[Bioc-devel] shiny, Bioconductor, and reproducible research

Tim Triche, Jr. tim.triche at gmail.com
Wed Jul 31 18:38:27 CEST 2013

Right this is what I meant with the captureOutput() snippet. Perhaps the whole reactive dispatch loop could be run to log instead of the clever force- directed graph of closures updating that Joe showed off after presenting Wednesday. 

No good deed goes unpunished, and this suggests that logging what is being dispatched is possible, especially for a group of smart fellers like the Rstudio guys 


On Jul 31, 2013, at 8:57 AM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote:

> I don't know how this actually works in practice. But conceptually, I think
> of moving a slider in an Shiny app as possibly executing some R code.  It
> will be important for production quality code release that we are able to
> test that this code works in a easy and portable way.  I realize we may not
> be able to simulate moving the slider without actually doing it, but some
> of us wants to test the underlying R code, which is especially important
> when you code up against packages in heavy development.  Perhaps this is
> easily done by adhering to a certain coding style.  If so, we are happy to
> get advice.
> Best,
> Kasper
> On Wed, Jul 31, 2013 at 11:45 AM, Winston Chang <winston at stdout.org> wrote:
>> On Mon, Jul 29, 2013 at 4:46 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>> Hi Winston,
>>> On Mon, Jul 29, 2013 at 2:39 PM, Winston Chang <winston at stdout.org>
>>> wrote:
>>>> Hi everyone -
>>>> Great to hear from you all on your thoughts about Shiny. I've tried to
>>>> answer some of Dan's questions below...
>>>>>> 1) Testing shiny apps
>>>>>> Typically, bioconductor packages have man page examples, vignettes,
>>>>>> and (sometimes) unit tests, so when we build the packages every day on
>>>>>> our build system, the code in all of these is evaluated and we have
>>>>>> some idea of whether the package is working as it's supposed to.
>>>>>> I'm not clear on how to do similar testing of a shiny application.
>>>>>> Since launching a shiny app takes away the R console (until the app is
>>>>>> closed), shiny apps should probably not be launched in example or test
>>>>>> code (unless interactive() is TRUE).
>>>>>> Do the shiny folks (or anyone else) have thoughts on testing shiny
>>> apps?
>>>> With regard to testing, we have unit tests for various components, and
>>> we're
>>>> working on end-to-end tests using Selenium.
>>>> We do have some unit tests in inst/tests/, but they are entirely on the
>>> R
>>>> side - they don't test interaction with the browser. We have some other
>>>> tests in inst/tests-js/, which exercise the client (Javascript) side,
>>> but
>>>> they don't test interaction with the server.
>>>> Of course it's important to have tests for client-server communication.
>>>> We're also in the process of setting up some end-to-end tests using
>>>> Selenium, but that's just in the beginning stages right now. Hopefully
>>> in
>>>> the future we'll have more to say about these kinds of tests.
>>> My feeling (and I could be wrong) is that Bioconductor package
>>> developers will be more concerned with testing the basic logic of
>>> shiny apps, and that therefore testing only in R would be sufficient
>>> for the most part. For example, if you could simulate a slider in a
>>> unit test by just changing a reactive value, it would not be necessary
>>> to make sure it works in the deployed context (with browser and
>>> server).
>> Unfortunately, the testing of logic in a Shiny app does require an active
>> connection from web browser, since the state of a Shiny app includes both
>> the server and client. In other words, you can't simulate a slider value
>> change without actually starting a web browser -- although it may be
>> possible to automate these tests using something like phantom.js, which is
>> a headless web browser that can be used for testing. As I mentioned, we're
>> working on setting up some tests like this.
>> On a related note, someone on the Shiny-Discuss mailing list just posted
>> about a project he's working on which makes it possible to have R and
>> Selenium WebDriver commuicate:
>> https://github.com/johndharrison/RSelenium
>> Best,
>> -Winston
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