8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

poikilotherm · 2022-11-02T15:49:18Z

What this PR does / why we need it:

Payara 5 is going EOL for community usage (= without a payed support contract). Payara 6 is the successor, but allows to use Jakarta EE 10 only.

Which issue(s) this PR closes:

Closes Upgrade to Payara 6 and from EE 8 to EE 10 (end of Payara 5 Community Edition security patches Q2/2022) #8305

Special notes for your reviewer:

Do not move this to QA until Payara 6.2022.1 is out and we can test with it.
Resolved upstream with Prettyfaces 6.0 Do not move this to QA until we've made a final decision to go with the Rewrite/PrettyFaces library I built on my Mac and put in local_lib. Check EE9 Compatible Release ocpsoft/rewrite#304 for progress toward a compatible release from upstream.
Instead of d86e220 should we preserve backward compatibility of the SWORD API by inserting attachment; for the user if it isn't supplied?
The Perl installer has not been updated. Honestly, @pdurbin and I are ok with deleting it (and references to it, of course, if any).
The release note snippet needs work. Upgrades have not been tested.

Suggestions on how to test this:

Make sure API tests pass.
A test server is coming, similar to the one for Payara 5: https://groups.google.com/g/dataverse-dev/c/5hfiXl4Hpd8/m/awzoSpupAQAJ
Test everything. Test, test, test, just like the last major version change.

Does this PR introduce a user interface change? If mockups are available, please link/include them here:

No

Is there a release notes update needed for this change?:

Yes, a stub is included.

Additional documentation:

None but references in the guides to Payara 5 have been switched to Payara 6.

…ces #8305

1. The Jersey dependencies in use did not use the versions imported via the Payara BOM (which itself imports a Jersey BOM). 2. The coordinates for the server package changed, re-aligned.

…nly #8305 This avoids potential trouble were it's unclear from where the higher exceptions come from, javax or jakarta namespace.

https://stackoverflow.com/questions/52737981/rebuilding-primefaces-jar-file-missing-pushservlet

Also add provided dependency of our persistence provider to POM to allow class resolution in IDEs.

For now this is payara-6.2022.1.Alpha2 (the latest).

update docker-aio for Payara 6 #8305

The jars were built from this commit (scratch work): pdurbin/rewrite@d494160

Conflicts (just javax vs. jakarta imports): src/main/java/edu/harvard/iq/dataverse/TemplatePage.java

…22.1.Alpha2.zip

#8305 Vagrantfile.payara6 deploys 8305-payara6 warfile on payara-6-A2

Also, in docker-aio, restore lines to publish root dataverse collection (uses SWORD, known to be broken) and grant perms. Also update scripts and config related to installer or dev environments.

Otherwise, at runtime, SWORD APIs fail (and who knows what else). Note that CDI 4.0 is coming with Jakarta EE 10 and we'll need to switch to "annotated" then.

In EditDDI I was seeing a NullPointerException on line 136 (createNewDraftVersion). Switch from `@Context HttpServletRequest` to our ordinary way of API auth fixed it. In DataversesIT I was seeing an OptimisticLockException so I added a sleep.

Conflicts (all javax vs jakarata): src/main/java/edu/harvard/iq/dataverse/EditDatafilesPage.java src/main/java/edu/harvard/iq/dataverse/UserNotification.java src/main/java/edu/harvard/iq/dataverse/UserNotificationServiceBean.java src/main/java/edu/harvard/iq/dataverse/api/Notifications.java src/main/java/edu/harvard/iq/dataverse/api/datadeposit/MediaResourceManagerImpl.java src/main/java/edu/harvard/iq/dataverse/authorization/providers/builtin/DataverseUserPage.java src/main/java/edu/harvard/iq/dataverse/authorization/users/AuthenticatedUser.java src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java src/main/java/edu/harvard/iq/dataverse/util/json/JsonPrinter.java src/test/java/edu/harvard/iq/dataverse/util/json/JsonPrinterTest.java

Note that we need to swap Payara 6.2022.1.Alpha2 for the final version.

mreekie · 2023-01-18T23:16:19Z

Backlog grooming:

Removed the size
Added the label: bklog: Collection
I hope that this communicates more clearly that this has become a collection of 1 or more smaller issues that are being decomposed from this bigger issue.

mreekie · 2023-01-23T15:04:54Z

sizing:

PM added to ordered sizing queue
Leave in the ordered sizing queue as we break off new pieces

mreekie · 2023-02-13T19:26:40Z

sizing:

PM added to ordered sizing queue

Leave in the ordered sizing queue as we break off new pieces

Phil has started keeping track of the work needed for this in Spike: Upgrade to Payara 6 and from EE 8 to EE 10 (end of Payara 5 Community Edition security patches Q2/2022) so this issue is no longer being used as described.

I've created a new temporary column Upgrade to "Jakarta EE 10 and Payara 6" and added this there.

mreekie · 2023-04-19T15:43:15Z

Sizing:
-To move this specific pull request forward a small bit, the next step is to resolve the conflicts. (pretty straightforward. a 3)
Separately we'll create a new issue to track the fixing of the issues that are triggered when this code is committed.

Get the API test suite to pass (hard. alot of uncertainty around what's broken. at least 33)

Notes
Context:
Prior to June

5.14 released
- Payara and solr upgrades are not in that.
6.0 release
- Payara, solr, java included in this.

Next steps:

meet to get the DV 6.0 release plan in writing.
meet to get more of the details specific to the Payara 6 upgrade thought out and in writting

poikilotherm · 2023-04-19T15:56:57Z

Sizing: -To move this specific pull request forward a small bit, the next step is to resolve the conflicts. (pretty straightforward. a 3)

Please be aware that the last merge was not correctly executed! It is no easy task to merge this because of the Jakarta EE switch! This is at least a size 10 task, as the last merge needs to be reverted as well!

cmbz · 2023-05-15T18:53:27Z

Prioritizing Payara 6 release
Sizing needed

cmbz · 2023-05-17T15:26:24Z

This appears to be a flawed PR.
Oliver will create a new PR and close this one.

cmbz · 2023-05-17T15:29:51Z

See related: #8305

diego-guillen · 2023-06-14T01:38:08Z

I'm trying to install the latest version of IQSS Dataverse, 5.13:

Dataverse 5.13 installation recommends Payara 5.2022.3, but it cannot be downloaded:

sudo wget https://s3-eu-west-1.amazonaws.com/payara.fish/Payara+Downloads/5.2022.3/payara-5.2022.3.zip
Responds: ERROR 404: Not Found.

What can be done in this case?

poikilotherm · 2023-06-14T16:28:58Z

@diego-guillen please see #9638. Your question is beyond scope for this PR 😉

poikilotherm · 2023-06-28T22:08:13Z

I am going to close this pull request now, as we will operate on a new branch and a new pull request for the actual move for Payara 6 after the release of Dataverse 5.14. See #9685 for the successor PR.

poikilotherm and others added 30 commits May 17, 2022 19:44

build!(deps): move dependencies to Jakarta EE 9.1 and Payara 6 #8305

8ae137e

refactor!(dataverse): move all usage of Java EE to Jakarta EE namespa…

3463aeb

…ces #8305

build!(deps): switch to Primefaces 11 Jakarta Edition #8305

177bd3d

build(sword): switch to Jakarta-enabled SWORD2 preview release #8305

d8f1315

build(api): align Jersey deps with BOMs #8305

194607b

1. The Jersey dependencies in use did not use the versions imported via the Payara BOM (which itself imports a Jersey BOM). 2. The coordinates for the server package changed, re-aligned.

fix(sword): add exception signature in service doc servlet init() #8305

7943bdf

build(deps): update to Jakartafied JSONLD library version #8305

9b5aa41

refactor(webapp): migrate web.xml to Jakarta Faces #8305

8ef62d8

docs: fix Jakarta occurences in code comments #8305

4b331ca

fix(ingest): migrate JMS interface class string to Jakarta #8305

aff1e25

refactor(api): make Index API check on most specific exception type o…

4f9f0c5

…nly #8305 This avoids potential trouble were it's unclear from where the higher exceptions come from, javax or jakarta namespace.

style(webapp): switch URL path to Jakarta Faces #8305

35a5c34

fix(webapp): remove deleted Primefaces PushServlet from web.xml #8305

099ad54

https://stackoverflow.com/questions/52737981/rebuilding-primefaces-jar-file-missing-pushservlet

chore(persistence): migrate persistence.xml to Jakarta EE 9 #8305

10d85b4

Also add provided dependency of our persistence provider to POM to allow class resolution in IDEs.

chore(jsf): migrate Faces config and web.xml to Jakarta EE 9 #8305

340f773

chore(cdi): migrate Bean config to Jakarta EE 9 #8305

f7234c4

update docker-aio for Payara 6 #8305

b771d83

For now this is payara-6.2022.1.Alpha2 (the latest).

Merge pull request #546 from IQSS/8305-payara6-docker-aio

7e8c71e

update docker-aio for Payara 6 #8305

get prettyfaces/rewrite working on EE9+

d37af1d

The jars were built from this commit (scratch work): pdurbin/rewrite@d494160

Merge branch 'develop' into payara6

ebcbb84

Conflicts (just javax vs. jakarta imports): src/main/java/edu/harvard/iq/dataverse/TemplatePage.java

#8305 Vagrantfile.payara6 deploys 8305-payara6 warfile on payara-6.20…

5083d63

…22.1.Alpha2.zip

#8305 update Vagrantfile, don't provide second/testing copy

dfa2aa9

Merge pull request #8741 from OdumInstitute/origin/8305-payara6

1c4595c

#8305 Vagrantfile.payara6 deploys 8305-payara6 warfile on payara-6-A2

update installer and dev guide for Payara 6 #8305

1fce7cd

Also, in docker-aio, restore lines to publish root dataverse collection (uses SWORD, known to be broken) and grant perms. Also update scripts and config related to installer or dev environments.

revert f7234c4 (stick with bean-discovery-mode="all" for now) #8305

6f54d1f

Otherwise, at runtime, SWORD APIs fail (and who knows what else). Note that CDI 4.0 is coming with Jakarta EE 10 and we'll need to switch to "annotated" then.

as of Payara 6, "attachment; " required to upload files to SWORD #8305

d86e220

change Payara 5 to 6 in guides #8305

b1323e5

Note that we need to swap Payara 6.2022.1.Alpha2 for the final version.

change payara5 to 6 for jhove, other scripts #8305

ca7d3ab

mreekie removed the Size: 210 A percentage of a sprint. 147 hours. label Jan 18, 2023

mreekie added the Size: Queued PM has called this issue out specifically for sizing label Jan 23, 2023

mreekie added the bklog: NeedsDiscussion label Jan 24, 2023

This was referenced Jan 26, 2023

Upgrade to Payara 6 and from EE 8 to EE 10 (end of Payara 5 Community Edition security patches Q2/2022) #8305

Closed

Upgrade from Payara 5 to 6 #8774

Closed

tiny doc change to trigger CI (not sure which version) #8305

d58c507

mreekie removed bklog: Collection labels Mar 3, 2023

Merge branch 'develop' into 8305-payara6-ee10

53559a4

scolapasta added this to the 6.0 milestone May 15, 2023

pdurbin mentioned this pull request May 24, 2023

create clean Payara 6 branch #9615

Closed

poikilotherm mentioned this pull request Jun 28, 2023

Big sweep: migrate codebase to Jakarta EE 10 and use Payara 6 now (third iteration) #9685

Merged

poikilotherm closed this Jun 28, 2023

pdurbin removed this from the 6.0 milestone Jul 17, 2023

pdurbin deleted the 8305-payara6-ee10 branch August 15, 2023 14:33

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8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

poikilotherm commented Nov 2, 2022

mreekie commented Jan 18, 2023

mreekie commented Jan 23, 2023 •

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cmbz commented May 15, 2023

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diego-guillen commented Jun 14, 2023

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poikilotherm commented Jun 28, 2023

8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

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poikilotherm commented Nov 2, 2022

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