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."
1---2name: deployment-artifact-documentation3description: 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.4license: CC-BY-4.05---67# deployment-artifact-documentation89## Summary1011Document 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.1213## When to use1415Apply 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.1617## When NOT to use1819- Application has no external database dependency or all credentials are embedded in code (use secrets management instead).20- Deployment target is a containerized environment (e.g., Docker) where configuration is already captured in a Dockerfile or compose file.21- App is a standalone CLI tool with no app-server runtime or shared library requirements.2223## Inputs2425- app-server type and version identifier26- database connection parameters (URL, credentials, JDBC driver)27- required library list with version numbers and file names28- JNDI or data-source configuration schema for target app server2930## Outputs3132- deployment configuration manifest or README33- data-source configuration template (XML or app-server format)34- documented list of prerequisite contacts and procedures35- JAR dependency inventory with installation paths3637## How to apply3839Document 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.4041## Related tools4243- **javax.faces-2.2.12.jar** (JSF (Java Server Faces) library required on app-server classpath for CEU Mass Mediator runtime)44- **CEU Mass Mediator** (metabolite annotation tool requiring documented deployment configuration) — https://github.com/albertogilf/ceuMassMediator4546## Evaluation signals4748- README explicitly names the database contact person and email ([redacted-email]) so a new operator does not have to search the codebase.49- Data-source configuration template includes all required parameters: database URL, username, password placeholder, and JNDI binding name.50- 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).51- Deployment steps are in execution order: access request → credential receipt → data-source creation → library installation → validation.52- A practitioner unfamiliar with the project can follow the README and deploy the tool without modifying code or contacting original authors.5354## Limitations5556- 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.57- No changelog was found in the source repository, making it difficult to track deployment changes across versions.58- JDBC data-source configuration syntax varies by app-server type (JBoss, Tomcat, WebSphere, etc.); a single generic template may not cover all targets.59- This skill documents static configuration but does not cover runtime environment validation (e.g., confirming database connectivity, JAR version compatibility at startup).6061## Evidence6263- [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]."64- [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."65- [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"66- [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."67- [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."
HolobiomicsLab 