add docker files

previously they have been stored in a separate project: https://gitlab.hzdr.de/model-data-explorer/docker-workspace/

.gitignore

@@ -138,4 +138,13 @@ dmypy.json
 cython_debug/
 .vscode/settings.json
 
-docs/workspace/build
\ No newline at end of file
+# build documentation files
+docs/workspace/build
+
+# docker-related workspace and other files that are cloned during installation
+workspace
+!*/**/workspace
+users_config/
+code-server.env
+!docker/workspace/templates/*.env
+docker/workspace/config/extensions/*.vsix
\ No newline at end of file

Dockerfile

+# syntax=docker/dockerfile:1
+FROM ghcr.io/linuxserver/code-server
+
+ENV PYTHONUNBUFFERED=1
+
+# install necessary libraries using apt-get
+RUN apt-get update && \
+  apt-get install -y \
+    bash-completion vim \
+    graphviz \
+    libpq-dev build-essential \
+    python3-venv python3-dev python3-psycopg2 \
+    python3.8-venv python3.8-dev
+
+# install git-mob
+RUN npm i -g git-mob
+
+COPY docker/workspace/config /config
+COPY docker/workspace/git-user-management /config/git-user-management
+RUN make -C /config/git-user-management install
+
+ADD . /config/workspace_src
+
+EXPOSE 8443

docker-compose.yml

+version: "3.7"
+
+networks:
+  frontend:
+  backend:
+
+volumes:
+  pgdata:
+  thredds-data:
+  thredds-config:
+
+x-op-restart-policy: &restart_policy
+  restart: unless-stopped
+x-mde-pg-env: &pg-env
+  POSTGRES_PASSWORD: "${POSTGRES_PASSWORD:-changeme}"
+  POSTGRES_USER: "${POSTGRES_USER:-django_mde_user}"
+  POSTGRES_DB: "${POSTGRES_DB:-django_mde}"
+
+services:
+  db:
+    image: postgres:13
+    <<: *restart_policy
+    stop_grace_period: "3s"
+    volumes:
+      - "pgdata:/var/lib/postgresql/data"
+    environment: *pg-env
+    networks:
+      - backend
+
+  cache:
+    image: memcached
+    <<: *restart_policy
+    networks:
+      - backend
+
+  code-server:
+    build: "."
+    <<: *restart_policy
+    volumes:
+      - "thredds-data:/config/workspace/thredds/data"
+      - "thredds-config:/config/workspace/thredds/config"
+      - "./workspace:/config/workspace"
+      - "./users_config:/config/users_config"
+    networks:
+      - frontend
+      - backend
+    expose:
+      - "8443"
+    ports:
+      - "${PORT:-8443}:8443"
+    env_file:
+      - code-server.env
+    environment:
+      <<: *pg-env
+      PUID: "${PUID:-1000}"
+      PGID: "${PGID:-1000}"
+      TZ: "${TZ:-Europe/Berlin}"
+      DEFAULT_GIT_USER_NAME: "${DEFAULT_GIT_USER_NAME:-}"
+      DEFAULT_GIT_USER_EMAIL: "${DEFAULT_GIT_USER_EMAIL:-}"
+    depends_on:
+      - db
+      - cache

docker/workspace/README.md

+# Model Data Explorer Workspace
+
+Docker-based Workspace for developing the Model Data Explorer
+
+
+Please checkout the docs to learn how to use and install this workspace:
+
+https://model-data-explorer.readthedocs.io/projects/workspace

docker/workspace/config/.bashrc

+# ~/.bashrc: executed by bash(1) for non-login shells.
+# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
+# for examples
+
+# If not running interactively, don't do anything
+case $- in
+    *i*) ;;
+      *) return;;
+esac
+
+# don't put duplicate lines or lines starting with space in the history.
+# See bash(1) for more options
+HISTCONTROL=ignoreboth
+
+# append to the history file, don't overwrite it
+shopt -s histappend
+
+# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
+HISTSIZE=1000
+HISTFILESIZE=2000
+
+# check the window size after each command and, if necessary,
+# update the values of LINES and COLUMNS.
+shopt -s checkwinsize
+
+# If set, the pattern "**" used in a pathname expansion context will
+# match all files and zero or more directories and subdirectories.
+#shopt -s globstar
+
+# make less more friendly for non-text input files, see lesspipe(1)
+[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"
+
+# set variable identifying the chroot you work in (used in the prompt below)
+if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
+    debian_chroot=$(cat /etc/debian_chroot)
+fi
+
+# set a fancy prompt (non-color, unless we know we "want" color)
+case "$TERM" in
+    xterm-color|*-256color) color_prompt=yes;;
+esac
+
+# uncomment for a colored prompt, if the terminal has the capability; turned
+# off by default to not distract the user: the focus in a terminal window
+# should be on the output of commands, not on the prompt
+#force_color_prompt=yes
+
+if [ -n "$force_color_prompt" ]; then
+    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
+	# We have color support; assume it's compliant with Ecma-48
+	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
+	# a case would tend to support setf rather than setaf.)
+	color_prompt=yes
+    else
+	color_prompt=
+    fi
+fi
+
+if [ "$color_prompt" = yes ]; then
+    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\] - \[\e[36m\]\A\[\e[m\] - \[\033[01;34m\]\w\[\033[00m\]\$ '
+else
+    PS1='${debian_chroot:+($debian_chroot)}\u@\h - \A - \w\$ '
+fi
+unset color_prompt force_color_prompt
+
+# If this is an xterm set the title to user@host:dir
+case "$TERM" in
+xterm*|rxvt*)
+    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
+    ;;
+*)
+    ;;
+esac
+
+# enable color support of ls and also add handy aliases
+if [ -x /usr/bin/dircolors ]; then
+    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
+    alias ls='ls --color=auto'
+    #alias dir='dir --color=auto'
+    #alias vdir='vdir --color=auto'
+
+    alias grep='grep --color=auto'
+    alias fgrep='fgrep --color=auto'
+    alias egrep='egrep --color=auto'
+fi
+
+# colored GCC warnings and errors
+#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'
+
+# some more ls aliases
+alias ll='ls -alF'
+alias la='ls -A'
+alias l='ls -CF'
+
+# Add an "alert" alias for long running commands.  Use like so:
+#   sleep 10; alert
+alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'
+
+# Alias definitions.
+# You may want to put all your additions into a separate file like
+# ~/.bash_aliases, instead of adding them here directly.
+# See /usr/share/doc/bash-doc/examples in the bash-doc package.
+
+if [ -f ~/.bash_aliases ]; then
+    . ~/.bash_aliases
+fi
+
+# enable programmable completion features (you don't need to enable
+# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
+# sources /etc/bash.bashrc).
+if ! shopt -oq posix; then
+  if [ -f /usr/share/bash-completion/bash_completion ]; then
+    . /usr/share/bash-completion/bash_completion
+  elif [ -f /etc/bash_completion ]; then
+    . /etc/bash_completion
+  fi
+fi
+
+# add intials of current co-authors
+function git_initials {
+  local initials=$(git mob-print --initials)
+  if [[ -n "${initials}" ]]; then
+    echo " [${initials}]"
+  fi
+}
+
+export PS1="\$(pwd)\$(git_initials) -> "
+
+export GPG_TTY="$(tty || :)"

docker/workspace/config/.inputrc

+"\e[A": history-search-backward
+"\e[B": history-search-forward

docker/workspace/config/custom-cont-init.d/create_workspace.sh

+#!/bin/bash
+# populate the workspace
+#
+# This script clones the workspace repository at https://gitlab.hzdr.de/model-data-explorer/workspace.git
+# and installs it at /config/workspace, including the python virtual
+# environment. Additionally, it starts some static file servers to host the
+# documentation. They are accessible with the browser at
+#
+# /proxy/9001 https://gitlab.hzdr.de/model-data-explorer/model-data-explorer.pages.hzdr.de
+# /proxy/9002 https://gitlab.hzdr.de/model-data-explorer/prototype
+#
+# NOTE: We do not overwrite any existing folder here
+
+set -e
+cd /config/workspace
+
+cp -r /config/workspace_src/. .
+
+if [[ ! -d venv ]]; then
+    echo "**** setting up python ****"
+
+    PYTHON=python3.8 install.sh
+else
+    echo "**** python already setup. skipping ****"
+fi
+
+# build and serve the docs
+source venv/bin/activate
+
+# main repo
+[ ! -d docs/main/build/html ] && sphinx-build docs/main/source docs/main/build/html
+nohup python -m http.server --directory docs/main/build/html 9001 &
+
+# prototype repo
+[ ! -d docs/prototype/build/html ] && sphinx-build docs/prototype/source docs/prototype/build/html
+nohup python -m http.server --directory docs/prototype/build/html 9002 &
+
+chown -R abc: .

docker/workspace/config/custom-cont-init.d/install_extensions.sh

+#!/bin/bash
+
+code-server --extensions-dir /config/extensions --install-extension ms-python.python
+code-server --extensions-dir /config/extensions --install-extension lextudio.restructuredtext
+code-server --extensions-dir /config/extensions --install-extension gitlab.gitlab-workflow
+code-server --extensions-dir /config/extensions --install-extension njpwerner.autodocstring
+
+if [ ! -z "$(ls -A /config/extensions/*.vsix)" ]; then
+  for FNAME in /config/extensions/*.vsix; do
+    code-server --extensions-dir /config/extensions --install-extension ${FNAME}
+  done
+fi

docker/workspace/config/custom-cont-init.d/setup_gitconfig.sh

+#!/bin/bash
+# Configure command line git
+#
+# In this script, we set the global git user.name and user.email, and we add
+# create the .git-coauthors file (if not already existing).
+#
+# We then check for GPG keys in /config/certs and add the corresponding names
+# to the .git-coauthors file.
+#
+# Furthermore we give the user the possibility to specify the global git
+# user.name via the DEFAULT_GIT_USER_NAME environment variable, and the global
+# git user.email via the DEFAULT_GIT_USER_EMAIL environment variable.
+
+set -e
+
+git config --global commit.gpgsign true
+
+if [[ ! -e ~/users_config/.git-coauthors ]]; then
+  mkdir -p ~/users_config
+  echo '{"coauthors": {}}' > ~/users_config/.git-coauthors
+fi
+
+if [[ ! -e ~/users_config/.gnupg ]]; then
+  mkdir -p ~/users_config/.gnupg
+fi
+chmod 700 ~/users_config/.gnupg
+
+ln -sf ~/users_config/.git-coauthors ~/.git-coauthors
+ln -sf ~/users_config/.gnupg ~/.gnupg
+
+git add-coauthors
+
+if [[ ${DEFAULT_GIT_USER_NAME} ]]; then
+    git config --global user.name ${DEFAULT_GIT_USER_NAME}
+fi
+
+if [[ ${DEFAULT_GIT_USER_EMAIL} ]]; then
+    git config --global user.email ${DEFAULT_GIT_USER_EMAIL}
+fi
+
+if [ "${DEFAULT_GIT_USER_NAME}" != "" ] && [ "${DEFAULT_GIT_USER_EMAIL}" != "" ]; then
+    INITIALS=""
+    for NAME in ${DEFAULT_GIT_USER_NAME}; do
+        INITIALS="${INITIALS}${NAME:0:1}"
+    done
+    git add-coauthor ${INITIALS,,} "${DEFAULT_GIT_USER_NAME}" ${DEFAULT_GIT_USER_EMAIL}
+fi
+
+chown -R abc: /config/users_config

docker/workspace/config/data/User/settings.json

+{
+    "python.defaultInterpreterPath": "/config/workspace/venv/bin/python",
+    "python.pythonPath": "/config/workspace/venv/bin/python",
+    "python.terminal.activateEnvInCurrentTerminal": true,
+    "editor.defaultFormatter": "ms-python.python",
+    "files.trimTrailingWhitespace": true,
+    "editor.formatOnType": true,
+    "editor.rulers": [
+        79
+    ],
+    "python.formatting.provider": "black",
+    "python.formatting.blackArgs": [
+        "--line-length",
+        "79"
+    ],
+    "python.formatting.autopep8Path": "/config/workspace/venv/bin/autopep8",
+    "python.formatting.blackPath": "/config/workspace/venv/bin/black",
+    "python.linting.mypyCategorySeverity.note": "Hint",
+    "python.linting.mypyEnabled": true,
+    "python.linting.mypyPath": "/config/workspace/venv/bin/mypy",
+    "python.linting.pylintPath": "/config/workspace/venv/bin/pylint",
+    "python.linting.pycodestylePath": "/config/workspace/venv/bin/pycodestyle",
+    "python.linting.pydocstylePath": "/config/workspace/venv/bin/pydocstyle",
+    "python.linting.flake8Path": "/config/workspace/venv/bin/flake8",
+    "python.linting.flake8Enabled": true,
+    "gitlab.instanceUrl": "https://gitlab.hzdr.de",
+    "restructuredtext.sphinxBuildPath": "/config/workspace/venv/bin/sphinx-build",
+    "restructuredtext.preview.scrollEditorWithPreview": false,
+    "restructuredtext.preview.scrollPreviewWithEditor": false,
+    "restructuredtext.languageServer.disabled": true,
+    "autoDocstring.docstringFormat": "numpy",
+    "autoDocstring.includeExtendedSummary": true,
+    "terminal.integrated.env.linux": {
+        "LC_ALL": "en_US.UTF-8",
+        "LANG": "en_US.UTF-8",
+        "LANGUAGE": "en_US.UTF-8",
+        "DISPLAY": ":0"
+    },
+    "editor.formatOnSave": true,
+    "git.enableCommitSigning": true,
+    "git.enableSmartCommit": true
+}

docker/workspace/git-user-management/Makefile

+# PREFIX is environment variable, but if it is not set, then set default value
+BINDIR = $(DESTDIR)/usr/bin
+COMPLETIONDIR = $(DESTDIR)/etc/bash_completion.d
+
+install:
+	install git-* $(BINDIR)/
+	install -m 644 git_user_management.sh $(COMPLETIONDIR)/
+
+uninstall:
+	rm $(BINDIR)/git-add-user
+	rm $(COMPLETIONDIR)/git_user_management.sh

docker/workspace/git-user-management/git-add-coauthors

+#!/bin/bash
+# Add all GPG UIDs as git-coauthors
+
+set -e
+
+function Help() {
+    cat << EOF
+Add all GPG UIDs as git-coauthors
+
+This command looks up the GPG keys and adds one entry for each key to the
+~/.git-coauthors file.
+
+Call syntax::
+
+    git add-coauthors
+
+
+Syntax: git add-coauthors [-h]
+
+options:
+h     Print this Help.
+EOF
+}
+
+function trim() {
+    local STRING="$*"
+    # remove leading spaces
+    STRING="${STRING#"${STRING%%[![:space:]]*}"}"
+    # remove trailing spaces
+    STRING="${STRING%"${STRING##*[![:space:]]}"}"
+    printf '%s' "$STRING"
+}
+
+while getopts ":h" option; do
+   case $option in
+      h) # display Help
+         Help
+         exit;;
+     \?) # incorrect option
+         echo "Error: Invalid option"
+         exit 1;;
+   esac
+done
+
+
+function get_initials() {
+    local INITIALS
+    local FULLNAME="${1}"
+    local INITIALS=""
+    for NAME in $FULLNAME; do
+        INITIALS="${INITIALS}${NAME:0:1}"
+    done
+    echo ${INITIALS}
+}
+
+
+while IFS= read -r GPG_UID; do
+    EMAIL=`echo "${GPG_UID}" | grep -Po '<\K[^>]+(?=>)'`
+    FULLNAME=`echo "${GPG_UID}" | grep -Po  '.*?(?=\<)'`
+    FULLNAME="`trim ${FULLNAME}`"
+
+    INITIALS=$(get_initials "${FULLNAME}")
+
+    git add-coauthor ${INITIALS,,} "${FULLNAME}" "${EMAIL}"
+done < <(git show-users)

docker/workspace/git-user-management/git-add-user

+#!/bin/bash
+# Convenience command to create a GPG key and add a git co-author
+
+set -e
+
+function Help() {
+    cat << EOF
+Convenience command to create a GPG key and add a git co-author
+
+This command takes a full name and an email as argument and creates a
+GPG key (the user is asked for a passphrase). At the end, this function
+adds the newly created user to ~/.git-coauthors and opens the public
+key using code-server to import it at gitlab.
+
+Call syntax::
+
+    git add-user "Full Name" full.name@example.com
+
+
+Syntax: git add-user [-h] FullName Email
+
+mandatory arguments:
+FullName    The full name of the user
+Email       The email of the user
+
+options:
+h     Print this Help.
+EOF
+}
+
+function get_initials() {
+    local INITIALS
+    local FULLNAME="${1}"
+    local INITIALS=""
+    for NAME in $FULLNAME; do
+        INITIALS="${INITIALS}${NAME:0:1}"
+    done
+    echo ${INITIALS}
+}
+
+while getopts ":h" option; do
+   case $option in
+      h) # display Help
+         Help
+         exit;;
+     \?) # incorrect option
+         echo "Error: Invalid option"
+         exit 1;;
+   esac
+done
+
+FULLNAME="${1}"
+EMAIL="${2}"
+
+if [[ "${FULLNAME}" == "" ]] || [[ "${EMAIL}" == "" ]]; then
+    >&2 echo "Please specify FULLNAME and EMAIL"
+    echo ""
+    Help
+    exit 1
+fi
+
+GPG_UID="${FULLNAME} <${EMAIL}>"
+
+INITIALS=$(get_initials "${FULLNAME}")
+
+gpg --quick-generate-key "${GPG_UID}"
+
+FPR=`git get-user-fpr "${GPG_UID}"`
+
+echo ""
+git add-coauthor ${INITIALS} "${FULLNAME}" "${EMAIL}"
+
+echo ""
+
+git switch-user "${GPG_UID}"
+echo ""
+
+TMPDIR=$(mktemp -d /tmp/gpg.XXXXXXXXX)
+TMPFILE=${TMPDIR}/${FPR}.asc
+
+gpg --armor --export ${FPR} > ${TMPFILE}
+
+code-server ${TMPFILE}
+
+cat << EOF
+
+You are almost done! We created a file at ${TMPFILE} for you. You see it in the
+editor above. Just paste the public key at https://gitlab.hzdr.de/-/profile/gpg_keys
+and you're done.
+EOF

docker/workspace/git-user-management/git-get-user-fpr

+#!/bin/bash
+# Get the fingerprint of a UID
+
+
+function Help() {
+    cat << EOF
+Get the fingerprint of a UID
+
+This function takes one argument, the UID as "Full Name <email>" and
+returns the corresponding fingerprint (if there is one)
+
+Call syntax::
+
+    git get-user-fpr "Full Name <full.name@example.com>"
+
+
+Syntax: git get-user-fpr [-h] UID
+
+mandatory arguments:
+UIDorFile    The UID of the GPG Key or the path to a key
+
+options:
+h     Print this Help.
+EOF
+}
+
+while getopts ":h" option; do
+   case $option in
+      h) # display Help
+         Help
+         exit;;
+     \?) # incorrect option
+         echo "Error: Invalid option"
+         exit 1;;
+   esac
+done
+
+FPR=""
+GPG_UID="${1}"
+
+if [[ "${GPG_UID}" == "" ]]; then
+    >&2 echo "Please specify the UID of the GPG Key to lookup"