Mutalyzer configuration

[drtconway]

Hi Mutalyzer,

We run an instance of Mutalyzer from your Ansible script, and we need to alter the configuration to unlimit request line length.

I posted previously (https://github.com/mutalyzer/mutalyzer/issues/490) and you explained that we need to change limit_request_line to do that, but our OPs folks have not been able to make the change work.

Can you please give detailed instructions about where/what the change should look like? Other than that we are running Mutalyzer unmodified.

Thanks,
Tom.

[mihailefter]

Dear Tom,

A way would be to pass it as a command line argument here:

...
ExecStart=/opt/mutalyzer/versions/971bde8/virtualenv/bin/gunicorn --limit-request-line 0 ...
...

Best regards,
Mihai

[christopherwelsh]

Hi Mihai,

Changes were made to the following configs (and then server restarted) but as you will see below there is still a failure.

TESTSCRIPT
#!/bin/bash
##MUTHOST=vmts-mutalyzer1.unix.petermac.org.au
##MUTHOST=vmts-mutalyzer1.unix.petermac.org.au

##dat=$(echo 'chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAAT' | base64)
dat=$(echo 'chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAAT' | base64)
uuid=$(curl -s -k -d 'process=SyntaxChecker' -d 'argument=hg19' -d "data=${dat}" 'https://vmts-mutalyzer1.unix.petermac.org.au/json/submitBatchJob' | tr -d '"')
sleep 10
if (curl -s -k https://vmts-mutalyzer1.unix.petermac.org.au/batch-job-result/batch-job-${uuid}.txt | grep OK > /dev/null)
then
echo success
exit 0
else
curl -s -k https://vmts-mutalyzer1.unix.petermac.org.au/batch-job-result/batch-job-${uuid}.txt
exit 1
fi

CHANGES I incrementally have made
mutalyzer-service-json-cb0a70a.service:ExecStart=/opt/mutalyzer/versions/cb0a70a/virtualenv/bin/gunicorn --limit-request-line 0 --pid /opt/mutalyzer/versions/cb0a70a/run/service-json.pid -c /opt/mutalyzer/versions/cb0a70a/conf/service-json.conf mutalyzer.entrypoints.service_json

mutalyzer-service-soap-cb0a70a.service:ExecStart=/opt/mutalyzer/versions/cb0a70a/virtualenv/bin/gunicorn --limit-request-line 0 --pid /opt/mutalyzer/versions/cb0a70a/run/service-soap.pid -c /opt/mutalyzer/versions/cb0a70a/conf/service-soap.conf mutalyzer.entrypoints.service_soap

mutalyzer-website-cb0a70a.service:ExecStart=/opt/mutalyzer/versions/cb0a70a/virtualenv/bin/gunicorn --limit-request-line 0 --pid /opt/mutalyzer/versions/cb0a70a/run/website.pid -c /opt/mutalyzer/versions/cb0a70a/conf/website.conf mutalyzer.entrypoints.website

LONG IINDEL TEST OUTCOME
[root@vmpr-res-cluster1 ~]# ./teps.sh
Input Status
InputFields: chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACAGCAATCAGGAAGACA... (Scheduler): Entry could not be formatted correctly, check batch input file help for details

SHORT INDEL OUTCOME
[root@vmpr-res-cluster1 ~]# ./teps.sh
success

[mihailefter]

Hi Christopher,

For the batch job interface the maximum line size allowed is 200 characters. If you wish to go this way, i.e., using the batch job interface, you have to change the code.

Otherwise, you could make use of the web services. Configuring Gunicorn as presented above should allow you to have "unlimited" input size. By default it seems to be 4096, which may already suffice your needs from the start.

With your largest description:

 $ curl --url "https://mutalyzer.nl/json/checkSyntax?variant=chr1:g.33479002_33479003insTCTGAGAACAGGAAGACAGCAATGAAAGGCTGGGACTGTTAGCAAGGTTTTCTTATTCCATGCCAGATGCAGATTTGAGATGGGACCATTCTGCCCAGGATGCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTCCTGTCTGTTCCCAAAGCCCATCAGAGACAAAGACAGGCAATCCAGACCCTC"

{"valid": true, "messages": []}

Best regards,
Mihai