DOCK-2312: Add "is this Entry automatically syncing?" endpoint

[svonworl]

Description This PR adds an isSyncing endpoint to the webservice that indicates whether or not the specified Entry is being automatically synced (currently, via our GitHub app).

Regarding the design and functionality of this endpoint, there were a number of different options as to complexity and effectiveness:

• We could use the newly-logged UNINSTALL LambdaEvent (https://github.com/dockstore/dockstore/pull/5852) to tell if the GitHub App was uninstalled (on or after the date we first deploy the UNINSTALL logging).
• Charles thought that it might be problematic to use the GitHub API to determine if the GitHub App was installed in a given repo, dynamically in the endpoint, so I didn't further investigate that option.
• We could use various techniques to guesstimate whether the GitHub App is currently installed, in bulk/offline, create a special "run one time" endpoint to calculate that information for all entries/repos in production, store it somewhere, etc...

In the end, I decided to go with the most basic approach, which is to conclude that an entry is not syncing iff the latest LambdaEvent for the entry's repo is an UNINSTALL. All the other approaches were much more involved. Sure, they would give us more visibility for older entries, but everyone I consulted with seemed to [slightly grudgingly] agree that the basic solution is good enough. I would love it to be perfect and give us useful information about preexisting uninstalls, but I don't think the engineering cost justifies the payoff. As it is, it's a quick little addition that will help us diagnose new issues.

Access to the endpoint is limited to entry owners and admins.

Note that since LambdaEvents can be delivered to the webservice out of order, and we don't log the GitHub creation date (because in general, the webhook events don't include one), it's theoretically possible that an UNINSTALL will get logged after events that were actually created later, and cause the endpoint to report that an entry is not syncing. Similar issues can happen if we fail to log an event that directly follows an UNINSTALL for whatever reason. Such cases should be fairly rare, and will tend to heal on their own, because when the next non-UNINSTALL event gets logged, the endpoint will report that the entry is syncing.

There will be a companion UI PR, coming soon. Currently, the plan is to display some sort of warning on the private .dockstore.yml-based entry page if the entry is not syncing, and leave the UI as-is otherwise.

Review Instructions Register an entry in a test GitHub repository via the GitHub App / .dockstore.yml path. Query this endpoint and confirm that it indicates that the entry is syncing. Uninstall the GitHub App from the repo and wait five minutes. Query this endpoint and confirm that it indicates that the entry is not syncing. Reinstall the GitHub App on the repo and wait five minutes. Query this endpoint and confirm that it indicates the the entry is syncing.

Issue https://ucsc-cgl.atlassian.net/browse/DOCK-2312 https://github.com/dockstore/dockstore/issues/5331

Security and Privacy

No concerns.

• [x] Security and Privacy assessed

e.g. Does this change...

• Any user data we collect, or data location?
• Access control, authentication or authorization?
• Encryption features?

Please make sure that you've checked the following before submitting your pull request. Thanks!

• [x] Check that you pass the basic style checks and unit tests by running mvn clean install
• [x] Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
• [x] Follow the existing JPA patterns for queries, using named parameters, to avoid SQL injection
• [x] If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
• [x] Assume that inputs to the API can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
• [x] Do not serve user-uploaded binary images through the Dockstore API
• [x] Ensure that endpoints that only allow privileged access enforce that with the @RolesAllowed annotation
• [x] Do not create cookies, although this may change in the future
• [x] If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 76.47059% with 4 lines in your changes are missing coverage. Please review.

Project coverage is 72.88%. Comparing base (7347da6) to head (6cec07d).

Files	Patch %	Lines
...n/java/io/dockstore/webservice/api/SyncStatus.java	66.66%	2 Missing :warning:
.../dockstore/webservice/resources/EntryResource.java	77.77%	0 Missing and 2 partials :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #5865 +/- ## ============================================= - Coverage 74.49% 72.88% -1.62% + Complexity 5244 5110 -134 ============================================= Files 368 369 +1 Lines 18945 18960 +15 Branches 1992 1993 +1 ============================================= - Hits 14114 13819 -295 - Misses 3880 4191 +311 + Partials 951 950 -1 ``` | [Flag](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | Coverage Δ | | |---|---|---| | [bitbuckettests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `27.22% <5.88%> (-0.02%)` | :arrow_down: | | [integrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `58.92% <76.47%> (+0.01%)` | :arrow_up: | | [languageparsingtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `11.08% <5.88%> (-0.01%)` | :arrow_down: | | [localstacktests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `21.70% <5.88%> (-0.02%)` | :arrow_down: | | [toolintegrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `30.60% <5.88%> (-0.02%)` | :arrow_down: | | [unit-tests_and_non-confidential-tests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `23.41% <5.88%> (-5.17%)` | :arrow_down: | | [workflowintegrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5865/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `38.86% <5.88%> (-0.03%)` | :arrow_down: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore#carryforward-flags-in-the-pull-request-comment) to find out more.

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[svonworl]

Lots of conflicting feedback, took a crack at getting closer to consensus. In the end, I:

• Changed the endpoint to return an object, which currently has one property that indicates if the github app is installed or not. We can add more fields when we want to return other information, good idea Denis.
• Changed the endpoint name to syncStatus. This dovetails with the notion that "sync" means different things to different people, but broadly, could encompass the act/process/result of automatically updating an entry, and thus, can return other related info in the future, or refer to other methods of automatically, should we someday implement them.
• Left the value of gitHubAppInstalled as a boolean. If we determine that we really need a three-phase TRUE/FALSE/UNKNOWN result, we can add it later.

[sonarcloud[bot]]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
86.2% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud