From e7316e6543966f53eeb75f7822eb38bd08cfe914 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Fri, 12 Jul 2024 17:06:09 -0500
Subject: [PATCH 1/9] First pass at theia installation

Working from https://jupyter-server-proxy.readthedocs.io/en/latest/convenience/packages/theia.html
---
 singleuser/Dockerfile                  |  6 ++++++
 singleuser/config/apt_install.sh       |  8 +++++--
 singleuser/config/pip_requirements.txt |  3 ++-
 singleuser/theia/package.json          | 30 ++++++++++++++++++++++++++
 4 files changed, 44 insertions(+), 3 deletions(-)
 create mode 100644 singleuser/theia/package.json

diff --git a/singleuser/Dockerfile b/singleuser/Dockerfile
index 312e251..d33131b 100644
--- a/singleuser/Dockerfile
+++ b/singleuser/Dockerfile
@@ -10,6 +10,7 @@ RUN if [ "$(python -c 'import sys; print(".".join(map(str, sys.version_info[:2])
 USER root
 COPY ./config /tmp/config
 COPY ./ipython-datajoint-creds-updater /tmp/ipython-datajoint-creds-updater
+COPY ./theia/ /tmp/theia
 RUN \
     # Install dependencies: apt
     bash /tmp/config/apt_install.sh \
@@ -23,7 +24,12 @@ RUN \
     # Autoload extension in IPython kernel config
     && mkdir -p /etc/ipython \
     && echo "c.IPKernelApp.extensions = ['ipython_datajoint_creds_updater.extension']" > /etc/ipython/ipython_kernel_config.py
+RUN \
+    cd /tmp/theia \
+    && yarn \
+    && yarn theia build
 
+ENV PATH="/tmp/theia/node_modules/.bin:${PATH}"
 USER $NB_UID
 RUN \
     # remove default work directory
diff --git a/singleuser/config/apt_install.sh b/singleuser/config/apt_install.sh
index 33e15fd..4ee3213 100644
--- a/singleuser/config/apt_install.sh
+++ b/singleuser/config/apt_install.sh
@@ -3,10 +3,14 @@
 sudo apt update
 
 # Install
-sudo apt-get install mysql-client gcc -y --no-install-recommends
+sudo apt-get install mysql-client gcc nodejs npm -y --no-install-recommends
 sudo apt-get clean
 rm -rf /var/lib/apt/lists/*
 
+# Install Yarn
+# npm install --global yarn
+corepack enable
+
 # Other installation
 wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O /usr/bin/yq
-chmod +x /usr/bin/yq
\ No newline at end of file
+chmod +x /usr/bin/yq
diff --git a/singleuser/config/pip_requirements.txt b/singleuser/config/pip_requirements.txt
index e1e3589..6fd6afd 100644
--- a/singleuser/config/pip_requirements.txt
+++ b/singleuser/config/pip_requirements.txt
@@ -1,2 +1,3 @@
 gh
-# jupyter-collaboration
\ No newline at end of file
+# jupyter-collaboration
+jupyter-server-proxy
diff --git a/singleuser/theia/package.json b/singleuser/theia/package.json
new file mode 100644
index 0000000..64aeb4e
--- /dev/null
+++ b/singleuser/theia/package.json
@@ -0,0 +1,30 @@
+{
+  "private": true,
+  "dependencies": {
+      "@theia/callhierarchy": "latest",
+      "@theia/editor-preview": "latest",
+      "@theia/file-search": "latest",
+      "@theia/git": "latest",
+      "@theia/json": "latest",
+      "@theia/languages": "latest",
+      "@theia/markers": "latest",
+      "@theia/merge-conflicts": "latest",
+      "@theia/messages": "latest",
+      "@theia/mini-browser": "latest",
+      "@theia/monaco": "latest",
+      "@theia/navigator": "latest",
+      "@theia/outline-view": "latest",
+      "@theia/preferences": "latest",
+      "@theia/preview": "latest",
+      "@theia/python": "latest",
+      "@theia/search-in-workspace": "latest",
+      "@theia/terminal": "latest",
+      "@theia/textmate-grammars": "latest",
+      "@theia/typescript": "latest",
+      "typescript": "latest",
+      "yarn": "^1.12.3"
+  },
+  "devDependencies": {
+      "@theia/cli": "latest"
+  }
+}

From 6ddcec7df9a8743bebe09486c52a3fabd77e5661 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Fri, 12 Jul 2024 18:28:48 -0500
Subject: [PATCH 2/9] Docker build working

---
 singleuser/config/apt_install.sh |  3 ++-
 singleuser/theia/package.json    | 39 ++++++++++++--------------------
 2 files changed, 17 insertions(+), 25 deletions(-)

diff --git a/singleuser/config/apt_install.sh b/singleuser/config/apt_install.sh
index 4ee3213..446f35e 100644
--- a/singleuser/config/apt_install.sh
+++ b/singleuser/config/apt_install.sh
@@ -3,13 +3,14 @@
 sudo apt update
 
 # Install
-sudo apt-get install mysql-client gcc nodejs npm -y --no-install-recommends
+sudo apt-get install mysql-client gcc-12 build-essential pkg-config libsecret-1-dev nodejs npm -y --no-install-recommends
 sudo apt-get clean
 rm -rf /var/lib/apt/lists/*
 
 # Install Yarn
 # npm install --global yarn
 corepack enable
+npm i -g node-gyp
 
 # Other installation
 wget https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64 -O /usr/bin/yq
diff --git a/singleuser/theia/package.json b/singleuser/theia/package.json
index 64aeb4e..15d331f 100644
--- a/singleuser/theia/package.json
+++ b/singleuser/theia/package.json
@@ -1,30 +1,21 @@
 {
   "private": true,
   "dependencies": {
-      "@theia/callhierarchy": "latest",
-      "@theia/editor-preview": "latest",
-      "@theia/file-search": "latest",
-      "@theia/git": "latest",
-      "@theia/json": "latest",
-      "@theia/languages": "latest",
-      "@theia/markers": "latest",
-      "@theia/merge-conflicts": "latest",
-      "@theia/messages": "latest",
-      "@theia/mini-browser": "latest",
-      "@theia/monaco": "latest",
-      "@theia/navigator": "latest",
-      "@theia/outline-view": "latest",
-      "@theia/preferences": "latest",
-      "@theia/preview": "latest",
-      "@theia/python": "latest",
-      "@theia/search-in-workspace": "latest",
-      "@theia/terminal": "latest",
-      "@theia/textmate-grammars": "latest",
-      "@theia/typescript": "latest",
-      "typescript": "latest",
-      "yarn": "^1.12.3"
+    "@theia/callhierarchy": "latest",
+    "@theia/file-search": "latest",
+    "@theia/git": "latest",
+    "@theia/markers": "latest",
+    "@theia/messages": "latest",
+    "@theia/mini-browser": "latest",
+    "@theia/navigator": "latest",
+    "@theia/outline-view": "latest",
+    "@theia/plugin-ext-vscode": "latest",
+    "@theia/preferences": "latest",
+    "@theia/preview": "latest",
+    "@theia/search-in-workspace": "latest",
+    "@theia/terminal": "latest"
   },
   "devDependencies": {
-      "@theia/cli": "latest"
+    "@theia/cli": "latest"
   }
-}
+}
\ No newline at end of file

From 1555f77ae4b5d571a77219a541c023b94f992356 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Mon, 15 Jul 2024 18:07:20 -0500
Subject: [PATCH 3/9] Add theia demo as separate service

---
 singleuser/docker-compose.yaml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/singleuser/docker-compose.yaml b/singleuser/docker-compose.yaml
index 75606d6..02c79ff 100644
--- a/singleuser/docker-compose.yaml
+++ b/singleuser/docker-compose.yaml
@@ -19,3 +19,16 @@ services:
     extends: singleuser
     container_name: djlab
     image: datajoint/djlab:inherit-hub-${JUPYTERHUB_VERSION}-py${PYTHON_VERSION}
+  theia:
+    extends: singleuser
+    container_name: theia
+    ports:
+      - 8080:8080
+    command:
+      - yarn
+      - --cwd=/tmp/theia
+      - theia
+      - start
+      - --plugins=local-dir:plugins
+      - --hostname=0.0.0.0
+      - --port=8080

From 4df6571b36c98807283df113ad539f909fbf7942 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Tue, 16 Jul 2024 14:45:19 -0500
Subject: [PATCH 4/9] theia service returning 500

---
 singleuser/config/pip_requirements.txt |  2 ++
 singleuser/docker-compose.yaml         | 16 ++++++++--------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/singleuser/config/pip_requirements.txt b/singleuser/config/pip_requirements.txt
index 6fd6afd..58bed61 100644
--- a/singleuser/config/pip_requirements.txt
+++ b/singleuser/config/pip_requirements.txt
@@ -1,3 +1,5 @@
 gh
 # jupyter-collaboration
 jupyter-server-proxy
+jupyter-theia-proxy
+
diff --git a/singleuser/docker-compose.yaml b/singleuser/docker-compose.yaml
index 02c79ff..0ddf1fb 100644
--- a/singleuser/docker-compose.yaml
+++ b/singleuser/docker-compose.yaml
@@ -24,11 +24,11 @@ services:
     container_name: theia
     ports:
       - 8080:8080
-    command:
-      - yarn
-      - --cwd=/tmp/theia
-      - theia
-      - start
-      - --plugins=local-dir:plugins
-      - --hostname=0.0.0.0
-      - --port=8080
+    # command:
+    #   - yarn
+    #   - --cwd=/tmp/theia
+    #   - theia
+    #   - start
+    #   - --plugins=local-dir:plugins
+    #   - --hostname=0.0.0.0
+    #   - --port=8080

From 8bf28e254b32340c83f44c1ce432ea585659a162 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Tue, 16 Jul 2024 14:57:23 -0500
Subject: [PATCH 5/9] Theia IDE working with WORKDIR /tmp/theia

---
 singleuser/Dockerfile | 1 +
 1 file changed, 1 insertion(+)

diff --git a/singleuser/Dockerfile b/singleuser/Dockerfile
index d33131b..c85ff96 100644
--- a/singleuser/Dockerfile
+++ b/singleuser/Dockerfile
@@ -36,3 +36,4 @@ RUN \
     [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work \
     # Install dependencies: pip
     && pip install /tmp/ipython-datajoint-creds-updater -r /tmp/config/pip_requirements.txt
+WORKDIR /tmp/theia

From aba5479eb58a735778bf618adca2246c07a3eeb3 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Tue, 16 Jul 2024 14:59:31 -0500
Subject: [PATCH 6/9] Skip repo clone for service theia

---
 singleuser/docker-compose.yaml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/singleuser/docker-compose.yaml b/singleuser/docker-compose.yaml
index 0ddf1fb..e7ccc32 100644
--- a/singleuser/docker-compose.yaml
+++ b/singleuser/docker-compose.yaml
@@ -24,6 +24,10 @@ services:
     container_name: theia
     ports:
       - 8080:8080
+    environment:
+      - DJLABHUB_REPO=
+      - DJLABHUB_REPO_BRANCH=
+      - DJLABHUB_REPO_INSTALL=FALSE
     # command:
     #   - yarn
     #   - --cwd=/tmp/theia

From a3222a6b7515c31c6b6447513a499980ca3f7421 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Tue, 16 Jul 2024 15:14:05 -0500
Subject: [PATCH 7/9] Clean up docker build

---
 singleuser/Dockerfile | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/singleuser/Dockerfile b/singleuser/Dockerfile
index c85ff96..8bd2857 100644
--- a/singleuser/Dockerfile
+++ b/singleuser/Dockerfile
@@ -10,7 +10,6 @@ RUN if [ "$(python -c 'import sys; print(".".join(map(str, sys.version_info[:2])
 USER root
 COPY ./config /tmp/config
 COPY ./ipython-datajoint-creds-updater /tmp/ipython-datajoint-creds-updater
-COPY ./theia/ /tmp/theia
 RUN \
     # Install dependencies: apt
     bash /tmp/config/apt_install.sh \
@@ -24,16 +23,20 @@ RUN \
     # Autoload extension in IPython kernel config
     && mkdir -p /etc/ipython \
     && echo "c.IPKernelApp.extensions = ['ipython_datajoint_creds_updater.extension']" > /etc/ipython/ipython_kernel_config.py
+
+# Install Theia IDE
+COPY ./theia/ /tmp/theia
 RUN \
     cd /tmp/theia \
     && yarn \
-    && yarn theia build
-
+    && yarn theia build \
+    && ln -s /tmp/theia/package.json /home/jovyan/package.json \
+    && ln -s /tmp/theia/src-gen /home/jovyan/src-gen
 ENV PATH="/tmp/theia/node_modules/.bin:${PATH}"
+
 USER $NB_UID
 RUN \
     # remove default work directory
     [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work \
     # Install dependencies: pip
     && pip install /tmp/ipython-datajoint-creds-updater -r /tmp/config/pip_requirements.txt
-WORKDIR /tmp/theia

From 4557de9674c218adde024cc85a06a1b63cdee340 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Sun, 28 Jul 2024 13:35:44 -0500
Subject: [PATCH 8/9] Extensions working in Theia

---
 singleuser/Dockerfile         | 14 ++++++++------
 singleuser/theia/package.json | 26 +++++++++++++++++++++++++-
 2 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/singleuser/Dockerfile b/singleuser/Dockerfile
index 8bd2857..5d30cd3 100644
--- a/singleuser/Dockerfile
+++ b/singleuser/Dockerfile
@@ -25,14 +25,15 @@ RUN \
     && echo "c.IPKernelApp.extensions = ['ipython_datajoint_creds_updater.extension']" > /etc/ipython/ipython_kernel_config.py
 
 # Install Theia IDE
-COPY ./theia/ /tmp/theia
+COPY ./theia/ /home/jovyan/.theia
+ENV THEIA_DEFAULT_PLUGINS=local-dir:/home/jovyan/.theia/plugins
 RUN \
-    cd /tmp/theia \
+    cd /home/jovyan/.theia \
     && yarn \
-    && yarn theia build \
-    && ln -s /tmp/theia/package.json /home/jovyan/package.json \
-    && ln -s /tmp/theia/src-gen /home/jovyan/src-gen
-ENV PATH="/tmp/theia/node_modules/.bin:${PATH}"
+    && yarn theia --app-target browser build \
+    && chown -R "$(id -u):$(id -g)" /home/jovyan/.theia \
+    && chmod -R g+rx,u+rwx,o+rwx /home/jovyan/.theia
+ENV PATH="/home/jovyan/.theia/node_modules/.bin:${PATH}"
 
 USER $NB_UID
 RUN \
@@ -40,3 +41,4 @@ RUN \
     [ -d "/home/jovyan/work" ] && rm -r /home/jovyan/work \
     # Install dependencies: pip
     && pip install /tmp/ipython-datajoint-creds-updater -r /tmp/config/pip_requirements.txt
+WORKDIR /home/jovyan/.theia
\ No newline at end of file
diff --git a/singleuser/theia/package.json b/singleuser/theia/package.json
index 15d331f..78d015e 100644
--- a/singleuser/theia/package.json
+++ b/singleuser/theia/package.json
@@ -17,5 +17,29 @@
   },
   "devDependencies": {
     "@theia/cli": "latest"
-  }
+  },
+  "scripts": {
+    "prepare": "yarn run clean && yarn run build && yarn run download:plugins",
+    "clean": "theia --app-target=browser clean",
+    "build": "theia --app-target=browser build",
+    "start": "theia --app-target=browser start --plugins=local-dir:/home/jovyan/.theia/plugins /home/jovyan",
+    "download:plugins": "theia --app-target=browser download:plugins"
+  },
+  "theiaPluginsDir": "plugins",
+  "theiaPlugins": {
+    "vscode-builtin-extensions-pack": "https://open-vsx.org/api/eclipse-theia/builtin-extension-pack/1.50.1/file/eclipse-theia.builtin-extension-pack-1.50.1.vsix",
+    "jupyter-keymap": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "jupyter-renderers": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "vscode-jupyter-slideshow": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "vscode-jupyter-cell-tags": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix"
+  },
+  "theiaPluginsExcludeIds": [
+    "ms-vscode.js-debug-companion",
+    "vscode.extension-editing",
+    "vscode.git",
+    "vscode.git-ui",
+    "vscode.github",
+    "vscode.github-authentication",
+    "vscode.microsoft-authentication"
+  ]
 }
\ No newline at end of file

From bc6c282190d0496d4c7ee684c22875fcd6625818 Mon Sep 17 00:00:00 2001
From: Ethan Ho <53266718+ethho@users.noreply.github.com>
Date: Mon, 29 Jul 2024 10:59:57 -0500
Subject: [PATCH 9/9] Fix plugin names

---
 singleuser/theia/package.json | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/singleuser/theia/package.json b/singleuser/theia/package.json
index 78d015e..ffa9aef 100644
--- a/singleuser/theia/package.json
+++ b/singleuser/theia/package.json
@@ -28,10 +28,10 @@
   "theiaPluginsDir": "plugins",
   "theiaPlugins": {
     "vscode-builtin-extensions-pack": "https://open-vsx.org/api/eclipse-theia/builtin-extension-pack/1.50.1/file/eclipse-theia.builtin-extension-pack-1.50.1.vsix",
-    "jupyter-keymap": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
-    "jupyter-renderers": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
-    "vscode-jupyter-slideshow": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
-    "vscode-jupyter-cell-tags": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix"
+    "ms-toolsai.jupyter-keymap": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "ms-toolsai.jupyter-renderers": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "ms-toolsai.vscode-jupyter-slideshow": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix",
+    "ms-toolsai.vscode-jupyter-cell-tags": "https://open-vsx.org/api/ms-toolsai/jupyter/2024.6.0/file/ms-toolsai.jupyter-2024.6.0.vsix"
   },
   "theiaPluginsExcludeIds": [
     "ms-vscode.js-debug-companion",