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8947 Update to Payara 5.2022.3#8949

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pdurbin merged 5 commits intoIQSS:developfrom
poikilotherm:8947-payara-5-2022-3
Sep 21, 2022
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8947 Update to Payara 5.2022.3#8949
pdurbin merged 5 commits intoIQSS:developfrom
poikilotherm:8947-payara-5-2022-3

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@poikilotherm poikilotherm commented Aug 31, 2022 •
edited by pdurbin
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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.

@poikilotherm poikilotherm added this to the 5.12 milestone Aug 31, 2022
This was referenced Aug 31, 2022
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coveralls commented Aug 31, 2022 •
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Coverage Status

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

qqmyers
qqmyers approved these changes Aug 31, 2022
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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?

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.
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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.

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@poikilotherm poikilotherm Aug 31, 2022

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I absolutely agree!

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@poikilotherm poikilotherm Sep 12, 2022

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

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poikilotherm commented Aug 31, 2022 •
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-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 pdurbin mentioned this pull request Sep 7, 2022
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pdurbin commented Sep 7, 2022

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.

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poikilotherm commented Sep 12, 2022

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

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I added a suggestion.

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pdurbin commented Sep 12, 2022

@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!

@donsizemore donsizemore mentioned this pull request Sep 12, 2022
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@sekmiller sekmiller self-assigned this Sep 19, 2022
sekmiller
sekmiller reviewed Sep 19, 2022
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@poikilotherm
chore(deps): update to Payara 5.2022.3 everywhere IQSS#8947
41c8f61
@poikilotherm
docs(deps): add release notes about Payara Update IQSS#8947
db4e82c
@poikilotherm
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
fix,docs(deps): delete lib/databases folder in scripts IQSS#8947
46f6066 
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
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poikilotherm commented Sep 20, 2022

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

sekmiller
sekmiller reviewed Sep 20, 2022
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doc/release-notes/8947-payara-update.md
3. Move the current Payara directory out of the way

```shell
mv $PAYARA $PAYARA.MOVED
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Where does PAYARA.MOVED get set/exported?

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@poikilotherm poikilotherm Sep 20, 2022

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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".

@pdurbin pdurbin requested a review from landreev September 21, 2022 17:04
@pdurbin pdurbin merged commit b0f967c into IQSS:develop Sep 21, 2022
poikilotherm added a commit to poikilotherm/dataverse that referenced this pull request Sep 22, 2022
@poikilotherm
chore(deps): remove Payara version from Maven ct profile
0959c84 
With the merge of IQSS#8949 the custom version is no longer necessary.
@donsizemore donsizemore mentioned this pull request Sep 22, 2022
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@pdurbin pdurbin mentioned this pull request Sep 23, 2022
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@poikilotherm poikilotherm deleted the 8947-payara-5-2022-3 branch May 21, 2023 19:15
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Update to Payara 5.2022.3

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