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hardcopy instead of symlink of build files

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This commit is contained in:
Christoph Schranz 2020-02-22 15:33:19 +01:00
parent 42f22e1630
commit d4b4e66228
6 changed files with 277 additions and 13 deletions
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15
generate_Dockerfile.sh
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@ -15,7 +15,7 @@ cd $STACKS_DIR && git pull && cd -
# Write the contents into the DOCKERFILE and start with the header # Write the contents into the DOCKERFILE and start with the header
cat src/Dockerfile.header > $DOCKERFILE cat src/Dockerfile.header > $DOCKERFILE
cp src/jupyter_notebook_config.json .build/ cp src/jupyter_notebook_config.json .build/
ln -sf .build/jupyter_notebook_config.json jupyter_notebook_config.json cp src/jupyter_notebook_config.json .
echo " echo "
############################################################################ ############################################################################
@ -24,19 +24,18 @@ echo "
" >> $DOCKERFILE " >> $DOCKERFILE
cat $STACKS_DIR/base-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE cat $STACKS_DIR/base-notebook/Dockerfile | grep -v BASE_CONTAINER >> $DOCKERFILE
# copy files that are used during the build # copy files that are used during the build in two directories:
cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .build/ cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .build/
cp $STACKS_DIR/base-notebook/fix-permissions .build/ cp $STACKS_DIR/base-notebook/fix-permissions .build/
cp $STACKS_DIR/base-notebook/start.sh .build/ cp $STACKS_DIR/base-notebook/start.sh .build/
cp $STACKS_DIR/base-notebook/start-notebook.sh .build/ cp $STACKS_DIR/base-notebook/start-notebook.sh .build/
cp $STACKS_DIR/base-notebook/start-singleuser.sh .build/ cp $STACKS_DIR/base-notebook/start-singleuser.sh .build/
# create softlinks for files used during the build cp $STACKS_DIR/base-notebook/jupyter_notebook_config.py .
ln -sf .build/jupyter_notebook_config.py jupyter_notebook_config.py cp $STACKS_DIR/base-notebook/fix-permissions .
ln -sf .build/fix-permissions fix-permissions cp $STACKS_DIR/base-notebook/start.sh .
ln -sf .build/start.sh start.sh cp $STACKS_DIR/base-notebook/start-notebook.sh .
ln -sf .build/start-notebook.sh start-notebook.sh cp $STACKS_DIR/base-notebook/start-singleuser.sh .
ln -sf .build/start-singleuser.sh start-singleuser.sh
echo " echo "
############################################################################ ############################################################################

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jupyter_notebook_config.json
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.build/jupyter_notebook_config.json

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jupyter_notebook_config.json Normal file
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@ -0,0 +1,6 @@
{
"NotebookApp": {
"password": "sha1:e49e73b0eb0e:32edae7a5fd119045e699a0bd04f90819ca90cd6"
}
}

1
jupyter_notebook_config.py
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.build/jupyter_notebook_config.py

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jupyter_notebook_config.py Normal file
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# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
from jupyter_core.paths import jupyter_data_dir
import subprocess
import os
import errno
import stat
c = get_config()
c.NotebookApp.ip = '0.0.0.0'
c.NotebookApp.port = 8888
c.NotebookApp.open_browser = False
# https://github.com/jupyter/notebook/issues/3130
c.FileContentsManager.delete_to_trash = False
# Generate a self-signed certificate
if 'GEN_CERT' in os.environ:
dir_name = jupyter_data_dir()
pem_file = os.path.join(dir_name, 'notebook.pem')
try:
os.makedirs(dir_name)
except OSError as exc: # Python >2.5
if exc.errno == errno.EEXIST and os.path.isdir(dir_name):
pass
else:
raise
# Generate an openssl.cnf file to set the distinguished name
cnf_file = os.path.join(os.getenv('CONDA_DIR', '/usr/lib'), 'ssl', 'openssl.cnf')
if not os.path.isfile(cnf_file):
with open(cnf_file, 'w') as fh:
fh.write('''\
[req]
distinguished_name = req_distinguished_name
[req_distinguished_name]
''')
# Generate a certificate if one doesn't exist on disk
subprocess.check_call(['openssl', 'req', '-new',
'-newkey', 'rsa:2048',
'-days', '365',
'-nodes', '-x509',
'-subj', '/C=XX/ST=XX/L=XX/O=generated/CN=generated',
'-keyout', pem_file,
'-out', pem_file])
# Restrict access to the file
os.chmod(pem_file, stat.S_IRUSR | stat.S_IWUSR)
c.NotebookApp.certfile = pem_file
# Change default umask for all subprocesses of the notebook server if set in
# the environment
if 'NB_UMASK' in os.environ:
os.umask(int(os.environ['NB_UMASK'], 8))

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start-notebook.sh
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.build/start-notebook.sh

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start-notebook.sh Normal file
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#!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
wrapper=""
if [[ "${RESTARTABLE}" == "yes" ]]; then
wrapper="run-one-constantly"
fi
if [[ ! -z "${JUPYTERHUB_API_TOKEN}" ]]; then
# launched by JupyterHub, use single-user entrypoint
exec /usr/local/bin/start-singleuser.sh "$@"
elif [[ ! -z "${JUPYTER_ENABLE_LAB}" ]]; then
. /usr/local/bin/start.sh $wrapper jupyter lab "$@"
else
. /usr/local/bin/start.sh $wrapper jupyter notebook "$@"
fi

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start-singleuser.sh
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.build/start-singleuser.sh

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start-singleuser.sh Normal file
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#!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# set default ip to 0.0.0.0
if [[ "$NOTEBOOK_ARGS $@" != *"--ip="* ]]; then
NOTEBOOK_ARGS="--ip=0.0.0.0 $NOTEBOOK_ARGS"
fi
# handle some deprecated environment variables
# from DockerSpawner < 0.8.
# These won't be passed from DockerSpawner 0.9,
# so avoid specifying --arg=empty-string
if [ ! -z "$NOTEBOOK_DIR" ]; then
NOTEBOOK_ARGS="--notebook-dir='$NOTEBOOK_DIR' $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_PORT" ]; then
NOTEBOOK_ARGS="--port=$JPY_PORT $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_USER" ]; then
NOTEBOOK_ARGS="--user=$JPY_USER $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_COOKIE_NAME" ]; then
NOTEBOOK_ARGS="--cookie-name=$JPY_COOKIE_NAME $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_BASE_URL" ]; then
NOTEBOOK_ARGS="--base-url=$JPY_BASE_URL $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_HUB_PREFIX" ]; then
NOTEBOOK_ARGS="--hub-prefix=$JPY_HUB_PREFIX $NOTEBOOK_ARGS"
fi
if [ ! -z "$JPY_HUB_API_URL" ]; then
NOTEBOOK_ARGS="--hub-api-url=$JPY_HUB_API_URL $NOTEBOOK_ARGS"
fi
if [ ! -z "$JUPYTER_ENABLE_LAB" ]; then
NOTEBOOK_BIN="jupyter labhub"
else
NOTEBOOK_BIN="jupyterhub-singleuser"
fi
. /usr/local/bin/start.sh $NOTEBOOK_BIN $NOTEBOOK_ARGS "$@"

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start.sh
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.build/start.sh

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start.sh Normal file
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#!/bin/bash
# Copyright (c) Jupyter Development Team.
# Distributed under the terms of the Modified BSD License.
set -e
# Exec the specified command or fall back on bash
if [ $# -eq 0 ]; then
cmd=( "bash" )
else
cmd=( "$@" )
fi
run-hooks () {
# Source scripts or run executable files in a directory
if [[ ! -d "$1" ]] ; then
return
fi
echo "$0: running hooks in $1"
for f in "$1/"*; do
case "$f" in
*.sh)
echo "$0: running $f"
source "$f"
;;
*)
if [[ -x "$f" ]] ; then
echo "$0: running $f"
"$f"
else
echo "$0: ignoring $f"
fi
;;
esac
done
echo "$0: done running hooks in $1"
}
run-hooks /usr/local/bin/start-notebook.d
# Handle special flags if we're root
if [ $(id -u) == 0 ] ; then
# Only attempt to change the jovyan username if it exists
if id jovyan &> /dev/null ; then
echo "Set username to: $NB_USER"
usermod -d /home/$NB_USER -l $NB_USER jovyan
fi
# Handle case where provisioned storage does not have the correct permissions by default
# Ex: default NFS/EFS (no auto-uid/gid)
if [[ "$CHOWN_HOME" == "1" || "$CHOWN_HOME" == 'yes' ]]; then
echo "Changing ownership of /home/$NB_USER to $NB_UID:$NB_GID with options '${CHOWN_HOME_OPTS}'"
chown $CHOWN_HOME_OPTS $NB_UID:$NB_GID /home/$NB_USER
fi
if [ ! -z "$CHOWN_EXTRA" ]; then
for extra_dir in $(echo $CHOWN_EXTRA | tr ',' ' '); do
echo "Changing ownership of ${extra_dir} to $NB_UID:$NB_GID with options '${CHOWN_EXTRA_OPTS}'"
chown $CHOWN_EXTRA_OPTS $NB_UID:$NB_GID $extra_dir
done
fi
# handle home and working directory if the username changed
if [[ "$NB_USER" != "jovyan" ]]; then
# changing username, make sure homedir exists
# (it could be mounted, and we shouldn't create it if it already exists)
if [[ ! -e "/home/$NB_USER" ]]; then
echo "Relocating home dir to /home/$NB_USER"
mv /home/jovyan "/home/$NB_USER" || ln -s /home/jovyan "/home/$NB_USER"
fi
# if workdir is in /home/jovyan, cd to /home/$NB_USER
if [[ "$PWD/" == "/home/jovyan/"* ]]; then
newcwd="/home/$NB_USER/${PWD:13}"
echo "Setting CWD to $newcwd"
cd "$newcwd"
fi
fi
# Change UID:GID of NB_USER to NB_UID:NB_GID if it does not match
if [ "$NB_UID" != $(id -u $NB_USER) ] || [ "$NB_GID" != $(id -g $NB_USER) ]; then
echo "Set user $NB_USER UID:GID to: $NB_UID:$NB_GID"
if [ "$NB_GID" != $(id -g $NB_USER) ]; then
groupadd -g $NB_GID -o ${NB_GROUP:-${NB_USER}}
fi
userdel $NB_USER
useradd --home /home/$NB_USER -u $NB_UID -g $NB_GID -G 100 -l $NB_USER
fi
# Enable sudo if requested
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
echo "Granting $NB_USER sudo access and appending $CONDA_DIR/bin to sudo PATH"
echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/notebook
fi
# Add $CONDA_DIR/bin to sudo secure_path
sed -r "s#Defaults\s+secure_path=\"([^\"]+)\"#Defaults secure_path=\"\1:$CONDA_DIR/bin\"#" /etc/sudoers | grep secure_path > /etc/sudoers.d/path
# Exec the command as NB_USER with the PATH and the rest of
# the environment preserved
run-hooks /usr/local/bin/before-notebook.d
echo "Executing the command: ${cmd[@]}"
exec sudo -E -H -u $NB_USER PATH=$PATH XDG_CACHE_HOME=/home/$NB_USER/.cache PYTHONPATH=${PYTHONPATH:-} "${cmd[@]}"
else
if [[ "$NB_UID" == "$(id -u jovyan)" && "$NB_GID" == "$(id -g jovyan)" ]]; then
# User is not attempting to override user/group via environment
# variables, but they could still have overridden the uid/gid that
# container runs as. Check that the user has an entry in the passwd
# file and if not add an entry.
STATUS=0 && whoami &> /dev/null || STATUS=$? && true
if [[ "$STATUS" != "0" ]]; then
if [[ -w /etc/passwd ]]; then
echo "Adding passwd file entry for $(id -u)"
cat /etc/passwd | sed -e "s/^jovyan:/nayvoj:/" > /tmp/passwd
echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
cat /tmp/passwd > /etc/passwd
rm /tmp/passwd
else
echo 'Container must be run with group "root" to update passwd file'
fi
fi
# Warn if the user isn't going to be able to write files to $HOME.
if [[ ! -w /home/jovyan ]]; then
echo 'Container must be run with group "users" to update files'
fi
else
# Warn if looks like user want to override uid/gid but hasn't
# run the container as root.
if [[ ! -z "$NB_UID" && "$NB_UID" != "$(id -u)" ]]; then
echo 'Container must be run as root to set $NB_UID'
fi
if [[ ! -z "$NB_GID" && "$NB_GID" != "$(id -g)" ]]; then
echo 'Container must be run as root to set $NB_GID'
fi
fi
# Warn if looks like user want to run in sudo mode but hasn't run
# the container as root.
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
echo 'Container must be run as root to grant sudo permissions'
fi
# Execute the command
run-hooks /usr/local/bin/before-notebook.d
echo "Executing the command: ${cmd[@]}"
exec "${cmd[@]}"
fi