WIP: Paraview express

Dockerfile

@@ -46,12 +46,12 @@ ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /bin/
 RUN chmod +x /bin/tini
 
 # ffmpeg
-# RUN apt update \
-#     && apt install -y --no-install-recommends --allow-unauthenticated \
-#         ffmpeg \
-#     && rm -rf /var/lib/apt/lists/* \
-#     && mkdir /usr/local/ffmpeg \
-#     && ln -s /usr/bin/ffmpeg /usr/local/ffmpeg/ffmpeg
+ RUN apt update \
+     && apt install -y --no-install-recommends --allow-unauthenticated \
+         ffmpeg \
+     && rm -rf /var/lib/apt/lists/* \
+     && mkdir /usr/local/ffmpeg \
+     && ln -s /usr/bin/ffmpeg /usr/local/ffmpeg/ffmpeg
 
 # python library
 COPY image/usr/local/lib/web/backend/requirements.txt /tmp/
@@ -105,25 +105,32 @@ FROM system
 
 COPY --from=builder /src/web/dist/ /usr/local/lib/web/frontend/
 
-# Install QGIS
+# Install Paraview
+
+RUN apt update \ 
+    && apt upgrade -y \
+    && apt install build-essential -y
+
+RUN apt-get update && apt-get install -y xterm paraview
+RUN apt-get install -y qt5-default
+RUN curl -sL https://deb.nodesource.com/setup_8.x | bash
+RUN apt-get install -y nodejs protobuf-compiler
+RUN npm install -g pvw-visualizer
+RUN ldconfig && \
+    mkdir /usr/local/opt/ && \
+    mkdir /Applications
+
+EXPOSE 8000
+CMD ["python", "/opt/cdatweb/run.py", "--port", "8000", "--upload-directory", "/opt/uvcdat/sample_data"]
 
 RUN apt update \
     && apt install -y \
-    python3-pip \
-    python3-dev \
-    python3-setuptools \
-    dirmngr \
-    xterm \
-    && apt autoclean \
-    && apt autoremove \
-    && rm -rf /var/lib/apt/lists/*
-
-RUN echo "deb     http://qgis.org/ubuntu bionic main" >> /etc/apt/sources.list
-RUN echo "deb-src http://qgis.org/ubuntu bionic main" >> /etc/apt/sources.list
+    libxkbcommon-x11-0
 
-RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-key CAEB3DC3BDF7FB45
+ADD docker-paraviewweb/startup.sh startup.sh
 
-RUN apt update && apt-get install -y qgis python3-qgis qgis-plugin-grass
+RUN chmod +x /startup.sh
+CMD /startup.sh
 
 COPY image /
 EXPOSE 6080
@@ -135,8 +142,6 @@ RUN groupadd --gid 816877 G-816877
 RUN useradd --uid 458981 --create-home --shell /bin/bash --user-group --groups G-816877,adm,sudo ubuntu && chown ubuntu:G-816877 /home/ubuntu
 RUN usermod -g G-816877 ubuntu
 RUN mkdir -p /home/ubuntu/.config/pcmanfm/LXDE/ && cp /usr/local/share/doro-lxde-wallpapers/desktop-items-0.conf /home/ubuntu/.config/pcmanfm/LXDE/ && chown -R ubuntu:G-816877 /home/ubuntu/.config
+
 COPY kill.py /
-# COPY /etc/pki/tls/certs/designsafe-exec-01.tacc.utexas.edu.cer /etc/nginx/ssl/
-# COPY /etc/pki/tls/private/designsafe-exec-01.tacc.utexas.edu.key /etc/nginx/ssl/
-# HEALTHCHECK --interval=30s --timeout=5s CMD curl --fail http://127.0.0.1:6079/api/health
-ENTRYPOINT ["/startup.sh"]
+ENTRYPOINT ["/startup.sh"]

Paraview.sh

@@ -0,0 +1,25 @@
+#!/bin/sh
+
+appname=`basename $0 | sed s,\.sh$,,`
+
+dirname=`dirname $0`
+tmp="${dirname#?}"
+
+if [ "${dirname%$tmp}" != "/" ]; then
+dirname=$PWD/$dirname
+fi
+
+core=$dirname/lib/core
+coredep=$dirname/lib/coredep
+export QTTOOLDIR=/opt/Qt5.12.4/5.12.4/gcc_64/bin
+export QTLIBDIR=/opt/Qt5.12.4/5.12.4/gcc_64/lib
+LD_LIBRARY_PATH=$dirname:$core:$coredep:$QTLIBDIR:$LD_LIBRARY_PATH
+export LD_LIBRARY_PATH
+#export QT_DEBUG_PLUGINS=1
+#echo "$0 = "$0
+#echo "appname = "$appname
+#echo "dirname = "$dirname
+#echo "tmp = "$tmp
+echo "LD_LIBRARY_PATH = "$LD_LIBRARY_PATH
+
+$dirname/$appname "$@"

README_Paraview.md

@@ -0,0 +1,11 @@
+ app
+--------
+Here are some notes on this app's image.
+
+
+Building Docker image
+================
+This Dockerfile will download, unzip, and run Paraview 5.6 for Ubuntu 18.04. 
+```
+docker build -t tagname  .
+```

docker-paraviewweb/.travis.yml

@@ -0,0 +1,14 @@
+sudo: required
+
+language: python
+python: 2.7
+
+services:
+  - docker
+
+before_install:
+  - docker build -t bmcv/galaxy-paraviewweb .
+  - docker run -d -p 8777:8777 bmcv/galaxy-paraviewweb
+
+script:
+  - docker ps

docker-paraviewweb/Dockerfile

@@ -0,0 +1,40 @@
+FROM nginx
+
+MAINTAINER Thomas Wollmann <[email protected]>
+
+ENV CONDA /miniconda/
+ENV PATH $CONDA/bin:$PATH
+
+RUN apt-get update && apt-get install -y wget bzip2 npm nodejs-legacy && \
+	wget -q http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh && \
+	bash Miniconda2-latest-Linux-x86_64.sh -p /miniconda -b && \
+	rm Miniconda2-latest-Linux-x86_64.sh && \
+	rm -rf /var/lib/apt/lists/* && \
+	apt-get purge -y wget && \
+	conda install paraview -c bioconda -c conda-forge -y && \
+        npm install -g pvw-visualizer
+
+RUN echo $CONDA/lib/paraview-5.2/ > /etc/ld.so.conf.d/paraview.conf && \
+    ldconfig && \
+    mkdir /usr/local/opt/ && \
+    mkdir /Applications
+
+ADD nginx.conf /etc/nginx/nginx.conf
+
+WORKDIR /input
+
+ENV DEBUG=false \
+    GALAXY_WEB_PORT=10000 \
+    NOTEBOOK_PASSWORD=none \
+    CORS_ORIGIN=none \
+    DOCKER_PORT=none \
+    API_KEY=none \
+    HISTORY_ID=none \
+    REMOTE_HOST=none \
+    GALAXY_URL=none
+
+EXPOSE 8777
+
+ADD startup.sh /
+RUN chmod +x /startup.sh
+CMD /startup.sh

docker-paraviewweb/LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2016 
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

docker-paraviewweb/README.md

@@ -0,0 +1,46 @@
+
+[![Build Status](https://travis-ci.org/BMCV/docker-paraviewweb.svg?branch=master)](https://travis-ci.org/BMCV/docker-paraviewweb)
+[![Docker Pulls](https://img.shields.io/docker/pulls/bmcv/galaxy-paraviewweb.svg)](https://hub.docker.com/r/bmcv/galaxy-paraviewweb/) 
+[![Docker Stars](https://img.shields.io/docker/stars/bmcv/galaxy-paraviewweb.svg)](https://hub.docker.com/r/bmcv/galaxy-paraviewweb/) 
+
+Docker ParaViewWeb Container
+========================
+
+
+This [ParaViewWeb](http://paraviewweb.kitware.com/) Docker container is used by the [Galaxy Project](https://galaxyproject.org/).
+
+![screenshot](screenshot.png)
+
+Usage
+=====
+
+* Build your own image and run it
+
+ [Docker](https://www.docker.com) is a pre-requirement for this project. You can build the container with:
+ ```bash
+  docker build -t paraviewweb .
+ ```
+ The build process can take some time, but if finished you can run your container with:
+ ```bash
+  docker run -p 8777:8777 -v /home/user/paraviewweb/input/:/input/ -v /home/user/paraviewweb/output/:/output/ paraviewweb
+ ```
+ and you will have a running [ParaViewWeb](http://paraviewweb.kitware.com/) instance on ``http://localhost:8777/apps/Visualizer``.
+
+ Environment Variables
+ =====================
+
+ Some environment variables are made available to the user which will allow for configuring the behaviour of individual instances.
+
+ Variable            | Use
+ ------------------- | ---
+ `DATASET_HID`           | Path of file relative to /input which is loaded on startup
+
+Acknowledgment
+========================
+This work was supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within the German Network for Bioinformatics Infrastructure (de.NBI) #031A537C.
+
+Works best with
+=====================
+
+ * [Galaxy Image Analysis Tools](https://github.com/ThomasWollmann/galaxy-image-analysis)
+ * [Galaxy Imaging](https://github.com/bgruening/docker-galaxy-imaging)

docker-paraviewweb/nginx.conf

@@ -0,0 +1,28 @@
+events {
+    worker_connections  128;
+}
+
+http {
+	map $http_upgrade $connection_upgrade {
+	       	default upgrade;
+	       	''      close;
+	}
+
+	server {
+		listen   8777;
+		server_name 0.0.0.0; 
+
+		location / {
+			proxy_pass http://127.0.0.1:9777;
+
+			add_header Access-Control-Allow-Origin *;
+			add_header 'Access-Control-Allow-Credentials' 'true';
+			add_header 'Access-Control-Allow-Methods' 'GET, POST, PUT, DELETE, OPTIONS';
+			add_header 'Access-Control-Allow-Headers' 'Accept,Authorization,Cache-Control,Content-Type,DNT,If-Modified-Since,Keep-Alive,Origin,User-Agent,X-Mx-ReqToken,X-Requested-With';
+
+			proxy_http_version 1.1;
+			proxy_set_header Upgrade $http_upgrade;
+		        proxy_set_header Connection $connection_upgrade;
+		}
+	}
+}

docker-paraviewweb/startup.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+
+service nginx start
+
+if [ -z "$DATASET_HID" ]
+then
+    Visualizer --paraview $CONDA/lib/paraview-5.2/ \
+        --data /input \
+        --port 8777 \
+	--server-only
+else
+    Visualizer --paraview $CONDA/lib/paraview-5.2/ \
+        --data /input \
+        --port 8777 \
+	--server-only \
+        --load-file $DATASET_HID
+fi

image/etc/supervisor/conf.d/supervisord.conf

@@ -60,19 +60,19 @@ command=bash /usr/local/lib/web/frontend/static/novnc/utils/launch.sh --listen 6
 stopasgroup=true
 stdout_logfile=/var/log/novnc.log
 
-[program:qgis]
+[program:paraview]
 priority=35
 directory=/home/ubuntu/mydata
-command=xterm -r -ls -geometry 80x24+10+10 -title '*** Exit this window to kill your QGIS session ***' -e '/usr/bin/qgis --nologo'
+command=xterm -r -ls -geometry 80x24+10+10 -title '*** Exit this window to kill your Paraview session ***' -e 'paraview'
 user=ubuntu
 autostart=true
 autorestart=false
 stopsignal=QUIT
 environment=DISPLAY=":1",HOME="/home/ubuntu"
-stdout_logfile=/var/log/qgis.log
+stdout_logfile=/var/log/paraview.log
 redirect_stderr=true
 
 [eventlistener:exit]
 command=/kill.py
-process_name=qgis
+process_name=paraview
 events=PROCESS_STATE_EXITED

kill.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python
+import sys
+import os
+import signal
+
+def write_stdout(s):
+   sys.stdout.write(s)
+   sys.stdout.flush()
+def write_stderr(s):
+   sys.stderr.write(s)
+   sys.stderr.flush()
+def main():
+   while 1:
+       write_stdout('READY\n')
+       line = sys.stdin.readline()
+       write_stdout('This line kills supervisor: ' + line);
+       try:
+               pidfile = open('/var/run/supervisord.pid','r')
+               pid = int(pidfile.readline());
+               os.kill(pid, signal.SIGQUIT)
+       except Exception as e:
+               write_stdout('Could not kill supervisor: ' + e.strerror + '\n')
+       write_stdout('RESULT 2\nOK')
+if __name__ == '__main__':
+   main()
+   import sys