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HGVS variant nomenclature checker
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Maximum variant length #490

Closed drtconway closed 4 years ago

drtconway commented 4 years ago

Hi Mutalyzers,

We have some cases where our pipeline is generating some long insertions (e.g. ~180-200bp), which we send to a local Mutalyzer instance, for which we get back malformed output. This appears to be a case of input being rejected possibly to avoid DOSing the server.

We're running on a private network behind a firewall, so we're not to concerned about protecting ourselves from such cases.

Is there a configuration parameter somewhere that we can set to allow long insertions?

(I apologise for the lack of a detailed variant. I'll dig up an example and add it as a comment.)

drtconway commented 4 years ago 
$cat inp.txt
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAAT
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAG
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAGATTTGAGATGGGACCATTCTGCCCAGGATGCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTC
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAG
$ curl -k -d 'process=SyntaxChecker' -d 'argument=hg19' -d "data=$(cat inp.txt | base64)" 'https://vmpr-res-mutalyzer1.unix.petermac.org.au/json/submitBatchJob'
"5de2cc96-023f-47b1-b4a2-a92a5321f58c"$
$curl -k https://vmpr-res-mutalyzer1.unix.petermac.org.au/batch-job-result/batch-job-5de2cc96-023f-47b1-b4a2-a92a5321f58c.txt
Input   Status
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAAT  OK
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAG OK
InputFields: chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAGATTTGAGATGGGACCATTCTGCCCAGGATGCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTC...    (Scheduler): Entry could not be formatted correctly, check batch input file help for details
chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAG OK
$

I've also run against your site and the same behaviour occurs.

mihailefter commented 4 years ago

Hi Tom,

You can try to set the gunicorn limit_request_line parameter to 0 for your local Mutalyzer instance.

Best regards, Mihai

drtconway commented 4 years ago

You guys are awesome. Thank you!