diff options
| -rw-r--r-- | genenetwork-local-container.scm | 1 | ||||
| -rwxr-xr-x | genenetwork-local-container.sh | 220 |
2 files changed, 212 insertions, 9 deletions
diff --git a/genenetwork-local-container.scm b/genenetwork-local-container.scm index 8dc02c7..4399796 100644 --- a/genenetwork-local-container.scm +++ b/genenetwork-local-container.scm @@ -21,7 +21,6 @@ ;;; tux04. (use-modules (gnu) - (genenetwork services genenetwork) (gnu build linux-container) ((gn packages genenetwork) #:select (genenetwork2 genenetwork3 gn-auth gn-libs gn-uploader)) ((gnu packages admin) #:select (shepherd shadow)) diff --git a/genenetwork-local-container.sh b/genenetwork-local-container.sh index 1db01dd..16492c6 100755 --- a/genenetwork-local-container.sh +++ b/genenetwork-local-container.sh @@ -26,6 +26,7 @@ set -euo pipefail BASE_DIR="${HOME:-/home/$USER}/genenetwork" SYSTEM_DIRECTORIES=( + "$BASE_DIR" "$BASE_DIR/var/log" "$BASE_DIR/var/genenetwork" "$BASE_DIR/etc/genenetwork/conf" @@ -43,8 +44,8 @@ SYSTEM_DIRECTORIES=( ) GN_PROJECTS=( - "genenetwork2:git@github.com:genenetwork/genenetwork2" - "genenetwork3:git@github.com:genenetwork/genenetwork3" + "genenetwork2:https://github.com/genenetwork/genenetwork2.git" + "genenetwork3:https://github.com/genenetwork/genenetwork3.git" "gn-transform-databases:https://git.genenetwork.org/gn-transform-databases/" "gn-auth:https://git.genenetwork.org/gn-auth" "gn-docs:https://git.genenetwork.org/gn-docs" @@ -96,8 +97,8 @@ if [ -z "${HOME:-}" ]; then exit 1 fi -if [ "$1" = "--init-container" ]; then - log "INFO" "Creating system directories..." +init_container() { + log "INFO" "Creating system directories..." for dir in "${SYSTEM_DIRECTORIES[@]}"; do # Check if directory exists and is accessible if [ -d "$dir" ]; then @@ -125,7 +126,7 @@ if [ "$1" = "--init-container" ]; then exit 1 fi # Set ownership to current user if created with sudo - if ! sudo chown "$USER:$USER" "$dir"; then + if ! sudo chown -R "$USER" "$dir"; then log "WARNING" "Failed to set ownership for: $dir" fi fi @@ -282,9 +283,13 @@ if [ "$1" = "--init-container" ]; then log "INFO" "Run with: $CONTAINER_BIN" log "INFO" "Email: test@development.user" log "INFO" "Password: testpasswd" +} +if [ "$1" = "--init-container" ]; then + init_container + exit 0 fi -if [ "$1" = "--init-sql" ]; then +init_sql() { # Configuration URL="https://files.genenetwork.org/database/db_webqtl_s-2025-02-18.sql.xz" DOWNLOAD_DIR="/tmp" @@ -370,10 +375,14 @@ if [ "$1" = "--init-sql" ]; then rm -f "$DOWNLOAD_DIR/$EXTRACTED_FILE" log INFO "Database import completed successfully" +} + +if [ "$1" = "--init-sql" ]; then + init_sql exit 0 fi -if [ "$1" = "--init-rdf" ]; then +init_rdf() { # Check for required tools for cmd in guix; do if ! command -v "$cmd" &> /dev/null; then @@ -401,10 +410,14 @@ if [ "$1" = "--init-rdf" ]; then guix shell guile-dbi -m "manifest.scm" -- guile load-rdf.scm \ "$curr_dir/etc/conn.scm" cd $curr_dir +} + +if [ "$1" = "--init-rdf" ]; then + init_rdf exit 0 fi -if [ "$1" = "--init-xapian" ]; then +init_xapian() { # Check for required tools log INFO "Please make sure your container is running for this to work" log INFO "This takes some time to run" @@ -432,5 +445,196 @@ if [ "$1" = "--init-xapian" ]; then mv "$BASE_DIR/var/lib/xapian/build/*" "$BASE_DIR/var/lib/xapian/" \ && rmdir "$BASE_DIR/var/lib/xapian/build/" log INFO "Please restart the container to set the correct permissions" +} + +if [ "$1" = "--init-xapian" ]; then + init_xapian + exit 0 +fi + + +# Function to handle yes/no prompts +prompt_yes_no() { + local prompt="$1" + while true; do + read -p "$prompt (yes/no): " response + case "$response" in + [Yy][Ee][Ss]|[Yy] ) return 0 ;; + [Nn][Oo]|[Nn] ) return 1 ;; + * ) echo "Please answer 'yes' or 'no'." ;; + esac + done +} + +# Main tutorial function +run_beginner_setup_tutorial() { + clear + # Step 1: Initialize Container + echo "Step 1: Setting Up the Container" + echo "--------------------------------" + echo "Before we begin, make sure you are using the correct guix-profile that has:" + echo "" + echo " guix-bioinformatics" + echo "" + echo "Otherwise, I will terminate early. If you don't know how to do that, read:" + echo "" + echo " https://issues.genenetwork.org/topics/guix/guix-profiles" + echo "" + echo "This step prepares the container environment where GeneNetwork runs." + echo "It ensures all necessary files, folders, and configurations are in place." + echo "" + echo "This step is similar to running:" + echo "" + echo "./genenetwork-local-container.sh --init-container" + echo "" + echo "NOTE: If you have any of the following projects:" + echo " genenetwork2" + echo " genenetwork3" + echo " gn-uploader" + echo "" + echo "Move/copy them to $BASE_DIR. This is where'll you'll be hacking" + echo "on them from. Because of how we mount things inside the container," + echo "make sure the names appear as above." + echo "" + echo "Now, some things to note. AI search won't work. To get this working, if you want so," + echo "Get into the container, and modify FAHAMU_AUTH_TOKEN in:" + echo " /etc/genenetwork/conf/gn3/secrets.py" + echo "" + echo "Similarly, e-mail functionality ala resetting passwords or confirming a new user" + echo "won't work unless you modify:" + echo " SMTP_HOST = 'XXXX'" + echo " SMTP_USER = 'XXXX'" + echo " SMTP_PASSWORD = 'XXXX'" + echo " SMTP_PORT = 'XXXX'" + echo " EMAIL_ADDRESS = 'XXXX'" + echo " EMAIL_DISPLAY_NAME = 'XXXX'" + echo "inside:" + echo " /etc/genenetwork/conf/gn-auth/secrets.py" + echo "" + if prompt_yes_no "Would you like to set up the container now?"; then + init_container + clear + echo "Container setup complete!" + echo "" + echo "Right now you have a working container. You need to set-up sql, upload rdf data" + echo "and build a xapian index to have a fully functioning system akin to production and" + echo "our test environment." + echo "" + else + clear + echo "Skipping container setup. Moving to the next step." + fi + echo "" + + # Step 2: Initialize SQL Database + echo "Step 2: Setting Up the SQL Database" + echo "-----------------------------------" + echo "Please make sure you have a working MariaDB installation on your Linux system." + echo "" + echo "This step creates and configures the database for storing GeneNetwork data." + echo "" + echo "It sets up tables and initial data needed for Genenetwork to run" + echo "" + echo "This step is similar to running:" + echo "./genenetwork-local-container.sh --init-sql" + echo "" + echo "Make sure your container, if not, is running for this to work:" + echo "" + echo "sudo /usr/local/bin/genenetwork-local-container" + if prompt_yes_no "Would you like to set up the database now?"; then + init_sql + clear + echo "Database setup complete!" + else + clear + echo "Skipping database setup. Moving to the next step: Importing RDF" + fi + echo "" + + # Step 3: Initialize RDF + echo "" + echo "Step 3: Importing RDF into your local set-up" + echo "---------------------------------------------" + echo "This step adds RDF (Resource Description Framework) data." + echo "" + echo "RDF helps organize and link data for GeneNetwork." + echo "" + echo "IMPORTANT. This step requires you to have a running container instance." + echo " Otherwise, it will fail." + echo "To run your container, in a different shell, run:" + echo "sudo /usr/local/bin/genenetwork-local-container" + echo "" + echo "This step is similar to running:" + echo "./genenetwork-local-container.sh --init-rdf" + echo "" + echo "Make sure your container, if not, is running for this to work:" + echo "" + echo "sudo /usr/local/bin/genenetwork-local-container" + if prompt_yes_no "Would you like to set up RDF now?"; then + init_rdf + clear + echo "RDF setup complete!" + else + clear + echo "Skipping RDF setup." + fi + echo "" + + # Step 4: Initialize XAPIAN + clear + echo "Step 3: Setting up XAPIAN search locally" + echo "---------------------------------------------" + echo "This indexes all your data from GeneNetwork and indexes it using XAPIAN" + echo "" + echo "Read more here:" + echo "https://issues.genenetwork.org/topics/xapian/xapian-search" + echo "" + echo "IMPORTANT. This step requires you to have a running container instance." + echo " Otherwise, it will fail." + echo " To run your container, in a different shell, run:" + echo " sudo /usr/local/bin/genenetwork-local-container" + echo "" + echo "This step is similar to running:" + echo "./genenetwork-local-container.sh --init-xapian" + echo "" + echo "Make sure your container, if not, is running for this to work:" + echo "" + echo "sudo /usr/local/bin/genenetwork-local-container" + if prompt_yes_no "Would you like to build the xapian index now?"; then + init_xapian + clear + echo "XAPIAN setup complete!" + else + clear + echo "Skipping RDF setup." + fi + echo "" + + # Completion Message + echo "=============================================================" + echo "Congratulations! You've completed the GeneNetwork Beginner Setup Tutorial!" + echo "=============================================================" + echo "You may have skipped some steps. To complete them, run the tutorial again." + echo "Your environment is ready to the extent you chose to set it up." + echo "If you run your container, you can access the different web-services at:" + echo "gn-guile : localhost:8091" + echo "genenetwork2 : localhost:8082" + echo "genenetwork3 : localhost:8083" + echo "gn-uploader : localhost:8085" + echo "sparql web ui: localhost:7082/sparql" + echo "" + echo "To access virtuoso back-end service, run:" + echo "guix shell virtuoso-ose isql -- 7081" + echo "" + echo "To login in gn-uploader/genenetwork2, use the following credentials:" + echo " Email: test@development.user" + echo " Password: testpasswd" + exit 0 +} + +# Check for --beginner-set-up flag or run tutorial interactively +if [ "$1" = "--beginner-set-up" ]; then +# Interactive mode: run the tutorial + run_beginner_setup_tutorial exit 0 fi |