Fix WASM e2e regressions: genetic-code numeric ID and tree-source mount race - #138
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Two regressions in v0.1.0-beta.32 blocking WASM e2e tests. Regression 1: The Bug 4 fix in #136 switched --code to pass the numeric geneticCodeId on the assumption that HyPhy WASM's CLI accepts it. It does not. HyPhy rejects --code 0 with "'0' is not a valid value for parameter 'Choose Genetic Code'", breaking every analysis since beta.32. Revert to passing the descriptive name. The original Bug 4 (multi-word names like 'Vertebrate mitochondrial' getting space-split by aioli) returns, but only affects users who pick a non-Universal code — the proper fix is to pass args as an array to cliObj.exec(cmd, argsArray), which is a larger refactor tracked separately. Regression 2: The Bug 3 fix's reactive switch fired at component mount before any file was loaded. At that point treeStore is empty, so hasInferredTree is false and selectedTreeSource gets switched away from 'inferred'. When the user later loads a file with a valid NJ tree, the state is stuck at 'upload-new' and clicking Run throws "No uploaded tree file available". Gate the reactive on $fileMetricsStore so it only runs after datareader has completed.
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Summary
Two regressions in v0.1.0-beta.32 (PR #136) blocking WASM e2e tests. Caught by the failing `FEL analysis end-to-end` job — screenshot showed the analysis crashing with `HyPhy error: '0' is not a valid value for parameter 'Choose Genetic Code'`, which led to the second regression once the first was fixed.
Regression 1 — `--code` numeric ID rejected by HyPhy
The Bug 4 fix in #136 switched `--code` from passing the descriptive name to passing the numeric `geneticCodeId`, on the assumption (taken from `BackendAnalysisRunner`) that HyPhy accepts numeric codes. It does not. HyPhy WASM rejects `--code 0` with `'0' is not a valid value for parameter 'Choose Genetic Code'`, breaking every analysis since beta.32.
Revert to passing the descriptive name. The original Bug 4 (multi-word names like `'Vertebrate mitochondrial'` getting space-split by aioli's `exec()` into `--code Vertebrate` + stray `mitochondrial`) returns, but only affects users who pick a non-Universal code.
Proper fix tracked separately: refactor `WasmAnalysisRunner.js` to pass args as an array to `cliObj.exec(cmd, argsArray)` instead of building a single space-joined string. The aioli worker source confirms this bypasses the split entirely.
Regression 2 — tree-source auto-switch race
The Bug 3 fix added a reactive in `AnalyzeTab.svelte` to switch `selectedTreeSource` away from `'inferred'` when `hasInferredTree` was false. That reactive fired at component mount, before any file was loaded. At that point `treeStore` is empty and `hasInferredTree` is false, so it switched the state to `'upload-new'`. When the user then loaded a file with a valid NJ tree, the state was stuck and clicking Run threw "No uploaded tree file available".
Gate the reactive on `$fileMetricsStore` so it only runs after datareader has completed. At that point `treeStore` has been populated (in the same synchronous block as `fileMetricsStore.set`), so the reactive sees the correct `hasInferredTree` value.
Test plan
Follow-up