Commit 2d79456a authored by Ivo Fokkema's avatar Ivo Fokkema

Reverted changes made for supporting full_group_by in the graphs.

parent 69390026
...@@ -4,10 +4,10 @@ ...@@ -4,10 +4,10 @@
* LEIDEN OPEN VARIATION DATABASE (LOVD) * LEIDEN OPEN VARIATION DATABASE (LOVD)
* *
* Created : 2012-06-11 * Created : 2012-06-11
* Modified : 2017-02-07 * Modified : 2019-08-06
* For LOVD : 3.0-19 * For LOVD : 3.0-22
* *
* Copyright : 2004-2017 Leiden University Medical Center; http://www.LUMC.nl/ * Copyright : 2004-2019 Leiden University Medical Center; http://www.LUMC.nl/
* Programmers : Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl> * Programmers : Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
* David Baux <david.baux@inserm.fr> * David Baux <david.baux@inserm.fr>
* M. Kroon <m.kroon@lumc.nl> * M. Kroon <m.kroon@lumc.nl>
...@@ -353,15 +353,15 @@ class LOVD_Graphs { ...@@ -353,15 +353,15 @@ class LOVD_Graphs {
// I guess this should be called "exonic", also removing both UTR regions, but I will leave this for some other time, if ever. // I guess this should be called "exonic", also removing both UTR regions, but I will leave this for some other time, if ever.
if ($bUnique) { if ($bUnique) {
if ($Data == '*') { if ($Data == '*') {
$qPositions = $_DB->query('SELECT MAX(position_c_cds_end), MAX(position_c_start), MAX(position_c_start_intron), MAX(position_c_end), MAX(position_c_end_intron), 1 FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`'); $qPositions = $_DB->query('SELECT position_c_cds_end, position_c_start, position_c_start_intron, position_c_end, position_c_end_intron, 1 FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`');
} else { } else {
$qPositions = $_DB->query('SELECT MAX(position_c_cds_end), MAX(position_c_start), MAX(position_c_start_intron), MAX(position_c_end), MAX(position_c_end_intron), 1 FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data)); $qPositions = $_DB->query('SELECT position_c_cds_end, position_c_start, position_c_start_intron, position_c_end, position_c_end_intron, 1 FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data));
} }
} else { } else {
if ($Data == '*') { if ($Data == '*') {
$qPositions = $_DB->query('SELECT MAX(position_c_cds_end), MAX(position_c_start), MAX(position_c_start_intron), MAX(position_c_end), MAX(position_c_end_intron), COUNT(*) FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`'); $qPositions = $_DB->query('SELECT position_c_cds_end, position_c_start, position_c_start_intron, position_c_end, position_c_end_intron, COUNT(*) FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`');
} else { } else {
$qPositions = $_DB->query('SELECT MAX(position_c_cds_end), MAX(position_c_start), MAX(position_c_start_intron), MAX(position_c_end), MAX(position_c_end_intron), COUNT(*) FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data)); $qPositions = $_DB->query('SELECT position_c_cds_end, position_c_start, position_c_start_intron, position_c_end, position_c_end_intron, COUNT(*) FROM ' . TABLE_TRANSCRIPTS . ' AS t INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot ON (t.id = vot.transcriptid) INNER JOIN ' . TABLE_VARIANTS . ' AS vog ON (vot.id = vog.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vot.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data));
} }
} }
} else { } else {
...@@ -482,9 +482,9 @@ class LOVD_Graphs { ...@@ -482,9 +482,9 @@ class LOVD_Graphs {
// Restricting to a certain gene, or full database ($Data == '*'). // Restricting to a certain gene, or full database ($Data == '*').
if ($bUnique) { if ($bUnique) {
if ($Data == '*') { if ($Data == '*') {
$qData = $_DB->query('SELECT MIN(type), COUNT(DISTINCT type) FROM ' . TABLE_VARIANTS . ' AS vog WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`'); $qData = $_DB->query('SELECT type, COUNT(DISTINCT type) FROM ' . TABLE_VARIANTS . ' AS vog WHERE 1=1' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`');
} else { } else {
$qData = $_DB->query('SELECT MIN(type), COUNT(DISTINCT type) FROM ' . TABLE_VARIANTS . ' AS vog INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING (id) INNER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data)); $qData = $_DB->query('SELECT type, COUNT(DISTINCT type) FROM ' . TABLE_VARIANTS . ' AS vog INNER JOIN ' . TABLE_VARIANTS_ON_TRANSCRIPTS . ' AS vot USING (id) INNER JOIN ' . TABLE_TRANSCRIPTS . ' AS t ON (vot.transcriptid = t.id) WHERE t.geneid = ?' . ($bNonPublic? '' : ' AND statusid >= ' . STATUS_MARKED) . (!$bPathogenicOnly? '' : ' AND (LEFT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ' OR RIGHT(vog.effectid, 1) >= ' . $nPathogenicThreshold . ')') . ' GROUP BY `VariantOnGenome/DBID`', array($Data));
} }
$aData = array(); $aData = array();
while (list($sType, $nCount) = $qData->fetchRow()) { while (list($sType, $nCount) = $qData->fetchRow()) {
......
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