Nickakhmetov/HMP-152 protocols fix #3165

NickAkhmetov · 2023-07-11T20:59:37Z

Added handling for multiple protocols links in one field
Added logic for trimming/fixing the protocols links has been edited to handle all of the cases in protocols.io failure on some Donor pages #2925 except for the typo case where commas took the place of periods
Added specs for the trimming logic
Added client authentication to Protocols.io requests
Targeted the v4 API protocol API instead of the legacy v3 API (takes care of HMP-254)

NickAkhmetov · 2023-07-12T15:58:10Z

After taking some time to review the documentation for the protocols.io authorization, I can summarize it:

I have obtained a client ID, client secret, and client access token
- The ID is safe to expose publicly
- The client secret is not safe to expose publicly
- The client access token is probably best not to expose publicly but would be visible in user-space if we made client-side requests with it
  - i.e. if the associated account has any private protocols shared with it, they are visible to requests made with this key.
We can make requests with either
- with the client access token
  - Allows access to all publicly visible protocols and the protocols associated with the given account, as mentioned above, but does not provide access to private protocols
  - We would likely want to forward these requests through our back-end to avoid sending the client access token down in session information
- with an OAuth key generated via an authorization link
  - User clicks the link, authenticates with protocols.io account, and gets redirected to a URL we specify with the auth code/scope in URL parameters
  - This allows the user to access any private protocols that are shared with them
  - This key is valid for up to a year
  - This requires us to pass the client secret so we'll need to make a python handler for this similar to the login handler

For a first pass, we can try just using the client auth key; we can build out OAuth support in a future iteration.

Logic for trimming/revising the links works Corresponding specs are failing (`Cannot read properties of null (reading 'useMemo'`) Also need to set up protocols API auth flow

NickAkhmetov · 2023-07-12T16:10:45Z

Rebased following the squash-merge of the base branch.

context/app/static/js/hooks/useProtocolData.js

…ol links

Refactored to avoid requiring multifetcher for this case, but still keeping introduced multifetcher for other cases

…rom the split string

NickAkhmetov · 2023-07-18T15:47:23Z

Donor fde7ac63c666fdaebe21e187293a8685 on prod has multiple protocol links, which we can now properly display:

NickAkhmetov · 2023-07-18T16:19:26Z

Zhou added the client ID entries to the various environments; once I fix the specs here this should be all set

john-conroy

Thanks! I made a few comments that you can take or leave.

CHANGELOG-fix-protocol-links.md

context/app/static/js/components/Providers.jsx

john-conroy · 2023-07-21T13:46:30Z

context/app/static/js/components/detailPage/Protocol/Protocol.jsx

+    <SectionItem label="Error loading protocol info">
+      This protocol may be private or otherwise inaccessible.
+    </SectionItem>;
+  }
+  if (loading || !data) {
+    <SectionItem label="Loading protocol info">Please wait...</SectionItem>;


@tsliaw do you want to weigh in on the language used here?

@NickAkhmetov Yes that language should be changed. Please change to "Protocols are loading. If protocols take a significant time to load, please contact [email protected] about this issue and mention the HuBMAP ID." And add the email icon after the email. The styling of that loader might need to change in the future since it doesn't match the rest of the portal, but this should be sufficient for now.

I've modified the text accordingly:

I've also added handling to make sure that the loading message is only displayed once in cases where there's more than one protocol URL.

john-conroy · 2023-07-21T13:52:09Z

context/app/static/js/helpers/multiFetcher.ts

 export const multiFetcher = (...urls: string[]) => {
  const f = (url: string) => fetch(url).then((response) => response.json());
+  if (urls.length === 0) {
+    return Promise.resolve([]);
+  }
+  return Promise.all(urls.map((url) => f(url)));
+};
+
+export const multiFetcherWithToken = (token: string, ...urls: string[]) => {
+  const f = (url: string) =>
+    fetch(url, {
+      headers: {
+        Authorization: `Bearer ${token}`,
+      },
+    }).then((response) => response.json());
+  if (urls.length === 0) {
+    return Promise.resolve([]);
+  }


Could we refactor out the commonalities and enable the multiFetcher to accept fetch options as a an arg with a default value of an empty obj?

fetcher and multiFetcher moved to a single swr file in helpers

Both functions take in an optional requestInit object

fetcher uses multiFetcher to minimize duplication

Added JSDoc explanations for usage which appear on hover in VS Code

context/app/static/js/hooks/useProtocolData.js

…on, add documentation for usage of fetcher functions

john-conroy

Looks great!

Base automatically changed from nickakhmetov/hmp-144-react-18-upgrade to main July 12, 2023 16:08

NickAkhmetov added 3 commits July 12, 2023 12:09

Upgrade nuka-carousel

2fde159

remove weird submodule thing?

2157b14

WIP

aab15dd

Logic for trimming/revising the links works Corresponding specs are failing (`Cannot read properties of null (reading 'useMemo'`) Also need to set up protocols API auth flow

NickAkhmetov force-pushed the nickakhmetov/hmp-152-protocols-fix branch from 3ac9107 to aab15dd Compare July 12, 2023 16:09

github-advanced-security bot found potential problems Jul 12, 2023

View reviewed changes

context/app/static/js/hooks/useProtocolData.js Fixed Show fixed Hide fixed

NickAkhmetov added 9 commits July 12, 2023 12:31

add changelog, fix regex

70f6ff3

add protocols API values context, pull values from app conf

64f7b3b

Merge branch 'main' into nickakhmetov/hmp-152-protocols-fix

688efb8

make authenticated requests; now seeing data, still not seeing protoc…

8c8bd1b

…ol links

Restore protocol links! 🎉

cfa962e

Refactored to avoid requiring multifetcher for this case, but still keeping introduced multifetcher for other cases

remove console log, add explanatory comment, add changelog

7e8d852

undefined safety for new app conf items

d218794

Fix handling of multi-url case by removing any resulting whitespace f…

f4c9bde

…rom the split string

add space to multi-protocol spec to match the real data

5b849ac

NickAkhmetov marked this pull request as ready for review July 18, 2023 15:48

NickAkhmetov requested review from lchoy, kevinyooky and john-conroy and removed request for kevinyooky July 18, 2023 15:48

expect v4 api

8bc9cff

fix tests, fix handling of empty string input

0b62fec

john-conroy previously approved these changes Jul 21, 2023

View reviewed changes

NickAkhmetov added 2 commits July 21, 2023 11:51

Remove duplicate changelog

756d038

revise ProtocolApiContext import

dd31b34

NickAkhmetov added 2 commits July 21, 2023 11:58

change protocolapicontext import and add global swr config

b16c164

Refactor and reorganize fetcher/multiFetcher to reduce code duplicati…

d13330b

…on, add documentation for usage of fetcher functions

NickAkhmetov dismissed john-conroy’s stale review via d13330b July 21, 2023 16:23

Updated loading message

4f8f269

john-conroy approved these changes Jul 21, 2023

View reviewed changes

NickAkhmetov merged commit 3cc7b44 into main Jul 21, 2023
8 checks passed

NickAkhmetov deleted the nickakhmetov/hmp-152-protocols-fix branch July 21, 2023 18:58

NickAkhmetov mentioned this pull request Oct 3, 2023

protocols.io failure on some Donor pages #2925

Closed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Nickakhmetov/HMP-152 protocols fix #3165

Nickakhmetov/HMP-152 protocols fix #3165

NickAkhmetov commented Jul 11, 2023 •

edited

Loading

NickAkhmetov commented Jul 12, 2023 •

edited

Loading

NickAkhmetov commented Jul 12, 2023

NickAkhmetov commented Jul 18, 2023

NickAkhmetov commented Jul 18, 2023

john-conroy left a comment

john-conroy Jul 21, 2023

tsliaw Jul 21, 2023

NickAkhmetov Jul 21, 2023

john-conroy Jul 21, 2023

NickAkhmetov Jul 21, 2023

john-conroy left a comment

Nickakhmetov/HMP-152 protocols fix #3165

Nickakhmetov/HMP-152 protocols fix #3165

Conversation

NickAkhmetov commented Jul 11, 2023 • edited Loading

NickAkhmetov commented Jul 12, 2023 • edited Loading

NickAkhmetov commented Jul 12, 2023

NickAkhmetov commented Jul 18, 2023

NickAkhmetov commented Jul 18, 2023

john-conroy left a comment

Choose a reason for hiding this comment

john-conroy Jul 21, 2023

Choose a reason for hiding this comment

tsliaw Jul 21, 2023

Choose a reason for hiding this comment

NickAkhmetov Jul 21, 2023

Choose a reason for hiding this comment

john-conroy Jul 21, 2023

Choose a reason for hiding this comment

NickAkhmetov Jul 21, 2023

Choose a reason for hiding this comment

john-conroy left a comment

Choose a reason for hiding this comment

NickAkhmetov commented Jul 11, 2023 •

edited

Loading

NickAkhmetov commented Jul 12, 2023 •

edited

Loading