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Reporting Format (as of )
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# Count warnings and errors per locus :
# Replace all # by newline, get the lines with locus errors, then pick the first part before: , sort it, and count unique values
tr '#' '\n' < testreport.txt |grep 'at locu' | cut -d':' -f1 | sort | uniq -c
32 Error at locus A*
24 Error at locus B*
112 Error at locus C*
16 Error at locus DQB1*
57 Error at locus DRB1*
76 Warning at locus A*
80 Warning at locus B*
# Give all ID's that have HLA warnings
tr ':' '|' <testreport.txt | cut -d'|' -f1,3,5 | grep -i 'HLA'
# Give ID from records that have a rejection due to invalid SEX field
grep -i 'sex.*rejected' testreport.txt | cut -d'|' -f3
737849095
# get deprecated HLA stats
tr '#' '\n' < testreport.txt |grep 'depr' | cut -d':' -f2 | sort | uniq -c
67 deprecated HLA code A*01
2 deprecated HLA code A*02
113 deprecated HLA code A*03 |
...
User contributed code samples
Getting and parsing report (sample by Marco Vitale )
| Code Block | ||||||
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<?php
// Retrieve the last couple of reports generated (donors and cords)
$ion="7450";
$remote_url = "https://dataupload.wmda.info/api/v2/fs/reports-ion".$ion."/?children=f";
include("wmda_credentials.php");
// Create a stream
$opts = array(
'http'=>array(
'method'=>"GET",
'header' => "Authorization: Basic " . base64_encode("$username:$password")
)
);
$context = stream_context_create($opts);
// Open the file using the HTTP headers set above
$file = file_get_contents($remote_url, false, $context);
$xml = simplexml_load_string($file);
$json = json_encode($xml);
$array = json_decode($json,TRUE);
$mod_c='';$mod_d='';$file_c='';$file_d='';
foreach ($array["tree"] as $ar_file)
foreach ( $ar_file["@attributes"] as $key => $value )
{
if ($key=="filename"){if (strpos($value,$ion."-C")>0){$tipo="C";$file_c=$value;}else{$tipo="D";$file_d=$value;}}
else if ($key=="ajxp_modiftime")
{
if ($tipo=="C"){if ($value>$mod_c){$mod_c=$value;}}
else {if ($value>$mod_d){$mod_d=$value;}}
}
}
echo $file_c."\n";
echo $file_d."\n";
?>
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