Generate alternatives#113
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Translates node status (Keep/Ban/Vary) and edge status (chain/break) into APE constraint objects and assembles the full synthesis config JSON including I/O EDAM tuples, tool taxonomy paths, and generation parameters.
…e initialization Handles CWL file upload via POST /alternatives/parse, builds the ReactFlow graph from the parsed DAG, and initialises all tool nodes to Keep status (§4.3 conservative strategy). Node clicks cycle through Keep/Vary/Ban; edge clicks toggle chain/break constraints.
… modal Shows active Keep/Ban/Chain/Break constraints, APE synthesis parameters (min/max length, timeout, solutions), a generate button with loading state, and a modal to inspect the generated APE config JSON.
…w, and synthesis Shows a drag-and-drop CWL upload zone before a file is loaded, then switches to a ReactFlow graph with a filename pill overlay. Builds the APE synthesis config from the current constraint state and navigates to /explore/results after successful synthesis.
…aStore Accepts a pre-built APE config object and an optional input tool sequence string. After synthesis, filters out any solution whose descriptive_name matches the input workflow's tool sequence to ensure all returned alternatives genuinely differ from the uploaded workflow.
Call GET /ape/alternatives/warm when GenerateAlternatives mounts. Show a full-page spinner while the backend loads the EDAM ontology; show an error state if loading fails. Upload zone renders only after warm-up completes.
EDAM loading is handled transparently by the backend on the first /parse request. No explicit frontend warm-up needed.
APE generates step names from a tool's label, but use_m/not_use_m/connected_op constraints must reference the taxonomy id, which differs for some tools (e.g. mzRecal -> mzrecal1, Sage -> Sage-proteomics, idconvert -> two ids). Add LABEL_TO_TOOL_IDS to map each label to its id(s); unknown labels fall back to the label itself.
Convert runSynthesisWithRawConfig to async/await, retry the synthesis call once on failure (1.5s delay), and include the response body in the error so transient backend issues surface clearly. Add ExploreDataStore tests for the post-filtering of identical tool sequences.
Two-line tool cards with a clipped accent bar for status; compact dashed data nodes for inputs/outputs. Dagre now uses separate dimensions per node type (tool 210x70, data 180x38) for correct automatic layout.
InfoTooltip renders configurable contextual help on the graph canvas, the active-constraints panel, and the APE-settings panel. The Show-JSON modal highlights the generated config without an external dependency. Canvas height now scales with the viewport.
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@eladrion And here is the corresponding PR for the frontend. Tagging you directly again due to missing assignment permissions. |
eladrion
reviewed
Jun 29, 2026
eladrion
reviewed
Jun 29, 2026
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Contributor
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@aaronstrachardt No worries, that's what reviews are for. I looked a bit into the RestApe PR and left you comments. When we have streamlined that one a bit, I can test on the internal instance. |
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Overview
This PR adds the user interface and client-side logic for the "Alternative Workflows" prototype component. It allows users to upload a CWL file, interact with it as a graph, and generate structural alternatives. It is designed to work together with the new
/alternatives/parseendpoint introduced in the correspondingrestapePR.Changes
Alternative Workflowscomponent usingReactFlowfor the graph visualization anddagrefor automated top-down layoutingMobX) to handle cyclic node and edge interactions (Keep/Vary/Ban and Chain/Break)generateApeConfig) to translate the visual UI markers directly into APE JSON constraints on the client sideLABEL_TO_TOOL_IDS) to resolve discrepancies between tool labels and EDAM taxonomy IDsTesting
The code has been tested via the added unit tests in Jest. I also tested the complete end-to-end flow manually on my local machine by running this branch against the updated
restapebackend branch.Checklist