Upgrade Fedora

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Nikolay Gannev

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Feb 1, 2024, 8:26:06 AMFeb 1
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Hi there, 

We are planning to upgrade our current Fedora 4.7.1 to Fedora 5 (most probably 5.1.1).
I have done some high level research, but still no specific step by step migration instructions. I see some threads for that, but not much help at this time. 
We might go to Fedora 6 at some point (and I see a lot more information for migration to 6), but bc of JDK requirement we need to do Fedora 5 migration first. 

Please let me know if you have some more detailed info regarding Fedora 4-5 migration. 

Thanks, 
Nikolay.

Jared Whiklo

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Feb 1, 2024, 12:47:31 PMFeb 1
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Hi Nikolay,

It's been a while, but as I recall the process is.

1. Because all upgrades were from the last version, you'll need to get from 4.7.1 to 4.7.5.

https://wiki.lyrasis.org/display/FF/Releases

I would pay special attention to warning on the 4.7.3 notes in case they apply to you.

2. Once you are at 4.7.5, you need to use the fcrepo-import-export tooling to make an export of your Fedora 4 repository on disk. 

https://github.com/fcrepo-exts/fcrepo-import-export

3. Then you run the fcrepo-upgrade-utils to convert the on-disk representation to that of a Fedora 5 repository. 

https://github.com/fcrepo-exts/fcrepo-upgrade-utils

4. Lastly you use the fcrepo-import-export tool from above to import your on-disk representation into a new Fedora 5.

Because of issues the Fedora project moved away from using the Modeshape JCR repository. Because of this I would recommend storing your export just in-case any issues arise so you have a backup of some of your data.

cheers,
jared

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Nikolay Gannev

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Feb 2, 2024, 1:59:54 PMFeb 2
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Thanks Jared! Appreciate it.

Nikolay Gannev

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Feb 9, 2024, 5:14:54 PMFeb 9
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Hi Jared, 

In the meantime we have upgraded MySQL to 8 and we need to configure Fedora 4.7.1. I have downloaded mysql-connector-j-8.2.0 and bundled in the war and redeployed but getting errors like
ERROR 16:50:34.093 (ContextLoader) Context initialization failed
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'modeshapeRepofactory': Invocation of init method failed; nested exception is org.fcrepo.kernel.api.exception.RepositoryRuntimeException: java.lang.RuntimeException: java.lang.ExceptionInInitializerError

Any ideas or suggestions?
Thanks,
Nikolay.

Michael Ritter

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Feb 9, 2024, 5:45:45 PMFeb 9
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Hi Nikolay,

mysql-connector-j changes the package for the mysql Driver class so that could be causing problems with Fedora starting. I'm not familiar with how Fedora 4 manages its configuration, but the updated class would be 'com.mysql.cj.jdbc.Driver'. From my experience the 5.x versions of mysql-connector-java have been compatible with every version of mysql I've tried, so you could try rolling that back as well.

-Mike

Nikolay Gannev

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Feb 9, 2024, 6:18:01 PMFeb 9
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Thanks Mike, 

I actually see similar error for this issue:

WARN 16:50:22.002 (DriverDataSource) Registered driver with driverClassName=com.mysql.jdbc.Driver was not found, trying direct instantiation.
WARN 16:50:33.890 (arjuna) ARJUNA012218: cant create new instance of {0}
java.lang.reflect.InvocationTargetException: null

We are in a process of upgrading Fedora, so maybe the best option (if that is valid option for us, need to clarify) is to simply upgrade Fedora with the new MySQL. 

Nikolay Gannev

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Mar 19, 2024, 3:30:22 PMMar 19
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Hi Jared, 

I'm trying to go through the steps you mentioned here. For simplicity I have a repo with only 10 objects and ran the first 2 steps to export and upgrade. 
When I tried to import though I was getting an error like below.
Looks like the backslash in the path is causing the issue. 
tmp/fedora5 folder where the upgraded content is looks fine. 
Any thoughts?

Thanks,
Nikolay.

C:\Users\drx9-aws>java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m import -r http://localhost:9030/fcrepo/rest/objects -d /tmp/fedora5 -b -a
INFO 15:17:51.250 (Importer) Running importer...
INFO 15:17:52.085 (RdfWriterHelper) Loading JENA 3.1.1 Patched RDF Output Writers
ERROR 15:17:53.321 (ImportExportDriver) Error performing import/export: Illegal character in path at index 28: http://localhost:9030/fcrepo\rest\objects\0e\35\a9\8b\0e35a98b-52fd-4980-b524-6ea75e0933aa

On Thursday, February 1, 2024 at 12:47:31 PM UTC-5 Jared Whiklo wrote:

Dan Field

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Mar 20, 2024, 9:18:29 AMMar 20
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Hi Nikolay. This looks to be related to the forward-slash characters in the URL. It might be that the import-export tool has not been tested on Windows thoroughly. You could try adding the file.separator property on the command line e.g.

 java  -Dfile.separator=/ -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m import -r http://localhost:9030/fcrepo/rest/objects -d /tmp/fedora5 -b -a


however, this may well have a knock on effect of breaking filesystem access 


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Subject: Re: [fedora-tech] Upgrade Fedora
 

Nikolay Gannev

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Mar 20, 2024, 12:23:35 PMMar 20
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Thanks Dan, 

yeah I see your point, but I'm getting another error now

C:\Users\drx9-aws>java -Dfile.separator=/ -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m import -r http://localhost:9030/fcrepo/rest/objects -d /tmp/fedora5 -b -a
Error: Could not find or load main class org.fcrepo.importexport.ImportExportDriver

Is there a version that has been fully tested on Windows?

Thanks, 
Nikolay

Nikolay Gannev

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Mar 21, 2024, 4:26:09 PMMar 21
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Hi Dan,

I upgraded to  fcrepo-import-export 1.0.0 and that helped with the original issue, but I'm now getting 403 error!
Any suggestions?


2024-03-21 16:18:43,874 Error importing C:\tmp\fedora5\fcrepo\rest\objects\0e\35\a9\8b\0e35a98b-52fd-4980-b524-6ea75e0933aa.ttl to http://localhost:9030/fcrepo/rest/objects/0e/35/a9/8b/0e35a98b-52fd-4980-b524-6ea75e0933aa, received 403
2024-03-21 16:18:43,956 Error importing C:\tmp\fedora5\fcrepo\rest\objects\0e\35\a9\8b\0e35a98b-52fd-4980-b524-6ea75e0933aa\THUMBNAIL_LARGE\fcr%3Ametadata.ttl to http://localhost:9030/fcrepo/rest/objects/0e/35/a9/8b/0e35a98b-52fd-4980-b524-6ea75e0933aa/THUMBNAIL_LARGE, received 403
2024-03-21 16:18:44,014 Error importing C:\tmp\fedora5\fcrepo\rest\objects\44\c7\a8\ae\44c7a8ae-3bcf-4851-86ed-72b9cfc07266.ttl to http://localhost:9030/fcrepo/rest/objects/44/c7/a8/ae/44c7a8ae-3bcf-4851-86ed-72b9cfc07266, received 403
2024-03-21 16:18:44,140 Error importing C:\tmp\fedora5\fcrepo\rest\objects\44\c7\a8\ae\44c7a8ae-3bcf-4851-86ed-72b9cfc07266\DS1\fcr%3Ametadata.ttl to http://localhost:9030/fcrepo/rest/objects/44/c7/a8/ae/44c7a8ae-3bcf-4851-86ed-72b9cfc07266/DS1, received 403
2024-03-21 16:18:44,190 Error importing C:\tmp\fedora5\fcrepo\rest\objects\44\c7\a8\ae\44c7a8ae-3bcf-4851-86ed-72b9cfc07266\DS2\fcr%3Ametadata.ttl to http://localhost:9030/fcrepo/rest/objects/44/c7/a8/ae/44c7a8ae-3bcf-4851-86ed-72b9cfc07266/DS2, received 403
....................................
On Wednesday, March 20, 2024 at 9:18:29 AM UTC-4 Dan Field wrote:

Nikolay Gannev

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Mar 26, 2024, 9:48:03 PMMar 26
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Hi everyone, 

I wanted to give you an update of the current migration process. 

1. Upgraded to Fedora 4.7.5 - that did not require any changes, only the new fcrepo.war file.
2. To simplify the process I have deleted the repo and only ingested two records. We have an application that has ingest functionality and requires to have objects container in Fedora as top level which I manually created. 
3. Based on documentation I downloaded fcrepo-import-export-0.3.0.jar and setup command to export the records to file system:
java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m export -r http://localhost:9030/fcrepo/rest/objects -d /tmp/fedora4 -b -a
4. Based on documentation I downloaded fcrepo-upgrade-utils-6.0.0.jar and setup command to run the upgrade from 4.7.5 to 5+. Note that I had to get later version of JDK to be able to run it.
D:\JDK\jdk-17.0.10\bin\java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-upgrade-utils\fcrepo-upgrade-utils-6.0.0.jar -i C:\tmp\fedora4 -s 4.7.5 -t 5+ -o C:\tmp\fedora5
5. Deleted Fedora repo.
6. Downloaded fcrepo_5.1.1.war file and deployed. Had to change web.xml to comment out shiro filter to bypass authentication/authorization to be able to run the import in the next step, otherwise I was getting 403 error. 
7. Finally setup command to import the records from file system back to Fedora. Note that I had some issues with backslash (when using fcrepo-import-export-0.3.0.jar version) discussed in the previous reply and found out that this issue was resolved in fcrepo-import-export-1.0.0.jar. 
java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-1.0.0.jar -m import -r http://localhost:9030/fcrepo/rest/objects -d /tmp/fedora5 -b -a

So far, export and upgrade finished with no errors, but I have some errors on the import:

NFO 14:09:29.051 (Importer) Importing binary fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\DS1\fcr%3Ametadata.ttl
INFO 14:09:29.237 (Importer) Imported binary: http://localhost:9030/fcrepo/rest/objects/cc/cc/1e/35/cccc1e35-9a2f-44fa-8217-7d8d6db328dd/DS1
ERROR 14:09:29.311 (Importer) Error while importing C:\tmp\fedora5_test5\fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\DS1\fcr%3Ametadata.ttl (400):
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModifiedBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModified) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#createdBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#created) cannot be modified by the client.
INFO 14:09:29.323 (Importer) Importing binary fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\MODS\fcr%3Ametadata.ttl
INFO 14:09:29.421 (Importer) Imported binary: http://localhost:9030/fcrepo/rest/objects/cc/cc/1e/35/cccc1e35-9a2f-44fa-8217-7d8d6db328dd/MODS
ERROR 14:09:29.475 (Importer) Error while importing C:\tmp\fedora5_test5\fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\MODS\fcr%3Ametadata.ttl (400):
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModifiedBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModified) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#createdBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#created) cannot be modified by the client.
INFO 14:09:29.492 (Importer) Importing binary fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\POLICY\fcr%3Ametadata.ttl
INFO 14:09:29.605 (Importer) Imported binary: http://localhost:9030/fcrepo/rest/objects/cc/cc/1e/35/cccc1e35-9a2f-44fa-8217-7d8d6db328dd/POLICY
ERROR 14:09:29.652 (Importer) Error while importing C:\tmp\fedora5_test5\fcrepo\rest\objects\cc\cc\1e\35\cccc1e35-9a2f-44fa-8217-7d8d6db328dd\POLICY\fcr%3Ametadata.ttl (400):
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModifiedBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#lastModified) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#createdBy) cannot be modified by the client.,
The server managed predicates (http://fedora.info/definitions/v4/repository#created) cannot be modified by the client.
.......

Also, the structure of Records in Fedora is broken.
For ex, before export there were two direct children of objects container in the repo:



After the import I see all records as direct children of objects container:


Please let me know if I'm not doing any step correctly and more specifically the import. Not sure if I need to set any other parameters when I call the tools.

Thanks, 
Nikolay

Jared Whiklo

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Mar 28, 2024, 11:25:39 AMMar 28
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Hi Nikolay,

For the first error you can add the "-Dfcrepo.properties.management=relaxed" Java system property to allow you to update certain system managed properties.

More information here (https://wiki.lyrasis.org/display/FEDORA5x/How+to+allow+user-updates+to+certain+server+managed+triples)

For the second issue...I'm less sure.

Do the "parent" objects exist with their own *.ttl files in the export on disk? It's been a while but if they don't then I believe they are just pairtree resources and might be treated differently in Fedora 5 from Fedora 4.

cheers,
jared

Nikolay Gannev

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Mar 28, 2024, 2:34:16 PMMar 28
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Hi Jared, 

Thanks for your reply. 

Yes, objects comes with it's own ttl and also ttl.headers  files (in upgraded 5 folder).

Nikolay Gannev

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Apr 3, 2024, 12:52:19 PMApr 3
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Hi Jared, 

When I added that configuration on fcrepo 5.1.1 it resolved the errors on import and actually it fixed the structure too!
I'm going to add another step to migrate content from 5 + to 6 + and let you know if I have any issues. 

Also do you recommend using latest version of fcrepo 6.5.0? 


Thanks again.
Nikolay.

Jared Whiklo

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Apr 4, 2024, 9:50:51 AMApr 4
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Hi Nikolay,

Glad to hear it is working for you and yes, I would recommend the latest version (6.5.0).

cheers,
jared

Nikolay Gannev

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Apr 9, 2024, 5:15:08 PMApr 9
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Thanks Jared, 

I was also able to migrate content (just few test records) to 6 and view in Fedora 6. 

I have some issues when I try to setup MySQL DB (I'm currently using fcrepo 6.4.0). If I don't provide url user and password params it still uses H2 by default and working fine. But when I provide MySQL credentials it throws errors on startup:


SEVERE: Exception sending context initialized event to listener instance of class [org.fcrepo.http.commons.FedoraContextLoaderListener]
org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'shiroFilter' defined in org.fcrepo.webapp.AuthConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.apache.shiro.spring.web.ShiroFilterFactoryBean]: Factory method 'shiroFilter' threw exception; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'securityManager' defined in org.fcrepo.webapp.AuthConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [org.apache.shiro.web.mgt.WebSecurityManager]: Factory method 'securityManager' threw exception; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'webACAuthorizingRealm': Unsatisfied dependency expressed through field 'rolesProvider'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'webACRolesProvider': Unsatisfied dependency expressed through field 'resourceFactory'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'resourceFactoryImpl': Unsatisfied dependency expressed through field 'persistentStorageSessionManager'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'ocflPersistentSessionManager': Unsatisfied dependency expressed through field 'objectSessionFactory'; nested exception is org.springframework.beans.factory.UnsatisfiedDependencyException: Error creating bean with name 'ocflPersistenceConfig': Unsatisfied dependency expressed through field 'dataSource'; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'dataSource' defined in org.fcrepo.config.DatabaseConfig: Bean instantiation via factory method failed; nested exception is org.springframework.beans.BeanInstantiationException: Failed to instantiate [javax.sql.DataSource]: Factory method 'dataSource' threw exception

Thanks again for all your help!
Nikolay.

Nikolay Gannev

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Apr 10, 2024, 9:35:03 AMApr 10
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I forgot to mention that I'm running fcrepo 6.4.0 on Tomcat 9 and JDK 11.

Jared Whiklo

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Apr 10, 2024, 10:27:17 AMApr 10
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Hi Nikolay,

Is there any more to the stack trace below this,

On 2024-04-10 8:35 a.m., Nikolay Gannev wrote:
> Failed to instantiate [javax.sql.DataSource]: Factory method
> 'dataSource' threw exception

I feel like the actual reason should be there but perhaps I'm just being
hopeful there is an easy answer.

cheers,
jared

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Nikolay Gannev

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Apr 10, 2024, 11:40:05 AMApr 10
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Hi Jared, 

Attached is the log file with all errors. 
Also Tomcat lib using mysql-connector-j-8.2.0.jar. All other libs should be standard with fcrepo 6.4.0.

Thanks, 
Nikolay.
tomcat-stdout.2024-04-10.log

Jared Whiklo

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Apr 10, 2024, 11:55:11 AMApr 10
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Hi Nikolay,

The issue seems to be this
> Found non-empty schema(s) `fcrepo` but no schema history table. Use baseline() or set baselineOnMigrate to true to initialize the schema history table.

We use FlywayDB to manage our database changes and it defines a schema history table to track what updates have or have not been applied.

It looks like Fedora has been pointed at a database but that database was not created by Fedora 6 or perhaps it didn't start up correctly. 

If this is the database from a previous version of Fedora, then I would recommend setting up a new database (i.e. fcrepo-6) and point to it.

If this is a new database specifically for Fedora 6, I would suggest dropping all the tables and trying again.

cheers,
jared

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Nikolay Gannev

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Apr 10, 2024, 12:16:21 PMApr 10
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Awesome! that was the issue. I was pointing to the old fcrepo DB (modeshape_repository table). I was thinking about this the other day (to create new DB) and totally forgot and got confused by many different errors and thought that  mysql connector lib version may affect this... 

Thanks a lot Jared, I appreciate your help and everyone who helped me on this journey :).
I'm going to hit the real data for this migration (we have more than 100k records) and see how it goes! 

Thanks,
Nikolay

Nikolay Gannev

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Apr 15, 2024, 9:13:05 AMApr 15
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Hi again everyone, 

So after successful migration for few test records, I have restored our DB (about 120k records), setup fcrepo 4.7.5 and tried to export all records. 
The process paused for about 10mins and threw an error, here is more info:

C:\Users\drx9-aws>java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m export -r http://localhost:9030/fcrepo/rest -d /tmp/fedora4_test12 -b -a
INFO 08:49:58.634 (Exporter) Running exporter...
INFO 08:49:58.639 (Exporter) Attempting to automatically determine the repository root
INFO 08:49:59.708 (RdfWriterHelper) Loading JENA 3.1.1 Patched RDF Output Writers
INFO 08:50:03.418 (Exporter) Exporting description: http://localhost:9030/fcrepo/rest
INFO 08:50:03.470 (Exporter) Exported http://localhost:9030/fcrepo/rest to C:\tmp\fedora4_test12\fcrepo\rest.ttl
java.lang.RuntimeException: Export operation failed: unexpected status 500 for http://localhost:9030/fcrepo/rest/objects
        at org.fcrepo.importexport.common.TransferProcess.checkValidResponse(TransferProcess.java:203)
        at org.fcrepo.importexport.exporter.Exporter.exportDescription(Exporter.java:331)
        at org.fcrepo.importexport.exporter.Exporter.export(Exporter.java:267)
        at org.fcrepo.importexport.exporter.Exporter.exportMembers(Exporter.java:393)
        at org.fcrepo.importexport.exporter.Exporter.exportDescription(Exporter.java:362)
        at org.fcrepo.importexport.exporter.Exporter.export(Exporter.java:267)
        at org.fcrepo.importexport.exporter.Exporter.run(Exporter.java:220)
        at org.fcrepo.importexport.ImportExportDriver.run(ImportExportDriver.java:58)
        at org.fcrepo.importexport.ImportExportDriver.main(ImportExportDriver.java:47)


Please let me know if you have any suggestion of the possible issue?

Thanks again! 
Nikolay.

Jared Whiklo

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Apr 15, 2024, 10:08:31 AMApr 15
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Hi Nikolay,

What happens if you attempt to view the resource at http://localhost:9030/fcrepo/rest/objects with a web browser or via cURL?

cheers,
jared

Nikolay Gannev

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Apr 15, 2024, 12:21:07 PMApr 15
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Hi Jared,,

Everything looks fine when I tried to access these records in a web browser. 

Thanks,
Nikolay

Nikolay Gannev

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Apr 16, 2024, 9:44:59 AMApr 16
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Hi everyone, 

Made couple of changes for the issue with export.
We added another drive with enough storage space for all records to be exported - that did not help as the same error showed up.
Ran the tool with Java 11 and no error this time, however it looks like the process is frozen as it did not update for several hours. Here is what I see in the console:

C:\Users\drx9-aws>D:\JDK\jdk-11.0.22\bin\java -jar C:\Users\drx9-aws\Documents\SWAT\Fedora\fcrepo-import-export\fcrepo-import-export-0.3.0.jar -m export -r http://localhost:9030/fcrepo/rest -d G:/fedora/fedora4 -b -a
INFO 15:39:50.920 (Exporter) Running exporter...
INFO 15:39:50.922 (Exporter) Attempting to automatically determine the repository root
INFO 15:39:51.713 (RdfWriterHelper) Loading JENA 3.1.1 Patched RDF Output Writers   

Any suggestions?

Thanks,
Nikolay.

Jared Whiklo

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Apr 25, 2024, 12:40:24 PMApr 25
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Hi Nikolay,

Sorry for the delay. It does seem frozen.

Do you see any files being generated in G:/fedora/fedora4 ?

Could try adding "-Dfcrepo.log.importexport=DEBUG" between "D:\JDK\jdk-11.0.22\bin\java" and "-jar C:\Users\..." to get some additional logging.

Nikolay Gannev

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Apr 29, 2024, 5:12:55 PMApr 29
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Hi Jared, 

Thanks for following on my issue! 

In the meantime I was able to export smaller repo (about 10k records) and migrate content. I was in a middle of something else now, but the issue (exporting large repo, over 120k records) still remains. 
We are going to try to run this export from another machine (non Windows) and see if that would work out for us.

Thanks again, 
Nikolay. 

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