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Bugfix for Sequence Customization #1516

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merged 3 commits into from
Oct 22, 2024
Merged

Bugfix for Sequence Customization #1516

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87b7f7b
Replace string output for customized sequence
cartermak Oct 20, 2024
caa100b
Make sure output is string or undefined
mattdailis Oct 21, 2024
057d24e
Explicitly handle object, undefined, and null cases
mattdailis Oct 22, 2024
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13 changes: 11 additions & 2 deletions src/components/sequencing/SequenceEditor.svelte
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Original file line number Diff line number Diff line change
Expand Up @@ -265,10 +265,19 @@
const sequence = viewUpdate.state.doc.toString();
disableCopyAndExport = sequence === '';
const tree = syntaxTree(viewUpdate.state);
const output = await selectedOutputFormat?.toOutputFormat?.(tree, sequence, commandDictionary, sequenceName);
let output = await selectedOutputFormat?.toOutputFormat?.(tree, sequence, commandDictionary, sequenceName);

if ($sequenceAdaptation?.modifyOutput !== undefined && output !== undefined) {
$sequenceAdaptation?.modifyOutput(output, parameterDictionaries, channelDictionary);
const modifiedOutput = $sequenceAdaptation.modifyOutput(output, parameterDictionaries, channelDictionary);
if (modifiedOutput === null) {
output = 'modifyOutput returned null. Verify your adaptation is correct';
} else if (modifiedOutput === undefined) {
output = 'modifyOutput returned undefined. Verify your adaptation is correct';
} else if (typeof modifiedOutput === 'object') {
output = JSON.stringify(modifiedOutput);
} else {
output = `${modifiedOutput}`;
}
}

editorOutputView.dispatch({ changes: { from: 0, insert: output, to: editorOutputView.state.doc.length } });
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21 changes: 14 additions & 7 deletions src/utilities/sequence-editor/extension-points.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -54,15 +54,22 @@ export async function toInputFormat(
channelDictionary: ChannelDictionary | null,
) {
const modifyOutputParse = get(sequenceAdaptation).modifyOutputParse;
let modifiedOutput = null;

if (modifyOutputParse !== undefined) {
modifiedOutput = await modifyOutputParse(output, parameterDictionaries, channelDictionary);
}

const input = await get(inputFormat)?.toInputFormat?.(modifiedOutput ?? output);
let modifiedOutput = await modifyOutputParse(output, parameterDictionaries, channelDictionary);
if (modifiedOutput === null) {
modifiedOutput = 'modifyOutputParse returned null. Verify your adaptation is correct';
} else if (modifiedOutput === undefined) {
modifiedOutput = 'modifyOutputParse returned undefined. Verify your adaptation is correct';
} else if (typeof modifiedOutput === 'object') {
modifiedOutput = JSON.stringify(modifiedOutput);
} else {
modifiedOutput = `${modifiedOutput}`;
}

return input;
return await get(inputFormat)?.toInputFormat?.(modifiedOutput);
} else {
return await get(inputFormat)?.toInputFormat?.(output);
}
}

export function inputLinter(
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