starting dspace 6.3

[Jose Blanco]

I'm getting this error when trying to deploy webapp via tomcat:

2020-02-12 12:55:16,566 FATAL org.dspace.core.Context @ Cannot obtain the bean which provides a database connection. Check previous entries in the dspace.log to find why the db failed to initialize. The schema validator returned: Could not determine type for: org.dspace.core.Context, at table: bitstreamformatregistry, for columns: [org.hibernate.mapping.Column(bfContext)]

Not sure what it means.

[José Geraldo]

Check o dspace.log  [dspace]/log/dspace.log

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At.te,

José Geraldo

[Jose Blanco]

The dspace.log does not have much info.  I think the error happens when the code tries to do this:

https://github.com/DSpace/DSpace/blob/dspace-6.3/dspace-api/src/main/java/org/dspace/core/Context.java#L160

Not sure why it was not able to get the db connection in:

https://github.com/DSpace/DSpace/blob/dspace-6.3/dspace-api/src/main/java/org/dspace/core/Context.java#L160

I see I get the same error when I try this:

> /l1/dspace/repository/dev63/bin/dspace create-administrator

Exception: The schema validator returned: Could not determine type for: org.dspace.core.Context, at table: bitstreamformatregistry, for columns: [org.hibernate.mapping.Column(bfContext)]

org.dspace.core.exception.DatabaseSchemaValidationException: The schema validator returned: Could not determine type for: org.dspace.core.Context, at table: bitstreamformatregistry, for columns: [org.hibernate.mapping.Column(bfContext)]
at org.dspace.core.Context.init(Context.java:173)
at org.dspace.core.Context.<init>(Context.java:129)
at org.dspace.administer.CreateAdministrator.<init>(CreateAdministrator.java:101)
at org.dspace.administer.CreateAdministrator.main(CreateAdministrator.java:70)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:607)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)

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[Jose Blanco]

Still stuck on this issue.

[Tim Donohue]

Jose,

Have you customized the v6.3 "Context" class in some way?  The error line numbers there do not seem to match up with the out-of-the-box DSpace 6.3 codebase.  These are the error lines I'm talking about

at org.dspace.core.Context.init(Context.java:173)
at org.dspace.core.Context.<init>(Context.java:129)

In the v6.3 codebase, lines #129 and #173 in the Context class are both empty lines:
https://github.com/DSpace/DSpace/blob/dspace-6.3/dspace-api/src/main/java/org/dspace/core/Context.java#L129

https://github.com/DSpace/DSpace/blob/dspace-6.3/dspace-api/src/main/java/org/dspace/core/Context.java#L173

​It's difficult to help you debug the issue here as it doesn't look like your Context class is the same as out-of-the-box DSpace 6.3.  So, my immediate guess is that your customizations may be causing an issue here -- either customizations in the Context class, or some sort of database customizations or both.  If you didn't mean to customize the Context class, then you might want to try and re-sync it with the one in DSpace 6.3.

Tim

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From: dspac...@googlegroups.com <dspac...@googlegroups.com> on behalf of Jose Blanco <bla...@umich.edu>
Sent: Thursday, February 13, 2020 11:35 AM
To: José Geraldo <jos...@gmail.com>
Cc: DSpace Technical Support <dspac...@googlegroups.com>
Subject: Re: [dspace-tech] starting dspace 6.3

 

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[Jose Blanco]

I did add the following, but did not think it would cause an issue:

private String sessionStatus;

this gets initialized:

sessionStatus = "";

And these two methods:

>     public void setSessionStatus(String info)

>     {

>         sessionStatus = info;

>     }

> 

>     public String getSessionStatus()

>     {

>         return sessionStatus;

>     }

[Jose Blanco]

Tim,

I build an out of the box 6.3, and before I did an "ant fresh_install"  I removed all the tables from my database, but the fresh_install did not build all the tables.  Do I have to start over with a new db?

Thanks!

-Jose

[Tim Donohue]

Hi Jose,

The error says: "Could not determine type for: org.dspace.core.Context, at table: bitstreamformatregistry, for columns: [org.hibernate.mapping.Column(bfContext)]"

Have you modified the org.dspace.content.BitstreamFormat class in some way?  Does "bfContext" maybe represent something you've added to the codebase?  I'm not sure myself what "bfContext" is (as I don't see anything by that name in DSpace code). But, the error makes it sound like Hibernate thinks "bfContext" is supposed to be a Database column in the "bitstreamformatregistry" table, and cannot find it.  

So, maybe some sort of custom code in the "BitstreamFormat" class (which corresponds to the "bitstreamformatregistry" table) is confusing Hibernate & causing this error?

Tim

---

From: Jose Blanco <bla...@umich.edu>
Sent: Thursday, February 13, 2020 12:10 PM
To: Tim Donohue <tim.d...@lyrasis.org>
Cc: José Geraldo <jos...@gmail.com>; DSpace Technical Support <dspac...@googlegroups.com>

[Jose Blanco]

When I merged the code, I had this:   

 private Context bfContext;


which actually, I'm not sure what purpose it served, so I'm going to comment it out, and try again.


Thanks!

[Jose Blanco]

Tim,

How do I get the database to be recreated. I have the db, but it has not tables.  I dropped them.  I thought the fresh_install would create them.

[geneviev...@anu.edu.au]

The tables are created when you start up the application.

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At.te,

José Geraldo

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[Tim Donohue]

Yes, Genevieve is correct, the database tables should be automatically created when you start Tomcat.

If that is not happening, you also can run 

[dspace]/bin/dspace database migrate

This will update (or create) your database tables (where needed) based on its current status.  More info on this command is in the documentation at https://wiki.lyrasis.org/display/DSDOC6x/Database+Utilities

If for some reason one of these commands is not working, you should check your logs for errors being reported there.

Tim

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Sent: Thursday, February 13, 2020 4:19 PM
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