View subtree in MicrobeTrace

[ikb6]

Hi I am from the MicrobeTrace team.
When I select 'View in MicrobeTrace " on the nextstrain site, I had two different issues for 2 trees. A measles tree could not open, but I saw the stats table and link source file displayed, and the modal kept spinning.

We have also tried other small trees without success.
I doubt Nextstrain has changed anything in the way the query is sent to MicrobeTrace, so I am asking our developers to look at MicrobeTrace as well, but one of our folks who had expertise in this has left the team.

Could you pl. take a look to see if something has changed in the way Nextstrain sends the URL query out or the way JSON files are generated?

For a lassa virus tree, it seems stuck on loading page, no modal- it was unable even to load the info. See MP4 below

(https://api.zenhub.com/attachedFiles/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBd0dPQ2c9PSIsImV4cCI6bnVsbCwicHVyIjoiYmxvYl9pZCJ9fQ==--b2730665fa160040c800dc9ee7c89fee6a15d82f/NextSTrain_TreeViewinMT2.0_Bug.mp4)

[joverlee521]

Hi @ikb6,

Based on the description in the original PR for implementing the link to MicrobeTrace, I believe there is a 500 tip limit for loading trees in MicrobeTrace. The measles tree is probably unable to load because it has >500 tips. I am able to open the smaller yellow-fever tree in MicrobeTrace, although it still takes a couple minutes to load the results.

As for the community lassa virus tree, I believe this tree likely never worked with MicrobeTrace because the underlying dataset in the GitHub repo uses the old v1 JSON format of splitting a single dataset into separate _tree.json and _meta.json files.

[joverlee521]

Ah, we can support the v1 -> v2 JSON conversion through the server if we link out with our /charon API.
For example, the lassa virus tree is viewable via
https://microbetrace.cdc.gov/MicrobeTrace/?url=https:%2F%2Fnextstrain.org%2Fcharon%2FgetDataset%3Fprefix%3Dcommunity%2Fpauloluniyi%2Flassa%2Fl

This will require a change in the Auspice code for creating the url for MicrobeTrace

[ikb6]

Thanks for the prompt response @joverlee521. I have two questions.

1. Is it possible to add a pop up when someone clicks on the View In MicrobeTrace button for a tree with >500 taxa?
2. Even when I look at a subtree just to decrease the number of taxa, it is still too large ( perhaps because the JSON file still contains all the inf). Is there any fix for the subtree issue? If not, this feature would become very limited...

[joverlee521]

Is it possible to add a pop up when someone clicks on the View In MicrobeTrace button for a tree with >500 taxa?

Looks like this is currently noted in our link out modal

---

Even when I look at a subtree just to decrease the number of taxa, it is still too large ( perhaps because the JSON file still contains all the inf). Is there any fix for the subtree issue? If not, this feature would become very limited...

Even if you are looking at a subtree, we pass the entire JSON file to MicrobeTrace. There's currently no easy fix for this because we do not generate the JSON file on the fly. We can consider this feature in the bigger picture improvement to Download dataset JSON(s) from redux state.

[joverlee521]

Ah, we can support the v1 -> v2 JSON conversion through the server if we link out with our /charon API. For example, the lassa virus tree is viewable via https://microbetrace.cdc.gov/MicrobeTrace/?url=https:%2F%2Fnextstrain.org%2Fcharon%2FgetDataset%3Fprefix%3Dcommunity%2Fpauloluniyi%2Flassa%2Fl

This will require a change in the Auspice code for creating the url for MicrobeTrace

Discussion about this on Slack w/ @victorlin made me realize that we can also resolve this be tackling the TODO in our endpoints to support v1.