Swagger UI

From c9f8cd864a2b72e7330b8095691fa5c16fea83aa Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Fri, 30 Aug 2019 11:14:50 +0200 Subject: Dockerfile and start script added --- docker/Dockerfile | 73 +++++++++++++++++++++++++++++++++++ docker/start.sh | 12 ++++++ docker/swagger.html | 107 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 192 insertions(+) create mode 100644 docker/Dockerfile create mode 100755 docker/start.sh create mode 100644 docker/swagger.html (limited to 'docker') diff --git a/docker/Dockerfile b/docker/Dockerfile new file mode 100644 index 0000000..a606b9a --- /dev/null +++ b/docker/Dockerfile @@ -0,0 +1,73 @@ +FROM archlinux/base +MAINTAINER in-silico toxicology Gmbh + +RUN pacman-db-upgrade +RUN pacman -Syyu --noconfirm +RUN pacman -S --noconfirm \ + base-devel \ + boost-libs \ + cmake \ + eigen3 \ + fontconfig \ + gcc-fortran \ + git \ + gsl \ + jre10-openjdk-headless \ + r \ + ruby \ + swig \ + python-pip \ + catdoc \ + wget +RUN pacman -Scc --noconfirm + +RUN R -e "install.packages('Rserve', repos='http://rforge.net/')" +RUN pip install xlsx2csv +RUN useradd -ms /bin/bash ist + +# mongodb has been removed from main repositories +USER ist +WORKDIR /home/ist +RUN mkdir data +RUN mkdir src +WORKDIR /home/ist/src +RUN wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz +RUN tar -xvzf mongodb-bin.tar.gz +WORKDIR /home/ist/src/mongodb-bin +RUN makepkg -s --noconfirm + +# installation requires root +USER root +RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz + +# install lazar-gui gem +RUN echo 'gem: --no-document' > /etc/gemrc + +#RUN gem install lazar-gui +RUN gem install lazar +RUN gem install qsar-report +RUN gem install sinatra haml sass rdiscount unicorn + +USER ist +WORKDIR /home/ist +RUN rm -r src + +# lazar-gui +RUN git clone https://git.in-silico.ch/lazar-gui +WORKDIR lazar-gui +RUN git checkout prerelease + +# SWAGGER for API +WORKDIR /home/ist +RUN git clone https://github.com/swagger-api/swagger-ui.git +COPY swagger.html /home/ist/swagger-ui/dist/index.html + +# TODO adjust to lazar-gui gem path +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js /home/ist/lazar-gui/public/swagger-ui-bundle.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js /home/ist/lazar-gui/public/swagger-ui-standalone-preset.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css /home/ist/lazar-gui/public/swagger-ui.css + +# start script +COPY start.sh /home/ist/start.sh + +ENTRYPOINT ["/home/ist/start.sh"] diff --git a/docker/start.sh b/docker/start.sh new file mode 100755 index 0000000..ad40a0e --- /dev/null +++ b/docker/start.sh @@ -0,0 +1,12 @@ +#!/bin/sh + +# start basic services +mongod --bind_ip 127.0.0.1 --dbpath ~/data & +R CMD Rserve --vanilla & + +# import data +ruby -e "require 'lazar'; include OpenTox; Import.public_data" + +# start lazar service +cd $HOME/lazar-gui +unicorn -p 8088 -E production diff --git a/docker/swagger.html b/docker/swagger.html new file mode 100644 index 0000000..239e4f1 --- /dev/null +++ b/docker/swagger.html @@ -0,0 +1,107 @@ + + + + + + Swagger UI + + + + + + + + +

+ + + + + + -- cgit v1.2.3 From a84d9eabf1b921086a688f81df28b0f21ba4df19 Mon Sep 17 00:00:00 2001 From: Christoph Helma Date: Tue, 3 Sep 2019 13:06:00 +0200 Subject: docker installation as gem, links with port numbers, version 1.4.0 --- docker/Dockerfile | 46 ++++++++++++++++++---------------------------- docker/start.sh | 4 ++-- 2 files changed, 20 insertions(+), 30 deletions(-) (limited to 'docker') diff --git a/docker/Dockerfile b/docker/Dockerfile index a606b9a..b7ba3c1 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -23,12 +23,17 @@ RUN pacman -Scc --noconfirm RUN R -e "install.packages('Rserve', repos='http://rforge.net/')" RUN pip install xlsx2csv + +# install lazar-gui gem +RUN echo 'gem: --no-document' > /etc/gemrc +RUN gem install lazar-gui + RUN useradd -ms /bin/bash ist -# mongodb has been removed from main repositories USER ist WORKDIR /home/ist RUN mkdir data +# mongodb has been removed from main repositories, AUR installation RUN mkdir src WORKDIR /home/ist/src RUN wget https://aur.archlinux.org/cgit/aur.git/snapshot/mongodb-bin.tar.gz @@ -36,38 +41,23 @@ RUN tar -xvzf mongodb-bin.tar.gz WORKDIR /home/ist/src/mongodb-bin RUN makepkg -s --noconfirm -# installation requires root -USER root -RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz - -# install lazar-gui gem -RUN echo 'gem: --no-document' > /etc/gemrc - -#RUN gem install lazar-gui -RUN gem install lazar -RUN gem install qsar-report -RUN gem install sinatra haml sass rdiscount unicorn - -USER ist -WORKDIR /home/ist -RUN rm -r src - -# lazar-gui -RUN git clone https://git.in-silico.ch/lazar-gui -WORKDIR lazar-gui -RUN git checkout prerelease - -# SWAGGER for API +# rest api swagger gui WORKDIR /home/ist RUN git clone https://github.com/swagger-api/swagger-ui.git COPY swagger.html /home/ist/swagger-ui/dist/index.html -# TODO adjust to lazar-gui gem path -RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js /home/ist/lazar-gui/public/swagger-ui-bundle.js -RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js /home/ist/lazar-gui/public/swagger-ui-standalone-preset.js -RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css /home/ist/lazar-gui/public/swagger-ui.css - # start script COPY start.sh /home/ist/start.sh +# mongodb installation requires root +USER root +RUN pacman -U --noconfirm /home/ist/src/mongodb-bin/mongodb-bin*.pkg.tar.xz + +# swagger links +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-bundle.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-bundle.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui-standalone-preset.js $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui-standalone-preset.js +RUN ln -s /home/ist/swagger-ui/dist/swagger-ui.css $(gem which "lazar-gui"|sed 's#/lib/lazar-gui.rb/##')/public/swagger-ui.css + +USER ist +RUN rm -r /home/ist/src ENTRYPOINT ["/home/ist/start.sh"] diff --git a/docker/start.sh b/docker/start.sh index ad40a0e..07fefde 100755 --- a/docker/start.sh +++ b/docker/start.sh @@ -5,8 +5,8 @@ mongod --bind_ip 127.0.0.1 --dbpath ~/data & R CMD Rserve --vanilla & # import data -ruby -e "require 'lazar'; include OpenTox; Import.public_data" +ruby -e "require 'lazar'; include OpenTox; Import.public_data if Model::Validation.all.empty?" # start lazar service -cd $HOME/lazar-gui +cd $(gem which lazar-gui|sed 's#/lib/lazar-gui.rb/##') unicorn -p 8088 -E production -- cgit v1.2.3