Tima Entry Point Validation

---
name: tima-entry-point-validation
description: Use when when you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.
license: CC-BY-4.0
metadata:
  edam_operation: http://edamontology.org/operation_0335
  edam_topics:
  - http://edamontology.org/topic_3520
  tools:
  - R
  - Docker
  - tima-r Docker image
  - tima
derived_from:
- doi: 10.3389/fpls.2019.01329
  title: tima
evidence_spans:
- The initial work is available at <https://doi.org/10.3389/fpls.2019.01329>
claims: []
provenance:
  collection: https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v1
  assembled_by: scripts/collect_metabolomics_collection.py
  sources:
  - build: coll_tima
    doi: 10.3389/fpls.2019.01329
    title: tima
  dedup_kept_from: coll_tima
schema_version: 0.2.0
---

# tima-entry-point-validation

## Summary

Verify that a tima Docker container (adafede/tima-r) successfully pulls from Docker Hub and launches without errors, confirming the container's entry point is accessible and functional.

## When to use

When you have obtained or are considering use of the tima Docker image (adafede/tima-r) and need to confirm that the containerized environment is operational before proceeding with metabolite annotation workflows. This is a smoke test to catch environment or registry issues early.

## When NOT to use

- You are using a native R installation of tima instead of a container — use R package import validation instead.
- You have already validated the container in a previous step in the same workflow — do not repeat unnecessarily.
- Docker is not available or Docker daemon is not running in your environment.

## Inputs

- Docker Hub registry URL (adafede/tima-r)
- Docker daemon (local or remote)

## Outputs

- Pulled Docker image (adafede/tima-r)
- stdout/stderr from tima help or version command (text output confirming functional entry point)

## How to apply

Pull the Docker image adafede/tima-r from Docker Hub using `docker pull`. Launch a container instance from the pulled image. Execute a tima help or version command within the running container to confirm the entry point is accessible and functional. A successful invocation should return version information or help text without errors, confirming the R environment and tima package are correctly installed and callable within the container.

## Related tools

- **Docker** (Container platform used to pull and launch the tima-r image) — https://www.docker.com/
- **tima-r Docker image** (Containerized R environment with tima package and dependencies pre-installed) — https://hub.docker.com/r/adafede/tima-r/
- **tima** (R package executed within the container to validate entry point functionality) — https://github.com/taxonomicallyinformedannotation/tima

## Examples

```
docker pull adafede/tima-r && docker run --rm adafede/tima-r R --version
```

## Evaluation signals

- docker pull command completes without 'manifest not found' or authentication errors
- docker run successfully creates and starts a container instance without immediate exit or crash
- tima help or version command executes within container and returns non-empty output
- Command exit code is 0 (success), not a non-zero error code
- No errors related to missing R packages, library linking, or entry point are reported in stderr

## Limitations

- This smoke test validates only the container's basic operability and R environment; it does not validate the correctness of tima's underlying algorithms or dependencies (e.g., SIRIUS, GNPS libraries).
- Network access to Docker Hub is required to pull the image; offline environments or restricted registries will fail.
- The test does not verify data input/output workflows or the Shiny app interface (`run_app()`) — only the CLI entry point.

## Evidence

- [other] Does the tima Docker container (adafede/tima-r) successfully pull and launch without errors?: "Does the tima Docker container (adafede/tima-r) successfully pull and launch without errors?"
- [other] Workflow steps from task_003: "1. Pull the Docker image adafede/tima-r from Docker Hub using docker pull. 2. Launch a container instance from the pulled image. 3. Execute a tima help or version command within the running container"
- [readme] Docker badge and availability: "[![Docker](https://img.shields.io/badge/Docker-2496ED?logo=docker&logoColor=white.png)](https://hub.docker.com/r/adafede/tima-r/)"
- [readme] Docker pull and launch instructions from README: "docker pull adafede/tima-r"