Merge branches 'master' and 'master' of https://github.com/sib-swiss/…

…AWS-docker

docs/index.md

@@ -37,12 +37,12 @@ git clone https://github.com/GeertvanGeest/AWS-docker.git
 
 ## Generate credentials
 
-You can generate credentials from a tab-delimited list of users, with two columns: first name and last name. Do not use column names. Here's an example:
+You can generate credentials from a comma separated list of users, with two columns: first name and last name. Do not use column names. Here's an example:
 
 ```
-Jan	de Wandelaar
-Piet	Kopstoot
-Joop	Zoetemelk
+Jan,de Wandelaar
+Piet,Kopstoot
+Joop,Zoetemelk
 ```
 
 Run the script `generate_credentials.sh` like this (use `-l` to specify the user list):
@@ -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. 
 - Some firewalls do not support http connections. In that case, use port forwarding instead of using the public IP address. This would require an extra user to set up the port forwarding:
     - Create a new user on the EC2 instance with public and private keys

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