Upgrade from Payara 5 to 6 #8774

pdurbin · 2022-06-03T19:45:36Z

What this PR does / why we need it:

Payara 5 is going EOL.

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 Alpha 3 is out and we can test with it.
Do not move this to QA until Payara 6 Final is out and we can test with it.
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, I'm 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.

landreev

It looks like there's been some movement on the Payara side, a good time for this to go back into dev.
(Also, note that it's showing a few conflicts now)

donsizemore · 2022-07-20T14:49:21Z

It looks like there's been some movement on the Payara side, a good time for this to go back into dev. (Also, note that it's showing a few conflicts now)

Correct - a mvn package results in controlledvocabulary and other language bundle errors, but there is concern that a merge with develop could take several hours. I have the full Maven output if anyone is interested, but I'm less inclined to waste anyone's time with it until the branch is current with develop.

coveralls · 2022-07-20T15:20:01Z

Coverage decreased (-0.007%) to 19.758% when pulling d1a19f3 on 8305-payara6 into 567e506 on develop.

@pdurbin

With the release of prettyfaces/rewrite 5.0.0.Alpha1 they finally released a version compatible with at least Jakarta EE 9. This includes the patches @pdurbin applied to our local build, too. Removing the local built, too. See also: ocpsoft/rewrite#304

poikilotherm · 2022-11-02T08:21:38Z

@pdurbin what do we do with this PR? It's based on Jakarta EE 9.1, but we need EE 10. I did that in https://github.com/IQSS/dataverse/tree/8305-payara6-ee10. Should we open a new PR?

pdurbin · 2022-11-02T13:16:34Z

@poikilotherm yes, a new PR is better. I'm closing this one. Thanks!

pdurbin · 2023-01-26T13:54:33Z

This is the new PR (thanks, @poikilotherm!):

8305 Upgrade to Jakarta EE 10 and Payara 6 #9116

I deleted the old branch to reduce confusion. 😄

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

This was referenced Jun 3, 2022

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

Closed

payara5 hard-coded in ec2-create-instance.sh (rsync logs) gdcc/dataverse-ansible#242

Open

qqmyers mentioned this pull request Jun 3, 2022

GDCC/HDC 3B-Bi-directional LDN messaging, Template Instructions #8775

Merged

pdurbin assigned landreev Jun 8, 2022

landreev reviewed Jul 20, 2022

View reviewed changes

landreev removed their assignment Jul 20, 2022

Merge branch 'develop' into 8305-payara6

d1a19f3

poikilotherm force-pushed the 8305-payara6 branch from 9f45769 to 74ef320 Compare July 26, 2022 19:24

mreekie added the bk2211 label Nov 1, 2022

pdurbin closed this Nov 2, 2022

pdurbin deleted the 8305-payara6 branch January 26, 2023 13:49

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Upgrade from Payara 5 to 6 #8774

Upgrade from Payara 5 to 6 #8774

pdurbin commented Jun 3, 2022

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donsizemore commented Jul 20, 2022

coveralls commented Jul 20, 2022

poikilotherm commented Nov 2, 2022 •

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pdurbin commented Nov 2, 2022

pdurbin commented Jan 26, 2023

Upgrade from Payara 5 to 6 #8774

Upgrade from Payara 5 to 6 #8774

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