Improve/variant creation form

src/ajax/mobidetails.php

@@ -111,10 +111,14 @@
     $_SESSION['csrf_tokens']['mobidetails_confirm'] = md5(uniqid());
     $sFormConfirmation = str_replace('{{CSRF_TOKEN}}', $_SESSION['csrf_tokens']['mobidetails_confirm'], $sFormConfirmation);
 
+    // This print statement and flush do not work.
+    // It seems that flush successfully forces the output
+    //  to the browser, but the browser does not seem to
+    //  execute the JS until the page has finished loading. (Chrome)
     print('
     $("#mobidetails_dialog").html("<IMG src=\'gfx/ajax_loading.gif\' alt=\'Please wait...\' width=\'100\' height=\'100\'>");
     ');
-    ob_end_flush();
+    @ob_end_flush();
     flush();
 
     // Now check with MobiDetails.

src/class/object_custom.php

@@ -299,6 +299,12 @@ function buildForm ($sPrefix = '')
                 $aFormData[$sPrefix . $sCol] = $aEntry;
             }
 
+            // The element data will be passed on, so that viewForm() can make sure it will be added to the HTML.
+            // NOTE: Element data is not stored in the database, but added by, for instance, getForm().
+            if (!empty($aCol['element_data'])) {
+                $aFormData[$sPrefix . $sCol][] = $aCol['element_data'];
+            }
+
             // Any custom links we want to mention?
             if (!empty($aCol['custom_links'])) {
                 $sLinks = '';

src/class/object_genome_builds.php

@@ -123,7 +123,7 @@ function prepareData ($zData = '', $sView = 'list')
             $sDNAColumn = 'VariantOnGenome/DNA' . (!$zData['column_suffix']? '' : '/') . $zData['column_suffix'];
             $nPercentComplete = (int) $_DB->query(
                 'SELECT ROUND(
-                   (SELECT COUNT(*) FROM ' . TABLE_VARIANTS. '
+                   (SELECT COUNT(*) FROM ' . TABLE_VARIANTS . '
                     WHERE `' . $sDNAColumn . '` IS NOT NULL AND
                       `' . $sDNAColumn . '` != "") / (
                     SELECT COUNT(*) FROM ' . TABLE_VARIANTS . ') * 100)')->fetchColumn();

src/class/object_genome_variants.php

@@ -222,20 +222,6 @@ function __construct ()
 
 
 
-    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, $_SETT;
@@ -268,6 +254,26 @@ function checkFields ($aData, $zData = false, $aOptions = array())
             }
         }
 
+        foreach ($aData as $sField => $sVariant) {
+            if (strpos($sField, '/DNA/') !== false) {
+                // We want to check the input of all DNA fields: are these variant
+                //  descriptions indeed cleanly formatted? And if our check seems
+                //  to fail, is this perhaps because it holds syntax that we do
+                //  not support? If we DO support the syntax but the variant does
+                //  not seem to be HGVS, we will send an error.
+                if (lovd_isHGVS($sVariant)) {
+                    // The variant looks good!
+                    continue;
+                }
+                $aVariantInfo = lovd_getVariantInfo($sVariant, false);
+                if (array_diff(array_keys($aVariantInfo['errors']), array('ENOTSUPPORTED')) // Are there any errors other than ENOTSUPPORTED?
+                    || array_diff(array_keys($aVariantInfo['warnings']), array('WNOTSUPPORTED'))) { // Are there any warnings other than WNOTSUPPORTED?
+                    // There are problems that are not caused by lack of syntax support.
+                    lovd_errorAdd($sField, 'The variant ' . $sVariant . ' did not pass our checks. Please take another look and try again.');
+                }
+            }
+        }
+
         // Do this before running checkFields so that we have time to predict the DBID and fill it in.
         if (!empty($aData['VariantOnGenome/DNA']) // DNA filled in.
             && isset($this->aColumns['VariantOnGenome/DBID']) // DBID column active.
@@ -351,9 +357,15 @@ function getForm ()
             }
         }
 
-        // 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']);
+        // Add genome build name and element data to VOG/DNA fields, and add in the link to the HGVS website.
+        $aActiveBuilds = $_DB->query('SELECT id, name, column_suffix FROM ' . TABLE_GENOME_BUILDS)->fetchAllGroupAssoc();
+        foreach ($aActiveBuilds as $sBuild => $aBuild) {
+            $sColumn = 'VariantOnGenome/DNA' . (!$aBuild['column_suffix']? '' : '/' . $aBuild['column_suffix']);
+            $this->aColumns[$sColumn]['description_form'] = '<B>Relative to ' . $aBuild['name'] . '.</B>' .
+                (!$this->aColumns[$sColumn]['description_form']? '' : '<BR>' . $this->aColumns[$sColumn]['description_form']);
+            $this->aColumns[$sColumn]['element_data'] = array('genome_build' => $sBuild);
+            $this->aColumns[$sColumn]['form_type'][0] = str_replace('(HGVS format)', '(<A href="https://varnomen.hgvs.org/recommendations/DNA" target="_blank">HGVS format</A>)', $this->aColumns[$sColumn]['form_type'][0]);
+        }
 
         // 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.

src/class/variant_validator.php

@@ -882,7 +882,7 @@ public function verifyVariant ($sVariant, $aOptions = array())
             //  NM, we end up with only one NM here.
             $aJSON = current($aJSON);
 
-            // Add a warning in case we submitted a intronic variant while not
+            // Add a warning in case we submitted an intronic variant while not
             //  using an NC reference sequence.
             if (preg_match('/^N[MR]_.+[0-9]+[+-][0-9]+/', $sVariant)) {
                 $aData['warnings']['WINTRONICWITHOUTNC'] = 'Without using a genomic reference sequence, intronic bases can not be verified.' .

src/inc-init.php

@@ -360,6 +360,7 @@
                             'hg18' =>
                                      array(
                                             'ncbi_name'      => 'Build 36.1',
+                                            'supported_by_VV' => false,
                                          // FIXME: This information is also stored in the chromosomes table.
                                          // Remove it from here?
                                             'ncbi_sequences' =>
@@ -394,6 +395,7 @@
                             'hg19' =>
                                      array(
                                             'ncbi_name'      => 'GRCh37',
+                                            'supported_by_VV' => true,
                                          // FIXME: This information is also stored in the chromosomes table.
                                          // Remove it from here?
                                             'ncbi_sequences' =>
@@ -429,6 +431,7 @@
                             'hg38' =>
                                      array(
                                             'ncbi_name'      => 'GRCh38',
+                                            'supported_by_VV' => true,
                                          // FIXME: This information is also stored in the chromosomes table.
                                          // Remove it from here?
                                             'ncbi_sequences' =>