8947 Update to Payara 5.2022.3 #8949

poikilotherm · 2022-08-31T11:59:32Z

What this PR does / why we need it:

Upgrade to Payara 5.2022.3. Security and bug fixing.

Which issue(s) this PR closes:

Closes #8947
Closes IQSS/dataverse-security#66

Special notes for your reviewer:
None.

Suggestions on how to test this:
Follow instructions. @donsizemore says to check for greatly increased logging when using S3 (#8219). We might need to document how to lower the logging level.

Does this PR introduce a user interface change? If mockups are available, please link/include them here:
None.

Is there a release notes update needed for this change?:
Yes. 🔋 included.

Additional documentation:
None.

coveralls · 2022-08-31T12:02:12Z

Coverage increased (+0.001%) to 20.1% when pulling 6167940 on poikilotherm:8947-payara-5-2022-3 into 454f3f1 on IQSS:develop.

qqmyers

Looks like a find/replace of all instances of 5.2021.6 - except

dataverse/src/main/java/edu/harvard/iq/dataverse/util/DataSourceProducer.java

Line 41 in 094c90a

    
           // of properties can be found at https://docs.payara.fish/community/docs/5.2021.6/documentation/payara-server/jdbc/advanced-connection-pool-properties.html#full-list-of-properties

-should that be changed too?

qqmyers · 2022-08-31T13:49:08Z

doc/release-notes/8947-payara-update.md

+
+*NOTE: this might be rephrased to "required" depending on https://github.com/IQSS/dataverse/pull/8915 being merged.*
+
+With lots of bug and security fixes included, we encourage everyone to update to Payara 5.2022.3 as soon as possible.


I expect others will want to wordsmith the release notes more, but I'll note that we should probably not make this optional - while I think v5.12 will be compatible with earlier versions, after this PR we're not testing that anymore.

I absolutely agree!

@pdurbin WDYT - should we make a bold statement? (Especially as it seems to be another good reason to update because of #8823)

poikilotherm · 2022-08-31T14:52:02Z

-should that be changed too?

Actually that one was on purpose. The docs links changed upstream and I was really hoping for #8915 being merged as it is fairly small and helps people. That PR is already updating this place.

pdurbin · 2022-09-07T15:43:37Z

I'm pulling this out of QA and assigning it to @poikilotherm because he offered to document the extra steps around lib/databases and such as originally written up by @qqmyers at #8064 (comment)

I assume this should go in the guides? I found a few related references:

$ ack osgi source
source/admin/troubleshooting.rst
101:- Remove the ``generated`` and ``osgi-cache`` directories;

source/_static/util/clear_timer.sh
20:rm -rf ${PAYARA_DIR}/${DV_DIR}/osgi-cache/felix

source/installation/installation-main.rst
210:- Remove the ``generated`` and ``osgi-cache`` directories;

There's also stuff in "scripts":

$ ack generated scripts
scripts/dev/dev-rebuild.sh
18:echo "Deleting \"generated\" directory..."
19:rm -rf $PAYARA_DIR/glassfish/domains/domain1/generated

scripts/installer/dvinstall/as-setup.sh
168:    rm -rf /usr/local/payara5/glassfish/domains/domain1/generated

@PaulBoon thanks for pinging us about this.

poikilotherm · 2022-09-12T11:59:25Z

@pdurbin @qqmyers @donsizemore I added the notes and modifications regarding #8230. Please take a look.

pdurbin

I added a suggestion.

doc/release-notes/8947-payara-update.md

pdurbin · 2022-09-12T15:35:56Z

@poikilotherm thanks for the updates. At standup we talked about how next we need someone to review this so I unassigned you.

On a related note, @donsizemore is testing with Ansible. Thanks, Don!

doc/release-notes/8947-payara-update.md

@qqmyers

As documented by @qqmyers in IQSS#8230 one needs to remove the `lib/databases` folder from the domain dir on update to a Payara version beyond 5.2021.8.

With the update to a Payara version past 5.2021.8, the `lib/databases` folder needs to be removed by scripts etc (as with osgi-cache and generated folders) during rebuild/upgrade of a domain to avoid incompatibilities. See also: IQSS#8230

poikilotherm · 2022-09-20T07:48:33Z

I'm sorry but I had to force push this after rebasing on latest develop to avoid the merge conflict.

sekmiller · 2022-09-20T15:05:30Z

doc/release-notes/8947-payara-update.md

+3. Move the current Payara directory out of the way
+
+```shell
+    mv $PAYARA $PAYARA.MOVED


Where does PAYARA.MOVED get set/exported?

Oh this was just copy-pasta from the v5.6 instructions.

The shell expansion will stop at the ".", so if $PAYARA is "x", it'll be "x.MOVED".

With the merge of IQSS#8949 the custom version is no longer necessary.

poikilotherm added Component: Code Infrastructure formerly "Feature: Code Infrastructure" Feature: Installer Feature: Installation Guide dependencies labels Aug 31, 2022

poikilotherm added this to the 5.12 milestone Aug 31, 2022

poikilotherm added this to On Deck 🛎 in IQSS/dataverse (TO BE RETIRED / DELETED in favor of project 34) via automation Aug 31, 2022

This was referenced Aug 31, 2022

7980 enhanced dsd #8915

Merged

Bump payara-bom from 5.2021.6 to 5.2022.3 in /modules/dataverse-parent #8946

Closed

qqmyers approved these changes Aug 31, 2022

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IQSS/dataverse (TO BE RETIRED / DELETED in favor of project 34) automation moved this from On Deck 🛎 to QA ✅ Aug 31, 2022

pdurbin mentioned this pull request Sep 7, 2022

7000 mpconfig basic infra #8823

Merged

pdurbin moved this from QA ✅ to Review 🔎 in IQSS/dataverse (TO BE RETIRED / DELETED in favor of project 34) Sep 7, 2022

pdurbin assigned poikilotherm Sep 7, 2022

poikilotherm force-pushed the 8947-payara-5-2022-3 branch from 0cd17e8 to 3a67df6 Compare September 12, 2022 11:58

poikilotherm requested review from qqmyers, pdurbin and donsizemore September 12, 2022 11:59

pdurbin reviewed Sep 12, 2022

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pdurbin unassigned poikilotherm Sep 12, 2022

donsizemore mentioned this pull request Sep 12, 2022

upgrade to Payara-5.2022.3 gdcc/dataverse-ansible#252

Closed

scolapasta moved this from Review 🔎 to QA ✅ in IQSS/dataverse (TO BE RETIRED / DELETED in favor of project 34) Sep 14, 2022

sekmiller self-assigned this Sep 19, 2022

sekmiller reviewed Sep 19, 2022

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poikilotherm force-pushed the 8947-payara-5-2022-3 branch from 6167940 to f2ddc04 Compare September 20, 2022 07:46

chore(deps): update to Payara 5.2022.3 everywhere IQSS#8947

41c8f61

poikilotherm added 3 commits September 20, 2022 09:47

docs(deps): add release notes about Payara Update IQSS#8947

db4e82c

docs(deps): add step in rel. notes for Payara update IQSS#8947

b6a502f

As documented by @qqmyers in IQSS#8230 one needs to remove the `lib/databases` folder from the domain dir on update to a Payara version beyond 5.2021.8.

poikilotherm force-pushed the 8947-payara-5-2022-3 branch from f2ddc04 to 46f6066 Compare September 20, 2022 07:47

sekmiller reviewed Sep 20, 2022

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pdurbin requested a review from landreev September 21, 2022 17:04

clearing out lib/databases is one-time during the upgrade IQSS#8947

71e4912

pdurbin merged commit b0f967c into IQSS:develop Sep 21, 2022

IQSS/dataverse (TO BE RETIRED / DELETED in favor of project 34) automation moved this from QA ✅ to Done 🚀 Sep 21, 2022

poikilotherm added a commit to poikilotherm/dataverse that referenced this pull request Sep 22, 2022

chore(deps): remove Payara version from Maven ct profile

0959c84

With the merge of IQSS#8949 the custom version is no longer necessary.

donsizemore mentioned this pull request Sep 22, 2022

Bump to payara 5 2022 3 gdcc/dataverse-ansible#256

Merged

pdurbin mentioned this pull request Sep 23, 2022

switch to our regular createDataverseRequest pattern #8992 #8993

Merged

poikilotherm deleted the 8947-payara-5-2022-3 branch May 21, 2023 19:15

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8947 Update to Payara 5.2022.3 #8949

8947 Update to Payara 5.2022.3 #8949

poikilotherm commented Aug 31, 2022 •

edited by pdurbin

coveralls commented Aug 31, 2022 •

edited

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qqmyers Aug 31, 2022

poikilotherm Aug 31, 2022

poikilotherm Sep 12, 2022

poikilotherm commented Aug 31, 2022 •

edited

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pdurbin commented Sep 12, 2022

poikilotherm commented Sep 20, 2022

sekmiller Sep 20, 2022

poikilotherm Sep 20, 2022


		NOTE: this might be rephrased to "required" depending on https://github.com/IQSS/dataverse/pull/8915 being merged.

		With lots of bug and security fixes included, we encourage everyone to update to Payara 5.2022.3 as soon as possible.

8947 Update to Payara 5.2022.3 #8949

8947 Update to Payara 5.2022.3 #8949

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poikilotherm commented Aug 31, 2022 • edited by pdurbin

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