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Workflomics
restape
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Generate alternatives
- #101
#101
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eladrion
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Workflomics:feat_workflow_alternative_generation
Workflomics/restape:feat_workflow_alternative_generation
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Jul 3, 2026
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Generate alternatives
#101
eladrion
merged 18 commits into
Workflomics:feat_workflow_alternative_generation
Workflomics/restape:feat_workflow_alternative_generation
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aaronstrachardt:generate-alternatives
aaronstrachardt/restape:generate-alternatives
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Commits on Jun 29, 2026
fix: replace Lombok annotations with explicit Java code
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feat: add snakeyaml dependency for CWL v1.2 parsing
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feat: add DTOs for CWL parse response
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feat: add EDAMTaxonomyService for async EDAM OWL label resolution
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feat: add CwlParser to extract DAG from CWL v1.2 workflows
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feat: add /alternatives/parse REST endpoint
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revert: restore Lombok annotations (target Java 17)
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refactor: replace OWL-based taxonomy loading with static JSON lookup
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refactor: load EDAM OWL lazily on demand instead of static JSON
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refactor: remove /alternatives/warm endpoint
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test: add T-PAR-01, T-TAX-01, T-ROB-01 for CwlParser and EdamLabels
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test: add @SpringBootTest to CwlParserTest and EdamLabelsTest for style consistency
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test: add AlternativesControllerTest integration tests for POST /alternatives/parse
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test: rename test methods to camelCase, fix two failing tests in AlternativesControllerTest
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refactor: load EDAM labels from static JSON instead of live OWL download
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refactor: remove unnecessary references
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refactor: replace ApeTaxTuple.java with the existing TaxonomyElem.java as suggested in the review
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refactor: Use @Getter/@AllArgsConstructor on GraphEdge.java, GraphNode.java and ParseResponse.java and replace GraphNode's string type with a enum, as suggested in review.
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