# Deployment Artifact Documentation

> Use when preparing a scientific application (such as a metabolite annotation tool) for deployment to a shared or production app server, particularly when the deployment requires external database access, Java library dependencies, and credential management.

- Skill: `holobiomicslab/deployment-artifact-documentation` (Agent Skill)
- Install (CLI): `npx skillmds@latest add holobiomicslab/deployment-artifact-documentation`
- Raw SKILL.md: https://api.skillmd.com/api/skills/holobiomicslab/deployment-artifact-documentation/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Docs & Writing
- License: CC-BY-4.0
- Author: HolobiomicsLab (https://skillmd.com/u/holobiomicslab)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/holobiomicslab/deployment-artifact-documentation

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# deployment-artifact-documentation

## Summary

Document deployment configuration artifacts (data sources, library dependencies, credentials, JNDI bindings) for reproducible app-server deployment of metabolomics tools. This skill ensures future operators and collaborators can reconstruct the exact runtime environment without trial-and-error.

## When to use

Apply this skill when preparing a scientific application (such as a metabolite annotation tool) for deployment to a shared or production app server, particularly when the deployment requires external database access, Java library dependencies, and credential management. Trigger on: (1) need to hand off deployment to another team member or institution, (2) app requires JDBC data-source configuration, (3) specific JAR library versions are non-standard, or (4) database access is gated behind a contact procedure.

## When NOT to use

- Application has no external database dependency or all credentials are embedded in code (use secrets management instead).
- Deployment target is a containerized environment (e.g., Docker) where configuration is already captured in a Dockerfile or compose file.
- App is a standalone CLI tool with no app-server runtime or shared library requirements.

## Inputs

- app-server type and version identifier
- database connection parameters (URL, credentials, JDBC driver)
- required library list with version numbers and file names
- JNDI or data-source configuration schema for target app server

## Outputs

- deployment configuration manifest or README
- data-source configuration template (XML or app-server format)
- documented list of prerequisite contacts and procedures
- JAR dependency inventory with installation paths

## How to apply

Document the deployment configuration in a structured README or manifest that captures: (1) prerequisite steps (e.g., contact person and email for database access), (2) data-source configuration syntax and required credentials (database URL, username placeholder), (3) library dependencies with exact version numbers and installation location (app-server lib path or classpath), and (4) JNDI binding name and connection parameters. Ground each step in the application's actual architecture: for CEU Mass Mediator, this means explicitly naming the javax.faces library version, specifying that a data-source XML must be created on the app server, and providing [redacted-email] as the contact for CEU database access. Validate completeness by ensuring a new operator could follow the steps without needing to reverse-engineer the original deployment.

## Related tools

- **javax.faces-2.2.12.jar** (JSF (Java Server Faces) library required on app-server classpath for CEU Mass Mediator runtime)
- **CEU Mass Mediator** (metabolite annotation tool requiring documented deployment configuration) — https://github.com/albertogilf/ceuMassMediator

## Evaluation signals

- README explicitly names the database contact person and email ([redacted-email]) so a new operator does not have to search the codebase.
- Data-source configuration template includes all required parameters: database URL, username, password placeholder, and JNDI binding name.
- Library inventory lists exact version numbers (e.g., javax.faces-2.2.12.jar, not just 'javax.faces') and specifies installation location (app-server lib path).
- Deployment steps are in execution order: access request → credential receipt → data-source creation → library installation → validation.
- A practitioner unfamiliar with the project can follow the README and deploy the tool without modifying code or contacting original authors.

## Limitations

- Documentation is only as current as its maintenance; credentials, contact emails, and library URLs may become stale if not kept in sync with actual deployment.
- No changelog was found in the source repository, making it difficult to track deployment changes across versions.
- JDBC data-source configuration syntax varies by app-server type (JBoss, Tomcat, WebSphere, etc.); a single generic template may not cover all targets.
- This skill documents static configuration but does not cover runtime environment validation (e.g., confirming database connectivity, JAR version compatibility at startup).

## Evidence

- [readme] It is necessary to access an internal database of CEU. Request access to [redacted-email].: "It is necessary to access an internal database of CEU. Request access to [redacted-email]."
- [readme] Once you have access to the database, it is needed a data-source from the app server used with the credentials provided.: "Once you have access to the database, it is needed a data-source from the app server used with the credentials provided."
- [readme] The next library is needed in the app server: javax.faces-2.2.12.jar: "The next library is needed in the app server: javax.faces-2.2.12.jar"
- [other] Obtain or verify availability of javax.faces-2.2.12.jar library and prepare it for inclusion in the application server library path or classpath.: "Obtain or verify availability of javax.faces-2.2.12.jar library and prepare it for inclusion in the application server library path or classpath."
- [other] Document the deployment configuration (data-source name, JNDI binding, database URL, username, and JAR dependency location) in a configuration manifest or README.: "Document the deployment configuration (data-source name, JNDI binding, database URL, username, and JAR dependency location) in a configuration manifest or README."