matdoering / openPrimeR

An R Package for Multiplex PCR Primer Design and Analysis
http://openprimer.mpi-inf.mpg.de
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Error data from IMGT running Retrieve Template #11

Closed mickael-decastro closed 1 year ago

mickael-decastro commented 1 year ago

Hello,

I deployed openPrimeR in docker following the Readme and docker image on docker hub. When I check Third-party tools status I have selenium-python in unvailable state. To fix it I installed manually python 2.7, pip and module selenium. After that everything is ok on this part.

When I run Retrieve Template on "Mus musculus" I receive the following message on GUI.

IMGT Data Unavailable
It was not possible to retrieve the selected data from IMGT. Possible reasons could be having no internet connection or missing dependencies (selenium for python).

And on docker container log

Warning in openPrimeRui:::retrieve.IMGT.templates(input$IMGT_DB_species,  :
  Failed to retrieve templates from IMGT for unknown reason.
/usr/local/lib/python2.7/dist-packages/selenium/webdriver/phantomjs/webdriver.py:49: UserWarning: Selenium support for PhantomJS has been deprecated, please use headless versions of Chrome or Firefox instead
  warnings.warn('Selenium support for PhantomJS has been deprecated, please use headless '
Traceback (most recent call last):
  File "/usr/local/lib/R/site-library/openPrimeRui/shiny/shiny_server/extra_IMGT_template_set_extractor.py", line 104, in <module>
    set_option(driver, field, value)
  File "/usr/local/lib/R/site-library/openPrimeRui/shiny/shiny_server/extra_IMGT_template_set_extractor.py", line 44, in set_option
    element = Select(driver.find_element_by_name(field))
  File "/usr/local/lib/python2.7/dist-packages/selenium/webdriver/remote/webdriver.py", line 496, in find_element_by_name
    return self.find_element(by=By.NAME, value=name)
  File "/usr/local/lib/python2.7/dist-packages/selenium/webdriver/remote/webdriver.py", line 978, in find_element
    'value': value})['value']
  File "/usr/local/lib/python2.7/dist-packages/selenium/webdriver/remote/webdriver.py", line 321, in execute
    self.error_handler.check_response(response)
  File "/usr/local/lib/python2.7/dist-packages/selenium/webdriver/remote/errorhandler.py", line 242, in check_response
    raise exception_class(message, screen, stacktrace)
selenium.common.exceptions.NoSuchElementException: Message: {"errorMessage":"Unable to find element with name 'model.subgroup'","request":{"headers":{"Accept":"application/json","Accept-Encoding":"identity","Content-Length":"97","Content-Type":"application/json;charset=UTF-8","Host":"127.0.0.1:34687","User-Agent":"selenium/3.141.0 (python linux)"},"httpVersion":"1.1","method":"POST","post":"{\"using\": \"name\", \"sessionId\": \"80b91d40-7d7e-11ed-861b-b1bd0a075e2a\", \"value\": \"model.subgroup\"}","url":"/element","urlParsed":{"anchor":"","query":"","file":"element","directory":"/","path":"/element","relative":"/element","port":"","host":"","password":"","user":"","userInfo":"","authority":"","protocol":"","source":"/element","queryKey":{},"chunks":["element"]},"urlOriginal":"/session/80b91d40-7d7e-11ed-861b-b1bd0a075e2a/element"}}
Screenshot: available via screen
Warning in openPrimeRui:::retrieve.IMGT.templates(input$IMGT_DB_species,  :
  Failed to retrieve templates from IMGT for unknown reason.

Can you help me ?

thanks

matdoering commented 1 year ago

Looks like the parser for the IMGT data doesn't work anymore. I'd recommend to just download the data from IMGT directly.