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HGVS variant nomenclature checker
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Mutalyzer configuration #493

Open drtconway opened 4 years ago

drtconway commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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 commented 4 years ago

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