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Store the original variant description as the source of the submission #561

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merged 4 commits into from
Oct 5, 2021
Merged

Store the original variant description as the source of the submission #561

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6951429
Add source to VOG when creating new variants
loeswerkman Oct 1, 2021
dfcbb78
Add source to existing VOG table when upgrading LOVD
loeswerkman Oct 5, 2021
49bf4a1
Apply fixes after comments on pull request
loeswerkman Oct 5, 2021
8a17146
Fixed missing whitespace and some clarifications.
ifokkema Oct 5, 2021
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2 changes: 1 addition & 1 deletion src/inc-init.php
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Original file line number Diff line number Diff line change
Expand Up @@ -174,7 +174,7 @@
$_SETT = array(
'system' =>
array(
'version' => '3.5-pre-02',
'version' => '3.5-pre-03',
),
'user_levels' =>
array(
Expand Down
16 changes: 14 additions & 2 deletions src/inc-js-variants.php
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Expand Up @@ -4,14 +4,15 @@
* LEIDEN OPEN VARIATION DATABASE (LOVD)
*
* Created : 2011-11-08
* Modified : 2020-07-23
* For LOVD : 3.0-25
* Modified : 2020-10-01
* For LOVD : 3.5-pre-02
*
* Copyright : 2004-2020 Leiden University Medical Center; http://www.LUMC.nl/
* Programmers : Ivar C. Lugtenburg <[email protected]>
* Ivo F.A.C. Fokkema <[email protected]>
* Daan Asscheman <[email protected]>
* M. Kroon <[email protected]>
* L. Werkman <[email protected]>
*
*
* This file is part of LOVD.
Expand Down Expand Up @@ -179,6 +180,17 @@ function lovd_convertPosition (oElement)
// Function that can map a variant to other transcripts or the genome.

var oThisDNA = $(oElement).siblings('input:first');
var oVariantSource = $('input[name$="source"]');
if (oVariantSource.val() == "") {
var sSource = "";
if (oThisDNA.attr("name").indexOf("VariantOnTranscript") >= 0) {
sSource = "VOT";
} else {
pos = oThisDNA.attr("name").lastIndexOf("/");
sSource = oThisDNA.attr("name").substr(pos + 1);
}
oVariantSource.val(sSource);
}
var oAllDNA = $('input[name$="_VariantOnTranscript/DNA"]');
$(oAllDNA).removeClass().siblings('img:first').attr({
src: 'gfx/trans.png',
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6 changes: 6 additions & 0 deletions src/inc-upgrade.php
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Expand Up @@ -833,6 +833,12 @@ function lovd_addConditionalSQL ($sCondition, $aConditionArgs, $sSQL)
VALUES ("' . $_CONF['refseq_build'] . '", "' . $_CONF['refseq_build'] . ' / ' .
$_SETT['human_builds'][$_CONF['refseq_build']]['ncbi_name'] . '", 0, NOW())',
),
'3.5-pre-03' => array(
'ALTER TABLE ' . TABLE_VARIANTS . ' ADD COLUMN source VARCHAR(4) AFTER type',
'UPDATE ' . TABLE_VARIANTS . ' AS vog' .
' SET source = (SELECT id FROM ' . TABLE_GENOME_BUILDS . ' WHERE column_suffix = "")' .
' WHERE vog.id NOT IN (SELECT id FROM ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ')',
),
);

if ($sCalcVersionDB < lovd_calculateVersion('3.0-alpha-01')) {
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6 changes: 4 additions & 2 deletions src/install/inc-sql-tables.php
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Expand Up @@ -4,13 +4,14 @@
* LEIDEN OPEN VARIATION DATABASE (LOVD)
*
* Created : 2009-10-22
* Modified : 2021-04-22
* For LOVD : 3.0-27
* Modified : 2021-10-01
* For LOVD : 3.5-pre-02
*
* Copyright : 2004-2021 Leiden University Medical Center; http://www.LUMC.nl/
* Programmers : Ivo F.A.C. Fokkema <[email protected]>
* Ivar C. Lugtenburg <[email protected]>
* M. Kroon <[email protected]>
* L. Werkman <[email protected]>
*
*
* This file is part of LOVD.
Expand Down Expand Up @@ -351,6 +352,7 @@
position_g_start INT(10) UNSIGNED,
position_g_end INT(10) UNSIGNED,
type VARCHAR(10),
source VARCHAR(4),
mapping_flags TINYINT(3) UNSIGNED NOT NULL DEFAULT 0,
average_frequency FLOAT,
owned_by SMALLINT(5) UNSIGNED ZEROFILL,
Expand Down
31 changes: 27 additions & 4 deletions src/variants.php
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@
* LEIDEN OPEN VARIATION DATABASE (LOVD)
*
* Created : 2010-12-21
* Modified : 2021-08-13
* For LOVD : 3.0-27
* Modified : 2021-10-01
* For LOVD : 3.5-pre-02
*
* Copyright : 2004-2021 Leiden University Medical Center; http://www.LUMC.nl/
* Programmers : Ivar C. Lugtenburg <[email protected]>
Expand All @@ -14,6 +14,7 @@
* Zuotian Tatum <[email protected]>
* Daan Asscheman <[email protected]>
* M. Kroon <[email protected]>
* L. Werkman <[email protected]>
*
*
* This file is part of LOVD.
Expand Down Expand Up @@ -805,7 +806,7 @@ function(sData) {
if (!lovd_error()) {
// Prepare the fields to be used for both genomic and transcript variant information.
$aFieldsGenome = array_merge(
array('allele', 'effectid', 'chromosome', 'position_g_start', 'type', 'position_g_end', 'owned_by', 'statusid', 'created_by', 'created_date'),
array('allele', 'effectid', 'chromosome', 'position_g_start', 'type', 'source', 'position_g_end', 'owned_by', 'statusid', 'created_by', 'created_date'),
$_DATA['Genome']->buildFields());

// Prepare values.
Expand All @@ -823,6 +824,27 @@ function(sData) {
$_POST['type'] = NULL;
}

// Add the source of the variant if a source can be found.
if (empty($_POST['source'])) {
// If nothing is given, the source is set to null, meaning that the source is unknown.
unset($aFieldsGenome[array_search('source', $aFieldsGenome)]);
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} elseif ($_POST['source'] == 'VOT') {
// If the source is a transcript, we describe it with an empty string.
$_POST['source'] = '';

} else {
// If the source of the variant is not a transcript, it is a genome build.
// We will then send the ID of this genome build to the database.
$sColumnSuffix = ($_POST['source'] == 'DNA'? '' : $_POST['source']);

// Get the ID by its column suffix and give this as the source.
$sID = $_DB->query(
'SELECT id FROM ' . TABLE_GENOME_BUILDS .
'WHERE column_suffix = ?', array($sColumnSuffix))->fetchColumn();
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Not sure how this is possible, but there is another space missing. I thought we tested this code - this should have caused a query error. Anyway, I'll fix it.

$_POST['source'] = $sID;
}

$_POST['owned_by'] = ($_AUTH['level'] >= LEVEL_CURATOR? $_POST['owned_by'] : $_AUTH['id']);
$_POST['statusid'] = ($_AUTH['level'] >= LEVEL_CURATOR? $_POST['statusid'] : STATUS_IN_PROGRESS);
$_POST['created_by'] = $_AUTH['id'];
Expand Down Expand Up @@ -932,7 +954,8 @@ function(sData) {
lovd_includeJS('inc-js-custom_links.php');

// Table.
print(' <FORM id="variantForm" action="' . CURRENT_PATH . '?create&amp;reference=' . $_GET['reference'] . (isset($sGene)? '&amp;geneid=' . rawurlencode($sGene) : '') . (isset($_POST['screeningid'])? '&amp;target=' . $_GET['target'] : '') . '" method="post">' . "\n");
print(' <FORM id="variantForm" action="' . CURRENT_PATH . '?create&amp;reference=' . $_GET['reference'] . (isset($sGene)? '&amp;geneid=' . rawurlencode($sGene) : '') . (isset($_POST['screeningid'])? '&amp;target=' . $_GET['target'] : '') . '" method="post">' . "\n" .
' <INPUT name="source" type="hidden" value="' . (empty($_POST['source'])? '' : $_POST['source']) . '"> ' . "\n");

// Array which will make up the form table.
$aForm = array_merge(
Expand Down