From 59c587a0aa13fd4d9436092bf35c53be5329ad84 Mon Sep 17 00:00:00 2001
From: Filippo Ledda <filippo@metacell.us>
Date: Tue, 7 Nov 2023 14:47:09 +0100
Subject: [PATCH] Simplify netpyne build

---
 applications/netpyne/Dockerfile               | 87 +------------------
 .../geppetto/GeppettoConfiguration.json       | 21 -----
 2 files changed, 1 insertion(+), 107 deletions(-)
 delete mode 100644 applications/netpyne/overrides/geppetto/GeppettoConfiguration.json

diff --git a/applications/netpyne/Dockerfile b/applications/netpyne/Dockerfile
index 0f93b09d..1b8f38a4 100644
--- a/applications/netpyne/Dockerfile
+++ b/applications/netpyne/Dockerfile
@@ -1,90 +1,5 @@
-FROM node:14 as jsbuild
-ENV REPO=https://github.com/MetaCell/NetPyNE-UI.git
-ENV BRANCH_TAG=release/1.0.0
-ENV FOLDER=netpyne
-RUN echo "no-cache 2023-7-14"
-RUN git clone $REPO -b $BRANCH_TAG $FOLDER
-RUN rm -Rf .git
-
-COPY overrides/geppetto/GeppettoConfiguration.json $FOLDER/webapp/GeppettoConfiguration.json
-
-WORKDIR $FOLDER/webapp
-RUN yarn install  --network-timeout 1000000000
-RUN yarn build-dev
-
-RUN rm -Rf node_modules/*
-
-
-
-###
-FROM jupyter/base-notebook:hub-1.4.2
-ENV NB_UID=jovyan
-ENV FOLDER=netpyne
-ENV NP_LFPYKIT_HEAD_FILE=/home/jovyan/nyhead.mat
-
-USER root
-
-RUN rm -rf /var/lib/apt/lists
-RUN apt-get update -qq &&\
-    apt-get install python3-tk vim nano unzip git make libtool g++ -qq pkg-config libfreetype6-dev libpng-dev libopenmpi-dev -y
-RUN apt-get install openjdk-11-jre-headless -y
-RUN conda install python=3.7 -y
-
-
-WORKDIR $FOLDER
-COPY --from=jsbuild --chown=1000:1000 $FOLDER/requirements.txt requirements.txt
-RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
-    pip install -r requirements.txt --prefer-binary
-
-COPY --from=jsbuild --chown=1000:1000 $FOLDER .
-
-# ToDo: fixme, for now remove the jupyter hub config json file because it overrides the default
-# and thus removes the frame ancestor cors settings
-RUN rm -f ~/.jupyter/*.json
-RUN chown $NB_UID .
-RUN chown $NB_UID /opt
-RUN rm -Rf workspace
-
-USER $NB_UID
-
-# sym link workspace pvc to $FOLDER
-RUN mkdir -p /opt/workspace
-RUN mkdir -p /opt/user
-
-
-
-
-ENV NEURON_HOME=/opt/conda
-
-
-USER root
-
-RUN jupyter nbextension install --py --symlink --sys-prefix jupyter_geppetto
-RUN jupyter nbextension enable --py --sys-prefix jupyter_geppetto
-RUN jupyter nbextension enable --py --sys-prefix widgetsnbextension
-RUN jupyter serverextension enable --py --sys-prefix jupyter_geppetto
-
-RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\ 
-  python utilities/install.py --npm-skip --no-test
+FROM gcr.io/metacellllc/netpyne-ui:1.0.0-osb
 
 COPY overrides/requirements.txt overrides/requirements.txt
 RUN --mount=type=cache,target=/root/.cache python -m pip install --upgrade pip &&\
     pip install -r overrides/requirements.txt
-
-RUN mv workspace /opt/workspace/tutorials
-RUN chown -R $NB_UID /opt/workspace/tutorials
-RUN ln -s /opt/workspace workspace
-
-RUN jupyter labextension disable @jupyterlab/hub-extension
-RUN wget --no-check-certificate -O $NP_LFPYKIT_HEAD_FILE https://www.parralab.org/nyhead/sa_nyhead.mat
-
-USER $NB_UID
-
-
-EXPOSE 8888
-
-ENTRYPOINT ["tini", "-g", "--"]
-
-
-
-CMD ./NetPyNE-UI
diff --git a/applications/netpyne/overrides/geppetto/GeppettoConfiguration.json b/applications/netpyne/overrides/geppetto/GeppettoConfiguration.json
deleted file mode 100644
index cb076391..00000000
--- a/applications/netpyne/overrides/geppetto/GeppettoConfiguration.json
+++ /dev/null
@@ -1,21 +0,0 @@
-{
-    "_README": "http://docs.geppetto.org/en/latest/build.html",
-    "contextPath": "org.geppetto.frontend",
-    "useSsl": true,
-    "embedded": true,
-    "embedderURL": [
-        "/"
-    ],
-    "rootRedirect": "",
-    "noTest": false,
-    "themes": "css/colors",
-    "properties": {
-        "title": "NetPyNE",
-        "description": "NetPyNE-UI is a user interface for building, visualizing and simulationg neuronal network models using NetPyNE.",
-        "type": "website",
-        "url": "https://github.com/MetaCell/NetPyNE-UI",
-        "icon": "https://d30y9cdsu7xlg0.cloudfront.net/png/38902-200.png",
-        "image": "http://www.geppetto.org/images/logo.png"
-    },
-    "notebookName": "notebook.ipynb"
-}
\ No newline at end of file