Fedora 4.7.1 upgrade error

[dsanfo...@gmail.com]

Hello,

Moving this from the Fedora Community to Fedora Tech, I'm working on testing an upgrade from Fedora 4.7.0 to 4.7.1 and running into a data problem. Right now I've got an Ubuntu box running Fedora on Tomcat7, with Postgres 9.5 serving as the database back end. I've cloned the fedora data disk and made a full backup via pg_dump of the database to try the upgrade on test machine. When I start the machine up the first time with Fedora 4.7.1's WAR file everything works fine, but if I take tomcat down for any reason and attempt to restart I get the following error in Tomcat's log:

WARN (XmlWebApplicationContext) Exception encountered during context initialization - cancelling refresh attempt: org.springframework.beans.factory.org.fcrepo.kernel.api.string to a Name
ERROR (ContextLoader) Context initialization failed
org.springframework.beans.nested exception is org.fcrepo.kernel.api.
s019:Proxy" from String to a Name
Full error: https://gist.github.com/sanfordd/57ca6868ccccce95e0a2933a66aed583

As far as I can tell, when I use the 4.7.1 WAR on the initial startup it works well, but it runs a few odd commands on the postgres database which I am fairly sure are messing things up:
[26363] user@fcrepo LOG:  00000: execute S_4: INSERT INTO MODESHAPE_REPOSITORY (ID, CONTENT) VALUES ($1, $2)
[26363] user@fcrepo DETAIL:  parameters: $1 = '936198c317f1e7mode:http://fedora.info/', $2 = [pile of rbinary data removed to keep this short]
[26363] user@fcrepo LOG:  00000: execute S_4: INSERT INTO MODESHAPE_REPOSITORY (ID, CONTENT) VALUES ($1, $2)
[26363] user@fcrepo DETAIL:  parameters: $1 = '936198c317f1e7mode:http://www.w3.org/', $2 = [pile of rbinary data removed to keep this short]
[26363] user@fcrepo LOG:  00000: execute S_4: INSERT INTO MODESHAPE_REPOSITORY (ID, CONTENT) VALUES ($1, $2)
[26363] user@fcrepo DETAIL:  parameters: $1 = '936198c317f1e7mode:http://www.w3.org/', $2 = [pile of rbinary data removed to keep this short]
[26363] user@fcrepo LOG:  00000: execute S_4: INSERT INTO MODESHAPE_REPOSITORY (ID, CONTENT) VALUES ($1, $2)
[26363] user@fcrepo DETAIL:  parameters: $1 = '936198c317f1e7mode:

Doing the same with 4.7.0 doesn't generate the INSERT_INTO statements. Andrew Woods noted, in the initial e-mail to the Fedora Community list this may be connected to the ModeShape upgrade in 4.7.1.

For further help here's a copy of the postgres configuration for Fedora:

https://gist.github.com/sanfordd/6f5fe840d22f850cffe413271903c07c

Here's the repo.xml for spring:

https://gist.github.com/sanfordd/18ee28ea98914f947dd5d58da73fbe99


Thanks for any advice,
Daniel

[Anna Headley]

Bump.

Has anyone else done a successful upgrade to 4.7.1? If so could you share your steps in case we've missed something?

Has anyone done with using this method of cloning the data disk and migrating the db with pg_dump? Any notes or documentation you may have could be useful to us.

Is anyone else seeing this error in a production context?

ERROR (ContextLoader) Context initialization failed
org.springframework.beans.nested exception is org.fcrepo.kernel.api.
s019:Proxy" from String to a Name

Really wanting this bugfix upgrade!

Thanks,

Anna

 

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[Durbin, Michael (md5wz)]

Anna,

I did the upgrade from 4.7.0 to 4.7.1 (shortly after doing a 4.5.2-SNAPSHOT to 4.7.0). 

The relevent upgrade was from 4.5.2-SNAPSHOT to 4.7.0 though, because it involved an upgrade in place to 4.6.1 then an fcr:backup then an upgrade to an empty 4.7.0 and an fcr:restore.

The exact steps I followed are attached (I replaced some server names and removed passwords)

I retained the old data directories but never had to try to use them again since the backup and restore worked.  I had a second fedora 4.7.0 instance on a separate machine for the sanity checks.

-Mike

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From: fedor...@googlegroups.com [fedor...@googlegroups.com] on behalf of Anna Headley [anna.h...@gmail.com]
Sent: Wednesday, April 26, 2017 9:14 AM
To: fedor...@googlegroups.com
Subject: Re: [fedora-tech] Fedora 4.7.1 upgrade error

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[Benjamin Armintor]

Hello!

There's some weird truncation in the original email here, but judging from the linked stacktrace: That's the kind of error that shows up when Java can't parse a string value as a XML name, which might happen  because of bad characters or (in this case) because of a missing namespace if the string is formatted as if it has a namespace prefix.

In this case, what appears to be the critical message is the cause of the ContextLoader error: 'Caused by: org.modeshape.jcr.value.NamespaceException: There is no namespace registered for the prefix "ns019"'

Is it possible that your new MODE config doesn't have some namespace mappings the previous one did?

- Ben

[dsanfo...@gmail.com]

Ben,

For the 4.7.0 to 4.7.1 upgrade all that's being changed is the fcrepo.war file, the change to the namespace seems to be happening in postgres when the fcrepo 4.7.1 boots up and runs the insert into statements on what look like namespace entires in the modeshape_repository database. I don't think any of the MODE config should change when the war files are swapped, but I could be wrong.

Daniel

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[Embry, Randall Paul]

A different error, here. I’m running 4.7.0 on MySQL. I copied my production database and files to a test server and started up 4.7.0 fine. Then I swapped to 4.7.2 and see the following error on the first and subsequent startups:

ERROR 13:51:22.960 (RepositoryNodeTypeManager) Node types were read from the system content, and appear to be inconsistent or invalid: repo

java.lang.NullPointerException: null

        at org.modeshape.jcr.SystemContent.first(SystemContent.java:932) 

I’ve pasted the full stacktrace here: https://gist.github.com/rpembry/697aa35a3a3a568fc005c2e8cd7f35e8

Casual inspection through the REST GUI seems like things are running ok, but I’m also seeing a fair number of messages like these in catalina.out:

ERROR 13:57:18.532 (WebApplicationExceptionMapper) WebApplicationException intercepted by WebApplicationExceptionMapper: HTTP 304 Not Modified

Thanks,

--Randall

[Benjamin Armintor]

Daniel,

I see where your hypothesis is coming from, but it's perplexing to think that it would work the first time if it were the case that the namespaces were being overwritten on start-up, right?

I'm looking through the MODE changesets to see if anything jumps out.

- Ben

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