Merge pull request #561 from LOVDnl/gb/sourceVariant

Gb/source variant
LOVDnl · Oct 5, 2021 · 53e22a7 · 53e22a7
2 parents 47d0070 + 8a17146
commit 53e22a7
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Showing 5 changed files with 54 additions and 9 deletions.
diff --git a/src/inc-init.php b/src/inc-init.php
@@ -174,7 +174,7 @@
 $_SETT = array(
                 'system' =>
                      array(
-                            'version' => '3.5-pre-02',
+                            'version' => '3.5-pre-03',
                           ),
                 'user_levels' =>
                      array(

diff --git a/src/inc-js-variants.php b/src/inc-js-variants.php
@@ -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 <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>
+ *               L. Werkman <L.Werkman@LUMC.nl>
  *
  *
  * This file is part of LOVD.
@@ -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',

diff --git a/src/inc-upgrade.php b/src/inc-upgrade.php
@@ -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')) {

diff --git a/src/install/inc-sql-tables.php b/src/install/inc-sql-tables.php
@@ -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 <I.F.A.C.Fokkema@LUMC.nl>
  *               Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
  *               M. Kroon <m.kroon@lumc.nl>
+ *               L. Werkman <L.Werkman@LUMC.nl>
  *
  *
  * This file is part of LOVD.
@@ -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,

diff --git a/src/variants.php b/src/variants.php
@@ -4,8 +4,8 @@
  * LEIDEN OPEN VARIATION DATABASE (LOVD)
  *
  * Created     : 2010-12-21
- * Modified    : 2021-08-13
- * For LOVD    : 3.0-27
+ * Modified    : 2021-10-05
+ * For LOVD    : 3.5-pre-03
  *
  * Copyright   : 2004-2021 Leiden University Medical Center; http://www.LUMC.nl/
  * Programmers : Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
@@ -14,6 +14,7 @@
  *               Zuotian Tatum <Z.Tatum@LUMC.nl>
  *               Daan Asscheman <D.Asscheman@LUMC.nl>
  *               M. Kroon <m.kroon@lumc.nl>
+ *               L. Werkman <L.Werkman@LUMC.nl>
  *
  *
  * This file is part of LOVD.
@@ -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.
@@ -823,6 +824,29 @@ 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', $aFieldsGenome)]);
+
+            } elseif ($_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.
+                // We have received the last piece of the field used, which may
+                //  be a genome build (from VOG/DNA/hg38) or "DNA" (from VOG/DNA).
+                $sColumnSuffix = ($_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();
+                $_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'];
@@ -932,7 +956,8 @@ 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(