Updatet shiny image

Services/Rocker/Dockerfile

@@ -1,13 +1,13 @@
 
 #
-# VERSION 0.7
+# VERSION 0.8
 # DOCKER-VERSION  17.05.0-ce
 # AUTHOR:         Paolo Cozzi <[email protected]>
 # DESCRIPTION:    A rocker container with some packages and users added
 # TO_BUILD:       docker build --rm -t ptp/rstudio .
-# TO_TAG:         docker tag ptp/rstudio:latest ptp/rstudio:0.7
-# CREATE_VOLUME:  docker create --name rstudio_volume ptp/rstudio:0.7 /bin/true
-# TO_RUN:         docker run -d -p 8787:8787 -P --name rstudio --volumes-from rstudio_volume -v /etc/localtime:/etc/localtime:ro -v /mnt/storage/:/storage/ ptp/rstudio:0.7
+# TO_TAG:         docker tag ptp/rstudio:latest ptp/rstudio:0.8
+# CREATE_VOLUME:  docker create --name rstudio_volume ptp/rstudio:0.8 /bin/true
+# TO_RUN:         docker run -d -p 8787:8787 -P --name rstudio --volumes-from rstudio_volume -v /etc/localtime:/etc/localtime:ro -v /mnt/storage/:/storage/ ptp/rstudio:0.8
 #
 
 FROM rocker/rstudio
@@ -34,24 +34,9 @@ RUN rm -rf /var/lib/apt/lists/ && \
     texlive-fonts-recommended \
     texlive-latex-recommended \
     texlive-latex-extra && \
+    openjdk-9-jdk && \
     apt-get clean && rm -rf /var/lib/apt/lists/
 
-# Instructions to install java JDK under rstudio image: https://github.com/cardcorp/card-rocker/blob/master/r-java/Dockerfile
-RUN echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" \
-      | tee /etc/apt/sources.list.d/webupd8team-java.list \
-    &&  echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" \
-      | tee -a /etc/apt/sources.list.d/webupd8team-java.list \
-    && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys EEA14886 \
-    && echo "oracle-java8-installer shared/accepted-oracle-license-v1-1 select true" \
-        | /usr/bin/debconf-set-selections \
-    && apt-get update \
-    && apt-get install -y oracle-java8-installer \
-    && update-alternatives --display java \
-    && rm -rf /var/lib/apt/lists/* \
-    && apt-get clean \
-    && R CMD javareconf \
-    && apt-get clean && rm -rf /var/lib/apt/lists/
-
 # Runnig rstudio instance need to be restarted (rstudio-server restart). There are no problems when building
 # a new rstudio image
 
@@ -98,11 +83,6 @@ RUN addgroup --gid 505 biscarinif && \
     adduser biscarinif --uid 505 --gid 505 --disabled-password --gecos "Filippo Biscarini" && \
     echo 'biscarinif:biscarinif' | chpasswd
 
-# Another user
-RUN addgroup --gid 517 capreraa && \
-    adduser capreraa --uid 517 --gid 517 --disabled-password --gecos "Andrea Caprera" && \
-    echo 'capreraa:capreraa' | chpasswd
-
 # Another user
 RUN addgroup --gid 533 masettig && \
     adduser masettig --uid 533 --gid 533 --disabled-password --gecos "Giulia Masetti" && \
@@ -115,7 +95,7 @@ RUN addgroup --gid 1002 ngs && \
     usermod -a -G ngs cozzip && \
     usermod -a -G ngs giannicor && \
     usermod -a -G ngs lazzarib && \
-    usermod -a -G ngs capreraa
+    usermod -a -G ngs biscarinif
 
 # By default RStudio Server only allows normal (as opposed to system) users to
 # successfully authenticate. The minimum user id is determined by reading the

TODO.md

@@ -12,7 +12,6 @@ TODO
   * more info on deleting images: [here][delete-images1] and [here][delete-images2]
   * registri [API][registry-api]?
 
-
 [delete-docker-registry-image]: https://github.com/burnettk/delete-docker-registry-image
 [deploying-registry]: https://docs.docker.com/registry/deploying/
 [registry-storage]: https://docs.docker.com/registry/configuration/#storage
@@ -21,3 +20,19 @@ TODO
 [delete-images1]: https://stackoverflow.com/questions/25436742/deleting-images-from-a-private-docker-registry
 [delete-images2]: https://forums.docker.com/t/delete-repository-from-v2-private-registry/16767
 [registry-api]: https://docs.docker.com/registry/spec/api/
+
+* Use [environment file][environment-file] to store environment variables in
+  docker composed images
+
+[environment-file]: https://docs.docker.com/compose/compose-file/#environment
+
+* Add [django-debug-toolbar][django-toolbar] to composed django image
+
+[django-toolbar]: https://django-debug-toolbar.readthedocs.io/en/stable/index.html
+
+* manage sensitive data using secret in docker-compose, as described
+  [here][secret1] and [here][secret2]
+
+[secret1]: https://docs.docker.com/engine/swarm/secrets/#use-secrets-in-compose
+[secret2]: https://docs.docker.com/compose/compose-file/#secrets
+

compose/registry/README.md

@@ -331,6 +331,32 @@ Pull it back
 $ docker pull registry.ptp/myfirstimage
 ```
 
+Using docker-registry
+---------------------
+
+### Listing images
+
+List all images in catalog (using httpie):
+
+```
+$ http https://<user>:<password>@registry.ptp/v2/_catalog
+```
+
+Getting all version for an image:
+
+```
+$ http  https://<user>:<password>@registry.ptp/v2/<image>/tags/list
+```
+
+### Deleting images using delete-docker-registry-image
+
+Deleting an image using the latest version of [delete-docker-registry-image](delete-docker-registry-image):
+
+```
+$ sudo ./delete_docker_registry_image.py --image <image>:latest
+$ sudo ./delete_docker_registry_image.py --image <image>:<tag>
+```
+
 <!-- References -->
 
 [docker-registry]: https://docs.docker.com/registry/
@@ -341,5 +367,6 @@ $ docker pull registry.ptp/myfirstimage
 [private-docker-registry-configuration]: http://blog.agilepartner.net/private-docker-registry-configuration/
 [supervisor-and-nginx]: https://www.kf-interactive.com/blog/roll-your-own-docker-registry-with-docker-compose-supervisor-and-nginx/
 [nginx-proxy-examples]: https://github.com/kwk/docker-registry-frontend/wiki/nginx-proxy-examples
+[delete-docker-registry-image]: https://github.com/burnettk/delete-docker-registry-image.git
 
 <!-- Not used: http://blog.agilepartner.net/private-docker-registry-behind-an-httpd-reverse-proxy/ -->

compose/shiny/shiny/Dockerfile

@@ -1,11 +1,11 @@
 #
-# VERSION 0.1
-# DOCKER-VERSION  1.7.1
+# VERSION 0.2
+# DOCKER-VERSION  17.05.0-ce
 # AUTHOR:         Paolo Cozzi <[email protected]>
 # DESCRIPTION:    A shiny container based on rocker-shiny
 # TO_BUILD:       docker build --rm -t ptp/shiny .
 # TO_RUN:         docker run -d -P ptp/shiny
-# TO_TAG:         docker tag ptp/shiny:latest <name>:0.1
+# TO_TAG:         docker tag ptp/shiny:latest <name>:0.2
 #
 
 # Get the last rocker/shiny image
@@ -17,7 +17,9 @@ MAINTAINER Paolo Cozzi <[email protected]>
 # install package dependencies
 RUN apt-get update && apt-get install -y \
     libssl-dev \
-    libxml2-dev
+    libxml2-dev \
+    openjdk-9-jdk \
+ && apt-get clean && rm -rf /var/lib/apt/lists/
 
 # Install R packages. Packages are listed in packages.txt
 COPY install.r packages.txt /root/