_VARIANTS . ' SET statusid = ? WHERE id IN (?' . str_repeat(', ?', count($aSubmit['variants']) - 1) . ')', array_merge(array(STATUS_PENDING), $aSubmit['variants']));
            }
            if (!empty($aSubmit['phenotypes'])) {
                $q = $_DB->query('UPDATE ' . TABLE_PHENOTYPES . ' SET statusid = ? WHERE id IN (?' . str_repeat(', ?', count($aSubmit['phenotypes']) - 1) . ')', array_merge(array(STATUS_PENDING), $aSubmit['phenotypes']));
            }
            if ($_PE[2] == 'individual') {
                $q = $_DB->query('UPDATE ' . TABLE_INDIVIDUALS . ' SET statusid = ? WHERE id = ?', array(STATUS_PENDING, $nID));
            }
        } elseif ($_AUTH['level'] == LEVEL_CURATOR && !empty($aSubmit['variants'])) {
            foreach ($aSubmit['variants'] as $nVariantID) {
                // $_AUTH['level'] will be set here to properly check the level for this variant. We have to keep in mind that the $_AUTH['level'] of the individual/screening check is overwritten.
                lovd_isAuthorized('variant', $nVariantID, true);
                if ($_AUTH['level'] == LEVEL_OWNER) {
                    $q = $_DB->query('UPDATE ' . TABLE_VARIANTS . ' SET statusid = ? WHERE id = ?', array_merge(array(STATUS_PENDING), array($nVariantID)));
                }
            }
        }
        $_DB->commit();

        // Remove the submission information from $_SESSION and close the session file, so that other scripts can use it without having to wait for this script to finish.
        unset($_SESSION['work']['submits'][$_PE[2]][$nID]);
        if (isset($_AUTH['saved_work']['submissions'][$_PE[2]][$nID])) {
            unset($_AUTH['saved_work']['submissions'][$_PE[2]][$nID]);
            lovd_saveWork();
        }

    } else {
        if ($_PE[2] != 'individual') {
            $aSubmit[$_PE[2] . 's'] = array($nID);
        }
    }

    session_write_close();
    define('LOG_EVENT', (ACTION != 'edit'? 'Submit' : 'Edit') . ucfirst($_PE[2]));
    define('PAGE_TITLE', (ACTION != 'edit'? 'Submit ' : 'Edit ') . $sTitle);

    $_T->printHeader();
    $_T->printTitle();
    $aCurators = array();
    $aManagers = array();
    $sCurators = ''; // For intragenic variants.
    $sManagers = ''; // For intergenic variants.
    if (!empty($aGenes)) {
        // Check if there are any genomic variants without a variant on transcript entry, in which case we would need to mail all managers.
        switch ($_PE[2]) {
            case 'individual':
            case 'screening':
            case 'variant':
            case 'confirmedVariants':
                $nNullTranscript = 0;
                if (!empty($aSubmit['variants'])) {
                    $nNullTranscript = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING (id) WHERE vot.id IS NULL AND v.id IN (?' . str_repeat(', ?', count($aSubmit['variants']) - 1) . ')', $aSubmit['variants'])->fetchColumn();
                }
                if (!empty($aSubmit['uploads'])) {
                    $a = array();
                    foreach ($aSubmit['uploads'] as $nUploadID => $aUpload) {
                        $a[] = $aUpload['upload_date'];
                    }
                    $nNullTranscript += $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING(id) WHERE vot.id IS NULL AND v.created_date IN (?' . str_repeat(', ?', count($a) - 1) . ') AND v.created_by = ?', array_merge($a, array($_AUTH['id'])))->fetchColumn();
                }
                if (!empty($aSubmit['confirmedVariants'])) {
                    $a = array();
                    foreach ($aSubmit['confirmedVariants'] as $nScreeningID => $aVariants) {
                        $a = array_merge($a, $aVariants);
                    }
                    $a = array_unique($a);
                    $nNullTranscript += $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING (id) WHERE vot.id IS NULL AND v.id IN (?' . str_repeat(', ?', count($a) - 1) . ')', $a)->fetchColumn();
                }
                break;
            case 'phenotype':
                $nNullTranscript = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_PHENOTYPES . ' AS p LEFT OUTER JOIN ' . TABLE_SCREENINGS . ' AS s USING (individualid) INNER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (s.id = s2v.screeningid) LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (s2v.variantid = vot.id) WHERE vot.id IS NULL AND p.id = ?', array($nID))->fetchColumn();
                break;
            case 'upload':
                $nNullTranscript = $_DB->query('SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING(id) WHERE vot.id IS NULL AND v.created_date = ? AND v.created_by = ?', array($aSubmit['uploads'][$nID]['upload_date'], $_AUTH['id']))->fetchColumn();
                break;
        }

        if ($nNullTranscript) {
            $aManagers = $_DB->query('SELECT name, email FROM ' . TABLE_USERS . ' WHERE level = ' . LEVEL_MANAGER)->fetchAllRow();
        }
        // Select all curators that need to be mailed.
        $aCurators = $_DB->query('SELECT DISTINCT u.name, u.email FROM ' . TABLE_CURATES . ' AS c, ' . TABLE_USERS . ' AS u WHERE c.userid = u.id ' . (count($aManagers)? 'AND u.level != ' . LEVEL_MANAGER . ' ' : '') . 'AND c.geneid IN (?' . str_repeat(', ?', count($aGenes) - 1) . ') AND allow_edit = 1 ORDER BY u.level DESC, u.name', $aGenes)->fetchAllRow();
    } else {
        // If there are no genes then we can only mail managers.
        $aManagers = $_DB->query('SELECT name, email FROM ' . TABLE_USERS . ' WHERE level = ' . LEVEL_MANAGER)->fetchAllRow();
    }
    // Put their names in the email also.
    foreach ($aManagers as $aUser) {
        $sManagers .= (!$sManagers? '' : ', ') . $aUser[0];
    }
    foreach ($aCurators as $aUser) {
        $sCurators .= (!$sCurators? '' : ', ') . $aUser[0];
    }
    $aTo = array_merge($aCurators, $aManagers);

    // Arrays containing submitter & data fields.
    $aSubmitterDetails =
        array(
            '_AUTH',
            'id' => 'User ID',
            'name' => 'Name',
            'institute' => 'Institute',
            'department' => 'Department',
            'address' => 'Address',
            'city' => 'City',
            'country_' => 'Country',
            'email' => 'Email address',
            'telephone' => 'Telephone',
            'reference' => 'Reference',
        );
    $aIndividualFields =
        array(
            'zIndividualDetails',
            'id' => 'Individual ID',
            'panel_' => 'Panel?',
            'panel_size' => 'Panel size',
        );
    $aPhenotypeFields =
        array(
            '',
            'individualid' => 'Individual ID',
            'diseaseid_' => 'Disease',
            'id' => 'Phenotype ID',
        );
    $aScreeningFields =
        array(
            '',
            'individualid' => 'Individual ID',
            'id' => 'Screening ID',
            'variants_found_' => 'Variants found',
        );
    $aVariantOnGenomeFields =
        array(
            '',
            'screeningid' => 'Screening ID',
            'id' => 'Variant ID',
            'allele_' => 'Allele',
            'effect_reported' => 'Affects function (reported)',
            'effect_concluded' => 'Affects function (concluded)',
            'chromosome' => 'Chromosome',
        );
    $aVariantOnTranscriptFields =
        array(
            '',
            'id_ncbi_' => 'On transcript',
            'effect_reported' => 'Affects function (reported)',
            'effect_concluded' => 'Affects function (concluded)',
        );
    $aUploadFields =
        array(
            '',
            'screeningid' => 'Screening ID',
            'file_name' => 'File name',
            'file_type' => 'File type',
            'upload_date' => 'Timestamp',
            'num_variants' => 'Variants imported',
            'num_variants_unsupported' => 'Variants not imported',
            'num_genes' => 'Genes created',
            'num_transcripts' => 'Transcripts created',
            'num_variants_on_transcripts' => 'Transcript variants imported',
            'mapping_flags_' => 'Automatic mapping',
        );

    // Load the non-shared custom columns and add them to the fields list.
    $qCols = $_DB->query('SELECT c.id, c.head_column FROM ' . TABLE_COLS . ' AS c INNER JOIN ' . TABLE_ACTIVE_COLS . ' AS ac ON (c.id = ac.colid) WHERE c.id NOT LIKE "VariantOnTranscript/%" ' . (empty($aSubmit['screenings']) && $_PE[2] != 'confirmedVariants'? 'AND c.id NOT LIKE "Screening/%" ' : '') . ($_PE[2] != 'individual'? 'AND c.id NOT LIKE "Individual/%" ' : '') . 'AND c.id NOT LIKE "Phenotype/%" ORDER BY c.col_order', array());
    if ($_PE[2] == 'individual') {
        unset($aScreeningFields['individualid']);
        unset($aPhenotypeFields['individualid']);
        unset($aVariantOnGenomeFields['screeningid']);
        unset($aUploadFields['screeningid']);
    } elseif ($_PE[2] == 'screening') {
        unset($aVariantOnGenomeFields['screeningid']);
        unset($aUploadFields['screeningid']);
    } elseif ($_PE[2] == 'confirmedVariants') {
        unset($aScreeningFields['individualid']);
    }

    while ($aCol = $qCols->fetchAssoc()) {
        $aFieldsName = explode('/', $aCol['id']);
        $sFieldsName = 'a' . $aFieldsName[0] . 'Fields';
        ${$sFieldsName}[$aCol['id']] = $aCol['head_column'];
    }

    // Load all VariantOnTranscript custom columns for each gene and put them in seperate variable variables
    foreach ($aGenes as $sGene) {
        $sColNamesVOT = 'VOTCols_' . $sGene;
        $$sColNamesVOT = $aVariantOnTranscriptFields;
        $qCols = $_DB->query('SELECT c.id, c.head_column FROM ' . TABLE_COLS . ' AS c INNER JOIN ' . TABLE_SHARED_COLS . ' AS sc ON (sc.colid = c.id) WHERE c.id LIKE "VariantOnTranscript/%" AND sc.geneid = ? ORDER BY sc.col_order', array($sGene));
        while ($aCol = $qCols->fetchAssoc()) {
            ${$sColNamesVOT}[$aCol['id']] = $aCol['head_column'];
        }
    }

    // Load all Phenotype custom columns for each disease and put them in separate variable variables
    foreach ($aDiseases as $sDisease) {
        $sColNamesPhen = 'PhenCols_' . $sDisease;
        $$sColNamesPhen = $aPhenotypeFields;
        $qCols = $_DB->query('SELECT c.id, c.head_column FROM ' . TABLE_COLS . ' AS c INNER JOIN ' . TABLE_SHARED_COLS . ' AS sc ON (sc.colid = c.id) WHERE c.id LIKE "Phenotype/%" AND sc.diseaseid = ? ORDER BY sc.col_order', array($sDisease));
        while ($aCol = $qCols->fetchAssoc()) {
            ${$sColNamesPhen}[$aCol['id']] = $aCol['head_column'];
        }
    }

    $_AUTH['country_'] = $_DB->query('SELECT name FROM ' . TABLE_COUNTRIES . ' WHERE id = ?', array($_AUTH['countryid']))->fetchColumn();

    // Build up the arrays that will create the data blocks in the email.
    // Select all data from the database that belong to this submission and put it in a variable.
    $bUnpublished = false;
    if ($_PE[2] == 'individual') {
        $zIndividualDetails = $_DB->query('SELECT i.*, u.name AS owned_by_ FROM ' . TABLE_INDIVIDUALS . ' AS i LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (i.owned_by = u.id) WHERE i.id = ?', array($nID))->fetchAssoc();
        $zIndividualDetails = lovd_prepareSubmitData('individual', $zIndividualDetails);
        if (ACTION == 'edit') {
            $aEdits = $_SESSION['work']['edits']['individual'][$nID];
            $aEdits = lovd_prepareSubmitData('individual', $aEdits);
        }
        $bUnpublished = ($bUnpublished || $zIndividualDetails['statusid'] < STATUS_MARKED);
        if ($zIndividualDetails['panel_size'] <= 1) {
            unset($aIndividualFields['panel_size']);
        } else {
            unset($aIndividualFields['panel_']);
        }
        $aOwner = array(); // Owners krijgen Cc van de email.
        if ($zIndividualDetails['owned_by'] != $_AUTH['id'] || (ACTION == 'edit' && $zIndividualDetails['owned_by'] != $aEdits['owned_by'])) {
            $aIndividualFields['owned_by_'] = 'Data owner';
            $aOwner[] = $zIndividualDetails['owned_by'];
        }
        $aIndividualFields['statusid_'] = 'Data status';
        if ($zIndividualDetails['edited_by'] != null) {
            $aIndividualFields['edited_by'] = 'Edited by';
            $aIndividualFields['edited_date'] = 'Edited date';
        }

        if (ACTION == 'edit') {
            $aFields = array_keys($aIndividualFields);
            unset($aFields[0]);
            foreach ($aFields as $sField) {
                if (is_array($aEdits[$sField])) {
                    $aEdits[$sField] = implode(';', $aEdits[$sField]);
                }
                if ($zIndividualDetails[$sField] != $aEdits[$sField]) {
                    $zIndividualDetails[$sField] .= "\n\t" . (empty($aEdits[$sField])? '(Was previously empty)' : 'Previous value:' . "\n" . $aEdits[$sField]);
                }
            }
            if (!in_array($aEdits['owned_by'], array($_AUTH['id'], $zIndividualDetails['owned_by']))) {
                $aOwner[] = $aEdits['owned_by'];
            }
        }
        $aIndividualDetails = $aIndividualFields;
    }

    if (!empty($aSubmit['phenotypes'])) {
        $aPhenotypeDetails = array();
        if (ACTION == 'edit') {
            $aEdits = $_SESSION['work']['edits']['phenotype'][$nID];
            $aEdits = lovd_prepareSubmitData('phenotype', $aEdits);
        }
        foreach ($aSubmit['phenotypes'] as $nPhenotypeID) {
            $z = $_DB->query('SELECT p.*, d.id AS diseaseid, d.name AS diseaseid_, u.name AS owned_by_ FROM ' . TABLE_PHENOTYPES . ' AS p LEFT OUTER JOIN ' . TABLE_DISEASES . ' AS d ON (p.diseaseid = d.id) LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (p.owned_by = u.id) WHERE p.id = ?', array($nPhenotypeID))->fetchAssoc();
            $z = lovd_prepareSubmitData('phenotype', $z);
            $bUnpublished = ($bUnpublished || $z['statusid'] < STATUS_MARKED);
            $sVariableNamePhen = 'zPhenotypeDetails_' . $nPhenotypeID;
            $sColNamesPhen = 'PhenCols_' . $z['diseaseid'];
            $a = $$sColNamesPhen;
            $a[0] = $sVariableNamePhen;
            $aOwner = array(); // Owners krijgen Cc van de email.
            if ($z['owned_by'] != $_AUTH['id'] || (ACTION == 'edit' && $z['owned_by'] != $aEdits['owned_by'])) {
                $a['owned_by_'] = 'Data owner';
                $aOwner[] = $z['owned_by'];
            }
            $a['statusid_'] = 'Data status';
            if ($z['edited_by'] != null) {
                $a['edited_by'] = 'Edited by';
                $a['edited_date'] = 'Edited date';
            }
            if (ACTION == 'edit') {
                $aFields = array_keys($a);
                unset($aFields[0]);
                foreach ($aFields as $sField) {
                    if (is_array($aEdits[$sField])) {
                        $aEdits[$sField] = implode(';', $aEdits[$sField]);
                    }
                    if ($z[$sField] != $aEdits[$sField]) {
                        $z[$sField] .= "\n\t" . (empty($aEdits[$sField])? '(Was previously empty)' : 'Previous value:' . "\n" . $aEdits[$sField]);
                    }
                }
                if (!in_array($aEdits['owned_by'], array($_AUTH['id'], $z['owned_by']))) {
                    $aOwner[] = $aEdits['owned_by'];
                }
            }
            $aPhenotypeDetails[] = $a;
            $$sVariableNamePhen = $z;
        }
    }

    if (!empty($aSubmit['screenings'])) {
        $aScreeningDetails = array();
        if (ACTION == 'edit') {
            $aEdits = $_SESSION['work']['edits']['screening'][$nID];
            $aEdits = lovd_prepareSubmitData('screening', $aEdits);
        }
        foreach ($aSubmit['screenings'] as $nScreeningID) {
            $sVariableNameSCR = 'zScreeningsDetails_' . $nScreeningID;
            $a = $aScreeningFields;
            $a[0] = $sVariableNameSCR;
            $$sVariableNameSCR = $_DB->query('SELECT s.*, u.name AS owned_by_ FROM ' . TABLE_SCREENINGS . ' AS s LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (s.owned_by = u.id) WHERE s.id = ?', array($nScreeningID))->fetchAssoc();
            $$sVariableNameSCR = lovd_prepareSubmitData('screening', $$sVariableNameSCR);
            if (${$sVariableNameSCR}['variants_found']) {
                ${$sVariableNameSCR}['variants_found_'] = $_DB->query('SELECT COUNT(variantid) FROM ' . TABLE_SCR2VAR . ' WHERE screeningid = ?', array($nScreeningID))->fetchColumn();
                if (${$sVariableNameSCR}['variants_found_'] && isset($aSubmit['confirmedVariants'][$nScreeningID])) {
                    ${$sVariableNameSCR}['variants_found_'] .= ' (inc. ' . count($aSubmit['confirmedVariants'][$nScreeningID]) . ' confirmed)';
                } elseif (!${$sVariableNameSCR}['variants_found_']) {
                    ${$sVariableNameSCR}['variants_found_'] = 0;
                }
            } else {
                ${$sVariableNameSCR}['variants_found_'] = 'None';
            }
            $aOwner = array(); // Owners krijgen Cc van de email.
            if (${$sVariableNameSCR}['owned_by'] != $_AUTH['id'] || (ACTION == 'edit' && ${$sVariableNameSCR}['owned_by'] != $aEdits['owned_by'])) {
                $a['owned_by_'] = 'Data owner';
                $aOwner[] = ${$sVariableNameSCR}['owned_by'];
            }
            if (${$sVariableNameSCR}['edited_by'] != null) {
                $a['edited_by'] = 'Edited by';
                $a['edited_date'] = 'Edited date';
            }
            if (ACTION == 'edit') {
                $aFields = array_keys($a);
                unset($aFields[0]);
                foreach ($aFields as $sField) {
                    if (is_array($aEdits[$sField])) {
                        $aEdits[$sField] = implode(';', $aEdits[$sField]);
                    }
                    if (${$sVariableNameSCR}[$sField] != $aEdits[$sField]) {
                        ${$sVariableNameSCR}[$sField] .= "\n\t" . (empty($aEdits[$sField])? '(Was previously empty)' : 'Previous value:' . "\n" . $aEdits[$sField]);
                    }
                }
                if (!in_array($aEdits['owned_by'], array($_AUTH['id'], ${$sVariableNameSCR}['owned_by']))) {
                    $aOwner[] = $aEdits['owned_by'];
                }
            }
            $aScreeningDetails[] = $a;
        }
    } elseif (!empty($aSubmit['confirmedVariants']) && $_PE[2] == 'confirmedVariants') {
        $aScreeningDetails = array();
        $sVariableNameSCR = 'zScreeningsDetails_' . $nID;
        $a = $aScreeningFields;
        $a[0] = $sVariableNameSCR;
        $$sVariableNameSCR = $_DB->query('SELECT s.*, u.name AS owned_by_ FROM ' . TABLE_SCREENINGS . ' AS s LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (s.owned_by = u.id) WHERE s.id = ?', array($nID))->fetchAssoc();
        ${$sVariableNameSCR}['variants_found_'] = $_DB->query('SELECT COUNT(variantid) FROM ' . TABLE_SCR2VAR . ' WHERE screeningid = ?', array($nID))->fetchColumn();
        ${$sVariableNameSCR}['variants_found_'] = (${$sVariableNameSCR}['variants_found_'] - count($aSubmit['confirmedVariants'][$nID])) . ' + ' . count($aSubmit['confirmedVariants'][$nID]) . ' additionaly confirmed';
        (${$sVariableNameSCR}['owned_by'] != $_AUTH['id']? $a['owned_by_'] = 'Data owner' : false);
        $aScreeningDetails[] = $a;
    }

    if (!empty($aSubmit['variants'])) {
        $aVariantDetails = array();
        if (ACTION == 'edit') {
            $aEdits = $_SESSION['work']['edits']['variant'][$nID];
            $aEdits = lovd_prepareSubmitData('variant', $aEdits);
        }
        foreach ($aSubmit['variants'] as $nVariantID) {
            $sVariableNameVOG = 'zVariantOnGenomeDetails_' . $nVariantID;
            $a = $aVariantOnGenomeFields;
            $a[0] = $sVariableNameVOG;
            if ($_PE[2] == 'variant') {
                $$sVariableNameVOG = $_DB->query('SELECT v.*, a.name AS allele_, u.name AS owned_by_, IFNULL(s2v.screeningid, "") AS screeningid FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (v.id = s2v.variantid) LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (v.owned_by = u.id) LEFT OUTER JOIN ' . TABLE_ALLELES . ' AS a ON (v.allele = a.id) WHERE v.id = ?', array($nVariantID))->fetchAssoc();
            } else {
                $$sVariableNameVOG = $_DB->query('SELECT v.*, a.name AS allele_, u.name AS owned_by_ FROM ' . TABLE_VARIANTS . ' AS v LEFT OUTER JOIN ' . TABLE_USERS . ' AS u ON (v.owned_by = u.id) LEFT OUTER JOIN ' . TABLE_ALLELES . ' AS a ON (v.allele = a.id) WHERE v.id = ?', array($nVariantID))->fetchAssoc();
            }
            $$sVariableNameVOG = lovd_prepareSubmitData('variant', $$sVariableNameVOG);
            $bUnpublished = ($bUnpublished || ${$sVariableNameVOG}['statusid'] < STATUS_MARKED);
            if (empty(${$sVariableNameVOG}['screeningid'])) {
                unset($a['screeningid']);
            }
            $aOwner = array(); // Owners krijgen Cc van de email.
            if (${$sVariableNameVOG}['owned_by'] != $_AUTH['id'] || (ACTION == 'edit' && ${$sVariableNameVOG}['owned_by'] != $aEdits['owned_by'])) {
                $a['owned_by_'] = 'Data owner';
                $aOwner[] = ${$sVariableNameVOG}['owned_by'];
            }
            $a['statusid_'] = 'Data status';
            if (${$sVariableNameVOG}['edited_by'] != null) {
                $a['edited_by'] = 'Edited by';
                $a['edited_date'] = 'Edited date';
            }
            if (ACTION == 'edit') {
                $aFields = $a;
                unset($aFields['screeningid']);
                $aFields = array_keys($aFields);
                unset($aFields[0]);
                foreach ($aFields as $sField) {
                    if (is_array($aEdits[$sField])) {
                        $aEdits[$sField] = implode(';', $aEdits[$sField]);
                    }
                    if (${$sVariableNameVOG}[$sField] != $aEdits[$sField]) {
                        ${$sVariableNameVOG}[$sField] .= "\n\t" . (empty($aEdits[$sField])? '(Was previously empty)' : 'Previous value:' . "\n" . $aEdits[$sField]);
                    }
                }
                if (!in_array($aEdits['owned_by'], array($_AUTH['id'], ${$sVariableNameVOG}['owned_by']))) {
                    $aOwner[] = $aEdits['owned_by'];
                }
            }
            $aVariantDetails[] = $a;

            $q = $_DB->query('SELECT vot.*, CONCAT(t.id_ncbi, " (", t.geneid, ")") AS id_ncbi_, t.geneid FROM ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE vot.id = ?', array($nVariantID));
            while ($z = $q->fetchAssoc()) {
                $z['statusid'] = 9;
                $z = lovd_prepareSubmitData('variant', $z);
                $sVariableNameVOT = 'zVariantOnTranscriptDetails_' . $nVariantID . '_' . $z['transcriptid'];
                $sColNamesVOT = 'VOTCols_' . $z['geneid'];
                ${$sColNamesVOT}[0] = $sVariableNameVOT;
                if (ACTION == 'edit') {
                    $aFields = $$sColNamesVOT;
                    unset($aFields['id_ncbi_']);
                    $aFields = array_keys($aFields);
                    unset($aFields[0]);
                    foreach ($aFields as $sField) {
                        if (is_array($aEdits[$z['transcriptid'] . '_' . $sField])) {
                            $aEdits[$z['transcriptid'] . '_' . $sField] = implode(';', $aEdits[$z['transcriptid'] . '_' . $sField]);
                        }
                        if ($z[$sField] != $aEdits[$z['transcriptid'] . '_' . $sField]) {
                            $z[$sField] .= "\n\t" . (empty($aEdits[$z['transcriptid'] . '_' . $sField])? '(Was previously empty)' : 'Previous value:' . "\n" . $aEdits[$z['transcriptid'] . '_' . $sField]);
                        }
                    }
                }
                $aVariantDetails[] = $$sColNamesVOT;
                $$sVariableNameVOT = $z;
            }
            $aVariantDetails[] = 'skip';
            $aVariantDetails[] = 'hr';
        }
        array_pop($aVariantDetails);
        array_pop($aVariantDetails);
    }

    if (!empty($aSubmit['uploads'])) {
        $aUploadDetails = array();
        foreach ($aSubmit['uploads'] as $nUploadID => $zUploadDetails) {
            $sVariableNameUpload = 'zUploadDetails_' . $nUploadID;
            $a = $aUploadFields;
            $a[0] = $sVariableNameUpload;
            $$sVariableNameUpload = $zUploadDetails;
            foreach (array('num_variants_unsupported', 'num_genes', 'num_transcripts') as $sKey) {
                if ($zUploadDetails[$sKey] == 0) {
                    // Don't show the 'Variants not imported', 'Genes created' and/or 'Transcripts created' fields if they are 0.
                    // Note that the Genes and Transcripts counters are always zero for VCF files.
                    unset($a[$sKey]);
                }
            }
            if ($zUploadDetails['file_type'] == 'VCF') {
                // Also don't show the VOT counter for VCF files.
                unset($a['num_variants_on_transcripts']);
            } else {
                // And don't show the mapping flags field for SeattleSeq files.
                unset($a['mapping_flags_']);
            }
            if (!isset($zUploadDetails['screeningid']) || $_PE[2] == 'screening') {
                // Hide the screening ID field if the upload is not added to an existing screening.
                unset($a['screeningid']);
            }
            if ($zUploadDetails['owned_by'] != $_AUTH['id']) {
                // Include 'Data owner' field if owner is not the submitter.
                $a['owned_by_'] = 'Data owner';
                ${$sVariableNameUpload}['owned_by_'] = $_DB->query('SELECT name FROM ' . TABLE_USERS . ' WHERE id = ?', array($zUploadDetails['owned_by']))->fetchColumn();
            }
            ${$sVariableNameUpload}['mapping_flags_'] = (($zUploadDetails['mapping_flags'] & MAPPING_ALLOW)? 'On' . (($zUploadDetails['mapping_flags'] & MAPPING_ALLOW_CREATE_GENES)? ', creating genes as needed' : '') : 'Off');

            // Include 'Data status' as the very last field.
            $a['statusid_'] = 'Data status';
            ${$sVariableNameUpload}['statusid_'] = $_SETT['data_status'][$zUploadDetails['statusid']];
            $aUploadDetails[] = $a;
        }
    }

    // Introduction message to curators/managers.
    $sHead = '';
    $sMessage = 'Dear ';
    if ($sCurators) {
        $sHead .= 'Curator' . (count($aCurators) > 1? 's' : '') . ': ' . $sCurators . "\n";
        $sMessage .= 'Curator' . (count($aCurators) > 1? 's' : '');
    }
    if ($sManagers) {
        $sHead .= 'Manager' . (count($aManagers) > 1? 's' : '') . ': ' . $sManagers . "\n";
        $sMessage .= (!$sCurators? '' : ' and ') . 'Manager' . (count($aManagers) > 1? 's' : '');
    }
    $sMessage = $sHead . "\n" .
                $sMessage . ',' . "\n\n" .
                $_AUTH['name'] . ($_PE[2] == 'confirmedVariants'? ' has indicated that additional variants were also confirmed by an existing screening.' : ' has ' . (ACTION != 'edit'? 'submitted an addition to' : 'made changes to an existing entry in') . ' the LOVD database.') . "\n";
    if ($bUnpublished) {
        $sMessage .= '(Part of) this submission won\'t be viewable to the public until you as curator agree with the additions. You can do so by viewing the entry in LOVD (make sure you\'re logged in), and selecting "Publish" in the options menu. Below is a ' . (ACTION != 'edit'? 'copy of the submission.' : 'overview of the changes.') . "\n\n";
    }

    if ($_CONF['location_url']) {
        $sMessage .= 'To view the ' . (ACTION != 'edit'? ($_PE[2] == 'confirmedVariants'? 'screening ' : 'new ') : '') . 'entry, click this link (you may need to log in first):' . "\n" .
                     $_CONF['location_url'] . $sURI . $nID . "\n\n";
    }
    $sMessage .= 'Regards,' . "\n" .
                 '    LOVD system at ' . $_CONF['institute'] . "\n\n";

    // Build the mail format.
    $aBody = array($sMessage, 'submitter_details' => $aSubmitterDetails);
    if ($_PE[2] == 'individual') {
        $aBody['individual_details'] = $aIndividualDetails;
    }
    if (!empty($aSubmit['phenotypes'])) {
        $aBody['phenotype_details'] = $aPhenotypeDetails;
    }
    if (!empty($aSubmit['screenings']) || $_PE[2] == 'confirmedVariants') {
        $aBody['screening_details'] = $aScreeningDetails;
    }
    if (!empty($aSubmit['variants'])) {
        $aBody['variant_details'] = $aVariantDetails;
    }
    if (!empty($aSubmit['uploads'])) {
        $aBody['upload_details'] = $aUploadDetails;
    }
    require ROOT_PATH . 'inc-lib-form.php';
    $sBody = lovd_formatMail($aBody);

    // Set proper subject.
    $sSubject = 'LOVD submission' . (ACTION != 'edit'? '' : ' update') . (!empty($aGenes)? ' (' . implode(', ', array_slice($aGenes, 0, 20)) . (count($aGenes) > 20? ', ...' : '') . ')' : ''); // Don't just change this; lovd_sendMail() is parsing it.

    $aCC = array();
    // Set submitter address.
    $aCC[] = array($_AUTH['name'], $_AUTH['email']);

    // Get owners address.
    if (!empty($aOwner)) {
        $aCC = array_merge($aCC, $_DB->query('SELECT name, email FROM ' . TABLE_USERS . ' WHERE id IN (?' . str_repeat(', ?', count($aOwner) - 1) . ')', $aOwner)->fetchAllRow());
    }

    // Send mail.
    $bMail = lovd_sendMail($aTo, $sSubject, $sBody, $_SETT['email_headers'], true, $_CONF['send_admin_submissions'], $aCC);

    // FIXME; When messaging system is built in, maybe queue message for curators?
    if ($bMail) {
        lovd_showInfoTable('Successfully processed your submission and sent an email notification to the relevant curator(s)!', 'success');

        // Forward only if there was no error sending the email.
        print('      <SCRIPT type="text/javascript">setTimeout("window.location.href=\'' . lovd_getInstallURL() . $sURI . $nID . '\'", 3000);</SCRIPT>' . "\n");
    } else {
        lovd_showInfoTable('Successfully processed your submission, but LOVD wasn\'t able to send an email notification to the relevant curator(s)!<BR>Please contact one of the relevant curators and notify them of your submission so that they can curate your data!', 'warning');
    }

    $_T->printFooter();
    exit;
}
?>
