Auto-generated Pull Request for feat/goldenbraid-dagu-workflows#685
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github-actions[bot] wants to merge 18 commits intodevelopfrom
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Auto-generated Pull Request for feat/goldenbraid-dagu-workflows#685github-actions[bot] wants to merge 18 commits intodevelopfrom
github-actions[bot] wants to merge 18 commits intodevelopfrom
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- Created dagu-goldenbraid-plasmid.yaml and dagu-goldenbraid-inventory.yaml - Updated dagu-plasmid-ontology.yaml for consistency - Configured mandatory parameters using JSON schema validation for all goldenbraid dagu workflows
- Remove ONTOLOGY_TERM from required list in dagu schema - Provide 'vector' as the default value
Dagu parameters defined only in schema may not be exported to the shell, triggering 'parameter not set' errors when using set -u. This ensures a fallback to 'vector' directly in the script.
…ment variable Remove the explicit --kubeconfig flag in favor of setting the KUBECONFIG environment variable.
Standardize indentation by replacing spaces with tabs to comply with Go formatting conventions and improve consistency across the codebase.
- Update `dagu-plasmid-ontology.yaml` to accept `ENV` and `NAMESPACE` parameters, allowing execution outside of the dev cluster. - Implement dynamic `KUBECONFIG` resolution in Dagu to support custom kubeconfig paths or local dev clusters. - Refactor `justfile` commands to accept a `k8s_namespace` argument, replacing hardcoded "dev" namespaces. - Add a private `check-kubeconfig` task to ensure environment connectivity before running jobs. The previous implementation was tightly coupled to a local k3d dev cluster. These changes decouple the orchestration logic from the infrastructure, enabling the deployment of plasmid ontology jobs to staging and production environments by providing the appropriate namespace and kubeconfig credentials.
…-kubeconfig
- Redirect check-kubeconfig echo to stderr to prevent stdout pollution
- Convert all kubectl apply + fixed name to kubectl create + generateName
- Append -o jsonpath='{.metadata.name}' to all job creations to ensure only the job name is output
- This allows clean orchestration capture in dagu without parsing
- Add ENV, NAMESPACE, and KUBE_CFG to dagu-goldenbraid-inventory.yaml and dagu-goldenbraid-plasmid.yaml - Inject dynamic KUBECONFIG resolution block into both workflows - Remove fragile string parsing (grep/head) from all three workflow submit steps - Explictly pass k8s_namespace to downstream just commands (wait, logs, debug) - This standardizes all three Dagu files to utilize the refactored justfile outputs
…ug flag - Add debug parameter to run-goldenbraid, run-goldenbraid-inventory, and run-goldenbraid-plasmid-ontology - Implement conditional logic for TTL, generateName, and debug logging arguments - Fix inventory-debug TTL (120 -> 300) - Remove redundant -debug recipes to reduce boilerplate (~80 lines removed)
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## develop #685 +/- ##
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- Coverage 3.92% 2.42% -1.50%
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Files 624 616 -8
Lines 69583 68530 -1053
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- Hits 2731 1662 -1069
- Misses 66791 66810 +19
+ Partials 61 58 -3
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…ters Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Introduce new JSON schema files to define and validate configuration parameters for GoldenBraid inventory, plasmid imports, and ontology assignments.
Move parameter schemas to external JSON files to reduce duplication and improve maintainability. Standardize the KUBECONFIG generation logic across workflows by using a consistent shell pattern and moving the logic into a handler init block for better lifecycle management. Update the justfile to parse the new external JSON schema format using jq.
Remove the implicit check-kubeconfig dependency and require an explicit k8s_config argument for all Kubernetes-related tasks.
Move the kubernetes configuration logic from the `handler_on` init block into a dedicated `k8s-generate` step. Update the pipeline steps to use the generated `KPATH` output. The previous approach using `dotenv` and `handler_on` was less explicit and harder to debug. By moving the configuration logic into a standard step, the pipeline flow becomes more transparent, dependencies are explicitly managed, and the `preconditions` feature allows for cleaner separation between successful log retrieval and failure debugging.
- Remove check-kubeconfig dependency from run-goldenbraid and run-goldenbraid-inventory - Add k8s_config parameter to both recipes - Use --kubeconfig flag instead of KUBECONFIG environment variable - Align with run-goldenbraid-plasmid-ontology pattern for consistency
…dling - Replace KUBECONFIG environment variable with k8s-generate step - Pass kubeconfig path as explicit parameter to just recipes - Align with plasmid-ontology workflow pattern for consistency
- Replace KUBECONFIG environment variable with k8s-generate step - Pass kubeconfig path as explicit parameter to just recipes - Complete consistency across all goldenbraid Dagu workflows
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Pulling 'feat/goldenbraid-dagu-workflows into develop. Please review and merge.