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

2020-02-26 Thread 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
>
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> .
>


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

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Re: [dspace-tech] DSpace deletion

2020-02-26 Thread Paul Münch 
Hello,

remove all DSpace components from your system:

- DSpace directories
- Tomcat server
- Postgresql server

That's all.

Kind regards,

Paul Münch


Am 14.02.20 um 13:39 schrieb Maiia Zbitnieva:
> Good day!
> Help me please. I installed DSpace 6.x on ubuntu 18. How to delete
> DSpace 6.x from ubuntu 18?
> With respect.
>
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Re: [dspace-tech] Difficulty setting up dspace 6.3

2020-02-26 Thread Mark H. Wood 
On Wed, Feb 26, 2020 at 05:12:49PM +0530, Ashim Kapoor wrote:
[snip]
> Also in BOTH cases I get this warning :-
> 
> $ mvn package
> [INFO] Scanning for projects...
> [WARNING] The project org.dspace:dspace-parent:pom:6.3 uses prerequisites
> which is only intended for maven-plugin projects but not for non
> maven-plugin projects. For such purposes you should use the
> maven-enforcer-plugin. See
> https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html

That warning can be ignored, and I think it will be fixed in DSpace 7.

-- 
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] Permissions of the [dspace] directory

2020-02-26 Thread Mark H. Wood 
On Wed, Feb 26, 2020 at 10:30:57AM +0530, Ashim Kapoor wrote:
> I am reading this
> 
> 
> At one place it says :
> # Change [dspace] and all subfolders to be owned by "tomcat"
> chown -R tomcat:tomcat [dspace]
> 
> At another place it says :
> mkdir [dspace]
> chown dspace [dspace]

Thank you for pointing this out.  I thought we had removed all of that
confusion.

> I think that FIRST we have to do :-
> 
> 1. chown dspace [dpspace]
> 2. Then run maven and ant
> 
> When I am building the webapp using maven and ant the user dspace needs
> ownership over the [dspace] directory.
> 
> Once it is built, THEN we should do :-
> 
> chown -R tomcat:tomcat [dspace]
> 
> So that tomcat has permissions over dspace directory.
> 
> Do I understand this correctly?

I think that would work.  But, read on.

> Query: Suppose after running maven and ant, I do:-
> 
> cp -R [dspace]/webapps/* [tomcat]/webapps*
> 
> Then does tomcat still need to have permissions over [dpsace] ? In other
> words, do I still need to do:-
> 
> chown -R tomcat:tomcat [dspace]

Tomcat needs read access to all of the files in [dspace], and write
access to many of them.  The easiest way to do this is to have them
all owned by the account which runs Tomcat, with rwx access for
owner.  The documentation calls that account 'tomcat', but on your
system Tomcat may have been installed to use an account with a
different name.  Whatever that account is called, it should own the
files that make up the installed instance of DSpace ([dspace]).

The build directory ([dspace-source]) can be owned by any account you
choose.  You just need a way to run the installer so that it can read
the [dspace-source] directory tree and write the [dspace] directory
tree.

There is no need for a separate 'dspace' account.  We need to finish
removing that from the documentation.  DSpace does not know or care
about OS accounts.  Tomcat has to care because it is what needs the
permissions -- DSpace runs inside Tomcat and uses Tomcat's
permissions.

-- 
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] new table in 6.3

2020-02-26 Thread Mark H. Wood 
On Tue, Feb 25, 2020 at 02:22:01PM -0500, Jose Blanco wrote:
> I just tried:
> 
>Query q = getHibernateSession(context).createSQLQuery("SELECT * FROM
> EPerson  WHERE uuid in (SELECT proxy_id from proxies where depositor_id = '"
> + depositor_id.toString() + "')");
> 
>q.setResultTransformer(Transformers.aliasToBean(EPerson.class));
> 
>List results = q.list();
> 
>return results;
> 
> 
> 
> And I'm getting:
> 
> 
> org.hibernate.MappingException: No Dialect mapping for JDBC type: 
> 
> 
> in this line:
> 
>List results = q.list();

I haven't dealt with this myself, but the first thing I would check is
whether Hibernate understands that proxies.proxy_id is of type UUID.

I would guess that you'll continue to fight issues like this so long
as "proxies" is not associated with an ORM entity type.  That would
mean writing an entity class 'Proxies' to tell Hibernate all about
your table.  You can find examples in
'dspace-api/src/main/java/org/dspace/content'.  To fit in with the
patterns of DSpace's object-relational mapping, you probably should
also write:

  ProxiesDAO
  ProxiesDAOImpl
  ProxiesService
  ProxiesServiceImpl

You'll also need to add a  element to
dspace/config/hibernate.cfg.xml so that Hibernate knows that it should
expect to find your entity class.

Yes, I know:  it looks like more frosting than cake.  But, if you use
Hibernate, then Hibernate needs a lot of information about what it is
to manipulate for you.  And, it will be easier to use other types as
examples if you follow the complete pattern.

-- 
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] JAVA_OPTS

2020-02-26 Thread Paul Münch 
Hello,

if you don't define $JAVA_OPTS it's set in the start script
(https://github.com/DSpace/DSpace/blob/master/dspace/bin/dspace#L36-L40).

Kind regards,

Paul Münch

Am 14.02.20 um 18:59 schrieb Maiia Zbitnieva (Майя Збитнева):
> I use Java 8 as indicated in DSpace installation instruction. An I use
> Tomcat 9 because there isn't restriction in DSpace documentation on
> version of Tomcat. Why did say that problems can be with version 9 of 
> Tomcat? 
>
> пятница, 14 февраля 2020 г., 18:53:29 UTC+2 пользователь Michael Plate
> написал:
>
> Am 14.02.20 um 10:40 schrieb Майя Збитнева:
> > I use ubuntu 18 and tomcat 9. I couldn`t found file
> > /etc/default/tomcat9. But I found in Internet the following
> > recommendation: "/etc/systemd/system/tomcat.service". Is that
> right?
>
>
> Don't know Ubuntu 18, sorry.
> You might get problems anyway with tomcat9 and Java newer than
> Version 8
> - you can run DSpace with Java 11, but can't install presumably.
>
> CU
>
> Michael
>
>
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Re: [dspace-tech] Difficulty setting up dspace 6.3

2020-02-26 Thread Sean Carte 
I don't know about your maven-enforcer-plugin error, but the first error is
a permissions problem. As root:
 chown -R dspace:dspace /home/dspace/dspace-6.3-release/

On Wed, 26 Feb 2020 at 13:43, Ashim Kapoor 
wrote:

> Dear All,
>
> I am following instructions on this page:-
>
> https://wiki.lyrasis.org/display/DSDOC6x/Installing+DSpace
>
> When I do mvn package as root I don't get the following error.
>
> However when I do mvn package as unix user dspace I get the following
> error:-
>
>
> [INFO] Reactor Summary for DSpace Parent Project 6.3:
> [INFO]
> [INFO] DSpace Parent Project .. SUCCESS [
>  1.209 s]
> [INFO] DSpace Addon Modules ... SUCCESS [
>  0.038 s]
> [INFO] DSpace Kernel :: Additions and Local Customizations  SUCCESS [
>  6.209 s]
> [INFO] DSpace XML-UI (Manakin) :: Local Customizations  SUCCESS [
> 15.203 s]
> [INFO] DSpace JSP-UI :: Local Customizations .. SUCCESS [
>  7.210 s]
> [INFO] DSpace RDF :: Local Customizations . SUCCESS [
>  6.657 s]
> [INFO] DSpace REST :: Local Customizations  SUCCESS [
>  8.845 s]
> [INFO] DSpace SWORD :: Local Customizations ... SUCCESS [
>  6.799 s]
> [INFO] DSpace SWORD v2 :: Local Customizations  SUCCESS [
>  6.757 s]
> [INFO] DSpace SOLR :: Local Customizations  FAILURE [
>  3.155 s]
> [INFO] DSpace OAI-PMH :: Local Customizations . SKIPPED
> [INFO] DSpace Assembly and Configuration .. SKIPPED
> [INFO]
> 
> [INFO] BUILD FAILURE
> [INFO]
> 
> [INFO] Total time:  01:02 min
> [INFO] Finished at: 2020-02-26T17:04:45+05:30
> [INFO]
> 
> [ERROR] Failed to execute goal
> org.apache.maven.plugins:maven-war-plugin:2.6:war (default-war) on project
> solr: Failed to copy file for artifact
> [org.dspace:dspace-solr:jar:classes:6.3:compile]:
> /home/dspace/dspace-6.3-release/dspace/modules/solr/target/solr-6.3/WEB-INF/lib/dspace-solr-6.3-classes.jar
> (Permission denied) -> [Help 1]
> [ERROR]
> [ERROR] To see the full stack trace of the errors, re-run Maven with the
> -e switch.
> [ERROR] Re-run Maven using the -X switch to enable full debug logging.
> [ERROR]
> [ERROR] For more information about the errors and possible solutions,
> please read the following articles:
> [ERROR] [Help 1]
> http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
> [ERROR]
> [ERROR] After correcting the problems, you can resume the build with the
> command
> [ERROR]   mvn  -rf :solr
> $
>
> Also in BOTH cases I get this warning :-
>
> $ mvn package
> [INFO] Scanning for projects...
> [WARNING] The project org.dspace:dspace-parent:pom:6.3 uses prerequisites
> which is only intended for maven-plugin projects but not for non
> maven-plugin projects. For such purposes you should use the
> maven-enforcer-plugin. See
> https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html
>
>
> Can someone please help me ?
>
> Thank you,
> Ashim
>
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> .
>


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

2020-02-26 Thread 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
>>
>> --
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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] Maximum number of DB connections in pool

2020-02-26 Thread 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
>
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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] Difficulty setting up dspace 6.3

2020-02-26 Thread Ashim Kapoor 
Dear All,

I am following instructions on this page:-

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

When I do mvn package as root I don't get the following error.

However when I do mvn package as unix user dspace I get the following
error:-


[INFO] Reactor Summary for DSpace Parent Project 6.3:
[INFO]
[INFO] DSpace Parent Project .. SUCCESS [
 1.209 s]
[INFO] DSpace Addon Modules ... SUCCESS [
 0.038 s]
[INFO] DSpace Kernel :: Additions and Local Customizations  SUCCESS [
 6.209 s]
[INFO] DSpace XML-UI (Manakin) :: Local Customizations  SUCCESS [
15.203 s]
[INFO] DSpace JSP-UI :: Local Customizations .. SUCCESS [
 7.210 s]
[INFO] DSpace RDF :: Local Customizations . SUCCESS [
 6.657 s]
[INFO] DSpace REST :: Local Customizations  SUCCESS [
 8.845 s]
[INFO] DSpace SWORD :: Local Customizations ... SUCCESS [
 6.799 s]
[INFO] DSpace SWORD v2 :: Local Customizations  SUCCESS [
 6.757 s]
[INFO] DSpace SOLR :: Local Customizations  FAILURE [
 3.155 s]
[INFO] DSpace OAI-PMH :: Local Customizations . SKIPPED
[INFO] DSpace Assembly and Configuration .. SKIPPED
[INFO]

[INFO] BUILD FAILURE
[INFO]

[INFO] Total time:  01:02 min
[INFO] Finished at: 2020-02-26T17:04:45+05:30
[INFO]

[ERROR] Failed to execute goal
org.apache.maven.plugins:maven-war-plugin:2.6:war (default-war) on project
solr: Failed to copy file for artifact
[org.dspace:dspace-solr:jar:classes:6.3:compile]:
/home/dspace/dspace-6.3-release/dspace/modules/solr/target/solr-6.3/WEB-INF/lib/dspace-solr-6.3-classes.jar
(Permission denied) -> [Help 1]
[ERROR]
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e
switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR]
[ERROR] For more information about the errors and possible solutions,
please read the following articles:
[ERROR] [Help 1]
http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR]
[ERROR] After correcting the problems, you can resume the build with the
command
[ERROR]   mvn  -rf :solr
$

Also in BOTH cases I get this warning :-

$ mvn package
[INFO] Scanning for projects...
[WARNING] The project org.dspace:dspace-parent:pom:6.3 uses prerequisites
which is only intended for maven-plugin projects but not for non
maven-plugin projects. For such purposes you should use the
maven-enforcer-plugin. See
https://maven.apache.org/enforcer/enforcer-rules/requireMavenVersion.html


Can someone please help me ?

Thank you,
Ashim

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