Import and Export Rmarkdown documents to/from Rmarkdown files
CSS JavaScript R HTML
Latest commit a0c1ea2 Dec 19, 2016 @gordonwoodhull gordonwoodhull committed on GitHub Merge pull request #21 from att/feature/readme
README, with user and dev docs

README.md

Install

  1. Install this package on RCloud, using devtools::install_github(), or install-github.me: R source("https://install-github.me/att/rcloud.rmd")
  2. In the RCloud Settings menu, in the Enable Extensions line, add rcloud.rmd, so that the package is loaded automatically.
  3. Reload RCloud in the browser. This loads the package, and you should have the Import Rmarkdown file and Export Rmarkdown file items added int the Advanced menu on the top.

Usage

In RCloud

Choose the Import Rmarkdown file item from the Advanced menu and then select the file to import from your computer.

In R Studio

rcloud.rmd contains an RStudio addin, that can be used to export R Markdown files from RStudio to RCloud.

  1. Open the R Markdown file in RStudio, and then select the Export to RCloud notebook item from the Addins menu.
  2. This will open a new tab or window in your default browser, with a form. Select or type in the URL of your RCloud installation, and click on Export. The browser will load RCloud, with the newly created RCloud notebook. If you are not logged in to RCloud, then before the notebook is added you will need to log in, the usual way.

If used from RStudio, the package also needs the jsonlite, rstudioapi and whisker packages to be installed.

Conversion details

The text chunks of the Rmd will be converted to markdown cells in the RCLoud notebook. The code chunks will be imported as R cells. If the Rmd file has a YAML header, that is converted to a markdown cell as well.

Chunk headers are parsed and inserted into the code chunk they refer to, as R comments. When exporting the notebook from RCloud to R Markdown, these will be converted back to proper chunk options. While chunk options are kept, they are not interpreted by the converter in any way.

The title of the Rmd document will be used as the name of the new notebook. If it does not have a title, then its file name is used.

Developer notes

The Rmd parser

The parser currently uses internal functions from the knitr package to parse the Rmd file. Unfortunately there is no publicly available, supported Rmd parser that returns the parsed document as an object.

The advantage of the current implementation is that is will always be compatible with knitr, which has the de-facto standard Rmd parser. The downside is that we are using internal functions, and their API is subject to change without notice.

One alternative to this would be writing a parser from scratch, but that would require extensive testing to make sure that it is equivalent to the knitr parser.

Another alternative is copying the current knitr implementation into the rcloud.rmd package. This is unfortunately technically difficult, because the parser is using non-pure functions, and a global state in knitr.

The RStudio Addin

The addin is relatively straightforward, the most difficult part is the HTTP submission and its authentication.

We currently use a static HTML web page, and a static JS file (submit.js), created by the addin. The JS file contains the JSON version of the Rmd already. It also contains the JS code to submit the form to RCloud.

Doing a form submission instead of a proper HTTP POST API call has the advantage that we can use the token from the user's browser to authenticate to RCloud. With a proper API call, the user would have to handle the token manually, although apart this hurdle, this way is technically superior, and probably should be used in the future.

The list of RCloud URLs is currently built into the app. For a better solution and storing the previously used URLs locally on the client, we would need to use a proper Shiny app instead of a static HTML page. A previous version of the addin did use a Shiny app indeed, this is here in git: https://github.com/att/rcloud.rmd/commit/0cd1a560c2e2d2a1fbd74880f056dc9ee3abc710

See the next subsection for the server-side part of the notebook submission.

The RCLoud API

The htdocs/api.R file contains the code for the /api.R/create endpoint that implements the server side of the notebook submission. This is a POST request, and if the user is logged in, then the token/cookie automatically submitted by the browser is enough to authenticate the request, and the notebook can be created right away.

If the user is not logged in, then the situation is tricker, because we need to redirect them to the login page, which invokes more redirects to GitHub, potentially. The login.R page can redirect to another page after a successful login, so we ask it to redirect back to the /api.R/create page. These redirects lose the POSTed notebooks, of course. So if the user is not logged in, then before performing the redirects, we store the notebook in a temporary file, where the file name is the digest of the file. We pass this token as a query parameter to login.R, and we will get it back at the end of the redirect chain. Then we get retrieve the submitted file using the token, and create the notebook.