<?php
/*******************************************************************************
 *
 * LEIDEN OPEN VARIATION DATABASE (LOVD)
 *
 * Created     : 2010-12-20
 * Modified    : 2022-02-10
 * For LOVD    : 3.0-28
 *
 * Copyright   : 2004-2022 Leiden University Medical Center; http://www.LUMC.nl/
 * Programmers : Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
 *               Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
 *               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/>.
 *
 *************/

// Don't allow direct access.
if (!defined('ROOT_PATH')) {
    exit;
}
// Require parent class definition.
require_once ROOT_PATH . 'class/object_custom.php';





class LOVD_GenomeVariant extends LOVD_Custom
{
    // This class extends the Custom class and it handles the Variants On Genome.
    var $sObject = 'Genome_Variant';
    var $sCategory = 'VariantOnGenome';
    var $sTable = 'TABLE_VARIANTS';





    function __construct ()
    {
        // Default constructor.
        global $_AUTH, $_CONF, $_SETT;

        // SQL code for loading an entry for an edit form.
        $this->sSQLLoadEntry = 'SELECT vog.*, ' .
                               'uo.name AS owned_by_ ' .
                               'FROM ' . TABLE_VARIANTS . ' AS vog ' .
                               'LEFT OUTER JOIN ' . TABLE_USERS . ' AS uo ON (vog.owned_by = uo.id) ' .
                               'WHERE vog.id = ?';

        // SQL code for viewing an entry.
        $this->aSQLViewEntry['SELECT']   = 'vog.*, ' .
                                           'a.name AS allele_, ' .
                                           'GROUP_CONCAT(DISTINCT i.id, ";", i.statusid SEPARATOR ";;") AS __individuals, ' .
                                           'GROUP_CONCAT(s2v.screeningid SEPARATOR "|") AS screeningids, ' .
                                           'GROUP_CONCAT(DISTINCT IFNULL(NULLIF(i.license, ""), IFNULL(iuc.default_license, uc.default_license)) SEPARATOR ";;") AS license, ' .
                                           'uo.name AS owned_by_, CONCAT_WS(";", uo.id, uo.name, uo.email, uo.institute, uo.department, IFNULL(uo.countryid, "")) AS _owner, ' .
                                           'uc.name AS created_by_, ' .
                                           'ue.name AS edited_by_';
        $this->aSQLViewEntry['FROM']     = TABLE_VARIANTS . ' AS vog ' .
                                           'LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (vog.id = s2v.variantid) ' .
                                           'LEFT OUTER JOIN ' . TABLE_SCREENINGS . ' AS s ON (s.id = s2v.screeningid) ' .
                                           'LEFT OUTER JOIN ' . TABLE_INDIVIDUALS . ' AS i ON (s.individualid = i.id) ' .
                                           'LEFT OUTER JOIN ' . TABLE_ALLELES . ' AS a ON (vog.allele = a.id) ' .
                                           'LEFT OUTER JOIN ' . TABLE_USERS . ' AS iuc ON (i.created_by = iuc.id) ' .
                                           'LEFT OUTER JOIN ' . TABLE_USERS . ' AS uo ON (vog.owned_by = uo.id) ' .
                                           'LEFT OUTER JOIN ' . TABLE_USERS . ' AS uc ON (vog.created_by = uc.id) ' .
                                           'LEFT OUTER JOIN ' . TABLE_USERS . ' AS ue ON (vog.edited_by = ue.id)';
        $this->aSQLViewEntry['GROUP_BY'] = 'vog.id';

        // SQL code for viewing the list of variants.
        $this->aSQLViewList['SELECT'] =
            'vog.*, ' .
            'a.name AS allele_, ' .
            'e.name AS effect, ' .
            'uo.name AS owned_by_, ' .
            'CONCAT_WS(";", uo.id, uo.name, uo.email, uo.institute, uo.department, IFNULL(uo.countryid, "")) AS _owner, ' .
            'ds.name AS status';
        $this->aSQLViewList['FROM'] =
            TABLE_VARIANTS . ' AS vog ' .
            // Added so that Curators and Collaborators can view the variants for which they have
            // viewing rights in the genomic variant VL.
            // The WHERE condition is set in object_custom.php.
            ($_AUTH && $_AUTH['level'] == LEVEL_SUBMITTER && (count($_AUTH['curates']) || count($_AUTH['collaborates']))?
                'LEFT OUTER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (vog.id = vot.id) ' .
                'LEFT OUTER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) '
            : '') .
            'LEFT OUTER JOIN ' . TABLE_SCR2VAR . ' AS s2v ON (vog.id = s2v.variantid) ' .
            'LEFT OUTER JOIN ' . TABLE_ALLELES . ' AS a ON (vog.allele = a.id) ' .
            'LEFT OUTER JOIN ' . TABLE_EFFECT . ' AS e ON (vog.effectid = e.id) ' .
            'LEFT OUTER JOIN ' . TABLE_USERS . ' AS uo ON (vog.owned_by = uo.id) ' .
            'LEFT OUTER JOIN ' . TABLE_DATA_STATUS . ' AS ds ON (vog.statusid = ds.id)';
        $this->aSQLViewList['GROUP_BY'] = 'vog.id';

        parent::__construct();

        // List of columns and (default?) order for viewing an entry.
        $this->aColumnsViewEntry = array_merge(
            array(
                'individualid_' => 'Individual ID',
                'chromosome' => 'Chromosome',
                'allele_' => 'Allele',
                'effect_reported' => 'Affects function (as reported)',
                'effect_concluded' => 'Affects function (by curator)',
                'curation_status_' => 'Curation status',
                'confirmation_status_' => 'Confirmation status',
            ),
            $this->buildViewEntry(),
            array(
                'mapping_flags_' => array('Automatic mapping', $_SETT['user_level_settings']['see_nonpublic_data']),
                'average_frequency_' => 'Average frequency (gnomAD v.2.1.1)',
                'owned_by_' => 'Owner',
                'status' => array('Variant data status', $_SETT['user_level_settings']['see_nonpublic_data']),
                'license_' => 'Database submission license',
                'created_by_' => 'Created by',
                'created_date_' => array('Date created', $_SETT['user_level_settings']['see_nonpublic_data']),
                'edited_by_' => array('Last edited by', $_SETT['user_level_settings']['see_nonpublic_data']),
                'edited_date_' => array('Date last edited', $_SETT['user_level_settings']['see_nonpublic_data']),
            )
        );
        if (!LOVD_plus) {
            unset($this->aColumnsViewEntry['curation_status_']);
            unset($this->aColumnsViewEntry['confirmation_status_']);
        }

        // List of columns and (default?) order for viewing a list of entries.
        $this->aColumnsViewList = array_merge(
            array(
                'id' => array(
                    'view' => false,
                    'db'   => array('vog.id', 'ASC', true)),
                'screeningids' => array(
                    'view' => false,
                    'db'   => array('s2v.screeningid', 'ASC', true)),
                'id_' => array(
                    'auth' => LEVEL_CURATOR,
                    'view' => array('Variant ID', 75, 'style="text-align : right;"'),
                    'db'   => array('vog.id', 'ASC', true)),
                'effect' => array(
                    'view' => array('Effect', 70),
                    'db'   => array('e.name', 'ASC', true),
                    'legend' => array(
                        'The variant\'s effect on the function of the gene/protein, displayed in the format \'R/C\'. R is the value ' . (LOVD_plus? 'initially reported and C is the value finally concluded;' : 'reported by the source (publication, submitter) and C is the value concluded by the curator;') . ' values ranging from \'+\' (variant affects function) to \'-\' (does not affect function).',
                        'The variant\'s effect on the function of the gene/protein, displayed in the format \'R/C\'. R is the value ' . (LOVD_plus? 'initially reported and C is the value finally concluded.' : 'reported by the source (publication, submitter) and this classification may vary between records. C is the value concluded by the curator. Note that in some database the curator uses Summary records to give details on the classification of the variant.') . 'Values used: \'+\' indicating the variant affects function, \'+?\' probably affects function, \'-\' does not affect function, \'-?\' probably does not affect function, \'?\' effect unknown, \'.\' effect was not classified.')),
                'allele_' => array(
                    'view' => array('Allele', 120),
                    'db'   => array('a.name', 'ASC', true),
                    'legend' => array(
                        'On which allele is the variant located? Does not necessarily imply inheritance!',
                        'On which allele is the variant located? Does not necessarily imply inheritance! \'Paternal\' (confirmed or inferred), \'Maternal\' (confirmed or inferred), \'Parent #1\' or #2 for compound heterozygosity without having screened the parents, \'Unknown\' for heterozygosity without having screened the parents, \'Both\' for homozygozity.')),
                'chromosome' => array(
                    'view' => array('Chr', 50),
                    'db'   => array('vog.chromosome', 'ASC', true)),
                'position_g_start' => array(
                    'view' => false,
                    'db'   => array('vog.position_g_start', 'ASC', true)),
                'position_g_end' => array(
                    'view' => false,
                    'db'   => array('vog.position_g_end', 'ASC', true)),
            ),
            $this->buildViewList(),
            array(
                'owned_by_' => array(
                    'view' => array('Owner', 160),
                    'db'   => array('uo.name', 'ASC', true)),
                'owner_countryid' => array(
                    'view' => false,
                    'db'   => array('uo.countryid', 'ASC', true)),
                'status' => array(
                    'view' => array('Status', 70),
                    'db'   => array('ds.name', false, true),
                    'auth' => $_SETT['user_level_settings']['see_nonpublic_data']),
                'created_by' => array(
                    'view' => false,
                    'db'   => array('vog.created_by', false, true)),
                'created_date' => array(
                    'view' => false,
                    'db'   => array('vog.created_date', 'ASC', true)),
            )
        );

        if ($_SETT['customization_settings']['variants_hide_observation_features']) {
            foreach (array('allele_', 'owned_by_', 'status') as $sCol) {
                unset($this->aColumnsViewEntry[$sCol]);
                unset($this->aColumnsViewList[$sCol]);
            }
        }
        if (!$_SETT['customization_settings']['variants_VL_show_effect']) {
            unset($this->aColumnsViewList['effect']);
        }

        $this->sSortDefault = 'VariantOnGenome/DNA';

        // 2015-10-09; 3.0-14; Add genome build name to the VOG/DNA field.
        $this->aColumnsViewEntry['VariantOnGenome/DNA'] .= ' (Relative to ' . $_CONF['refseq_build'] . ' / ' . $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_name'] . ')';
        $this->aColumnsViewList['VariantOnGenome/DNA']['view'][0] .= ' (' . $_CONF['refseq_build'] . ')';

        // Because the information is publicly available, remove some columns for the public.
        $this->unsetColsByAuthLevel();

        $this->sRowLink = 'variants/{{ID}}';
    }





    function buildForm ($sPrefix = '')
    {
        $aForm = parent::buildForm($sPrefix);
        // Link to HGVS for nomenclature.
        if (isset($aForm[$sPrefix . 'VariantOnGenome/DNA'])) {
            $aForm[$sPrefix . 'VariantOnGenome/DNA'][0] = str_replace('(HGVS format)', '(<A href="http://varnomen.hgvs.org/recommendations/DNA" target="_blank">HGVS format</A>)', $aForm[$sPrefix . 'VariantOnGenome/DNA'][0]);
        }
        return $aForm;
    }





    function checkFields ($aData, $zData = false, $aOptions = array())
    {
        global $_AUTH, $_SETT;

        // Mandatory fields.
        $this->aCheckMandatory =
                 array(
                        'chromosome',
                        'effect_reported',
                        'owned_by',
                        'statusid',
                      );

        if ($_AUTH['level'] >= LEVEL_CURATOR) {
            // This still allows for "Unclassified", which anyway is the default.
            $this->aCheckMandatory[] = 'effect_concluded';
        }

        if (isset($aData['effect_reported']) && $aData['effect_reported'] === '0') {
            // `effect_reported` is not allowed to be '0' (Not classified)
            //  when user is a submitter or when the variant is set to Marked or Public.
            if ($_AUTH['level'] < LEVEL_CURATOR) {
                // Remove the mandatory `effect_reported` field to throw an error.
                unset($aData['effect_reported']);
            } elseif (isset($aData['statusid']) && $aData['statusid'] >= STATUS_MARKED) {
                // Show error for curator/manager trying to publish variant without effect.
                lovd_errorAdd('effect_reported', 'The \'Affects function (as reported)\' field ' .
                    'may not be "' . $_SETT['var_effect'][0] . '" when variant status is "' .
                    $_SETT['data_status'][STATUS_MARKED] . '" or "' . $_SETT['data_status'][STATUS_OK] . '".');
            }
        }

        // Do this before running checkFields so that we have time to predict the DBID and fill it in.
        if (!empty($aData['VariantOnGenome/DNA']) // DNA filled in.
            && isset($this->aColumns['VariantOnGenome/DBID']) // DBID column active.
            && ($this->aColumns['VariantOnGenome/DBID']['public_add'] || $_AUTH['level'] >= LEVEL_CURATOR) // Submitters are allowed to fill it in, or you're curator or up.
            && !(lovd_getProjectFile() == '/import.php' && isset($zData['VariantOnGenome/DBID']) && $aData['VariantOnGenome/DBID'] == $zData['VariantOnGenome/DBID']) // And we're not updating without touching the DBID.
            ) {
            // VOGs with at least one VOT, which still have a chr* DBID, will get an error. So we'll empty the DBID field, allowing the new VOT value to be autofilled in.
            if (!empty($aData['aTranscripts']) && !empty($aData['VariantOnGenome/DBID']) && strpos($aData['VariantOnGenome/DBID'], 'chr' . $aData['chromosome'] . '_') !== false) {
                $aData['VariantOnGenome/DBID'] = '';
            }
            if (empty($aData['VariantOnGenome/DBID'])) {
                if (lovd_getProjectFile() != '/import.php') {
                    // Only predict an DBID, if we're actually going to use it (which doesn't happen when we're importing).
                    $aData['VariantOnGenome/DBID'] = $_POST['VariantOnGenome/DBID'] = lovd_fetchDBID($aData);
                }
            } elseif (!lovd_checkDBID($aData)) {
                lovd_errorAdd('VariantOnGenome/DBID', 'Please enter a valid ID in the ' . (lovd_getProjectFile() == '/import.php'? 'VariantOnGenome/DBID' : '\'ID\'') . ' field or leave it blank and LOVD will predict it. Incorrect ID: "' . htmlspecialchars($aData['VariantOnGenome/DBID']) . '".');
            }
        }

        parent::checkFields($aData, $zData, $aOptions);

        lovd_checkXSS($aData);
    }





    function getForm ()
    {
        // Build the form.
        global $_AUTH, $_CONF, $_DB, $_SETT, $zData, $_DATA;

        // If we've built the form before, simply return it. Especially imports will repeatedly call checkFields(), which calls getForm().
        if (!empty($this->aFormData)) {
            return parent::getForm();
        }

        $aSelectAllele = $_DB->query('SELECT id, name FROM ' . TABLE_ALLELES . ' ORDER BY display_order')->fetchAllCombine();

        if (!empty($_GET['geneid'])) {
            $aFormChromosome = array('Chromosome', '', 'print', $_POST['chromosome']);
        } elseif (ACTION == 'edit') {
            $aFormChromosome = array('Chromosome', '', 'print', $zData['chromosome']);
        } else {
            $aChromosomes = array_keys($_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_sequences']);
            $aSelectChromosome = array_combine($aChromosomes, $aChromosomes);
            $aFormChromosome = array('Chromosome', '', 'select', 'chromosome', 1, $aSelectChromosome, false, false, false);
        }

        if ($_AUTH['level'] >= LEVEL_CURATOR) {
            $aSelectOwner = $_DB->query('SELECT id, CONCAT(name, " (#", id, ")") as name_id FROM ' . TABLE_USERS .
                ' ORDER BY name')->fetchAllCombine();
            $aFormOwner = array('Owner of this data', '', 'select', 'owned_by', 1, $aSelectOwner, false, false, false);
            $aSelectStatus = $_SETT['data_status'];
            if (lovd_getProjectFile() == '/import.php') {
                // During an import the status pending is allowed, therefore only status in progress is unset.
                unset($aSelectStatus[STATUS_IN_PROGRESS]);
            } else {
                unset($aSelectStatus[STATUS_PENDING], $aSelectStatus[STATUS_IN_PROGRESS]);
            }
            $aFormStatus = array('Status of this data', '', 'select', 'statusid', 1, $aSelectStatus, false, false, false);
        } else {
            $aFormOwner = array();
            $aFormStatus = array();
        }

        $aTranscriptEffects = array();
        $aTranscriptsForm = array();
        if (is_array($_DATA) && !empty($_DATA['Transcript'])) {
            foreach (array_keys($_DATA['Transcript']) as $sGene) {
                $aTranscriptsForm = array_merge($aTranscriptsForm, $_DATA['Transcript'][$sGene]->getForm());

                // Collect variant effect for all transcripts in $aTranscriptEffects.
                foreach (array_keys($_DATA['Transcript'][$sGene]->aTranscripts) as $sTranscript) {
                    if (isset($zData[$sTranscript . '_effectid'])) {
                        $aTranscriptEffects[$sTranscript] = $zData[$sTranscript . '_effectid'];
                    }
                }
            }
        }

        // Add genome build name to VOG/DNA field.
        $this->aColumns['VariantOnGenome/DNA']['description_form'] = '<B>Relative to ' . $_CONF['refseq_build'] . ' / ' . $_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_name'] . '.</B>' .
            (!$this->aColumns['VariantOnGenome/DNA']['description_form']? '' : '<BR>' . $this->aColumns['VariantOnGenome/DNA']['description_form']);

        // FIXME; right now two blocks in this array are put in, and optionally removed later. However, the if() above can build an entire block, such that one of the two big unset()s can be removed.
        // A similar if() to create the "authorization" block, or possibly an if() in the building of this form array, is easier to understand and more efficient.
        // Array which will make up the form table.
        $this->aFormData = array_merge(
                 array(
                        array('POST', '', '', '', '35%', '14', '65%'),
                      ),
                $aTranscriptsForm,
                array(
                        array('', '', 'print', '<B>Genomic variant information</B>'),
                        'hr',
                        array('Allele', '', 'select', 'allele', 1, $aSelectAllele, false, false, false),
                        array('', '', 'note', 'If you wish to report an homozygous variant, please select "Both (homozygous)" here.'),
                        $aFormChromosome,
                      ),
                 $this->buildForm(),
                 array(
   'effect_reported' => array('Affects function (as reported)', '', 'select', 'effect_reported', 1, $_SETT['var_effect'], false, false, false),
  'effect_concluded' => array('Affects function (by curator)', '', 'select', 'effect_concluded', 1, $_SETT['var_effect'], false, false, false),
                        'hr',
      'general_skip' => 'skip',
           'general' => array('', '', 'print', '<B>General information</B>'),
       'general_hr1' => 'hr',
             'owner' => $aFormOwner,
            'status' => $aFormStatus,
       'general_hr2' => 'hr',
                        'skip',
     'authorization' => array('Enter your password for authorization', '', 'password', 'password', 20),
                      ));

        // Check if we actually have any transcripts enabled. When creating a variant, the user may disable them.
        // We need to know for the variant effect fields.
        $nTranscripts = 0;
        if (ACTION == 'create' && !empty($_POST['aTranscripts'])) {
            foreach (array_keys($_POST['aTranscripts']) as $nTranscriptID) {
                if (empty($_POST['ignore_' . $nTranscriptID])) {
                    $nTranscripts ++;
                }
            }
        } elseif (!empty($_POST['aTranscripts'])) {
            $nTranscripts = count($_POST['aTranscripts']);
        }

        if (ACTION == 'create' || (ACTION == 'publish' && GET)) {
            // When creating, or when publishing without any changes, unset the authorization.
            unset($this->aFormData['authorization']);
        }
        if ($_AUTH['level'] < LEVEL_CURATOR) {
            unset($this->aFormData['effect_concluded'], $this->aFormData['general_skip'], $this->aFormData['general'], $this->aFormData['general_hr1'], $this->aFormData['owner'], $this->aFormData['status'], $this->aFormData['general_hr2']);
        } elseif ($nTranscripts) {
            // Determine whether to show the `effect_concluded` field.
            // When a variant is linked to one or more transcripts, its effect
            //  on the genomic level will be determined by the "worst" effect on the
            //  transcript levels. Only if the currently set effect is non-concordant
            //  with the current effects on the transcripts and not set to
            //  'not classified', will the form field be shown so that the user
            //  must manually correct the current value.
            $bHideEffectConcluded = false;
            $nVOGEffectConcluded = (!isset($zData['effectid'])? 0 : intval($zData['effectid'][1]));
            if ($nVOGEffectConcluded === 0) {
                // Set to "Not classified", we'll fill it in.
                $bHideEffectConcluded = true;
            } else {
                $nMaxEffectReported = max(array_map(function ($sEffectID) {
                    return intval($sEffectID[1]);
                }, $aTranscriptEffects));
                if ($nVOGEffectConcluded == $nMaxEffectReported) {
                    $bHideEffectConcluded = true;
                }
            }

            if ($bHideEffectConcluded) {
                $this->aFormData['effect_concluded'] = array(
                    $this->aFormData['effect_concluded'][0], '', 'note',
                    'Effect on genomic level will be determined by the variant\'s effect on transcript(s).');
            }
        }

        // Determine whether to show the `effect_reported` field.
        if ($nTranscripts) {
            // When a variant is linked to one or more transcripts, its effect
            //  on the genomic level will be determined by the "worst" effect on the
            //  transcript levels. Only if the currently set effect is non-concordant
            //  with the current effects on the transcripts and not set to
            //  'not classified', will the form field be shown so that the user
            //  must manually correct the current value.
            $bHideEffectReported = false;
            $nVOGEffectReported = (!isset($zData['effectid'])? 0 : intval($zData['effectid'][0]));
            if ($nVOGEffectReported === 0) {
                // Set to "Not classified", we'll fill it in.
                $bHideEffectReported = true;
            } else {
                $nMaxEffectReported = max(array_map(function ($sEffectID) {
                    return intval($sEffectID[0]);
                }, $aTranscriptEffects));
                if ($nVOGEffectReported == $nMaxEffectReported) {
                    $bHideEffectReported = true;
                }
            }

            if ($bHideEffectReported) {
                $this->aFormData['effect_reported'] = array(
                    $this->aFormData['effect_reported'][0], '', 'note',
                    'Effect on genomic level will be determined by the variant\'s effect on transcript(s).');
            }
        }

        return parent::getForm();
    }




    function prepareData ($zData = '', $sView = 'list')
    {
        // Prepares the data by "enriching" the variable received with links, pictures, etc.

        global $_AUTH, $_DB, $_SETT;

        if (!in_array($sView, array('list', 'entry'))) {
            $sView = 'list';
        }

        // Makes sure it's an array and htmlspecialchars() all the values.
        $zData = parent::prepareData($zData, $sView);

        if ($sView == 'entry') {
            $zData['individualid_'] = '';
            // While in principle a variant should only be connected to one patient, due to database model limitations, through several screenings, one could link a variant to more individuals.
            foreach ($zData['individuals'] as $aIndividual) {
                list($nID, $nStatusID) = $aIndividual;
                if ($_AUTH && $_AUTH['level'] >= $_SETT['user_level_settings']['see_nonpublic_data']) {
                    $zData['individualid_'] .= ($zData['individualid_']? ', ' : '') .
                        '<A href="individuals/' . $nID . '">' . $nID . '</A> ' .
                        '<SPAN style="color: #' . $this->getStatusColor($nStatusID) . '">(' . $_SETT['data_status'][$nStatusID] . ')</SPAN>';
                } elseif ($nStatusID >= STATUS_MARKED) {
                    $zData['individualid_'] .= ($zData['individualid_']? ', ' : '') . '<A href="individuals/' . $nID . '">' . $nID . '</A>';
                }
            }
            if (empty($zData['individualid_'])) {
                unset($this->aColumnsViewEntry['individualid_']);
            }
            $zData['effect_reported'] = $_SETT['var_effect'][$zData['effectid'][0]];
            $zData['effect_concluded'] = $_SETT['var_effect'][$zData['effectid'][1]];

            if (!empty($zData['VariantOnGenome/DBID'])) {
                // Allow linking to view of all these variants.
                $sQ = 'SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ' WHERE chromosome = ? AND `VariantOnGenome/DBID` = ?';
                $aArgs = array($zData['chromosome'], $zData['VariantOnGenome/DBID']);
                if (!$_AUTH || $_AUTH['level'] < LEVEL_CURATOR) {
                    $sQ .= ' AND statusid >= ?';
                    $aArgs[] = STATUS_MARKED;
                }
                $n = $_DB->query($sQ, $aArgs)->fetchColumn();
                if ($n > 1 && (!LOVD_plus || !lovd_verifyInstance('mgha', false))) {
                    list($sPrefix,) = explode('_', $zData['VariantOnGenome/DBID'], 2);
                    $sLink = '<A href="' . (substr($sPrefix, 0, 3) == 'chr'? 'variants' : 'view/' . $sPrefix) . '?search_VariantOnGenome%2FDBID=%3D%22' . $zData['VariantOnGenome/DBID'] . '%22">See all ' . $n . ' reported entries</A>';
                    if (LOVD_plus) {
                        $sLink = '<A href="variants/DBID/' . $zData['VariantOnGenome/DBID'] .'">See all ' . $n . ' reported entries</A>';
                    }
                    // This is against our coding policy of never modifying actual contents of values (we always create a copy with _ appended), but now I simply can't without
                    // modifying the column list manually. If only array_splice() would work on associative arrays... I'm not going to create a workaround here.
                    $zData['VariantOnGenome/DBID'] .= ' <SPAN style="float:right">' . $sLink . '</SPAN>';
                }
            }

            if ($zData['mapping_flags'] & MAPPING_ALLOW) {
                $sMappingLinkText  = '';
                $sMappingLinkTitle = '';
                if ($zData['mapping_flags'] & MAPPING_NOT_RECOGNIZED) {
                    $zData['mapping_flags_'] = 'Variant not recognized';
                    if ($zData['mapping_flags'] & MAPPING_ALLOW_CREATE_GENES) {
                        $zData['mapping_flags_'] .= ' (would have created genes as needed)';
                    }
                    $sMappingLinkText = 'Retry';
                } elseif ($zData['mapping_flags'] & MAPPING_DONE) {
                    $zData['mapping_flags_'] = 'Done';
                    if ($zData['mapping_flags'] & MAPPING_ALLOW_CREATE_GENES) {
                        $zData['mapping_flags_'] .= ' (created genes as needed)';
                    }
                    $sMappingLinkText  = 'Map again';
                    $sMappingLinkTitle = 'If new transcripts have been added to LOVD, this will try to map this variant to them.';
                } else {
                    $zData['mapping_flags_'] = 'Scheduled';
                    if ($zData['mapping_flags'] & MAPPING_ALLOW_CREATE_GENES) {
                        $zData['mapping_flags_'] .= ', creating genes as needed';
                    }
                    if ($zData['mapping_flags'] & MAPPING_ERROR) {
                        $zData['mapping_flags_'] .= ' (encountered a problem on the last attempt)';
                    }
                    $sMappingLinkText = 'Map now';
                }
                if ($_AUTH && $_AUTH['level'] >= LEVEL_OWNER) {
                    $zData['mapping_flags_'] .= ' <SPAN style="float: right" id="mapOnRequest"><A href="#" onclick="return lovd_mapOnRequest();"' . (!$sMappingLinkTitle? '' : ' title="' . $sMappingLinkTitle . '"') . '>' . $sMappingLinkText . '</A></SPAN>';
                }
            } else {
                $zData['mapping_flags_'] = 'Off';
            }

            // 2013-09-27; 3.0-08; Frequences retrieved from the LOVD WGS install.
            if (!$zData['chromosome'] || !$zData['position_g_start'] || !$zData['position_g_end']) {
                $zData['average_frequency_'] = 'Genomic location of variant could not be determined';
            } elseif ($zData['average_frequency'] === '') {
                $zData['average_frequency_'] = '<A href="#" onclick="lovd_openWindow(\'' . ROOT_PATH . 'scripts/fetch_frequencies.php\', \'FetchFrequencies\', \'500\', \'150\'); return false;">Retrieve</A>';
            } elseif ($zData['average_frequency'] === '0') {
                $zData['average_frequency_'] = 'Variant not found in online data sets';
            } else {
                $zData['average_frequency_'] = round($zData['average_frequency'], 5) . ' <SPAN style="float: right"><A href="https://gnomad.broadinstitute.org/region/' . $zData['chromosome'] . '-' . $zData['position_g_start'] . '-' . $zData['position_g_end'] . '?dataset=gnomad_r2_1" target="_blank">View details</A></SPAN>';
            }
            if (LOVD_plus && !empty($zData['curation_status_'])) {
                // Add a link to the curation status to show the curation status history for this variant.
                $zData['curation_status_'] .= '<SPAN style="float: right"><A href="#" onclick="lovd_openWindow(\'' . lovd_getInstallURL(). 'variants/' . $zData['id'] . '?curation_status_log&in_window\', \'curationStatusHistory\', 1050, 450);return false;">View History</A></SPAN>';
            }
            if (LOVD_plus && !empty($zData['confirmation_status_'])) {
                // Add a link to the confirmation status to show the confirmation status history for this variant.
                $zData['confirmation_status_'] .= '<SPAN style="float: right"><A href="#" onclick="lovd_openWindow(\'' . lovd_getInstallURL(). 'variants/' . $zData['id'] . '?confirmation_status_log&in_window\', \'confirmationStatusHistory\', 1050, 450);return false;">View History</A></SPAN>';
            }
        }
        // Replace rs numbers with dbSNP links.
        if (!empty($zData['VariantOnGenome/dbSNP'])) {
            $zData['VariantOnGenome/dbSNP'] = preg_replace('/(rs\d+)/', '<SPAN' . ($sView != 'list'? '' : ' onclick="cancelParentEvent(event);"') . '><A href="https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=' . "$1" . '" target="_blank">' . "$1" . '</A></SPAN>', $zData['VariantOnGenome/dbSNP']);
        }

        return $zData;
    }





    function setDefaultValues ()
    {
        global $_AUTH;

        $_POST['statusid'] = STATUS_OK;
        $_POST['owned_by'] = $_AUTH['id'];
        $this->initDefaultValues();
    }
}
?>
