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[theosanderson]

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[johnpage09]

Hi Theo,
I am trying to create a basic tree that I upload and run in Taxonium. The aim is to create a Taxonomy tree of various species in our database but unfortunately I am unable to get any results from the UI.

I have seen the tfci.jsonl but am unable to get the data model or the main fields that I need in order to get the visualisation to work.
Could you please help by supplying a file that has 10 nodes. It will help me understand the datamodel better.
Thanks,
John

[johnpage09]

Thank you Theo. I will discuss the path you have indicated with my team.
If you do get a chance to run my file, it would be much appreciated.
I have been unable to run a file with 5 to 10 nodes. Is there any restriction that the tree size has to have a certain number of nodes at a minimum ?

[theosanderson]

Hi @johnpage09 ,

I had a quick look at your file. I think that Taxonium is probably designed such that node_ids always have to go 0, 1, 2, 3 etc. (and then parent_ids have to match them).

[johnpage09]

Very good. Thanks. I will make the change and try,

[johnpage09]

Hi Theo,
I have made the changes suggested by you and checked the file for dangling pointers etc. It still hangs after 500 nodes and I can't see any errors in the Dev Console.
test_taxonium_2.zip
If you notice anything else in my file, please let me know.
Thanks

[theosanderson]

Hi John,

There is an error in the console

I believe the first node in the list (in the second line of the JSONL file) needs to be 0 then the next node needs to be 1, etc. Really the node_id was just an identifier I added to help manual look up in the file

[johnpage09]

Thank you Theo. The error was not coming up in Chrome but I see it in Edge.
I have also fixed the part where I was missing node_id = parent_id. I will continue with the debugging and also look into your original suggestion.
Regards,
John

[johnpage09]

I think I have nearly got it working. However, I have another error related to the x_dist

Could you please advise if there is a specific logic related to calculating these values.
My latest file is
test_taxonium_2.zip
Many thanks

[theosanderson]

Your node ids go 1, 2, 3, 4, then 9, 22. They would need to be entirely sequential.

Sorry I likely won't be able to continue iterating on this much further. I would suggest you use the technique that Angie suggested to get yourself an example JSONL that works. If you continue to have problems I'd suggest using the Newick and TSV approach that I mentioned.

[johnpage09]

Thank you Theo.