hardcopy instead of symlink of build files
This commit is contained in:
Christoph Schranz
parent
42f22e1630
commit
d4b4e66228
@ -15,7 +15,7 @@ cd $STACKS_DIR && git pull && cd -
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# Write the contents into the DOCKERFILE and start with the header
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cat src/Dockerfile.header > $DOCKERFILE
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cp src/jupyter_notebook_config.json .build/
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ln -sf .build/jupyter_notebook_config.json jupyter_notebook_config.json
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cp src/jupyter_notebook_config.json .
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echo "
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############################################################################
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@ -24,19 +24,18 @@ echo "
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" >> $DOCKERFILE
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cat $STACKS_DIR/base-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
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# copy files that are used during the build
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# copy files that are used during the build in two directories:
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cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .build/
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cp $STACKS_DIR/base-notebook/fix-permissions .build/
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cp $STACKS_DIR/base-notebook/start.sh .build/
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cp $STACKS_DIR/base-notebook/start-notebook.sh .build/
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cp $STACKS_DIR/base-notebook/start-singleuser.sh .build/
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# create softlinks for files used during the build
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ln -sf .build/jupyter_notebook_config.py jupyter_notebook_config.py
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ln -sf .build/fix-permissions fix-permissions
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ln -sf .build/start.sh start.sh
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ln -sf .build/start-notebook.sh start-notebook.sh
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ln -sf .build/start-singleuser.sh start-singleuser.sh
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cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .
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cp $STACKS_DIR/base-notebook/fix-permissions .
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cp $STACKS_DIR/base-notebook/start.sh .
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cp $STACKS_DIR/base-notebook/start-notebook.sh .
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cp $STACKS_DIR/base-notebook/start-singleuser.sh .
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echo "
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############################################################################
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@ -1 +0,0 @@
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.build/jupyter_notebook_config.json
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6
jupyter_notebook_config.json
Normal file
6
jupyter_notebook_config.json
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@ -0,0 +1,6 @@
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{
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"NotebookApp": {
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"password": "sha1:e49e73b0eb0e:32edae7a5fd119045e699a0bd04f90819ca90cd6"
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}
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}
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@ -1 +0,0 @@
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.build/jupyter_notebook_config.py
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55
jupyter_notebook_config.py
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55
jupyter_notebook_config.py
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@ -0,0 +1,55 @@
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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from jupyter_core.paths import jupyter_data_dir
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import subprocess
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import os
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import errno
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import stat
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c = get_config()
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c.NotebookApp.ip = '0.0.0.0'
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c.NotebookApp.port = 8888
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c.NotebookApp.open_browser = False
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# https://github.com/jupyter/notebook/issues/3130
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c.FileContentsManager.delete_to_trash = False
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# Generate a self-signed certificate
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if 'GEN_CERT' in os.environ:
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dir_name = jupyter_data_dir()
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pem_file = os.path.join(dir_name, 'notebook.pem')
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try:
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os.makedirs(dir_name)
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except OSError as exc: # Python >2.5
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if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
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pass
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else:
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raise
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# Generate an openssl.cnf file to set the distinguished name
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cnf_file = os.path.join(os.getenv('CONDA_DIR', '/usr/lib'), 'ssl', 'openssl.cnf')
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if not os.path.isfile(cnf_file):
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with open(cnf_file, 'w') as fh:
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fh.write('''\
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[req]
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distinguished_name = req_distinguished_name
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[req_distinguished_name]
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''')
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# Generate a certificate if one doesn't exist on disk
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subprocess.check_call(['openssl', 'req', '-new',
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'-newkey', 'rsa:2048',
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'-days', '365',
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'-nodes', '-x509',
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'-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
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'-keyout', pem_file,
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'-out', pem_file])
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# Restrict access to the file
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os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
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c.NotebookApp.certfile = pem_file
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# Change default umask for all subprocesses of the notebook server if set in
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# the environment
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if 'NB_UMASK' in os.environ:
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os.umask(int(os.environ['NB_UMASK'], 8))
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@ -1 +0,0 @@
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.build/start-notebook.sh
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19
start-notebook.sh
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19
start-notebook.sh
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#!/bin/bash
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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set -e
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wrapper=""
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if [[ "${RESTARTABLE}" == "yes" ]]; then
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wrapper="run-one-constantly"
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fi
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if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
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# launched by JupyterHub, use single-user entrypoint
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exec /usr/local/bin/start-singleuser.sh "$@"
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elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
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. /usr/local/bin/start.sh $wrapper jupyter lab "$@"
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else
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. /usr/local/bin/start.sh $wrapper jupyter notebook "$@"
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fi
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@ -1 +0,0 @@
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.build/start-singleuser.sh
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43
start-singleuser.sh
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43
start-singleuser.sh
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@ -0,0 +1,43 @@
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#!/bin/bash
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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set -e
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# set default ip to 0.0.0.0
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if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
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NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
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fi
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# handle some deprecated environment variables
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# from DockerSpawner < 0.8.
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# These won't be passed from DockerSpawner 0.9,
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# so avoid specifying --arg=empty-string
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if [ ! -z "$NOTEBOOK_DIR" ]; then
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NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_PORT" ]; then
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NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_USER" ]; then
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NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_COOKIE_NAME" ]; then
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NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_BASE_URL" ]; then
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NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_HUB_PREFIX" ]; then
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NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JPY_HUB_API_URL" ]; then
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NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
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fi
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if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
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NOTEBOOK_BIN="jupyter labhub"
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else
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NOTEBOOK_BIN="jupyterhub-singleuser"
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fi
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. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@"
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147
start.sh
Normal file
147
start.sh
Normal file
@ -0,0 +1,147 @@
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#!/bin/bash
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# Copyright (c) Jupyter Development Team.
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# Distributed under the terms of the Modified BSD License.
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set -e
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# Exec the specified command or fall back on bash
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if [ $# -eq 0 ]; then
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cmd=( "bash" )
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else
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cmd=( "$@" )
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fi
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run-hooks () {
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# Source scripts or run executable files in a directory
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if [[ ! -d "$1" ]] ; then
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return
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fi
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echo "$0: running hooks in $1"
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for f in "$1/"*; do
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case "$f" in
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*.sh)
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echo "$0: running $f"
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source "$f"
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;;
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*)
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if [[ -x "$f" ]] ; then
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echo "$0: running $f"
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"$f"
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else
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echo "$0: ignoring $f"
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fi
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;;
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esac
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done
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echo "$0: done running hooks in $1"
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}
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run-hooks /usr/local/bin/start-notebook.d
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# Handle special flags if we're root
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if [ $(id -u) == 0 ] ; then
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# Only attempt to change the jovyan username if it exists
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if id jovyan &> /dev/null ; then
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echo "Set username to: $NB_USER"
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usermod -d /home/$NB_USER -l $NB_USER jovyan
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fi
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# Handle case where provisioned storage does not have the correct permissions by default
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# Ex: default NFS/EFS (no auto-uid/gid)
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if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then
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echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'"
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chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER
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fi
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if [ ! -z "$CHOWN_EXTRA" ]; then
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for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do
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echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'"
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chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir
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done
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fi
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# handle home and working directory if the username changed
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if [[ "$NB_USER" != "jovyan" ]]; then
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# changing username, make sure homedir exists
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# (it could be mounted, and we shouldn't create it if it already exists)
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if [[ ! -e "/home/$NB_USER" ]]; then
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echo "Relocating home dir to /home/$NB_USER"
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mv /home/jovyan "/home/$NB_USER" || ln -s /home/jovyan "/home/$NB_USER"
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fi
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# if workdir is in /home/jovyan, cd to /home/$NB_USER
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if [[ "$PWD/" == "/home/jovyan/"* ]]; then
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newcwd="/home/$NB_USER/${PWD:13}"
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echo "Setting CWD to $newcwd"
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cd "$newcwd"
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fi
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fi
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# Change UID:GID of NB_USER to NB_UID:NB_GID if it does not match
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if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then
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echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID"
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if [ "$NB_GID" != $(id -g $NB_USER) ]; then
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groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
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fi
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userdel $NB_USER
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useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER
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fi
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# Enable sudo if requested
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if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
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echo "Granting $NB_USER sudo access and appending $CONDA_DIR/bin to sudo PATH"
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echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook
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fi
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# Add $CONDA_DIR/bin to sudo secure_path
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sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
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# Exec the command as NB_USER with the PATH and the rest of
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# the environment preserved
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run-hooks /usr/local/bin/before-notebook.d
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echo "Executing the command: ${cmd[@]}"
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exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
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else
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if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then
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# User is not attempting to override user/group via environment
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# variables, but they could still have overridden the uid/gid that
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# container runs as. Check that the user has an entry in the passwd
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# file and if not add an entry.
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STATUS=0 && whoami &> /dev/null || STATUS=$? && true
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if [[ "$STATUS" != "0" ]]; then
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if [[ -w /etc/passwd ]]; then
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echo "Adding passwd file entry for $(id -u)"
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cat /etc/passwd | sed -e "s/^jovyan:/nayvoj:/" > /tmp/passwd
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echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
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cat /tmp/passwd > /etc/passwd
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rm /tmp/passwd
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else
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echo 'Container must be run with group "root" to update passwd file'
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fi
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fi
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# Warn if the user isn't going to be able to write files to $HOME.
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if [[ ! -w /home/jovyan ]]; then
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echo 'Container must be run with group "users" to update files'
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fi
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else
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# Warn if looks like user want to override uid/gid but hasn't
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# run the container as root.
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if [[ ! -z "$NB_UID" && "$NB_UID" != "$(id -u)" ]]; then
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echo 'Container must be run as root to set $NB_UID'
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fi
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if [[ ! -z "$NB_GID" && "$NB_GID" != "$(id -g)" ]]; then
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echo 'Container must be run as root to set $NB_GID'
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fi
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fi
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# Warn if looks like user want to run in sudo mode but hasn't run
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# the container as root.
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if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
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echo 'Container must be run as root to grant sudo permissions'
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fi
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# Execute the command
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run-hooks /usr/local/bin/before-notebook.d
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echo "Executing the command: ${cmd[@]}"
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exec "${cmd[@]}"
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fi
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