Merge pull request #24 from yacchin1205/fix/my-binder

Fixed a problem that did not work on mybinder.org.

Dockerfile

@@ -1,12 +1,12 @@
 FROM solr:8 AS solr
 
-FROM niicloudoperation/notebook:latest
+FROM jupyter/scipy-notebook:latest
 
 USER root
 
 # Install OpenJDK and lsyncd
 RUN apt-get update && apt-get install -yq supervisor lsyncd uuid-runtime \
-    openjdk-11-jre gnupg curl tinyproxy \
+    openjdk-11-jre gnupg curl tinyproxy netcat \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
@@ -32,17 +32,27 @@ RUN mkdir -p /opt/minio/bin/ && \
 
 COPY . /tmp/nbsearch
 RUN pip install -e /tmp/nbsearch && \
-    pip install 'notebook>=7' jupyter_nbextensions_configurator jupyter-server-proxy && \
+    pip install --no-cache jupyter_nbextensions_configurator \
+        git+https://github.com/NII-cloud-operation/Jupyter-LC_nblineage.git@feature/lab \
+        git+https://github.com/NII-cloud-operation/Jupyter-LC_notebook_diff.git@feature/lab \
+        git+https://github.com/NII-cloud-operation/Jupyter-LC_index.git@feature/lab \
+        jupyter-server-proxy && \
     jupyter server extension enable --sys-prefix jupyter_server_proxy && \
     jupyter labextension develop /tmp/nbsearch --overwrite && \
-    jupyter server extension enable nbsearch
+    jupyter server extension enable nbsearch && \
+    jupyter labextension enable nbsearch && \
+    jupyter labextension enable lc_notebook_diff && \
+    jupyter labextension enable lc_index
+
 RUN mkdir -p /usr/local/bin/before-notebook.d && \
-    cp /tmp/nbsearch/example/*.sh /usr/local/bin/before-notebook.d/ && \
+    cp /tmp/nbsearch/example/00-add-config.sh /usr/local/bin/before-notebook.d/ && \
+    cp /tmp/nbsearch/example/99-run-supervisor.sh /usr/local/bin/before-notebook.d/ && \
     chmod +x /usr/local/bin/before-notebook.d/*.sh && \
     cp /tmp/nbsearch/example/update-index /usr/local/bin/ && \
     chmod +x /usr/local/bin/update-index && \
     mkdir -p /opt/nbsearch/ && \
-    cp -fr /tmp/nbsearch/solr /opt/nbsearch/
+    cp -fr /tmp/nbsearch/solr /opt/nbsearch/ && \
+    mkdir -p /jupyter_notebook_config.d && chown jovyan:users /jupyter_notebook_config.d
 
 # Boot scripts to perform /usr/local/bin/before-notebook.d/* on JupyterHub
 RUN mkdir -p /opt/nbsearch/original/bin/ && \
@@ -54,30 +64,32 @@ RUN mkdir -p /opt/nbsearch/original/bin/ && \
     cp /tmp/nbsearch/example/jupyter-notebook /opt/conda/bin/ && \
     cp /tmp/nbsearch/example/jupyter-lab /opt/conda/bin/ && \
     cp /tmp/nbsearch/example/run-hook.sh /opt/nbsearch/bin/ && \
+    cp /tmp/nbsearch/example/build-index.sh /opt/nbsearch/bin/ && \
     chmod +x /opt/conda/bin/jupyterhub-singleuser /opt/conda/bin/jupyter-notebook /opt/conda/bin/jupyter-lab \
-        /opt/nbsearch/bin/run-hook.sh
+        /opt/nbsearch/bin/*.sh
 
 RUN jupyter nbclassic-extension install --py --sys-prefix nbsearch && \
     jupyter nbclassic-serverextension enable --py --sys-prefix nbsearch && \
     jupyter nbclassic-extension enable --py --sys-prefix nbsearch && \
-    jupyter nbclassic-extension enable --py --sys-prefix lc_notebook_diff
+    jupyter nbclassic-extension enable --py --sys-prefix lc_notebook_diff && \
+    jupyter nblineage quick-setup --sys-prefix
 
 # Configuration for Server Proxy
 RUN cat /tmp/nbsearch/example/jupyter_notebook_config.py >> $CONDA_DIR/etc/jupyter/jupyter_notebook_config.py
 
 USER $NB_UID
 
 RUN mkdir -p /home/$NB_USER/.nbsearch && \
-    cp /tmp/nbsearch/example/config_*.py /home/$NB_USER/.nbsearch/
-
-RUN mkdir /home/$NB_USER/.nbsearch/conf.d && \
+    cp /tmp/nbsearch/example/config_*.py /home/$NB_USER/.nbsearch/ && \
+    mkdir /home/$NB_USER/.nbsearch/conf.d && \
     cp /tmp/nbsearch/example/supervisor.conf /home/$NB_USER/.nbsearch/supervisor.conf && \
-    cp /tmp/nbsearch/example/update-index.lua /home/$NB_USER/.nbsearch/update-index.lua
+    cp /tmp/nbsearch/example/update-index.lua /home/$NB_USER/.nbsearch/update-index.lua && \
+    cp -fr /tmp/nbsearch/example/notebooks/* /home/$NB_USER/ && \
+    cp /tmp/nbsearch/images/* /home/$NB_USER/images/ && \
+    cp /tmp/nbsearch/README.md /home/$NB_USER/
 
 # Create Solr schema
 RUN precreate-core jupyter-notebook /opt/nbsearch/solr/jupyter-notebook/ && \
     precreate-core jupyter-cell /opt/nbsearch/solr/jupyter-cell/
 
-ENV DOCKER_STACKS_JUPYTER_CMD=lab
-
 VOLUME /var/solr /var/minio

README.md

@@ -1,41 +1,65 @@
 # nbsearch
 
-[![Github Actions Status](https://github.com/NII-cloud-operation/nbsearch//workflows/Build/badge.svg)](https://github.com/NII-cloud-operation/nbsearch//actions/workflows/build.yml)[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NII-cloud-operation/nbsearch//main?urlpath=lab)
+[![Release](https://github.com/NII-cloud-operation/nbsearch/actions/workflows/release.yml/badge.svg)](https://github.com/NII-cloud-operation/nbsearch/actions/workflows/release.yml) [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/NII-cloud-operation/nbsearch/feature/lab?urlpath=lab)
 
 nbsearch extension provides search capabilities for Jupyter Notebooks, which you created. It supports search by MEME in addition to search by keywords and modified times like a search engine. Therefore, users can easily find cells of the same origin in sticky notes added by sidestickies.
 
+## Try it out on mybinder.org
+
+You can try out the extension on mybinder.org by clicking the Binder badge above, and refer to the [Usage](#usage) section for more information.
+
+The following software is installed in this environment.
+
+- Services
+  - JupyterLab
+  - Jupyter Notebook 7
+  - [Apache Solr](https://solr.apache.org/)
+  - [MinIO](https://min.io/)
+
+- Extensions
+  - nbsearch
+  - [nblineage](https://github.com/NII-cloud-operation/Jupyter-LC_nblineage)
+  - [lc_notebook_diff](https://github.com/NII-cloud-operation/Jupyter-LC_notebook_diff)
+
+If you create a Notebook file in this environment, it will be automatically indexed in Solr and you will be able to search for it using the Search. Please refer to the [Usage](#usage) section for more information.
+
+> **Note**: It may take some time for Apache Solr and MinIO to start up. If your search fails, please wait a while and try again.
+
 ## Requirements
 
 - JupyterLab >= 4.0.0
+- Jupyter Notebook >= 7.0.0
 
 ## Install
 
 To install the extension, execute:
 
-*TBD*
-
 ```bash
 pip install git+https://github.com/NII-cloud-operation/nbsearch
 ```
 
 To use nbsearch extension, you will also need to install and enable. You can use Jupyter subcommand:
 
-*TBD*
-
 ```
-jupyter nbextension install --py nbsearch
-jupyter serverextension enable --py nbsearch
-jupyter nbextension enable --py nbsearch
+jupyter server extension enable nbsearch
+jupyter labextension enable nbsearch
+
+# If you want to use the extension with the classic notebook,
+# you need to install and enable the nbclassic notebook extension.
+jupyter nbclassic-extension install --py --sys-prefix nbsearch
+jupyter nbclassic-serverextension enable --py --sys-prefix nbsearch
+jupyter nbclassic-extension enable --py --sys-prefix nbsearch
 ```
 
 To compare multiple Notebooks, you need to install [Jupyter-LC_notebook_diff](https://github.com/NII-cloud-operation/Jupyter-LC_notebook_diff), as shown below.
 
-*TBD*
-
 ```
-pip install git+https://github.com/NII-cloud-operation/Jupyter-LC_notebook_diff
-jupyter nbextension install --py lc_notebook_diff
-jupyter nbextension enable --py lc_notebook_diff
+pip install git+https://github.com/NII-cloud-operation/Jupyter-LC_notebook_diff.git@feature/lab
+jupyter labextension enable lc_notebook_diff
+
+# If you want to use the extension with the classic notebook,
+# you need to install and enable the nbclassic notebook extension.
+jupyter nbclassic-extension enable --py --sys-prefix lc_notebook_diff
 ```
 
 then restart Jupyter notebook.

example/00-add-config.sh

@@ -1,7 +1,11 @@
 #!/bin/bash
 
+set -xe
+
+TARGET_CONFIG_DIR=/jupyter_notebook_config.d
+
 if [[ -f /home/$NB_USER/.nbsearch/config_local.py ]] ; then
-    cat /home/$NB_USER/.nbsearch/config_local.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py
+    cp /home/$NB_USER/.nbsearch/config_local.py ${TARGET_CONFIG_DIR}/nbsearch-config.py
 else
-    cat /home/$NB_USER/.nbsearch/config_base.py >> /home/$NB_USER/.jupyter/jupyter_notebook_config.py
+    cp /home/$NB_USER/.nbsearch/config_base.py ${TARGET_CONFIG_DIR}/nbsearch-config.py
 fi

example/99-run-supervisor.sh

@@ -5,17 +5,19 @@ set -xe
 # For Solr
 supervisord -c /home/jovyan/.nbsearch/supervisor.conf
 
-if [[ ! -f /home/$NB_USER/.nbsearch/config_local.py ]] ; then
-    while ! nc -z localhost 8983; do
-      sleep 0.5
-    done
-    while ! nc -z localhost 9000; do
-      sleep 0.5
-    done
-    while ! curl http://localhost:8983/solr/jupyter-cell/admin/ping | grep '"status":"OK"'; do
-      sleep 0.5
-    done
-    jupyter nbsearch update-index --debug /home/$NB_USER/.jupyter/jupyter_notebook_config.py local
+if [ ! -z "$WAIT_FOR_SOLR_READY" ]; then
+    if [[ ! -f /home/$NB_USER/.nbsearch/config_local.py ]] ; then
+        while ! nc -z localhost 8983; do
+          sleep 0.5
+        done
+        while ! nc -z localhost 9000; do
+          sleep 0.5
+        done
+        while ! curl http://localhost:8983/solr/jupyter-cell/admin/ping | grep '"status":"OK"'; do
+          sleep 0.5
+        done
+        jupyter nbsearch update-index --debug $CONDA_DIR/etc/jupyter/jupyter_notebook_config.py local
+    fi
 fi
 
 export SUPERVISOR_INITIALIZED=1

example/build-index.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+set -xe
+
+if [[ ! -f /home/$NB_USER/.nbsearch/config_local.py ]] ; then
+    while ! nc -z localhost 8983; do
+        sleep 0.5
+    done
+    while ! nc -z localhost 9000; do
+        sleep 0.5
+    done
+    while ! curl http://localhost:8983/solr/jupyter-cell/admin/ping | grep '"status":"OK"'; do
+        sleep 0.5
+    done
+    jupyter nbsearch update-index --debug $CONDA_DIR/etc/jupyter/jupyter_notebook_config.py local
+fi

example/jupyter_notebook_config.py

@@ -1,4 +1,5 @@
 # Solr
+import os
 import tempfile
 
 def _run_solr_proxy(port):
@@ -25,3 +26,13 @@ def _run_solr_proxy(port):
     'timeout': 30,
   }
 }
+
+# load additional config files
+additional_config_path = os.environ.get('JUPYTER_ADDITIONAL_CONFIG_PATH',
+                                        '/jupyter_notebook_config.d')
+if os.path.exists(additional_config_path):
+    for filename in sorted(os.listdir(additional_config_path)):
+        _, ext = os.path.splitext(filename)
+        if ext.lower() != '.py':
+            continue
+        load_subconfig(os.path.join(additional_config_path, filename))