From fa401226cbc4bd8a0b25ba968244a85aaf8a9cc2 Mon Sep 17 00:00:00 2001
From: Emmanuel Bruno <emmanuel.bruno@univ-tln.fr>
Date: Tue, 18 Apr 2023 16:07:33 +0200
Subject: [PATCH] moves to postgresql package and entrypoint.
---
Artefacts/apt_packages | 4 +++-
Dockerfile | 19 +++++++++----------
entrypoint.sh | 15 +++++++++++++++
initDB.sh | 5 -----
run.sh | 11 +++++------
5 files changed, 32 insertions(+), 22 deletions(-)
create mode 100755 entrypoint.sh
delete mode 100755 initDB.sh
diff --git a/Artefacts/apt_packages b/Artefacts/apt_packages
index 4351315..5ec23d1 100644
--- a/Artefacts/apt_packages
+++ b/Artefacts/apt_packages
@@ -5,5 +5,7 @@ inkscape
iputils-ping
net-tools
postgresql-client
+postgresql
procps
-tree
\ No newline at end of file
+tree
+rsync
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
index 6e4fabe..8634023 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -2,27 +2,26 @@ FROM brunoe/jupyter-base:develop
USER root
+COPY Artefacts/apt_packages /tmp/apt_packages
+
RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
apt-get update && \
apt-get install -qq --yes --no-install-recommends \
$(cat /tmp/apt_packages) && \
- rm -rf /var/lib/apt/lists/*
+ chown jovyan /var/run/postgresql/ && \
+ rm -rf /var/lib/apt/lists/*
# Postgresql python library
# SQL support for ipython and PlantUML
RUN conda install --quiet --yes psycopg2 && \
- conda install -y -c conda-forge postgresql pgspecial && \
- conda clean -tipy && \
- pip install ipython-sql iplantuml mocodo && \
+ conda clean -tipy && \
+ pip install pgspecial ipython-sql iplantuml mocodo && \
fix-permissions "${CONDA_DIR}" && \
fix-permissions "/home/${NB_USER}"
-ENV PGDATA=/home/jovyan/work/pgdata
-
-COPY initDB.sh /usr/local/bin/before-notebook.d/
-
-#RUN ipython profile create && \
-# sed -i -e '/c.InteractiveShellApp.extensions = / s/= [^\]]*/= ["mocodo_magic","sql"]/' -e 's/# \(c.InteractiveShellApp.extensions\)/\1/' ~/.ipython/profile_default/ipython_config.py
+COPY ./entrypoint.sh /
+RUN chmod +x /entrypoint.sh
# Switch back to jovyan to avoid accidental container runs as root
USER $NB_UID
+ENTRYPOINT ["/entrypoint.sh"]
\ No newline at end of file
diff --git a/entrypoint.sh b/entrypoint.sh
new file mode 100755
index 0000000..ab0841f
--- /dev/null
+++ b/entrypoint.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+set -e
+
+PGDATA=${PGDATA:-/home/jovyan/srv/postgresql}
+DB_NAME=DEMO_DB
+PG_PATH=$(echo /usr/lib/postgresql/*/bin/)
+
+
+rm -rf $PGDATA/$DB_NAME
+sudo -u jovyan $PG_PATH/initdb -D $PGDATA/$DB_NAME --auth-host=trust --encoding=UTF8
+chown -R jovyan:users /var/run/postgresql
+sudo -u jovyan $PG_PATH/pg_ctl -D $PGDATA/$DB_NAME -l $PGDATA/../$DB_NAME.log start
+sudo -u jovyan createdb --owner=jovyan jovyandb
+
+exec "$@"
diff --git a/initDB.sh b/initDB.sh
deleted file mode 100755
index 08ffbf6..0000000
--- a/initDB.sh
+++ /dev/null
@@ -1,5 +0,0 @@
-DB_NAME=DEMO_DB
-rm -rf $PGDATA/$DB_NAME
-sudo -u jovyan initdb -D $PGDATA/$DB_NAME
-sudo -u jovyan pg_ctl -D $PGDATA/$DB_NAME -l $PGDATA/../$DB_NAME.log start
-sudo -u jovyan createdb --owner=jovyan jovyandb
\ No newline at end of file
diff --git a/run.sh b/run.sh
index 58704a4..039f285 100755
--- a/run.sh
+++ b/run.sh
@@ -1,8 +1,7 @@
#!/usr/bin/env bash
-WORKDIR=$HOME/JUPYTER_WORK_DIR
-
-echo brunoe/${PWD##*/}:$(git rev-parse --abbrev-ref HEAD)
+WORKDIR=$HOME/JUPYTER_WORK
+IMAGE_REPO=brunoe
docker run --rm -it \
--user root \
@@ -10,6 +9,6 @@ docker run --rm -it \
--volume $WORKDIR:/home/jovyan/work \
--publish 8888:8888 \
--env NB_UID=$UID \
- brunoe/${PWD##*/}:$(git rev-parse --abbrev-ref HEAD) $@
-# --env CHOWN_HOME_OPTS='-R' --env CHOWN_HOME=yes \
-
\ No newline at end of file
+ ${IMAGE_REPO}/${PWD##*/}:$(git rev-parse --abbrev-ref HEAD) start-notebook.sh
+
+# start-notebook.sh --notebook-dir=/home/jovyan/notebooks/
\ No newline at end of file
--
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