[Dspace-tech] Idle In Transaction Problem
Hi,
This may have been fixed in more recent versions of DSpace; we're on 1.8.2.
I'd been getting this problem a lot, to the point where our tomcat was
shutting down about once a week.
https://wiki.duraspace.org/display/DSPACE/Idle+In+Transaction+Problem
I wrote a script to try and find what DSpace code coincides with the idle
processes, see below.
It's not airtight, but I did find that /feed/* came up a lot (10%) in the
list of requests. Has anyone ever looked at the feeds code to see if it is
closing transactions properly?
Regards,
Joseph
Guts of the bash script:
pgIdle=($(ps -ef | grep 'postgres.*idle')) #array of idle processes
idleProcs=$(( ${#pgIdle[@]} - 1 )) #count the idle processes, minus one to
get rid of the grep command
while [ $idleProcs -le $1 ]
do
pgIdle=($(ps -ef | grep 'postgres.*idle'))
idleProcs=$(( ${#pgIdle[@]} - 1 ))
done (tail -n 0 -f /var/log/apache2/access.log ./pgtest.out) #output
the logfile as long as the while loop runs
Collected data for a week using cron, running every five minutes until two
idle processes built up:
*/5 * * * * /home/dspace/pgtest.sh 2
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Re: [Dspace-tech] Shibboleth and role based groups?
Thanks Tim, You might be hitting this bug: https://jira.duraspace.org/browse/DS-2527 Yes, it does look like what I'm experiencing, but I've tried the fix and it didn't seem to do the job for me - I uncommented the following in dspace.cfg: org.dspace.content.Collection.findAuthorizedPerformanceOptimize = false - and restarted Tomcat, but no joy. In authentication-shibboleth.cfg, I have: -- # The shibboleth header to do role-based mappings role-header = affiliation # Whether to ignore the attribute's scope or value. role-header.ignore-scope = true #role-header.ignore-value = false # Default mappings of roles values to a comma separated list of DSpace group # names (Case Sensitive). #role.faculty = Faculty, Member role.staff = STIR_USERS -- But, when I log on as a user with the appropriate role defined, they are not allocated to the named group (which should give them deposit permissions as the special group has deposit permissions in my one and only test group). With logging at DEBUG, I can see the role header (affiliation) being passed over (amongst others): eppn='m...@stir.ac.uk' affiliation='st...@stir.ac.uk;mem...@stir.ac.uk' unscoped-affiliation='' entitlement='' targeted-id='' persistent-id='' sn='White' givenname='Michael' mail='michael.wh...@stir.ac.uk' netid='mw6' o='Information Services' ou='eLearning Liaison and Development' However, I'm not seeing any of the log lines from the getSpecialGroups function in ShibAuthentication.java - so it still looks like this function isn't being called? So, just wanted to report that the simple fix didn't seem to resolve the problem for me. However, It isn't life or death for me to solve this now as allocation to a single special group wasn't quite what I wanted to do anyway - I ideally wanted to allocate Researchers to deposit groups for the Collections for their department (pulled from ou header), so instead I extended the ShibAuthentication code to use a mapping of departments to deposit groups (abstracted to authentication-shibboleth.cfg) to add users to their department's deposit group during logon (which I now have working a treat). Not sure why the stipulated fix for the original problem didn't work for me though :-( Cheers, Mike Michael White eLearning Developer Information Services T: (01786) 466877 E: michael.wh...@stir.ac.uk A: S8, Library, University of Stirling, Stirling, FK9 4LA -Original Message- From: Tim Donohue [mailto:tdono...@duraspace.org] Sent: 12 June 2015 15:25 To: Michael White; dspace-tech@lists.sourceforge.net Subject: Re: [Dspace-tech] Shibboleth and role based groups? Mike, You might be hitting this bug: https://jira.duraspace.org/browse/DS-2527 If so, there's a quick fix listed in the bug report. Good luck, - Tim On 6/9/2015 5:21 AM, Michael White wrote: Hi, I can't seem to get the auto population of this group working. Just to add to what I've already said - I upped the log level to DEBUG and ran some more tests, but that didn't seem to shine any additional light. So I've been looking through the Shibboleth authentication code (in ShibAuthentication.java) - In the code I can see the function: public int[] getSpecialGroups(Context context, HttpServletRequest request) - which appears to be the code that adds the user to the special group(s). This code contains lots of INFO and DEBUG logging lines, but I'm not seeing any of these lines appearing in my logs - suggesting that this code to populate the special groups isn't actually being called . . . . . ? It certainly isn't called from within ShibAuthentication.java as far as I can tell . . . . Am I missing some config somewhere to turn this feature on? It all looks like it should work, so I feel like I'm missing something obvious (assuming this feature is working for others)? Any pointers welcome! Cheers, Mike Michael White eLearning Developer Information Services T: (01786) 466877 E: michael.wh...@stir.ac.uk A: S8, Library, University of Stirling, Stirling, FK9 4LA -Original Message- From: Michael White Sent: 09 June 2015 10:17 To: dspace-tech@lists.sourceforge.net Subject: Shibboleth and role based groups? Hi, DSpace v5.2/JSPUI. I've set up Shibboleth authentication for a new v5.2 installation - the authentication part appears to be working well, but I'm struggling with automatically placing authenticated users into role based groups based on their (scoped) affiliation and I'm hoping someone might be able to help. I've configured authentication-shibboleth.cfg to add staff users into the group ALL_Collections_Submit (and I've double checked the group name/case etc): # The shibboleth header to do role-based mappings
[Dspace-tech] Repec export
(Apologies for cross-posting) Hi all, We run a Perl script (dspace2redif.pl) periodically that uses OAI-PMH to generate a file which we use to update http://repec.org/. I've forgotten the origins of the script but it was downloaded and I believe is used at other sites. Anyway, we recently upgraded DSpace to 4.2 and the script stopped working as it has hardcoded assumptions about the OAI resumption tokens which are no longer valid at 4.2. I'm emailing on the off chance that others have experienced the same problems and have already fixed the script? Cheers, Robin. Robin Taylor Main Library University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
[Dspace-tech] Question Rest Javadoc
Hello everyone, I have a little question on how to compile the Javadoc of the Dspace-Rest-API. The command mvn javadoc:javadoc (as described in https://wiki.duraspace.org/display/DSDOC5x/REST+API) does not create the commentaries from the classes in org.dspace.rest. Is that a bug or did I do something wrong? :) Sincerely yours Paul Kloss -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Question Rest Javadoc
Hi Paul, there certainly is some JavaDoc for classes under org.dspace.rest in DSpace 5 as you can see here: http://demo.dspace.org/javadocs/5/apidocs/ Perhaps you ran mvn javadoc:javadoc in ~/dspace-src/dspace-rest/ ? Try running it in ~/dspace-src/ instead. Regards, ~~helix84 Compulsory reading: DSpace Mailing List Etiquette https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] discovery facet by collection
I'm using the configuration of a filter that works ok, so seems that no bad configuration could affect here, any hint? -- View this message in context: http://dspace.2283337.n4.nabble.com/discovery-facet-by-collection-tp4678162p4678364.html Sent from the DSpace - Tech mailing list archive at Nabble.com. -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Ordering community collection listings
For collections I think the best way is to modify the sql query of the function that returns all the collections. This function is located here https://github.com/DSpace/DSpace/blob/master/dspace-api/src/main/java/org/dspace/content/Community.java#L661 so playing with the sql clause ORDER BY you can reorder the list anyway you like. -- View this message in context: http://dspace.2283337.n4.nabble.com/Ordering-community-collection-listings-tp4662451p4678362.html Sent from the DSpace - Tech mailing list archive at Nabble.com. -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
[Dspace-tech] Fwd: How to search items by metadata using REST API?
Hi all,
This reminds me of a related issue I was thinking about the other day - as
the REST API evolves and starts to see production use, we might want to
think about versioning it somehow, keeping support for previous
schemas/endpoint functionality, etc (within reason) so that we don't break
existing integrations and UIs with new releases, and to help with
documentation.
I don't know how easy this is to achieve in practice, and I already need to
brush up on my JAX-RS...perhaps it could be something like keeping note of
which REST versions are compatible with which DSpace kernel versions, so
that during the maven build, a particular REST module release tag can be
pulled down if it's still compatible with the dspace-api being built.
Thoughts?
Cheers
Kim
M: k...@shepherd.nz
T: @kimshepherd
P: +6421883635
0CCB D957 0C35 F5C1 497E CDCF FC4B ABA3 2A1A FAEC
https://keybase.io/kshepherd
On 16 June 2015 at 11:52, Terry Brady terry.br...@georgetown.edu wrote:
Alan,
The following PR has some code that will search metadata via the API:
https://github.com/DSpace/DSpace/pull/954
I am also on 4.3, so this code is compatible with DSpace4.3.
Terry
On Thu, Jun 11, 2015 at 5:58 AM, Alan Orth alan.o...@gmail.com wrote:
Ah, it seems the `/rest/items/find-by-metadata-field` endpoint doesn't
exist in DSpace 4.x. Neither does the `/rest/login` endpoint. The docs need
to make more of a point to say which versions these are supposed to work
in... ;)
Alan
On Thu, Jun 11, 2015 at 12:24 PM Alan Orth alan.o...@gmail.com wrote:
Thanks. It seems my query is well formed but it returns an HTTP 405
Method Not Allowed response. Perhaps DSpace 4.x's REST API isn't
sufficient for the find-by-metadata-field query. Or perhaps I need to log
in as you illustrated here:
https://github.com/BrunoNZ/dspace-rest-requests
I guess I'll fork that repo and give this a more structured test. I
already found some syntax and usability bugs there (mixing sh and bash, not
reading the sourced variables, etc).
Alan
On Wed, Jun 10, 2015 at 8:30 PM, Bruno Zanette brunonzane...@gmail.com
wrote:
Hey Alan,
Take a look at the commentaries on the REST-API's documentation's page.
I've answered a similar question there.
https://wiki.duraspace.org/display/DSDOC5x/REST+API?focusedCommentId=68068154#comment-68068154
But basically, the request that you have to send is something like this:
curl -k -4 -H accept: application/json -H Content-Type:
application/json -X POST
https://demo.dspace.org/rest/items/find-by-metadata-field; -d '{key:
dc.title,value: Test Webpage,language: en_US}'
Em qua, 10 de jun de 2015 às 14:08, Alan Orth alan.o...@gmail.com
escreveu:
Hey,
I'm using DSpace 4.3 and trying to search for items matching certain
metadata. The REST API docs on GitHub[0] mention that you can POST to
`rest/items/find-by-metadata-field`, but it doesn't give any more
information than that (like how to specify query parameters).
I've tried several variations of the following:
$ http --print Hhb POST '
http://localhost:8080/rest/items/find-by-metadata-field'
dc.subject=LACTATION
It always returns with an HTTP 405. What is the proper way to use
this? Does the POST require I login first or something?
Thanks,
[0] https://github.com/DSpace/DSpace/tree/master/dspace-rest
--
Alan Orth
alan.o...@gmail.com
https://alaninkenya.org
https://mjanja.ch
In heaven all the interesting people are missing. -Friedrich
Nietzsche
GPG public key ID: 0x8cb0d0acb5cd81ec209c6cdfbd1a0e09c2f836c0
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alan.o...@gmail.com
https://alaninkenya.org
https://mjanja.ch
In heaven all the interesting people are missing. -Friedrich Nietzsche
GPG public key ID: 0x8cb0d0acb5cd81ec209c6cdfbd1a0e09c2f836c0
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Georgetown University Library Information Technology
https://www.library.georgetown.edu/lit/code
425-298-5498 (Seattle, WA)
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[Dspace-tech] DSpace questions on StackOverflow?
Hi- I was at the Open Repositories conference last week and there was some mention of asking questions on StackOverflow rather than in the list. Is StackOverflow the preferred place for questions? Thanks, susan - Susan Borda Digital Technologies Development Librarian Montana State University Library 406-994-1873 -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] How to alter word 'DSpace' with another desired word
You need to edit the message catalog see Where to find the message cataloghttps://wiki.duraspace.org/display/DSDOC5x/Localization+L10n#LocalizationL10n-Wheretofindthemessagecatalog for XMLUI or Where to find the message cataloghttps://wiki.duraspace.org/display/DSDOC5x/Localization+L10n#LocalizationL10n-Wheretofindthemessagecatalog.1 for JSPUI Monika — Monika Mevenkamp Digital Repository Infrastructure Developer Phone: 609-258-4161 333C 701 Carnegie, Princeton University, Princeton, NJ 08544 On Jun 12, 2015, at 8:53 AM, Shivraj Thorat thoratshiv...@gmail.commailto:thoratshiv...@gmail.com wrote: Dear Professional I have installed DSpace 3.1 JSPUI, and customized layout etc. as per my requirement. Now I have to use repository name against the word DSPACE from the layout and other messges. etc. Assist me in this issues. -- Regards Mr. Shivraj Thorat Librarian BVDU, Institute of Management Entrepreneurship Development Paud Rd, Kothrud, Pune-38 -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.netmailto:DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
[Dspace-tech] ldap configuration on windows
Hi everyone, I install dspace on my machine as a test instance for own institutional repository. I want to configure ldap login but it not working. Kindly help. Regards Binta DISCLAIMER: This message is private and confidential. If you have received this message in error please notify us and remove it from your system. Any views and opinions expressed in this message are those of the individual sender and do not necessarily represent the views and opinions of Medical Research Council Unit, The Gambia ___ This communication is confidential and may contain privileged information intended solely for the named recipient(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient, you must not copy, distribute, take any action or reliance on it. If you have received this communication in error, do not open any attachments but please notify the Help Desk by e-mailing h...@mrc.gm quoting the sender details, and then delete this message along with any attached files. E-mail messages are not secure and attachments could contain software viruses which may damage your computer system. Whilst every reasonable precaution has been taken to minimise this risk, The MRC Unit The Gambia cannot accept any liability for any damage sustained as a result of these factors. You are advised to carry out your own virus checks before opening any attachments. Unless expressly stated, opinions in this message are those of the e-mail author and not of the Medical Research Council Unit The Gambia. -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] DSpace questions on StackOverflow?
Hi Susan, Either StackOverflow or dspace-tech are fine, to be honest. It's mostly a matter of preference. But, it's also worth noting that StackOverflow tends to encourage questions that are more development oriented..e.g. How do I do this in DSpace? or I'm trying to do this, but it's not working. So, for example, StackOverflow itself doesn't approve of questions which relate to getting DSpace installed, or getting feedback on error messages. We have some guidelines on this support page: https://wiki.duraspace.org/display/DSPACE/Support - Tim On 6/15/2015 11:10 AM, Borda, Susan wrote: Hi- I was at the Open Repositories conference last week and there was some mention of asking questions on StackOverflow rather than in the list. Is StackOverflow the preferred place for questions? Thanks, susan — Susan Borda Digital Technologies Development Librarian Montana State University Library 406-994-1873 -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] Repec export
We have a highly-customised version of the same script which I believe has this defect fixed. http://researcharchive.vuw.ac.nz/local/RePEc/dspace2redif.pl This version of the script also does some quality control checking and squawks if the metadata doesn't meet the RePEc minimums (which usually indicates a user error somewhere at our end). We run it with crontab lines that look like: 32 12 * * * cd /var/www/html/local/RePEc/ ; /var/www/html/local/RePEc/dspace2redif.pl /var/www/html/local/RePEc/vuwecf.conf cheers stuart -- I have a new phone number: 04 463 5692 https://www.facebook.com/VUWLibrary / https://www.facebook.com/TKMPC From: TAYLOR Robin robin.tay...@ed.ac.uk Sent: Monday, 15 June 2015 9:17 p.m. To: dspace-tech; DSpace Developers Subject: [Dspace-tech] Repec export (Apologies for cross-posting) Hi all, We run a Perl script (dspace2redif.pl) periodically that uses OAI-PMH to generate a file which we use to update http://repec.org/. I've forgotten the origins of the script but it was downloaded and I believe is used at other sites. Anyway, we recently upgraded DSpace to 4.2 and the script stopped working as it has hardcoded assumptions about the OAI resumption tokens which are no longer valid at 4.2. I'm emailing on the off chance that others have experienced the same problems and have already fixed the script? Cheers, Robin. Robin Taylor Main Library University of Edinburgh -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
Re: [Dspace-tech] How to search items by metadata using REST API?
Alan,
The following PR has some code that will search metadata via the API:
https://github.com/DSpace/DSpace/pull/954
I am also on 4.3, so this code is compatible with DSpace4.3.
Terry
On Thu, Jun 11, 2015 at 5:58 AM, Alan Orth alan.o...@gmail.com wrote:
Ah, it seems the `/rest/items/find-by-metadata-field` endpoint doesn't
exist in DSpace 4.x. Neither does the `/rest/login` endpoint. The docs need
to make more of a point to say which versions these are supposed to work
in... ;)
Alan
On Thu, Jun 11, 2015 at 12:24 PM Alan Orth alan.o...@gmail.com wrote:
Thanks. It seems my query is well formed but it returns an HTTP 405
Method Not Allowed response. Perhaps DSpace 4.x's REST API isn't
sufficient for the find-by-metadata-field query. Or perhaps I need to log
in as you illustrated here:
https://github.com/BrunoNZ/dspace-rest-requests
I guess I'll fork that repo and give this a more structured test. I
already found some syntax and usability bugs there (mixing sh and bash, not
reading the sourced variables, etc).
Alan
On Wed, Jun 10, 2015 at 8:30 PM, Bruno Zanette brunonzane...@gmail.com
wrote:
Hey Alan,
Take a look at the commentaries on the REST-API's documentation's page.
I've answered a similar question there.
https://wiki.duraspace.org/display/DSDOC5x/REST+API?focusedCommentId=68068154#comment-68068154
But basically, the request that you have to send is something like this:
curl -k -4 -H accept: application/json -H Content-Type:
application/json -X POST
https://demo.dspace.org/rest/items/find-by-metadata-field; -d '{key:
dc.title,value: Test Webpage,language: en_US}'
Em qua, 10 de jun de 2015 às 14:08, Alan Orth alan.o...@gmail.com
escreveu:
Hey,
I'm using DSpace 4.3 and trying to search for items matching certain
metadata. The REST API docs on GitHub[0] mention that you can POST to
`rest/items/find-by-metadata-field`, but it doesn't give any more
information than that (like how to specify query parameters).
I've tried several variations of the following:
$ http --print Hhb POST '
http://localhost:8080/rest/items/find-by-metadata-field'
dc.subject=LACTATION
It always returns with an HTTP 405. What is the proper way to use this?
Does the POST require I login first or something?
Thanks,
[0] https://github.com/DSpace/DSpace/tree/master/dspace-rest
--
Alan Orth
alan.o...@gmail.com
https://alaninkenya.org
https://mjanja.ch
In heaven all the interesting people are missing. -Friedrich Nietzsche
GPG public key ID: 0x8cb0d0acb5cd81ec209c6cdfbd1a0e09c2f836c0
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--
Alan Orth
alan.o...@gmail.com
https://alaninkenya.org
https://mjanja.ch
In heaven all the interesting people are missing. -Friedrich Nietzsche
GPG public key ID: 0x8cb0d0acb5cd81ec209c6cdfbd1a0e09c2f836c0
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--
Terry Brady
Applications Programmer Analyst
Georgetown University Library Information Technology
https://www.library.georgetown.edu/lit/code
425-298-5498 (Seattle, WA)
--
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[Dspace-tech] metadata fields for google cholar
Hi. Wich metadata fields are recommended to me used for google metadata fields, such as citation_firstpage, citation_lastpage or citation_conference? Is it good way to make my own metadata registry (for example, local) and make fields local.conference.name, local.conference.date and local.firstpage or it is not good and I should make dc.description.firstpage field? -- ___ DSpace-tech mailing list DSpace-tech@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/dspace-tech List Etiquette: https://wiki.duraspace.org/display/DSPACE/Mailing+List+Etiquette
