Merge pull request #8 from sib-swiss/improve-vscode

Improve vscode

docs/index.md

@@ -153,7 +153,7 @@ There are three volumes mounted to each container:
 
 - The volume `data` is mounted to `/data`. This volume is meant to harbour read-only data (e.g. raw data). 
 - The volume `group_work` is mounted to `/group_work`. The group volume is meant as a shared directory, where everybody can read and write.
-- Each user has a personal volume, named after the username (output of `generate_credentials`). This volume is mounted to `/home/rstudio/workdir/` for rstudio, `/home/jovyan/workdir` for jupyter, and `/config/workdir` for vscode. 
+- Each user has a personal volume, named after the username (output of `generate_credentials`). This volume is mounted to `/home/rstudio/workdir/` for rstudio, `/home/jovyan/workdir` for jupyter, and `/config/project` for vscode. 
 
 Below you can find an example of the container infrastructure. Blue squares are containers, yellow are volumes. Arrows indicate accessibility. 
 

docs/tutorial.md

@@ -57,12 +57,12 @@ Now, clone this repository into your home directory on the instance (`/home/ubun
 git clone https://github.com/sib-swiss/AWS-docker.git
 ```
 
-First, we generate some credentials (link + password). We have prepared a tab delimited file with user information to test inside the repository at `examples/user_list_credentials.txt`. It's just tab-delimited file with first names and last names:
+First, we generate some credentials (link + password). We have prepared a comma delimited file with user information to test inside the repository at `examples/user_list_credentials.txt`. It's just comma-delimited file with first names and last names:
 
 ```
-Jan     de Wandelaar
-Piet    Kopstoot
-Joop    Zoetemelk
+Jan,de Wandelaar
+Piet,Kopstoot
+Joop,Zoetemelk
 ```
 
 Now that we have the user list ready we can generate the credentials with the script `generate_credentials`:

docs/usage.md

@@ -11,7 +11,7 @@ In this chapter there is some general information for people (e.g. teachers/cour
 - In the container, you can find the following shared directories:
     - `/data`: read only, and shared between all running containers. This directory is used to have a single place to store data
     - `/group_work`: read and write enabled for all participants, and shared between all containers. This can be used to share data/scripts between students. This directory can be backed up. 
-    - `~/workdir`: read and write enabled, and only shared between containers assigned to the same participant. This directory can be backed up and shared as a tarball at the end of the course. 
+    - `~/project` or `~/workdir`: read and write enabled, and only shared between containers assigned to the same participant. This directory can be backed up and shared as a tarball at the end of the course. 
 - All directories other than the shared directories only exist within the container. 
 
 ## Jupyter containers

examples/user_list_credentials.txt

@@ -1,3 +1,3 @@
-Jan	de Wandelaar
-Piet	Kopstoot
-Joop	Zoetemelk
+Jan,de Wandelaar
+Piet,Kopstoot
+Joop,Zoetemelk

generate_credentials

@@ -4,7 +4,7 @@ USAGE="Usage: generate_credentials -l <user list> [-o <outdir>] \n
 \n
 This command generates credentials for users\n
 \n
--l  tab-delimited list of users, with 2 columns: first name and last name. Required. \n
+-l  CSV file with users, with 2 columns: first name and last name. Required. \n
 -o  output directory. Default: ./credentials \n
 -p  port start. Generates ports and starts counting from this port. E.g. for Rstudio server count from 9001. Default: 10001\n
 -a  address to use in the link (usually IP address). Required."
@@ -75,12 +75,12 @@ cat $LIST | tr -d '\015\040' > $TMPULIST
 
 LIST=$TMPULIST
 
-FIRSTL=`cat "$LIST" | cut -f 1 | tr -cd '\11\12\15\40-\176' | tr [:upper:] [:lower:] | cut -c-1`
-LASTN=`cat "$LIST" | cut -f 2 | tr -cd '\11\12\15\40-\176' | tr [:upper:] [:lower:]`
+FIRSTL=`cat "$LIST" | cut -f 1 -d ',' | tr -cd '\11\12\15\40-\176' | tr [:upper:] [:lower:] | cut -c-1`
+LASTN=`cat "$LIST" | cut -f 2 -d ',' | tr -cd '\11\12\15\40-\176' | tr [:upper:] [:lower:]`
 
 USERNAMES=$(paste -d '-' <(echo "$FIRSTL") <(echo "$LASTN") | tr -d '-')
 
-cat "$LIST" > $TMPTNAMES
+cat "$LIST" | tr ',' '\t' > $TMPTNAMES
 
 paste $TMPTNAMES <(echo $USERNAMES | tr ' ' '\n') >> $TMPUNAMES
 
@@ -95,7 +95,7 @@ fi
 
 for user in $USERNAMES
 do
-    openssl rand -base64 14 >> $TMPPASSWD
+    openssl rand -hex 4 >> $TMPPASSWD
 done
 
 paste $TMPUNAMES $TMPPASSWD > $TMPCOMB

run_vscode_server

@@ -65,7 +65,6 @@ docker volume create group
 
 docker run \
 -d \
--e SUDO_PASSWORD=$MASTERPW \
 -p 7000:8443 \
 --name vscode_admin \
 -e PASSWORD=$MASTERPW \
@@ -96,8 +95,8 @@ do
   -e PASSWORD=$password \
   -e PUID=1000 \
   -e PGID=1000 \
-  -e DEFAULT_WORKSPACE=/config/workdir \
-  --mount source=$user,target=/config/workdir \
+  -e DEFAULT_WORKSPACE=/config/project \
+  --mount source=$user,target=/config/project \
   --mount source=data,target=/data,readonly \
   --mount source=group,target=/group_work \
   $IMAGE