By Berry Boessenkool, 2020-2023, [email protected]
jump to students / teachers / developers
Watch lesson 1.4 in the fundamentals of programming course.
- Create a folder for all the exercises
- Run the following code (in R / Rstudio) to install the
codeoceanRpackage:
install.packages("remotes") # ignore the Rtools warning
remotes::install_github("openHPI/codeoceanR")For potential installation issues (and solutions), see below.
prepare exercise:
- through OpenHPI, go to the CodeOcean exercise
- download it to the folder mentioned above, no need to unzip
- close the CodeOcean browser tab
- run (in R / Rstudio Console)
codeoceanR::rt_create() - confirm to have closed the tab
- select the exercise file. If unzipped (the default on Mac OS Safari), any file within the task folder.
use rt_create only once per excercise. Start the project later by opening the zz_*.Rproj file in your file browser.
download several exercise files (without unzupping!) and run codeoceanR::rt_create_all() to process them all in one go.
take exercise:
- work on task 1
- save & source the script with
CTRL + SHIFT + S, this will runcodeoceanR::rt_score() - work on task 2
CTRL + SHIFT + S- ...
codeoceanR::rt_score() transfers your code to CodeOcean for scoring. Run this frequently.
rt_create() should
- create a new folder with a
.Rprojfile - open the Project in Rstudio
- with the
script_n.Rfiles already opened - have everything prepared so
rt_score()works out of the box.
use rt_create(deletezip=FALSE) to not delete the zip file if task creation was successful.
Don't open several tabs of an exercise. The autosave could overwrite all you've done from a second (unused=empty) tab.
For the same reason, don't use the back button of your browser.
Thanks to autosave, you can refresh the tab or reopen it later to continue working on the tasks.
Remember to always access this from the openHPI platform.
- Click
RUNto source the script. Read the output, fix your code if it throws an error.RUNagain. - Click
SCOREto see how many of the tests you pass. Change your solutions if needed.SCOREagain.
Ignore messages for tasks you haven't worked on yet (they show how much work is left). RUNandSCOREoften to easily find the location of mistakes.
The tasks are split in separate files. Each can be run independently. Scoring happens for all files at once.
I suggest to always read the entire task before starting to work on it ;-)
Remember to explicitely call an object to see its value in the RUN output.
head(x) / str(x) / summary(x) work fine.
plot(x) outputs are only shown if the call is between rt_plot1()/rt_plot2().
If SCORE tells you 'script_x.R' can not be executed, you cannot get points for tasks (in that script) after the error.
If the top line shows RENDER instead of RUN, you're probably in a data text file. Just click on the desired script.R again.
Click the arrow on the top left (or hide at the bottom right) to hide the instructions for more screen-space for the code.
To reset a complete exercise, click the backwards clock button in the file panel on the left.
To reset only a single file, click the button on the bottom right of the screen.
Occasionally, the installation of the codeoceanR package from github causes issues.
Here are some solutions that may help you.
- On Windows: If you want to install Rtools (this is optional), install it at e.g.
C:/Rtools(compiler paths may not have spaces) and run in R:cat('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', file= "~/.Renviron", append=TRUE) - On Linux: first run in terminal (STRG+ALT+T):
sudo add-apt-repository ppa:c2d4u.team/c2d4u4.0+andsudo apt-get updateandsudo apt install libcurl4-openssl-dev libssl-dev r-cran-rjson. Then in R the code above. If it fails, follow the instructions from installing the dependencies in R:install.packages("curl")and then with"openssl","httr"and"rjson". - For "Failed to install ... Permission denied": set write permissions (rightclick on folder - properties - security - edit - select user - full control - OK). Turn off virus scanner or reboot computer.
- Permanently use custom folder for packages: in R
cat('R_LIBS_USER="C:/path/to/library"', file= "~/.Renviron", append=TRUE). After R restart, should be the first result from.libPaths(). - For "Failed to R CMD build package":
remotes::install_github("openHPI/codeoceanR", build=FALSE) - If only an old version of R is possible: for rjson
remotes::install_version("rjson", "0.2.20") - If you use another editor than Rstudio: don't run
rt_create()below, instead unzip the file manually. - For
rt_create()error message "Could not load the Qt platform plugin xcb": MAYBE! AT OWN RISK:sudo apt remove libxcb-xinerama0andsudo apt install libxcb-xinerama0, see here
Watch lesson 1.4 in the fundamentals of programming course.
It takes a bit of effort to initialize interactive R coding exercises in openHPI / CodeOcean, but it's worth it. The mostly automatic system enables you to put most day-to-day focus on developing good exercises instead of grading them.
For more on CodeOcean and CodeHarbor, see the corresponding article and slides at the SPLICE 2021 workshop.
Exercises are accessed through openHPI but run and tested at CodeOcean, from which grades are passed back. The tasks can also be solved in Rstudio, which is greatly recommended because it is the habitual and future environment with interactivity, autocompletion, debugging, keyboard shortcuts and integrated graphics, help, package manager, ...
Some participants had a hard time getting started in a time-pressed graded exercise setting.
I suggest to first use the system at least twice(!) non-graded or non-time-pressured!
You can't stress enough that participants need to run "Score" / rt_score() very often.
The openHPI admins will have to create a CodeOcean exercise in OpenHPI for you the first time.
To be logged in, open CodeOcean from openHPI through "Launch exercise tool".
Then you can either go to https://codeocean.openhpi.de/exercises/new
or copy my master template exercise.
Potentially, admins must first duplicate it for you and set you as the author.
On OpenHPI, go to Course administration - Course structure and content, e.g.
url for fprog2020.
In the desired section, click "Add item"
- Title: e.g. exercise 3
- Type: External exercise tool
- Exercise type: Self Test (ungraded) or Main (graded)
- Maximal points: e.g. 10
- Submission deadline: optional: time before which the CodeOcean task must be started.
The actual deadline and grace period (20% score reduction) must be set in the CO task itself (if wanted). - Submission publishing date: not relevant, can be left empty
- Instructions: e.g. Click the button below to launch the exercise.
- LTI provider: CodeOcean
- Additional parameters: locale=en&token=
xxxxxxxx&embed_options_disable_redirect_to_rfcs=true&embed_options_disable_redirect_to_feedback=true&embed_options_disable_interventions=true
replacexxxxxxxxwith the token from your CodeOcean exercise!
embedding options:redirect_to_rfcs: finished users can be lead to open Request for Comments (RfCs).redirect_to_feedback: after "Submit", if there are no open RfCs, a feedback form is presented to 10% of users (min 20) without full score.interventions: popups like "You seem to have trouble. Request comments here" while users are working.- all options
All file types & roles etc can be seen in my master template exercise at https://codeocean.openhpi.de/exercises/721
You can only have one 'main' file, the rest must be 'executable file (similar to main file)'.
The structure of task and test scripts can also be seen at https://github.com/openHPI/codeoceanR/tree/main/inst/extdata
A collection of tasks can be requested through Berry or Sebastian.
There's an overview of all R exercises at https://codeocean.openhpi.de/exercises?&q[execution_environment_id_eq]=28
The Makefile run: could have Rscript ${FILENAME} as well,
but then the run output does not contain the calls, making error sources harder to find.
Hide your exercices if wanted (e.g. during development) by unchecking the 'Public' box.
The admins would like you to use a prefix in the exercise name, e.g. Fprog21 for my course.
If you have data files to be read, make sure to check the box for Read-only.
Otherwise users might change the file and your test script might fail,
e.g. if you have a file with meta data in the first lines and you want to
emphasize to never touch raw data and use read.table(...,skip=n) instead.
I suggest developing (and testing) the tasks within Rstudio.
In the test script, have rt_run_script() right before the actual tests.
That way, you can check for the value of n even if students create n
for other purposes in a later script, e.g. in a student-defined loop.
Always test the entire exercise on CodeOcean as well.
If possible, recruit two student assistants just to test-run the exercise. They might find errors you overlooked.
Example: in a statement combination task, the solution was meant to be c(A=4, C=1, D=3),
and I had not thought of students using a different order (which is OK). The solution for the test script:
if(exists("obj")) obj <- obj[order(names(obj))]
Instead of checking code like in the write.table task and test, your tests can also execute the code and you test the resulting file. This gives participants more freedom in how they structure the task.
In tests, never use an object created by the students for reference.
Even results from a previous task should be created in the test-script.
Students can have their own copy of e.g. iris, hence use datasets::iris
If students use CodeOcean directly instead of downloading and working locally, the following hints are especially important.
You can split up tests to several files (like with the scripts).
Users will get several score boxes with green boxes for the successful files.
This is probably motivating, but also takes up a lot of screen space.
Yes you could urge people to use PC pool computers with large screens,
but having participants use their own (small) laptops has the advantage of
easier logins on their side and keyboards they are used to.
You can technically have a single script file, but be aware that non-runnning files are common, frustrating and no points are given for tasks after an error.
Prefixing data files with t*_filename.txt is good to have the main script_1.R
at the top of the page, also for statistics.
replace 721 with the number of your exercise.
https://codeocean.openhpi.de/exercises/721/edit
https://codeocean.openhpi.de/exercises/721/implement
https://codeocean.openhpi.de/exercises/721/statistics
https://codeocean.openhpi.de/exercises/721/requests_for_comments (not auto-updated)
https://codeocean.openhpi.de/exercises/721/study_group_dashboard/32 live view (RfCs auto-updated)
All functions in the package are prefixed with rt_ (R test) for nice autocomplete selection.
This entire project profited from great info from Sebastian Serth, [email protected].
Experiences are based on the 2019 class "fundamentals of programming in digital health" with 31 participants.
For the 2020 class, code was bundeled into an R package. Exercises can now be run locally in Rstudio.
For the 2021 class and the 2022 MOOC, the test suite was completely rewritten and test script length reduced greatly.
The source code for codeOcean itself is online at https://github.com/openHPI/codeocean/
Updating codeoceanR on the CO-server is a two-step process:
- In GH docker actions (be logged in), click 'Run workflow' then again 'Run workflow'. Wait 5 minutes.
- In CO execution environment, from the dropdown next to 'Edit', click 'Synchronize'. Should be done in a few seconds. Try to do this when no one is scoring exercises, as all running containers are interrupted. Note that changes to the run/test commands in the Dockerfile are not synchronized.
- Copy
packageVersion("codeoceanR")to any script and run it to check whether the update was successfull.