[fcrepo-user] upgrading to 3.7.1

[Adam Wead]

With fedora stopped, when I run fedora-rebuild.sh on the new version, I get:

ERROR 14:26:44.741 (Server) Module
(org.fcrepo.server.storage.DOManager) failed to initialize
org.fcrepo.server.errors.ModuleInitializationException: Error checking
for and creating non-existing tables

I'm getting this even with an empty database, which seems odd. I know
there's the new table fcrepoRebuildStatus. Should I create this
manually?

TIA,
...adam
____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Benjamin Armintor]

Adam-

  Can you walk me through what you've done so far?

- Ben

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[Adam Wead]

so... with the new jar file,

java -jar installer.3.7.1.jar /old/FEDORA_HOME/install/install.properties
cd /new/FEDORA_HOME
copy fedora, fedora-users and akubra configs from old fedora to new
copy fedora-xacml-policies from old fedora to new
set environment variables (FEDORA_HOME, CATALINA_HOME)
run fedora-rebuild.sh
BOOM!

That's what I did with the 3.7.0 upgrade. Perhaps there's a better way...

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Adam Wead]

So, I'm getting the same problem even with a new install of 3.7.1.
When I execute the jar file and go through the custom install process,
I point fedora to our mysql server with an empt database.

When I startup fedora, I get:

https://gist.github.com/anonymous/7321053

Try to rebuild:

https://gist.github.com/anonymous/7321206

Here's the install properties file that was created when I ran the
custom install:

https://gist.github.com/anonymous/7321222

I didn't change any of the config files. They are as-is from the
installer. I also tried updating the mysql-connector to the latest
5.1.27, but no dice.

I'm seeing the errors: Duplicate key name 'rebuildDate' and Error:

Error checking for and creating non-existing tables

If you want to send me the specs on the that new table, I can try
creating it manually in mysql and see if that has any effect.

FYI: The installer works with the "quick" installation option which
uses the jdbc driver, so I imagine this is some odd issue with mysql.

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Benjamin Armintor]

The dbSpec is at https://github.com/fcrepo/fcrepo/blob/master/fcrepo-server/src/main/resources/dbspec/server/org/fcrepo/server/storage/resources/DefaultDOManager.dbspec

The new table is defined at the end of the file.

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[Adam Wead]

Sorry, no dice there. Is anyone else having this problem?

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Jeff Minelli]

Silly questions, but can you access the database from the CLI?

-jeff

---

From: Adam Wead Adam Wead
Reply: Support and info exchange list for Fedora users. fedora-com...@lists.sourceforge.net
Date: November 5, 2013 at 11:30:22 AM
To: Support and info exchange list for Fedora users. fedora-com...@lists.sourceforge.net
Subject:  Re: [fcrepo-user] upgrading to 3.7.1

[Benjamin Armintor]

First of all, let me say: Aargh.

I think the mySQL jdbc driver is barking that a columnSpec marked as unique and indexed is trying to build 2 indexes with the same name. Try this:

1. Start tomcat- it will fail, but it will unpack the WAR.

2. shut down tomcat

3. Grab this file: https://raw.github.com/fcrepo/fcrepo/master/fcrepo-server/src/main/resources/dbspec/server/org/fcrepo/server/storage/resources/DefaultDOManager.dbspec

4. edit the last table spec to remove the "index" attribute

5. copy the edited file to $CATALINE_HOME/webapps/fedora/WEB-INF/classes/org/fcrepo/storage/resources

6. start tomcat (it should work now)

7. stop tomcat.

8. run the rebuilder (if desired)

[Benjamin Armintor]

More specifically for #4, edit the table spec for fcrepoRebuildStatus to remove the index attribute "index='rebuildDate'" from the rebuildDate column.

[Benjamin Armintor]

Edit for #5: $CATALINA_HOME/webapps/fedora/WEB-INF/classes/org/fcrepo/server/storage/resources

[Adam Wead]

OK, it creates the table! But, now I'm getting:

https://gist.github.com/awead/7324228

Never saw this before and don't have the xsd file in any of my
previous fedora installs.

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Adam Wead]

Alright... turned out it was some stale config files that had old file names.

I'm now happy to report that it's working! Thanks for the help...

Should there be a new release, something like 3.7.1.1 to address the fix?

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Benjamin Armintor]

I'm going to put that decision in the steering group's lap. There's hypothetically another RC to be ready in a week or so.

[Adam Wead]

Oh, if it's that soon, then I'm fine waiting until 3.7.2

____________________________________________
Adam Wead
Systems and Digital Collections Librarian
Rock and Roll Hall of Fame and Museum
216.515.1960 (t)
215.515.1964 (f)

[Andrew Woods]

Thanks for raising the flag on this issue, Adam. 

Having the update roll in with 3.7.2 seems very reasonable, versus yet another minor release.

Andrew

[Korcynski, Michael T.]

I just started a 3.7.1 upgrade at Tufts as well. While running the
installer we ran into a different initial problem, and having resolved
that have caught up the problem reported here, so first off, thanks for
the info here in this thread. The problem we initially hit is that in our
install we specify the low level storage option as legacy-fs, which upon
start up results in the following error:

ERROR 13:46:21.014 (Server) Module
(org.fcrepo.server.storage.lowlevel.ILowlevelStorage) failed to initialize
org.fcrepo.server.errors.ModuleInitializationException: couldn't set up
path_algorithm for objectPaths Class
org.fcrepo.server.storage.lowlevel.defaultstore.Store can not access a
member of class org.fcrepo.server.storage.lowlevel.TimestampPathAlgorithm
with modifiers "public"
at
org.fcrepo.server.storage.lowlevel.DefaultLowlevelStorageModule.postInitMod
ule(DefaultLowlevelStorageModule.java:44) ~[fcrepo-server-3.7.1.jar:na]

Looking at the fcrepo-server source it seemed to be related to this commit:

https://github.com/fcrepo/fcrepo/commit/5ad360edf39bfeca57038974639b41073af
1fd1b#diff-644ddc1704c65930c61becbd9826bee1



Where the Store class moved from being a support within
DefaultLowlevelStorage in the org.fcrepo.server.storage.lowlevel package
to the org.fcrepo.server.storage.lowlevel.default package as a top level
class.

I confirmed that by making the TimestampPathAlgorithm class public this
issue goes away at startup since Store would then have access. Not sure
if this is the correct fix or if Store should've stayed in the previous
package.

Hope this helps,
Mike

[Benjamin Armintor]

That looks like a bug to me, Mike. If you have time to create a JIRA ticket for it, I'll patch it in master.

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[Gervais de Montbrun]

Hi All,

I'm having trouble installing 3.7.1. I just downloaded the fcrepo-installer-3.7.1.jar from the fedora-commons.org web page to do a new install. It seems that this bug is still present in the jar file that is on the fedora-commons.org web page, but that the fix below no longer works...

I downloaded the linked to DefaultDOManager.dbspec file (which seems to already be updated as step 4's reference to "index='rebuildDate'" is not there). NP...

The path where the file is supposed to be save to ($CATALINA_HOME/webapps/fedora/WEB-INF/classes/org/fcrepo/server/storage/resources) in step 5 doesn't exist on my fresh install... Problem...

I created the path and stuck the file there on the off chance that this would correct the issue. As I expected, it does not.

Any suggestions on how to get fedora 3.7.1 working? Again, this is a fresh, clean install.

Cheers,

Gervais

[Benjamin Armintor]

Gervais,

  The fact that the path you copied to didn't exist is suspicious.  Are you quite sure that you're working in the operative CATALINA_HOME? If you had tried and failed to start Fedora, the web application should still have been unpacked.

- Ben

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[Gervais de Montbrun]

The apache tomcat manager page loads up…  "Thanks for using Tomcat!”

:-)

I set up a vm to test on and I find the same result.

[root@Islandora ~]# cd $CATALINA_HOME/webapps/fedora/WEB-INF/classes

[root@Islandora classes]# ls

carol.properties  default.properties  images  META-INF  ri

There is no “org” dir. I don’t have an org dir in classes in any of my fedora installs (checked a working 3.6.2 install).

Cheers,
Gervais

[Benjamin Armintor]

Right, this file is usually in a JAR- you're overriding it by creating the resource in the WEB-INF-classes directory.

Ok, so you've created the override file, and copied it into $CATALINA_HOME/webapps/fedora/WEB-INF/classes/org/fcrepo/server/storage/resources (this is an edit further down in this email chain, please double-check the path you are copying to).  What message do you get in the Fedora logs?

- Ben 

[Gervais de Montbrun]

Hi Ben,

I saw the correction in the tread about CATALINA…  Let me go back a bit… This is what I am doing:

cd ~

wget http://downloads.sourceforge.net/fedora-commons/fcrepo-installer-3.7.1.jar

sudo java -jar fcrepo-installer-3.7.1.jar install.properties

cat /usr/local/fedora/install/install.properties 
#Install Options
#Thu Feb 20 12:18:00 AST 2014
keystore.file=included
ri.enabled=true
messaging.enabled=true
apia.auth.required=false
database.jdbcDriverClass=com.mysql.jdbc.Driver
tomcat.ssl.port=8443
ssl.available=true
database.jdbcURL=jdbc\:mysql\://localhost/fedora3?useUnicode\=true&characterEncoding\=UTF-8&autoReconnect\=true
messaging.uri=vm\:(broker\:(tcp\://localhost\:61616))
database.password=islandora
database.mysql.driver=included
database.username=fedoraAdmin
fesl.authz.enabled=false
tomcat.shutdown.port=8055
deploy.local.services=true
xacml.enabled=true
database.mysql.jdbcDriverClass=com.mysql.jdbc.Driver
tomcat.http.port=8080
fedora.serverHost=localhost
database=mysql
database.driver=included
fedora.serverContext=fedora
llstore.type=akubra-fs
tomcat.home=/usr/local/fedora/tomcat
fesl.authn.enabled=true
database.mysql.jdbcURL=jdbc\:mysql\://localhost/fedora3?useUnicode\=true&characterEncoding\=UTF-8&autoReconnect\=true
fedora.home=/usr/local/fedora
install.type=custom
servlet.engine=included
apim.ssl.required=false
fedora.admin.pass=islandora
apia.ssl.required=false

I set my JAVA_OPTS, FEDORA_HOME and CATALINA_HOME up in a /etc/profile.d/fedora.sh file

cat /etc/profile.d/fedora.sh 
export FEDORA_HOME=/usr/local/fedora
export CATALINA_HOME=/usr/local/fedora/tomcat
export JAVA_OPTS="-Xms1024m -Xmx1024m -XX:MaxPermSize=512m -XX:+CMSClassUnloadingEnabled -Djavax.net.ssl.trustStore=/usr/local/fedora/server/truststore -Djavax.net.ssl.trustStorePassword=tomcat"
export JAVA_HOME=/usr/java/jdk1.6.0_38
export FEDORA_USER=fedora

I run my tomcat stack as the FEDORA_USER so I chown the dir to fedora

chown -R $FEDORA_USER:$FEDORA_USER $FEDORA_HOME

We have an init script that we use to stop and start tomcat…so I 

service tomcat start

Tomcat starts, but fedora.log throws an error when it tries to create the table:

INFO 2014-02-20 12:18:25.702 [main] (SQLUtilityImpl) Creating new table 'fcrepoRebuildStatus' with command(s):

CREATE TABLE fcrepoRebuildStatus (

  rebuildDate bigint NOT NULL,

  complete boolean NOT NULL,

  UNIQUE KEY rebuildDate (rebuildDate),

  KEY rebuildDate (rebuildDate)

);

ERROR 2014-02-20 12:18:25.730 [main] (Server) Module (org.fcrepo.server.storage.DOManager) failed to initialize

org.fcrepo.server.errors.ModuleInitializationException: Error while attempting to check for and create non-existing table(s): com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Duplicate key name 'rebuildDate'

        at org.fcrepo.server.storage.DefaultDOManager.postInitModule(DefaultDOManager.java:410) ~[fcrepo-server-3.7.1.jar:na]

There is no org dir to copy the file into as suggested…

[root@Islandora ~]# echo $CATALINA_HOME

/usr/local/fedora/tomcat

[root@Islandora ~]# cd $CATALINA_HOME/webapps/fedora/WEB-INF/classes/org/fcrepo/server/storage/resources

-bash: cd: /usr/local/fedora/tomcat/webapps/fedora/WEB-INF/classes/org/fcrepo/server/storage/resources: No such file or directory

Anything else I can tell you that might help you help me?

:)

Cheers,
Gervais
--

Gervais de Montbrun  | Systems Team Lead 

discoverygarden inc. | www.discoverygarden.ca

Skype: GervaisdeM    | GTalk: ger...@discoverygarden.ca

[Edward Garrett]

Hi there,

i just ran into this problem myself. fixes #4 and #5 above worked for me.

it's a year on; perhaps there should be a minor release so that others don't run into the same problem, or perhaps 3.7.2 is near??

edward

[Edward Garrett]

looks like this issue should point to:

https://groups.google.com/forum/#!topic/fedora-community/UXH7jyJY4x4

where it is suggested to install fedora 3.8

On Friday, November 1, 2013 6:33:25 PM UTC, awoods wrote:

[Scott Prater]

Fedora 3.8.0 is very near.

-- Scott

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