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< h2 class = "blog-post-title" > < a href = "https://alanorth.github.io/cgspace-notes/2016-08/" > August, 2016< / a > < / h2 >
2016-09-27 22:54:30 +02:00
< p class = "blog-post-meta" > < time datetime = "2016-08-01T15:53:00+03:00" > Mon Aug 01, 2016< / time > by Alan Orth in
2016-09-28 16:03:11 +02:00
< i class = "fa fa-tag" aria-hidden = "true" > < / i > < a href = "/cgspace-notes/tags/notes" rel = "tag" > Notes< / a >
2016-09-27 22:54:30 +02:00
< / p >
2016-09-21 14:24:28 +02:00
< / header >
2016-10-03 17:28:33 +02:00
< h2 id = "2016-08-01" > 2016-08-01< / h2 >
2016-08-01 14:45:50 +02:00
< ul >
< li > Add updated distribution license from Sisay (< a href = "https://github.com/ilri/DSpace/issues/259" > #259< / a > )< / li >
2016-08-02 00:06:47 +02:00
< li > Play with upgrading Mirage 2 dependencies in < code > bower.json< / code > because most are several versions of out date< / li >
< li > Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more< / li >
< li > bower stuff is a dead end, waste of time, too many issues< / li >
< li > Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of < code > fonts< / code > )< / li >
< li > Start working on DSpace 5.1 < / li >
< / ul >
< pre > < code > $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
< / code > < / pre >
2016-10-03 17:28:33 +02:00
< p > < / p >
2016-08-02 00:06:47 +02:00
< ul >
< li > Lots of conflicts that don’ t make sense (ie, shouldn’ t conflict!)< / li >
< li > This file in particular conflicts almost 10 times: < code > dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss< / code > < / li >
< li > Checking out a clean branch at 5.5 and cherry-picking our commits works where that file would normally have a conflict< / li >
< li > Seems to be related to merge commits< / li >
< li > < code > git rebase --preserve-merges< / code > doesn’ t seem to help< / li >
< li > Eventually I just turned on git rerere and solved the conflicts and completed the 403 commit rebase< / li >
< li > The 5.5 code now builds but doesn’ t run (white page in Tomcat)< / li >
2016-08-02 14:03:28 +02:00
< / ul >
2016-08-03 09:09:36 +02:00
< h2 id = "2016-08-02" > 2016-08-02< / h2 >
2016-08-02 14:03:28 +02:00
< ul >
< li > Ask Atmire for help with DSpace 5.5 issue< / li >
< li > Vanilla DSpace 5.5 deploys and runs fine< / li >
< li > Playing with DSpace in Ubuntu 16.04 and Tomcat 7< / li >
< li > Everything is still fucked up, even vanilla DSpace 5.5< / li >
2016-08-05 13:05:32 +02:00
< / ul >
< h2 id = "2016-08-04" > 2016-08-04< / h2 >
< ul >
< li > Ask on DSpace mailing list about duplicate authors, Discovery and author text values< / li >
< li > Atmire responded with some new DSpace 5.5 ready versions to try for their modules< / li >
2016-08-01 14:45:50 +02:00
< / ul >
2016-08-05 15:38:43 +02:00
< h2 id = "2016-08-05" > 2016-08-05< / h2 >
< ul >
< li > Fix item display incorrectly displaying Species when Breeds were present (< a href = "https://github.com/ilri/DSpace/pull/260" > #260< / a > )< / li >
< li > Experiment with fixing more authors, like Delia Grace:< / li >
< / ul >
< pre > < code > dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';
< / code > < / pre >
2016-08-06 15:55:17 +02:00
< h2 id = "2016-08-06" > 2016-08-06< / h2 >
< ul >
< li > Finally figured out how to remove “ View/Open” and “ Bitstreams” from the item view< / li >
< / ul >
2016-08-08 22:22:50 +02:00
< h2 id = "2016-08-07" > 2016-08-07< / h2 >
< ul >
< li > Start working on Ubuntu 16.04 Ansible playbook for Tomcat 8, PostgreSQL 9.5, Oracle 8, etc< / li >
< / ul >
< h2 id = "2016-08-08" > 2016-08-08< / h2 >
< ul >
< li > Still troubleshooting Atmire modules on DSpace 5.5< / li >
< li > Vanilla DSpace 5.5 works on Tomcat 7… < / li >
< li > Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!< / li >
< li > Some notes about setting up Tomcat 8, since it’ s new on this machine… < / li >
< li > Install latest Oracle Java 8 JDK< / li >
< li > Create < code > setenv.sh< / code > in Tomcat 8 < code > libexec/bin< / code > directory:
< br / > < / li >
< / ul >
< pre > < code > CATALINA_OPTS=" -Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8"
CATALINA_OPTS=" $CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib"
JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home
< / code > < / pre >
< ul >
< li > Edit Tomcat 8 < code > server.xml< / code > to add regular HTTP listener for solr< / li >
< li > Symlink webapps:< / li >
< / ul >
< pre > < code > $ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/oai
$ ln -sv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/jspui
$ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/rest
$ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/solr
< / code > < / pre >
2016-08-09 11:31:06 +02:00
< h2 id = "2016-08-09" > 2016-08-09< / h2 >
< ul >
< li > More tests of Atmire’ s 5.5 modules on a clean, working instance of < code > 5_x-prod< / code > < / li >
< li > Still fails, though perhaps differently than before (Flyway): < a href = "https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2" > https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2< / a > < / li >
< li > More work on Tomcat 8 and Java 8 stuff for Ansible playbooks< / li >
2016-08-10 12:19:46 +02:00
< / ul >
< h2 id = "2016-08-10" > 2016-08-10< / h2 >
< ul >
< li > Turns out DSpace 5.x isn’ t ready for Tomcat 8: < a href = "https://jira.duraspace.org/browse/DS-3092" > https://jira.duraspace.org/browse/DS-3092< / a > < / li >
< li > So we’ ll need to use Tomcat 7 + Java 8 on Ubuntu 16.04< / li >
< li > More work on the Ansible stuff for this, allowing Tomcat 7 to use Java 8< / li >
< li > Merge pull request for fixing the type Discovery index to use < code > dc.type< / code > (< a href = "https://github.com/ilri/DSpace/pull/262" > #262< / a > )< / li >
< li > Merge pull request for removing “ Bitstream” text from item display, as it confuses users and isn’ t necessary (< a href = "https://github.com/ilri/DSpace/pull/263" > #263< / a > )< / li >
2016-08-09 11:31:06 +02:00
< / ul >
2016-08-11 07:50:33 +02:00
< h2 id = "2016-08-11" > 2016-08-11< / h2 >
< ul >
< li > Finally got DSpace (5.5) running on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5 via the updated Ansible stuff< / li >
< / ul >
2016-09-21 14:24:28 +02:00
< p > < img src = "2016/08/dspace55-ubuntu16.04.png" alt = "DSpace 5.5 on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5" / > < / p >
2016-08-11 07:50:33 +02:00
2016-08-15 10:34:55 +02:00
< h2 id = "2016-08-14" > 2016-08-14< / h2 >
< ul >
< li > Update Mirage 2 build notes for Ubuntu 16.04: < a href = "https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0" > https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0< / a > < / li >
< / ul >
< h2 id = "2016-08-15" > 2016-08-15< / h2 >
< ul >
< li > Notes on NodeJS + nginx + systemd: < a href = "https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1" > https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1< / a > < / li >
< / ul >
2016-09-21 14:24:28 +02:00
< p > < img src = "2016/08/nodejs-nginx.png" alt = "ExpressJS running behind nginx" / > < / p >
2016-08-15 10:34:55 +02:00
2016-08-17 06:19:11 +02:00
< h2 id = "2016-08-16" > 2016-08-16< / h2 >
< ul >
< li > Troubleshoot Paramiko connection issues with Ansible on ILRI servers: < a href = "https://github.com/ilri/rmg-ansible-public/issues/37" > #37< / a > < / li >
< li > Turns out we need to add some MACs to our < code > sshd_config< / code > : hmac-sha2-512,hmac-sha2-256< / li >
< li > Update DSpace Test’ s Java to version 8 to start testing this configuration (< a href = "https://wiki.apache.org/solr/ShawnHeisey" > seeing as Solr recommends it< / a > )< / li >
2016-08-17 13:40:16 +02:00
< / ul >
< h2 id = "2016-08-17" > 2016-08-17< / h2 >
< ul >
< li > More work on Let’ s Encrypt stuff for Ansible roles< / li >
< li > Yesterday Atmire responded about DSpace 5.5 issues and asked me to try the < code > dspace database repair< / code > command to fix Flyway issues< / li >
< li > The < code > dspace database< / code > command doesn’ t even run: < a href = "https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5" > https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5< / a > < / li >
< li > Oops, it looks like the missing classes causing < code > dspace database< / code > to fail were coming from the old < code > ~/dspace/config/spring< / code > folder< / li >
< li > After removing the spring folder and running ant install again, < code > dspace database< / code > works< / li >
< li > I see there are missing and pending Flyway migrations, but running < code > dspace database repair< / code > and < code > dspace database migrate< / code > does nothing: < a href = "https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70" > https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70< / a > < / li >
2016-08-17 06:19:11 +02:00
< / ul >
2016-08-18 14:48:32 +02:00
< h2 id = "2016-08-18" > 2016-08-18< / h2 >
< ul >
< li > Fix “ CONGO,DR” country name in < code > input-forms.xml< / code > (< a href = "https://github.com/ilri/DSpace/pull/264" > #264< / a > )< / li >
< li > Also need to fix existing records using the incorrect form in the database:< / li >
< / ul >
< pre > < code > dspace=# update metadatavalue set text_value='CONGO, DR' where resource_type_id=2 and metadata_field_id=228 and text_value='CONGO,DR';
< / code > < / pre >
2016-08-18 15:35:08 +02:00
< ul >
< li > I asked a question on the DSpace mailing list about updating “ preferred” forms of author names from ORCID< / li >
2016-08-21 16:10:08 +02:00
< / ul >
< h2 id = "2016-08-21" > 2016-08-21< / h2 >
< ul >
< li > A few days ago someone on the DSpace mailing list suggested I try < code > dspace dsrun org.dspace.authority.UpdateAuthorities< / code > to update preferred author names from ORCID< / li >
< li > If you set < code > auto-update-items=true< / code > in < code > dspace/config/modules/solrauthority.cfg< / code > it is supposed to update records it finds automatically< / li >
< li > I updated my name format on ORCID and I’ ve been running that script a few times per day since then but nothing has changed< / li >
2016-08-21 17:10:52 +02:00
< li > Still troubleshooting Atmire modules on DSpace 5.5< / li >
< li > I sent them some new verbose logs: < a href = "https://gist.github.com/alanorth/700748995649688148ceba89d760253e" > https://gist.github.com/alanorth/700748995649688148ceba89d760253e< / a > < / li >
2016-08-22 18:29:35 +02:00
< / ul >
< h2 id = "2016-08-22" > 2016-08-22< / h2 >
< ul >
< li > Database migrations are fine on DSpace 5.1:< / li >
< / ul >
< pre > < code > $ ~/dspace/bin/dspace database info
Database URL: jdbc:postgresql://localhost:5432/dspacetest
Database Schema: public
Database Software: PostgreSQL version 9.3.14
Database Driver: PostgreSQL Native Driver version PostgreSQL 9.1 JDBC4 (build 901)
+----------------+----------------------------+---------------------+---------+
| Version | Description | Installed on | State |
+----------------+----------------------------+---------------------+---------+
| 1.1 | Initial DSpace 1.1 databas | | PreInit |
| 1.2 | Upgrade to DSpace 1.2 sche | | PreInit |
| 1.3 | Upgrade to DSpace 1.3 sche | | PreInit |
| 1.3.9 | Drop constraint for DSpace | | PreInit |
| 1.4 | Upgrade to DSpace 1.4 sche | | PreInit |
| 1.5 | Upgrade to DSpace 1.5 sche | | PreInit |
| 1.5.9 | Drop constraint for DSpace | | PreInit |
| 1.6 | Upgrade to DSpace 1.6 sche | | PreInit |
| 1.7 | Upgrade to DSpace 1.7 sche | | PreInit |
| 1.8 | Upgrade to DSpace 1.8 sche | | PreInit |
| 3.0 | Upgrade to DSpace 3.x sche | | PreInit |
| 4.0 | Initializing from DSpace 4 | 2015-11-20 12:42:52 | Success |
| 5.0.2014.08.08 | DS-1945 Helpdesk Request a | 2015-11-20 12:42:53 | Success |
| 5.0.2014.09.25 | DS 1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2014.09.26 | DS-1582 Metadata For All O | 2015-11-20 12:42:55 | Success |
| 5.0.2015.01.27 | MigrateAtmireExtraMetadata | 2015-11-20 12:43:29 | Success |
| 5.1.2015.12.03 | Atmire CUA 4 migration | 2016-03-21 17:10:41 | Success |
| 5.1.2015.12.03 | Atmire MQM migration | 2016-03-21 17:10:42 | Success |
+----------------+----------------------------+---------------------+---------+
< / code > < / pre >
< ul >
< li > So I’ m not sure why they have problems when we move to DSpace 5.5 (even the 5.1 migrations themselves show as “ Missing” )< / li >
2016-08-23 15:16:10 +02:00
< / ul >
< h2 id = "2016-08-23" > 2016-08-23< / h2 >
< ul >
< li > Help Paola from CCAFS with her thumbnails again< / li >
< li > Talk to Atmire about the DSpace 5.5 issue, and it seems to be caused by a bug in FlywayDB< / li >
< li > They said I should delete the Atmire migrations
< br / > < / li >
< / ul >
< pre > < code > dspacetest=# delete from schema_version where description = 'Atmire CUA 4 migration' and version='5.1.2015.12.03.2';
dspacetest=# delete from schema_version where description = 'Atmire MQM migration' and version='5.1.2015.12.03.3';
< / code > < / pre >
< ul >
< li > After that DSpace starts up by XMLUI now has unrelated issues that I need to solve!< / li >
< / ul >
< pre > < code > org.apache.avalon.framework.configuration.ConfigurationException: Type 'ThemeResourceReader' does not exist for 'map:read' at jndi:/localhost/themes/0_CGIAR/sitemap.xmap:136:77
context:/jndi:/localhost/themes/0_CGIAR/sitemap.xmap - 136:77
< / code > < / pre >
< ul >
< li > Looks like we’ re missing some stuff in the XMLUI module’ s < code > sitemap.xmap< / code > , as well as in each of our XMLUI themes< / li >
< li > Diff them with these to get the < code > ThemeResourceReader< / code > changes:
< ul >
< li > < code > dspace-xmlui/src/main/webapp/sitemap.xmap< / code > < / li >
< li > < code > dspace-xmlui-mirage2/src/main/webapp/sitemap.xmap< / code > < / li >
< / ul > < / li >
< li > Then we had some NullPointerException from the SolrLogger class, which is apparently part of Atmire’ s CUA module< / li >
< li > I tried with a small version bump to CUA but it didn’ t work (version < code > 5.5-4.1.1-0< / code > )< / li >
< li > Also, I started looking into huge pages to prepare for PostgreSQL 9.5, but it seems Linode’ s kernels don’ t enable them< / li >
2016-08-18 15:35:08 +02:00
< / ul >
2016-08-25 10:09:07 +02:00
< h2 id = "2016-08-24" > 2016-08-24< / h2 >
< ul >
< li > Clean up and import 48 CCAFS records into DSpace Test< / li >
< li > SQL to get all journal titles from dc.source (55), since it’ s apparently used for internal DSpace filename shit, but we moved all our journal titles there a few months ago:< / li >
< / ul >
< pre > < code > dspacetest=# select distinct text_value from metadatavalue where metadata_field_id=55 and text_value !~ '.*(\.pdf|\.png|\.PDF|\.Pdf|\.JPEG|\.jpg|\.JPG|\.jpeg|\.xls|\.rtf|\.docx?|\.potx|\.dotx|\.eqa|\.tiff|\.mp4|\.mp3|\.gif|\.zip|\.txt|\.pptx|\.indd|\.PNG|\.bmp|\.exe|org\.dspace\.app\.mediafilter).*';
< / code > < / pre >
< h2 id = "2016-08-25" > 2016-08-25< / h2 >
< ul >
< li > Atmire suggested adding a missing bean to < code > dspace/config/spring/api/atmire-cua.xml< / code > but it doesn’ t help:< / li >
< / ul >
< pre > < code > ...
Error creating bean with name 'MetadataStorageInfoService'
...
2016-08-25 13:59:59 +02:00
< / code > < / pre >
< ul >
< li > Atmire sent an updated version of < code > dspace/config/spring/api/atmire-cua.xml< / code > and now XMLUI starts but gives a null pointer exception:< / li >
< / ul >
< pre > < code > Java stacktrace: java.lang.NullPointerException
at org.dspace.app.xmlui.aspect.statistics.Navigation.addOptions(Navigation.java:129)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
at sun.reflect.GeneratedMethodAccessor126.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.cocoon.core.container.spring.avalon.PoolableProxyHandler.invoke(PoolableProxyHandler.java:71)
at com.sun.proxy.$Proxy103.startElement(Unknown Source)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.environment.internal.EnvironmentChanger.startElement(EnvironmentStack.java:140)
at org.apache.cocoon.xml.AbstractXMLPipe.startElement(AbstractXMLPipe.java:94)
...
< / code > < / pre >
< ul >
< li > Import the 47 CCAFS records to CGSpace, creating the SimpleArchiveFormat bundles and importing like:< / li >
< / ul >
< pre > < code > $ ./safbuilder.sh -c /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/3546.csv
$ JAVA_OPTS=" -Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/bin/dspace import -a -e aorth@mjanja.ch -c 10568/3546 -s /tmp/Thumbnails\ to\ Upload\ to\ CGSpace/SimpleArchiveFormat -m 3546.map
2016-08-25 10:09:07 +02:00
< / code > < / pre >
2016-08-25 20:09:55 +02:00
< ul >
< li > Finally got DSpace 5.5 working with the Atmire modules after a few rounds of back and forth with Atmire devs< / li >
2016-08-26 22:49:43 +02:00
< / ul >
< h2 id = "2016-08-26" > 2016-08-26< / h2 >
< ul >
< li > CGSpace had issues tonight, not entirely crashing, but becoming unresponsive< / li >
< li > The dspace log had this:< / li >
< / ul >
< pre > < code > 2016-08-26 20:48:05,040 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error - org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
< / code > < / pre >
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< li > Related to /rest no doubt< / li >
2016-08-27 09:20:02 +02:00
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< h2 id = "2016-08-27" > 2016-08-27< / h2 >
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< li > Run corrections for Delia Grace and < code > CONGO, DR< / code > , and deploy August changes to CGSpace< / li >
< li > Run all system updates and reboot the server< / li >
2016-08-25 20:09:55 +02:00
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< aside class = "col-sm-3 offset-sm-1 blog-sidebar" >
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< h4 > Recent Posts< / h4 >
< ol class = "list-unstyled" >
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< li > < a href = "/cgspace-notes/2016-10/" > October, 2016< / a > < / li >
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< li > < a href = "/cgspace-notes/2016-09/" > September, 2016< / a > < / li >
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< li > < a href = "/cgspace-notes/2016-08/" > August, 2016< / a > < / li >
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< li > < a href = "/cgspace-notes/2016-07/" > July, 2016< / a > < / li >
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< li > < a href = "/cgspace-notes/2016-06/" > June, 2016< / a > < / li >
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< section class = "sidebar-module" >
< h4 > Links< / h4 >
< ol class = "list-unstyled" >
< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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Blog template created by < a href = "https://twitter.com/mdo" > @mdo< / a > , ported to Hugo by < a href = 'https://twitter.com/mralanorth' > @mralanorth< / a > .
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< a href = "#" > Back to top< / a >
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