--- name: multi-service-dependency-management description: Use when your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed and initialized in a coordinated sequence, with explicit dependency declarations and network communication paths between. license: CC-BY-4.0 metadata: edam_topics: - http://edamontology.org/topic_0605 tools: - MAGMa - Docker Compose - Docker derived_from: - doi: 10.5702/massspectrometry.S0033 title: magma evidence_spans: - MAGMa is a abbreviation for 'Ms Annotation based on in silico Generated Metabolites'. - MAGMa is a abbreviation for 'Ms Annotation based on in silico Generated Metabolites' claims: [] provenance: collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v1 assembled_by: scripts/collect_metabolomics_collection.py sources: - build: coll_magma doi: 10.5702/massspectrometry.S0033 title: magma dedup_kept_from: coll_magma schema_version: 0.2.0 --- # multi-service-dependency-management ## Summary Orchestrate and manage interdependencies among multiple containerized microservices by defining service topology, inter-service networking, health checks, and startup ordering. This skill is essential when deploying a multi-component research system (e.g., MAGMa's four subprojects) as Docker services with explicit dependency chains. ## When to use Your research software comprises multiple independent subprojects or microservices (calculation engines, web services, data processors, websites) that must be deployed and initialized in a coordinated sequence, with explicit dependency declarations and network communication paths between services. ## When NOT to use - Your system is monolithic or consists of a single service—use standard single-container Docker deployment instead. - Services have no explicit interdependencies or can be deployed and run independently in isolation. - You are deploying to a Kubernetes cluster or other orchestration platform with native service mesh support; use Helm charts or native orchestration manifests instead. ## Inputs - GitHub repository containing multiple subproject directories with Dockerfiles - Existing build scripts and documentation describing service configurations - Service interdependency documentation or README statements of which services depend on which ## Outputs - docker-compose.yml manifest file with all services, ports, environment variables, volumes, and depends_on declarations - Validated and tested multi-service orchestration that runs successfully end-to-end ## How to apply Parse the project structure and documentation to identify all distinct service components and their runtime dependencies. For MAGMa, this means recognizing that the web application (magmaweb) depends on joblauncher, which in turn depends on the job calculation service, and that the job service requires a pubchem lookup database. Extract service configurations (ports, environment variables, volume mounts) from existing Dockerfiles and build scripts. Define a docker-compose.yml manifest that specifies each service's image, exposed ports, environment configuration, and volume mounts. Use the `depends_on` directive to enforce startup ordering and health checks to verify service readiness before dependent services begin. Configure inter-service networking to allow joblauncher to reach the job service, magmaweb to reach joblauncher, and the job service to access the pubchem database. Validate the manifest syntax and test the full orchestration workflow by building and running all composed services together to confirm the dependency chain resolves correctly. ## Related tools - **Docker Compose** (Primary orchestration tool used to define, configure, and manage multi-service deployment with dependency declarations and networking) - **MAGMa** (Target multi-service system consisting of four subprojects (emetabolomics_site, job, joblauncher, pubchem) that require coordinated containerized deployment) — https://github.com/NLeSC/MAGMa - **Docker** (Container runtime underlying docker-compose; used to build and run individual service images referenced in the composition) ## Evaluation signals - docker-compose.yml is syntactically valid (verified by `docker-compose config`) - All four service images (magmaweb, joblauncher, job, pubchem) build successfully without errors - Services start in the correct dependency order: pubchem before job, job before joblauncher, joblauncher before magmaweb - Health checks (if configured) report all services healthy before dependent services attempt to communicate - Inter-service network communication succeeds: magmaweb can reach joblauncher, joblauncher can reach job, job can query pubchem lookup database ## Limitations - Docker Compose is suitable for development and single-node deployment; for production multi-node clusters, Kubernetes or similar platforms are required. - The success of this skill depends critically on accurate extraction of service dependencies from incomplete or scattered documentation; missing or incorrectly inferred dependencies will cause runtime failures. - Health check configurations (e.g., HTTP endpoints, database connectivity checks) must be tailored to each service; generic health checks may not catch all failure modes. ## Evidence - [readme] Subprojects: emetabolomics_site, job, joblauncher, pubchem, web: "Subprojects: - emetabolomics_site - The http://www.emetabolomics.org website - job - Runs MAGMa calculation - joblauncher - Webservice to execute jobs - pubchem - Processing of PubChem database" - [readme] Service interdependencies chain: "The `emetabolomics_site` website can be used as starting pages for the `web` application. - The `job` calculation requires a pubchem lookup database which can be made using the `pubchem`" - [readme] MAGMa repository source: "To contribute contact me via Github issue or pull request at https://github.com/NLeSC/MAGMa" - [readme] Docker readiness indicator: ".. image:: https://img.shields.io/badge/docker-ready-blue.svg :target: https://hub.docker.com/r/nlesc/magma"