diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 00000000..21742c08 --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +conductorscripts/**/*.sh text eol=lf diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..71c8bd46 --- /dev/null +++ b/Makefile @@ -0,0 +1,20 @@ +platform: + PROFILE=platform docker compose --profile platform up --attach conductor + +stageDev: + PROFILE=stageDev docker compose --profile stageDev up --attach conductor + +arrangerDev: + PROFILE=arrangerDev docker compose --profile arrangerDev up --attach conductor + +maestroDev: + PROFILE=maestroDev docker compose --profile maestroDev up --attach conductor + +songDev: + PROFILE=songDev docker compose --profile songDev up --attach conductor + +scoreDev: + PROFILE=scoreDev docker compose --profile scoreDev up --attach conductor + +down: + PROFILE=platform docker compose --profile platform down diff --git a/README.md b/README.md index b35e004c..8d828dc8 100644 --- a/README.md +++ b/README.md @@ -1,33 +1,69 @@ -# Overture QuickStart +# Conductor -The Overture QuickStart provides those interested in gaining hands-on experience using an Overture platform a fast and frictionless local installation. +Conductor is a flexible Docker Compose setup that simplifies the process of spinning up Overture development and deployment configurations using Docker profiles and extensible scripting events. -## Getting Started +## Key Features -**1. Download and configure Docker Desktop** +- **Profile-based Deployments**: Uses Docker profiles to manage different environment setups. +- **Conductor-driven Execution**: The Conductor service executes ordered scripts based on the `PROFILE` environment variable. -In Docker Desktop click the cog icon , then resources. We recommend at minimum setting your CPU limit to 8, memory to 8GB, swap to 2GB, with64GB of virtual disk space available. If you have Docker already installed ensure it is up to date. +## Getting Started -**2. Clone the QuickStart Repository** +**1. Clone the repo's `main` branch** -```bash -git clone https://github.com/overture-stack/composer.git && cd composer ``` +git clone -b concerto https://github.com/overture-stack/composer.git && cd composer +``` + +**2. Run one of the following commands to spin up different environments:** + +| Environment | Unix/macOS | Windows | +|-------------|------------|---------| +| Overture Platform | `make platform` | `make.bat platform` | +| Stage Dev | `make stageDev` | `make.bat stageDev` | +| Arranger Dev | `make arrangerDev` | `make.bat arrangerDev` | +| Maestro Dev | `make maestroDev` | `make.bat maestroDev` | +| Song Dev | `make songDev` | `make.bat songDev` | +| Score Dev | `make scoreDev` | `make.bat scoreDev` | -**3. Run the Docker Compose with attach mode enabled** +Each command spins up complementary services for the specified development environment. -```bash -docker compose up --attach conductor +## Repository Structure + +``` +. +├── conductorScripts/ +│ ├── deployments +│ └── services +├── configurationFiles/ +│ ├── arrangerConfigs +│ ├── elasticsearchConfigs +│ └── keycloakConfigs +├── guideMaterials +├── persistentStorage/ +│ ├── data-keycloak-db +│ ├── data-minio +│ └── data-song-db +├── Makefile +└── make.bat ``` -Your portal will be accessible from your `localhost:3000` +- **`conductorScripts/`** Contains scripts for orchestrating the deployment process. + - `deployments/`: Scripts that execute service scripts sequentially based on the deployment configuration. These also include custom post-deployment logs with essential next steps for the deployment scenario. + - `services/`: Modular scripts for individual service setup tasks. Each file is named according to its purpose, with inline comments documenting the code. + +- **`configurationFiles/`** Stores all required configuration files, including: + - `arrangerConfigs/`: Configuration files specific to Arranger. + - `elasticsearchConfigs/`: Configuration files for Elasticsearch, encompassing indexing mappings and documents for seeding data. + - `keycloakConfigs/`: Configuration files for Keycloak, including preconfigured realm files and Overture API key provider details. + +- **`guideMaterials/`** Supplementary folders and files for use with the [Overture guides](https://www.overture.bio/documentation/guides/). -## Rational +- **`persistentStorage/`** Directory for storing persistent data during container startups and restarts. These folders come pre-loaded with mock data. + - `data-keycloak-db/`: Persistent local storage for the Keycloak database. + - `data-minio/`: Persistent local storage for MinIO object storage. + - `data-song-db/`: Persistent local storage for the Song database. -With Overture we want to provide new users the following: +- **`Makefile`** Contains [`make` commands](https://www.gnu.org/software/make/manual/make.html#Overview-of-make) for Unix-based systems (macOS, Linux) to streamline Docker operations. -|Purpose|Solution| -|---|---| -| **A way to look at it**|[Overture Demo Portal](https://demo.overture.bio/)| -| **A way to try it**| Overture QuickStart | -| **A way to own it**| [Product Documentation](https://www.overture.bio/documentation/) *and* [Platform Guides](https://github.com/overture-stack/website/pull/385)| +- **`make.bat`** Windows equivalent of the Makefile, featuring batch commands tailored for Windows systems. diff --git a/conductorScripts/deployments/arrangerDev.sh b/conductorScripts/deployments/arrangerDev.sh new file mode 100755 index 00000000..80f4eafe --- /dev/null +++ b/conductorScripts/deployments/arrangerDev.sh @@ -0,0 +1,43 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔═════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the ArrangerDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚═════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Elasticsearch Setup +echo -e "\033[1;35m[1/2]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticSearchSetup.sh + +# Update Conductor to Healthy Status +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Stage +echo -e "\033[1;35m[2/2]\033[0m Checking Stage" +rs /scripts/services/stageCheck.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Arranger Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m\n" +echo -e "\033[1m1️⃣ To run Arranger locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/arranger.git\033[0m\n" +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd arranger\033[0m\n" +echo -e "\033[1m3️⃣ Copy the example environment file:\033[0m\n" +echo -e " \033[1;32mcp .env.arrangerDev .env\033[0m\n" +echo -e "\033[1m4️⃣ Install the dependencies:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" +echo -e "\033[1m5️⃣ Bootstrap the project:\033[0m\n" +echo -e " \033[1;32mnpm run bootstrap\033[0m\n" +echo -e "\033[1m6️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run server\033[0m\n" diff --git a/conductorScripts/deployments/maestroDev.sh b/conductorScripts/deployments/maestroDev.sh new file mode 100755 index 00000000..899a9302 --- /dev/null +++ b/conductorScripts/deployments/maestroDev.sh @@ -0,0 +1,56 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the MaestroDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/6]\033[0m Setting up Song & Keycloak databases" +rs /scripts/services/keycloakDbSetup.sh +rs /scripts/services/songDbSetup.sh + +# Minio Check +echo -e "\033[1;35m[2/6]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/6]\033[0m Checking on Score" +rs /scripts/services/scoreCheck.sh + +# Song Check +echo -e "\033[1;35m[4/6]\033[0m Checking Song" +rs /scripts/services/songCheck.sh + +# Elasticsearch Setup +echo -e "\033[1;35m[5/6]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticsearchSetup.sh + +# Check Keycloak +echo -e "\033[1;35m[6/6]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + +# Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ MaestroDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/maestro.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd maestro\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -pl maestro-app\033[0m\n" + +echo -e "\033[1mMaestro's Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:11235/api-docs\033[0m\n" diff --git a/conductorScripts/deployments/platform.sh b/conductorScripts/deployments/platform.sh new file mode 100755 index 00000000..ded7c1c7 --- /dev/null +++ b/conductorScripts/deployments/platform.sh @@ -0,0 +1,71 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔═══════════════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the Overture Platform QuickStart ║\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Cleanup any existing healthcheck file +rs scripts/services/healthcheckCleanup.sh + +# Database Setups +echo -e "\033[1;35m[1/9]\033[0m Setting up Song & Keycloak databases" +rs /scripts/services/songDbSetup.sh +rs /scripts/services/keycloakDbSetup.sh + +# Minio Check +echo -e "\033[1;35m[2/9]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/9]\033[0m Checking on Score" +rs /scripts/services/scoreCheck.sh + +# Song Setup +echo -e "\033[1;35m[4/9]\033[0m Checking on Song" +rs /scripts/services/songCheck.sh + +# Elasticsearch Setup +echo -e "\033[1;35m[5/9]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticSearchSetup.sh + +# Update Conductor to Healthy Status, this signals search and exploration services (maestro, arranger, stage) to startup +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Stage +echo -e "\033[1;35m[7/9]\033[0m Checking Stage" +rs /scripts/services/stageCheck.sh + +# Check Arranger +echo -e "\033[1;35m[6/9]\033[0m Checking Arranger" +rs /scripts/services/arrangerCheck.sh + +# Check Maestro +echo -e "\033[1;35m[8/9]\033[0m Checking Maestro" +rs /scripts/services/maestroCheck.sh + +# Check Keycloak +echo -e "\033[1;35m[9/9]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Overture QuickStart Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" +echo -e "\n" +echo -e "\033[1m🌐 Front-end Portal:\033[0m" +echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" +echo -e "\033[1m📚 Overture Platform Guides:\033[0m" +echo -e " \033[1;32mhttps://www.overture.bio/documentation/guides/\033[0m\n" +echo -e "\033[1m🛠️ QuickStart Information:\033[0m" +echo -e " Check the \033[1;33mdocker-compose.yml\033[0m file for details on this QuickStart," +echo -e " including links to relevant sections of our deployment guide.\n" diff --git a/conductorScripts/deployments/scoreDev.sh b/conductorScripts/deployments/scoreDev.sh new file mode 100755 index 00000000..57a045e2 --- /dev/null +++ b/conductorScripts/deployments/scoreDev.sh @@ -0,0 +1,48 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the ScoreDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Song & Keycloak databases" +rs /scripts/services/keycloakDbSetup.sh +rs /scripts/services/songDbSetup.sh + +# Minio Check +echo -e "\033[1;35m[2/4]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Song Setup +echo -e "\033[1;35m[3/6]\033[0m Checking Song" +rs /scripts/services/songCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + +# Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ ScoreDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Score locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/score.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd score\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application \033[1;34m(requires JDK11 & Maven3)\033[0m:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -Dspring-boot.run.profiles=default,s3,secure,dev -pl score-server\033[0m\n" + +echo -e "\033[1mScores Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:8087/swagger-ui.html\033[0m\n" diff --git a/conductorScripts/deployments/songDev.sh b/conductorScripts/deployments/songDev.sh new file mode 100755 index 00000000..879ca012 --- /dev/null +++ b/conductorScripts/deployments/songDev.sh @@ -0,0 +1,48 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔═════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the SongDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚═════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Keycloak and Song Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Song and Keycloak databases" +rs /scripts/services/keycloakDbSetup.sh +rs /scripts/services/songDbSetup.sh + +# Minio Check +echo -e "\033[1;35m[2/4]\033[0m Checking Minio Object Storage" +rs /scripts/services/minioCheck.sh + +# Score Setup +echo -e "\033[1;35m[3/4]\033[0m Checking Score" +rs /scripts/services/scoreCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + +# Success and Next Steps +echo -e "\033[1;36m╔══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ SongDev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Song locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/song.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd song\033[0m\n" + +echo -e "\033[1m3️⃣ Build the application \033[1;34m(Requires JDK11)\033[0m:\033[0m\n" +echo -e " \033[1;32m./mvnw clean install -DskipTests\033[0m\n" + +echo -e "\033[1m4️⃣ Start the development server:\033[0m\n" +echo -e " \033[1;32m./mvnw spring-boot:run -Dspring-boot.run.profiles=default,dev,secure -pl song-server\033[0m\n" + +echo -e "\033[1mSongs Swagger UI can be accessed from:\n" +echo -e " \033[1;32mhttp://localhost:8080/swagger-ui.html\033[0m\n" diff --git a/conductorScripts/deployments/stageDev.sh b/conductorScripts/deployments/stageDev.sh new file mode 100755 index 00000000..d36544fc --- /dev/null +++ b/conductorScripts/deployments/stageDev.sh @@ -0,0 +1,61 @@ +#!/bin/sh + +# Welcome +echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Welcome to the StageDev QuickStart ║\033[0m" +echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" + +# rs = "Run Script" a simple function to apply permissions and run scripts +rs() { + chmod +x "$1" && "$1" + } + +# Keycloak Db Setup +echo -e "\033[1;35m[1/4]\033[0m Setting up Keycloak database" +rs /scripts/services/keycloakDbSetup.sh + +# Elasticsearch Setup +echo -e "\033[1;35m[2/4]\033[0m Setting up Elasticsearch" +rs /scripts/services/elasticSearchSetup.sh + +# Update Conductor to Healthy Status +echo "healthy" > /health/conductor_health +echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" + +# Check Arranger +echo -e "\033[1;35m[3/4]\033[0m Checking Arranger" +rs /scripts/services/arrangerCheck.sh + +# Keycloak Check +echo -e "\033[1;35m[4/4]\033[0m Checking Keycloak" +rs /scripts/services/keycloakCheck.sh + +# Remove Health Check File +rm /health/conductor_health + +# Success and Next Steps +echo -e "\033[1;36m╔═══════════════════════════════════════╗\033[0m" +echo -e "\033[1;36m║ Stage Dev Service Setup Complete ║\033[0m" +echo -e "\033[1;36m╚═══════════════════════════════════════╝\033[0m\n" + +echo -e "\033[1m1️⃣ To run Stage locally, start by cloning the repo:\033[0m\n" +echo -e " \033[1;32mgit clone https://github.com/overture-stack/stage.git\033[0m\n" + +echo -e "\033[1m2️⃣ Navigate to the cloned directory:\033[0m\n" +echo -e " \033[1;32mcd stage\033[0m\n" + +echo -e "\033[1m3️⃣ Copy the example environment file:\033[0m\n" +echo -e " \033[1;32mcp .env.stageDev .env\033[0m\n" + +echo -e "\033[1m4️⃣ Install the dependencies:\033[0m\n" +echo -e " \033[1;32mnpm ci\033[0m\n" + +echo -e "\033[1m This will require:\033[0m" +echo -e "\033[1;34m - Node v16 or higher\033[0m" +echo -e "\033[1;34m - npm v8.3.0 or higher\033[0m\n" + +echo -e "\033[1m5️⃣ Run the development server:\033[0m\n" +echo -e " \033[1;32mnpm run dev\033[0m\n" + +echo -e "\033[1mYour development server will be accessible at:\n" +echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" diff --git a/conductorScripts/services/arrangerCheck.sh b/conductorScripts/services/arrangerCheck.sh new file mode 100755 index 00000000..5a9a5709 --- /dev/null +++ b/conductorScripts/services/arrangerCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +echo -e "Checking if Arranger is reachable" + until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do + echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 + done +echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" diff --git a/conductorScripts/services/elasticsearchSetup.sh b/conductorScripts/services/elasticsearchSetup.sh new file mode 100755 index 00000000..6587a161 --- /dev/null +++ b/conductorScripts/services/elasticsearchSetup.sh @@ -0,0 +1,45 @@ +#!/bin/sh + +# Wait for Elasticsearch +echo -e "\033[1;36mElasticsearch:\033[0m Starting up (this may take a few minutes)" +sleep 20 +until curl -s -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/_cluster/health" > /dev/null; do + echo -e "\033[1;36mElasticsearch:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Elasticsearch is reachable" + +# Set up Elasticsearch index template +echo -e "Setting up the Elasticsearch index template" +if ! curl -s -u elastic:myelasticpassword "http://elasticsearch:9200/_template/index_template" | grep -q "\"index_patterns\""; then + curl -s -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/_template/index_template" \ + -H "Content-Type: application/json" -d @/usr/share/elasticsearch/config/quickstart_index_template.json > /dev/null && + echo -e "\033[1;32mSuccess:\033[0m Elasticsearch index template created successfully" +else + echo -e "\033[1;36mElasticsearch:\033[0m Index template already exists, skipping creation" +fi + +# Set up Elasticsearch index and alias (needs failure check) +echo -e "Setting up the Elasticsearch index and alias" +echo -e "\033[1;36mElasticsearch:\033[0m Checking if Elasticsearch index exists" +if ! curl -s -f -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/overture-quickstart-index" > /dev/null 2>&1; then + echo -e "\033[1;36mElasticsearch:\033[0m Creating Elasticsearch index and alias" + response=$(curl -s -w "\n%{http_code}" -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/overture-quickstart-index" \ + -H "Content-Type: application/json" -d "{\"aliases\": {\"file_centric\": {\"is_write_index\": true}}}") + http_code=$(echo "$response" | tail -n1) + body=$(echo "$response" | sed '$d') + echo -e "\033[1;32mSuccess:\033[0m Index and alias created successfully, Elasticsearch setup complete" +else + echo -e "\033[1;36mElasticsearch:\033[0m Index already exists, skipping creation" +fi + +# Importing Elasticsearch Documents +echo -e "Importing Elasticsearch Documents" +for f in ./es-docs/*.json; do + object_id=$(basename "$f" .json) + curl --user elastic:myelasticpassword -sL -X POST \ + -H "Content-Type: application/json" \ + "http://elasticsearch:9200/overture-quickstart-index/_doc/$object_id" \ + -d "@$f" > /dev/null +done +echo -e "\033[1;32mSuccess:\033[0m Document import complete" diff --git a/conductorScripts/services/healthcheckCleanup.sh b/conductorScripts/services/healthcheckCleanup.sh new file mode 100755 index 00000000..8cb3521c --- /dev/null +++ b/conductorScripts/services/healthcheckCleanup.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +# If the health check file exists on startup it needs to be removed +rm /health/conductor_health 2>/dev/null diff --git a/conductorScripts/services/kafkaSetup.sh b/conductorScripts/services/kafkaSetup.sh new file mode 100755 index 00000000..6589fc96 --- /dev/null +++ b/conductorScripts/services/kafkaSetup.sh @@ -0,0 +1,21 @@ +#!/bin/sh + +# Quick check if Kafka is ready +until /bin/kafka-topics --bootstrap-server kafka:9092 --list > /dev/null 2>&1; do + echo -e "\033[1;33mWaiting:\033[0m Kafka not ready yet..." + sleep 5 +done + +# Create topic if it doesn't exist +echo -e "\033[1;36mSetting up Kafka:\033[0m Creating Kafka topic for Song" +/bin/kafka-topics --bootstrap-server kafka:9092 --create --if-not-exists \ + --topic song-analysis \ + --partitions 1 \ + --replication-factor 1 \ + --config cleanup.policy=delete \ + --config retention.ms=604800000 + +# Update healthcheck to just verify +echo "Verifying Kafka topic creation" +/bin/kafka-topics --bootstrap-server kafka:9092 --describe --topic song-analysis +echo -e "\033[1;32mSuccess:\033[0m Kafka Overture Setup Script Complete" diff --git a/conductorScripts/services/keycloakCheck.sh b/conductorScripts/services/keycloakCheck.sh new file mode 100755 index 00000000..4cf752d1 --- /dev/null +++ b/conductorScripts/services/keycloakCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +# Check for Keycloak +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://keycloak:8080/health/live")" = "200" ]; do + echo -e "\033[1;36mKeycloak:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Keycloak is reachable" diff --git a/conductorScripts/services/keycloakDbSetup.sh b/conductorScripts/services/keycloakDbSetup.sh new file mode 100755 index 00000000..3af80fa0 --- /dev/null +++ b/conductorScripts/services/keycloakDbSetup.sh @@ -0,0 +1,17 @@ +#!/bin/sh + +# Create missing empty directories not tracked by git and needed by postgres +echo -e "Setting up empty directories for Keycloaks postgres database" +mkdir -p keycloak/db-folder-init/pg_tblspc +mkdir -p keycloak/db-folder-init/pg_stat +mkdir -p keycloak/db-folder-init/pg_stat_tmp +mkdir -p keycloak/db-folder-init/pg_replslot +mkdir -p keycloak/db-folder-init/pg_dynshmem +mkdir -p keycloak/db-folder-init/pg_twophase +mkdir -p keycloak/db-folder-init/pg_notify +mkdir -p keycloak/db-folder-init/pg_serial +mkdir -p keycloak/db-folder-init/pg_snapshots +mkdir -p keycloak/db-folder-init/pg_commit_ts +mkdir -p keycloak/db-folder-init/pg_wal/archive_status +mkdir -p keycloak/db-folder-init/pg_logical/snapshots +mkdir -p keycloak/db-folder-init/pg_logical/mappings diff --git a/conductorScripts/services/maestroCheck.sh b/conductorScripts/services/maestroCheck.sh new file mode 100755 index 00000000..7a60c551 --- /dev/null +++ b/conductorScripts/services/maestroCheck.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +# Check Maestro +echo -e "Checking if Maestro is reachable (this may take a few minutes)" +until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study/demo" -H "accept: */*" -d "{}" | grep -q "true"; do + echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" + sleep 30 +done +echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" diff --git a/conductorScripts/services/minioCheck.sh b/conductorScripts/services/minioCheck.sh new file mode 100755 index 00000000..8af12e6d --- /dev/null +++ b/conductorScripts/services/minioCheck.sh @@ -0,0 +1,7 @@ +#!/bin/sh + +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://minio:9000/minio/health/live")" = "200" ]; do + echo -e "\033[1;36mMinio:\033[0m Not yet reachable, checking again in 15 seconds" + sleep 15 +done +echo -e "\033[1;32mSuccess:\033[0m Minio is reachable" diff --git a/conductorScripts/services/scoreCheck.sh b/conductorScripts/services/scoreCheck.sh new file mode 100755 index 00000000..cba7bcec --- /dev/null +++ b/conductorScripts/services/scoreCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +# Check for Score +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://score:8087/download/ping" -H "accept: */*" -H "Authorization: 68fb42b4-f1ed-4e8c-beab-3724b99fe528" -H "User-Agent: unknown")" = "200" ]; do + echo -e "\033[1;36mScore:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 +done +echo -e "\033[1;32mSuccess:\033[0m Score is now reachable" diff --git a/conductorScripts/services/songCheck.sh b/conductorScripts/services/songCheck.sh new file mode 100755 index 00000000..fd515161 --- /dev/null +++ b/conductorScripts/services/songCheck.sh @@ -0,0 +1,8 @@ +#!/bin/sh + +# Check for Song +until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do + echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 20 seconds" + sleep 20 +done +echo -e "\033[1;32mSuccess:\033[0m Song is now reachable" diff --git a/conductorScripts/services/songDbSetup.sh b/conductorScripts/services/songDbSetup.sh new file mode 100755 index 00000000..8d1b1950 --- /dev/null +++ b/conductorScripts/services/songDbSetup.sh @@ -0,0 +1,14 @@ +#!/bin/sh + +# Create missing empty directories not tracked by git and needed by postgres +echo -e "Setting up empty directories for Songs postgres database" +mkdir -p song/db-folder-init/pg_tblspc +mkdir -p song/db-folder-init/pg_stat +mkdir -p song/db-folder-init/pg_stat_tmp +mkdir -p song/db-folder-init/pg_twophase +mkdir -p song/db-folder-init/pg_snapshots +mkdir -p song/db-folder-init/pg_commit_ts +mkdir -p song/db-folder-init/pg_logical/snapshotss +mkdir -p song/db-folder-init/pg_logical/mappings +mkdir -p song/db-folder-init/pg_replslot +mkdir -p song/db-folder-init/pg_logical/snapshots diff --git a/conductorScripts/services/stageCheck.sh b/conductorScripts/services/stageCheck.sh new file mode 100755 index 00000000..f07d08b9 --- /dev/null +++ b/conductorScripts/services/stageCheck.sh @@ -0,0 +1,9 @@ +#!/bin/sh + +# Check Stage +echo -e "Checking if Stage is reachable" + until curl -s -o /dev/null -w "%{http_code}" "http://stage:3000" | grep -q "200"; do + echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" + sleep 10 + done +echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" diff --git a/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json b/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json new file mode 100644 index 00000000..56c836ba --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/02732061-9daf-5a64-99f5-c550320c7916.json @@ -0,0 +1 @@ +{"object_id": "02732061-9daf-5a64-99f5-c550320c7916", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "CRAM", "file_access": "controlled", "analysis": {"analysis_id": "4ab918ab-a6e9-4cc8-b918-aba6e98cc8b1", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110840020, "first_published_at": 1720110840007, "published_at": 1720110840007, "experiment": {"model": "PromethION", "platform": "ONT", "sequencingDate": "2022-12-12T19:00:00.000Z", "sequencingCenter": "GATC", "experimentalStrategy": "WXS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:34:00.007328"}], "collaborator": [{"name": "OICR", "contactEmail": "sturedman@micr.ca"}], "createdAt": "2024-07-04T16:20:48.424137", "donor": {"primarySite": "Brain", "vitalStatus": "Deceased", "causeOfDeath": "Died of cancer", "survivalTime": 1092, "primaryDiagnosis": [{"followUp": [{"relapseType": null, "intervalOfFollowUp": 95, "submitterFollowUpId": "FO923401", "submitterTreatmentId": "TR923401", "diseaseStatusAtFollowUp": "Relapse or recurrence"}], "treatment": [{"radiation": [{"anatomicalSiteIrradiated": "Neck", "radiationTherapyModality": "Heavy Ions"}], "chemotherapy": [{"drugName": "Azacitidine"}], "treatmentType": ["Chemotherapy", "Radiation therapy"], "treatmentDuration": 1, "responseToTreatment": "Partial response", "submitterTreatmentId": "TR923401", "treatmentStartInterval": 50}], "ageAtDiagnosis": 40, "cancerTypeCode": "C71.8", "clinicalStageGroup": "Stage I", "clinicalTumourStagingSystem": "Rai staging system", "submitterPrimaryDiagnosisId": "PD923401"}, {"followUp": [{"relapseType": null, "intervalOfFollowUp": 67, "submitterFollowUpId": "FO923402", "submitterTreatmentId": "TR923402", "diseaseStatusAtFollowUp": "No evidence of disease"}], "treatment": [{"chemotherapy": [{"drugName": "Tamoxifen"}], "treatmentType": ["Chemotherapy"], "treatmentDuration": 66, "responseToTreatment": "Complete response", "submitterTreatmentId": "TR923402", "treatmentStartInterval": 78}], "ageAtDiagnosis": 75, "cancerTypeCode": "C71.7", "clinicalStageGroup": "Stage II", "clinicalTumourStagingSystem": "St Jude staging system", "submitterPrimaryDiagnosisId": "PD923402"}], "submitterDonorId": "DO9234"}, "publication": {"doi": "10.1038/s41591-023-02650-10", "publication": "Nature"}, "specimen": {"tumourGrade": "G2", "submitterSpecimenId": "SP923402", "tumourGradingSystem": "Three-tier grading system", "specimenAnatomicLocation": "C60", "submitterPrimaryDiagnosisId": "PD923401"}, "workflow": {"runId": "RI9234", "inputs": [{"analysisId": "00000000-0000-0000-0000-0000000009234", "analysisType": "sequencing_experiment"}], "sessionId": "SI9234", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "Bowtie2 Alignment", "workflowVersion": "0.1.0", "workflowShortName": "Bowtie2Aln"}}, "file": {"name": "SP923412.cram", "md5sum": "cc20167c878bd3302e91be057701686b", "size": 116014, "data_type": "Aligned Reads", "index_file": {"object_id": "f701f36d-c795-5dd4-9e4c-e9c33a9dd284", "name": "SP923412.cram.crai", "file_type": "CRAI", "md5sum": "114d6d5a7568666bb5fe3b365197f137", "data_type": "Aligned Reads", "size": 52, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "986121a4-adf0-570b-8a4d-7ef5e63ad06a", "submitter_donor_id": "DO9234", "gender": "Male", "specimens": [{"specimen_id": "40d1385d-6a3c-575c-994b-3fab94bc9c66", "specimen_type": "Tumour - unknown if derived from primary or metastatic", "submitter_specimen_id": "SP923412", "samples": [{"sample_id": "40d1385d-6a3c-575c-994b-3fab94bc9c66", "submitter_sample_id": "SP923412", "sample_type": "Total DNA", "matched_normal_submitter_sample_id": "SP923402"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Lymph node"}]}], "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/configurationFiles/elasticsearchConfigs/es-docs/190e1812-563f-5158-9b35-0925edea4a1d.json b/configurationFiles/elasticsearchConfigs/es-docs/190e1812-563f-5158-9b35-0925edea4a1d.json new file mode 100644 index 00000000..383187b0 --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/190e1812-563f-5158-9b35-0925edea4a1d.json @@ -0,0 +1 @@ +{"object_id": "190e1812-563f-5158-9b35-0925edea4a1d", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "BAM", "file_access": "controlled", "analysis": {"analysis_id": "dc444dde-ffe1-4ffd-844d-deffe19ffd49", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110731277, "first_published_at": 1720110731270, "published_at": 1720110731270, "experiment": {"model": "PromethION", "platform": "ONT", "sequencingDate": "2022-12-12T19:00:00.000Z", "sequencingCenter": "GATC", "experimentalStrategy": "WGS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:32:11.270145"}], "collaborator": [{"name": "OICR", "contactEmail": "sturedman@micr.ca"}], "createdAt": "2024-07-04T16:20:30.946428", "donor": {"primarySite": "Bronchus and lung", "vitalStatus": "Alive", "causeOfDeath": null, "survivalTime": null, "primaryDiagnosis": [{"followUp": [{"relapseType": null, "intervalOfFollowUp": 74, "submitterFollowUpId": "FO745301", "submitterTreatmentId": "TR745301", "diseaseStatusAtFollowUp": "Relapse or recurrence"}], "treatment": [{"treatmentType": ["Hormonal therapy"], "hormoneTherapy": [{"drugName": "Letrozole"}], "treatmentDuration": 32, "responseToTreatment": "Partial response", "submitterTreatmentId": "TR745301", "treatmentStartInterval": 38}], "ageAtDiagnosis": 30, "cancerTypeCode": "C34.3", "clinicalStageGroup": "Stage IB1", "clinicalTumourStagingSystem": "FIGO staging system", "submitterPrimaryDiagnosisId": "PD745301"}, {"followUp": [{"relapseType": null, "intervalOfFollowUp": 46, "submitterFollowUpId": "FO745302", "submitterTreatmentId": "TR745302", "diseaseStatusAtFollowUp": "Relapse or recurrence"}], "treatment": [{"chemotherapy": [{"drugName": "Tamoxifen"}], "treatmentType": ["Chemotherapy"], "treatmentDuration": 44, "responseToTreatment": "Disease progression", "submitterTreatmentId": "TR745302", "treatmentStartInterval": 82}], "ageAtDiagnosis": 20, "cancerTypeCode": "C34.8", "clinicalStageGroup": "Stage III", "clinicalTumourStagingSystem": "Ann Arbor staging system", "submitterPrimaryDiagnosisId": "PD745302"}], "submitterDonorId": "DO7453"}, "publication": {"doi": "10.1038/s41591-023-02650-10", "publication": "Nature"}, "specimen": {"tumourGrade": "Grade Group 3", "submitterSpecimenId": "SP745302", "tumourGradingSystem": "Gleason grade group system", "specimenAnatomicLocation": "C53", "submitterPrimaryDiagnosisId": "PD745301"}, "workflow": {"runId": "RI7453", "inputs": [{"analysisId": "00000000-0000-0000-0000-0000000007453", "analysisType": "sequencing_experiment"}], "sessionId": "SI7453", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "BWA mem2 Alignment", "workflowVersion": "0.8", "workflowShortName": "BWAmem2Aln"}}, "file": {"name": "SP745312.bam", "md5sum": "99a812795e2c6cb4df2fcfe9c26981fe", "size": 125283, "data_type": "Aligned Reads", "index_file": {"object_id": "0dc8a919-fdd0-5c59-b2ea-c654f93279b9", "name": "SP745312.bam.bai", "file_type": "BAI", "md5sum": "4b3a3c832b21ef7f7278b071f2245169", "data_type": "Aligned Reads", "size": 27136, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "663b8536-90a9-51d3-abda-695771e751d0", "submitter_donor_id": "DO7453", "gender": "Male", "specimens": [{"specimen_id": "0874380c-c470-5844-a4a4-5310ddbbac4b", "specimen_type": "Metastatic tumour - additional metastatic", "submitter_specimen_id": "SP745312", "samples": [{"sample_id": "0874380c-c470-5844-a4a4-5310ddbbac4b", "submitter_sample_id": "SP745312", "sample_type": "ctDNA", "matched_normal_submitter_sample_id": "SP745302"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Solid tissue"}]}], "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/configurationFiles/elasticsearchConfigs/es-docs/22a0f109-77ac-5c09-b3e4-26a783e898c1.json b/configurationFiles/elasticsearchConfigs/es-docs/22a0f109-77ac-5c09-b3e4-26a783e898c1.json new file mode 100644 index 00000000..a4616e92 --- /dev/null +++ b/configurationFiles/elasticsearchConfigs/es-docs/22a0f109-77ac-5c09-b3e4-26a783e898c1.json @@ -0,0 +1 @@ +{"object_id": "22a0f109-77ac-5c09-b3e4-26a783e898c1", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "BAM", "file_access": "controlled", "analysis": {"analysis_id": "d99bcc91-7dfd-415b-9bcc-917dfdd15bee", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110980483, "first_published_at": 1720110980465, "published_at": 1720110980465, "experiment": {"model": "SEQUEL IIe", "platform": "PacBio", "sequencingDate": "2021-03-08T19:00:00.000Z", "sequencingCenter": "CGTA", "experimentalStrategy": "WGS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:36:20.465757"}], "collaborator": [{"name": "AICR", "contactEmail": "raygarraty@aicr.ca"}], "createdAt": "2024-07-04T16:21:10.418976", "donor": {"primarySite": "Hematopoietic and reticuloendothelial systems", "vitalStatus": "Alive", "causeOfDeath": null, "survivalTime": null, "primaryDiagnosis": [{"followUp": [{"relapseType": null, "intervalOfFollowUp": 90, "submitterFollowUpId": "FO849001", "submitterTreatmentId": "TR849001", "diseaseStatusAtFollowUp": "Loco-regional progression"}], "treatment": [{"chemotherapy": [{"drugName": "Tamoxifen "}], "treatmentType": ["Chemotherapy", "Hormonal therapy"], "hormoneTherapy": [{"drugName": "Letrozole "}], "treatmentDuration": 72, "responseToTreatment": "Partial response", "submitterTreatmentId": "TR849001", "treatmentStartInterval": 9}], "ageAtDiagnosis": 78, "cancerTypeCode": "C88.3", "clinicalStageGroup": "Stage C", "clinicalTumourStagingSystem": "Binet staging system", "submitterPrimaryDiagnosisId": "PD849001"}], "submitterDonorId": "DO8490"}, "publication": {"doi": "10.1093/nar/gkae188", "publication": "NAR"}, "specimen": {"tumourGrade": "Grade III", "submitterSpecimenId": "SP849001", "tumourGradingSystem": "WHO grading system for CNS tumours", "specimenAnatomicLocation": "C42", "submitterPrimaryDiagnosisId": "PD849001"}, "workflow": {"runId": "RI8490", "inputs": [{"analysisId": "00000000-0000-0000-0000-0000000008490", "analysisType": "sequencing_experiment"}], "sessionId": "SI8490", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "BWA mem2 Alignment", "workflowVersion": 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-0,0 +1 @@ +{"object_id": "ff7b8ca2-2b43-5503-b407-35dc8b0591b0", "study_id": "demo", "data_type": "Aligned Reads", "file_type": "BAM", "file_access": "controlled", "analysis": {"analysis_id": "d7fe62b5-3bab-47b0-be62-b53bab77b0e7", "analysis_type": "quickStartSchema", "analysis_version": 1, "analysis_state": "PUBLISHED", "updated_at": 1720110461116, "first_published_at": 1720110461106, "published_at": 1720110461106, "experiment": {"model": "SEQUEL IIe", "platform": "PacBio", "sequencingDate": "2021-03-08T19:00:00.000Z", "sequencingCenter": "CGTA", "experimentalStrategy": "WGS"}, "analysisStateHistory": [{"initialState": "UNPUBLISHED", "updatedState": "PUBLISHED", "updatedAt": "2024-07-04T16:27:41.106551"}], "collaborator": [{"name": "MICR", "contactEmail": "susannorton@micr.ca"}], "createdAt": "2024-07-04T16:19:40.628302", "donor": {"primarySite": "Bronchus and lung", "vitalStatus": "Alive", "causeOfDeath": null, "survivalTime": null, "primaryDiagnosis": [{"followUp": [{"relapseType": 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"ageAtDiagnosis": 20, "cancerTypeCode": "C34.8", "clinicalStageGroup": "Stage III", "clinicalTumourStagingSystem": "Ann Arbor staging system", "submitterPrimaryDiagnosisId": "PD745302"}], "submitterDonorId": "DO7453"}, "publication": {"doi": "10.1093/nar/gkae188", "publication": "NAR"}, "specimen": {"tumourGrade": "G3", "submitterSpecimenId": "SP745301", "tumourGradingSystem": "Four-tier grading system", "specimenAnatomicLocation": "C11", "submitterPrimaryDiagnosisId": "PD745301"}, "workflow": {"runId": "RI7453", "inputs": [{"analysisId": "00000000-0000-0000-0000-0000000007453", "analysisType": "sequencing_experiment"}], "sessionId": "SI7453", "genomeBuild": "GRCh38_hla_decoy_ebv", "workflowName": "BWA mem2 Alignment", "workflowVersion": "0.8", "workflowShortName": "BWAmem2Aln"}}, "file": {"name": "SP745311.bam", "md5sum": "7df44e073f73923d05893764889039d2", "size": 125255, "data_type": "Aligned Reads", "index_file": {"object_id": "a36547ca-da4a-5591-a0fc-4e11e03a829c", "name": "SP745311.bam.bai", "file_type": "BAI", "md5sum": "dd2b54ec315db4ef29ffeec3777fc8a0", "data_type": "Aligned Reads", "size": 27160, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"}, "repositories": [{"code": "song.overture", "organization": "Overture", "name": "Overture", "type": "S3", "country": "CA", "url": "http://song:8080"}], "donors": [{"donor_id": "663b8536-90a9-51d3-abda-695771e751d0", "submitter_donor_id": "DO7453", "gender": "Male", "specimens": [{"specimen_id": "6473c26f-b273-5172-9bb0-7e95ea9f5020", "specimen_type": "Metastatic tumour", "submitter_specimen_id": "SP745311", "samples": [{"sample_id": "6473c26f-b273-5172-9bb0-7e95ea9f5020", "submitter_sample_id": "SP745311", "sample_type": "Total DNA", "matched_normal_submitter_sample_id": "SP745301"}], "tumour_normal_designation": "Tumour", "specimen_tissue_source": "Blood derived - peripheral blood"}]}], "dataCategory": "Sequencing Reads", "jbrowseCoordinates": "hg38:chr1:100000-200000"} \ No newline at end of file diff --git a/docker-compose.yml b/docker-compose.yml index 5134f693..3c405f50 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -1,10 +1,6 @@ services: - # ====================================== - # Conductor - # -------------------------------------- - # Orchestrates setup with health checks, data population and logging - # -------------------------------------- conductor: + profiles: ["platform", "songDev", "scoreDev", "maestroDev", "arrangerDev", "stageDev"] image: alpine/curl:8.8.0 container_name: conductor ports: @@ -13,124 +9,59 @@ services: - ./persistentStorage/data-keycloak-db:/keycloak/db-folder-init - ./persistentStorage/data-song-db:/song/db-folder-init - ./configurationFiles/elasticsearchConfigs/quickstart_index_template.json:/usr/share/elasticsearch/config/quickstart_index_template.json + - ./configurationFiles/elasticsearchConfigs/es-docs:/es-docs + - ./conductorScripts:/scripts - ./health:/health + environment: + - PROFILE=${PROFILE:-platform} command: > sh -c ' set -e - - echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" - echo -e "\033[1;36m║ Welcome to the Overture QuickStart ║\033[0m" - echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" - # Create missing empty directories not tracked by git and needed by postgres - echo -e "\033[1;35m[1/7]\033[0m Setting up empty directories for postgres" - mkdir -p keycloak/db-folder-init/pg_tblspc - mkdir -p keycloak/db-folder-init/pg_stat - mkdir -p keycloak/db-folder-init/pg_replslot - mkdir -p keycloak/db-folder-init/pg_dynshmem - mkdir -p keycloak/db-folder-init/pg_twophase - mkdir -p keycloak/db-folder-init/pg_notify - mkdir -p keycloak/db-folder-init/pg_serial - mkdir -p keycloak/db-folder-init/pg_snapshots - mkdir -p keycloak/db-folder-init/pg_commit_ts - mkdir -p keycloak/db-folder-init/pg_wal/archive_status - mkdir -p keycloak/db-folder-init/pg_logical/snapshots - mkdir -p keycloak/db-folder-init/pg_logical/mappings - mkdir -p song/db-folder-init/pg_tblspc - mkdir -p song/db-folder-init/pg_stat - mkdir -p song/db-folder-init/pg_replslot - mkdir -p song/db-folder-init/pg_twophase - mkdir -p song/db-folder-init/pg_snapshots - mkdir -p song/db-folder-init/pg_commit_ts - mkdir -p song/db-folder-init/pg_logical/snapshots - mkdir -p song/db-folder-init/pg_logical/mappings - echo -e "\033[1;32mSuccess:\033[0m Databases ready" - - # Wait for Elasticsearch - echo -e "\033[1;35m[2/7]\033[0m Waiting for Elasticsearch (this may take a few minutes)" - sleep 20 - until curl -s -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/_cluster/health" > /dev/null; do - echo -e "\033[1;36mElasticsearch:\033[0m Not yet reachable, checking again in 30 seconds" - sleep 30 - done - echo -e "\033[1;32mSuccess:\033[0m Elasticsearch is reachable" - - # Set up Elasticsearch index template - echo -e "\033[1;35m[3/7]\033[0m Setting up Elasticsearch index template" - if ! curl -s -u elastic:myelasticpassword "http://elasticsearch:9200/_template/index_template" | grep -q "\"index_patterns\"" > /dev/null; then - curl -s -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/_template/index_template" -H "Content-Type: application/json" -d @/usr/share/elasticsearch/config/quickstart_index_template.json > /dev/null && - echo -e "\033[1;32mSuccess:\033[0m Elasticsearch index template created successfully" - else - echo -e "\033[1;36mElasticsearch:\033[0m Index template already exists, skipping creation" - fi - - # Set up Elasticsearch index and alias (needs failure check) - echo -e "\033[1;35m[4/7]\033[0m Setting up Elasticsearch index and alias" - echo -e "\033[1;36mElasticsearch:\033[0m Checking if Elasticsearch index exists" - if ! curl -s -f -u elastic:myelasticpassword -X GET "http://elasticsearch:9200/overture-quickstart-index" > /dev/null 2>&1; then - echo -e "\033[1;32mElasticsearch:\033[0m Creating Elasticsearch index and alias" - response=$$(curl -s -w "\n%{http_code}" -u elastic:myelasticpassword -X PUT "http://elasticsearch:9200/overture-quickstart-index" -H "Content-Type: application/json" -d "{\"aliases\": {\"file_centric\": {\"is_write_index\": true}}}") - http_code=$$(echo "$$response" | tail -n1) - body=$$(echo "$$response" | sed "$$d") - echo -e "\033[1;32mSuccess:\033[0m Index and alias created successfully, Elasticsearch setup complete" - else - echo -e "\033[1;36mElasticsearch:\033[0m Index already exists, skipping creation" - fi - - # Check for Song - echo -e "\033[1;35m[5/7]\033[0m Checking if Song is ready" - until [ "$(curl -s -o /dev/null -w "%{http_code}" "http://song:8080/isAlive" -H "accept: */*")" = "200" ]; do - echo -e "\033[1;36mSong:\033[0m Not yet reachable, checking again in 2 seconds" - sleep 20 - done - echo -e "\033[1;32mSuccess:\033[0m Song is now reachable" - - # Updating health status of the conductor image - # This health file signals container readiness, fulfilling dependencies for search & discovery components, Maestro, Arranger & Stage - echo "healthy" > /health/conductor_health - echo -e "\033[1;36mConductor:\033[0m Updating Container Status. Health check file created" - - # Check Maestro - echo -e "\033[1;35m[6/8]\033[0m Checking if Maestro is reachable (this may take a few minutes)" - until curl -s -X POST "http://maestro:11235/index/repository/song.overture/study/demo" -H "accept: */*" -d "{}" | grep -q "true"; do - echo -e "\033[1;36mMaestro:\033[0m Not yet reachable, checking again in 30 seconds" - sleep 30 - done - echo -e "\033[1;32mSuccess:\033[0m Maestro is now reachable" - - # Check Arranger - echo -e "\033[1;35m[7/8]\033[0m Checking if Arranger is reachable" - until curl -s -o /dev/null -w "%{http_code}" "http://arranger-server:5050/graphql" | grep -q "200"; do - echo -e "\033[1;36mArranger:\033[0m Not yet reachable, checking again in 10 seconds" - sleep 10 - done - echo -e "\033[1;32mSuccess:\033[0m Arranger is now reachable" - - # Check Stage - echo -e "\033[1;35m[8/8]\033[0m Checking if Stage is reachable" - until curl -s -o /dev/null -w "%{http_code}" "http://stage:3000" | grep -q "200"; do - echo -e "\033[1;36mStage:\033[0m Not yet reachable, checking again in 10 seconds" - sleep 10 - done - echo -e "\033[1;32mSuccess:\033[0m Stage is now reachable" - echo -e "\033[1;36m╔══════════════════════════════════════════╗\033[0m" - echo -e "\033[1;36m║ Overture QuickStart Setup Complete ║\033[0m" - echo -e "\033[1;36m╚══════════════════════════════════════════╝\033[0m" - echo -e "\033[1m🌐 Front-end Portal:\033[0m" - echo -e " \033[1;32mhttp://localhost:3000\033[0m\n" - echo -e "\033[1m📚 Overture Platform Guides:\033[0m" - echo -e " \033[1;32mhttps://www.overture.bio/documentation/guides/\033[0m\n" - echo -e "\033[1m🛠️ QuickStart Information:\033[0m" - echo -e " Check the \033[1;33mdocker-compose.yml\033[0m file for details on this QuickStart," - echo -e " including links to relevant sections of our deployment guide.\n" - rm /health/conductor_health + echo "Profile is set to: $PROFILE" + case "$PROFILE" in + platform) + echo "Running platform deployment..." + chmod +x scripts/deployments/platform.sh + scripts/deployments/platform.sh + ;; + stageDev) + echo "Running Stage development environment..." + chmod +x scripts/deployments/stageDev.sh + scripts/deployments/stageDev.sh + ;; + arrangerDev) + echo "Running Arranger development environment..." + chmod +x scripts/deployments/arrangerDev.sh + scripts/deployments/arrangerDev.sh + ;; + maestroDev) + echo "Running Maestro development environment..." + chmod +x scripts/deployments/maestroDev.sh + scripts/deployments/maestroDev.sh + ;; + songDev) + echo "Running Song development environment..." + chmod +x scripts/deployments/songDev.sh + scripts/deployments/songDev.sh + ;; + scoreDev) + echo "Running Score development environment..." + chmod +x scripts/deployments/scoreDev.sh + scripts/deployments/scoreDev.sh + ;; + *) + echo "Invalid profile: $PROFILE. Available options are [platform, songDev, scoreDev, maestroDev, arrangerDev, stageDev]." + exit 1 + ;; + esac exit 0 ' healthcheck: test: ["CMD", "test", "-f", "/health/conductor_health"] - interval: 30s - timeout: 10s + interval: 5s + timeout: 40s retries: 100 - start_period: 45s + start_period: 30s # ================================================================================== # OAuth (KeyCloak) @@ -139,15 +70,16 @@ services: # ====================================== # Keycloak Database # -------------------------------------- - # Pre-populated with a system side API key: 68fb42b4-f1ed-4e8c-beab-3724b99fe528, required for Songs SCORE_ACCESSTOKEN env variable + # Pre-populated with a system wide API key: 68fb42b4-f1ed-4e8c-beab-3724b99fe528, required for Songs SCORE_ACCESSTOKEN env variable # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-the-keycloak-database # -------------------------------------- keycloak-db: + profiles: ["platform", "songDev" , "scoreDev" ,"maestroDev", "stageDev"] depends_on: - conductor image: postgres:14 - container_name: keycloak-db platform: linux/amd64 + container_name: keycloak-db environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 @@ -168,6 +100,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/oauth/#setting-up-keycloak # -------------------------------------- keycloak: + profiles: ["platform", "songDev", "scoreDev", "maestroDev", "stageDev"] image: quay.io/keycloak/keycloak:22.0 container_name: keycloak platform: linux/amd64 @@ -207,31 +140,60 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-kafka # -------------------------------------- kafka: - image: confluentinc/cp-kafka:7.6.1 - container_name: kafka - platform: linux/amd64 - ports: - - "9092:9092" - - "29092:29092" - environment: - KAFKA_PROCESS_ROLES: broker,controller - KAFKA_NODE_ID: 1 - KAFKA_LISTENERS: PLAINTEXT://kafka:9092,CONTROLLER://kafka:9093 - KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092 - KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: PLAINTEXT:PLAINTEXT,CONTROLLER:PLAINTEXT - KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT - KAFKA_CONTROLLER_QUORUM_VOTERS: 1@kafka:9093 - KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER - KAFKA_LOG_DIRS: /var/lib/kafka/data - KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1 - KAFKA_AUTO_CREATE_TOPICS_ENABLE: false - KAFKA_NUM_PARTITIONS: 1 - CLUSTER_ID: "q1Sh-9_ISia_zwGINzRvyQ" - healthcheck: - test: ["CMD", "sh", "-c", "echo stats | nc localhost 9092"] - interval: 30s - timeout: 10s - retries: 5 + profiles: ["platform", "maestroDev"] + image: confluentinc/cp-kafka:7.6.1 + container_name: kafka + platform: linux/amd64 + ports: + - "9092:9092" + - "29092:29092" + volumes: + - ./conductorScripts/services/kafkaSetup.sh:/scripts/kafkaSetup.sh + environment: + # Core Kafka Configuration + KAFKA_PROCESS_ROLES: broker,controller + KAFKA_NODE_ID: 1 + KAFKA_ADVERTISED_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://localhost:29092 + KAFKA_LISTENERS: PLAINTEXT://kafka:9092,EXTERNAL://0.0.0.0:29092,CONTROLLER://kafka:9093 + KAFKA_LISTENER_SECURITY_PROTOCOL_MAP: PLAINTEXT:PLAINTEXT,EXTERNAL:PLAINTEXT,CONTROLLER:PLAINTEXT + KAFKA_INTER_BROKER_LISTENER_NAME: PLAINTEXT + KAFKA_CONTROLLER_QUORUM_VOTERS: 1@kafka:9093 + KAFKA_CONTROLLER_LISTENER_NAMES: CONTROLLER + # Storage Configuration + KAFKA_LOG_DIRS: /var/lib/kafka/data + KAFKA_LOG_RETENTION_HOURS: 168 # 7 days + KAFKA_LOG_RETENTION_BYTES: -1 # Unlimited size + # Topic Configuration + KAFKA_OFFSETS_TOPIC_REPLICATION_FACTOR: 1 + KAFKA_AUTO_CREATE_TOPICS_ENABLE: false + KAFKA_NUM_PARTITIONS: 1 + KAFKA_DEFAULT_REPLICATION_FACTOR: 1 + KAFKA_MIN_INSYNC_REPLICAS: 1 + # Performance Tuning + KAFKA_MESSAGE_MAX_BYTES: 5242880 # 5MB max message size + KAFKA_REPLICA_FETCH_MAX_BYTES: 5242880 + # Logging Configuration + KAFKA_LOG4J_LOGGERS: "kafka.controller=INFO,kafka.producer.async.DefaultEventHandler=INFO,state.change.logger=INFO" + KAFKA_LOG4J_ROOT_LOGLEVEL: INFO + # Cluster Configuration + CLUSTER_ID: "q1Sh-9_ISia_zwGINzRvyQ" + command: > + sh -c ' + echo "Setting up Kafka..." + chmod +x /scripts/kafkaSetup.sh + /scripts/kafkaSetup.sh & + + # Start Kafka broker + /etc/confluent/docker/run + ' + healthcheck: + test: + - "CMD-SHELL" + - > + /bin/kafka-topics --bootstrap-server kafka:9092 --list + interval: 10s + timeout: 5s + retries: 10 # ====================================== # Song Database @@ -240,11 +202,14 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song-db: + profiles: ["platform", "songDev", "scoreDev", "maestroDev"] + depends_on: + - conductor image: postgres:11.1 container_name: song-db platform: linux/amd64 - depends_on: - - conductor + ports: + - "5433:5432" environment: POSTGRES_USER: admin POSTGRES_PASSWORD: admin123 @@ -265,6 +230,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-song # -------------------------------------- song: + profiles: ["platform", "scoreDev", "maestroDev"] image: ghcr.io/overture-stack/song-server:5.2.0 container_name: song platform: linux/amd64 @@ -272,7 +238,7 @@ services: keycloak: condition: service_started kafka: - condition: service_started + condition: service_healthy song-db: condition: service_healthy ports: @@ -305,7 +271,7 @@ services: SPRING_DATASOURCE_USERNAME: admin SPRING_DATASOURCE_PASSWORD: admin123 # Kafka Variables - SPRING_KAFKA_BOOTSTRAPSERVERS: http://kafka:9092 + SPRING_KAFKA_BOOTSTRAPSERVERS: kafka:9092 SPRING_KAFKA_TEMPLATE_DEFAULTTOPIC: song-analysis # Swagger Variable SWAGGER_ALTERNATEURL: /swagger-api @@ -319,6 +285,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#setting-up-object-storage # -------------------------------------- minio: + profiles: ["platform", "scoreDev", "songDev", "maestroDev"] image: minio/minio:RELEASE.2018-05-11T00-29-24Z container_name: minio platform: linux/amd64 @@ -343,14 +310,13 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/datamanagement/#running-score # -------------------------------------- score: + profiles: ["platform", "songDev", "maestroDev"] image: ghcr.io/overture-stack/score-server:5.11.0 container_name: score platform: linux/amd64 depends_on: keycloak: condition: service_started - song: - condition: service_started ports: - "8087:8087" environment: @@ -399,6 +365,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-elasticsearch # -------------------------------------- elasticsearch: + profiles: ["platform", "stageDev", "arrangerDev", "maestroDev"] image: docker.elastic.co/elasticsearch/elasticsearch:7.17.1 container_name: elasticsearch platform: linux/amd64 @@ -431,6 +398,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-maestro # -------------------------------------- maestro: + profiles: ["platform"] image: ghcr.io/overture-stack/maestro:4.3.0 container_name: maestro platform: linux/amd64 @@ -453,7 +421,7 @@ services: MAESTRO_REPOSITORIES_0_CODE: song.overture MAESTRO_REPOSITORIES_0_URL: http://song:8080 MAESTRO_REPOSITORIES_0_NAME: Overture - MAESTRO_REPOSITORIES_0_ORGANIZATION: Overture + MAESTRO_REPOSITORIES_0_ORGANIZATION: OICR MAESTRO_REPOSITORIES_0_COUNTRY: CA # Elasticsearch Variables MAESTRO_ELASTICSEARCH_CLUSTER_NODES: http://elasticsearch:9200 @@ -465,7 +433,7 @@ services: MAESTRO_ELASTICSEARCH_INDEXES_FILECENTRIC_NAME: overture-quickstart-index MAESTRO_ELASTICSEARCH_INDEXES_FILECENTRIC_ALIAS: file_centric MAESTRO_ELASTICSEARCH_CLIENT_BASICAUTH_ENABLED: true - MANAGEMENT_HEALTH_ELASTICSEARCH_ENABLED: "false" + MANAGEMENT_HEALTH_ELASTICSEARCH_ENABLED: false # Spring Variables SPRING_MVC_ASYNC_REQUESTTIMEOUT: -1 SPRINGDOC_SWAGGERUI_PATH: /swagger-api @@ -480,6 +448,7 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#running-arranger # -------------------------------------- arranger-server: + profiles: ["platform", "stageDev"] image: ghcr.io/overture-stack/arranger-server:3.0.0-beta.33 container_name: arranger-server platform: linux/amd64 @@ -501,9 +470,6 @@ services: ES_HOST: http://elasticsearch:9200 ES_USER: elastic ES_PASS: myelasticpassword - # Stage Variables - REACT_APP_BASE_URL: http://stage:3000 - REACT_APP_ARRANGER_ADMIN_ROOT: http://arranger-server:5050/graphql # ================================================================================== # F. Discovery (Stage) @@ -516,14 +482,13 @@ services: # Documentation Link: https://www.overture.bio/documentation/guides/deployment/dataportal/#setting-up-stage # -------------------------------------- stage: + profiles: ["platform", "arrangerDev"] image: ghcr.io/overture-stack/stage:a211593 container_name: stage platform: linux/amd64 depends_on: conductor: condition: service_healthy - arranger-server: - condition: service_started ports: - "3000:3000" environment: @@ -542,10 +507,8 @@ services: NEXT_PUBLIC_KEYCLOAK_CLIENT_ID: webclient KEYCLOAK_CLIENT_SECRET: ikksyrYaKX07acf4hpGrpKWcUGaFkEdM NEXT_PUBLIC_KEYCLOAK_PERMISSION_AUDIENCE: dms - # Score Variables - NEXT_PUBLIC_SCORE_API_URL: http://score:8087 # Arranger Variables NEXT_PUBLIC_ARRANGER_DOCUMENT_TYPE: file NEXT_PUBLIC_ARRANGER_INDEX: file_centric NEXT_PUBLIC_ARRANGER_API_URL: http://arranger-server:5050 - NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS: repositories.code, analysis.analysis_id, object_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id \ No newline at end of file + NEXT_PUBLIC_ARRANGER_MANIFEST_COLUMNS: repositories.code, analysis.analysis_id, object_id, study_id, file_type, file.name, file.size, file.md5sum, file.index_file.object_id, donors.donor_id, donors.specimens.samples.sample_id diff --git a/make.bat b/make.bat new file mode 100644 index 00000000..9e86a98a --- /dev/null +++ b/make.bat @@ -0,0 +1,51 @@ +@echo off +setlocal enabledelayedexpansion + +if "%1"=="" goto help + +if "%1"=="platform" ( + set PROFILE=platform + goto run +) +if "%1"=="stageDev" ( + set PROFILE=stageDev + goto run +) +if "%1"=="arrangerDev" ( + set PROFILE=arrangerDev + goto run +) +if "%1"=="maestroDev" ( + set PROFILE=maestroDev + goto run +) +if "%1"=="songDev" ( + set PROFILE=songDev + goto run +) +if "%1"=="scoreDev" ( + set PROFILE=scoreDev + goto run +) +if "%1"=="down" ( + set PROFILE=platfrom + docker compose down + goto :eof +) + +goto help + +:run +docker compose --profile %PROFILE% up --attach conductor +goto :eof + +:help +echo Usage: build.bat [target] +echo Available targets: +echo platform +echo stageDev +echo arrangerDev +echo maestroDev +echo songDev +echo scoreDev +echo down