You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 12 Next »

Reporting Format (as of )


LineContent
1-5Meta processing information
6-9Totals
10 and further

Details per records:

Field separator : |

Column 1 : R (rejection) or W (warning)
Column 2 : POOL (ION)
Column 3 : GRID
Column 4 : Error messages.

Please note that HLA errors and warnings may contain multiple messages on the same line.
The messages are separated by #

last 2 linesProcessing statistics (performance)

 

Sample file

 

File: ION-XXXX-D.xml.gpg 2018-05-21 08:04:35
Pool(s): XXXX
Content Type: D
Start processing: 2018-05-21 08:05:00
Schema version: 2.1
Total records processed: 3427
Total records with warnings: 280
Total records rejected: 51
Total valid records: 3376
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
W | XXXX | 947522905891 | N/A | HLA:   #Error at locus DRB1*: invalid HLA code DRB1*8:04. Locus blanked.
R | XXXX | 947529306154 | N/A | BIRTH_DATE (Record Rejected) Field type must be [date]. (Record Rejected) Date is not provided in the correct format. The format must be [YYYY-MM-DD].
W | XXXX | 947532906148 | N/A | HLA:  #Warning at locus A*: deprecated HLA code A*23:AHENZ 
W | XXXX | 947534106167 | N/A | HLA:   #Error at locus B*: invalid HLA code B*7:XX. Locus blanked. #Error at locus B*: invalid HLA code B*8:XX. Locus blanked.
R | XXXX | 947534106167 | N/A | (Record Rejected) Incomplete typing found: HLA-A, HLA-B are required for DONOR and CBU. HLA-DRB1 is required for CBU.
W | XXXX | 947535306189 | N/A | HLA:   #Error at locus A*: invalid HLA code A*3:XX. Locus blanked.
R | XXXX | 947535306189 | N/A | (Record Rejected) Incomplete typing found: HLA-A, HLA-B are required for DONOR and CBU. HLA-DRB1 is required for CBU.
R | XXXX | 947537206209 | N/A | BIRTH_DATE (Record Rejected) Field type must be [date]. (Record Rejected) Date is not provided in the correct format. The format must be [YYYY-MM-DD].
W | XXXX | 947537506212 | N/A | HLA:   #Error at locus DRB1*: invalid HLA code DRB1*8:XX. Locus blanked.
W | XXXX | 733230748329 | N/A | HLA:   #Error at locus DRB1*: invalid HLA code DRB1*1101. Locus blanked. #Error at locus DRB1*: invalid HLA code DRB1*1111. Locus blanked.
W | XXXX | 734555524080 | N/A | HLA:   #Error at locus C*: invalid HLA code C*0102. Locus blanked. #Error at locus C*: invalid HLA code C*0401/15. Locus blanked.
W | XXXX | 733260938482 | N/A | HLA:   #Error at locus C*: invalid HLA code C*0401. Locus blanked. #Error at locus C*: invalid HLA code C*0501. Locus blanked.
............
Processing finished at: 2018-05-21 08:06:32
Total processing time: 1 minutes.

 

Parsing reports

You may use standard text processing tools like SED, AWK and TR to process the report file, eg to collect statistics: please note that these are only examples

 

Sample processing directives (suggestions)
# 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 )

Fetch last report 
<?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";
?>


 

 

 

  • No labels