Add external links #1763

jameshadfield · 2024-04-09T00:35:18Z

Adds Taxonium & MicrobeTrace link-outs to Auspice. Each of those sites allows accessing Nextstrain datasets by using a GET call to the path provided to them with with an {accept: "application/json"} header. As such some datasets don't work (if we don't support that route), and private datasets don't work for obvious reasons. But most datasets do work for Taxonium, which is cool! MicrobeTrace seems to only load with trees of 500 tips or less and a warning is added if you have more than this, but this functionality closes https://github.com/nextstrain/private/issues/106.

See commit messages for implementation details.

@theosanderson you may be interested in the taxonium link-out, especially the query params I'm using which I've mainly figured out by playing around in Taxonium. And are you OK with us including this on nextstrain.org?!

Testing Taxonium

is a little hard because the site running Auspice must support the appropriate GET request and build Auspice with customisations enabling this functionality. The review app from nextstrain/nextstrain.org#816 works nicely. E.g.

View a flu dataset
Change the color-by and/or distance metric
scroll to the bottom and click "view in other platforms" then click the taxonium button
Taxonium should load and preserve as many view settings as possible

Testing MicrobeTrace

is even harder because (I'm guessing) the url query is checked and so only "nextstrain.org" or "next.nextstrain.org" will work, despite the review app site supporting the relevant GET route. Not a big problem if it doesn't work on review apps tho. To test you can do the following (and kind of trust me that it'll work like this when we've merged the PRs):

E.g. for MicrobeTrace:

View a dataset with <500 tips, e.g. measles/genome
scroll to the bottom and click "view in other platforms" then click the MicrobeTrace button
MicrobeTrace will get stuck on a "loading file" page
Change the URL by replacing nextstrain-s-james-link-2gqxtm.herokuapp.com with nextstrain.org (i.e. to this one)
MicrobeTrace should now load the data

Checks pass
If making user-facing changes, add a message in CHANGELOG.md summarizing the changes in this PR

See <nextstrain/auspice#1763> for context

huddlej

Just reviewing the UI experience and not the code, but I really dig this new modal interface. The new link at the bottom of the page to "View in other platforms" feels consistent with the "Download data" link and the modal interface behaves just like I'd expect based on having used the data window.

I like how the modal window has the potential to expand to support other platforms besides these two. It's really cool to see how well Taxonium handles the Auspice JSONs even to the point of using the dataset title from the JSON in the display. 💯

I also liked this warning for the MicrobeTrace link that tells the user how many tips there are: "Note that trees with over 500 tips may have trouble loading (this one has 2983)."

Finally, I appreciate that the links open in new windows/tabs, which might seem like an obvious thing to do, but it is reassuring to find I don't lose my place on Nextstrain by clicking a link to view in the other platforms. Your use of the "open in new window" icon next to the "View in other platforms" link primes the user to expect that behavior from the modal window.

joverlee521

Nice, glad this was pretty straightforward! I only left some non-blocking comments.

joverlee521 · 2024-04-09T17:37:58Z

src/components/modal/LinkOutModalContents.jsx

+        // Taxonium should work with most nextstrain.org URLs, including /fetch and public /groups
+        // (checking authn status is not something Auspice should be doing), but it doesn't work
+        // with /community URLs.
+        if (pathname.startsWith('/community/')) return false;


I was curious why community builds don't work in Taxonium.

I can enter a community URL (https://nextstrain.org/community/blab/measurements-panel/flu/seasonal/h3n2/ha) on Taxonium and it loads the community dataset.

Was there one particular community build that didn't work?

The inrb-drc/ebola-nord-kivu build doesn't work in taxonium. I didn't do enough digging and assumed we didn't handle those routes in our {GET + application/json} routing (that's why taxonium doesn't load it, it 404s), but the corresponding {GET + application/json} route for the flu dataset you used did work. My guess is that the bug is related to EBOV being a "default" dataset... but the bug is on us, so I'll open up all community links for this PR.

Relevant commands, if interested:

200 OK: curl -I -H 'Accept: application/json' https://nextstrain.org/community/blab/measurements-panel/flu/seasonal/h3n2/ha
404 Not Found: curl -I -H 'Accept: application/json' https://nextstrain.org/community/inrb-drc/ebola-nord-kivu

My guess is that the bug is related to EBOV being a "default" dataset...

More likely it's because that repo is using v1 (meta + tree) JSONs

I've updated the PR to no longer filter out /community URLs. I'll leave this thread open as it's got some interesting information in it!

src/components/modal/LinkOutModalContents.jsx

joverlee521 · 2024-04-09T18:18:12Z

src/components/modal/LinkOutModalContents.jsx

+        // (checking authn status is not something Auspice should be doing), but it doesn't work
+        // with /community URLs.
+        if (pathname.startsWith('/community/')) return false;
+        if (tangle) return false;


I think it'd be helpful to have a hint as to why the data source or view settings aren't compatible with the external platform. If we don't want to clutter the modal, maybe a brief console message/warning that says tangle trees aren't supported?

Good suggestion! I've updated the styles - here's what it now looks like when viewing a tanglegram

joverlee521 · 2024-04-09T18:25:10Z

src/components/framework/fine-print.js

+        style={Object.assign({}, materialButton, {backgroundColor: "rgba(0,0,0,0)", color: medGrey, margin: 0, padding: 0})}
+        onClick={() => { this.props.dispatch({ type: SET_MODAL, modal: "linkOut" }); }}
+      >
+        <FaExternalLinkAlt />


I think this icon is a little misleading because the button actually opens a modal and is not an external link. Maybe add this icon next to the actual links within the modal?

You're good at picking icons - do you have one in mind I should use?

Maybe add this icon next to the actual links within the modal?

I tried this but it felt a little messy so I think I'll keep the modal contents as-is

I actually didn't find the modal result from the arrow-out icon surprising. But maybe there is something more semantically appropriate?

I think it's fine to just leave out the icon, but if you want one, maybe a cloudshare icon?

FaExternalLinkSquareAlt might be less associated directly with "new window" while still giving the same general meaning. For Taxonium I use FaShare or an equivalent (curvy arrow).

I've gone with FaExternalLinkSquareAlt - thanks for all the suggestions!

P.S. Jover, I liked TbCloudShare but it would require an update to react-icons so FaExternalLinkSquareAlt won out!

theosanderson · 2024-04-09T19:31:39Z

Just so say this is super cool! Thanks for taking the time to make sense of Taxonium's query parameters. These bidirectional integrations are really great. There's definitely a lot I can improve on the Taxonium side, e.g. with surfacing 404s as seen here - and my parsing of your JSONs could still be more complete! - I hope to make more progress there. This is a great motivation!

The original design had only one modal so the modal design was wrapped up with the contents shown in the modal. Here we separate them to allow different modals in future commits. There should be no user-facing changes with this change.

Doesn't include any actual links yet, but sets out the interface

See <nextstrain/auspice#1763> for context

ikb6 · 2024-04-17T16:04:09Z

@jameshadfield , I am on the MicrobeTrace team at the CDC. Sorry, but herokuapp gave me an error when I tried clicking on the measles genome to test the option to view on MicrobeTrace. It says there was no content there. Could you see what the issue is? Thanks!

jameshadfield · 2024-04-17T19:41:58Z

Sorry, but herokuapp gave me an error when I tried clicking on the measles genome to test the option to view on MicrobeTrace. It says there was no content there. Could you see what the issue is? Thanks!

The heroku review app no longer exists since this PR has been merged. The code will be included in the next Auspice release (possibly today) and then it should appear on nextstrain.org some time after that. (Note that the functionality in this PR is only enabled for Auspice running on nextstrain.org, as both Taxonum & Microbetrace get the JSON data via {GET + accept: application/json} requests, and these API routes are not part of Auspice.)

ikb6 · 2024-04-26T13:41:10Z

Sorry, but herokuapp gave me an error when I tried clicking on the measles genome to test the option to view on MicrobeTrace. It says there was no content there. Could you see what the issue is? Thanks!

The heroku review app no longer exists since this PR has been merged. The code will be included in the next Auspice release (possibly today) and then it should appear on nextstrain.org some time after that. (Note that the functionality in this PR is only enabled for Auspice running on nextstrain.org, as both Taxonum & Microbetrace get the JSON data via {GET + accept: application/json} requests, and these API routes are not part of Auspice.)

@jameshadfield , we are eager to try/test this feature. No rush, but just wanted to make sure I am not missing something. nextstrain.org is still showing the Feb version of Auspice. I presume we just wait for the new release? Thanks!

jameshadfield · 2024-04-28T22:10:54Z

@ikb6 this has been released as part of Auspice 2.53.0 and this should propagate through to the nextstrain.org server in the coming 24 hours

nextstrain-bot temporarily deployed to auspice-external-links-wvnjdi1 April 9, 2024 00:35 Inactive

nextstrain-bot mentioned this pull request Apr 9, 2024

[bot] [DO NOT MERGE] Test Auspice PR 1763 nextstrain/nextstrain.org#815

Closed

jameshadfield force-pushed the external-links branch from 12cdab3 to 899e75a Compare April 9, 2024 02:51

nextstrain-bot temporarily deployed to auspice-external-links-wvnjdi1 April 9, 2024 02:51 Inactive

jameshadfield added a commit to nextstrain/nextstrain.org that referenced this pull request Apr 9, 2024

Add auspice "link out modal" extension

fc4f838

See <nextstrain/auspice#1763> for context

jameshadfield mentioned this pull request Apr 9, 2024

[auspice] Add link out modal nextstrain/nextstrain.org#816

Merged

jameshadfield requested a review from huddlej April 9, 2024 03:24

huddlej reviewed Apr 9, 2024

View reviewed changes

joverlee521 approved these changes Apr 9, 2024

View reviewed changes

jameshadfield added 4 commits April 12, 2024 11:47

Separate Modal component from modal contents

fd77a61

The original design had only one modal so the modal design was wrapped up with the contents shown in the modal. Here we separate them to allow different modals in future commits. There should be no user-facing changes with this change.

Add link-out modal UI

343ca32

Doesn't include any actual links yet, but sets out the interface

Add Taxonium link-out

767be39

Add MicrobeTrace linkout

39b4ec6

jameshadfield force-pushed the external-links branch from 899e75a to 39b4ec6 Compare April 12, 2024 00:05

nextstrain-bot temporarily deployed to auspice-external-links-wvnjdi1 April 12, 2024 00:05 Inactive

jameshadfield merged commit a40c340 into master Apr 12, 2024
20 checks passed

jameshadfield deleted the external-links branch April 12, 2024 00:10

jameshadfield added a commit to nextstrain/nextstrain.org that referenced this pull request Apr 12, 2024

Add auspice "link out modal" extension

19147f0

See <nextstrain/auspice#1763> for context

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Add external links #1763

Add external links #1763

jameshadfield commented Apr 9, 2024 •

edited

Loading

huddlej left a comment •

edited

Loading

joverlee521 left a comment

joverlee521 Apr 9, 2024

jameshadfield Apr 9, 2024

jameshadfield Apr 10, 2024

jameshadfield Apr 10, 2024 •

edited

Loading

jameshadfield Apr 12, 2024

joverlee521 Apr 9, 2024

jameshadfield Apr 12, 2024

joverlee521 Apr 9, 2024

jameshadfield Apr 9, 2024

trvrb Apr 9, 2024

joverlee521 Apr 9, 2024

theosanderson Apr 9, 2024 •

edited

Loading

jameshadfield Apr 12, 2024 •

edited

Loading

theosanderson commented Apr 9, 2024

ikb6 commented Apr 17, 2024

jameshadfield commented Apr 17, 2024

ikb6 commented Apr 26, 2024

jameshadfield commented Apr 28, 2024

Add external links #1763

Add external links #1763

Conversation

jameshadfield commented Apr 9, 2024 • edited Loading

Testing Taxonium

Testing MicrobeTrace

huddlej left a comment • edited Loading

Choose a reason for hiding this comment

joverlee521 left a comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

jameshadfield Apr 10, 2024 • edited Loading

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

Choose a reason for hiding this comment

theosanderson Apr 9, 2024 • edited Loading

Choose a reason for hiding this comment

jameshadfield Apr 12, 2024 • edited Loading

Choose a reason for hiding this comment

theosanderson commented Apr 9, 2024

ikb6 commented Apr 17, 2024

jameshadfield commented Apr 17, 2024

ikb6 commented Apr 26, 2024

jameshadfield commented Apr 28, 2024

jameshadfield commented Apr 9, 2024 •

edited

Loading

huddlej left a comment •

edited

Loading

jameshadfield Apr 10, 2024 •

edited

Loading

theosanderson Apr 9, 2024 •

edited

Loading

jameshadfield Apr 12, 2024 •

edited

Loading