SEAB-6449: Improve TransactionHelper

[svonworl]

Description While investigating https://ucsc-cgl.atlassian.net/browse/SEAB-6448 and https://ucsc-cgl.atlassian.net/browse/SEAB-6449, it appeared beneficial to make some tweaks to TransactionHelper.

Accordingly, this PR improves TransactionHelper to make it more flexible and easy to use, as follows:

• Add a new transaction() method that returns a value produced by some user-supplied code.
• Add a new continueSession() method that instructs the next transaction() method call to not to clear the Session's entities, allowing multiple successive transactions to use the same managed entities, rather than have to "reload" them in each transaction.
• Make various helper methods private, and strike the related documentation which suggests they can be used "ala carte" to implement custom behavior. This change reduces the theoretical utility of TransactionHelper, but we don't currently use the helpers "ala carte", and not being able to do so will prevent us from shooting ourselves in the feet in the future.
• Add a "begin transaction" call after we commit/roll-back. Testing suggests that we need to do this after a rollback, if we want any entities subsequently modified (outside of TransactionHelper) to be committed. As far as I can tell, this doesn't affect any current code.
• Wrap internal database exceptions in TransactionHelperException and rethrow. Remove thrown() and code which used that idiom.

To demonstrate the new TransactionHelper transaction() method that returns a value, I used it to simplify the portion of the push processing code where we link the "version update" transaction to the "doi generation" transaction. Whilst doing so, I noticed a small bug: if the DOI generation code threw, two LambdaEvents would be logged, one a success, and the other, a failure. This PR fixes said bug.

Review Instructions Register a workflow via the .dockstore.yml path, and make sure the workflow appears correctly in Dockstore.

Issue https://ucsc-cgl.atlassian.net/browse/SEAB-6448 https://ucsc-cgl.atlassian.net/browse/SEAB-6449

Security and Privacy

If there are any concerns that require extra attention from the security team, highlight them here and check the box when complete.

• [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.

[sonarcloud[bot]]

Quality Gate failed

Failed conditions
70.4% Coverage on New Code (required ≥ 80%)

See analysis details on SonarCloud

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 66.66667% with 16 lines in your changes missing coverage. Please review.

Project coverage is 74.32%. Comparing base (b881d9c) to head (92f4e65). Report is 1 commits behind head on develop.

Files	Patch %	Lines
...ockstore/webservice/helpers/TransactionHelper.java	59.25%	9 Missing and 2 partials :warning:
...webservice/resources/AbstractWorkflowResource.java	76.19%	3 Missing and 2 partials :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #5909 +/- ## ============================================= - Coverage 74.36% 74.32% -0.05% + Complexity 5368 5367 -1 ============================================= Files 375 375 Lines 19418 19420 +2 Branches 2030 2031 +1 ============================================= - Hits 14441 14433 -8 - Misses 4007 4015 +8 - Partials 970 972 +2 ``` | [Flag](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/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/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `26.93% <0.00%> (-0.01%)` | :arrow_down: | | [hoverflytests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `27.40% <47.91%> (+0.01%)` | :arrow_up: | | [integrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `56.84% <66.66%> (-0.05%)` | :arrow_down: | | [languageparsingtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `11.09% <0.00%> (-0.01%)` | :arrow_down: | | [localstacktests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `21.59% <0.00%> (-0.01%)` | :arrow_down: | | [toolintegrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `30.33% <0.00%> (-0.01%)` | :arrow_down: | | [unit-tests_and_non-confidential-tests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `25.99% <0.00%> (-0.01%)` | :arrow_down: | | [workflowintegrationtests](https://app.codecov.io/gh/dockstore/dockstore/pull/5909/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=dockstore) | `38.22% <47.91%> (+0.01%)` | :arrow_up: | 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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