Merge branch 'master' into fix/strict_mysql_errors

LOVDnl · Jan 31, 2017 · c555a6c · c555a6c
2 parents 6e0d851 + fe06dbb
commit c555a6c
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Showing 4 changed files with 23 additions and 13 deletions.
diff --git a/src/changelog.txt b/src/changelog.txt
@@ -18,6 +18,10 @@
    Closes #143: "LOVD won't install with error "Invalid default value for
    'start_date'""
    Closes #173: "Installation failed on ubuntu 16"
+ * Fixed bug; The "all variants affecting transcripts" view showed only one
+   entry. This was caused by the recent changes making LOVD compatible with the
+   new default "ONLY_FULL_GROUP_BY" MySQL setting.
+   Closes #176: "Viewlist entry count differs from what is displayed".
 
 
 /**************************

diff --git a/src/class/object_custom_viewlists.php b/src/class/object_custom_viewlists.php
@@ -4,13 +4,13 @@
  * LEIDEN OPEN VARIATION DATABASE (LOVD)
  *
  * Created     : 2011-08-15
- * Modified    : 2017-01-13
+ * Modified    : 2017-01-25
  * For LOVD    : 3.0-19
  *
  * Copyright   : 2004-2017 Leiden University Medical Center; http://www.LUMC.nl/
- * Programmers : Ing. Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
- *               Ing. Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
- *               Msc. Daan Asscheman <D.Asscheman@LUMC.nl>
+ * Programmers : Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
+ *               Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
+ *               Daan Asscheman <D.Asscheman@LUMC.nl>
  *               M. Kroon <m.kroon@lumc.nl>
  *
  *
@@ -290,6 +290,11 @@ function __construct ($aObjects = array(), $sOtherID = '')
                             $aSQL['FROM'] .= 't.id = vot.transcriptid)';
                             // Nice, but if we're showing transcripts and variants on transcripts in one viewList, we'd only want to see the transcripts that HAVE variants.
                             $aSQL['WHERE'] .= (!$aSQL['WHERE']? '' : ' AND ') . 'vot.id IS NOT NULL';
+                            // Then also make sure we group on the VOT's ID, unless we're already grouping on something.
+                            if (!$aSQL['GROUP_BY']) {
+                                // t.geneid needs to be included because we order on this as well (otherwise, we could have used t.id).
+                                $aSQL['GROUP_BY'] = 't.geneid, vot.id';
+                            }
                         }
                         // We have no fallback, so we'll easily detect an error if we messed up somewhere.
                     }

diff --git a/src/class/progress_bar.php b/src/class/progress_bar.php
@@ -4,12 +4,12 @@
  * LEIDEN OPEN VARIATION DATABASE (LOVD)
  *
  * Created     : 2010-09-10
- * Modified    : 2016-10-14
- * For LOVD    : 3.0-18
+ * Modified    : 2017-01-27
+ * For LOVD    : 3.0-19
  *
- * Copyright   : 2004-2016 Leiden University Medical Center; http://www.LUMC.nl/
- * Programmers : Ing. Ivo F.A.C. Fokkema <I.F.A.C.Fokkema@LUMC.nl>
- *               Ing. Ivar C. Lugtenburg <I.C.Lugtenburg@LUMC.nl>
+ * Copyright   : 2004-2017 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>
  *
  *
  * This file is part of LOVD.
@@ -46,7 +46,7 @@ class ProgressBar {
 
 
 
-    function ProgressBar ($sID = '', $sMessageInit = '', $sMessageDone = '')
+    function __construct ($sID = '', $sMessageInit = '', $sMessageDone = '')
     {
         // Default constructor.
 

diff --git a/src/class/template.php b/src/class/template.php
@@ -4,7 +4,7 @@
  * LEIDEN OPEN VARIATION DATABASE (LOVD)
  *
  * Created     : 2012-03-27
- * Modified    : 2017-01-13
+ * Modified    : 2017-01-25
  * For LOVD    : 3.0-19
  *
  * Copyright   : 2004-2017 Leiden University Medical Center; http://www.LUMC.nl/
@@ -612,7 +612,7 @@ function lovd_changeURL ()
 <TABLE border="0" cellpadding="0" cellspacing="0" width="100%"><TR><TD>
 
 <!-- Have a DIV for the announcements together with the header, to make sure the announcements move with the sticky header. -->
-<DIV id="stickyheader" style="position : fixed; z-index : 10;">
+<DIV id="stickyheader" style="position : fixed; z-index : 10; width : 100%">
 <?php
 // Check for announcements. Ignore errors, in case the table doesn't exist yet.
 $qAnnouncements = @$_DB->query('SELECT id, type, announcement FROM ' . TABLE_ANNOUNCEMENTS . ' WHERE start_date <= NOW() AND end_date >= NOW()', array(), false);
@@ -645,7 +645,8 @@ function lovd_changeURL ()
               '      <H2 style="margin-bottom : 2px;">' . $_CONF['system_title'] . '</H2>');
 
         if ($sCurrSymbol && $sCurrGene) {
-            print('      <H5 id="gene_name" style="display:inline">' . $sCurrGene . ' (' . $sCurrSymbol . ')' . "\n");
+            $sGeneName = lovd_shortenString($sCurrSymbol . ' (' . $sCurrGene . ')', 55);
+            print('      <H5 id="gene_name" style="display:inline">' . $sGeneName . "\n");
             if (strpos($sGeneSwitchURL, '{{GENE}}') !== false) {
                 print('        <A href="#" onclick="lovd_switchGene(); return false;">' . "\n" .
                       '          <IMG src="gfx/lovd_genes_switch_inline.png" width="23" height="23" alt="Switch gene" title="Switch gene database" align="top">' . "\n" .