I've changed the search.server settings and changed all occurrences of "${dspace.dir}" with "/data/dspace" in dspace.cfg. Restarted Tomcat and no change.

Here is the diff output for the dspace.cfg file:

[root@dspacex /]# diff /data/dspace/config/dspace.cfg /data/dspace/config/dspace_DEFAULT.cfg
10c10
< # Revision: $Revision: 6830 $
---
> # Revision: $Revision$
12c12
< # Date:     $Date: 2011-10-28 18:30:14 -0500 (Fri, 28 Oct 2011) $
---
> # Date:     $Date$
25c25
< dspace.dir = /dspace
---
> dspace.dir = ${default.dspace.dir}
28,29c28
< #dspace.hostname = localhost
< dspace.hostname = dspacex.lib.uci.edu
---
> dspace.hostname = localhost
32c31
< dspace.baseUrl = http://dspacex.lib.uci.edu:8080
---
> dspace.baseUrl = http://localhost:8080
38,43c37
< #dspace.url = ${dspace.baseUrl}/xmlui
< dspace.url = http://dspacex.lib.uci.edu/xmlui
<
< #ucispace.url was created so generated sitemaps/handle server
< #point to ucispace.lib.uci.edu instead of dspace2.nacs.uci.edu MM 10/17/11
< ucispace.url = http://ucispace.lib.uci.edu
---
> dspace.url = ${dspace.baseUrl}/xmlui
46,47c40
< #dspace.name = DSpace at My University
< dspace.name = UCIspace @ the Libraries
---
> dspace.name = DSpace at My University
51a45
> db.name = ${default.db.name}
53d46
< db.name = postgres
57,58c50
< #db.url = jdbc:postgresql://localhost:5432/dspace
< db.url = jdbc:postgresql://localhost:5432/dspace
---
> db.url = ${default.db.url}
61a54
> db.driver = ${default.db.driver}
63d55
< db.driver = org.postgresql.Driver
65a58,59
> db.username = ${default.db.username}
> db.password = ${default.db.password}
68,69d61
< db.username = dspace
< db.password = 3c@psD
97,98c89
< #mail.server = smtp.example.com
< mail.server=localhost
---
> mail.server = ${default.mail.server}
108c99
< mail.from.address = libucispace@uci.edu
---
> mail.from.address = dspace-noreply@myu.edu
111c102
< feedback.recipient = libucispace@uci.edu
---
> feedback.recipient = dspace-help@myu.edu
114c105
< mail.admin = libucispace@uci.edu
---
> mail.admin = dspace-help@myu.edu
117c108
< alert.recipient = libucispace@uci.edu
---
> # alert.recipient = email-address-here
120c111
< registration.notify = libucispace@uci.edu
---
> # registration.notify = email-address-here
149c140
< assetstore.dir = /data/dspace/assetstore
---
> assetstore.dir = ${dspace.dir}/assetstore
224,225c215,216
< # log.init.config = /data/dspace/config/log4j.xml
< # log.init.config = /data/dspace/config/log4j-console.properties
---
> # log.init.config = ${dspace.dir}/config/log4j.xml
> # log.init.config = ${dspace.dir}/config/log4j-console.properties
227c218
< log.init.config = /data/dspace/config/log4j.properties
---
> log.init.config = ${dspace.dir}/config/log4j.properties
230c221
< log.dir = /data/dspace/log
---
> log.dir = ${dspace.dir}/log
240c231
< search.dir = /data/dspace/search
---
> search.dir = ${dspace.dir}/search
286c277
< search.index.1 = keyword:dc.*
---
> search.index.1 = author:dc.contributor.*
288,304c279,288
< search.index.3 = author:dc.contributor
< search.index.4 = title:dc.title.*
< search.index.5 = subject:dc.subject
<
< # Added for VAOHP collection search
< search.index.6 = narrator:dc.creator
< search.index.7 = interviewer:dc.contributor
< search.index.8 = dateofinterview:dc.date.created
< search.index.9 = decadeofbirth:dc.coverage.temporal
<
< #search.index.6 = author:dc.description.statementofresponsibility
< #search.index.7 = series:dc.relation.ispartofseries
< #search.index.8 = abstract:dc.description.tableofcontents
< #search.index.9 = mime:dc.format.mimetype
< #search.index.10 = sponsor:dc.description.sponsorship
< #search.index.11 = identifier:dc.identifier.*
< #search.index.12 = language:dc.language.iso
---
> search.index.3 = title:dc.title.*
> search.index.4 = keyword:dc.subject.*
> search.index.5 = abstract:dc.description.abstract
> search.index.6 = author:dc.description.statementofresponsibility
> search.index.7 = series:dc.relation.ispartofseries
> search.index.8 = abstract:dc.description.tableofcontents
> search.index.9 = mime:dc.format.mimetype
> search.index.10 = sponsor:dc.description.sponsorship
> search.index.11 = identifier:dc.identifier.*
> search.index.12 = language:dc.language.iso
330c314
< handle.prefix = 10575
---
> handle.prefix = 123456789
333c317
< handle.dir = /data/dspace/handle-server
---
> handle.dir = ${dspace.dir}/handle-server
417,418c401
<                                  Word Text Extractor, JPEG Thumbnail, \
<                                    PDF Thumbnail
---
>                                  Word Text Extractor, JPEG Thumbnail
425,426c408
<   org.dspace.app.mediafilter.XPDF2Text = PDF Text Extractor, \
<   org.dspace.app.mediafilter.XPDF2Thumbnail = PDF Thumbnail, \
---
>   org.dspace.app.mediafilter.PDFFilter = PDF Text Extractor, \
434c416,417
< filter.org.dspace.app.mediafilter.HTMLFilter.inputFormats = HTML, Text, CSV
---
> filter.org.dspace.app.mediafilter.PDFFilter.inputFormats = Adobe PDF
> filter.org.dspace.app.mediafilter.HTMLFilter.inputFormats = HTML, Text
439,440d421
< filter.org.dspace.app.mediafilter.XPDF2Thumbnail.inputFormats = Adobe PDF
< filter.org.dspace.app.mediafilter.XPDF2Text.inputFormats = Adobe PDF
452,455d432
< #XPDF paths
< xpdf.path.pdftotext = /usr/local/src/xpdf/xpdfbin-linux-3.03/bin32/pdftotext
< xpdf.path.pdftoppm = /usr/local/src/xpdf/xpdfbin-linux-3.03/bin32/pdftoppm
< xpdf.path.pdfinfo = /usr/local/src/xpdf/xpdfbin-linux-3.03/bin32/pdfinfo
662c639
< #event.dispatcher.default.consumers = search, browse, discovery, eperson, harvester
---
> # event.dispatcher.default.consumers = search, browse, discovery, eperson, harvester
699c676
< embargo.field.terms = dc.date.available
---
> embargo.field.terms = SCHEMA.ELEMENT.QUALIFIER
702c679
< embargo.field.lift = dc.date.available
---
> embargo.field.lift = SCHEMA.ELEMENT.QUALIFIER
724c701
< org.dspace.app.itemexport.work.dir = /data/dspace/exports
---
> org.dspace.app.itemexport.work.dir = ${dspace.dir}/exports
727c704
< org.dspace.app.itemexport.download.dir = /data/dspace/exports/download
---
> org.dspace.app.itemexport.download.dir = ${dspace.dir}/exports/download
778c755
< webui.submit.upload.required = false
---
> #webui.submit.upload.required = true
831,832c808,809
< webui.browse.thumbnail.maxheight = 100
< webui.browse.thumbnail.maxwidth = 100
---
> #webui.browse.thumbnail.maxheight = 80
> #webui.browse.thumbnail.maxwidth = 80
844,845c821,822
< thumbnail.maxwidth  = 300
< thumbnail.maxheight = 300
---
> thumbnail.maxwidth  = 80
> thumbnail.maxheight = 80
858c835
< webui.preview.brand.abbrev = UCISpace@theLibraries
---
> webui.preview.brand.abbrev = MyOrg
887c864
< webui.strengths.cache = true
---
> webui.strengths.cache = false
942,945c919,922
< #webui.browse.index.1 = dateissued:item:dateissued
< #webui.browse.index.2 = author:metadata:dc.contributor.*,dc.creator:text
< #webui.browse.index.3 = title:item:title
< #webui.browse.index.4 = subject:metadata:dc.subject.*:text
---
> webui.browse.index.1 = dateissued:item:dateissued
> webui.browse.index.2 = author:metadata:dc.contributor.*,dc.creator:text
> webui.browse.index.3 = title:item:title
> webui.browse.index.4 = subject:metadata:dc.subject.*:text
948,954d924
< webui.browse.index.1 = title:item:title
< webui.browse.index.2 = date:metadata:dc.date.created:date
< webui.browse.index.3 = author:metadata:dc.creator:text
< webui.browse.index.4 = subject:metadata:dc.subject:text
< webui.browse.index.5 = contributor:metadata:dc.contributor:text
< webui.browse.index.6 = decade:metadata:dc.coverage.temporal:date
<
979,982d948
< #webui.itemlist.sort-option.1 = title:dc.title:title
< #webui.itemlist.sort-option.2 = dateissued:dc.date.issued:date
< #webui.itemlist.sort-option.3 = dateaccessioned:dc.date.accessioned:date
<
984,992c950,951
< webui.itemlist.sort-option.2 = author:dc.creator:text
< webui.itemlist.sort-option.3 = collection:dc.relation.isPartOf:text
< webui.itemlist.sort-option.4 = date:dc.date.created:date
<
< #Added for VAOHP collection sort
< webui.itemlist.sort-option.5 = narrator:dc.creator:text
< webui.itemlist.sort-option.6 = interviewer:dc.contributor:text
< webui.itemlist.sort-option.7 = dateofinterview:dc.date.created:date
< webui.itemlist.sort-option.8 = decadeofbirth:dc.coverage.temporal:date
---
> webui.itemlist.sort-option.2 = dateissued:dc.date.issued:date
> webui.itemlist.sort-option.3 = dateaccessioned:dc.date.accessioned:date
1010c969
< webui.browse.metadata.case-insensitive = true
---
> # webui.browse.metadata.case-insensitive = true
1104,1106c1063
< #Put the recent submissions count to 0 so that discovery can use it's recent submissions,
< # not doing this when discovery is enabled will cause UI overlap issues
< #How many recent submissions should be displayed at any one time
---
> # how many recent submissions should be displayed at any one time
1108d1064
< #recent.submissions.count = 0
1246,1248c1202
<
< #Changing to allow inline (in-browser) serving of all bitstreams up to 20 Mb (default was 8 Mb) MM 11/2012
< xmlui.content_disposition_threshold = 20971520
---
> xmlui.content_disposition_threshold = 8388608
1274c1228
< sitemap.dir = /data/dspace/sitemaps
---
> sitemap.dir = ${dspace.dir}/sitemaps
1389c1343
< google-metadata.config = /data/dspace/config/crosswalks/google-metadata.properties
---
> google-metadata.config = ${dspace.dir}/config/crosswalks/google-metadata.properties
1401c1355
< upload.temp.dir = /data/dspace/upload
---
> upload.temp.dir = ${dspace.dir}/upload
1405c1359
< upload.max= 1048576000
---
> upload.max = 536870912
1416c1370
< report.dir = /data/dspace/reports/
---
> report.dir = ${dspace.dir}/reports/
1581c1535
< webui.suggest.enable = true
---
> webui.suggest.enable = false
1628,1629c1582,1583
< xmlui.user.registration=false
< xmlui.user.editmetadata=true
---
> #xmlui.user.registration=true
> #xmlui.user.editmetadata=true
1711,1713c1665
< #
< # Google Analytics key is already declared in structural.xsl and should not be redeclared here!
< #xmlui.google.analytics.key=UA-15607289-1
---
> #xmlui.google.analytics.key=UA-XXXXXX-X

Thanks!
Matthew


Matthew McKinley
Digital Project Specialist, University of California, Irvine
about.me



On Thu, Nov 29, 2012 at 12:50 AM, helix84 <helix84@centrum.sk> wrote:
On Thu, Nov 29, 2012 at 2:17 AM, Matthew McKinley
<matthewjamesmckinley@gmail.com> wrote:
> helix,
>
> Thanks for the reply.
>
> 1. The context path in tomcat6/server.xml is as follows, as it has been in
> previous (working) versions of dspace:
>
>         <!-- DEFINE A CONTEXT PATH FOR DSpace XML User Interface (Manakin)
> -->
>         <Context path="/xmlui"
>               docBase="/data/dspace/webapps/xmlui"
>               debug="0" reloadable="true"
>               cachingAllowed="false"
>               allowLinking="true"/>

That looks fine.

> 2. I've googled the "Threadlocal" errors before, as they happened many many
> times on a daily basis even while our dspace instance was running perfectly.
> Not being a formally trained IT guy, I couldn't really make heads or tails
> of a lot of the conversations, but the gist I got was that 99% of the time
> these messages are superfluous despite tomcat reporting them. I could be
> wrong about this but I'm not sure where to start in addressing, I spent a
> long while researching them about a year ago but quickly got out of my
> depth.
>
> 3. As a matter of fact I have modified the java files slightly to change the
> URLs in our sitemap/handle servers to list the CNAME "ucispace.lib.uci.edu"
> instead of the true server name "dspace2.nacs.uci.edu". However, the server
> not working is the test server dspacex.lib.uci.edu, so though I made the
> changes below they don't really apply to dspacex because A it's not running
> a handle server and B its address is different. Could this be causing
> problems? I can remove the following changes and try rebuilding/updating.
>
> I added this line to dspace.cfg:
>
> #ucispace.url was created so generated sitemaps/handle server
> #point to ucispace.lib.uci.edu instead of dspace2.nacs.uci.edu MM 10/17/11
> ucispace.url = http://ucispace.lib.uci.edu
>
> And changed ALL references of "dspace.url" to "ucispace.url" in the
> following java files:
>
> Source Location:
> /data/src/dspace-1.8.2-src-release/dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java
>
> Source Location:
> /data/src/dspace-1.8.2-src-release/dspace-api/src/main/java/org/dspace/handle/HandleManager.java
>
> 4. I started with a clean 1.8 config directory and added customizations
> (twice!)
>
> 5. In config/modules/discovery.cfg, the search.server value is set to:
>
>  http://dspacex.lib.uci.edu/solr/search

Set this to:
search.server = http://localhost:8080/solr/search


> Output of grep -RnI '\${.*}' data/dspace/config/* :

Go to /data/dspace/config/dspace.cfg and replace all occurences of
"${dspace.dir}" by "/data/dspace". Then restart Tomcat and see if it
fixes things. If not, we may try looking at your customizations (send
a complete diff).


Regards,
~~helix84

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