Newt 4 issues

[NoorMuhammad1]

Upon my testing of the current unstable branch of newt, I have encountered the following issues:

• 1. [@okg21] Color scheme not being properly loaded for sample maps.
• 2. [@NoorMuhammad1] SBGN bricks not working for Association. Can also test for other types as well.

If anybody finds any other issues or bugs please add it here.

[umut-er]

I have not been able to recreate the above-mentioned issues. Can you perhaps go into a little bit more into detail as to how to recreate them? Is the first issue related to #689? Does "SBGN bricks not working for Association" mean that it doesn't generate output at all or that there is something wrong with the output?
I have been testing for some time and haven't encountered any issues. I haven't looked at the query tab yet.

[NoorMuhammad1]

No that is precisely the issue that the options that we see in the video are not available when we run the application. To be more specific, There is no option to select simple molecule from the menu in SBGN brick. That is what I was referring to.

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On Tue, Jun 4, 2024 at 12:27 PM Umut Utku ERŞAHİNCE < ***@***.***> wrote: I have not been able to recreate the above-mentioned issues. Can you perhaps go into a little bit more into detail as to how to recreate them? Is the first issue related to #689 <#689>? Does "SBGN bricks not working for Association" mean that it doesn't generate output at all or that there is something wrong with the output? I have been testing for some time and haven't encountered any issues. I haven't looked at the query tab yet. — Reply to this email directly, view it on GitHub <#708 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALSZ5TUW4ZUUVMOQT3IV6VTZFWCB7AVCNFSM6AAAAABIWW6C7WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNBXGA2DQMBQGY> . You are receiving this because you were assigned.Message ID: ***@***.***>

[umut-er]

Same issue with:
metabolic reaction (input/output fields should include macromolecules)
dissociation (input/outputs field should include simple chemicals)
degradation (input/outputs field should include simple chemicals)

[ugurdogrusoz]

@amazein @adrienrougny can you please check this release candidate for Newt 4 in regards to our requirements for what input/outputs for above mentioned SGBN bricks should be (see under Edit > Add Using SBGN Bricks..)? We might have changed these when we extended the support for SBGN bricks.

Specs we had prepared earlier.

[NoorMuhammad1]

I checked and the SBGN bricks modal works and is following all the specified rules.

[ugurdogrusoz]

@amazein @adrienrougny can you please check this release candidate for Newt 4 in regards to our requirements for what input/outputs for above mentioned SGBN bricks should be (see under Edit > Add Using SBGN Bricks..)? We might have changed these when we extended the support for SBGN bricks.

Specs we had prepared earlier.

@NoorMuhammad1 checked and things looked fine according to this document

[okg21]

With this PR on sbgnviz iVis-at-Bilkent/sbgnviz.js#219, the color scheme issue for samples is fixed.