rapache.app.from.registry: rapache.app.from.registry

In apomatix/AnalysisPageServer: A framework for sharing interactive data and plots from R through the web

Description

Build rapache app from an AnalysisPageRegistry

Usage

rapache.app.from.registry(registry, page.param = "page",
  textarea.wrap.param = "textarea_wrap", device.param = "device",
  decoder.param = "decoder", max.regions.param = "max_annotated_regions",
  default.max.regions = 10000, force = FALSE,
  tmpdir = Sys.getenv("WEB_TMPDIR"), tmpdir.timeout.seconds = 600,
  devices = .default.device.list, other.mime.types = c(json =
  "application/json"), mime.types = c(sapply(devices, "[[", "mime.type"),
  other.mime.types),
  query.param.decoders = .build.default.query.param.decoders(),
  brand.builder = .default.brand.builder, logger = create.logger(stderr(),
  log4r:::FATAL))

Arguments

registry	AnalysisPageRegistry from which to build you app.
page.param	Character. Name for the parameter which specifies the page. Default "page"
textarea.wrap.param	Character. Name for the parameter which specifies whether the response should be wrapped in a <textarea> tag. This is needed to support file uploads in browsers, like IE9, that don't support XMLHttpRequest2. Default "textarea_wrap". In addition to wrapping in textarea the response type will be set to "text/html", another hack that such browsers require.
device.param	Character. Name for the parameter which specifices the plotting device. Default: "device".
decoder.param	Character. Name for the parameter which specifices the form query parameter decoding method. Default: "decoder".
max.regions.param	String. Name for the parameter which specifies the maximum number of regions for annotation. Default: "max_annotated_regions".
default.max.regions	Default maximum number of regions for annotation. If a plot has more than this many elements then it will not be annotated. Default: 10000.
force	Logical. If set then an invalid registry is a warning instead of an error.
tmpdir	Temporary directory into which plot files should be written. By default this is taken from the WEB_TMPDIR environment variable. It is checked upon opening. It is important under Apache that all of the processes use the same directory, otherwise they won't be able to find the plots made by other processes.
tmpdir.timeout.seconds	Temporary files will expire after this time. Default: 600 (10 minutes)
devices	Named list. The names of the vector are the names of allowed plotting devices. The values are themselves lists, each having a $mime.type and $function, being the ploting function. Default is given by the private variable .default.device.list, and includes svg and png (but uses a modified png function so that it accepts units inches). Which one to be used (in the default scenario, a choice between svg and png) is controlled by the special device.param parameter. If that is not provided then the first device from this vector is used (default default is therefore "svg", which is the best since it can be annotated, but older browsers such as IE8 will need to do PNGs).
other.mime.types	Named charvec giving a mapping from file extensions other than those already in devices to MIME types that can be served out of the temporary storage/retrieval area. Default: c(json = "application/json").
mime.types	This is a named charvec giving a mapping from file extensions to mime types. Only files with extensions in this list can be served from the temporary storage/retrieval area. The default is to take the extensions/MIME-types defined in devices and add to them those in other.mime.tpyes.
query.param.decoders	Names list. The names are the names of allowed query param decoders (valid values for the decoder.param parameter). The values are functions which do the decoding. Default is just list(url=urlDecode). urlDecode is a function supplied by RApache (or by testing framework).
brand.builder	This is a function that takes a single argument called "persistent" which is a list of key value pairs representing the internal "persistent" state of the app. The persistent state is a namespace that particular parameters of particular pages can draw from, with the possible option of locking those parameters to the values in the persistent namespace. The purpose of the brand.builder function is to return a string that should be used in the top-left corner of the web page to briefly summarize the current state. The default brand builder always returns the string "AnalysisPageServer".
logger	log4r object, optional

Details

This does most but not all of the work. You should create an R script that builds your page registry, then builds an rapache.app with this function. Within that R script you call add.handlers.to.global to install the 5 handlers (handle.pages/handle.params/handle.plot/handle.data/handle.meta.data).

Next you have to tell apache to source your script upon startup. The directive for your httpd.conf is as follows: RSourceOnStartup "/gne/home/friedmab/scr/apache-test/R-startup.R"

Finally, you have to register the five handlers. This is done as follows

Value

AnalysisPageRApacheApp

Author(s)

Brad Friedman

apomatix/AnalysisPageServer documentation built on May 26, 2019, 11:36 a.m.