In charlotte-ngs/lbgfs2021: Livestock Breeding and Genomics (ETHZ) - Fall Semester 2021

knitr::opts_chunk$set(echo = TRUE)

Disclaimer

The preparation of the docker container for the R exercise platform is documented here.

Dockerfile

The docker container that is built is based on the container rocker/verse. To have all packages available, we build a Dockerfile that installs all packages directly into the image. The content of the Dockerfile is shown below

$ cd /home/quagadmin/courses/gelasmss2021/docker
quagadmin@2-htz:~/courses/gelasmss2021/docker$ cat Dockerfile 
FROM rocker/verse

LABEL maintainer="[e-mail]"

RUN R -e "install.packages(c('pedigreemm', 'kableExtra', 'AlphaSimR', dependencies = TRUE))" && \
    R -e "remotes::install_github(repo = 'charlotte-ngs/rmdhelp')" && \
    R -e "remotes::install_github(repo = 'pvrqualitasag/rvcetools')"

From that Dockerfile, a docker image is built by the following command

cd courses/lbgfs2021/docker
docker build -t lbgfs2021 .

Testing The Image

The following command is used to test the command

STUDENTHOME=/home/quagadmin/courses/lbgfs2021/home/pvr
if [ ! -d "$STUDENTHOME" ];then mkdir -p ${STUDENTHOME};chmod 777 ${STUDENTHOME};fi
docker run -d -p 10187:8787 -e PASSWORD=pvrpass -v /home/quagadmin/courses/lbgfs2021/home/pvr:/home/rstudio --name pvr_rstudio lbgfs2021
# check
docker ps -a

Open the firewall to test it from outside

sudo ufw allow 10087/tcp
sudo ufw status

Stopping the Test Container

docker stop pvr_rstudio
docker rm $(docker ps --filter "status=exited" -q)

Creating Student Lists

Start with a download of the BelegungLerneinheit*.xlsx file from eDoz under https://www.lehrbetrieb.ethz.ch/edoz . We assume that this file is saved to the Downloads folder. From there, we extract the usernamens of the students.

vec_pkg <- c('openxlsx', 'dplyr', 'tidyr')
if (!all(is.element(vec_pkg, installed.packages())))
  install.packages(vec_pkg, dependencies = TRUE)

s_bl_path <- '~/Downloads/BelegungenLerneinheit_751630500L_Herbstsemester_2021.xlsx'
wb <- openxlsx::read.xlsx(xlsxFile = s_bl_path)

First create a list of students with their names, firstnames and e-mail addresses

library(dplyr)
(tbl_student_info <- wb %>% 
    select(Familienname, Rufname, Nummer, `E-Mail`) %>%
    mutate(UDName = `E-Mail`) %>%
    tidyr::separate(UDName, c("Username", NA), sep = '@') %>%
    select(Username, Familienname, Rufname, Nummer, `E-Mail`))

The student information is written to a file.

student_dir <- file.path(here::here(), 'students')
if (!dir.exists(student_dir)) fs::dir_create(path = student_dir)
student_file_path <- file.path(student_dir, "students_lbgfs2021.txt")
readr::write_csv(tbl_student_info, file = student_file_path, col_names = FALSE)

A test-student is created manually.

tbl_test_student_info <- tibble::tibble(Username     = c('vrohrp'),
                                        Familienname = c('von Rohr'), 
                                        Rufname      = c('Peter'), 
                                        Nummer       = c('00-000-000') , 
                                        `E-Mail`     = c('[e-mail]'))
test_student_file_path <- file.path(student_dir, "test_students_lbgfs2021.txt")
readr::write_csv(tbl_test_student_info, file = test_student_file_path, col_names = FALSE)

Student Usernames

From the e-mail addresses, we extract usernames as follows

(tbl_student_username <- tbl_student_info %>% select(Username))

Write the usernames to a file

user_file_path <- file.path(student_dir, "student_usernames_lbgfs2021.txt")
readr::write_csv(tbl_student_username, file = user_file_path, col_names = FALSE)

The username for the test-student is specified manually and is not extracted from the e-mail.

test_user_file_path <- file.path(student_dir, "test_student_usernames_lbgfs2021.txt")
tbl_test_student_username <- tbl_test_student_info %>% select(Username)
readr::write_csv(tbl_test_student_username, file = test_user_file_path, col_names = FALSE)

File Upload

Upload the created files to the server

$ cd /Users/peter/Data/Projects/GitHub/charlotte-ngs/lbgfs2021_ghroot/master/lbgfs2021
$ scp -r students [e-mail]:/home/quagadmin/courses/lbgfs2021
$ scp -r bash [e-mail]:/home/quagadmin/courses/lbgfs2021

Start Containers

cd /home/quagadmin/courses/lbgfs2021/bash
# test 604RcuhD
./docker_student_start.sh -f ../students/test_students_lbgfs2021.txt -c /home/quagadmin/courses/lbgfs2021/home -p 10187 -i "rocker/verse"
# real
./docker_student_start.sh -f ../students/students_lbgfs2021.txt -c /home/quagadmin/courses/lbgfs2021/home

Move Passwords to created folder

COURSEDIR=/home/quagadmin/courses/lbgfs2021
cd $COURSEDIR
CREATEDIR=$COURSEDIR/created
if [ ! -d "$CREATEDIR" ];then mkdir -p $CREATEDIR;fi
cat students/test_student_usernames_lbgfs2021.txt | while read s
do 
  echo " * Processing student $s ..."
  if [ -f "$COURSEDIR/bash/${s}_email.txt" ]
  then
    grep -i password $COURSEDIR/bash/${s}_email.txt | cut -d' ' -f2 > $CREATEDIR/.${s}.pwd
  fi
  sleep 2
done

Cloning Material

The exercise material must be cloned to the directories of the students. First start with preparing the branch.

# on mac
cd /Users/pvr/Data/Projects/Github/charlotte-ngs/lbgfs2021_gh-root
mkdir -p rexpf
cd rexpf
git clone https://github.com/charlotte-ngs/lbgfs2021.git
cd rexpf
git branch rexpf
git checkout rexpf
ls -1 | while read d
do
  echo " * Checking element: $d ..."
  if [ "$d" != "ex" ] 
  then
    echo " ** Deleting $d ..."
    rm -rf $d
  fi
  sleep 2
done
545  git add .
546  git commit -m"Deleted all unneeded material"
547  git push origin rexpf

Cloning the material

# on 2-htz
export GITURI=https://github.com/charlotte-ngs/lbgfs2021.git
export GELSRC=/home/quagadmin/courses/lbgfs2021
export GELHOME=${GELSRC}/home
cd $GELSRC
# test student
cat students/test_student_usernames_lbgfs2021.txt | while read s
do
  cd $GELHOME/$s
  echo " * Cloning repo for $s ..."
  git clone $GITURI -b rexpf
  sleep 2
done

# students
cd $GELSRC
# real student
cat students/student_usernames_lbgfs2021.txt | while read s
do
  cd $GELHOME/$s
  echo " * Cloning repo for $s ..."
  git clone $GITURI -b rexpf
  sleep 2
done

Sending E-Mails

The following commands are used to send e-mails to students

export GELSRC=/home/quagadmin/courses/lbgfs2021
cd $GELSRC
if [ ! -d "email_sent" ]; then mkdir -p email_sent;fi
cat students/test_students_lbgfs2021.txt  | while read s
do
  user=$(echo "$s" | cut -d ',' -f1)
  email=$(echo "$s" | cut -d ',' -f5)
  echo " * Sending ${user}_mail.txt to $email ..."
  cat bash/${user}_email.txt | ssmtp $email
  sleep 2
  mv bash/${user}_email.txt email_sent
done

# real students
cat students/students_lbgfs2021.txt  | while read s
do
  user=$(echo "$s" | cut -d ',' -f1)
  email=$(echo "$s" | cut -d ',' -f5)
  echo " * Sending ${user}_mail.txt to $email ..."
  cat bash/${user}_email.txt | ssmtp $email
  sleep 2
  mv bash/${user}_email.txt email_sent
done

Restart Containers

For an update of the docker image, we have to restart the docker container. First the running container are stopped.

# test
cd /home/quagadmin/courses/lbgfs2021/bash
# stop
./docker_student_stop.sh -f ../students/test_students_lbgfs2021.txt
# restart
./docker_student_start.sh -f ../students/test_students_lbgfs2021.txt -c /home/quagadmin/courses/lbgfs2021/home -p 10187 -w /home/quagadmin/courses/lbgfs2021/created -i lbgfs2021

The same can be done for all other students

# real
cd /home/quagadmin/courses/lbgfs2021/bash
# stop
./docker_student_stop.sh -f ../students/students_lbgfs2021.txt
# restart
./docker_student_start.sh -f ../students/students_lbgfs2021.txt -c /home/quagadmin/courses/lbgfs2021/home -w /home/quagadmin/courses/lbgfs2021/created -i lbgfs2021

charlotte-ngs/lbgfs2021 documentation built on Dec. 19, 2021, 3:01 p.m.