path: root/genenetwork-local-container.sh

#! /bin/sh -e

# genenetwork-machines --- Guix configuration for genenetwork machines
# Copyright © 2025 Munyoki Kilyungi <me@bonfacemunyoki.com>
#
# This file is part of genenetwork-machines.
#
# genenetwork-machines is free software: you can redistribute it
# and/or modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# genenetwork-machines is distributed in the hope that it will be
# useful, but WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with genenetwork-machines.  If not, see
# <https://www.gnu.org/licenses/>.

# Build and install genenetwork container on your local machine.

set -euo pipefail


BASE_DIR="${HOME:-/home/$USER}/genenetwork"
SYSTEM_DIRECTORIES=(
    "$BASE_DIR/var/log"
    "$BASE_DIR/var/genenetwork"
    "$BASE_DIR/etc/genenetwork/conf"
    "$BASE_DIR/etc/genenetwork"
    "$BASE_DIR/var/lib/redis"
    "$BASE_DIR/var/lib/virtuoso"
    "$BASE_DIR/var/lib/xapian"
    "$BASE_DIR/var/genenetwork/genotype-files/genotype/json"
    "$BASE_DIR/var/lib/genenetwork-sqlite"
    "$BASE_DIR/var/lib/genenetwork-gnqa"
    "/tmp/local-container"
)

GN_PROJECTS=(
    "genenetwork2:git@github.com:genenetwork/genenetwork2"
    "genenetwork3:git@github.com:genenetwork/genenetwork3"
    "gn-auth:https://git.genenetwork.org/gn-auth"
    "gn-docs:https://git.genenetwork.org/gn-docs"
)

# File mappings: source -> destination
declare -A FILE_MAPPINGS=(
    ["etc/auth.db"]="$BASE_DIR/var/genenetwork/auth.db"
    ["etc/llm.db"]="$BASE_DIR/var/lib/genenetwork-sqlite/llm.db"
    ["etc/gn2-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn2/secrets.py"
    ["etc/gn3-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn3/secrets.py"
    ["etc/gn-auth-secrets.py"]="$BASE_DIR/etc/genenetwork/conf/gn-auth/secrets.py"
)

CONTAINER_SCM="genenetwork-local-container.scm"
CONTAINER_BIN="/usr/local/bin/genenetwork-local-container"
GC_ROOT="/var/guix/gcroots/genenetwork-local-container"

log() {
    local level="$1"
    shift
    echo "[$(date '+%Y-%m-%d %H:%M:%S')] $level: $*" >&2
}

# Check dependencies
for cmd in git guix sudo diff cp; do
    if ! command -v "$cmd" &>/dev/null; then
        log "ERROR" "Required command '$cmd' not found"
        exit 1
    fi
done

# Validate HOME is set
if [ -z "${HOME:-}" ]; then
    log "ERROR" "HOME environment variable is not set"
    exit 1
fi

log "INFO" "Creating system directories..."
for dir in "${SYSTEM_DIRECTORIES[@]}"; do
    # Check if directory exists and is accessible
    if [ -d "$dir" ]; then
        if [ -w "$dir" ]; then
            log "DEBUG" "Directory exists and is writable: $dir"
        else
            log "WARNING" "Directory exists but is not writable: $dir.  Making this writable"
	    sudo chown -R "$USER" "$dir"
        fi
        continue
    fi

    # Attempt to create directory
    log "INFO" "Creating directory: $dir"
    if [ -w "$(dirname "$dir")" ]; then
        # Parent directory is writable, try without sudo
        if ! mkdir -p "$dir"; then
            log "ERROR" "Failed to create directory without sudo: $dir"
            exit 1
        fi
    else
        # Parent directory requires root, use sudo
        if ! sudo mkdir -p "$dir"; then
            log "ERROR" "Failed to create directory with sudo: $dir"
            exit 1
        fi
        # Set ownership to current user if created with sudo
        if ! sudo chown "$USER:$USER" "$dir"; then
            log "WARNING" "Failed to set ownership for: $dir"
        fi
    fi
done

# Check and copy configuration files
log "INFO" "Checking and copying configuration files..."
for src in "${!FILE_MAPPINGS[@]}"; do
    dest="${FILE_MAPPINGS[$src]}"
    log "INFO" "Processing $src -> $dest"

    # Check if source file exists
    if [ ! -f "$src" ]; then
        log "ERROR" "Source file does not exist: $src"
        exit 1
    fi

    # Check if destination file exists
    if [ ! -f "$dest" ]; then
        log "INFO" "Destination file does not exist, copying $src to $dest"
        mkdir -p "$(dirname "$dest")"
        if ! cp "$src" "$dest"; then
            log "ERROR" "Failed to copy $src to $dest"
            exit 1
        fi
        continue
    fi

    # Compare files using diff
    log "INFO" "Comparing $src with $dest"
    if diff_output=$(diff -u "$dest" "$src" 2>&1); then
        log "INFO" "Files $src and $dest are identical"
    else
        log "INFO" "Differences found between $src and $dest:"
        echo "$diff_output" >&2
        log "INFO" "Copying $src to $dest"
        if ! cp "$src" "$dest"; then
            log "ERROR" "Failed to copy $src to $dest"
            exit 1
        fi
    fi
done

is_git_repository() {
    local dir="$1"
    # Check for standard repository
    if [ -d "$dir/.git" ]; then
        if [ -f "$dir/.git/HEAD" ] && [ -d "$dir/.git/refs" ]; then
            log "DEBUG" "Detected standard Git repository: $dir"
            return 0
        else
            log "ERROR" "Directory $dir/.git exists but is not a valid Git repository"
            return 1
        fi
    # Check for bare repository
    elif [ -f "$dir/HEAD" ] && [ -d "$dir/refs" ] && [ -d "$dir/objects" ]; then
        log "DEBUG" "Detected bare Git repository: $dir"
        return 0
    else
        log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)"
        return 1
    fi
}
# Clone GeneNetwork projects
log "INFO" "Cloning GeneNetwork projects..."
for project_entry in "${GN_PROJECTS[@]}"; do
    IFS=':' read -r project repo_url <<< "$project_entry"
    dir="$BASE_DIR/$project"
    if [ ! -d "$dir" ]; then
        log "INFO" "Cloning $project from $repo_url to $dir"
        if ! git clone "$repo_url" "$dir"; then
            log "ERROR" "Failed to clone $project"
            exit 1
        fi
    else
        log "DEBUG" "Directory exists, skipping clone: $dir"
        if ! is_git_repository "$dir"; then
            log "ERROR" "$dir exists but is not a Git repository"
            exit 1
        fi
    fi
done

FLASK_SESSION="$BASE_DIR/genenetwork2/flask_session"
log "INFO" "Checking FLASK_SESSION directory: $FLASK_SESSION"
if [ ! -d "$FLASK_SESSION" ]; then
    log "INFO" "Creating FLASK_SESSION directory: $FLASK_SESSION"
    if ! mkdir -p "$FLASK_SESSION"; then
        log "ERROR" "Failed to create FLASK_SESSION directory: $FLASK_SESSION"
        exit 1
    fi
else
    log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION"
fi


# Verify container SCM file exists
if [ ! -f "$CONTAINER_SCM" ]; then
    log "ERROR" "Container SCM file not found: $CONTAINER_SCM"
    exit 1
fi

# Create Guix system container
log "INFO" "Creating Guix system container..."
SHARE_OPTS=(
    "--share=$BASE_DIR/var/log=/var/log"
    "--share=$BASE_DIR/var/genenetwork=/var/genenetwork"
    "--share=$BASE_DIR/etc/genenetwork/conf=/etc/genenetwork/conf"
    "--share=$BASE_DIR/etc/genenetwork=/etc/genenetwork"
    "--share=$BASE_DIR/var/lib/redis=/var/lib/redis"
    "--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso"
    "--share=$BASE_DIR/genenetwork2=/genenetwork2"
    "--share=$BASE_DIR/genenetwork3=/genenetwork3"
    "--share=$BASE_DIR/gn-auth=/gn-auth"
    "--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian"
    "--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite"
    "--share=$BASE_DIR/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa"
    "--share=/tmp/local-container=/tmp"
    "--share=$BASE_DIR/gn-docs=/var/lib/gn-docs"
    "--share=/run/mysqld=/run/mysqld"
)

container_script=$(guix system container \
    --network \
    --load-path=. \
    --verbosity=3 \
    "${SHARE_OPTS[@]}" \
    "$CONTAINER_SCM")

log $container_script

# Create symbolic links
log "INFO" "Creating symbolic links..."
if ! sudo ln -sf "$container_script" "$CONTAINER_BIN"; then
    log "ERROR" "Failed to create symbolic link: $CONTAINER_BIN"
    exit 1
fi

if ! sudo ln -sf "$container_script" "$GC_ROOT"; then
    log "ERROR" "Failed to create GC root link: $GC_ROOT"
    exit 1
fi

log "INFO" "Setup completed successfully!"
log "INFO" "Container script: $container_script"
log "INFO" "Run with: $CONTAINER_BIN"
log "INFO" "Email: test@development.user"
log "INFO" "Password: testpasswd"