Add "--init-container" option.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 159 insertions, 157 deletions

diff --git a/genenetwork-local-container.sh b/genenetwork-local-container.sh
index 5cf4655..0f873a7 100755
--- a/genenetwork-local-container.sh
+++ b/genenetwork-local-container.sh
@@ -79,180 +79,182 @@ if [ -z "${HOME:-}" ]; then
     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
+if [ "$1" = "--init-container" ]; then
+    log "INFO" "Creating system directories..."
+    for dir in "${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"
+	# 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 if source file exists
-    if [ ! -f "$src" ]; then
-        log "ERROR" "Source file does not exist: $src"
-        exit 1
-    fi
+    # Check and copy configuration files
+    log "INFO" "Checking and copying configuration files..."
+    for src in "${!FILE_MAPPINGS[@]}"; do
+	dest="${FILE_MAPPINGS[$src]}"
+	log "INFO" "Processing $src -> $dest"
 
-    # Check if 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 $dest"
+	# Check if source file exists
+	if [ ! -f "$src" ]; then
+            log "ERROR" "Source file does not exist: $src"
             exit 1
-        fi
-        continue
-    fi
+	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 $dest"
-            exit 1
-        fi
-    fi
-done
+	# Check if destination file exists
+	if [ ! -f "$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"
+    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" "Directory $dir/.git exists but is not a valid Git repository"
+	else
+            log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)"
             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 $project"
+	fi
+    }
+    # Clone GeneNetwork projects
+    log "INFO" "Cloning GeneNetwork projects..."
+    for project_entry in "${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
+	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
+	log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION"
     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: $FLASK_SESSION"
-        exit 1
+
+    # Verify container SCM file exists
+    if [ ! -f "$CONTAINER_SCM" ]; then
+	log "ERROR" "Container SCM file not found: $CONTAINER_SCM"
+	exit 1
     fi
-else
-    log "DEBUG" "FLASK_SESSION directory already exists: $FLASK_SESSION"
-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"
+    )
 
-# Verify container SCM file exists
-if [ ! -f "$CONTAINER_SCM" ]; then
-    log "ERROR" "Container SCM file not found: $CONTAINER_SCM"
-    exit 1
-fi
+    container_script=$(guix system container \
+			    --network \
+			    --load-path=. \
+			    --verbosity=3 \
+			    "${SHARE_OPTS[@]}" \
+			    "$CONTAINER_SCM")
 
-# 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
 
-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
 
-# 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
 
-if ! sudo ln -sf "$container_script" "$GC_ROOT"; then
-    log "ERROR" "Failed to create GC root link: $GC_ROOT"
-    exit 1
+    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"
 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"