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Update libraries/scripts connecting to external tools #654

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merged 4 commits into from
Jul 3, 2024
Merged

Update libraries/scripts connecting to external tools #654

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f4d5b10
Remove newlines in errors coming from Mobidetails.
ifokkema Jul 3, 2024
456a3fc
Make sure we follow redirects.
ifokkema Jul 3, 2024
6fcc0f8
Support more error strings for EREFSEQ.
ifokkema Jul 3, 2024
4b4f533
Support more error strings for IREFSEQUPDATED.
ifokkema Jul 3, 2024
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6 changes: 3 additions & 3 deletions src/ajax/mobidetails.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 : 2020-10-01
* Modified : 2024-05-07
* For LOVD : 3.0-30
* Modified : 2024-07-03
* For LOVD : 3.0-31
*
* Copyright : 2004-2024 Leiden University Medical Center; http://www.LUMC.nl/
* Programmer : Ivo F.A.C. Fokkema <[email protected]>
Expand Down Expand Up @@ -197,7 +197,7 @@
print('
$("#mobidetails_dialog").html("Error while requesting MobiDetails to annotate this variant.<BR>' .
implode(array_map(function ($sKey, $sVal) {
return $sKey . ': ' . $sVal . '<BR>';
return $sKey . ': ' . trim($sVal) . '<BR>';
}, array_keys($aJSON), array_values($aJSON))) . '");

// Select the right buttons.
Expand Down
13 changes: 10 additions & 3 deletions src/class/variant_validator.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 : 2020-03-09
* Modified : 2024-01-25
* For LOVD : 3.0-30
* Modified : 2024-07-03
* For LOVD : 3.0-31
*
* Copyright : 2004-2024 Leiden University Medical Center; http://www.LUMC.nl/
* Programmer : Ivo F.A.C. Fokkema <[email protected]>
Expand Down Expand Up @@ -131,7 +131,8 @@ private function addFault (&$aData, $sFault, $sVariant, $aVariantInfo = false)
// EREF error.
$aData['errors']['EREF'] = $sFault;
} elseif (strpos($sFault, 'is not associated with genome build') !== false
|| strpos($sFault, 'No transcript definition for') !== false) {
|| strpos($sFault, 'No transcript definition for') !== false
|| strpos($sFault, 'is not in our database. Please check the transcript') !== false) {
// EREFSEQ error.
$aData['errors']['EREFSEQ'] = $sFault;
} elseif (substr($sFault, 0, 5) == 'char '
Expand All @@ -152,6 +153,11 @@ private function addFault (&$aData, $sFault, $sVariant, $aVariantInfo = false)
$sFault, $aRegs)) {
// This is not that important, but we won't completely discard it, either.
$aData['messages']['IREFSEQUPDATED'] = 'Reference sequence ' . $aRegs[1] . ' can be updated to ' . $aRegs[2] . '.';
} elseif (preg_match(
'/^The following versions of the requested transcript are available in our database: (.+)$/',
$sFault, $aRegs)) {
// This is not that important, but we won't completely discard it, either.
$aData['messages']['IREFSEQUPDATED'] = 'Reference sequence can be updated to one of: ' . str_replace('|', ', ', $aRegs[1]) . '.';
} elseif (strpos($sFault, 'Caution should be used when reporting the displayed variant descriptions') !== false
|| strpos($sFault, 'The displayed variants may be artefacts of aligning') !== false) {
// Both these warnings are thrown at the same time when there are mismatches between the
Expand Down Expand Up @@ -199,6 +205,7 @@ private function callVV ($sMethod, $aArgs = array())
if (!$hCurl) {
$hCurl = curl_init();
curl_setopt($hCurl, CURLOPT_RETURNTRANSFER, true); // Return the result as a string.
curl_setopt($hCurl, CURLOPT_FOLLOWLOCATION, true); // Make sure we follow redirects.
if (!empty($_SETT['system']['version'])) {
curl_setopt($hCurl, CURLOPT_USERAGENT, 'LOVDv.' . $_SETT['system']['version']); // Return the result as a string.
}
Expand Down