adapt Dockerfile

beakerx-dist/configuration.yml

@@ -3,4 +3,14 @@ channels:
   - conda-forge
 dependencies:
   - python =3.7.5
-  - pip
+  - openjdk=11.0.1
+  - notebook>=5.7.6
+  - tornado>6
+  - ipywidgets>=7.5.1
+  - nodejs
+  - pandas
+  - maven
+  - py4j
+  - requests
+  - pyspark
+  - bottle

docker/Dockerfile

@@ -58,7 +58,7 @@ RUN echo 'export PATH=/opt/conda/bin:$PATH' > /etc/profile.d/conda.sh && \
 
 RUN apt-get clean
 
-COPY configuration.yml /home/beakerx/
+COPY beakerx/beakerx-dist/configuration.yml /home/beakerx/
 RUN conda env create -n beakerx -f /home/beakerx/configuration.yml
 RUN conda install -y -n beakerx -c conda-forge jupyterhub jupyterlab=1 pyzmq pytest
 
@@ -70,21 +70,22 @@ ENV SHELL /bin/bash
 ENV NB_UID 1000
 ENV HOME /home/$NB_USER
 
-COPY beakerx jitpack.yml js kernel test /home/beakerx/
-COPY docker/setup.sh / $HOME/
-COPY docker/start.sh docker/start-notebook.sh docker/start-singleuser.sh /usr/local/bin/
-COPY docker/jupyter_notebook_config.py /etc/jupyter/
+COPY beakerx beakerx_base beakerx_kernel_groovy beakerx_kernel_java beakerx_kernel_scala beakerx_kernel_kotlin beakerx_kernel_sql beakerx_kernel_clojure beakerx_kernel_autotranslation beakerx_base beakerx_tabledisplay beakerx_widgets $HOME/
+
+COPY beakerx/docker/setup.sh / $HOME/
+COPY beakerx/docker/start.sh beakerx/docker/start-notebook.sh beakerx/docker/start-singleuser.sh /usr/local/bin/
+COPY beakerx/docker/jupyter_notebook_config.py /etc/jupyter/
 
 WORKDIR $HOME
 
 ###################
 #      Build      #
 ###################
-RUN chown -R beakerx:beakerx /home/beakerx /opt/conda/envs/beakerx  && \
-    /home/beakerx/setup.sh
+RUN chown -R beakerx:beakerx $HOME/ /opt/conda/envs/beakerx  && \
+    $HOME/setup.sh
 
 # Add documentation
-COPY NOTICE README.md StartHere.ipynb doc /home/beakerx/
+COPY beakerx/NOTICE beakerx/README.md beakerx/StartHere.ipynb beakerx/doc $HOME/
 
 USER $NB_USER
 

docker/setup.sh

@@ -15,13 +15,23 @@
 
 set -ex
 source activate beakerx
-(cd beakerx; pip install -r requirements.txt --verbose)
-beakerx install
-beakerx_databrowser install
-jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
-(cd js/lab; jupyter labextension install . --no-build)
-(cd js/lab-theme-dark; jupyter labextension install . --no-build)
-(cd js/lab-theme-light; jupyter labextension install . --no-build)
-jupyter lab build
+
+(cd beakerx_kernel_base; ./gradlew clean install)
+(cd beakerx_kernel_groovy/groovy-dist; pip install -r requirements.txt --verbose; beakerx_kernel_groovy install)
+(cd beakerx_kernel_java/java-dist; pip install -r requirements.txt --verbose; beakerx_kernel_java install)
+(cd beakerx_kernel_scala/scala-dist; pip install -r requirements.txt --verbose; beakerx_kernel_scala install)
+(cd beakerx_kernel_kotlin/kotlin-dist; pip install -r requirements.txt --verbose; beakerx_kernel_kotlin install)
+(cd beakerx_kernel_sql/sql-dist; pip install -r requirements.txt --verbose; beakerx_kernel_sql install)
+(cd beakerx_kernel_clojure/clojure-dist; pip install -r requirements.txt --verbose; beakerx_kernel_clojure install)
+(cd beakerx_kernel_autotranslation; pip install -r requirements.txt --verbose; beakerx_kernel_autotranslation install)
+(cd beakerx_base; pip install -r requirements.txt --verbose)
+(cd beakerx_tabledisplay/beakerx_tabledisplay; pip install -r requirements.txt --verbose; beakerx_tabledisplay install)
+(cd beakerx_widgets/beakerx; pip install -r requirements.txt --verbose; beakerx install)
+
+#jupyter labextension install @jupyter-widgets/jupyterlab-manager --no-build
+#(cd js/lab; jupyter labextension install . --no-build)
+#(cd js/lab-theme-dark; jupyter labextension install . --no-build)
+#(cd js/lab-theme-light; jupyter labextension install . --no-build)
+#jupyter lab build
 
 rm -rf docker .DS_Store .git .gradle .idea jitpack.yml kernel RELEASE.md test .cache .yarn .local logs .ipynb_checkpoints