Re: [dspace-tech] Dspace-CRIS OAI-pmh Error

[陳彥棠]

Dear Bollini Andrea

1)   I'll wait to try.

2)   This is the build.properties that I use to mvn package and ant 
fresh_install
What do I miss of some key ?



Regards


Sincerly yours, Yen-Tang Chen


Bollini Andrea於 2016年11月29日星期二 UTC+8上午6時37分45秒寫道：
>
> Hi Yen-Tang Chen,
>
> 1) this is the default behavior of DSpace, it is not a bug or something 
> that you can configure nor in DSpace nor in DSpace-CRIS. It depends on the 
> metadata format that you use: oai_dc in your case that in turn involve 
> https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java
> .
>
> If you can try to use the qdc (Qualified Dublin Core) or the DIM as you 
> are harvesting another DSpace instance. Here you can find some 
> documentation about the Harvesting client
>
>
> https://wiki.duraspace.org/display/DSDOC5x/OAI#OAI-HarvestingfromanotherDSpace
>
> You can also configure the webui.itemlist.columns propert
>
>
> https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2234
>
> as you did in DSpace JSPUI 5.5 but I don't recommend that as you will keep 
> in your database records with very poor metadata and you will need to fix 
> the configuration in a lot of other places, as for instance define an 
> authority on dc.creator
>
>
> https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2321
>
> change the browse, the cris-enhancers, the ORCID mapping and much more.
>
>
> 2) I guess that you have rebuild dspace-cris using an old build.properties 
> that is missing of some key so in the generated configuration files you 
> have something like
>
> a-configuration-property = ${a-configuration-property}
>
> that result in an infinite loop when the application (or a script) start 
> so the out-of-memory
>
> Try to take the current build.properties 
>
> https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/build.properties
>
> and edit you configuration inside this file.
>
> Hope this help,
>
> Andrea
>
> Il 28/11/2016 07:27, 陳彥棠 ha scritto:
>
> Dear Bollini Andrea
>
> 1.
> I run oai-pmh on the linux(centos7) (dspace-cris-oai_02.PNG)
>
> My database format is like this (dspace-cris-oai_03.png)
> ex: 吳密察
> 1997-07-31
> dspace-cris database format
> 
> 
>
> My oai-pmh don't obtain author and date, How to set the settings?(Do 
> not change the data from the database)
> ex: dspace 5.5 jspui => dspace.cfg webui.itemlist.columns = thumbnail, 
> dc.date(date), dc.title, dc.creator
> Which dspace.cfg parameter?
>
> 2. 
>
> I install dspace-cris-5.6.1 on the windows 10
> add this line 126 " c.turnOffItemWrapper(); " in the " 
> C:\DSpace-dspace-cris-5.6.1\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java
>  
> "
> after mvn package is successful.
>
>
> but step " Administrator Account: Create an initial administrator 
> account"  has been wrong!
>
> dspace create-administrator error message => 
> dspace-cris-5.6.1-create-administrator.png
>
> "Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit 
> exceeded"
>
>
> Although dspace-cris-5.6.1 has started successfully , Administrator 
> account is alway failure
>
> I found that the use of dspace-cris-5.6.1([dspace]/bin) "dspace function" 
> will fail
>
> I try to use dspace-cris-5.5.0 in the same environment that ([dspace]/bin) 
> "dspace function" is successful 
> (dspace-cris-5.5.0-create-administrator.png)
>
>
> I don't know why this happened..
> magical!
>
> Installation environment
>
>   jdk1.8.0_101
>   postgresSQL 9.5
>   tomcat 8.0.37  
>   dspace-cris-5.6.1
>
> Regards
>
>
> Sincerly yours, Yen-Tang Chen
>
> 陳彥棠於 2016年11月25日星期五 UTC+8上午9時57分50秒寫道： 
>>
>>
>>
>>
>>
>>
>>
>>
>> *Dear Bollini Andrea Thank you so much Bollini Andrea :D I try again to 
>> run OAIHarvest  on windows 10 (dspace-cris-5.6.1). I'll report to you later 
>> on . Regards* 
>>
>>
>> *Sincerly yours, Yen-Tang Chen*
>>
>> Bollini Andrea於 2016年11月24日星期四 UTC+8下午7時30分28秒寫道： 
>>>
>>> Hi Yen-Tang Chen,
>>> the method turnOffItemWrapper() was introduced in April after the tag of 
>>> the 5.5.0 version so it is only available on the maintenance branch and in 
>>> the new versions (5.6.1).
>>> I think that on windows you are using old code, probably the one from 
>>> the 5.5.0 tag as your path suggest.
>>> It was unclear to me if with such change on centos you have run 
>>> successful the OAIHarvest or if right now you are just verified that the 
>>> proposed patch compile. Can you please confirm?
>>> Thanks,
>>> Andrea
>>>
>>> Il 24/11/2016 09:44, 陳彥棠 ha scritto:
>>>
>>>
>>>
>>> *Dear Bollini Andrea *
>>> *I try to add  this line 126  " c.turnOffItemWrapper(); " in the " 
>>> C:\DSpace-dspace-cris-5.5.0\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java
>>>  
>>> "*
>>> *on the linux(cetos 7) is successful!!! (dspace-cris-oai_01.png)*
>>> mvn package  ..ok
>>>
>>> but it is failure on the 

Re: [dspace-tech] Dspace-CRIS OAI-pmh Error

[Bollini Andrea]

Hi Yen-Tang Chen,

1) this is the default behavior of DSpace, it is not a bug or something that 
you can configure nor in DSpace nor in DSpace-CRIS. It depends on the metadata 
format that you use: oai_dc in your case that in turn involve 
https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-api/src/main/java/org/dspace/content/crosswalk/OAIDCIngestionCrosswalk.java.

If you can try to use the qdc (Qualified Dublin Core) or the DIM as you are 
harvesting another DSpace instance. Here you can find some documentation about 
the Harvesting client

https://wiki.duraspace.org/display/DSDOC5x/OAI#OAI-HarvestingfromanotherDSpace

You can also configure the webui.itemlist.columns propert

https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2234

as you did in DSpace JSPUI 5.5 but I don't recommend that as you will keep in 
your database records with very poor metadata and you will need to fix the 
configuration in a lot of other places, as for instance define an authority on 
dc.creator

https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace/config/dspace.cfg#L2321

change the browse, the cris-enhancers, the ORCID mapping and much more.


2) I guess that you have rebuild dspace-cris using an old build.properties that 
is missing of some key so in the generated configuration files you have 
something like

a-configuration-property = ${a-configuration-property}

that result in an infinite loop when the application (or a script) start so the 
out-of-memory

Try to take the current build.properties

https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/build.properties

and edit you configuration inside this file.

Hope this help,

Andrea

Il 28/11/2016 07:27, 陳彥棠 ha scritto:
Dear Bollini Andrea

1.
I run oai-pmh on the linux(centos7) (dspace-cris-oai_02.PNG)

My database format is like this (dspace-cris-oai_03.png)
ex: 吳密察
1997-07-31
dspace-cris database format



My oai-pmh don't obtain author and date, How to set the settings?(Do not 
change the data from the database)
ex: dspace 5.5 jspui => dspace.cfg webui.itemlist.columns = thumbnail, 
dc.date(date), dc.title, dc.creator
Which dspace.cfg parameter?

2.

I install dspace-cris-5.6.1 on the windows 10
add this line 126 " c.turnOffItemWrapper(); " in the " 
C:\DSpace-dspace-cris-5.6.1\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java
 "
after mvn package is successful.


but step " Administrator Account: Create an initial administrator account"  has 
been wrong!

dspace create-administrator error message => 
dspace-cris-5.6.1-create-administrator.png

"Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit 
exceeded"


Although dspace-cris-5.6.1 has started successfully , Administrator account is 
alway failure

I found that the use of dspace-cris-5.6.1([dspace]/bin) "dspace function" will 
fail

I try to use dspace-cris-5.5.0 in the same environment that ([dspace]/bin) 
"dspace function" is successful (dspace-cris-5.5.0-create-administrator.png)


I don't know why this happened..
magical!

Installation environment

  jdk1.8.0_101
  postgresSQL 9.5
  tomcat 8.0.37
  dspace-cris-5.6.1

Regards


Sincerly yours, Yen-Tang Chen

陳彥棠於 2016年11月25日星期五 UTC+8上午9時57分50秒寫道：
Dear Bollini Andrea

Thank you so much Bollini Andrea :D
I try again to run OAIHarvest  on windows 10 (dspace-cris-5.6.1).
I'll report to you later on .


Regards


Sincerly yours, Yen-Tang Chen

Bollini Andrea於 2016年11月24日星期四 UTC+8下午7時30分28秒寫道：
Hi Yen-Tang Chen,
the method turnOffItemWrapper() was introduced in April after the tag of the 
5.5.0 version so it is only available on the maintenance branch and in the new 
versions (5.6.1).
I think that on windows you are using old code, probably the one from the 5.5.0 
tag as your path suggest.
It was unclear to me if with such change on centos you have run successful the 
OAIHarvest or if right now you are just verified that the proposed patch 
compile. Can you please confirm?
Thanks,
Andrea

Il 24/11/2016 09:44, 陳彥棠 ha scritto:
Dear Bollini Andrea


I try to add  this line 126  " c.turnOffItemWrapper(); " in the " 
C:\DSpace-dspace-cris-5.5.0\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java
 "
on the linux(cetos 7) is successful!!! (dspace-cris-oai_01.png)
mvn package  ..ok

but it is failure on the windows 10..
Error message => dspace-cris-oai_error.png
mvn package  ..error


cetos 7  and windows 10 are same settings

Dspace-cris-5.6.1
tomcat 8.0.39
jdk 1.8.0
postgreSQL 9.5

I don't know error. Fantastic results!!



Regards


Sincerly yours, Yen-Tang Chen


陳彥棠於 2016年11月23日星期三 UTC+8上午10時14分30秒寫道：

Dear Bollini Andrea

I try to add  this line 126  " c.turnOffItemWrapper(); " in the " 
C:\DSpace-dspace-cris-5.5.0\dspace-api\src\main\java\org\dspace\harvest\OAIHarvester.java
 "

but it is errors for the mvn package  , I can not find the method " 
turnOffItemWrapper()"...
Would i need to add those 

Re: [dspace-tech] Checksum checker "Un-Checked Bitstream" report

[Monika Mevenkamp]

I rewrote the checker so I can trigger checking such that I can select the 
bitstreams to be checked based on  last checked date, or the last check result. 
The check can be limited to checking a max number of bitstreams. I added  a CLI 
utility that can list the check status of bitstreams or count the number of 
bitstreams in a given status - aka DELETED or NOT_FOUND. The output of the 2 
CLIs is easy to grep through, aka it makes it easy to look for relevant info. I 
use them in my daily cronjob to go round robin through bitstreams such that all 
my bitstreams are checked every 3 weeks. 

Here a two example usages with corresponding  output: 

> $DSPACE_HOME/bin/dspace checksum -d check -c 4000 -x BITSTREAM_MARKED_DELETED
# 
org.dspace.checker.CheckBitstreamIterator(without_result=[BITSTREAM_MARKED_DELETED])
# Action check
# Max-Count 4000
# Printing  m for CHECKSUM_MATCH, d for BITSTREAM_MARKED_DELETED, and E in all 
other cases


….

# worked on 4000 bitstreams

> $DSPACE_HOME/bin/dspace checksum -d print -c 1 -x BITSTREAM_MARKED_DELETED | 
> egrep -v '^#’
1 BITSTREAM.39318 CHECKSUM_MATCH 
internalId=9128636048098563653161844066534785665  delete=false  
lastDate=2016-11-06 01:02:03.83 


See documentation HERE 

There is a JIRA HERE 
And a PR THERE 

I’d be happy to help if you want to try this out 

Monika

 
Monika Mevenkamp
Digital Repository Infrastructure Developer
Princeton University
Phone: 609-258-4161
Skype: mo-meven



> On Nov 24, 2016, at 11:58 AM, do...@uoguelph.ca wrote:
> 
> Hi all, 
> 
> We'll occasionally get bitstreams showing up in this report, but I'm really 
> unclear on why or what it is that we should be doing to address it. 
> 
> What conditions cause a bitstream to be skipped and included in this report?
> 
> As an administrator, what actions should I take when this occurs? 
> 
> The report itself says "To add these bitstreams to be checked run the 
> checksum checker with the -u option" but the checker doesn't seem to have a 
> -u option 
> .
>  Running the checker with the -u option doesn't seem to make any noticeable 
> difference.
> 
> Digging into the most recent report where this occurred, I can see that the 
> item associated to the unchecked bitstreams has finished its workflow and has 
> been accepted to our repository. 
> 
> Any help or guidance that you folks could provide would be greatly 
> appreciated!
> 
> Thanks,
> -Adam
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "DSpace Technical Support" group.
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> .

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[dspace-tech] ElasticSearch in v5.6+

[Margaret Vail]

We have changed our statistics in DSpace v.5.6 to no longer use 
ElasticSearch since it is deprecated in DSpace v.6. Is statistics the only 
module using ElasticSearch? Would it be safe to turn off the ElasticSearch 
service at this point?

Thanks,

Margaret Vail

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[dspace-tech] Re: [dspace-community] Re: PostgreSQL question in upgrading to DSpace 6.0

[Mark Wood]

On Monday, November 28, 2016 at 8:43:12 AM UTC-5, wangyo wrote:
>
> Hi Mark,
>
> > You can change that last record from "md5" (which requires a password) 
> to "trust"...
>
> I did that.
>
> Then I restarted postgresql-9.5, and ran the cammond as follows:
>
> [root@dr data]# /usr/pgsql-9.5/bin/psql -U postgres -f 
> /dspace-backup/pg.out postgres
>
> The output as following:
>
> SET
> SET
> SET
> CREATE ROLE
> ALTER ROLE
> psql:/dspace-backup/pg.out:16: ERROR:  role "postgres" already exists 
> ALTER ROLE
> CREATE DATABASE
> REVOKE
> REVOKE
> GRANT
> GRANT
> You are now connected to database "dspace" as user "postgres".
> SET
> SET
> SET
> SET
> SET
> SET
> CREATE EXTENSION
> COMMENT
> ...
>
> ALTER TABLE
> COPY 1710
>  setval
> 
>1710
> (1 row)
>  ...
>
>
>
> It keeps going like this, and the last several lines:
>
> GRANT
> You are now connected to database "template1" as user "postgres".
> SET
> SET
> SET
> SET
> SET
> SET
> COMMENT
> CREATE EXTENSION
> COMMENT
> REVOKE
> REVOKE
> GRANT
> GRANT
>
>
> Does that mean the restore is successful?
>
>
Yes, that appears to be successful.  The error on line 16 is to be 
expected:  the DBMS already has a superuser account defined, so it cannot 
be created again.  That should not be a problem. 

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[dspace-tech] Re: Handle server in separate machine

[Mark Wood]

See https://github.com/DSpace/Remote-Handle-Resolver for one approach.

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Re: [dspace-tech] Dspace 5.5 OAI Error when request

[helix84]

It seems you've run into an item that doesn't have any parent
communities. This should not normally happen.

https://github.com/DSpace/DSpace/blob/dspace-5.5/dspace-oai/src/main/java/org/dspace/xoai/data/DSpaceSolrItem.java#L43

You can find out which one only if you're the admin of the server
you're trying to harvest. Running
[dspace]/bin/dspace oai import -c -v
will probably show you which item it fails on.


Regards,
~~helix84

Compulsory reading: DSpace Mailing List Etiquette
https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette


On Mon, Nov 28, 2016 at 4:46 PM, Pablo Crespo  wrote:
> Hi,
>
> I'm having a problem with a Dspace 5.5 Server.
>
> When I'm trying to access to the list of records It's all ok until 4200 but
> when I try to access to
> http://repository..edu.ec:8080/oai/request?verb=ListRecords=oai_dc4300
> I got this error.
>
>
> type Exception report
>
> message
>
> description The server encountered an internal error () that prevented it
> from fulfilling this request.
>
> exception
>
> org.springframework.web.util.NestedServletException: Request processing
> failed; nested exception is java.lang.NullPointerException
> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:894)
> org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
> javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
> javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
>
> root cause
>
> java.lang.NullPointerException
> org.dspace.xoai.data.DSpaceSolrItem.(DSpaceSolrItem.java:43)
> org.dspace.xoai.services.impl.xoai.DSpaceItemSolrRepository.retrieveItems(DSpaceItemSolrRepository.java:119)
> org.dspace.xoai.services.impl.xoai.DSpaceItemSolrRepository.getItems(DSpaceItemSolrRepository.java:102)
> com.lyncode.xoai.dataprovider.data.internal.ItemRepositoryHelper.getItems(ItemRepositoryHelper.java:174)
> com.lyncode.xoai.dataprovider.handlers.ListRecordsHandler.handle(ListRecordsHandler.java:75)
> com.lyncode.xoai.dataprovider.OAIDataProvider.handle(OAIDataProvider.java:213)
> org.dspace.xoai.controller.DSpaceOAIDataProvider.contextAction(DSpaceOAIDataProvider.java:104)
> sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> java.lang.reflect.Method.invoke(Method.java:606)
> org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:213)
> org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:126)
> org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:96)
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:617)
> org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:578)
> org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:80)
> org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:923)
> org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
> org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)
> org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
> javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
> javax.servlet.http.HttpServlet.service(HttpServlet.java:722)
>
>
> If anyone give me some lights to resolve this, I will appreciate to much.
>
>
> Thanks in advance.
>
>
> Pablo Cr.
>
>
> --
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[dspace-tech] Dspace 5.5 OAI Error when request

[Pablo Crespo]

Hi,

I'm having a problem with a Dspace 5.5 Server.

When I'm trying to access to the list of records It's all ok until 4200 but 
when I try to access to 
http://repository..edu.ec:8080/oai/request?verb=ListRecords=oai_dc4300
 
I got this error. 


*type* Exception report

*message*

*description* *The server encountered an internal error () that prevented 
it from fulfilling this request.*

*exception*

org.springframework.web.util.NestedServletException: Request processing failed; 
nested exception is java.lang.NullPointerException

org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:894)

org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
javax.servlet.http.HttpServlet.service(HttpServlet.java:722)

*root cause*

java.lang.NullPointerException
org.dspace.xoai.data.DSpaceSolrItem.(DSpaceSolrItem.java:43)

org.dspace.xoai.services.impl.xoai.DSpaceItemSolrRepository.retrieveItems(DSpaceItemSolrRepository.java:119)

org.dspace.xoai.services.impl.xoai.DSpaceItemSolrRepository.getItems(DSpaceItemSolrRepository.java:102)

com.lyncode.xoai.dataprovider.data.internal.ItemRepositoryHelper.getItems(ItemRepositoryHelper.java:174)

com.lyncode.xoai.dataprovider.handlers.ListRecordsHandler.handle(ListRecordsHandler.java:75)

com.lyncode.xoai.dataprovider.OAIDataProvider.handle(OAIDataProvider.java:213)

org.dspace.xoai.controller.DSpaceOAIDataProvider.contextAction(DSpaceOAIDataProvider.java:104)
sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)

sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
java.lang.reflect.Method.invoke(Method.java:606)

org.springframework.web.method.support.InvocableHandlerMethod.invoke(InvocableHandlerMethod.java:213)

org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:126)

org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:96)

org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:617)

org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:578)

org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:80)

org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:923)

org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)

org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:882)

org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:778)
javax.servlet.http.HttpServlet.service(HttpServlet.java:621)
javax.servlet.http.HttpServlet.service(HttpServlet.java:722)


If anyone give me some lights to resolve this, I will appreciate to much.


Thanks in advance.


Pablo Cr.


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