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AMAS Speed Up changes#104

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lognguyenle merged 3 commits intomasterfrom
AMASSpeedUp
May 30, 2025
Merged

AMAS Speed Up changes#104
lognguyenle merged 3 commits intomasterfrom
AMASSpeedUp

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@lognguyenle
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@lognguyenle lognguyenle commented May 28, 2025

Changes

Changes of the implementation of the AMAS algorithm as described in #65
Also fixes an issue with actually applying the annotations to a file due to no longer only having the IndexDB only open as version 1,

You can check a side by side of the changed algorithm in \AntimonyEditor\src\libs\AMAS-js\src\reaction_annotation.js

Testing

Code runs and builds

Expected Behavior:

  • AMAS should work and not take as long to generate annotations anymore
  • Annotations should be applied to files once you select it to and click Update annotations

@lognguyenle lognguyenle requested review from qndan and sophiaxzhang May 28, 2025 05:57
@qndan
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qndan commented May 29, 2025

I got this error when I ran it on biomodel 36. The annotating part ran fine, but it got to the creating table part then closed.

Screenshot 2025-05-28 at 7 37 29 PM

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I believe the AMAS settings you used to generate that had ABOVE selected as the MSSC setting?

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lognguyenle commented May 29, 2025

I got this error when I ran it on biomodel 36. The annotating part ran fine, but it got to the creating table part then closed.

Screenshot 2025-05-28 at 7 37 29 PM

Yeah I get this same error when using the ABOVE option on the currently deployed branch as well
But when I use TOP it should work. Probably?

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Just tested it on Kevin's older branches and same behavior on that ABOVE option for MSSC.

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That worked 👍

@lognguyenle lognguyenle merged commit 53eda7f into master May 30, 2025
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@lognguyenle lognguyenle deleted the AMASSpeedUp branch May 30, 2025 00:25
Comment on lines 295 to 301
setStep(3);
setGenInProgress(false);
} catch (error) {
console.error("Unable to generate annotation recommendations:", error);
setGenInProgress(false);
onClose();
}
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3 participants