Re: [dspace-tech] Re: How to update to DataCite Metdata Schema 4?

[Alan Orth]

Check this pull request for DSpace 8.0 which updates the DataCite crosswalk
to schema version 4.5:

https://github.com/DSpace/DSpace/pull/9339

Regards,

On Wed, Jul 17, 2024, 09:21 Olayiwola Lawal 
wrote:

> Hi Carolyn,
>
> You may want to have a look at this, I was able to update the schema of my
> 7.6 to Schema 4 using the information provided.
> https://groups.google.com/g/dspace-tech/c/pOiEpV7HUN0/m/un0w8QPSBAAJ
>
> Regards.
>
>
> On Wednesday 17 July 2024 at 17:11:41 UTC+1 Carolyn Sullivan wrote:
>
>> Hello,
>>
>> I'm wondering how we should update DataCite metadata schema 3 to schema 4
>> in our DSpace 7.6 repository.  The DataCite webpage gives general
>> instructions
>> 
>> but nothing platform specific.  Should I just be going through my code and
>> replacing everything that says http://datacite.org/schema/kernel-3 with
>> https://schema.datacite.org/meta/kernel-4/ ?  Do I need to tweak my item
>> submission forms somehow?  Help.
>>
>> Thanks,
>> Carolyn Sullivan.
>>
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Re: [dspace-tech] High CPU usage in DSpace 7.6 leading to server issues, lots of errors/examples (crossposted from Slack)

[Alan Orth]

Dear all,

Our experience with moving to DSpace 7.6 in production was that bots 
exhausted the SSR cache immediately. We effectively solved it by adding 
rate limiting of bots in nginx.

I also noticed that many applications have had performance issues with 
Angular SSR due to its use of `inlineCriticalCss`. See some discussions:

- https://github.com/angular/angular/issues/42098
- https://github.com/angular/universal/issues/2106
- https://github.com/GoogleChromeLabs/critters/issues/78

On that note there is a draft pull request for dspace-angular to allow 
disabling inlineCriticalCss: 
https://github.com/DSpace/dspace-angular/pull/2067

Regards,

On Wednesday, March 6, 2024 at 10:47:31 PM UTC+3 DSpace Technical Support 
wrote:

Hi all,

I wanted to chime in briefly to say that I appreciate everyone sharing your 
experiences with high CPU issues, as it does help the developers & I to 
hear what everyone is encountering under heavier load and/or bot activity.  
 The more that institutions can share your experiences, the more likely we 
can begin to narrow down the problem(s) and build better 
documentation/guidelines for everyone.

A few things that are clear is that Server Side Rendering (SSR) from 
Angular **does seem to be more CPU heavy than we anticipated**.  This is 
why the basic "SSR caching 
"
 
was added in the first place.  However, what's also starting to become 
clear is that the *basic SSR caching* may not be enough.  (In all honesty, 
we knew it would help in some scenarios but possibly not *all* scenarios.)

I can verify though that the existing basic SSR caching is *per instance*.  
So, when using "cluster mode" (and running several instances at once), 
there is no way to currently share that cache across instances (as the 
cache is literally just stored in the memory of each instance).  This means 
it has a more limited impact than we initially hoped.  

*This may mean we need to begin looking at some more advanced caching 
options for Angular SSR*. To be clear though,  this SSR performance/caching 
issue shouldn't be specific to DSpace 7, as we are just using the SSR tools 
from Angular.io. So, it's possible that tools may already exist out there 
from other sites/applications that use Angular SSR.

In the meantime, I would ask that sites which have this working well 
consider also sharing your experiences of how you "stabilized" your high 
CPU. I know there are sites out there who've done this (as there are a 
growing number of sites running DSpace 7 in production).  It'd just be 
helpful, for me (and others), if we can learn from each other in order to 
create better documentation & best practices for DSpace 7.  (All DSpace 
documentation & best practices have always been a collaborative/community 
effort because we don't have a central development team.)

Tim

On Wednesday, March 6, 2024 at 10:38:43 AM UTC-6 uOttawa Library wrote:

I would like to understand how memory is used by the node instances.

There are comments in the example frontend configuration file that mentions 
the following:

  # Maximum number of pages to cache for known bots. Set to zero (0) to 
disable server side caching for bots.
  # Default is 1000, which means the 1000 most recently accessed public 
pages will be cached.
  # As all pages are cached in server memory, increasing this value 
will increase memory needs.
  # Individual cached pages are usually small (<100KB), so max=1000 
should only require ~100MB of memory.

We have both bot cache and anonymous cache set to  max: 1000. This would 
mean a total of ~200MB cache (per instance?). We allocate 1.5GB to 
instances (max_memory_restart), so cache wouldn't be the main cause of the 
high memory usage. We have set max_old_space_size=1024 since the original 
post above, and this seems to make the instances stay alive longer 
(instance restart every ~90 min due to exceeding the 1.5GB memory).

It isn't clear is if cache is shared amongst instances (to avoid having to 
render the same frequently accessed content in every instance), but in any 
case, it wouldn't be the main source of memory use according to the 
comments.

François

On Tuesday, March 5, 2024 at 5:13:09 p.m. UTC-5 Edmund Balnaves wrote:

We are running DSpace 7 instances in a multi-tennanted environment in a 
reasonably stable way.

Our experience is that lots of memory is needed and we do see lockups in 
cluster instances periodically.   Even low levels of bot activity can 
stress the system and performance of DSpace7 is pretty under-whelming but 
we have managed to maintain stable instances. Trimming your caching 
would be wise to keep memory within reasonable bounds.  We have written 
shell scripts to monitor and restart instances that look to be locked up, 
and have put some memory limits for auto-restart per your approach.


Edmund 

Re: [dspace-tech] automatic start up for dspace front end at reboot

[Alan Orth]

Dear Joshua,

I am starting pm2 via a systemd service unit,
/etc/systemd/system/dspace-angular.service:

[Unit]
Description=DSpace Angular (PM2)
After=network.target tomcat9.service
Wants=tomcat9.service

[Service]
User=dspace
Group=dspace
LimitNOFILE=infinity
LimitNPROC=infinity
LimitCORE=infinity
Environment=NODE_ENV=production
Environment=PM2_HOME=/home/dspace/.pm2
Restart=on-failure
WorkingDirectory=/home/dspace/src/git/dspace-angular
ExecStart=/home/dspace/.node_modules/lib/node_modules/pm2/bin/pm2 start
./dist/server/main.js --name dspace-ui -i 4 --no-daemon
ExecReload=/home/dspace/.node_modules/lib/node_modules/pm2/bin/pm2 reload
dspace-ui
ExecStop=/home/dspace/.node_modules/lib/node_modules/pm2/bin/pm2 stop
dspace-ui
# Don't log pm2 to the systemd journal! Use pm2 logs instead.
StandardOutput=null

[Install]
WantedBy=multi-user.target

Then start and enable the service like you would any other system service.
Works well, but I'm surprised at how pm2 makes this difficult. I find pm2's
ergonomics very strange. In the service file above you can see I tell pm2
to not start its own management daemon. How can so much of the insanely
massive Node.js ecosystem depend on this random package for clustering? And
how can there be no other alternatives? Bizarre...

Hope that helps,

On Tue, Jan 9, 2024 at 12:15 AM Joshua Kim  wrote:

> Hello,
>
> Does anyone use automatic start for dspace front end at reboot by using
> service ? If so, would you share with us? The 7.x documentation shows only
> manual start like pm2 start dspace-ui.json.
>
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Re: [dspace-tech] How to stop DSpace to accept duplicates item / titles

[Alan Orth]

Dear Lewatle,

This is a commonly requested feature. For our repository we urge our
submitters to check titles before submission, but something built into
DSpace would be better.

There is a proposed patch for this that is will hopefully make it into
DSpace 8.0: https://github.com/DSpace/DSpace/pull/8415

Hoping to see this come in a future release as well.

Regards,

On Wed, Jan 17, 2024 at 4:14 PM Lewatle Johannes Phaladi 
wrote:

> Dear All,
>
> How to stop DSpace accepting deposits of one item twice especially with
> similar title, I have tested by depositing same item using one title and
> other metadata fields similar but DSpace is accepting that deposit. please
> see the following item deposited twice but DSpace is not recognizing that
> and block the deposit.
>
> [image: image_2024-01-17_151406327.png]
>
> Regards,
> Lewatle
>
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[dspace-tech] Too many boolean clauses

[Alan Orth]

Dear list,

We've recently migrated to DSpace 7.6 (from 6.3) and I notice one user who
is a member of very many groups having issues with workflow tasks. In
dspace.log I see:

2024-01-09 06:23:35,893 ERROR unknown unknown
org.dspace.authorize.AuthorizeServiceImpl @ Failed getting getting
community/collection admin status for foo...@example.org The search error
is: Error from server at http://localhost:8983/solr/search:
org.apache.solr.search.SyntaxError: Cannot parse
'search.resourcetype:Community AND
(admin:eef481147-daf3-4fd2-bb8d-e18af8131d8c OR
admin:g80199ef9-bcd6-4961-9512-501dea076607 OR
admin:g4ac29263-cf0c-48d0-8be7-7f09317d50ec OR
admin:g0e594148-a0f6-4f00-970d-6b7812f89540 OR
admin:g0265b87a-2183-4357-a971-7a5b0c7add3a OR
admin:g371ae807-f014-4305-b4ec-f2a8f6f0dcfa OR
admin:gdc5cb27c-4a5a-45c2-b656-a399fded70de OR
admin:ge36d0ece-7a52-4925-afeb-6641d6a348cc OR
admin:g15dc1173-7ddf-43cf-a89a-77a7f81c4cfc OR
admin:gc3a599d3-c758-46cd-9855-c98f6ab58ae4 OR
admin:g3d648c3e-58c3-4342-b500-07cba10ba52d OR
admin:g82bf5168-65c1-4627-8eb4-724fa0ea51a7 OR
admin:ge751e973-697d-419c-b59b-5a5644702874 OR
admin:g44dd0a80-c1e6-4274-9be4-9f342d74928c OR
admin:g4842f9c2-73ed-476a-a81a-7167d8aa7946 OR
admin:g5f279b3f-c2ce-4c75-b151-1de52c1a540e OR
admin:ga6df8adc-2e1d-40f2-8f1e-f77796d0eecd OR
admin:gfdfc1621-382e-437a-8674-c9007627565c OR
admin:g15cd114a-0b89-442b-a1b4-1febb6959571 OR
admin:g12aede99-d018-4c00-b4d4-a732541d0017 OR
admin:gc59529d7-002a-4216-b2e1-d909afd2d4a9 OR
admin:gd0806714-bc13-460d-bedd-121bdd5436a4 OR
admin:gce70739a-8820-4d56-b19c-f191855479e4 OR
admin:g7d3409eb-81e3-4156-afb1-7f02de22065f OR
admin:g54bc009e-2954-4dad-8c30-be6a09dc5093 OR
admin:gc5e1d6b7-4603-40d7-852f-6654c159dec9 OR
admin:g0046214d-c85b-4f12-a5e6-2f57a2c3abb0 OR
admin:g4c7b4fd0-938f-40e9-ab3e-447c317296c1 OR
admin:gcfae9b69-d8dd-4cf3-9a4e-d6e31ff68731 OR ...
admin:g20f366c0-96c0-4416-ad0b-46884010925f)': too many boolean clauses The
search resourceType filter was: search.resourcetype:Community

There are 1,805 OR clauses in the full error. In the past we did two things:

- Increase maxBooleanClauses in the Solr schema
- Disable access rights awareness¹

I'm wondering if other people are seeing this as well and what they have
done. Besides reducing the number of groups this user belongs to, is it
time to increase the defaults for maxBooleanClauses in DSpace? And is
disabling access rights awareness still a valid solution? What side effects
does that have?

Thanks!

¹
https://wiki.lyrasis.org/display/DSPACE/TechnicalFaq#TechnicalFAQ-I'mgetting%22SolrException:BadRequest%22followedbyalongqueryora%22tooManyClauses%22Exception
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Re: [dspace-tech] Re: How to set up load balance?

[Alan Orth]

Dear Augustina,

This sounds very interesting. We have a large self-hosted repository with
many users as well, and I'm thinking that we will need to do something
similar in the future. I would love to hear more about your setup. In
particular, how does load balancing handle authenticated users? I'm
thinking through this now... maybe it's not an issue because Angular itself
doesn't care about the session per se. Only the backend API and the client
care about sessions.

Thanks,

On Thu, Dec 21, 2023 at 6:13 PM Agustina Martinez-Garcia 
wrote:

> Hi Jack,
>
> The information from the DCAT notes is not fully correct. This is the
> setup that we have:
>
> - We have 3 frontend VMs, and load balancing is achieved through HAProxy
> - We have a single VM for the backend (single tomcat)
> - A separate VM for Solr
>
> I hope that clarifies.
>
> Best,
> Agustina
>
> On Thursday 21 December 2023 at 13:09:13 UTC Jack OE wrote:
>
>> Hi all,
>>
>> I discovered on this page that Shannon Searle mentioned Cambridge has set
>> up load balance for their servers:
>> https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+September+2023
>>
>> "Shannon Searle:
>>
>> Cambridge had some issues with slow connectors - they have a large
>> self-hosted repository. They have a separate Angular interface for
>> staff/students and another for public, a separate solr server and two
>> backend tomcat servers with a round-robin  load balance"
>>
>> How did they achieve load balance and how would I go about setting it up?
>>
>> Any help is appreciated
>> Thanks
>>
>> Jack
>>
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Re: [Extern] [dspace-tech] how to disable browse.comcol.by.srsc in 7.6?

[Alan Orth]

Dear Michael,

Yes, there is some discussion about this on the DSpace Slack and GitHub
issue tracker. This pull request proposes to make the automatic wiring of
hierarchical browses based on vocabularies configurable:

https://github.com/DSpace/DSpace/pull/8948

See the discussion there and add your comments about how this should be
considered and implemented.

Thanks,

On Fri, Jul 7, 2023 at 4:56 PM Michael Koch 
wrote:

> Removing from the submission form does not work for the display of items
> on community and collection pages - My current solution:
> Define browse.comcol.by.srsc as empty string in the language files ...
>
> Michael Plate schrieb am Freitag, 7. Juli 2023 um 13:28:31 UTC+2:
>
>> Hi,
>>
>> Am 07.07.23 um 11:33 schrieb Michael Koch:
>> > In the 7.6 user interface there is an additional tab in browsing
>> > communities and collections, using the srsc taxonomy?
>>
>> got the same problem, this is not bug but a "feature".
>> Would prefer this to be configurable at the usual place…
>>
>> >
>> > Is there a way to switch this off?
>>
>> https://wiki.lyrasis.org/display/DSDOC7x/Configuration+Reference#ConfigurationReference-HierarchicalBrowseIndexes
>>
>> remove it from the submission forms :(
>>
>> Michael
>>
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Re: [dspace-tech] Change image on taskbar

[Alan Orth]

Dear Matthias,

If you are looking in dspace.cfg then you are in the wrong place—that's the
DSpace backend. You should be looking in the DSpace Angular frontend.
According to GitHub, this config key is present in DSpace 7.2 as well, see:

https://github.com/DSpace/dspace-angular/blob/dspace-7.2/config/config.example.yml#L210

Hope that helps,

On Fri, Jun 16, 2023 at 11:30 AM Matthias Letsch 
wrote:

> Hello Tim and Lewatle,
>
> I would like to follow up on that question. The documentation doesn't fit
> for us unfortunately, because for some reason we don't have config.*.yml
> (in DSpace 7.2) where you could put something under a "themes" section.
>
> We only have a dspace.cfg with the following entry under OpenSearch
> settings:
>
> # location of favicon for service, if any must be 16X16 pixels
> websvc.opensearch.faviconurl = http://www.dspace.org/images/favicon.ico
>
> But I want to include a local file under images and not a URL. I don't
> even know if this is the right spot to change it.
>
> How do I do that now if I am missing what the documentation points to?
>
> Thank you and kind regards
> Matthias
>
> Lewatle Johannes Phaladi schrieb am Donnerstag, 27. Oktober 2022 um
> 14:00:21 UTC+2:
>
>> Hello Tim,
>>
>> Thanks a lot, favicon is updated.
>>
>> Regards,
>> Lewatle
>>
>> On Wednesday, 26 October 2022 at 18:07:52 UTC+2 Tim Donohue wrote:
>>
>>> Hi Lewatle,
>>>
>>> That icon in your browser tab is called the "Favicon" of a site.  We
>>> have documentation on how to change that for DSpace 7 here:
>>> https://wiki.lyrasis.org/display/DSDOC7x/User+Interface+Customization#UserInterfaceCustomization-CustomizeFaviconforsiteortheme
>>>
>>> Tim
>>> --
>>> *From:* dspac...@googlegroups.com  on behalf
>>> of Lewatle Johannes Phaladi 
>>> *Sent:* Wednesday, October 26, 2022 9:18 AM
>>> *To:* DSpace Technical Support 
>>> *Subject:* [dspace-tech] Change image on taskbar
>>>
>>> Dear DSpace Colleagues,
>>>
>>> How to change image that appear on address bar.
>>> see this picture :
>>>  [image: image_2022-10-26_161722772.png]
>>>
>>> Regards,
>>> Lewatle
>>>
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>>> <https://groups.google.com/d/msgid/dspace-tech/9082b31b-f67a-4ae3-b541-bebf54980af5n%40googlegroups.com?utm_medium=email_source=footer>
>>> .
>>>
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Re: [dspace-tech] Problem with Internationalization (i18n)

[Alan Orth]

Dear Maksim,

I just tried using Ukrainian and the Klaro popup is working for me, but I
am using the default Ukrainian i18n strings. Are you using a custom theme?
If so, you need to merge your theme's i18n keys to the main i18n files
after updating them in your theme. For example, if your theme is called
"mytheme":

$ yarn merge-i18n -s src/themes/mytheme/assets/i18n

Then check to see if the `src/assets/i18n/uk.json5` file is sane. I've
noticed that the merge script has one small bug¹ that causes it to unquote
the `title` key, so you will have to quote it again manually.

Hope that helps,

¹ https://github.com/DSpace/dspace-angular/issues/2309

On Fri, Jun 16, 2023 at 3:36 PM Mark H. Wood  wrote:

> On Fri, Jun 16, 2023 at 12:24:18AM -0700, Maksim Donchenko wrote:
> > Hi to all. I added a new translation language to /src/assets/i18n using
> > this guide:
> > https://wiki.lyrasis.org/pages/viewpage.action?pageId=117735441.
> Everything
> > was localized well, except for the Cookie notification. I have attached
> a
> > screenshot of the problem below. Maybe someone has encountered something
> > similar and can help? I use Dspace 7.4.
>
> There is another layer of mapping for cookie messages.  The keys that
> Klaro should be looking up are named in
> 'src/app/shared/cookies/klaro-configuration.ts'.  The first thing I
> would check is whether this file's mapping corresponds to the keys in
> your 'uk' message catalog.
>
> However:  this is the second time today that I've seen a message from
> someone having trouble specifically with translating cookie messages.
> There may be a deeper problem.  And all that I really know about Klaro
> is that it seems to take care of cookie management.
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
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Re: [dspace-tech] Re: handle server quits after ubuntu upgrade

[Alan Orth]

all-back solution at least.  Hopefully formal fix will be
>>> out soon.
>>>
>>> On Saturday, November 12, 2022 at 3:17:40 AM UTC+11 cpgr...@gmail.com
>>> wrote:
>>>
>>>> We did an upgrade to Ubuntu last night and now our handle server quits
>>>> immediately on trying to start it. Unfortunately, the person who set up
>>>> our handle server has left our organization.
>>>>
>>>> Our handle-server.log reports:
>>>>
>>>> "2022/11/11 10:27:43 EST" 25 Rotating log files
>>>> Error: null
>>>> (see the error log for details.)
>>>>
>>>> Shutting down...
>>>>
>>>> and the error.log reports:
>>>>
>>>> "2022/11/11 10:27:43 EST" 25 Started new run.
>>>> java.lang.UnsupportedOperationException
>>>>  at java.lang.Runtime.runFinalizersOnExit(Runtime.java:287)
>>>>  at java.lang.System.runFinalizersOnExit(System.java:1059)
>>>>  at net.handle.server.Main.initialize(Main.java:124)
>>>>  at net.handle.server.Main.main(Main.java:75)
>>>> Shutting down...
>>>>
>>>> Can anyone help with what is going wrong or how to diagnose this
>>>> further?
>>>
>>> --
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Re: [dspace-tech] Google analytics - abnormal increase of users

[Alan Orth]

Dear Willian,

I advise all management types in our organization to take any statistics
numbers with a grain of salt because measuring accurately is incredibly
difficult. Having said that, the best way to see real traffic hitting your
server is by looking at the web server logs. Our site has noticeably more
traffic on Sundays for some reason (I think it's something about harvesting
the REST API). So check the Apache or nginx logs.

Regards,

On Fri, Sep 30, 2022 at 11:27 PM WILLIAN  wrote:

> I recently migrated dspace from version 5.X to 7.3 and since migration I
> have noticed that the amount of active users has increased more than 10
> times already the next day. Has anyone gone through the same experience? Is
> it a bug of version 7.3?
>
> Note: This DSpace instance has been active since 2008, has gone through
> several migrations and has seen organic growth in analytics over time.
> <https://www.univates.br/assinatura-email/padrao>
>
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>


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Re: [dspace-tech] dspace.log is getting very big with continuous WARN and some ERROR messages

[Alan Orth]

Hey Fatih,

I was curious so I checked GitHub for issues with this error and bingo!

https://github.com/DSpace/DSpace/issues/8378

So it looks like you're not alone...

Cheers,

On Fri, Sep 30, 2022 at 10:15 PM Fatih Güneş  wrote:

> Hello everyone,
> My dspace log is getting bigger and bigger with continuous (nearly 5
> messages in every second) below messages. It is mostly WARN but ERROR line
> is seen sometimes as well.
> Do you have any idea, why I get these messages and how can I deep further?
>
> I am on Dspace 7.3.
>
> ERROR d4b3c8d5-5f04-48e6-bd5a-e0c55fc97740
> c10d26f3-2b24-4b38-a374-6c61048ee6cb
> org.dspace.app.rest.exception.DSpaceApiExceptionControllerAdvice @
> Unprocessable or invalid entity (status:422)
> WARN  d4b3c8d5-5f04-48e6-bd5a-e0c55fc97740
> 9fde6cee-4004-44e3-a812-6dc46853f8e6
> org.dspace.app.rest.exception.DSpaceApiExceptionControllerAdvice @
> Authentication is required (status:401 exception: Access is denied at:
> org.springframework.security.access.vote.AffirmativeBased.decide(AffirmativeBased.java:73))
>
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Re: [dspace-tech] DSpace 7.3 - create-administrator error

[Alan Orth]

Hi both,

If it works in DSpace 7.2.1, but not 7.3, it could be due to the database
dialect issue. DSpace 7.3 uses a newer Hibernate, which changes the
supported dialects. Make sure your local.cfg and dspace.cfg are using:

db.dialect = org.hibernate.dialect.PostgreSQL94Dialect

Previously the dialect was DSpacePostgreSQL82Dialect. This one bit me and I
was confused for weeks until someone mentioned it recently on the DSpace
Slack.

Hopefully that helps,

On Mon, Jul 11, 2022 at 6:29 PM 'Tim Donohue' via DSpace Technical Support <
dspace-tech@googlegroups.com> wrote:

> Hi Jan,
>
> That error appears to be saying you have a database connection issue.  I'd
> recommend checking your dspace.log file for more details... it's highly
> likely you have errors in that log file related to the database
> connection.  It's unclear what the exact problem may be though, so you'd
> need to check the dspace.log file.
>
> Tim
> --
> *From:* dspace-tech@googlegroups.com  on
> behalf of Jan Broulím 
> *Sent:* Monday, July 4, 2022 6:43 AM
> *To:* DSpace Technical Support 
> *Subject:* [dspace-tech] DSpace 7.3 - create-administrator error
>
>
> Hi,
>
> we are testing DSpace 7.3 and the installation fails with the installation
> of backend.
>
>
> This we get from the build as warning:
>
>  2022-07-04 12:56:15,162 WARN
> org.dspace.servicemanager.DSpaceServiceManager @ Unable to locate bean by
> name or id=database. Will try to look up bean by type next.
>
>
> and when running create-administrator command, it fails with:
>
> Exception: null
>
> java.lang.NullPointerException
>
> at
> org.dspace.core.AbstractHibernateDAO.getHibernateSession(AbstractHibernateDAO.java:59)
>
> at
> org.dspace.core.AbstractHibernateDAO.createQuery(AbstractHibernateDAO.java:137)
>
> at
> org.dspace.eperson.dao.impl.GroupDAOImpl.findByName(GroupDAOImpl.java:104)
>
> at
> org.dspace.eperson.GroupServiceImpl.findByName(GroupServiceImpl.java:401)
>
> at
> org.dspace.administer.CreateAdministrator.createAdministrator(CreateAdministrator.java:223)
>
> at
> org.dspace.administer.CreateAdministrator.negotiateAdministratorDetails(CreateAdministrator.java:197)
>
> at
> org.dspace.administer.CreateAdministrator.main(CreateAdministrator.java:84)
>
> at
> java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native
> Method)
>
> at
> java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
>
>
> When trying the same installation scrips with 7.2.1, it works fine.
>
> Thank you for any help
>
>
>
> Jan
>
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Re: [dspace-tech] mirage2 build problems

[Alan Orth]

Dear Anne,

DSpace 6.4 will be released "soon". ;) We (a group of volunteers) have been
doing preparations in the last few weeks, for example collating the list of
changes and contributors for the release notes, updating the DSpace wiki,
etc. DSpace 6.4 will be a massive bug fix release, an accumulation of years
of pull requests from members of the community, but it will likely be the
last DSpace 6.x release so we want to make sure it doesn't have any
show-stopping bugs that cause us more work immediately after. Now it's
essentially upon a few of us to see if it's in our schedules to actually do
the release (tag the commit in git, push to Maven central, etc).

If you are technical and adventurous I would highly recommend jumping on
DSpace 6.4-SNAPSHOT now using a source build. It's totally stable and has a
metric tonne of bug, security, and performance fixes, and then it will
become DSpace 6.4 in the near future.

Regards,

On Tue, Jun 7, 2022 at 6:49 PM al...@vt.edu  wrote:

> Alan,
>
> What is the plan for DSpace 6.4?
>
> Thanks,
>
> Anne
>
> On Tuesday, June 7, 2022 at 2:50:28 AM UTC-4 alan...@gmail.com wrote:
>
>> BTW this has been merged in to the 6.x branch that will soon become
>> DSpace 6.4:
>>
>> https://github.com/DSpace/DSpace/pull/8292
>>
>> Also note that Mirage 2 builds fine with Node.js 14, so I've sent another
>> pull request to update that as well:
>>
>> https://github.com/DSpace/DSpace/pull/8331
>>
>> This is important because Node.js 12 is no longer supported by the
>> upstream Node.js project and this might be the last DSpace 6.x release so
>> we don't want it shipping with dependencies that are dead on arrival
>> (within reason, given that DSpace 6 is soon EOL). I would appreciate any
>> feedback here or on GitHub for this pull request too.
>>
>> Regards,
>>
>> On Fri, May 13, 2022 at 3:16 PM Bill Tantzen  wrote:
>>
>>> Alan,
>>> Cool, if I can take ruby and bower out of the mix, so much the better!
>>> I think this should work just fine with 5.x with maybe a little tweak here
>>> and there.
>>> ~~Bill
>>>
>>> On Fri, May 13, 2022 at 3:13 AM Alan Orth  wrote:
>>>
>>>> Hi,
>>>>
>>>> Yes you're right that Mirage 2 build issues will be the same for DSpace
>>>> 5.x and 6.x, and the solution would be similar as what I proposed here:
>>>>
>>>> https://github.com/DSpace/DSpace/pull/8292
>>>>
>>>> Basically, we can remove the dependency on Ruby and bower *completely*,
>>>> moving entirely to npm for dependencies and node-sass (via npm) for Sass
>>>> processing. In addition this means we can build with newer versions of
>>>> Node.js (for example, the instructions say to use 0.10.31 but that is
>>>> beyond ancient!). I am currently building Mirage 2 successfully with
>>>> Node.js 10, 12, and even 14.
>>>>
>>>> I won't have time to look at a DSpace 5.x port of this Mirage 2 pull
>>>> request for some time, but you might be able to draw some inspiration from
>>>> the changes there on your own in the meantime...
>>>>
>>>> Regards,
>>>>
>>>> On Thu, May 12, 2022 at 6:14 PM 'Bill Tantzen' via DSpace Technical
>>>> Support  wrote:
>>>>
>>>>> Thanks Jose!
>>>>> I leveraged the instructions at
>>>>> https://github.com/DSpace/DSpace/tree/dspace-6_x/dspace-xmlui-mirage2#installation
>>>>>  and
>>>>> a single user installation of rvm to finally get my build to work.  Here's
>>>>> what finally did it for me:
>>>>>
>>>>> ## grab rvm and install for the dspace user only:
>>>>> curl -sSL https://get.rvm.io | bash -s stable
>>>>> source /home/dspace/.rvm/scripts/rvm
>>>>>
>>>>> ## install a newish version of ruby (I did need to install a couple
>>>>> RHEL packages, for which I have sudo)
>>>>> rvm install 3.1.2
>>>>> rvm use 3.1.2
>>>>>
>>>>> ## install nvm, node, bower, grunt, sass and compass
>>>>> curl -o-
>>>>> https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh | bash
>>>>> nvm install 12
>>>>> nvm alias default 12
>>>>> npm install -g bower
>>>>> npm install -g grunt && npm install -g grunt-cli
>>>>> gem install sass -v 3.3.14
>>>>> gem install compass -v 1.0.1 (compass install actually upgrades sass
>>>&

Re: [dspace-tech] Recommending Training for DSpace 7

[Alan Orth]

Dear Sarah,

I have not yet embarked on DSpace 7 customization, but this is what I'm
going to reference first (just saw it mentioned on Slack a few days ago):

https://wiki.lyrasis.org/display/DSDOC7x/User+Interface+Customization

Good luck, and share your progress!

On Mon, Jun 6, 2022 at 4:08 PM Sarah Butash  wrote:

> Good Morning Group,
>
> We are soon to launch our DSpace 7 upgrade project.  Do you have any
> recommended training that helped you prepare for the new UI customization
> process?
>
> Thank you!
> Sarah
>
> --
>
> Sarah Butash
>
> she / her
>
> Library Systems Analyst, OU Libraries
>
> Kresge Library, Room 227
>
> 100 Library Drive, Rochester, MI  48309-4479
>
> Phone: 248-370-2368
>
>
>
> --
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>


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Re: [dspace-tech] mirage2 build problems

[Alan Orth]

BTW this has been merged in to the 6.x branch that will soon become DSpace
6.4:

https://github.com/DSpace/DSpace/pull/8292

Also note that Mirage 2 builds fine with Node.js 14, so I've sent another
pull request to update that as well:

https://github.com/DSpace/DSpace/pull/8331

This is important because Node.js 12 is no longer supported by the upstream
Node.js project and this might be the last DSpace 6.x release so we don't
want it shipping with dependencies that are dead on arrival (within reason,
given that DSpace 6 is soon EOL). I would appreciate any feedback here or
on GitHub for this pull request too.

Regards,

On Fri, May 13, 2022 at 3:16 PM Bill Tantzen  wrote:

> Alan,
> Cool, if I can take ruby and bower out of the mix, so much the better!  I
> think this should work just fine with 5.x with maybe a little tweak here
> and there.
> ~~Bill
>
> On Fri, May 13, 2022 at 3:13 AM Alan Orth  wrote:
>
>> Hi,
>>
>> Yes you're right that Mirage 2 build issues will be the same for DSpace
>> 5.x and 6.x, and the solution would be similar as what I proposed here:
>>
>> https://github.com/DSpace/DSpace/pull/8292
>>
>> Basically, we can remove the dependency on Ruby and bower *completely*,
>> moving entirely to npm for dependencies and node-sass (via npm) for Sass
>> processing. In addition this means we can build with newer versions of
>> Node.js (for example, the instructions say to use 0.10.31 but that is
>> beyond ancient!). I am currently building Mirage 2 successfully with
>> Node.js 10, 12, and even 14.
>>
>> I won't have time to look at a DSpace 5.x port of this Mirage 2 pull
>> request for some time, but you might be able to draw some inspiration from
>> the changes there on your own in the meantime...
>>
>> Regards,
>>
>> On Thu, May 12, 2022 at 6:14 PM 'Bill Tantzen' via DSpace Technical
>> Support  wrote:
>>
>>> Thanks Jose!
>>> I leveraged the instructions at
>>> https://github.com/DSpace/DSpace/tree/dspace-6_x/dspace-xmlui-mirage2#installation
>>>  and
>>> a single user installation of rvm to finally get my build to work.  Here's
>>> what finally did it for me:
>>>
>>> ## grab rvm and install for the dspace user only:
>>> curl -sSL https://get.rvm.io | bash -s stable
>>> source /home/dspace/.rvm/scripts/rvm
>>>
>>> ## install a newish version of ruby (I did need to install a couple RHEL
>>> packages, for which I have sudo)
>>> rvm install 3.1.2
>>> rvm use 3.1.2
>>>
>>> ## install nvm, node, bower, grunt, sass and compass
>>> curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.0/install.sh
>>> | bash
>>> nvm install 12
>>> nvm alias default 12
>>> npm install -g bower
>>> npm install -g grunt && npm install -g grunt-cli
>>> gem install sass -v 3.3.14
>>> gem install compass -v 1.0.1 (compass install actually upgrades sass to
>>> 3.4.25)
>>>
>>> That's it, I was able to build successfully by
>>> setting -Dmirage2.deps.included=false which I think is the default anyway.
>>>
>>> ~~Bill
>>>
>>> On Thu, May 12, 2022 at 10:05 AM Jose Blanco  wrote:
>>>
>>>> Hi Bill,
>>>>
>>>> I had the same problem.  Take a look at last message in this thread:
>>>>
>>>> https://groups.google.com/g/dspace-tech/c/7_fUBxsxkhs
>>>>
>>>> I have not tried the patch yet.  What I did is, since I had a
>>>> successful Mirage2 build from a previous build in the webapp directory,
>>>> copy it to
>>>>
>>>> dspace-xmlui/src/main/webapp/themes/Mirage2
>>>>
>>>> And then build it using:
>>>> > mvn clean package
>>>>
>>>> From now on, if I need to make any changes to Mirage2, I will do it
>>>> from:
>>>>
>>>> dspace-xmlui/src/main/webapp/themes/Mirage2
>>>>
>>>> That got me over the issue.
>>>>
>>>> -Jose
>>>>
>>>> On Thu, May 12, 2022 at 9:56 AM 'Bill Tantzen' via DSpace Technical
>>>> Support  wrote:
>>>>
>>>>> I am recently required to rebuild my v5.10 instance with mirage2, and
>>>>> I'm encountering the same problems as many others here since
>>>>> torquebox.org is out of action.
>>>>>
>>>>> Does anybody have any tips?
>>>>>
>>>>> One major problem is that I cannot install rvm as root -- can I use
>>>>> rbenv a

Re: [dspace-tech] mirage2 build problems

[Alan Orth]

;>> at Module.load (module.js:356:32)
>>> at Function.Module._load (module.js:312:12)
>>> at Module.require (module.js:364:17)
>>> at require (module.js:380:17)
>>> at Object.
>>> (/home/dspace/.nvm/v0.10.31/lib/node_modules/grunt/node_modules/grunt-cli/node_modules/liftup/node_modules/findup-sync/index.js:12:10)
>>> at Module._compile (module.js:456:26)
>>> at Object.Module._extensions..js (module.js:474:10)
>>> at Module.load (module.js:356:32)
>>> ...
>>> ...
>>>
>>> Any suggestions on the right cocktail of versions and software I need to
>>> get this to build?
>>>
>>> Thanks all,
>>> ~~Bill
>>>
>>> --
>>> Human wheels spin round and round
>>> While the clock keeps the pace... -- John Mellencamp
>>> 
>>> Bill TantzenUniversity of Minnesota Libraries
>>> 612-626-9949 (U of M)612-325-1777 (cell)
>>>
>>> --
>>> All messages to this mailing list should adhere to the Code of Conduct:
>>> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
>>> ---
>>> You received this message because you are subscribed to the Google
>>> Groups "DSpace Technical Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to dspace-tech+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/dspace-tech/CADgrb7E3YVEmw12XQxkdssj9VHeHJFQTc%2BDAnK_YCj9V7FXwpA%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/dspace-tech/CADgrb7E3YVEmw12XQxkdssj9VHeHJFQTc%2BDAnK_YCj9V7FXwpA%40mail.gmail.com?utm_medium=email_source=footer>
>>> .
>>>
>>
>
> --
> Human wheels spin round and round
> While the clock keeps the pace... -- John Mellencamp
> 
> Bill TantzenUniversity of Minnesota Libraries
> 612-626-9949 (U of M)612-325-1777 (cell)
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
> ---
> You received this message because you are subscribed to the Google Groups
> "DSpace Technical Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dspace-tech/CADgrb7FftxA%2BJNDztoXgj1n-NjcxAozbG7Ad1CFmMt-0QcPCAw%40mail.gmail.com
> <https://groups.google.com/d/msgid/dspace-tech/CADgrb7FftxA%2BJNDztoXgj1n-NjcxAozbG7Ad1CFmMt-0QcPCAw%40mail.gmail.com?utm_medium=email_source=footer>
> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] error building

[Alan Orth]

c:
>
>
>
> export NVM_DIR="$HOME/.nvm"
>
> [ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"  # This loads nvm
>
> [ -s "$NVM_DIR/bash_completion" ] && \. "$NVM_DIR/bash_completion"  # This
> loads nvm bash_completion
>
>
>
> --
>
> Sean
>
>
>
> *From: *Jose Blanco 
> *Date: *Tuesday, May 3, 2022 at 4:46 PM
> *To: *Sean Kalynuk 
> *Cc: *DSpace Technical Support 
> *Subject: *Re: [dspace-tech] error building
>
> *Caution:* This message was sent from outside the University of Manitoba.
>
>
>
> Sean,
>
>
>
> Sorry to bother you, I just tried again and it fails like this:
>
>
>
> if [ ! -r node -o ! -L node ]; then \
>
>   ln -fs out/Release/node node; fi
>
> ln: failed to create symbolic link 'node': Operation not supported
>
> Makefile:104: recipe for target 'node' failed
>
> make: *** [node] Error 1
>
> nvm: install v12.22.12 failed!
>
>
>
>
>
> Why?
>
>
>
> -Jose
>
>
>
> On Tue, May 3, 2022 at 4:36 PM Sean Kalynuk 
> wrote:
>
> Hi Jose,
>
>
>
> Sorry, I don’t know about the status of torquebox.org, but since there
> have been issues with that domain before, I’m sticking with the locally
> installed Mirage 2 prerequisites now since I managed to get a full compile.
>
>
>
> When you installed nvm, it would have modified your account’s login
> scripts. In my case, it modified my .bashrc file. I logged out and back in
> again to make sure I had the right environment settings before running “nvm
> install 12”.
>
>
>
> --
>
> Sean
>
>
>
> *From: *Jose Blanco 
> *Date: *Tuesday, May 3, 2022 at 3:12 PM
> *To: *Sean Kalynuk 
> *Cc: *DSpace Technical Support 
> *Subject: *Re: [dspace-tech] error building
>
> *Caution:* This message was sent from outside the University of Manitoba.
>
>
>
> Sean, I'm doing the install and it takes a while and now I'm getting :
>
>
>
> nvm: install v12.22.12 failed!
>
>
>
> is there any chance we will be able to build without having to do this?
>
>
>
> -Jose
>
>
>
> On Tue, May 3, 2022 at 3:08 PM Sean Kalynuk 
> wrote:
>
> The torquebox.org domain has expired.
>
>
>
> See old discussion: https://groups.google.com/g/dspace-tech/c/RPL_qoTGvMI
>
>
>
> The workaround is to install the prerequisite software for building Mirage
> 2:
>
>
>
>
> https://github.com/DSpace/DSpace/tree/dspace-6_x/dspace-xmlui-mirage2#installation
>
>
>
> I’m currently setting up the workaround myself since I ran into this
> yesterday and can’t wait for torquebox.org to return. Will be more stable
> (and faster!) for builds in the long run too.
>
>
>
> --
>
> Sean
>
>
>
> *From: *dspace-tech@googlegroups.com  on
> behalf of Jose Blanco 
> *Date: *Tuesday, May 3, 2022 at 1:47 PM
> *To: *DSpace Technical Support 
> *Subject: *[dspace-tech] error building
>
> *Caution:* This message was sent from outside the University of Manitoba.
>
>
>
> Getting this error when building 6.3.  It was working fine a week ago
>
>
>
> [ERROR] Failed to execute goal on project xmlui-mirage2: Could not resolve
> dependencies for project org.dspace.modules:xmlui-mirage2:war:6.3: Failed
> to collect dependencies at rubygems:compass:gem:1.0.1 ->
> rubygems:sass:gem:[3.3.13,3.5): No versions available for
> rubygems:sass:gem:[3.3.13,3.5) within specified range -> [Help 1]
>
>
>
> -Jose
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
> ---
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> .
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
> ---
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> To unsubscribe from this group and stop receiving emails from it, send an
> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dspace-tech/YQBPR0101MB54048744D4D26658F47051DDE8C39%40YQBPR0101MB5404.CANPRD01.PROD.OUTLOOK.COM
> <https://groups.google.com/d/msgid/dspace-tech/YQBPR0101MB54048744D4D26658F47051DDE8C39%40YQBPR0101MB5404.CANPRD01.PROD.OUTLOOK.COM?utm_medium=email_source=footer>
> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Feedburner notifications for new items

[Alan Orth]

Dear list,

We used to use Feedburner to subscribe to various built-in
community/collection RSS feeds, which would then send emails to
subscribers. It was a great way for project administrators and budget
holders to know when there were new items/outputs in their program.

Now that Feedburner has been placed in read-only mode by Google we're
wondering what to do now. Does anyone have a similar use case and solution?
It occurs to me that this is what the built-in collection subscription
function is for. We have not used that much so I'm not sure. One cool thing
with the Feedburner solution was that you could create custom RSS feeds
using Open Search, for example for items with a certain budget code.

Thanks,

-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Remove a workspace item

[Alan Orth]

Asking again here. Is there any way to delete "abandoned" submissions from
the database? Our editors sometimes accept submissions at the
"Accept/Reject/Edit" step that end up being duplicates or mistakenly
accepted for other reasons. Once they've accepted them there is no way to
reject them, only send them back to the task pool. We have thousands of
these as our repository is over ten years old!

Appreciate any help or stories from the SQL trenches...

On Mon, Oct 11, 2021 at 3:53 PM Alan Orth  wrote:

> Hi all,
>
> I've looked at both of these PRs and unfortunately they are for the
> configurable workflow (aka XML workflow). We are using the basic workflow
> so these won't work for us. That's a real shame because I have thousands of
> abandoned submissions from hundreds of editors over the past twelve years
> and I'd love to find a way to get rid of them. We are on DSpace 6.3.
>
> Regards,
>
> On Fri, Oct 1, 2021 at 7:06 PM 'Alexander Vielhauer' via DSpace Technical
> Support  wrote:
>
>> After testing and rereading the PRs, I can say that the workflow
>> administration (in DSpace7) is limited to workflow items which have been
>> submitted. Sorry for the confusion.
>> On 30/09/2021 18:06, 'Alexander Vielhauer' via DSpace Technical Support
>> wrote:
>>
>> Dear Hrafn,
>>
>> Thank you very much! From the PR I learned that DSpace7 has a handy admin
>> feature for browsing and deleting workflow items - another reason to push
>> for the upgrade! :)
>>
>> Best,
>> Alexander
>> On 24/09/2021 17:35, Hrafn Malmquist wrote:
>>
>> Hello Alexander
>>
>> To the best of my knowledge, there is currently no supported way of doing
>> this using DSpace UI.
>>
>> There are two PRs to DSpace 6 (assuming that's the version you're using)
>> intended to support such functionality:
>> https://github.com/DSpace/DSpace/pull/2200
>> and
>> https://github.com/DSpace/DSpace/pull/2076
>>
>> I've mostly looked at the latter one. It applies only to the XML
>> Configurable Workflow which I could not try out as our production servers
>> only use the basic workflow setup.
>>
>> Unfortunately I can't help you more.
>>
>> Good luck, Hrafn
>>
>>
>> On Fri, Sep 24, 2021 at 4:13 PM 'Alexander Vielhauer' via DSpace
>> Technical Support  wrote:
>>
>>> Dear list,
>>>
>>> what is your recommended workflow for deleting abandoned workspace items?
>>>
>>> We have a rather large dataset stuck in submission since the author
>>> started a new submission (which is now archived) instead of resuming his
>>> old submission.
>>>
>>> I cannot find a way though to delete workspace items via a command line
>>> operation or an admin feature in the UI. I'd rather not manipulate the
>>> database directly to allow the cleanup utility to take care of deleting
>>> the bitstreams.
>>>
>>> If anyone keeps track of this in their repo: How do you scan for "stuck"
>>> submissions and what are your thresholds and deadlines for notifying the
>>> authors and deleting the submission?
>>>
>>> Thank you and kind regards
>>> Alexander
>>>
>>> --
>>> Alexander Vielhauer
>>> Philipps-Universität Marburg | UB
>>> Digitale Dienste | Deutschhausstraße 9 | D226
>>> Tel. +49 06421 28-25290
>>>
>>> --
>>> All messages to this mailing list should adhere to the Code of Conduct:
>>> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
>>> ---
>>> You received this message because you are subscribed to the Google
>>> Groups "DSpace Technical Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to dspace-tech+unsubscr...@googlegroups.com.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/dspace-tech/2b00b729-5b64-8f95-91b5-b3a6c9cb4b10%40staff.uni-marburg.de
>>> .
>>>
>> --
>> Alexander Vielhauer
>> Philipps-Universität Marburg | UB
>> Digitale Dienste | Deutschhausstraße 9 | D226
>> Tel. +49 06421 28-25290
>>
>> --
>> All messages to this mailing list should adhere to the Code of Conduct:
>> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
>> ---
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>> "DSpace Technical Support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to d

Re: [dspace-tech] Remove a workspace item

[Alan Orth]

Hi all,

I've looked at both of these PRs and unfortunately they are for the
configurable workflow (aka XML workflow). We are using the basic workflow
so these won't work for us. That's a real shame because I have thousands of
abandoned submissions from hundreds of editors over the past twelve years
and I'd love to find a way to get rid of them. We are on DSpace 6.3.

Regards,

On Fri, Oct 1, 2021 at 7:06 PM 'Alexander Vielhauer' via DSpace Technical
Support  wrote:

> After testing and rereading the PRs, I can say that the workflow
> administration (in DSpace7) is limited to workflow items which have been
> submitted. Sorry for the confusion.
> On 30/09/2021 18:06, 'Alexander Vielhauer' via DSpace Technical Support
> wrote:
>
> Dear Hrafn,
>
> Thank you very much! From the PR I learned that DSpace7 has a handy admin
> feature for browsing and deleting workflow items - another reason to push
> for the upgrade! :)
>
> Best,
> Alexander
> On 24/09/2021 17:35, Hrafn Malmquist wrote:
>
> Hello Alexander
>
> To the best of my knowledge, there is currently no supported way of doing
> this using DSpace UI.
>
> There are two PRs to DSpace 6 (assuming that's the version you're using)
> intended to support such functionality:
> https://github.com/DSpace/DSpace/pull/2200
> and
> https://github.com/DSpace/DSpace/pull/2076
>
> I've mostly looked at the latter one. It applies only to the XML
> Configurable Workflow which I could not try out as our production servers
> only use the basic workflow setup.
>
> Unfortunately I can't help you more.
>
> Good luck, Hrafn
>
>
> On Fri, Sep 24, 2021 at 4:13 PM 'Alexander Vielhauer' via DSpace Technical
> Support  wrote:
>
>> Dear list,
>>
>> what is your recommended workflow for deleting abandoned workspace items?
>>
>> We have a rather large dataset stuck in submission since the author
>> started a new submission (which is now archived) instead of resuming his
>> old submission.
>>
>> I cannot find a way though to delete workspace items via a command line
>> operation or an admin feature in the UI. I'd rather not manipulate the
>> database directly to allow the cleanup utility to take care of deleting
>> the bitstreams.
>>
>> If anyone keeps track of this in their repo: How do you scan for "stuck"
>> submissions and what are your thresholds and deadlines for notifying the
>> authors and deleting the submission?
>>
>> Thank you and kind regards
>> Alexander
>>
>> --
>> Alexander Vielhauer
>> Philipps-Universität Marburg | UB
>> Digitale Dienste | Deutschhausstraße 9 | D226
>> Tel. +49 06421 28-25290
>>
>> --
>> All messages to this mailing list should adhere to the Code of Conduct:
>> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "DSpace Technical Support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dspace-tech+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dspace-tech/2b00b729-5b64-8f95-91b5-b3a6c9cb4b10%40staff.uni-marburg.de
>> .
>>
> --
> Alexander Vielhauer
> Philipps-Universität Marburg | UB
> Digitale Dienste | Deutschhausstraße 9 | D226
> Tel. +49 06421 28-25290
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
> ---
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> https://groups.google.com/d/msgid/dspace-tech/ae874de6-b24e-5a97-68e7-d4ff3ba96383%40staff.uni-marburg.de
> <https://groups.google.com/d/msgid/dspace-tech/ae874de6-b24e-5a97-68e7-d4ff3ba96383%40staff.uni-marburg.de?utm_medium=email_source=footer>
> .
>
> --
> Alexander Vielhauer
> Philipps-Universität Marburg | UB
> Digitale Dienste | Deutschhausstraße 9 | D226
> Tel. +49 06421 28-25290
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://www.lyrasis.org/about/Pages/Code-of-Conduct.aspx
> ---
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> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on

Re: [dspace-tech] "No changes were detected" when importing metadata via XMLUI

[Alan Orth]

Apologies for bumping this very old thread. Just an FYI that this is still
an issue on DSpace 6.3 and DSpace 7.1-SNAPSHOT. It is not possible to
remove duplicates from multi-value fields using the CSV bulkedit metadata
importer.

I've filed an issue on GitHub: https://github.com/DSpace/DSpace/issues/7989

Hopefully someone can take a look!

Cheers,

On Wed, Nov 25, 2015 at 3:18 PM Kcho Lorenzetti  wrote:

> Hi, I think that could be the problem.
> I did something similar with the header that worked:
>
> id, collection, dc.contributor.author,
> dc.contributor.author[]
> "id_x", "collection_y", "author2::longid2::300||author1::longid1::300",
>
> Please note the final comma.
> Thank you!
>
> --
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Re: [dspace-tech] Configurations For large number of items and concurrent users

[Alan Orth]

Dear Arunendra MB,

You will find many examples of users with over 100,000 items in their
DSpace repository. We have ~95,000 and it's "fine".

As for specifics, our production server has 32GB of RAM, and we use DSpace
6 with Tomcat 7 and have a heap size of 8192M. I recommend stealing the JVM
settings from the Solr 4.10.x init script, as DSpace is essentially a Solr
frontend (and it runs Solr version 4.10.x currently). The 32GB of RAM is
surely overkill, but above and beyond DSpace itself, we of course have
PostgreSQL running and any other leftover memory is automatically used by
the Linux kernel as a cache (for example for Solr index data).

We only do a full Discovery re-index once a month, or less, when we do some
batch metadata cleanups. That takes about three hours and is an intensive
process. Otherwise there is no need to do such expensive indexing.

Also, you should make sure you're running the latest PostgreSQL possible
(PostgreSQL 10 with DSpace 6). On our web server we also aggressively limit
non-human clients because they are a waste of resources and cause
considerable load crawling useless and infinite combinations of /discovery
and /browse subject results pages.

Regards,

On Tue, Jul 27, 2021 at 12:10 PM ArunendraMB 
wrote:

> Thanks.
> I will check if it works.
> For *concurrent users*, I had come across this post :
> http://dspace.2283337.n4.nabble.com/Maximum-number-of-DB-connections-in-pool-td4692476.html
> The user had problem even after changing the value db.maxconnections.
> The solution provided appears to require a lot of changes.
> Can you please comment on that?
>
> For *large number of items*, cleaning and reindexing is definitely an
> option. But when there are say, 1 lakh items, simply reindexing might not
> work, I assume.
> What to do then?
>
> In terms of *hardware*/*memory allocation*, do you have any advice on-
> Memory or CPU cores?
>
>
> *From,*
> *Arunendra MB.*
>
>
>
> On Mon, Jul 26, 2021 at 7:49 PM Hrafn Malmquist 
> wrote:
>
>> Hi Arunendra
>>
>> That's a bit of an ask.
>>
>> Here =>
>> https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace#InstallingDSpace-HardwareRecommendations
>>
>> You will find hardware recommendations split into minimum, mid and
>> high-end.
>>
>> To optimize search you should run the index-discovery job see =>
>> https://wiki.lyrasis.org/display/DSDOC6x/Discovery#Discovery-DiscoverySolrIndexMaintenance
>>
>> Review the "Scheduled Tasks via Cron" for further information about
>> maintenance =>
>> https://wiki.lyrasis.org/display/DSDOC6x/Scheduled+Tasks+via+Cron
>>
>> With regards to concurrent users, the default settings should be fine,
>> but review the database settings =>
>> https://wiki.lyrasis.org/display/DSDOC6x/Configuration+Reference#ConfigurationReference-DSpaceDatabaseConfiguration
>>
>> As well as settings for the database you use in your setup, Postgres or
>> Oracle.
>>
>> Best regards, Hrafn
>>
>> On Mon, Jul 26, 2021 at 1:31 PM Projects Arunendra <
>> project.arunen...@gmail.com> wrote:
>>
>>>
>>> Hi,
>>> I believe there are related responses scattered through out this forum
>>> but I need a summarized idea:
>>> 1)What configurations are required when there are large number of items
>>> (i.e optimized search)?
>>> 2) What configurations are required when there are large number of
>>> concurrent users?
>>>
>>> Will only sufficient memory allocation to to Tomcat do?
>>> Or,
>>> Configurations are required in the Solar indexing too?
>>>
>>> Reqd. for DSpace 5.x and 6.x
>>>
>>>
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>>> .
>>>
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Re: [dspace-tech] JavaUpdate

[Alan Orth]

Dear Maya,

It's hard to say how the Bitcoin miner got installed. Did you install
OpenJDK via Ubuntu's package manager or by some other download method? In
my experience, these types of things generally get into your system via
bruteforce scanning of SSH, where some bot gets lucky guessing your SSH
username/password, for example: admin/admin. The fact that it was running
as the tomcat user is interesting, meaning either your tomcat user has SSH
enabled, or something managed to exploit your Tomcat server.

Regards,

On Thu, Jul 29, 2021 at 2:12 PM Maya Zbitneva  wrote:

> Good day!
>
> Michael, thank you very much for your professional recommendations!
> I will try to realize all of them.
>
> > Do you have the user of the running process (ps -xau) ?
>
> Yes, My cryptominer process was runned under "tomcat" user.
>
> Zbitnieva Maiia,
> System administrator,
> Ukraine.
>
>
> среда, 28 июля 2021 г. в 16:31:58 UTC+3, Michael Plate:
>
>> Hi,
>>
>> Am 28.07.21 um 13:16 schrieb Maya Zbitneva:
>> > Good day!
>> >
>> > Michael, thank you very much for your professional consultation. It was
>> > real cryptominer in OS Ubuntu!
>>
>> Outch.
>>
>> > I succedeed to kill it.
>>
>> Do you have the user of the running process (ps -xau) ?
>>
>> > But I have the question about it.
>> > How to find the vulnerability from which the malware got in?
>>
>> That is the hard part. You can try http://www.chkrootkit.org/ (should be
>> in Ubuntu) but this also can produce false positives. It might also be
>> not the right tool…
>>
>> If you have no idea, no log files or anything, IMHO:
>>
>> > Install a new machine !! <
>>
>> Make a new machine, setup (Apache / Nginx), Tomcat and after basically
>> running, copy the DSpace files.
>> Change passwords and hope nothing awful is copied to the new machine.
>> Keep it closed - only https and ssh, keep the logins local (no Windows
>> join).
>>
>> > Because even if I removed the malware, it can come again using the same
>> > vulnerability it exploited earlier.
>>
>> This is what makes admins sleep bad.
>>
>> > Help me please, what security measures need to be taken to prevent the
>> > virus from entering the operating system again?
>>
>> I only can give you some simple tips, because I don't know you
>> organization, and there are standards you should keep on any machine
>> running on the internet.
>>
>> Do not expose any service to the internet which you don't need there -
>> if you are behind a network firewall, only https (port 443) for DSpace
>> needs to be accessible from outside - no ssh, no network files systems
>> etc. Try a port scan from outside.
>>
>> Update your OS regulary, on DSpace especially Java.
>>
>> Backup - and restore ! Try the restore on a new machine an get a feeling
>> for that, note down the steps.
>>
>> If your DSpace is also file-, mail- and print-server, there is something
>> really wrong - try to split that.
>>
>> Find a local Linux community to get better help.
>>
>> But maybe you made everything OK - this still can happen :( .
>>
>> CU
>>
>> Michael
>>
>>
>> --
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Re: [dspace-tech] JavaUpdate

[Alan Orth]

Dear Maya,

What kind of server is this? Is it Windows? There should not be any Java
update service on Linux, as that is handled by the system's package manager.

Regards,

On Tue, Jul 13, 2021, 11:26 Maya Zbitneva  wrote:

> Good day!
>
> Help me please to solve the following problem.
> I have two running processes: java and JavaUpdate on my web server DSpace
> repository.
> JavaUpdate consumes almost all resources of processor of my web server
> DSpace repository.
> Can I kill JavaUpdate process so that my repository continues to work?
> so that my repository does not stop working?
>
>
> With respect,
> Zbitnieva Maiia,
> System administrator,
> Ukraine.
>
> --
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> .
>

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Re: [dspace-tech] Statistics not Updating since server move

[Alan Orth]

Dear Sarah,

Is this DSpace 5 or 6? I bet it's because of the MaxMind GeoIP1
deprecation. See these issues:

- DS-3986: https://jira.duraspace.org/browse/DS-3986
- DS-4020: https://jira.duraspace.org/browse/DS-4020
- DS-3832: https://jira.duraspace.org/browse/DS-3832

Basically, Solr silently fails to log statistics if the GeoLite database is
missing. DSpace 5.10 and 6.4 were modified to use GeoIP2 databases, but you
can also just find an old copy of the database and put it on the new
server. Otherwise you'll have to upgrade so you can use GeoIP2 versions of
the databases.

Cheers,

On Thu, Jul 8, 2021 at 11:17 PM Sarah Butash  wrote:

> Hello,
>
> Our Dspace environment was migrated to a new VM.  The new VM server is not
> capturing new statistics in SOLR.  I am able to successfully query
> statistics through SOLR.  Do you have any suggestions of why the statistics
> have not updated on the new VM?
>
> Thank you!
> Sarah
>
> --
>
> Sarah Butash
>
> she / her
>
> Library Systems Analyst, OU Libraries
>
> Kresge Library, Room 227
>
> 100 Library Drive, Rochester, MI  48309-4479
>
> Phone: 248-370-2368
>
>
>
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Re: [dspace-tech] Re: Messages about JNDI bean at boot time...then crash later?

[Alan Orth]

or invoking action
>> ...
>> Caused by: org.hibernate.exception.GenericJDBCException: Could not open
>> connection
>>
>> If any of this rings a bell, I'd appreciate any info.  Thanks!
>>
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Re: [dspace-tech] Extend REST API

[Alan Orth]

Dear Kpet,

You will need to work from a source release or git checkout in order to see
the Java code. The REST API lives in the `dspace-rest` directory of the
source release. After making your changes you will have to re-build the
code with Maven (mvn) and re-install with ant.

See the DSpace 6.x installation instructions:
https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace

But note that DSpace 6.x is very old and is (essentially) in
maintenance-only mode for the past few years as a massive amount of
engineering and planning resources have gone into the upcoming DSpace 7
release (currently beta 5). DSpace 7 includes a fully reworked REST API, so
you might want to look into that.

Cheers,

On Tue, Jun 22, 2021 at 10:51 AM kpet  wrote:

> Hello,
>
> I am using Dspace 6.3, and I would like to customize the rest api
> endpoints, add new ones, etc.
> However, I am unable to locate any .java files under my current
> installation, which I could directly edit to perform any such
> customizations.
>
> Do you know of any way this can be achieved?
>
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Re: [dspace-tech] Error with thumbnails not being created

[Alan Orth]

Dear Shaun,

Double check your mediafilter plugins (filter.plugins in dspace.cfg).
DSpace 6 configuration syntax changed in general, and more specifically a
new, default JPEG thumbnailer was added (PDFBox). I have no experience with
the new PDFBoxThumbnailer so this could be a bug or a site-specific
configuration issue. We use ImageMagick.

Cheers,

On Mon, Jun 21, 2021 at 4:24 PM Shaun donovan  wrote:

> Hi All.
>
> I am running version 6.x. I had to move up to it so that I could move my
> statistics cores from the old id to uuid, and 6.x is the only one that had
> the tools to do it.
>
> Now I have come across something strange. When I run filter-media, the
> output I get is:
>
> "FILTERED: bitstream 5dfd340b-f46b-485f-95bd-494c6d6bde2d (item:
> 10204/6053) and created 'Olwal_2012.pdf.jpg'"
>
> But when I edit that item, there is no thumbnail attached to it.
>
> If I run "filter-media -i 10204/6053", I get the same output, but now the
> thumbnail is properly created.
>
> I have tried "filter-media -f". It also says that it creates the
> thumbnail, but it doesn't.
>
> Any ideas?
>
> Kind Regards.
>
> Shaun.
>
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Re: [dspace-tech] Cloud Storage

[Alan Orth]

Dear Julio,

I have been running a large DSpace instance since 2010 and my advice would
be to avoid deploying DSpace in a container. I avoid containers in general,
but more specifically: the DSpace 6.x software is basically technology from
the early 2000s and is not well suited for container deployment. The newer
as-of-yet-unreleased version (7.0) seems to be designed with containers in
mind because it uses some newer components. Even so, it is very common for
database administrators to recommend against deploying relational databases
in containers.

Others on this mailing list might be more willing to help you with the
container thing, but not me!

Regards,

On Wed, May 26, 2021 at 4:45 PM Julio Isaias Peguero Santana <
juliomegacomp...@gmail.com> wrote:

> Hi,
>
> Thank Alan, to take the moment to answer 
>
> It's not a mandatory requirement, it's a own project, can change. But the
> way i would like to do it is separeted the storage from the app, i think is
> more secure for the data and i'm thinking to run the container directly
> using Azure container instances. I was testing with some Dspace image and
> when you restart the container the app reset, it's running in a sandbox and
> that worry me. Maybe i'm making wrong.
>
> By the way, i am open to suggestions   :D
>
> Thanks,
>
> Regards,
>
> PD: Sorry by my bad english
>
> El miércoles, 26 de mayo de 2021 a la(s) 06:37:45 UTC-4, alan...@gmail.com
> escribió:
>
>> Dear Julio,
>>
>> Is "cloud storage" a requirement? By default DSpace stores its files on
>> the disk where the server runs (for example /dspace/assetstore). It's much
>> more simple in my opinion anyways.
>>
>> Regards,
>>
>> On Wed, May 26, 2021 at 12:22 AM Julio Isaias Peguero Santana <
>> juliomeg...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> I'm student college who try implementation an institute repository for
>>> my college, my idea is to deploy Dspace 6.3 in a container on Microsoft
>>> Azure platform, i have been follow the documantation, but the doesnt spefic
>>> how can i connet to Azure storage service, only it talk about Amazon S3 and
>>> local storage.
>>>
>>> How can i connect Azure sotage to Dspace ??
>>>
>>> Dspace 6.3 on Ubuntu 18.04
>>>
>>> Thinks,
>>>
>>> Julio Isaias
>>>
>>> --
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>>> .
>>>
>>
>>
>> --
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>> alan...@gmail.com
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>> https://mjanja.ch
>>
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> email to dspace-tech+unsubscr...@googlegroups.com.
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>


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Re: [dspace-tech] DSpace 6.3 - Yet the expand parameter in the rest get collections

[Alan Orth]

Dear Ricardo,

So you mean that you're getting a list of all collections with the
parentCommunity expand parameter like this?

https://dspacetest.cgiar.org/rest/collections?expand=parentCommunity

In this example above I see that the response does not include
parentCommunity data for each collection. If you change the null to expand
on line 197 of CollectionsResource.java does it fix the problem? If so,
then you should definitely file a bug on Jira and make a pull request.
That's a good find!

Cheers,

On Wed, May 26, 2021 at 12:08 AM Ricardo Campos 
wrote:

> Hi, Alan.
>
> Thanks for your reply.
>
> There is a difference between your call to rest and mine. While you ask
> for a specific collection - you give an collection uuid in the url -, I'm
> asking a list of all collections in the repository. In terms of the java
> code, you call "getCollection" while I call "getCollection*s"*. In you
> case, the the call to the Collection class includes the expand parameter.
> Maybe the fact getCollections asks for a list of collections would have
> been the reason why the code for all collections does not refer to expand,
> i'd say on purpose: to minimize, to shorten the answer. The problem is that
> if you have the list of all collections you could find many of them with
> the same name, making impossible to identify which is which, if you
> understand me. I'd try to have the parent community name with collection
> name in order to make this identification unique, if possible (you could
> still have "homonimes" until a certain level).
>
> Thanks again.
>
>
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>
>  Livre
> de vírus. www.avast.com
> <https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail>.
> <#m_2311080036561454480_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
>
> Em ter., 25 de mai. de 2021 às 03:29, Alan Orth 
> escreveu:
>
>> Dear Ricardo,
>>
>> I don't understand the logic around that code block in
>> CollectionsResource.java, but I'm on DSpace 6.3 as well and I can use
>> expand on a collection to get the parent community, for example:
>>
>>
>> https://dspacetest.cgiar.org/rest/collections/8ea4b611-1f59-4d4e-b78d-a9921a72cfe7?expand=parentCommunity
>>
>> Were you doing something differently? You can check the git log for that
>> file to see its history.
>>
>> Cheers,
>>
>> On Tue, May 18, 2021 at 11:25 PM rdias...@gmail.com <
>> rdiascam...@gmail.com> wrote:
>>
>>> Hi,
>>>
>>> For some time now, I've been trying to get the parent Community for when
>>> reading the collections through the Rest API.
>>>
>>> Today I finally went to the source code and found, in
>>> CollectionsResource.java the line
>>>
>>> Collection collection = new
>>> org.dspace.rest.common.Collection(dspaceCollection, servletContext,
>>> *null*, context, limit, offset);
>>>
>>> I wish to know why the parameter  expand is set to null. I changed to expand
>>> (a string passed to the function getCollections) and it seems to work
>>> as expected.
>>>
>>> As I  think no code is made without a reason, I feel insecure to let it
>>> modified without further notice or advice.
>>>
>>> Any help is welcome.
>>>
>>> Thanks,
>>>
>>> Ricardo
>>>
>>> --
>>> All messages to this mailing list should adhere to the Code of Conduct:
>>> https://duraspace.org/about/policies/code-of-conduct/
>>> ---
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>>> Groups "DSpace Technical Support" group.
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>>> .
>>>
>>
>>
>> --
>> Alan Orth
>> alan.o...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>>
>

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Re: [dspace-tech] DSpace 6.3 - Yet the expand parameter in the rest get collections

[Alan Orth]

Dear Ricardo,

I don't understand the logic around that code block in
CollectionsResource.java, but I'm on DSpace 6.3 as well and I can use
expand on a collection to get the parent community, for example:

https://dspacetest.cgiar.org/rest/collections/8ea4b611-1f59-4d4e-b78d-a9921a72cfe7?expand=parentCommunity

Were you doing something differently? You can check the git log for that
file to see its history.

Cheers,

On Tue, May 18, 2021 at 11:25 PM rdias...@gmail.com 
wrote:

> Hi,
>
> For some time now, I've been trying to get the parent Community for when
> reading the collections through the Rest API.
>
> Today I finally went to the source code and found, in
> CollectionsResource.java the line
>
> Collection collection = new
> org.dspace.rest.common.Collection(dspaceCollection, servletContext, *null*,
> context, limit, offset);
>
> I wish to know why the parameter  expand is set to null. I changed to expand
> (a string passed to the function getCollections) and it seems to work as
> expected.
>
> As I  think no code is made without a reason, I feel insecure to let it
> modified without further notice or advice.
>
> Any help is welcome.
>
> Thanks,
>
> Ricardo
>
> --
> All messages to this mailing list should adhere to the Code of Conduct:
> https://duraspace.org/about/policies/code-of-conduct/
> ---
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> .
>


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Re: [dspace-tech] Is it normal for both the dspace and tomcat users to have crontab files?

[Alan Orth]

Dear Kerry,

That sounds strange and could cause some unexpected issues. Technically you
should put the cron jobs in the cron tab of the user who owns the DSpace
installation directory (ie, where the code is deployed, not the source
folder). In my case this is the `dspace` user, which is probably also the
user you are running Tomcat as. The reason is that the cron jobs read and
write files, indexes, logs, etc to the DSpace installation directory so if
the jobs are running as a user without permissions there they will fail.

Hope that helps!

On Wed, May 12, 2021 at 5:07 PM Kerry Bouchard  wrote:

> After adding a parameter to the filter-media command in our dspace user
> crontab file and not seeing any difference, I realized that the tomcat user
> on our system also has a crontab file with identical entries. As far as I
> can tell, it's the tomcat crontab that is actually being used. Is there a
> reason for the dspace user to have a crontab file when tomcat does?
>
> Thanks, Kerry
>
> --
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>


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[dspace-tech] Re: Mapped item does not appear in collection

[Alan Orth]

Dear list,

After looking at this a few weeks later with fresh eyes I realized that the
item was private! One of my editors must have done that on accident. I
spent an hour or two debugging this in good faith, assuming it was a bug!
Argh... once I made the item public again I could see it in the mapped
collection.

Regards,

On Wed, Mar 31, 2021 at 9:24 AM Alan Orth  wrote:

> Dear dspace-tech,
>
> I have mapped an item from one collection to another in DSpace 6.3. By
> several accounts it seems the mapping was successful:
>
> - The item appears in the collection's list of mapped items on the
> collection's item mapper interface
> - The item view page correctly shows all collections the item is mapped to
> - The "collection" column in a CSV export of the item correctly shows all
> mapped collections
>
> Yet for some reason I don't see the item when I browse the newly mapped
> collection, nor does it appear in REST API. I have tried to clear the XMLUI
> cache, force a full Discovery re-index, etc, but the item still does not
> appear.
>
> Has anyone seen this before? Should I file a bug on Jira?
> --
> Alan Orth
> alan.o...@gmail.com
> https://picturingjordan.com
> https://englishbulgaria.net
> https://mjanja.ch
>


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Re: [dspace-tech] System Crash

[Alan Orth]

Dear Derrick,

That's a strange issue to happen after a crash. It could be that something
happened to your Solr. The actual items are in PostgreSQL, but the DSpace
user interface reads the metadata from an index in Solr because it's
faster. You could try to re-index your Discovery:

$ /path/to/bin/dspace index-discovery -b

Regards,

On Tue, Apr 27, 2021 at 10:43 AM walakira Jibril Derrick <
walakira.derrick...@gmail.com> wrote:

> It does start up. But the number of items reduced from 1000 to 537
>
> On Tue, 27 Apr 2021, 10:41 am Alan Orth,  wrote:
>
>> Dear Derrick,
>>
>> How did your system crash? What is the error now? Does DSpace start up?
>> We need more information to help you start getting the system back up.
>>
>> Cheers,
>>
>> On Tue, Apr 20, 2021 at 5:00 PM walakira Jibril Derrick <
>> walakira.derrick...@gmail.com> wrote:
>>
>>> Hello,
>>> Good after, this derrick Walakira from Uganda.
>>>
>>> Qn 1: We are using DSpace but we got a system crash and I have been
>>> tasked to find a way to get a system backup for our data and restore the
>>> old system.
>>>
>>>
>>> Thank you,
>>> dwalak...@umu.ac.ug
>>> walakira.derrick...@gmail.com
>>>
>>> --
>>> All messages to this mailing list should adhere to the Code of Conduct:
>>> https://duraspace.org/about/policies/code-of-conduct/
>>> ---
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>>> .
>>>
>>
>>
>> --
>> Alan Orth
>> alan.o...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>>
>

-- 
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Re: [dspace-tech] System Crash

[Alan Orth]

Dear Derrick,

How did your system crash? What is the error now? Does DSpace start up? We
need more information to help you start getting the system back up.

Cheers,

On Tue, Apr 20, 2021 at 5:00 PM walakira Jibril Derrick <
walakira.derrick...@gmail.com> wrote:

> Hello,
> Good after, this derrick Walakira from Uganda.
>
> Qn 1: We are using DSpace but we got a system crash and I have been tasked
> to find a way to get a system backup for our data and restore the old
> system.
>
>
> Thank you,
> dwalak...@umu.ac.ug
> walakira.derrick...@gmail.com
>
> --
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>


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Re: [dspace-tech] Import and Export-Collection specific metadata

[Alan Orth]

Dear Arunendra,

Unfortunately, I don't think it's possible to do either of those things.

Regards,

On Sat, Apr 24, 2021 at 12:48 PM ArunendraMB 
wrote:

> Any responses?
>
>
> *From,*
> *Arunendra MB.*
>
>
>
> On Fri, Apr 16, 2021 at 8:06 PM Projects Arunendra <
> project.arunen...@gmail.com> wrote:
>
>> While batch uploading if somebody unintentionally *import*s metadata of
>> one type of collection into another collection, having separate metadata,
>> can Dspace prevent that?
>>
>> Similarly, while *export*ing, how do I export collection with its own
>> metadata only and not other metadata fields that are not part of that
>> Collection?
>>
>> I am using DSpace 5.10 but I guess the question will apply to recent
>> versions also.
>>
>> --
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>>
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Re: [dspace-tech] Beginning a new solution

[Alan Orth]

Dear Mike,

Absolutely we will help you. Lots of people here love sharing their
experiences and war stories (myself included). First, I'd say you should be
targeting DSpace 6.3 or the as-of-yet unreleased DSpace 6.4. The DSpace
documentation has a list of required software that is a bit busy, but
helpful nonetheless:

https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace

At this point I'd recommend deploying DSpace 6.x on Linux with OpenJDK Java
8, Tomcat 8.5, and PostgreSQL 10. You should be pretty familiar with Linux
command line administration stuff. Otherwise, you could look to a hosted
DSpace provider (there's a list somewhere on the wiki).

Regards,

On Fri, Apr 23, 2021 at 5:33 PM Mountain Man 
wrote:

> Hello,
>
> Will someone be willing to share lessons learned with me, as I begin using
> DSpace for a new digital archive solution for a museum, in the US, in the
> Atlanta, GA area.  For an architecture and technical discussion.  Thank you.
>
> --  Mike
>
> --
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Re: [dspace-tech] Upload huge datasets > 1TB

[Alan Orth]

Dear Philipp,

That sounds painful! I don't know how to register the data directly at S3.
Perhaps you could just upload it to an S3 bucket and add a link in the
metadata rather than using some tight DSpace–S3 integration. At our
institute we upload the data somewhere else and make a metadata-only
accession to our DSpace repository, for example *The genome of
Caenorhabditis bovis*:

https://hdl.handle.net/10568/107367

The data for this publication is deposited in the European Nucleotide
Archive.

Regards,

On Thu, Apr 22, 2021 at 6:36 PM Philipp Rehs  wrote:

> Hello,
>
> we are planing to publish some data which is processed on our hpc
> system. The dataset are up to 100tb (already packed) and need to be
> stored and published with dspace.
>
> I know it is possible to upload the file to the filesystem and assign it
> to an item but this does not scale well with huge datasets.
>
> Is there any way to upload the data directly to S3 storage and assign
> the object later? without uploading to dspace first.
>
> Kind regards
>
>  Philipp Rehs
>
> ---
>
> Zentrum für Informations- und Medientechnologie
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>
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> 40225 Düsseldorf / Germany
> Tel: +49-211-81-15557
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Re: [dspace-tech] Highest level of Java supported by DSpace?

[Alan Orth]

Dear Michael,

I have a standard JAVA_OPTS in bin/dspace:

JAVA_OPTS="-Xmx256m -Dfile.encoding=UTF-8"

The mean run time of four runs of `dspace index-discovery -h` on my
development server is 13.9 seconds. :P I suppose it could be that we have
some Atmire custom modules in our DSpace 6 code base.

So your tests show that there is not much improvement to startup time in a
vanilla DSpace environment. The article and these JDK tests show that
differences can be significant:

https://cl4es.github.io/2020/12/06/Towards-OpenJDK-17.html#startup-fixed

Regards,

P.S. I enabled G1GC on our development server today. I am curious to see if
there is any difference in the JVM GC "chainsaw" pattern. I will look at
our JVM graphs in a few days...

On Mon, Apr 19, 2021 at 12:46 PM Michael Plate <
pl...@bibliothek.uni-kassel.de> wrote:

> Hi Alan,
>
> Am 19.04.21 um 09:59 schrieb Alan Orth:
> > Dear dspace-tech,
>
> can you please share your JAVA_OPTS from ~/bin/dspace ?
>
> >
> > As I wait eleven seconds (!) for my `dspace index-discovery -h` command
> > to complete, I saw this blog post¹ about newer Java versions last week
> > and found it compelling:
> >
>
> I made some tests on production and testing systems and it made a
> difference on the JAVA_OPTS.
>
> So these figures are from the standard JAVA_OPTS (JAVA_OPTS="-Xmx256m
> -Dfile.encoding=UTF-8"), approx. mean of 4 measures from the "real" time:
>
> # time ~/bin/dspace index-discovery -h
> ~ 2,3s - 3,5s production Java 8
> ~ 3,65s testing Java 8
> ~ 4,15s testing Java 11
>
> (testing is same system using Debian 10 and update-alternatives with
> Java 8 and Java 11).
>
> […]
> > Not to mention the improvements in garbage collection and of course new
> > language features. So I ask: what is the highest version of Java that
> > DSpace 6 and 7 officially supported? I recall seeing people running with
> > Java 9 at least...
>
> DSpace 5 (and 6 presumable, too) run on both Java 8 and Java 11 (with
> warnings, not tested in production), but at least DSpace 5 only compiles
> with Java 8.
>
> Michael
>
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> .
>


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[dspace-tech] Highest level of Java supported by DSpace?

[Alan Orth]

Dear dspace-tech,

As I wait eleven seconds (!) for my `dspace index-discovery -h` command to
complete, I saw this blog post¹ about newer Java versions last week and
found it compelling:

> Recent comparisons show that, since Java 8, the application startup time
has already almost halved (compared to the early builds of Java 16),
consistently progressing towards better performance.

Not to mention the improvements in garbage collection and of course new
language features. So I ask: what is the highest version of Java that
DSpace 6 and 7 officially supported? I recall seeing people running with
Java 9 at least...

Also, on a related note, is anyone using the G1GC garbage collection
introduced in Java 8? It was lore² for the longest time that you should not
use G1GC with Solr, but it has been a few years since I checked.

Regards,

¹ https://mikemybytes.com/2021/03/16/you-cant-afford-to-run-java-8/
² https://cwiki.apache.org/confluence/display/SOLR/ShawnHeisey
-- 
Alan Orth
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https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] informal survey regarding bitstream limits and sizes

[Alan Orth]

Hi Bill,

We primarily host open access PDFs, PowerPoints, and documents in an
institutional/academic research setting. We limit uploads to 30MB in our
nginx frontend. Part of open access is ensuring that people on
low-bandwidth or bandwidth-limited connections can download files easily,
without incurring fees, on spotty connections, etc. If an editor reaches
out to me I can temporarily increase the limit. We have 90,000 items in our
repository and this has worked well for us.

Pragmatically we have avoided offering support for large uploads to our
users because it increases administrative burden for me (sysadmin) and for
our organization (server size, backups, architecture complexity, etc). If a
project has produced a video we have them upload it to Vimeo, YouTube, etc
and then we add a link in the metadata. For any large file type you can
think of—video, genome sequences, data dump, etc—there is a platform that
is better suited than DSpace where you can upload it.

Regards!

On Thu, Apr 15, 2021 at 10:59 PM 'Bill Tantzen' via DSpace Technical
Support  wrote:

> Sorry for the duplication -- I originally sent this to dspace-community,
> but I it did not generate a great deal of discussion, so I thought I would
> take my chances here:
>
> If you have a minute, I am trying to get a feel for some of the larger
> (reasonable) bitstreams the community is currently supporting.  On my site,
> we have removed the DSpace upload limits to allow for records containing
> research data, but of course there are practical limits that dictate what
> makes for a good user experience.
>
> What is the largest bitstream you support?  Do you enforce upload limits?
> Assuming download speeds are faster than upload speeds, what are some of
> the methods in use (besides the DSpace gui) to get large files onto the
> server?  What are some alternatives to simple DSpace upload currently
> utilized -- like globus for instance?
>
> I realize the answer to these questions will always include "it
> depends...", but are these all questions you have had at your institution
> and how have you dealt with them?
>
> Thanks for any discussion you wish to contribute!
> ~~ Bill
>
> --
> Human wheels spin round and round
> While the clock keeps the pace... -- John Mellencamp
> 
> Bill TantzenUniversity of Minnesota Libraries
> 612-626-9949 (U of M)612-325-1777 (cell)
>
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[dspace-tech] Mapped item does not appear in collection

[Alan Orth]

Dear dspace-tech,

I have mapped an item from one collection to another in DSpace 6.3. By
several accounts it seems the mapping was successful:

- The item appears in the collection's list of mapped items on the
collection's item mapper interface
- The item view page correctly shows all collections the item is mapped to
- The "collection" column in a CSV export of the item correctly shows all
mapped collections

Yet for some reason I don't see the item when I browse the newly mapped
collection, nor does it appear in REST API. I have tried to clear the XMLUI
cache, force a full Discovery re-index, etc, but the item still does not
appear.

Has anyone seen this before? Should I file a bug on Jira?
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] DSpace 6.3 - hibernate - really slow performance.

[Alan Orth]

org.dspace.eperson.Group.supervisedItems#4491bccf-303c-439234325-897b-d8092d655fb3],
>>>>> was:
>>>>> [org.dspace.eperson.Group.supervisedItems#4491bccf-303c-43243295-897b-d8092d655fb3]
>>>>> (uninitialized)
>>>>> 2021-01-25 17:50:26,746 DEBUG
>>>>> org.hibernate.engine.internal.Collections @ Collection found:
>>>>> [org.dspace.content.DSpaceObject.handles#0d2abd2f-e192-4a8234322-9e49-11e2e0f05c18],
>>>>> was:
>>>>> [org.dspace.content.DSpaceObject.handles#0d2abd2f-e192-4a8234322-9e49-11e2e0f05c18]
>>>>> (uninitialized)
>>>>> 2021-01-25 17:50:26,746 DEBUG
>>>>> org.hibernate.engine.internal.Collections @ Collection found:
>>>>> [org.dspace.content.DSpaceObject.metadata#0d2abd2f-e192-4a243282-9e49-11e2e0f05c18],
>>>>> was:
>>>>> [org.dspace.content.DSpaceObject.metadata#0d2abd2f-e192-4a2342382-9e49-11e2e0f05c18]
>>>>> (uninitialized)
>>>>>
>>>>> The problem exist with:
>>>>> - Create collection when i check
>>>>>* The submission workflow will include an *accept/reject* step
>>>>>* The submission workflow will include an *accept/reject/edit
>>>>> metadata* step
>>>>>* *The submission workflow will include an edit metadata step*
>>>>> ***This collection will have delegated collection administrators
>>>>> The same, when i edditing  new collection first time
>>>>> (accept/reject/edit etc).
>>>>>
>>>>> It looks like problem with new mechanism "hibernate". Is posible to
>>>>> increase performance ? For example by modify (hibernate.cfg.xml) or
>>>>> something else?
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Karol
>>>>>
>>>>>
>>>>> Thanks,
>>>>>
>>>>> --
>>>>> All messages to this mailing list should adhere to the DuraSpace Code
>>>>> of Conduct: https://duraspace.org/about/policies/code-of-conduct/
>>>>> ---
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>>>>> Groups "DSpace Technical Support" group.
>>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>>> an email to dspace-tech...@googlegroups.com.
>>>>> To view this discussion on the web visit
>>>>> https://groups.google.com/d/msgid/dspace-tech/e3a93319-958e-41fa-a447-ddcf5cc8af5dn%40googlegroups.com
>>>>> <https://groups.google.com/d/msgid/dspace-tech/e3a93319-958e-41fa-a447-ddcf5cc8af5dn%40googlegroups.com?utm_medium=email_source=footer>
>>>>> .
>>>>>
>>>>
>>>>
>>>> --
>>>> Alan Orth
>>>> alan...@gmail.com
>>>> https://picturingjordan.com
>>>> https://englishbulgaria.net
>>>> https://mjanja.ch
>>>>
>>> --
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>>> ---
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>>>
>> To view this discussion on the web visit
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>>> .
>>>
>>
>>
>> --
>> Alan Orth
>> alan...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>>
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> .
>


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Re: [dspace-tech] DSpace 6.3 - hibernate - really slow performance.

[Alan Orth]

lem exist with:
>>> - Create collection when i check
>>>* The submission workflow will include an *accept/reject* step
>>>* The submission workflow will include an *accept/reject/edit
>>> metadata* step
>>>* *The submission workflow will include an edit metadata step*
>>> ***This collection will have delegated collection administrators
>>> The same, when i edditing  new collection first time (accept/reject/edit
>>> etc).
>>>
>>> It looks like problem with new mechanism "hibernate". Is posible to
>>> increase performance ? For example by modify (hibernate.cfg.xml) or
>>> something else?
>>>
>>> Thanks,
>>>
>>> Karol
>>>
>>>
>>> Thanks,
>>>
>>> --
>>> All messages to this mailing list should adhere to the DuraSpace Code of
>>> Conduct: https://duraspace.org/about/policies/code-of-conduct/
>>> ---
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>>> Groups "DSpace Technical Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to dspace-tech...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/dspace-tech/e3a93319-958e-41fa-a447-ddcf5cc8af5dn%40googlegroups.com
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>>> .
>>>
>>
>>
>> --
>> Alan Orth
>> alan...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>>
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> .
>


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Re: [dspace-tech] Language and facets

[Alan Orth]

Good morning,

1. The messages.properties file is only used for the JSPUI. If you are
using the XMLUI then you need to edit the messages.xml file. If you are
building from source code then this file lives in
dspace-xmlui/src/main/webapp/i18n/messages.xml. The recommended best
practice is to copy that file to the modules directory and modify it there:
dspace/modules/xmlui/src/main/webapp/i18n/messages.xml. You can include
other files there as well for other languages, like messages_ua.xml,
messages_de.xml, etc. If a key does not exist for a language then the
default will be used from messages.xml.

2. I don't know.

3. You need to add a bean for type to
dspace/config/spring/api/discovery.xml, for example:





dc.type







And then add searchFilterType to the list of search filters and facets
elsewhere in the file (look for sidebarFacets). After that you need to do a
`dspace index-discovery -b` to re-index Discovery.

Hope that helps,

On Fri, Jan 29, 2021 at 5:06 PM István Molnár 
wrote:

>
> I've started to use DSpace 6.3  a few months ago and there are still 3
> problems I cannot solve.
> 1. I use it on 3 different languages, and it changes, but when I change
> the messages.properties file, and rebuild the dspace it uses the same
> values and keys.
> 2. I would like to add document type to change with languages too, but I
> cannot.
> 3. I would like to add the type facet on the main screen, but when I try
> it, the system collapses.
>
> Please give me some help and instruction.
> Waiting forward for your answer:
> Molnár István
>
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Re: [dspace-tech] Updated Handle Server Init Script

[Alan Orth]

Hello,

We start the handle server using systemd. Create this file
/etc/systemd/system/dspace-handle-server.service:

[Unit]
Description=DSpace Handle Server
# Only run if the DSpace Handle server is configured on this host
ConditionDirectoryNotEmpty=/dspace/handle-server

[Service]
Type=forking
User=tomcat7
ExecStart=/dspace/bin/start-handle-server

[Install]
WantedBy=multi-user.target

Then enable it with `systemctl enable dspace-handle-server.service` and it
will start up at boot. It doesn't do any restarting or reloading. Never
needed such things...

Regards,

On Fri, Jan 29, 2021 at 5:46 PM Ray W  wrote:

> Hi Sean,
>
> Thank you so very much for sending a copy of your init script. With your
> help, right now we are making modifications to our own script to move
> forward with our issue. Our institution uses JSPUI 6.3 at the moment and I
> am more than happy to answer questions in future if you need assistance
> debugging.
>
> Thank you and Take Care,
> Rachel
>
> On Friday, January 29, 2021 at 1:40:11 AM UTC-5 sean@gmail.com wrote:
>
>> Please find the init script that we use attached.
>>
>> On Thu, 28 Jan 2021 at 18:12, Ray W  wrote:
>>
>>> Hi Everyone,
>>>
>>> Hope you're all safe and well, I'm reaching out to ask if anyone is
>>> willing to share their handle server init scripts or point me to some newer
>>> resources. I found this conversation that links to a wiki which
>>> unfortunately has not been updated.
>>>
>>> We have had some issues with our handle server and we believe the root
>>> cause is our startup script, hoping to see if anyone has one we can compare
>>> against to troubleshoot our issues.
>>>
>>> https://groups.google.com/g/dspace-tech/c/O2joqROdx5A/m/wA7fQpjzBgAJ
>>>
>>> https://wiki.duraspace.org/display/DSPACE/Handle+Service+Startup+Scripts+for+Unix+or+Linux
>>>
>>> Thank you and Take Care,
>>> Rachel
>>>
>>> --
>>> All messages to this mailing list should adhere to the DuraSpace Code of
>>> Conduct: https://duraspace.org/about/policies/code-of-conduct/
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>>> .
>>>
>> --
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>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Re: Error in DSpace 6.3 "Export Search Metadata"

[Alan Orth]

Dear list, I have filed DS-4566 for this issue.

After a bit of digging I realized that the issue here is that DSpace
incorrectly escapes search filter parameters in the query string using a
backslash (\). Tomcat 7.0.107 (at least) returns an HTTP 400 due to invalid
characters in the URL. For example, if I try to search for author
containing "Alan Orth", the resulting "export search metadata" link causes
this error in Tomcat:

Jan 26, 2021 10:47:23 AM org.apache.coyote.http11.AbstractHttp11Processor
process
INFO: Error parsing HTTP request header
 Note: further occurrences of HTTP request parsing errors will be logged at
DEBUG level.
java.lang.IllegalArgumentException: Invalid character found in the request
target
[/discover/search/csv?query=*=~=author:(Alan\%20Orth)]. The
valid characters are defined in RFC 7230 and RFC 3986
at
org.apache.coyote.http11.InternalInputBuffer.parseRequestLine(InternalInputBuffer.java:213)
at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1108)
at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:654)
at
org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:317)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)

The string is already URL encoded so there is no need to add a backslash.
For some reason the query works on demo.dspace.org, though it should not. I
suspect that Tomcat has been configured to allow "\" in query parameters
using the relaxedQueryChars option.

Regards,

See: https://jira.lyrasis.org/browse/DS-4566. Note that I accidentally hit
Enter before I was done with the report and there is no edit function. :\

On Sun, Oct 18, 2020 at 3:11 PM Alan Orth  wrote:

> Dear DSpace community,
>
> I'm trying to test the "Export Search Metadata" feature of DSpace 6. I
> search my repository for authors containing a name like "Orth, Alan" where
> there are 22 results. When I try to export the results from the Context →
> Export Search Metadata link I see a blank page with an HTTP 400 in the
> browser's network console. The resulting URL is:
>
>
> http://localhost:8080/discover/search/csv?query=*=~=author:(Orth,\
> Alan)
>
> If I search for "Orth" instead then I do get a CSV. For what it's worth I
> see the same issue on demo.dspace.org when I search for "Lewis, Stuart":
>
>
> http://demo.dspace.org/xmlui/discover?filtertype_1=author_relational_operator_1=contains_1=Lewis%2C+Stuart_apply_filter===%2F
>
> The export works if I search for "Lewis" instead (note that you have to be
> logged in as a site admin to see the export link).
>
> Is this a known issue? Should I file one?
> --
> Alan Orth
> alan.o...@gmail.com
> https://picturingjordan.com
> https://englishbulgaria.net
> https://mjanja.ch
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Setting up a Postgres JDBC JNDI connection in Tomcat

[Alan Orth]

Dear Hrafn,

Actually, ironically, in the very same docs I linked above it specifically
states that adding a context in [appname]/META-INF/context.xml is allowed.
I hadn't heard of that method before! If it's not working for you that
sounds like a bug. In my opinion the [engine]/localhost/[appname].xml
method is better because I deploy the infrastructure using some templates
and I can pre-create those without having to build/install DSpace yet.
Anyways, I'm glad you solved it. All of this is relevant for your
discussion about documentation and pooling support in
https://github.com/DSpace/DSpace/issues/3070. I will try to contribute
there.

Regards,

P.S. for anyone reading this, Tomcat 8.0 has been deprecated for several
years now. It has been replaced by 8.5 and you should try to run that one
(or higher) if possible, unless your distribution provides an 8.0 package
that they maintain.

On Sat, Dec 5, 2020 at 7:10 PM Hrafn Malmquist 
wrote:

> Hi Alan
>
> Thanks for getting back to me. Yes, I resolved this by placing the context
> in an [appname].xml under the [engine] directory. I'm not sure if
> [appname]/META-INF/context.xml is allowed. The docs seem to suggest it's
> dependant on whether or not auto-deployment of applications is enabled
> (see: https://tomcat.apache.org/tomcat-8.0-doc/config/context.html).
>
> Anywho, I got it right finally.
>
> On a related note, if you or anyone else reading this, find the time to
> contribute to https://github.com/DSpace/DSpace/issues/3070 that would be
> great.
>
> Cheers, Hrafn
>
> On Wed, Dec 2, 2020 at 9:07 AM Alan Orth  wrote:
>
>> Dear Hrafn,
>>
>> You mention creating a context inside the webapp's META-INF directory. Is
>> that a valid Tomcat configuration? I only know about creating contexts in
>> Tomcat's server.xml (not recommended, according to Tomcat's docs¹) and in
>> the Tomcat conf.Catalina/[hostname] directory. Our DSpace instances use
>> Tomcat from the official binary releases rather than from our Linux
>> distribution, and I create the following, for example:
>>
>> # ls /usr/local/apache-tomcat-7.0.104/conf/Catalina/localhost/
>> jspui.xml  oai.xml  rest.xml  ROOT.xml  solr.xml
>>
>> Where each context looks something like this:
>>
>> # cat /usr/local/apache-tomcat-7.0.104/conf/Catalina/localhost/ROOT.xml
>> 
>>   > type="javax.sql.DataSource"/>
>> 
>>
>> The conf/Catalina/localhost directory doesn't exist in the binary Tomcat
>> distributions. I can't remember if conf/Catalina exists in the
>> CentOS/Ubuntu distribution. I hope that helps.
>>
>> Regards,
>>
>> ¹ https://tomcat.apache.org/tomcat-8.5-doc/config/context.html
>>
>>
>> On Mon, Nov 30, 2020 at 6:01 PM Hrafn Malmquist <
>> hrafn.malmqu...@gmail.com> wrote:
>>
>>> I am trying to set up a Postgres JNDI globally shared connection is
>>> running running several DSpace webapps.
>>>
>>> I have been largely assisted by the official documentation here [0] and
>>> here [1] as well as DSpace documentation here [2] and discussion on a user
>>> mailing list for DSpace here [3].
>>>
>>> I am running:
>>>
>>> CentOS Linux release 7.8.2003
>>> Tomcat 9.0.12
>>> PostgreSQL 9.5.23
>>> openjdk version "1.8.0_262"
>>> OpenJDK Runtime Environment (build 1.8.0_262-b10)
>>>
>>>
>>>1.  I downloaded postgresql-42.2.18.jar from
>>>https://jdbc.postgresql.org/download/postgresql-42.2.18.jar and
>>>placed it in /home/lib/dspace/apache-tomcat-9.0.12/lib
>>>2. In /home/lib/dspace/apache-tomcat-9.0.12/conf/server.xml I added
>>>the following Resource
>>>
>>>>>  factory="org.apache.tomcat.jdbc.pool.DataSourceFactory"
>>>  type="javax.sql.DataSource"
>>>  auth="Container"
>>>  username="*"
>>>  password="**"
>>>  driverClassName="org.postgresql.Driver"
>>>  url="jdbc:postgresql://localhost:5432/dspace"
>>>  initialSize="5"
>>>  maxTotal="50"
>>>  maxIdle="15"
>>>  minIdle="5" />
>>>
>>>There are a couple of issues that confuse me:
>>>a) the official documentation about JNDI datasource examples [0]
>>>says "*This author has not had success here, although others have
>>>

Re: [dspace-tech] Setting up a Postgres JDBC JNDI connection in Tomcat

[Alan Orth]

echnical Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dspace-tech/738f0710-f9a9-41ce-bb42-974bddff1a06n%40googlegroups.com
> <https://groups.google.com/d/msgid/dspace-tech/738f0710-f9a9-41ce-bb42-974bddff1a06n%40googlegroups.com?utm_medium=email_source=footer>
> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Re: DSpace 6 Hibernate exacerbating "idle in transaction" locking issues

[Alan Orth]

Update on this for posterity:

After a few days the connections and locks have gone down and we are now
able to submit items again. I have no clue what caused this "transaction
storm". See attached graphs from our monitoring now that it's ~1 week
later. Hoping someone else can comment on their DSpace 5 → 6 upgrade
experience with special consideration to the database configuration!

Regards,

On Wed, Nov 18, 2020 at 11:30 AM Alan Orth  wrote:

> Dear list,
>
> We upgraded from DSpace 5.8 to 6.3 a few days ago and the database load
> went up significantly. Users report very long wait times and timeouts
> during item submission, taking items from the workflow, and approving
> items. You can see in the attached graph that we have a large number of
> connections waiting for locks.
>
> When I look at the PostgreSQL status I see over 2,000 locks:
>
> $ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON
> pl.pid = psa.pid;' | wc -l
> 2071
>
> Looking at the locks I see at least half of them "idle in transaction"
> with the query being some SELECT statement. Why is Hibernate BEGINing
> transactions and not committing or rolling them back before returning them
> to the pool?
>
> We are using DSpace 6.3 on Tomcat 7.0.104 with Tomcat's JDBC connection
> pool provided via JNDI.
>
> Any help or pointers would be appreciated. Our editors can barely work
> now...
> --
> Alan Orth
> alan.o...@gmail.com
> https://picturingjordan.com
> https://englishbulgaria.net
> https://mjanja.ch
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] DSpace 6 Hibernate exacerbating "idle in transaction" locking issues

[Alan Orth]

Dear list,

We upgraded from DSpace 5.8 to 6.3 a few days ago and the database load
went up significantly. Users report very long wait times and timeouts
during item submission, taking items from the workflow, and approving
items. You can see in the attached graph that we have a large number of
connections waiting for locks.

When I look at the PostgreSQL status I see over 2,000 locks:

$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON
pl.pid = psa.pid;' | wc -l
2071

Looking at the locks I see at least half of them "idle in transaction" with
the query being some SELECT statement. Why is Hibernate BEGINing
transactions and not committing or rolling them back before returning them
to the pool?

We are using DSpace 6.3 on Tomcat 7.0.104 with Tomcat's JDBC connection
pool provided via JNDI.

Any help or pointers would be appreciated. Our editors can barely work
now...
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] DSpace 5.x on Ubuntu 20.04 and Tomcat 9

[Alan Orth]

Dear Agustina,

I looked in the DSpace Jira briefly and found these two issues:

- Failure to set dspace.current.user.id session cookie under Tomcat 8.5.x:
https://jira.lyrasis.org/browse/DS-4140
- Stop relying on alphabetical loading of jars in WEB-INF/lib:
https://jira.lyrasis.org/browse/DS-2437
- DSpace 6.3 REST-API fail to start on ubuntu 18.04 LTS's tomcat8:
https://jira.lyrasis.org/browse/DS-4160
- Meta issue tracking various Tomcat 8 issues:
https://jira.lyrasis.org/browse/DS-3092

Some of these are unresolved and some people report they are running on
Tomcat 8. I'm surprised to hear that! Good news if so... we need to move
with the ecosystem.

Regards,

On Tue, Nov 17, 2020 at 12:27 PM amgc...@gmail.com 
wrote:

> Hi Alan, Paul,
>
> Many thanks for the information. Alan, do you have examples of issues
> people reported / you've experienced?
>
> We've had DSpace 5.10 running on a test environment with Tomcat 9 and have
> been testing and haven't experienced any issue so far.
>
> Best and many thanks!
> Agustina
>
> On Monday, 16 November 2020 at 13:59:38 UTC alan...@gmail.com wrote:
>
>> Hi Agustina,
>>
>> Yes I suspect you will run into some problems. There were many issues
>> with DSpace 5.x on Tomcat versions beyond 7. As of DSpace 6 you can use
>> Tomcat 8.5, but I haven't heard of anyone using Tomcat 9. For what it's
>> worth, we are running Tomcat 7 on Ubuntu 18.04 via a binary distribution
>> from Apache's website (https://tomcat.apache.org/). I deploy the Tomcat
>> tarball into /usr/local and run it from there. This method works on any
>> Linux distribution. I created systemd service units that run Tomcat and it
>> all works really well actually, and I'm running the latest stable Tomcat 7.
>> I can share more tips and configs if you'd like.
>>
>> Regards,
>>
>> On Mon, Nov 16, 2020 at 11:35 AM amgc...@gmail.com 
>> wrote:
>>
>>> Dear all,
>>>
>>> We are upgrading our DSpace VMs to Ubuntu 20.04 and discovered that
>>> Tomcat 8 is no longer available in the repositories, only from Tomcat 9.x.
>>>
>>> Is anyone currently running DSpace 5.10 in Ubuntu 20.04 on Tomcat 9? It
>>> would be useful to know whether it is working OK for you or you've
>>> encountered any issues.
>>>
>>> Thanks a lot!
>>> Agustina
>>>
>>> --
>>> All messages to this mailing list should adhere to the DuraSpace Code of
>>> Conduct: https://duraspace.org/about/policies/code-of-conduct/
>>> ---
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>>> Groups "DSpace Technical Support" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to dspace-tech...@googlegroups.com.
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>>> https://groups.google.com/d/msgid/dspace-tech/94236c9f-de15-4de1-84e3-1d3b335be91cn%40googlegroups.com
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>>> .
>>>
>>
>>
>> --
>> Alan Orth
>> alan...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>>
> --
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> Conduct: https://duraspace.org/about/policies/code-of-conduct/
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] DSpace 5.x on Ubuntu 20.04 and Tomcat 9

[Alan Orth]

Hi Agustina,

Yes I suspect you will run into some problems. There were many issues with
DSpace 5.x on Tomcat versions beyond 7. As of DSpace 6 you can use Tomcat
8.5, but I haven't heard of anyone using Tomcat 9. For what it's worth, we
are running Tomcat 7 on Ubuntu 18.04 via a binary distribution from
Apache's website (https://tomcat.apache.org/). I deploy the Tomcat tarball
into /usr/local and run it from there. This method works on any Linux
distribution. I created systemd service units that run Tomcat and it all
works really well actually, and I'm running the latest stable Tomcat 7. I
can share more tips and configs if you'd like.

Regards,

On Mon, Nov 16, 2020 at 11:35 AM amgc...@gmail.com 
wrote:

> Dear all,
>
> We are upgrading our DSpace VMs to Ubuntu 20.04 and discovered that Tomcat
> 8 is no longer available in the repositories, only from Tomcat 9.x.
>
> Is anyone currently running DSpace 5.10 in Ubuntu 20.04 on Tomcat 9? It
> would be useful to know whether it is working OK for you or you've
> encountered any issues.
>
> Thanks a lot!
> Agustina
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
> ---
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> "DSpace Technical Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Re: Item Submission Upload step taking longer time to respond

[Alan Orth]

Dear list,

We upgraded from DSpace 5.8 to 6.3 yesterday and now our PostgreSQL
connections and locks have skyrocketed. I have a bunch of editors emailing
me that they can't edit or approve items in their workflows. Attaching
Munin usage graphs for PostgreSQL where you can obviously see the issue
beginning after the upgrade yesterday.

I have 1,344 locks currently, and the number keeps going up...

$ psql -c 'SELECT * FROM pg_locks pl LEFT JOIN pg_stat_activity psa ON
pl.pid = psa.pid;' | wc -l
1344

What are people doing about this? Are there any commits we can cherry-pick
from the upcoming DSpace 6.4? Should I file an issue? We are using
PostgreSQL 10.15. Any help or comments appreciated.

Thanks again,

On Wed, Oct 28, 2020 at 4:46 PM ayukap...@gmail.com 
wrote:

> Hi everyone,
> This problem of a very slow upload step is very collection specific. The
> collection has ~150 items in the workflow and ~4000 archived items.
> I would appreciate any help.
>
> This specific query to update/select metadata value is very slow both in
> PostgreSQL 12 and PostgreSQL 9.6 -  DSpace 6.3 tomcat 8
>
> * select metadata0_.dspace_object_id as dspace_o7_12_3_,
> metadata0_.metadata_value_id as metadata1_27_3_,
> metadata0_.metadata_value_id as metadata1_27_2_, metadata0_.authority as
> authorit2_27_2_, metadata0_.confidence as confiden3_27_2_,
> metadata0_.dspace_object_id as dspace_o7_27_2_, metadata0_.text_lang as
> text_lan4_27_2_, metadata0_.metadata_field_id as metadata8_27_2_,
> metadata0_.place as place5_27_2_, metadata0_.text_value as text_val6_27_2_,
> metadatafi1_.metadata_field_id as metadata1_25_0_, metadatafi1_.element as
> element2_25_0_, metadatafi1_.metadata_schema_id as metadata5_25_0_,
> metadatafi1_.qualifier as qualifie3_25_0_, metadatafi1_.scope_note as
> scope_no4_25_0_, metadatasc2_.metadata_schema_id as metadata1_26_1_,
> metadatasc2_.short_id as short_id2_26_1_, metadatasc2_.namespace as
> namespac3_26_1_ from public.metadatavalue metadata0_ left outer join
> public.metadatafieldregistry metadatafi1_ on
> metadata0_.metadata_field_id=metadatafi1_.metadata_field_id left outer join
> public.metadataschemaregistry met*
>
> On Wednesday, 21 October 2020 at 09:25:24 UTC+3 ayukap...@gmail.com wrote:
>
>> A quick update on this matter.  I have noticed that we are having more
>> than *100 table locks* just for one submission (no other user using the
>> system). And this slows down the transition from the access step to the
>> upload step by up to a minute or two.
>> Is this how it should work ? Any help with this is highly appreciated.
>>
>> [image: database_locks (2).PNG]
>> On Wednesday, 7 October 2020 at 06:02:55 UTC+3 ayukap...@gmail.com wrote:
>>
>>> Our item submission has been working fine until just a few days when the
>>> upload step would take *up to a minute or more* to load.
>>> It seems I cant figure out where the problem is as the server resources
>>> are still very adequate and all other steps are working ok.
>>> File upload also takes way longer than normal to load.
>>> Has anyone encountered this problem before?
>>>
>>>
>>> --
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-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Using secure LDAP without a certificate

[Alan Orth]

Hi Sean,

I'm using LDAPS on both DSpace 5.8 and 6.3. For DSpace 5 I have the
following in my sitename.properties:

ldap.provider_url = ldaps://blahblah.org:636/

For DSpace 6 I have this in my local.cfg:

authentication-ldap.provider_url = ldaps://blahblah.org:636/

I have not configured any STARTTLS parameters in DSpace or the system's
ldap.conf. We are using Ubuntu 18.04.

Regards,

On Thu, Nov 12, 2020 at 9:34 AM Sean Carte  wrote:

> I'm trying to configure DSpace-CRIS 5.10 and DSpace 6.3 to use ldaps, but
> get this error in the log:
>
> 2020-11-11 15:05:03,464 WARN  org.dspace.authenticate.LDAPAuthentication @
> anonymous:session_id=F261C03287498D5AEE67FFE7F53CBCAF:ip_addr=10.0.36.134:ldap_authentication:type=failed_auth
> javax.naming.CommunicationException\colon; simple bind failed\colon;
> \colon;636 [Root exception is
> javax.net.ssl.SSLHandshakeException\colon; PKIX path building failed\colon;
> sun.security.provider.certpath.SunCertPathBuilderException\colon; unable to
> find valid certification path to requested target]
>
> LDAP authentication is working without SSL. All I've changed in the
> configuration is ldap -> ldaps in the provider_url property.
>
> On the DSpace 6.3 server I've also tried:
> authentication-ldap.starttls=true
> while leaving the scheme at ldap
>
> That results in the following error:
>
> 2020-11-12 09:06:32,112 WARN  org.dspace.authenticate.LDAPAuthentication @
> anonymous:session_id=0BD2A90CE7458F21149D8505D76D7E78:ip_addr=10.0.36.134:ldap_authentication:type=failed_auth
> javax.net.ssl.SSLHandshakeException\colon; PKIX path building failed\colon;
> sun.security.provider.certpath.SunCertPathBuilderException\colon; unable to
> find valid certification path to requested target
>
> I also tried using ldapsearch and found that that fails on ldaps with the
> error 'TLS: peer cert untrusted or revoked (0x142)' unless I add the
> following line to /etc/ldap/ldap.conf:
>
> TLS_REQCERT NEVER
>
> That setting in ldap.conf doesn't seem to have any effect on DSpace; is
> there a way of telling DSpace to not expect a server certificate? Or is
> there a better way to get secure LDAP working?
>
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>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Error in DSpace 6.3 "Export Search Metadata"

[Alan Orth]

Dear DSpace community,

I'm trying to test the "Export Search Metadata" feature of DSpace 6. I
search my repository for authors containing a name like "Orth, Alan" where
there are 22 results. When I try to export the results from the Context →
Export Search Metadata link I see a blank page with an HTTP 400 in the
browser's network console. The resulting URL is:

http://localhost:8080/discover/search/csv?query=*=~=author:(Orth,\
Alan)

If I search for "Orth" instead then I do get a CSV. For what it's worth I
see the same issue on demo.dspace.org when I search for "Lewis, Stuart":

http://demo.dspace.org/xmlui/discover?filtertype_1=author_relational_operator_1=contains_1=Lewis%2C+Stuart_apply_filter===%2F

The export works if I search for "Lewis" instead (note that you have to be
logged in as a site admin to see the export link).

Is this a known issue? Should I file one?
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Curation tasks in DSpace 5 vs DSpace 6

[Alan Orth]

Dear list,

I've implemented a curation task to read country names from item metadata
and add new metadata fields with appropriate ISO 3166-1 Alpha2 codes if
they don't already exist. On DSpace 5 the task finishes in an hour or
sometimes two, but on DSpace 6 it runs for twelve hours and I end up
killing it. As far as I can tell I ported the DSpace 5 version¹ to DSpace 6
faithfully², though I'm wondering if I missed something with regards to
caching, as that seems to have been removed (or internalized) with the
service API / Hibernate overhaul. I would be grateful if someone could take
a look.

Another thing I note is that when I do "-i all" to process all items in the
repository the curation task will curate each item multiple times, one for
each collection it is mapped to. Our repository has ~90,000 items and in
our case that results in reprocessing ~25,000 items(!). Would it be better
to write a standalone Java utility for this rather than using the curation
interface?

Thank you,

¹
https://github.com/ilri/cgspace-java-helpers/blob/dspace5/src/main/java/io/github/ilri/cgspace/ctasks/CountryCodeTagger.java
²
https://github.com/ilri/cgspace-java-helpers/blob/dspace6/src/main/java/io/github/ilri/cgspace/ctasks/CountryCodeTagger.java

-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Re: Backup issues due to assetstore size

[Alan Orth]

Dear Michael,

Your assetstore doesn't seem unpractically large to me. We have ~90,000
items in our DSpace repository and our assetstore looks like this:

# du -sh /home/dspace/assetstore/
76G /home/dspace/assetstore/
# find /home/dspace/assetstore/ -type f | wc -l
143062

We do a simple `s3cmd sync` to Amazon S3 every night and have never, ever
had an issue in ten years. I regularly rsync our production assetstore to
dev and it's super fast... The overwhelming majority of your assetstore
won't change every day so backups should only copy new files and those that
have changed. If your colleagues are doing file-level backups it should be
trivial to only sync what has changed...? BTW even rsync can be
parallelized¹ with a little bit of shell scripting.

Regards,

¹ https://mjanja.ch/2014/07/parallelizing-rsync/

On Thu, Aug 13, 2020 at 10:46 AM Michael White 
wrote:

> Hi,
>
> I just want to thank folk for the replies and discussion around this issue
> - I will pass all this on to my network colleague and hopefully it will
> give him some food for thought and a way forwards.
>
> Cheers,
>
> Mike
>
> On Tuesday, August 11, 2020 at 2:34:52 PM UTC+1, Michael White wrote:
>>
>> Hi,
>>
>>
>>
>> Our DSpace instance has been steadily growing over the years and now has
>> over 18,000 records, all with one or more full text files attached (taking
>> up around 106GB of disk space). We are on DSpace 6.2 and currently only
>> have one assetstore configured.
>>
>>
>>
>> Whilst we have no issues with dspace operation/performance, my System and
>> Network colleagues are reporting problems when their scheduled backup jobs
>> of the DSpace server are trying to run as they are timing out, which they
>> suspect is due to the large number of files on the server.
>>
>>
>>
>> To resolve this, they have asked me about the possibility of splitting
>> the current dspace filesystem in to a number of smaller filesystems (which
>> they can then back up in parallel, reducing the overall time to back up the
>> dspace server).
>>
>>
>>
>> To that end they have asked about the possibility of splitting the
>> assetstore in to a number of filesystems and creating softlinks to these
>> from the assetstore - e.g. adding 9 new filesystems for clusters of 10
>> assetstore subdirectories - i.e.:
>>
>>
>>
>> .../dspace/assetstore/10 -> .../assetstores10-19/10
>>
>> .../dspace/assetstore/11 -> .../assetstores10-19/11
>>
>> .../dspace/assetstore/12 -> .../assetstores10-19/12
>>
>>  ...
>>
>> .../dspace/assetstore/20 -> ../assetstores20-29/20
>>
>>
>>
>> Has anyone ever done anything like this? Any reasons why that wouldn't
>> work?
>>
>>
>>
>> I can, of course, add another assetstore alongside the existing one, but
>> my understanding is that this would only be used going forwards, and so
>> wouldn't address the large number of files in the current assetstore -
>> unless there is a way to then distribute the existing assetstore across a
>> number of smaller assetstores?
>>
>>
>>
>> Has anyone else in the community had issues like this? And, if so, any
>> (other) suggestions on how best to address the problem?
>>
>>
>>
>> Cheers,
>>
>>
>>
>> Mike
>>
>>
>>
>>
>> *Michael White Senior Developer*
>>
>>
>> *Business Applications and Integrations Information Services*
>>
>>
>> 4B19, Cottrell
>>
>> University of Stirling
>> Stirling
>> FK9 4LA
>>
>> Tel:  +44 (0)1786 466877
>> Email:  michael.wh...@stir.ac.uk
>> Web: stir.ac.uk/informationservices
>> <http://www.stir.ac.uk/informationservices>
>>
>> <https://www.facebook.com/stirlinglibrary/>
>> <https://twitter.com/isstirling> <https://www.instagram.com/isstirling/>
>> <https://www.youtube.com/user/infoservicesatstir>
>>
>> [image: Banner] <https://www.stir.ac.uk/>
>>
>>
>>
>>
>> --
>> The University achieved an overall 5 stars in the QS World University
>> Rankings 2020
>> UK Sports University of the Year 2020 (Times Higher Good University Guide)
>> The University of Stirling is a charity registered in Scotland, number SC
>> 011159.
>>
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Re: [dspace-tech] cronjobs for 6.3 in discovery

[Alan Orth]

Dear Jose,

The second cron job is not needed because upstream Solr deprecated the
misleading "optimize" function. There's a note on the wiki somewhere with a
link to the upstream bug report, but I'm on mobile now and can't find it.

Cheers,

On Mon, Jul 20, 2020, 23:12 Jose Blanco  wrote:

> For 6.3, I think I just have to have these two commands run as part of my
> cron jobs, right?
>
> #ensures that any deleted documents are cleaned from the Discovery
> search/browse index
> [rep]/bin/dspace index-discovery
>
> #ensures that the Discovery Solr Index is re-optimized for better
> performance
> [rep]/bin/dspace index-discovery -o
>
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> 
> .
>

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Re: [dspace-tech] Thumbnails error

[Alan Orth]

Original poster is using Windows. Recursively change the permissions of the
assetstore to your Windows user and try filter-media again.

Regards,

On Fri, Jul 31, 2020, 17:25 Mark H. Wood  wrote:

> On Tue, Jul 28, 2020 at 01:57:39PM -0700, stefanabr...@gmail.com wrote:
> > Thanks for your response, Mark. Do you know if how to check/update
> > assetstore permissions is documented anywhere?
>
> I can't think of any place where this is documented, but it's really
> simple:  everything in and below [dspace]/assetstore (and any
> additional assetstores that you may have) should be owned by the user
> that runs Tomcat and should grant read/write permission to that user.
>
> I ran a quick experiment on a test instance of DSpace.  On this system
> Tomcat is run by the user 'tomcat'.  I am using GNU 'find'.  This
> command should list all files in 'assetstore' NOT owned by the user
> 'tomcat', *provided* that your current directory is the [dspace]
> directory and the assetstore is a subdirectory named "assetstore":
>
>   find assetstore -not -user tomcat
>
> This command should list all files under 'assetstore' that are not
> read/write for the owner, regardless of other permissions:
>
>   find assetstore -not -perm -600
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
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> .
>

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[dspace-tech] Re: Erroneous, duplicate item mappings

[Alan Orth]

Dear list,

Duplicate mappings continue to be a minor annoyance for us. It was brought
to my attention by someone consuming our content via the REST API that
items with duplicate mappings behave strangely in the REST API:

$ http 'http://localhost:8080/rest/collections/1445' | json_pp | grep
numberItems
   "numberItems" : 63,
$ http 'http://localhost:8080/rest/collections/1445/items' jq '. | length'
61

In this case the collection had two items that were mapped twice. So
my question is this: is there any legitimate reason to allow duplicate
mappings? I'm thinking of trying to write a curation task or database
query to programmatically find and fix these... should I create a
GitHub issue for this?

Regards,

On Tue, Jan 10, 2017 at 3:54 PM Alan Orth  wrote:

> Hello,
>
> I found an older thread (by Shaun Donovan, 2014) on the list discussing
> this issue and he offered some SQL commands for exploring the mappings of
> an item:
>
> dspace=# select * from collection2item where item_id = '80596';
>
> Using that, I removed all mappings except the legitimate ones:
>
> dspace=# delete from collection2item where item_id = '80596' and id
> not in (90792, 90806, 90807);
>
> After refreshing the item view for the particular item I now see only the
> three correct mappings remaining. Is this solution sufficient, or are there
> some other relationships I should take care of in the database?
>
> Thank you,
>
> On Tue, Jan 10, 2017 at 3:19 PM Alan Orth  wrote:
>
>> Hello,
>>
>> I tried to remedy this by exporting the item's metadata as CSV, deleting
>> the duplicate mappings in the file, and re-importing, but DSpace says that
>> "no changes were detected". Does anyone have any ideas about this?
>>
>> Thanks,
>>
>> On Mon, Jan 9, 2017 at 6:17 PM Alan Orth  wrote:
>>
>>> Hello,
>>>
>>> Has anyone ever had issues with duplicate item mappings? We have an item
>>> that has been mapped to the same collection 184 times (really). I doubt the
>>> editor did this on purpose!
>>>
>>> We are running DSpace 5.5 with XMLUI on PostgreSQL 9.5.
>>>
>>> Thanks,
>>> [image: Screen Shot 2017-01-09 at 17.59.32-fs8.png]
>>> --
>>>
>>> Alan Orth
>>> alan.o...@gmail.com
>>> https://englishbulgaria.net
>>> https://alaninkenya.org
>>> https://mjanja.ch
>>>
>> --
>>
>> Alan Orth
>> alan.o...@gmail.com
>> https://englishbulgaria.net
>> https://alaninkenya.org
>> https://mjanja.ch
>>
> --
>
> Alan Orth
> alan.o...@gmail.com
> https://englishbulgaria.net
> https://alaninkenya.org
> https://mjanja.ch
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Timeout waiting for idle object Dspace 4.1

[Alan Orth]

Dear Euler,

Yes the iplists are long gone. In fact that should even be removed from the
next 5.x and 6.x point releases. You can still update your spider *agent*
lists though. Just download the one I linked, or generate one from here:

https://github.com/atmire/COUNTER-Robots

That will at least cause bot user agents to not get logged in Solr. Last
year I removed 75 million (yes million) hits from our Solr statistics core
by feeding this user agent list into a script I wrote:

https://github.com/ilri/DSpace/blob/5_x-prod/check-spider-hits.sh

Neither of those things will help with load directly, but will massively
reduce memory and disk requirements. I cringe to think of how poorly
configured most DSpace instances are.

The thing to remember with the default connection pool settings is that
they are *per application*, meaning that XMLUI, REST, OAI, and any other
application all use those settings to create their own pools! It is really
worth looking into configuring a global pool with Tomcat JDBC.

BTW another thing I can recommend: block any request without a user agent!

Regards,

On Thu, Jul 9, 2020, 15:58 euler  wrote:

> Dear Alan,
>
> Many thanks for your prompt response. Today, before I wrote my response to
> you, I restarted my Tomcat many times because of the "Cannot get a
> connection, pool error Timeout waiting for idle object" issue. I updated my
> Tomcat's crawler session manager valve based from your response here.
> Unfortunately, I cannot apply some of the methods you used because we are
> using Apache 2.4 in front of Tomcat and I don't know how to translate your
> Nginx configuration into Apache configuration. I also discovered that when
> I run 'dspace stats-util -u' to update the spider files, it resulted
> in java.lang.NullPointerException because the site iplists.com has been
> suspended.
>
> I also modified the connection parameters by increasing the
> db.maxconnections, db.maxwait, and db.maxidle as suggested by Bram in the
> DCAT meeting that I mentioned earlier. I hope this would at least stabilize
> our repository for now.
>
> Many thanks again, the methods you posted here is very valuable not only
> to me but also for others that may be experiencing the same issues with
> these crawlers.
>
> Best regards,
> Euler
>
> On Thursday, July 9, 2020 at 4:10:21 PM UTC+8, Alan Orth wrote:
>>
>> Dear Euler,
>>
>> It's a constant struggle. You absolutely have to get aggressive with
>> non-human users. I have adopted a multi-faceted effort. I'm happy to share,
>> everything of ours is in open GitHub repositories.
>>
>> 1. Tagging and throttling bad bots in nginx (which sits in front of
>> Tomcat):
>> https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/nginx/default.conf.j2
>> 2. Force users with "bot" user agents to use the same JSESSION ID in
>> Tomcat Crawler Session Manager Valve:
>> https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L210
>> 3. Update DSpace's builtin "spider" user agents lists so it doesn't
>> record them in Solr stats (most of those come from COUNTER-Robots project):
>> https://github.com/ilri/DSpace/tree/5_x-prod/dspace/config/spiders/agents
>> 4. Aggressive PostgreSQL connection pooling in Tomcat JDBC (requires
>> special configuration in Tomcat contexts as well):
>> https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L50
>>
>> This has made our site more stable, but like I said it's still a constant
>> struggle. For a few months starting in 2020-04 or so we've had an
>> increasing number of "waiting for lock" connections in both production 5.x
>> and testing 6.x. I've tried upgrading PostgreSQL, upgrading the JDBC
>> driver, downgrading Tomcat, etc. Nothing works except restarting Tomcat.
>>
>> Would love to restart the discussion on all of this... BTW it helps if
>> your systems have something like Munin configured that graphs the
>> PostgreSQL connection status every five minutes. Helpful when some user
>> says they couldn't log in or submit an item yesterday afternoon.
>>
>> Regards,
>>
>> On Thu, Jul 9, 2020 at 10:10 AM euler  wrote:
>>
>>> Hello Alan,
>>>
>>> This thread is 3 years old now but our repositories are still
>>> experiencing the issues mentioned here. We are running DSpace 6.3 by the
>>> way. I've read from one of your CGSpace notes (
>>> https://alanorth.github.io/cgspace-notes/2018-11/) that when you
>>> encountered crawlers making a lot of requests from different IP addresses,
>>> you add them to your Tomcat's crawler 

[dspace-tech] What to do with "unmigrated" Solr statistics records in DSpace 6?

[Alan Orth]

Dear dspace-tech,

We're in the middle of an upgrade from DSpace 5.8 to DSpace 6.3. After
processing our Solr stats with the as-of-yet unreleased Dspace 6.4
SolrUpgradePre6xStatistics class we have a large number of Solr statistics
records with "-unmigrated" IDs. In my tests with only a small fraction of
our ten-year Solr history we have 300,000 unmigrated records, which leads
me to believe we'd have millions if I attempted to process our entire Solr
history.

I see that the records with "unmigrated" IDs have correct UUIDs for their
owningComm and owningColl fields, so all that's missing would be for them
to have a unique UUID for their ID. Why do these fail to migrate? Could I
generate UUIDs for them manually? What do other people do with these
records?

Thanks,

-- 
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Timeout waiting for idle object Dspace 4.1

[Alan Orth]

Dear Euler,

It's a constant struggle. You absolutely have to get aggressive with
non-human users. I have adopted a multi-faceted effort. I'm happy to share,
everything of ours is in open GitHub repositories.

1. Tagging and throttling bad bots in nginx (which sits in front of
Tomcat):
https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/nginx/default.conf.j2
2. Force users with "bot" user agents to use the same JSESSION ID in Tomcat
Crawler Session Manager Valve:
https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L210
3. Update DSpace's builtin "spider" user agents lists so it doesn't record
them in Solr stats (most of those come from COUNTER-Robots project):
https://github.com/ilri/DSpace/tree/5_x-prod/dspace/config/spiders/agents
4. Aggressive PostgreSQL connection pooling in Tomcat JDBC (requires
special configuration in Tomcat contexts as well):
https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L50

This has made our site more stable, but like I said it's still a constant
struggle. For a few months starting in 2020-04 or so we've had an
increasing number of "waiting for lock" connections in both production 5.x
and testing 6.x. I've tried upgrading PostgreSQL, upgrading the JDBC
driver, downgrading Tomcat, etc. Nothing works except restarting Tomcat.

Would love to restart the discussion on all of this... BTW it helps if your
systems have something like Munin configured that graphs the PostgreSQL
connection status every five minutes. Helpful when some user says they
couldn't log in or submit an item yesterday afternoon.

Regards,

On Thu, Jul 9, 2020 at 10:10 AM euler  wrote:

> Hello Alan,
>
> This thread is 3 years old now but our repositories are still experiencing
> the issues mentioned here. We are running DSpace 6.3 by the way. I've read
> from one of your CGSpace notes (
> https://alanorth.github.io/cgspace-notes/2018-11/) that when you
> encountered crawlers making a lot of requests from different IP addresses,
> you add them to your Tomcat's crawler session manager. I highly suspect
> that the cause of our repository 'hanging' is also because of this amount
> of requests from this crawlers (mostly from crawlers with user
> agent facebookexternalhit, Turnitin, and Unpaywall).
>
> With regards to this, I hope you don't mind if you can share here the
> setting of your Tomcat's crawler session manager. Note that I have modified
> my postgresql.conf based from the discussion mentioned here:
> https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+April+2017.
>
> Thanks and hoping for your positive response,
> euler
>
> On Friday, July 7, 2017 at 7:41:52 PM UTC+8, Alan Orth wrote:
>>
>> Hello,
>>
>> I've struggled with this in various forms over the seven years or so
>> we've been running DSpace. High load on public servers can easily exhaust
>> PostgreSQL connection slots. The easy answer is to increase the connection
>> limits, but before that it's better to understand why the system load is
>> increasing. Here are a few tips.
>>
>> The easiest thing is to enable DSpace's XML sitemaps. Search engines like
>> Google really hammer the repository as they crawl and click all sorts of
>> dynamic links in the Browse and Discovery sidebar. Instead, you register
>> your web property with Google Webmaster Tools and give them the path to
>> your sitemap so they can get to each item directly without crawling
>> haphazardly. Once you're sure Google is consuming your sitemap, you can
>> block them from the dynamic pages in robots.txt. Here's the link on the
>> wiki for DSpace 4:
>>
>> https://wiki.duraspace.org/display/DSDOC4x/Search+Engine+Optimization
>>
>> Second, look at your web server access logs. You might see many requests
>> from bots like Bing, Yandex, Google, Slurp, etc, and notice they will all
>> becoming from different IP addresses—sometimes from five or ten
>> concurrently! Another place you might see this is in the "Current Activity"
>> tab in the DSpace Admin UI control panel. The problem with this is that
>> each of these connections creates a new Tomcat session, which consumes
>> precious memory, CPU, and other resources. You can enable a Crawler Session
>> Manager Valve in your Tomcat config which will tell Tomcat to make all user
>> agents matching a certain pattern use a single session. There are some
>> notes from me in the comments here:
>>
>> https://wiki.duraspace.org/display/cmtygp/DCAT+Meeting+April+2017
>>
>> And finally, in the last link is a discussion about updating the DSpace
>> defaults for PostgreSQL connections from a recentl

Re: [dspace-tech] Re: Can't produce Thumbnails!

[Alan Orth]

Yes you're right. Those are quite large dimensions for a thumbnail. Also
DSpace's default Java heap size hasn't changed in a decade and PDFs have
all gotten bigger!

Regards,

On Wed, Jun 24, 2020, 01:21 Chris Clawson  wrote:

> Thank You.
> This limit will affect the ability to generate thumbnails for larger file
> size bitstreams. Once I lowered my image resolution, I found it easier for
> the system to produce thumbnails. Got it. Memory related, and using the
> command you describe will raise the limit.
>
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Re: [dspace-tech] Problem with blank thumbnails

[Alan Orth]

Dear Helen,

I downloaded one of the PDFs in the linked collection and was able to
create a nice thumbnail using ImageMagick directly on the command line:

$ convert -flatten CUCSSN8319.pdf\[0\] CUCSSN8319.pdf.jpg
$ convert -thumbnail x600 CUCSSN8319.pdf.jpg
CUCSSN8319-thumbnail.pdf.jpg

So the PDFs seem OK. It could be an issue with memory or ImageMagick
version/configuration on your server. Try running the dspace filter-media
command in verbose mode for one of the PDFs to see if there are any errors:

$ dspace filter-media -i 10976/167371 -f -v

Regards,

On Thu, Jun 11, 2020 at 12:15 AM Baer,Helen 
wrote:

> Hi everyone,
>
>
>
> One of our partner libraries has a recurring problem with blank thumbnails
> for pdf's. Their process is to create the original PDF from separate TIFFs
> in Adobe, then use Adobe Acrobat Pro 2017 to make a smaller sized file.
> Have any of you seen this before? We're thinking the problem is with the
> source content, not DSpace, but I thought I'd ask around and see if anyone
> has a solution.
>
>
>
> Here's an example: https://mountainscholar.org/handle/10976/167263
>
>
>
> Best,
>
>
>
> Helen Baer
>
> Colorado State University
>
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Re: [dspace-tech] Re: Can't produce Thumbnails!

[Alan Orth]

Dear Chris,

You can set it directly on the command line using JAVA_OPTS:

$ export JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8"
$ dspace filter-media

The default memory heap in the `dspace` script is 256m.

Regards,

On Sun, Jun 21, 2020 at 8:47 AM Chris Clawson 
wrote:

>
> Okay- Maybe this has something to do with the large image pixel size 4000
> x 6000 of the jpgs. Where can I adjust the amount of memory available for
> the 'dspace filter-media' command?
>
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>


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https://englishbulgaria.net
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Re: [dspace-tech] Re: Upgrading Tomcat?

[Alan Orth]

Dear Chris,

For what it's worth I have been running DSpace 5 and 6 with Tomcat 7.0.x
for several years so your issues are likely not due to having an older
Tomcat—you might want to look into those issues more (start another thread
on this mailing list describing them)! Also, the Apache Tomcat project has
announced (long ago) that the 8.0.x series is superseded by the 8.5.x
series¹. Lastly, I see that Ubuntu 18.04 ships Tomcat 8.5.x with its system
package manager². How did you manage to get 8.0.x? Are you on Ubuntu 16.04
perhaps?

Regards,

¹ https://tomcat.apache.org/whichversion.html
² https://packages.ubuntu.com/bionic/tomcat8

On Tue, Jun 2, 2020 at 1:10 AM Chris Clawson 
wrote:

> Thank you, Mark
>
> You have answered some real concerns. I am only using binaries installed
> using apt. I was concerned that ant might have built DSpace with
> dependencies from the Tomcat installation. I will also be installing the
> Tomcat binary, using apt. I am not a very advanced Linux/Ubuntu user, but I
> can still explore directories and check configuration files.
>
> On Monday, June 1, 2020 at 2:07:20 PM UTC-4, Chris Clawson wrote:
>>
>> My DSpace 6 installation is on a remote server, running Ubuntu 18.04. I
>> guess I goofed and installed Tomcat 8.0.37 instead of Tomcat 8.5. It works,
>> but with assorted issues which may be because of the older Tomcat. Could
>> you please suggest or link to a procedure to upgrade Tomcat, without
>> blowing my working configuration?
>>
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[dspace-tech] Mystery "edit item metadata" feature in DSpace Demo XMLUI

[Alan Orth]

Hi,

I was looking at the DSpace Demo XMLUI (version 6) and I noticed this cool
feature where the metadata values for certain fields are using controlled
lists instead of free text when editing an existing item's metadata. See
dc.type in the attached screenshot.

What is this feature? Is it related to authority control? I've never seen
it before.

Thanks!

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https://englishbulgaria.net
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Re: [dspace-tech] Date searching gone haywire.

[Alan Orth]

Dear Nathan,

Coming back to this thread three years later after I realized you were
right (a user of mine reported the same issue on our repository recently)!
The XMLUI's Discovery advanced search filters do not work correctly for
dates.

In my own example above you can't see the issue because there is only one
item matching the filter term. I edited one item's issue date on the DSpace
6 demo repository and you can clearly see that the second item in the
search results *should not* match. In this case the search filter for issue
date containing "1992-06" returns results for the item having an issue date
of 1992-06-26 as expected, but also includes one with an issue date of
1992-01-06.

This is actually a bug! I will file a bug report... it affects at least
DSpace 5 and DSpace 6.

Regards,

On Wed, Mar 8, 2017 at 11:49 AM Alan Orth  wrote:

> Hi, Nathan.
>
> What's the problem exactly? Say you have an item with a dc.date.issued of
> 1992-06-26, if you use the advanced search to search for items that have an
> issue date containing 1992-06, you should get the result. See this example
> on the DSpace Demo:
>
>
> http://demo.dspace.org/xmlui/discover?filtertype_1=dateIssued_relational_operator_1=contains_1=1992-06_apply_filter==
>
> Regards,
>
> On Mon, Mar 6, 2017 at 10:05 PM Nathan Fralick 
> wrote:
>
>> When using date searching in our repository, the search doesn't function
>> as one would think. It almost acts as a key word search. I am sure the
>> problem lies within the dc code, where date isn't referencing the right
>> index. I am a beginner at coding and could use some help/advice
>> troubleshooting. The date code for the form is below. Any help would be
>> appreciated.
>>
>> 
>>   dc
>>   date
>>   issued
>>   false
>>   Date of Document(s)
>>   date
>>   Enter the date of the minutes, reports, etc.
>>   You must enter at least the year.
>> 
>>
>> Nathan Fralick
>> Digital Resources Librarian
>> Allegheny College, Pelletier Library
>>
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>


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Re: [dspace-tech] Broken Community Links after upgrade to 6.3

[Alan Orth]

We are also using a customized version of Mirage 2 on DSpace 5.x, but the
same would work on 6.x. We actually have one master theme where most of the
theme logic and templates lives, then twenty-six child themes that inherit
from it. It saves us loads of time. In Mirage 1 we were maintaining all
child themes individually!

Repository: https://cgspace.cgiar.org/
Code: https://github.com/ilri/DSpace/

Regards,

On Thu, Mar 12, 2020 at 4:42 PM Anne Lawrence  wrote:

> https://vtechworks.lib.vt.edu/ is a lightly customized version of DSpace
> 6.3 with Mirage2.
>
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Re: [dspace-tech] Stop Downloading of PDF file from browser

[Alan Orth]

Hello,

It's not possible. Basically, the "open in the browser" versus "download"
distinction is superficial as, once the user has viewed the PDF in the
browser it is trivial to save it using the browser's own tools—Firefox's
own PDF viewer literally has a save button.

Also, I'm against this type of attempt to limit the free flow of
information. Especially within the context of an open-source software
system that is overwhelmingly developed with the aim of building open
access repositories!

Regards,

On Thu, Mar 12, 2020 at 4:04 PM Umeshwar Rai  wrote:

> Hi,
>
> Please any one help on this topic.
>
> I am using dspace xmlui 6.3. I want to restrict the PDF file view and
> download option user wise.
> Meaning by if the user is administrator then allow to download or print
> the pdf file when it open by the dspace is browser on click of view/open
> button.
> If the user is not administrator its allow to view the file only in
> browser and print and download button gets disabled.
>
> Thanks
>
> Umeshwar Roy
>
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Re: [dspace-tech] update-sequences.sql giving permission denied when run as root

[Alan Orth]

Dear Ashim,

"Peer authentication failed" means your PostgreSQL user could not log in.
Either the password was wrong, the user doesn't exist, or you have
incorrectly configured the "allowed" IPs / databases for that user in
pg_hba.conf. On my Ubuntu system the file is here:
/etc/postgresql/9.6/main/pg_hba.conf

Are you sure you have a "dspace" user in PostgreSQL? Check the DSpace wiki
for more information about the correct settings for pg_hba.conf:

https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace#InstallingDSpace-RelationalDatabase:(PostgreSQLorOracle)

Cheers,

On Wed, Mar 11, 2020 at 8:25 AM Ashim Kapoor 
wrote:

> Dear Mark,
>
> I did this :-
>
> root@DSpace:~# psql --user dspace -d dspace -f
> /home/dspace/dspace-install/etc/postgres/update-sequences.sql
> psql: FATAL:  Peer authentication failed for user "dspace"
> root@DSpace:~#
>
> Can you please correct me ?
>
> Thank you,
> Ashim
>
>
> On Mon, 9 Mar 2020 at 20:50, Mark H. Wood  wrote:
>
>> On Mon, Mar 09, 2020 at 12:38:57PM +0530, Ashim Kapoor wrote:
>> > Here is what I did:
>> >
>> > 1. I did an AIP backup and restore of a top level community.
>> > 2. Looks ok in the browser after restarting tomcat.
>> > 3. Then I stopped tomcat and as root did
>> > [dspace]/etc/postgresql/update-sequences.sql
>> >
>> > It says Permission denied.
>> >
>> > I am root, how can I get permission denied? Can some one please help me
>> ?
>>
>> Because the shell will not execute a command or script which does not
>> have the executable bit set in its mode, even if you are root.
>>
>> Also:  that is not an executable command or shell script; it is an SQL
>> script.  You need to give it to an SQL interpreter.  For PostgreSQL
>> that would be 'psql'.
>>
>> The DBMS has its own credentials and permissions, and doesn't give
>> special powers to 'root'.  As any OS user, use the database username
>> and password that you configured in [dspace]/config/local.cfg when
>> running 'psql':
>>
>>   psql --user dspace --dbname dspace --file
>> [dspace]/etc/postgres/update-sequences.sql
>>   Password:  secret
>>
>> See
>>
>>
>> https://wiki.lyrasis.org/display/DSDOC6x/Upgrading+DSpace#UpgradingDSpace-UpgradeSteps
>>
>> step 11b.
>>
>> --
>> Mark H. Wood
>> Lead Technology Analyst
>>
>> University Library
>> Indiana University - Purdue University Indianapolis
>> 755 W. Michigan Street
>> Indianapolis, IN 46202
>> 317-274-0749
>> www.ulib.iupui.edu
>>
>> --
>> All messages to this mailing list should adhere to the DuraSpace Code of
>> Conduct: https://duraspace.org/about/policies/code-of-conduct/
>> ---
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>> .
>>
> --
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> .
>


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https://englishbulgaria.net
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Re: [dspace-tech] 2 issues after setting up DSpace 6.3

[Alan Orth]

Dear Ashim,

It looks like Gmail isn't working on port 465 (can't connect), whereas port
587 was working, but simply needed you to turn on STARTTLS. Try adding this
to your dspace.cfg:

mail.extraproperties = mail.smtp.starttls.enable=true

Regards,

On Sun, Mar 8, 2020 at 8:26 AM Ashim Kapoor 
wrote:

>
> Dear Ayuka,
>
> here is the snippet from my local.cfg
>
> ###
> # EMAIL CONFIGURATION #
> ###
>
> # SMTP mail server (allows DSpace to send email notifications)
> mail.server = smtp.gmail.com
>
> # SMTP mail server authentication username and password (if required)
> mail.server.username = x...@gmail.com
> mail.server.password = yyy
>
> # SMTP mail server alternate port (defaults to 25)
> mail.server.port = 465
>
> # From address for mail
> # All mail from the DSpace site will use this 'from' address
> mail.from.address = x...@gmail.com
>
> # When feedback is submitted via the Feedback form, it is sent to this
> address
> # Currently limited to one recipient!
> feedback.recipient = x...@gmail.com
>
> # General site administration (Webmaster) e-mail
> mail.admin = x...@gmail.com
>
> # Recipient for server errors and alerts (defaults to mail.admin)
> #alert.recipient = ${mail.admin}
>
> # Recipient for new user registration emails (defaults to unspecified)
> #registration.notify =
> mail.extraproperites = mail.smtp.starttls.enable.true
>
> 
>
>
>
> root@DSpace:/home/dspace/dspace-install/bin# ./dspace test-email
>
> About to send test email:
>  - To: x...@gmail.com
>  - Subject: DSpace test email
>  - Server: smtp.gmail.com
>
> Error sending email:
>  - Error: javax.mail.SendFailedException: Send failure
> (javax.mail.MessagingException: Could not connect to SMTP host:
> smtp.gmail.com, port: 465, response: -1)
>
> Please see the DSpace documentation for assistance.
>
>
>
> root@DSpace:/home/dspace/dspace-install/bin#
>
>
> Many thanks for your help.
> Best,
> Ashim
>
> On Sat, 7 Mar 2020 at 21:57, Ayuka Phanuel  wrote:
>
>> And you have to add this to your local.cfg
>> mail.extraproperties = mail.smtp.starttls.enable=true
>>
>>
>>
>> On Sat, Mar 7, 2020 at 4:38 PM Ayuka Phanuel 
>> wrote:
>>
>>> While using port 587 ?
>>>
>>> --
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> .
>


-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Show and tell: DSpace Statistics API

[Alan Orth]

Dear list,

FYI I've updated my dspace-statistics-api to work with DSpace 6+ UUIDs.
Previous versions used the integer item IDs present in DSpace 4 and 5. You
can see more here:

https://github.com/ilri/dspace-statistics-api

This is a small tool that indexes your Solr item view and download
statistics into a PostgreSQL database and makes them available via a REST
API. It is written in Python and can be run using a WSGI server like
gunicorn.

Regards,

On Mon, Nov 5, 2018 at 8:43 PM Bruno Nocera Zanette 
wrote:

> Nice job, Alan!
> It may be very handy for our research group and the systems we mantain.
> Thanks!
> Em qui, 1 de nov de 2018 às 11:40, Alan Orth 
> escreveu:
> >
> > Dear list,
> >
> > We have recently been doing some integration with our DSpace repository
> using the REST API. Eventually we realized that it would be nice to be able
> to use the item views and downloads from the Solr statistics core, but
> those are not exposed by any externally accessible APIs. I wrote a small,
> lightweight Python-based tool that runs locally on the DSpace server to
> periodically index the Solr statistics core and expose the statistics via a
> simple API. And it's fast!
> >
> > The tool is called "dspace-statistics-api" and you can find the source
> code, documentation, and deployment instructions on GitHub:
> >
> > https://github.com/ilri/dspace-statistics-api
> >
> > You can see it in running on the public development instance of our
> DSpace repository:
> >
> > https://dspacetest.cgiar.org/rest/statistics
> >
> > I hope this is useful to some people and I would be very happy for
> comments, suggestions, and pull requests (see my list of TODOs in the
> project).
> >
> > Thank you!
> >
> > --
> > Alan Orth
> > alan.o...@gmail.com
> > https://picturingjordan.com
> > https://englishbulgaria.net
> > https://mjanja.ch
> > "In heaven all the interesting people are missing." ―Friedrich Nietzsche
> >
> > --
> > All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
> > ---
> > You received this message because you are subscribed to the Google
> Groups "DSpace Technical Support" group.
> > To unsubscribe from this group and stop receiving emails from it, send
> an email to dspace-tech+unsubscr...@googlegroups.com.
> > To post to this group, send email to dspace-tech@googlegroups.com.
> > Visit this group at https://groups.google.com/group/dspace-tech.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Bruno Nocera Zanette
> +55 41 2-2508
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Troubleshooting failed yearly Solr statistics sharding

[Alan Orth]

Dear Mark,

After having exported a slice of my 2019 statistics from production I've
just done two experiments in my development environment: manually create a
`statistics-2019` core and load the 2019 hits into it, and load data into
the main `statistics` core and initiate the `dspace stats-util -s` yearly
sharding process. In both cases the core's data is online and available
immediately after it is loaded. In the first case the manually created core
does not get loaded the next time I restart Tomcat, while in the second
case the DSpace-created core does.

Regarding DSpace doing something "hacky" in using multiple data-only cores
that share an instanceDir, I'm also wondering how that fits into the
official use cases of Solr! I want to add some debug logging to
SolrLoggerServiceImpl.java (DSpace 6.x) to try to understand why my
manually-created core doesn't get loaded. Possibly related, about half the
time we start Tomcat on our production server one of the cores fails to
load anyways! To be honest it's making me a bit nervous about running with
all these shards (we have ten, back to 2010!) and I am debating whether I
should just put everything back in the main statistics core. How does the
migration process to a more modern Solr with DSpace 7 look with our "hacky"
sharding?

Regards,

On Thu, Feb 6, 2020 at 5:03 PM Mark H. Wood  wrote:

> On Thu, Feb 06, 2020 at 02:50:43PM +0200, Alan Orth wrote:
> > Our yearly Solr statistics sharding (stats-util -s) failed this year
> > because our core is very large (43GiB) and apparently timed out
> somewhere.
> > It failed again when I tried to run it manually:
> >
> > Moving: 51633080 into core statistics-2019
> > ...
> > Exception: Read timed out
> > java.net.SocketTimeoutException: Read timed out
> >
> > As a test I used this really great tool called solr-import-export-json to
> > export some of my 2019 statistics to JSON on the production server, then
> > import them into a new core in my development instance:
> >
> > $ ./run.sh -s http://localhost:8081/solr/statistics -a export -o
> > /tmp/statistics-2019-01.json -f 'dateYearMonth:2019-01' -k uid
> > $ curl '
> >
> http://localhost:8080/solr/admin/cores?action=CREATE=statistics-2019=/home/aorth/dspace/solr/statistics=/home/aorth/dspace/solr/statistics-2019/data
> > '
> > $ ./run.sh -s http://localhost:8080/solr/statistics-2019 -a import -o
> > /tmp/statistics-2019-01.json -k uid
> >
> > This worked brilliantly... in fact I am very impressed with this tool and
> > recommend it to people!
> >
> > The problem is, this core does not get enumerated automatically by Solr
> > after I restart the servlet container. I got it to load by hard-coding
> the
> > core into dspace/solr/solr.xml config² but it seems hacky. How are these
> > core shards enumerated by DSpace's Solr application? What would cause
> > shards to not be loaded automatically?
> >
> > My environment is DSpace 5.8 with Tomcat 7.0.99 and OpenJDK 8.
>
> I think that a good place to look is
>
> 'dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl#initSolrYearCores'.
> Also #createCore in the same class.  This is where DSpace enumerates
> the cores that it will use for statistics.  It seems to be looking for
> directories 'solr/statistics-'.  It will call CREATE in Solr's
> CoreAdmin API, which would seem to register a core if it already
> exists.  You seem to be doing the same thing, but there must be
> something slightly different about your actions.  Or perhaps the way
> you are testing -- it looks to me as though Solr is unaware of the
> additional cores at startup and is told of them by DSpace when *it*
> starts up.
>
> But I think it is actually DSpace that is doing something hacky:
> using the same InstanceDir for multiple cores.  I have no idea why
> that works.
>
> Sadly, SolrJ is almost entirely undocumented, at least in this area.
> I have had to puzzle out a lot of its working by reference to the web
> API documentation in the Solr Ref Guide.
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
> ---
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> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on the web v

Re: [dspace-tech] Maximum number of DB connections in pool

[Alan Orth]

Dear Paolo,

I should also add the some of the benefits of managing the pool outside of
Tomcat is that they can be shared across web applications (rather than
having one per web application context), you can do connection re-use,
connection validation, etc.

Regards,

On Wed, Feb 26, 2020 at 2:58 PM Alan Orth  wrote:

> Dear Paolo,
>
> We had similar problems that were completely resolved by switching to a
> pool managed in Tomcat via JNDI, rather than via DSpace itself. We are
> using PostgreSQL, but the idea would be the same for Oracle. See my
> detailed dspace-tech mailing list post in December, 2017¹. Also, see the
> commits to our site's infrastructure repository on GitHub² for some insight
> on the Tomcat changes required. Lastly, we ended up setting up two pools³:
> one for the REST API and another for XMLUI and the others.
>
> Hope that helps,
>
> ¹
> http://dspace.2283337.n4.nabble.com/Notes-on-PostgreSQL-connection-pooling-with-a-Tomcat-JNDI-resource-td4687149.html
> ²
> https://github.com/ilri/rmg-ansible-public/commit/1959d9cb7a0e7a7318c77f769253e5e029bdfa3b
> ³
> https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L50
>
> On Mon, Feb 17, 2020 at 5:49 PM Paolo  wrote:
>
>> Dear All,
>>
>> I would like to submit you a fairly frequent problem in our cadmus.eui.eu
>> repository.
>>
>> Our DSpace 5.2 installation works as a front-end on a virtual machine
>> with 4 CPU and 8 GB RAM and the back-end with Oracle db on the Oracle
>> enterprise installation in our University ICT environment. The access to
>> the DMZ, where the front-end is located, is managed by linux server with an
>> Apache httpd.conf configuration apparently not limited by the number of
>> simultaneous connections. Our problem is the number of connections to the
>> db that quite frequently reach 200 as configured in dspace.cfg.
>>
>>
>> #Maximum number of DB connections in pool
>>
>> db.maxconnections = 200
>>
>>
>> Unfortunately, despite the fact that the 200 connections are inactive,
>> they blocked access to the server forcing tomcat to restart.
>>
>> Please find attached the result of an SQL query for inactive connections
>>
>>
>> Any suggestions or previous experience in this regard are extremely
>> welcome.
>>
>> Best Regards
>>
>>
>> Paolo Baglioni
>>
>> Library Systems Analyst
>>
>> European University Institute
>>
>> 50014 Firenze ITALY
>>
>> --
>> All messages to this mailing list should adhere to the DuraSpace Code of
>> Conduct: https://duraspace.org/about/policies/code-of-conduct/
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "DSpace Technical Support" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to dspace-tech+unsubscr...@googlegroups.com.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/dspace-tech/79f1fd7c-b1e2-4279-9b83-a1de82e74f5f%40googlegroups.com
>> <https://groups.google.com/d/msgid/dspace-tech/79f1fd7c-b1e2-4279-9b83-a1de82e74f5f%40googlegroups.com?utm_medium=email_source=footer>
>> .
>>
>
>
> --
> Alan Orth
> alan.o...@gmail.com
> https://picturingjordan.com
> https://englishbulgaria.net
> https://mjanja.ch
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

-- 
All messages to this mailing list should adhere to the DuraSpace Code of 
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Re: [dspace-tech] Maximum number of DB connections in pool

[Alan Orth]

Dear Paolo,

We had similar problems that were completely resolved by switching to a
pool managed in Tomcat via JNDI, rather than via DSpace itself. We are
using PostgreSQL, but the idea would be the same for Oracle. See my
detailed dspace-tech mailing list post in December, 2017¹. Also, see the
commits to our site's infrastructure repository on GitHub² for some insight
on the Tomcat changes required. Lastly, we ended up setting up two pools³:
one for the REST API and another for XMLUI and the others.

Hope that helps,

¹
http://dspace.2283337.n4.nabble.com/Notes-on-PostgreSQL-connection-pooling-with-a-Tomcat-JNDI-resource-td4687149.html
²
https://github.com/ilri/rmg-ansible-public/commit/1959d9cb7a0e7a7318c77f769253e5e029bdfa3b
³
https://github.com/ilri/rmg-ansible-public/blob/master/roles/dspace/templates/tomcat/server-tomcat7.xml.j2#L50

On Mon, Feb 17, 2020 at 5:49 PM Paolo  wrote:

> Dear All,
>
> I would like to submit you a fairly frequent problem in our cadmus.eui.eu
> repository.
>
> Our DSpace 5.2 installation works as a front-end on a virtual machine with
> 4 CPU and 8 GB RAM and the back-end with Oracle db on the Oracle enterprise
> installation in our University ICT environment. The access to the DMZ,
> where the front-end is located, is managed by linux server with an
> Apache httpd.conf configuration apparently not limited by the number of
> simultaneous connections. Our problem is the number of connections to the
> db that quite frequently reach 200 as configured in dspace.cfg.
>
>
> #Maximum number of DB connections in pool
>
> db.maxconnections = 200
>
>
> Unfortunately, despite the fact that the 200 connections are inactive,
> they blocked access to the server forcing tomcat to restart.
>
> Please find attached the result of an SQL query for inactive connections
>
>
> Any suggestions or previous experience in this regard are extremely
> welcome.
>
> Best Regards
>
>
> Paolo Baglioni
>
> Library Systems Analyst
>
> European University Institute
>
> 50014 Firenze ITALY
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
> ---
> You received this message because you are subscribed to the Google Groups
> "DSpace Technical Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to dspace-tech+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/dspace-tech/79f1fd7c-b1e2-4279-9b83-a1de82e74f5f%40googlegroups.com
> <https://groups.google.com/d/msgid/dspace-tech/79f1fd7c-b1e2-4279-9b83-a1de82e74f5f%40googlegroups.com?utm_medium=email_source=footer>
> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

-- 
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Re: [dspace-tech] Twitter cards and open graph in page-structure.xsl

[Alan Orth]

Dear Deborah,

This is a fantastic idea! I don't know why I never thought of it. Your work
is a great starting point... I will play with it some more and keep testing
in the Twitter Card validator to see how it looks:

https://cards-dev.twitter.com/validator

It would be great to get a high-quality thumbnail and a description.

Thanks!

On Wed, Feb 12, 2020 at 12:22 AM Fitchett, Deborah <
deborah.fitch...@lincoln.ac.nz> wrote:

> Kia ora koutou,
>
>
>
> Has anyone played around with Twitter cards and/or Open Graph with Dspace?
> The goal being that, if someone tweets a link to an item in the repository,
> Twitter (or Facebook or whoever) automatically displays a little preview of
> the item’s title, thumbnail etc. This seems likely to improve
> click-throughs/engagement.
>
>
>
> I’ve edited page-structure.xsl (we’re on XMLUI, Mirage2) to get some basic
> metadata in – following the Google Scholar Metadata section:
>
> 
>
>  content="article"/>
>
>  property="og:site_name" content="Research@Lincoln"/>
>
>  content="
> https://ltl.lincoln.ac.nz/wp-content/uploads/sites/20/2020/01/lincoln.png
> "/>
>
>  select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element =
> 'title']">
>
>  property="og:title" content="{.}"/>
>
> 
>
>  select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element =
> 'identifier']">
>
>  property="og:url" content="https://hdl.handle.net/{.}"/>
>
> 
>
> Which experiments on Twitter show works! J
>
>
>
> But note the image is a static logo, and I haven’t managed to get a
> description in. This content doesn’t appear to be included in the dri
> structure – except that dcterms.abstract is buried in the xhtml_head_item
> which is a giant blob-thing of xml as text so I can’t reach into it (unless
> maybe I play with substrings). Is there any other way to get at the
> abstract here?
>
>
>
> And is there a way to access the mets data from page-structure.xsl? (If
> so, I should be able to get the item’s thumbnail to use for the image.) We
> have in item-view.xsl and I don’t see why it wouldn’t be accessible from
> page-structure.xsl, but maybe that shows how much I know. In any case so
> far all my trial-and-error messing around trying to access it has resulted
> in errors.
>
>
>
> Ngā mihi,
>
>
>
> Deborah
>
> ––
>
> *Deborah Fitchett*
>
> Head of Department: Digital Services
>
>
>
> ––
>
> *Library, Teaching and Learning – Te Wharepūrākau*
>
> PO Box 85064, Lincoln University
>
> Lincoln 7647, Christchurch, New Zealand
>
> +64 3 423 0358
>
> deborah.fitch...@lincoln.ac.nz
>
> ltl.lincoln.ac.nz
>
>
>
> ––
>
> *Lincoln University*
>
> Te Whare Wānaka o Aoraki
>
> ––
>
>
>
>
>
> --
>
> "The contents of this e-mail (including any attachments) may be
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> .
>


-- 
Alan Orth
alan.o...@gmail.c

Re: [dspace-tech] Solr metadata statistics - query syntax

[Alan Orth]

Dear Filippo,

I only have a comment: if you have access to localhost you could query the
SQL database directly (the Solr search core is built from that data
anyways). I guess it all depends on your skill in writing Solr queries
versus SQL queries!

Regards,

On Mon, Feb 17, 2020 at 4:39 PM Filippo Santoro 
wrote:

> Hello to everyone,
> I have installed an instance of DSpace 6.3 on Windows Server 2016.
> Since for institutional policies cannot use default JSP frontend of DSpace
> (except for ordinary maintenance), I am using Solr for queries.
> However, I need to get statistics from a query (as provided by the
> Discovery module) using Solr. For example, if I perform a search by author:
>
> http:
> //localhost:8090/search/select?q=search.resourcetype:2=dc.contributor.author:MickeyMouse
>
> in addition to the assets in which MickeyMouse is the author, I would
> obtain the number by author:
>
> Mickey Mouse45
> Donald Duck 25
> Minnie Mouse13
> Pluto   5
> Goofy   3
> Daisy Duck  3
>
> How should I edit the query?
>
> Thanks in advance.
> Filippo
>
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>


-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] SOLR error: too many boolean clauses

[Alan Orth]

 ausschließlich final rechtsverbindlich, wenn sie in herkömmlicher
>> Schriftform (mit eigenhändiger Unterschrift) oder durch Übermittlung eines
>> solchen Schriftstücks per Telefax erfolgen.
>>
>> Important note: The information included in this e-mail is confidential.
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>> (with personal signature) or when such documents are sent by fax.
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>> https://groups.google.com/d/msgid/dspace-tech/018898d5-6a6c-6225-73df-6c69f6f5fc16%40tu-dortmund.de
>> .
>>
>
>
> --
>
> --
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] Slow Discovery indexing performance in DSpace 6

[Alan Orth]

Dear Mark,

I think flame graphs might be what we need to look into. Brendan more or
less pioneered this way of doing visualization of performance analysis
while troubleshooting MySQL in 2011, and now the tooling ecosystem has
really developed. We should definitely look into this. I've only ever done
amateur performance analysis with strace, iotop, VisualVM, etc, but I will
try to see if I can figure out how to generate a flame graph of DSpace
while it is indexing.

Regarding patches pending in 6.4, I've been testing 6.4-SNAPSHOT and it's
the same. :\

Cheers,

http://www.brendangregg.com/flamegraphs.html

Brendan is a pioneer in this type of performance visualization that I see

On Thu, Feb 6, 2020 at 4:15 PM Mark H. Wood  wrote:

> On Thu, Feb 06, 2020 at 09:46:49AM +0200, Alan Orth wrote:
> > Dear list,
> >
> > I'm testing an upgrade of a DSpace 5.8 instance to DSpace 6.3 and one of
> > the first things I notice is that Discovery indexing is about three or
> four
> > times slower than it was before. On the same hardware, my repository with
> > ~85,000 items takes 30 minutes to index with DSpace 5 and three hours
> with
> > DSpace 6.3 and DSpace 6.4-SNAPSHOT. My development environment is on
> Linux
> > with a fast SSD and lots of RAM, so I fear it will be even worse on our
> > production server.
> >
> > I have read that the new Hibernate database layer in DSpace 6 involves
> much
> > more complicated or time-consuming database queries. How are other people
> > handling this? We're using PostgreSQL 9.6. Could it be time to move to
> > something higher to hopefully gain something from PostgreSQL's own
> advances?
>
> I don't know that upgrading PostgreSQL will help your indexing
> performance all that much, but it shouldn't hurt.  We run production
> against Pg 10.9 and I develop DSpace 5, 6, and 7 against 12.1.
>
> Hibernate does tend to fetch more stuff, but it also caches very
> aggressively and rather well, so it's hard to say whether it is
> contributing to any particular slow-down.  There have been specific
> DSpace operations in which Hibernate was found to be a source of
> excess activity, but I think that most of them have been addressed in
> patches scheduled for 6.4.  I have no doubt that there are others.
>
> Probably the most methodical approach would be to run indexing with a
> profiler and find out where the time is being spent.  Since
> command-line indexing involves three processes (bin/dspace, Pg, and
> Tomcat (running Solr)) it would be good to pay particular attention to
> time spent waiting on another process.
>
> Short of profiling, tools like 'top' and 'iotop' will give a rough
> idea of whether the system is generally busier and suggest which parts
> are responsible.  You might be able to set up 'strace' or the like to
> log mainly I/O calls and grind some statistics out of the log.
>
> (I really should try some of these myself)
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Troubleshooting failed yearly Solr statistics sharding

[Alan Orth]

Dear list,

Our yearly Solr statistics sharding (stats-util -s) failed this year
because our core is very large (43GiB) and apparently timed out somewhere.
It failed again when I tried to run it manually:

Moving: 51633080 into core statistics-2019
...
Exception: Read timed out
java.net.SocketTimeoutException: Read timed out

As a test I used this really great tool called solr-import-export-json to
export some of my 2019 statistics to JSON on the production server, then
import them into a new core in my development instance:

$ ./run.sh -s http://localhost:8081/solr/statistics -a export -o
/tmp/statistics-2019-01.json -f 'dateYearMonth:2019-01' -k uid
$ curl '
http://localhost:8080/solr/admin/cores?action=CREATE=statistics-2019=/home/aorth/dspace/solr/statistics=/home/aorth/dspace/solr/statistics-2019/data
'
$ ./run.sh -s http://localhost:8080/solr/statistics-2019 -a import -o
/tmp/statistics-2019-01.json -k uid

This worked brilliantly... in fact I am very impressed with this tool and
recommend it to people!

The problem is, this core does not get enumerated automatically by Solr
after I restart the servlet container. I got it to load by hard-coding the
core into dspace/solr/solr.xml config² but it seems hacky. How are these
core shards enumerated by DSpace's Solr application? What would cause
shards to not be loaded automatically?

My environment is DSpace 5.8 with Tomcat 7.0.99 and OpenJDK 8.

Thanks,

¹ https://github.com/freedev/solr-import-export-json
²
https://cwiki.apache.org/confluence/display/solr/Solr.xml%20(supported%20through%204.x)
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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[dspace-tech] Slow Discovery indexing performance in DSpace 6

[Alan Orth]

Dear list,

I'm testing an upgrade of a DSpace 5.8 instance to DSpace 6.3 and one of
the first things I notice is that Discovery indexing is about three or four
times slower than it was before. On the same hardware, my repository with
~85,000 items takes 30 minutes to index with DSpace 5 and three hours with
DSpace 6.3 and DSpace 6.4-SNAPSHOT. My development environment is on Linux
with a fast SSD and lots of RAM, so I fear it will be even worse on our
production server.

I have read that the new Hibernate database layer in DSpace 6 involves much
more complicated or time-consuming database queries. How are other people
handling this? We're using PostgreSQL 9.6. Could it be time to move to
something higher to hopefully gain something from PostgreSQL's own advances?

Thanks for any comments or suggestions,
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch

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Re: [dspace-tech] "Invalid UUID string" in Solr search core after DSpace 6 upgrade

[Alan Orth]

Dear Mark,

Is there a difference in the automatic re-indexing that is triggered by the
existence of the `dspace/solr/search/conf/reindex.flag` and a manually
triggered `dspace index-discovery -b`? After my database migration was
completed I started Tomcat and then immediately triggered a manual
re-indexing. I lost a few hours investigating the cause of this, only to
stumble on the fact that the "automatic" re-indexing apparently does
something differently—the effects of which are only visible if the
"automatic" re-indexing actually completes without interruption! Very
strange...

Regards,

On Tue, Feb 4, 2020 at 4:37 PM Mark H. Wood  wrote:

> On Tue, Feb 04, 2020 at 12:11:22PM +0200, Alan Orth wrote:
> > I'm testing DSpace version 5.8 to 6.3 upgrade. Immediately after
> performing
> > the database migrations successfully and starting Tomcat I initiated a
> > `dspace index-discovery -b`. I thought something was strange because I
> > didn't see any indexing progress in dspace.log (despite high CPU usage),
> > and then when I browsed the home page I saw many errors such as this in
> > dspace.log:
> >
> > 2020-02-03 10:27:14,485 ERROR org.dspace.browse.ItemCountDAOSolr @
> > caught exception:
> > org.dspace.discovery.SearchServiceException: Invalid UUID string: 1
> > 2020-02-03 13:20:20,475 ERROR
> > org.dspace.app.xmlui.aspect.discovery.AbstractRecentSubmissionTransformer
> > @ Caught SearchServiceException while retrieving recent submission
> > for: home page
> > org.dspace.discovery.SearchServiceException: Invalid UUID string: 111210
> >
> > I checked Solr's search core and saw that the search.resourceid fields
> were
> > indeed integers instead of UUIDs. On a guess I stopped the indexing,
> > deleted the search cores¹, touched an empty file in
> > dspace/solr/search/conf/reindex.flag², and restarted Tomcat. After Tomcat
> > started back up the re-indexing started and correctly indexed
> > search.resourceid as UUIDs.
> >
> > After the initial reindex.flag indexing completes, subsequent manual
> > indexing runs with `dspace index-discovery -b` work correctly. This only
> > seems to happen the first time after upgrade—I tried deleting all search
> > documents and starting a `dspace index-discovery -b` and it behaved
> > correctly.
> >
> > Has anyone seen this? Is it worth filing a bug? Are there perhaps some
> > fixes in the as-of-yet-unreleased 6.4 that would address this?
> >
> > Regards,
> >
> > ¹ curl -s 'http://localhost:8080/solr/search/update?stream.body=
> > *:*=true'
> > ² https://wiki.lyrasis.org/display/DSDOC6x/Upgrading+DSpace
>
> According to https://wiki.lyrasis.org/display/DSDOC6x/Upgrading+DSpace
> the 'search' core should have been reindexed automatically, unless you
> disabled that (as discussed further down that page) and then did not
> follow through with a manual reindex.
>
> You should also be aware of a usage statistics issue which will be
> addressed in 6.4:
>
>
> https://wiki.lyrasis.org/display/DSDOC6x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-UpgradeLegacyDSpaceObjectIdentifiers(pre-6xstatistics)toDSpace6xUUIDIdentifiers
>   https://jira.lyrasis.org/browse/DS-4110
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
> ---
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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[dspace-tech] "Invalid UUID string" in Solr search core after DSpace 6 upgrade

[Alan Orth]

Dear list,

I'm testing DSpace version 5.8 to 6.3 upgrade. Immediately after performing
the database migrations successfully and starting Tomcat I initiated a
`dspace index-discovery -b`. I thought something was strange because I
didn't see any indexing progress in dspace.log (despite high CPU usage),
and then when I browsed the home page I saw many errors such as this in
dspace.log:

2020-02-03 10:27:14,485 ERROR org.dspace.browse.ItemCountDAOSolr @
caught exception:
org.dspace.discovery.SearchServiceException: Invalid UUID string: 1
2020-02-03 13:20:20,475 ERROR
org.dspace.app.xmlui.aspect.discovery.AbstractRecentSubmissionTransformer
@ Caught SearchServiceException while retrieving recent submission
for: home page
org.dspace.discovery.SearchServiceException: Invalid UUID string: 111210

I checked Solr's search core and saw that the search.resourceid fields were
indeed integers instead of UUIDs. On a guess I stopped the indexing,
deleted the search cores¹, touched an empty file in
dspace/solr/search/conf/reindex.flag², and restarted Tomcat. After Tomcat
started back up the re-indexing started and correctly indexed
search.resourceid as UUIDs.

After the initial reindex.flag indexing completes, subsequent manual
indexing runs with `dspace index-discovery -b` work correctly. This only
seems to happen the first time after upgrade—I tried deleting all search
documents and starting a `dspace index-discovery -b` and it behaved
correctly.

Has anyone seen this? Is it worth filing a bug? Are there perhaps some
fixes in the as-of-yet-unreleased 6.4 that would address this?

Regards,

¹ curl -s 'http://localhost:8080/solr/search/update?stream.body=
*:*=true'
² https://wiki.lyrasis.org/display/DSDOC6x/Upgrading+DSpace
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] Re: Exclude specific IPs from DSpace Solr Statistics?

[Alan Orth]

Dear James,

I only use block lists based on user agent strings, so I'm not entirely
sure, but it looks like you can just drop a list of IPs in here:

https://github.com/DSpace/DSpace/tree/dspace-6_x/dspace/config/spiders

Check your dspace.log and you will see them being loaded.

Cheers,

On Fri, Dec 6, 2019, 22:42 James Michelich 
wrote:

> Our goal is to get a more accurate view of statistics around views and
> downloads of content in our institutional repository.  Thus, I'm attempting
> to find a way to filter out stats generated by accesses from certain
> people/departments internal to our organization.
>
> On Wednesday, December 4, 2019 at 9:03:09 AM UTC-6, James Michelich wrote:
>>
>> I am new to DSpace and Solr, but have been tasked with finding a way to
>> exclude specific IPs (or IP ranges) from the pageview and download
>> statistics in our DSpace 6 install (XMLUI).  The idea is to exclude stats
>> generated by views from some of our internal departments.  Is this
>> possible?  Thanks.
>>
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Re: [dspace-tech] Re: LDAP Dspace 5.3

[Alan Orth]

Hello,

I'm using Active Directory for DSpace authentication for years. A few
comments and suggestions:

- comment out the object_context. I don't know what it does, but we have it
commented out and ours works
- set the search context to the root of the directory, ie:
DC=satc,DC=edu,Dc=br

You're using the subtree search scope (2) so it makes sense to start at the
top of the tree and let it search down for the user.

Regards,

On Wed, Nov 20, 2019 at 9:50 AM Anda  wrote:

>
> Dear Marcelo,
>
> Did You resolve this problem?
> We have the same issue. I don't know what to do.
>
> Thanks You!
>
> Anda
>
> trešdiena, 2017. gada 11. oktobris 02:05:49 UTC+3, Marcelo Silveira
> rakstīja:
>>
>> This is my LDAP configuration file.
>>
>> enable = true
>> autoregister = true
>> provider_url = ldap://satc.edu.br/
>> id_field = sAMAccountName
>> object_context = ou=Users,DC=satc,DC=edu,DC=br
>> search_context = OU=Users,DC=satc,DC=edu,DC=br
>> email_field = mail
>> surname_field = sn
>> givenname_field = givenName
>> phone_field = telephoneNumber
>> search_scope = 2
>> search.user = CN=Administrador,CN=Users,DC=satc,DC=edu,DC=br
>> search.password = Password
>>
>> If I try to perform a search on the server where dspace is installed,
>> using the command:
>>
>> *ldapsearch -h satc.edu.br <http://satc.edu.br> -b "DC=satc,DC=edu,Dc=br"
>> -D "CN=Administrador,CN=Users,DC=satc,DC=edu,DC=br" -w Password
>> "(sAMAccountName=marcelo.silveira)"*
>>
>> It returns me the user data normally
>>
>> But when I try to log in using LDAP, it informs that the user is invalid.
>> Any idea? I have already tried setting up using the \, without it, and
>> all cause the same problem.
>>
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-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] Marking robots by user agent with `stats-util -m` is not implemented

[Alan Orth]

Dear Sean, Fabricio, and others,

I've made a handful of improvements to the script. Notably it can now read
regular expressions from the patterns file, which greatly improves the
number of hits matched¹. In my repository's case, with statistics from 2010
to 2019, I identified and purged 1.4 million more hits (in addition to the
2 million from before). Please test the script again to see if there are
any more bot hits matched on your statistics. Find the latest version
below. Check the help options and make sure to run without the purge option
(-p) to see if things look OK.

https://raw.githubusercontent.com/ilri/DSpace/5_x-prod/check-spider-hits.sh

Regards,

¹ Parsing these from the patterns file is tricky in bash and, even so, the
regular expression syntax used in the patterns file differs from that used
in Solr. Where possible, I've tried to convert them to a compatible format
on the fly, and where not possible I've ignored them (for example patterns
that use + or % are really tricky to handle).

On Tue, Nov 12, 2019 at 5:18 PM Alan Orth  wrote:

> Dear Sean,
>
> That's great! I'm glad you found it useful. I hope your manager isn't too
> depressed to see the numbers go down. ;)
>
> Regarding the difference in between runs, it looks like it has to do with
> the order of the user agent patterns in the file. For example, there are
> 325498 hits from "Googlebot" which get purged first, then there's a later
> user agent "bot" which matches 520514 requests, but 325498 of those would
> have already been purged from the "Googlebot" match. There are also about
> 100,000 matches for "robot" and "robots", both of which overlap with the
> "bot" pattern and each other. Maybe I should add a note to the output of
> the total to say it's not a reliable number. The most accurate number would
> be the hits actually purged.
>
> Also, I think I'm going to change the purge option to just be "-p" without
> an argument like the debug flag... to be consistent and require less
> typing...
>
> Cheers,
>
> On Tue, Nov 12, 2019 at 2:50 PM Sean Carte  wrote:
>
>> Thanks, Alan!
>>
>> Total number of bot hits purged: 575004
>>
>> One thing I found curious is that I first ran it with -pno -d, then -pyes
>> and got a different result each time:
>>
>> dspace@ir:/home/dspace$ scripts/check-spider-hits.sh -u
>> http://localhost:8080/solr -f
>> /dspacecris-dut/config/spiders/agents/example -pno -d
>> (DEBUG) Using spiders pattern file:
>> /dspacecris-dut/config/spiders/agents/example
>> (DEBUG) Checking for hits from spider: AllenTrack
>> (DEBUG) Checking for hits from spider: Arachmo
>> (DEBUG) Checking for hits from spider: ContentSmartz
>> (DEBUG) Checking for hits from spider: DSurf
>> (DEBUG) Checking for hits from spider: EmailSiphon
>> (DEBUG) Checking for hits from spider: EmailWolf
>> (DEBUG) Checking for hits from spider: GetRight
>> (DEBUG) Checking for hits from spider: Googlebot
>> Found 325498 hits from Googlebot in statistics
>> (DEBUG) Checking for hits from spider: HTTrack
>> Found 1366 hits from HTTrack in statistics
>> (DEBUG) Checking for hits from spider: LOCKSS
>> (DEBUG) Checking for hits from spider: MSNBot
>> (DEBUG) Checking for hits from spider: Milbot
>> (DEBUG) Checking for hits from spider: MuscatFerre
>> (DEBUG) Checking for hits from spider: NABOT
>> (DEBUG) Checking for hits from spider: NaverBot
>> (DEBUG) Checking for hits from spider: OurBrowser
>> (DEBUG) Checking for hits from spider: Readpaper
>> (DEBUG) Checking for hits from spider: Strider
>> Found 1 hits from Strider in statistics
>> (DEBUG) Checking for hits from spider: Teoma
>> Found 2 hits from Teoma in statistics
>> (DEBUG) Checking for hits from spider: Wanadoo
>> Found 7 hits from Wanadoo in statistics
>> (DEBUG) Checking for hits from spider: WebCloner
>> (DEBUG) Checking for hits from spider: WebCopier
>> (DEBUG) Checking for hits from spider: WebReaper
>> (DEBUG) Checking for hits from spider: WebStripper
>> (DEBUG) Checking for hits from spider: WebZIP
>> (DEBUG) Checking for hits from spider: Webinator
>> (DEBUG) Checking for hits from spider: Webmetrics
>> (DEBUG) Checking for hits from spider: Wget
>> Found 170 hits from Wget in statistics
>> (DEBUG) Checking for hits from spider: alexa
>> Found 238 hits from alexa in statistics
>> (DEBUG) Checking for hits from spider: almaden
>> (DEBUG) Checking for hits from spider: appie
>> (DEBUG) Checking for hits from spider: architext
>> (DEBUG) Checking for hits from spider: arks
>> Found 18 hits from arks in statistics
>> (DEBUG) Ch

Re: [dspace-tech] Marking robots by user agent with `stats-util -m` is not implemented

[Alan Orth]

s from spider: scan4mail
> (DEBUG) Checking for hits from spider: scientificcommons
> (DEBUG) Checking for hits from spider: scirus
> (DEBUG) Checking for hits from spider: scooter
> (DEBUG) Checking for hits from spider: seekbot
> (DEBUG) Checking for hits from spider: seznambot
> (DEBUG) Checking for hits from spider: shoutcast
> (DEBUG) Checking for hits from spider: slurp
> Found 104 hits from slurp in statistics
> (DEBUG) Checking for hits from spider: sogou
> Found 2178 hits from sogou in statistics
> (DEBUG) Checking for hits from spider: speedy
> Found 139 hits from speedy in statistics
> (DEBUG) Checking for hits from spider: spider
> Found 23341 hits from spider in statistics
> (DEBUG) Checking for hits from spider: spiderman
> (DEBUG) Checking for hits from spider: spiderview
> (DEBUG) Checking for hits from spider: sunrise
> (DEBUG) Checking for hits from spider: superbot
> (DEBUG) Checking for hits from spider: surveybot
> (DEBUG) Checking for hits from spider: tailrank
> (DEBUG) Checking for hits from spider: technoratibot
> (DEBUG) Checking for hits from spider: titan
> (DEBUG) Checking for hits from spider: turnitinbot
> (DEBUG) Checking for hits from spider: twiceler
> (DEBUG) Checking for hits from spider: ucsd
> (DEBUG) Checking for hits from spider: ultraseek
> (DEBUG) Checking for hits from spider: urlaliasbuilder
> (DEBUG) Checking for hits from spider: urllib
> Found 66 hits from urllib in statistics
> (DEBUG) Checking for hits from spider: voila
> (DEBUG) Checking for hits from spider: webcollage
> (DEBUG) Checking for hits from spider: weblayers
> (DEBUG) Checking for hits from spider: webmirror
> (DEBUG) Checking for hits from spider: webreaper
> (DEBUG) Checking for hits from spider: wordpress
> (DEBUG) Checking for hits from spider: worm
> (DEBUG) Checking for hits from spider: xenu
> (DEBUG) Checking for hits from spider: yacy
> Found 2 hits from yacy in statistics
> (DEBUG) Checking for hits from spider: yahoo
> Found 153 hits from yahoo in statistics
> (DEBUG) Checking for hits from spider: yahoofeedseeker
> (DEBUG) Checking for hits from spider: yahooseeker
> (DEBUG) Checking for hits from spider: yandex
> Found 8591 hits from yandex in statistics
> (DEBUG) Checking for hits from spider: yodaobot
> (DEBUG) Checking for hits from spider: zealbot
> (DEBUG) Checking for hits from spider: zeus
> (DEBUG) Checking for hits from spider: zyborg
> (DEBUG) Checking for hits from spider: parsijoo
> Found 38 hits from parsijoo in statistics
> (DEBUG) Checking for hits from spider: validator
>
> Total number of hits from bots: 1361976
> dspace@ir:/home/dspace$ scripts/check-spider-hits.sh -u
> http://localhost:8080/solr -f
> /dspacecris-dut/config/spiders/agents/example -pyes
> Purging 325498 hits from Googlebot in statistics
> Purging 1366 hits from HTTrack in statistics
> Purging 1 hits from Strider in statistics
> Purging 2 hits from Teoma in statistics
> Purging 7 hits from Wanadoo in statistics
> Purging 170 hits from Wget in statistics
> Purging 238 hits from alexa in statistics
> Purging 18 hits from arks in statistics
> Purging 195014 hits from bot in statistics
> Purging 72 hits from bspider in statistics
> Purging 14714 hits from crawl in statistics
> Purging 4 hits from custo in statistics
> Purging 10626 hits from findlinks in statistics
> Purging 2271 hits from google in statistics
> Purging 765 hits from heritrix in statistics
> Purging 5 hits from ia_archiver in statistics
> Purging 598 hits from ichiro in statistics
> Purging 2 hits from java in statistics
> Purging 113 hits from libwww in statistics
> Purging 8 hits from motor in statistics
> Purging 1 hits from python in statistics
> Purging 103 hits from slurp in statistics
> Purging 2178 hits from sogou in statistics
> Purging 139 hits from speedy in statistics
> Purging 20938 hits from spider in statistics
> Purging 66 hits from urllib in statistics
> Purging 49 hits from yahoo in statistics
> Purging 38 hits from parsijoo in statistics
>
> Total number of bot hits purged: 575004
>
>
> On Sun, 10 Nov 2019 at 18:12, Alan Orth  wrote:
>
>> Dear list,
>>
>> I ended up writing a little bash script¹ to read known spider user agents
>> from a file such as DSpace's `example` pattern file and check for matching
>> documents in the Solr statistics core (or yearly statistics shards). It can
>> optionally purge the matched records, but this is disabled by default. In
>> our case, I purged 2 MILLION hits from our statistics core, which has data
>> going back nine years. It feels nice to know that our usage statistics are
>> more accurate now, though the repository managers will be depressed because
&

Re: [dspace-tech] Re: DSpace LDAP

[Alan Orth]

Dear Anda,

Which kind of LDAP are you using? Is it Active Directory? Make sure your
connection strings in config/modules/authentication-ldap.cfg are correct.
If it is Active Directory you will probably need at least the following:

ldap.provider_url = ldaps://ad.yourorganization.edu:636/
id_field = sAMAccountName
search_context = dc=yourorganization,dc=edu
search_scope = 2
search.user = ldap-u...@yourorganization.edu
search.password = yourpassword

If you have a Linux workstation you can try to verify your settings by
performing a search with the ldapsearch utility from the ldap-utils package:

$ ldapsearch -x -H ldaps://ad.yourorganization.edu:636/ -b
"dc=yourorganization,dc=edu" -D "ldap-u...@yourorganization.edu" -W
"(sAMAccountName=ldap-user)"

Hope that helps,


On Mon, Nov 11, 2019 at 4:34 PM Anda  wrote:

> Sorry, We use DSpace CRIS
>
> pirmdiena, 2019. gada 11. novembris 16:33:52 UTC+2, Anda rakstīja:
>>
>> Hello,
>>
>> How do I configure LDAP authorization correctly?
>>
>> We see the following window, but cannot login with LDAP. What is wrong?
>>
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> Conduct: https://duraspace.org/about/policies/code-of-conduct/
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] Marking robots by user agent with `stats-util -m` is not implemented

[Alan Orth]

Dear Fabricio,

Thank you for trying the script! It sounds like there is something wrong
with the  Solr query parameters that causes the XML result to be malformed
(it is parsed with xmllint in the script). I've added some additional logic
checks and a debug option to the script. Please get a new copy of the
script¹ and try again with the "-d" option to see if you can narrow the
issue down:

$ ./check-spider-hits.sh -d -u http://localhost:8080/solr -f
~/dspace/config/spiders/agents/example

Regards,

¹
https://raw.githubusercontent.com/ilri/DSpace/5_x-prod/check-spider-hits.sh

On Tue, Nov 12, 2019 at 6:26 AM Fabricio Costa  wrote:

> Hello, Alan.
>
> I tried the bash script and received the following message (several times).
>
> -:1: parser error : Document is empty
>
>
>
>
> Em domingo, 10 de novembro de 2019 14:12:23 UTC-2, Alan Orth escreveu:
>>
>> Dear list,
>>
>> I ended up writing a little bash script¹ to read known spider user agents
>> from a file such as DSpace's `example` pattern file and check for matching
>> documents in the Solr statistics core (or yearly statistics shards). It can
>> optionally purge the matched records, but this is disabled by default. In
>> our case, I purged 2 MILLION hits from our statistics core, which has data
>> going back nine years. It feels nice to know that our usage statistics are
>> more accurate now, though the repository managers will be depressed because
>> their content wasn't as popular as they thought. :)
>>
>> To use the script you need to be able to access your DSpace's Solr
>> instance directly, either by running the script on the same machine or by
>> making the port available via an SSH tunnel:
>>
>> $ ssh -L 8080:localhost:8080 dspace.example.edu
>>
>> Then you can run the script, specifying the location of the Solr instance
>> and the location of the patterns file:
>>
>> $ ./check-spider-hits.sh -u http://localhost:8080/solr -f
>> ~/dspace/config/spiders/agents/example
>>
>> Read the script source or check its help text with `-h` to see more
>> options. There is one implementation detail that is interesting: DSpace
>> uses the spider agents file from the COUNTER-Robots project², which
>> contains some plaintext names as well as regular expressions. Unfortunately
>> Solr 4.x as used in current DSpace 5 and 6 only has basic support for
>> regular expressions. For example, all patterns are anchored with ^ and $ by
>> default, you need to use [0-9] instead of \d, etc. As such, my script does
>> some basic filtering of the input pattern file to remove user agents that
>> are using regular expression characters. I imagine this is part of the
>> reason why DSpace's mark spider feature was never completed for user
>> agents, because the example agents file used by SpiderDetector.java cannot
>> be used when searching Solr later for marking spiders.
>>
>> I hope this is helpful for someone. Thanks to the contributors of the
>> COUNTER-Robots project for curating this list.
>>
>> Regards,
>>
>> ¹ https://github.com/ilri/DSpace/blob/5_x-prod/check-spider-hits.sh
>> ² https://github.com/atmire/COUNTER-Robots
>>
>> On Thu, Nov 7, 2019 at 3:55 PM Alan Orth  wrote:
>>
>>> Thank you, Mark. For now I'll just settle for an updated list of spider
>>> agents from COUNTER-Robots¹ (dropping the text file into
>>> dspace/config/spiders/agents seems to work).
>>>
>>> Regards,
>>>
>>> ¹ https://github.com/atmire/COUNTER-Robots
>>>
>>> On Tue, Nov 5, 2019 at 4:02 PM Mark H. Wood  wrote:
>>>
>>>> On Mon, Nov 04, 2019 at 11:10:25PM +0200, Alan Orth wrote:
>>>> > The DSpace 5.x (and presumably 6.x) documentation[0] suggests that it
>>>> is
>>>> > possible to mark existing Solr statistics records as being bots or
>>>> spiders
>>>> > using the following command:
>>>> >
>>>> > $ dspace stats-util -m
>>>> >
>>>> > After trying to test this with an updated list of user agents[1] for a
>>>> > while I realized that the feature is only implemented for IPs. As it
>>>> stands
>>>> > right now the code in StatisticsClient.java only marks robots based on
>>>> > their IPs, but not on their user agents or domains:
>>>> >
>>>> > else if (line.hasOption('m'))
>>>> > {
>>>> > SolrLogger.markRobotsByIP();
>>>> > }
>>>> >
>>>> > Strangely enough, SolrLogger has a markRobotByUserAgent() f

Re: [dspace-tech] Marking robots by user agent with `stats-util -m` is not implemented

[Alan Orth]

Thank you, Mark. For now I'll just settle for an updated list of spider
agents from COUNTER-Robots¹ (dropping the text file into
dspace/config/spiders/agents seems to work).

Regards,

¹ https://github.com/atmire/COUNTER-Robots

On Tue, Nov 5, 2019 at 4:02 PM Mark H. Wood  wrote:

> On Mon, Nov 04, 2019 at 11:10:25PM +0200, Alan Orth wrote:
> > The DSpace 5.x (and presumably 6.x) documentation[0] suggests that it is
> > possible to mark existing Solr statistics records as being bots or
> spiders
> > using the following command:
> >
> > $ dspace stats-util -m
> >
> > After trying to test this with an updated list of user agents[1] for a
> > while I realized that the feature is only implemented for IPs. As it
> stands
> > right now the code in StatisticsClient.java only marks robots based on
> > their IPs, but not on their user agents or domains:
> >
> > else if (line.hasOption('m'))
> > {
> > SolrLogger.markRobotsByIP();
> > }
> >
> > Strangely enough, SolrLogger has a markRobotByUserAgent() function that
> is
> > never called anywhere in the Java code base (also it seems to only be
> > partially implemented, as it does not iterate over agents).
> >
> > Should I file a bug? This issue affects DSpace 5.x and 6.x for sure.
>
> https://jira.duraspace.org/browse/DS-2431
>
> There are several Issues related to completing the work on extended
> spider marking and filtering.
>
> --
> Mark H. Wood
> Lead Technology Analyst
>
> University Library
> Indiana University - Purdue University Indianapolis
> 755 W. Michigan Street
> Indianapolis, IN 46202
> 317-274-0749
> www.ulib.iupui.edu
>
> --
> All messages to this mailing list should adhere to the DuraSpace Code of
> Conduct: https://duraspace.org/about/policies/code-of-conduct/
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> .
>


-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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[dspace-tech] Marking robots by user agent with `stats-util -m` is not implemented

[Alan Orth]

Dear list,

The DSpace 5.x (and presumably 6.x) documentation[0] suggests that it is
possible to mark existing Solr statistics records as being bots or spiders
using the following command:

$ dspace stats-util -m

After trying to test this with an updated list of user agents[1] for a
while I realized that the feature is only implemented for IPs. As it stands
right now the code in StatisticsClient.java only marks robots based on
their IPs, but not on their user agents or domains:

else if (line.hasOption('m'))
{
SolrLogger.markRobotsByIP();
}

Strangely enough, SolrLogger has a markRobotByUserAgent() function that is
never called anywhere in the Java code base (also it seems to only be
partially implemented, as it does not iterate over agents).

Should I file a bug? This issue affects DSpace 5.x and 6.x for sure.

Regards,

[0]
https://wiki.duraspace.org/display/DSDOC5x/SOLR+Statistics+Maintenance#SOLRStatisticsMaintenance-FilteringandPruningSpiders
[1] https://github.com/atmire/COUNTER-Robots
-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] REST-API in DSpace 5.8

[Alan Orth]

Dear Kosmas,

Yes this is a drawback of the current REST API. It is not possible to
specify a wildcard in the find-by-metadata-field endpoint. :(

I hope it will be better in the new DSpace 7 REST API!

Regards,

On Wed, Jul 31, 2019 at 10:06 AM Kosmas Kaifel 
wrote:

> Dear all,
>
> I want to list Items over the REST-API with the following command:
>
> curl -X POST -H "Content-Type: application/json" -d
> '{"key":"dc.contributor.author", _
> "value":", X", "language": null}'
> https:///rest/items/find-by-metadata-field
>
> With this command I receive only items with the language = null in the
> databasetable metadatavalue,
> but we have also metadataentries with the languages 'de' and 'en'.
>
> How can I list all items in one command with different languages like
> 'null', 'de', and 'en'.
>
> Thank yo for your help
> Kosmas
>
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>


-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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[dspace-tech] Pipeline to check and fix CSV metadata

[Alan Orth]

Dear list,

For years I've used OpenRefine to do basic sanity checks and cleaning of
CSV files before batch upload (either directly or with SAFBuilder).
OpenRefine makes it very easy to do things like trim whitespace, facet on
text values or custom patterns to eyeball outliers like invalid dates or
ISSNs, and you can even write Python (though it's Python 2 and quite
cumbersome). This is much more powerful and methodical than using a
spreadsheet application for the same task, but still becomes tedious when
you have dozens of metadata fields and hundreds or thousands of records.

To make a long story short, I've just written a metadata cleaning pipeline
geared towards working with CSVs in the DSpace ecosystem. Its
implementation is basically a series of checks and fixes applied as a
pipeline. For example, the order is roughly:

1. Strip leading, trailing, and excessive whitespace
2. Strip newlines
3. Remove "unnecessary" Unicode characters like non-breaking spaces
4. Fix invalid multi-value separators like "Kenya|Ethiopia"
5. Drop duplicate metadata values
6. Validate subject terms against AGROVOC REST API
7. Validate languages against ISO 639-2 or ISO 639-3
8. Validate ISSNs and ISBNs
9. Validate dates against ISO 8601 (and warn if date missing)

It is slightly geared towards our repository's workflow, but I think the
implementation is simple and powerful enough that many of you could benefit
from it. I will keep working to extend it. If you are interested in using
or improving it you can find the code on GitHub:

https://github.com/alanorth/csv-metadata-quality

Regards,
-- 
Alan Orth
alan.o...@gmail.com
https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] How to upgrade the PostgreSQL server

[Alan Orth]

Hello,

I'm not sure DSpace 4.x works with PostgreSQL 11. Support for PostgreSQL 10
was only just improved for DSpace 5, 6, and 7 in 2019-03:

https://jira.duraspace.org/browse/DS-3854

Regards,

On Thu, Jun 6, 2019 at 10:31 AM George Peterson 4th <667...@gmail.com>
wrote:

> try to login via commandline. it'll show you the problem, it can be a
> wrong password or postgres configuration issue.
> from dspace.cfg take the connection credentials:
>
> db.url = jdbc:postgresql://localhost:5432/dspace_dbname
> 
> # Database username and password
> db.username = dspace_dbuser
> db.password = a
>
> and issue this with 9.6 running (it'll prompt for a password):
> psql -Udspace_dbuser dspace_dbname
>
> then do the same with 11
>
> On Thu, Jun 6, 2019 at 12:16 AM Stan Orlov  wrote:
>
>> Greetings!
>>
>> I am running DSpace 4.X on a test server on a Windows 2008 server
>> machine. I decided to upgrade PostgreSQL 9.6 to 11.  So, I installed
>> PostgreSQL 11 and created the "dspace" user and an empty "dspace" database.
>> In 9.6 created a dump and imported it into 11.  Now, when I try to access
>> in a browser http://localhost/xmlui with 9.6 server running, I can see
>> my DSpace instance, but when I turn it off and turn on 11, I can only see a
>> blank page.
>>
>> What am I doing wrong?
>>
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>> .
>>
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-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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Re: [dspace-tech] Re: Solr lock obtained timeout

[Alan Orth]

Dear list,

I'm still experiencing sporadic occurrences of the "Error opening new
searcher" issue with the Solr statistics core. In our case Tomcat always
shuts down cleanly, and even so, manually deleting the write locks before
Tomcat startup doesn't seem to help. Thinking about this a bit more, it
sounds plausible to me that high load or slow disks could indeed cause a
timeout waiting for a write lock with large Solr cores. Our server has an
SSD, but is indeed busy, and we have nine years of statistics with hundreds
of millions of events.

Some Solr parameter that seems like it should help is writeLockTimeout. The
default in solrconfig.xml is 1000ms (1 sec). I tried setting it to 5000 and
1, neither of which helped. Should I try to bump this setting up to
some obscenely high value? Could there be another factor here, like JVM
heap size or settings? Happy to discuss experiences others are having.

Thanks,

P.S. I've been running Solr 4.10.4 in DSpace 5.8 production for over one
month now (versus 4.10.2 in DSpace pom.xml).

On Thu, Mar 21, 2019 at 11:54 PM Alan Orth  wrote:

> Thanks for the response, Mark.
>
> I have started testing Solr 4.10.4 in a few development environments will
> share my notes after some time. Regarding the lock files, I might be
> barking up the wrong tree because it seems like Solr never deletes these: I
> did a quick check by adding a `find /dspace -type f -iname '*.lock'` before
> and after the Tomcat service starts and stops, and the lock files are
> always there. I'm not sure what to make of that...
>
> Regards,
>
> On Tue, Mar 19, 2019 at 6:02 PM Mark H. Wood  wrote:
>
>> On Tuesday, March 19, 2019 at 11:35:47 AM UTC-4, Alan Orth wrote:
>>>
>>> Dear list,
>>>
>>> In the last few months we've been having issues with Solr throwing
>>> "Error creating core" errors one out of every two times we start Tomcat.
>>> This results in our statistics from previous years being inaccessible. For
>>> example, from the Solr log yesterday:
>>>
>>> 2019-03-18 12:32:39,799 ERROR org.apache.solr.core.CoreContainer @ Error
>>> creating core [statistics-2018]: Error opening new searcher
>>> ...
>>> Caused by: org.apache.solr.common.SolrException: Error opening new
>>> searcher
>>> at
>>> org.apache.solr.core.SolrCore.openNewSearcher(SolrCore.java:1565)
>>> at org.apache.solr.core.SolrCore.getSearcher(SolrCore.java:1677)
>>> at org.apache.solr.core.SolrCore.(SolrCore.java:845)
>>> ... 31 more
>>> Caused by: org.apache.lucene.store.LockObtainFailedException: Lock
>>> obtain timed out: NativeFSLock@
>>> /dspace/solr/statistics-2018/data/index/write.lock
>>>
>>> Some old Stack Overflow posts recommend setting Solr's address space to
>>> unlimited (ulimit -v unlimited), but the issue still occurs seemingly
>>> randomly for us.
>>>
>>
>>
>> I think that raising ulimit would only help if Tomcat's JVM memory
>> settings add up to more than the OS was configured to give the process.
>> Those recommendations may have been for stand-alone Solr running in its own
>> Jetty instance.
>>
>>
>>
>>> Now I usually just try to restart Tomcat again, or sometimes I shut it
>>> down cleanly, delete all the Solr write locks, and then start Tomcat back
>>> up. It's starting to feel a bit superstitious... maybe I should try to kill
>>> a chicken.
>>>
>>
>>
>>> We are running DSpace 5.8 with Tomcat 7.0.93 on Ubuntu 16.04. We
>>> upgraded from DSpace 5.5 in late 2018 and 2019 was the first year that the
>>> yearly stats-util sharding completed successfully (fixed in DSpace 5.7). I
>>> believe our problems are related to the existence of these shards. It feels
>>> like there is some kind of *race condition* because it only every so
>>> often and it's not always the same core that Solr is refusing to create.
>>> Sometimes it's statistics-2018, statistics-2015, etc.
>>>
>>
>>
>> So, sometimes Solr doesn't remove all of its locks when shut down.  Does
>> it log ([DSpace]log/solr*.log) anything interesting at shutdown? does
>> Tomcat?
>>
>>
>>
>>> On this note, is there any reason we are still using Solr 4.10.2 with
>>> DSpace 5.x and 6.x? The Solr project issued two bug fix releases in that
>>> series—4.10.3 and 4.10.4—and there are about fifty bug fixes in those
>>> releases, some of which address memory leaks and shard handling. See the
>>> change logs for 4.10.3¹ and 4.10.4². As an experiment I just bumped the
>>> 

Re: [dspace-tech] Re: Cannot expunge items in DSpace 5.8

[Alan Orth]

Thank you, Adan and Genevieve. It's good to know I'm not alone. There's
definitely a bug waiting to be filed here, though I'm not sure on which
component!

In this case the item seems to be in pre-submitted state (in the
workspaceitem table). After deleting the item's bitstream in the XMLUI and
running `dspace cleanup -v` to remove it from the assetstore, I removed the
item via SQL:

dspace=# DELETE FROM metadatavalue WHERE resource_id=74648;
dspace=# DELETE FROM workspaceitem WHERE item_id=74648;
dspace=# DELETE FROM item WHERE item_id=74648;

Are there any other tables where I should look to completely remove this
item from the database?

Regards,

On Wed, May 1, 2019 at 2:00 AM  wrote:

> Hi Alan,
>
> Just to be sure are they in a workflow currently?  You should be able to
> match the item_id's with the workflowitem table, also check that they
> aren't in the pre-submitted state i.e. the workspaceitem table..
>
> Regards,
>
> Genevieve
>
> On Tuesday, April 30, 2019 at 5:15:35 PM UTC+10, Alan Orth wrote:
>>
>> Dear list,
>>
>> I have discovered some items in my repository that are in some weird
>> state. They don't have handles, don't appear in any collections, are NOT in
>> the archive, and I can't delete them. I've tried to "permanently delete"
>> them via the XMLUI admin interface as well as "expunge" them by CSV
>> metadata upload action, but they are still present.
>>
>> Has anyone run into this issue before? Aside from the fact that these
>> items are in some weird limbo state, they are actually causing the REST
>> API's /items/find-by-metadata-value endpoint to throw an exception because
>> the anonymous user doesn't have permission to read some of these items that
>> are returned as having a metadata match (see my message last week on this
>> list regarding that).
>>
>> Thank you,
>>
>> --
>> Alan Orth
>> alan...@gmail.com
>> https://picturingjordan.com
>> https://englishbulgaria.net
>> https://mjanja.ch
>> "In heaven all the interesting people are missing." ―Friedrich Nietzsche
>>
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-- 
Alan Orth
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https://picturingjordan.com
https://englishbulgaria.net
https://mjanja.ch
"In heaven all the interesting people are missing." ―Friedrich Nietzsche

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