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2019-10-11 10:19:42 +02:00
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< h1 class = "blog-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" dir = "auto" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-08/" > August, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-08-01T11:52:54+03:00" > Wed Aug 01, 2018< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2018-08-01" > 2018-08-01< / h2 >
< ul >
< li > DSpace Test had crashed at some point yesterday morning and I see the following in < code > dmesg< / code > :< / li >
< / ul >
< pre > < code > [Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
< / code > < / pre > < ul >
< li > Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight< / li >
< li > From the DSpace log I see that eventually Solr stopped responding, so I guess the < code > java< / code > process that was OOM killed above was Tomcat’ s< / li >
< li > I’ m not sure why Tomcat didn’ t crash with an OutOfMemoryError… < / li >
< li > Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core< / li >
< li > The server only has 8GB of RAM so we’ ll eventually need to upgrade to a larger one because we’ ll start starving the OS, PostgreSQL, and command line batch processes< / li >
< li > I ran all system updates on DSpace Test and rebooted it< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-08/' > Read more →< / a >
< / article >
2020-02-02 16:15:48 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-07/" > July, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-07-01T12:56:54+03:00" > Sun Jul 01, 2018< / time > by Alan Orth in
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2018-07-01" > 2018-07-01< / h2 >
< ul >
< li > I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:< / li >
< / ul >
< pre > < code > $ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
< / code > < / pre > < ul >
< li > During the < code > mvn package< / code > stage on the 5.8 branch I kept getting issues with java running out of memory:< / li >
< / ul >
< pre > < code > There is insufficient memory for the Java Runtime Environment to continue.
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-07/' > Read more →< / a >
< / article >
2020-01-06 10:14:44 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-06/" > June, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-06-04T19:49:54-07:00" > Mon Jun 04, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
< h2 id = "2018-06-04" > 2018-06-04< / h2 >
< ul >
< li > Test the < a href = "https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560" > DSpace 5.8 module upgrades from Atmire< / a > (< a href = "https://github.com/ilri/DSpace/pull/378" > #378< / a > )
< ul >
2020-01-27 15:20:44 +01:00
< li > There seems to be a problem with the CUA and L& R versions in < code > pom.xml< / code > because they are using SNAPSHOT and it doesn’ t build< / li >
2020-01-06 10:14:44 +01:00
< / ul >
< / li >
< li > I added the new CCAFS Phase II Project Tag < code > PII-FP1_PACCA2< / code > and merged it into the < code > 5_x-prod< / code > branch (< a href = "https://github.com/ilri/DSpace/pull/379" > #379< / a > )< / li >
< li > I proofed and tested the ILRI author corrections that Peter sent back to me this week:< / li >
< / ul >
< pre > < code > $ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
< / code > < / pre > < ul >
< li > I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in < a href = "/cgspace-notes/2018-03/" > March, 2018< / a > < / li >
< li > Time to index ~70,000 items on CGSpace:< / li >
< / ul >
< pre > < code > $ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b
real 74m42.646s
user 8m5.056s
sys 2m7.289s
< / code > < / pre >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-06/' > Read more →< / a >
< / article >
2019-12-01 10:29:49 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-05/" > May, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-05-01T16:43:54+03:00" > Tue May 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-05-01" > 2018-05-01< / h2 >
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< ul >
< li > I cleared the Solr statistics core on DSpace Test by issuing two commands directly to the Solr admin interface:
< ul >
< li > http://localhost:3000/solr/statistics/update?stream.body=%3Cdelete%3E%3Cquery%3E*:*%3C/query%3E%3C/delete%3E< / li >
< li > http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E< / li >
< / ul >
< / li >
< li > Then I reduced the JVM heap size from 6144 back to 5120m< / li >
< li > Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the < a href = "https://github.com/ilri/rmg-ansible-public" > Ansible infrastructure scripts< / a > to support hosts choosing which distribution they want to use< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-05/' > Read more →< / a >
< / article >
2019-11-04 15:41:19 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-04/" > April, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-04-01T16:13:54+02:00" > Sun Apr 01, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-04-01" > 2018-04-01< / h2 >
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< ul >
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< li > I tried to test something on DSpace Test but noticed that it’ s down since god knows when< / li >
2019-11-04 15:41:19 +01:00
< li > Catalina logs at least show some memory errors yesterday:< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-04/' > Read more →< / a >
< / article >
2019-10-28 12:43:25 +01:00
< article class = "blog-post" >
< header >
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-03/" > March, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-03-02T16:07:54+02:00" > Fri Mar 02, 2018< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-03-02" > 2018-03-02< / h2 >
2019-10-28 12:43:25 +01:00
< ul >
< li > Export a CSV of the IITA community metadata for Martin Mueller< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-03/' > Read more →< / a >
< / article >
2019-10-01 16:31:40 +02:00
< article class = "blog-post" >
< header >
2019-10-11 10:19:42 +02:00
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-02/" > February, 2018< / a > < / h2 >
2019-10-01 16:31:40 +02:00
< p class = "blog-post-meta" > < time datetime = "2018-02-01T16:28:54+02:00" > Thu Feb 01, 2018< / time > by Alan Orth in
2020-01-28 11:01:42 +01:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-02-01" > 2018-02-01< / h2 >
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< ul >
< li > Peter gave feedback on the < code > dc.rights< / code > proof of concept that I had sent him last week< / li >
2020-01-27 15:20:44 +01:00
< li > We don’ t need to distinguish between internal and external works, so that makes it just a simple list< / li >
2019-10-01 16:31:40 +02:00
< li > Yesterday I figured out how to monitor DSpace sessions using JMX< / li >
2020-01-27 15:20:44 +01:00
< li > I copied the logic in the < code > jmx_tomcat_dbpools< / code > provided by Ubuntu’ s < code > munin-plugins-java< / code > package and used the stuff I discovered about JMX < a href = "/cgspace-notes/2018-01/" > in 2018-01< / a > < / li >
2019-10-01 16:31:40 +02:00
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-02/' > Read more →< / a >
< / article >
2019-09-01 09:41:30 +02:00
< article class = "blog-post" >
< header >
2019-10-11 10:19:42 +02:00
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2018-01/" > January, 2018< / a > < / h2 >
2019-09-01 09:41:30 +02:00
< p class = "blog-post-meta" > < time datetime = "2018-01-02T08:35:54-08:00" > Tue Jan 02, 2018< / time > by Alan Orth in
2020-01-28 11:01:42 +01:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2018-01-02" > 2018-01-02< / h2 >
2019-09-01 09:41:30 +02:00
< ul >
< li > Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time< / li >
2020-01-27 15:20:44 +01:00
< li > I didn’ t get any load alerts from Linode and the REST and XMLUI logs don’ t show anything out of the ordinary< / li >
2019-09-01 09:41:30 +02:00
< li > The nginx logs show HTTP 200s until < code > 02/Jan/2018:11:27:17 +0000< / code > when Uptime Robot got an HTTP 500< / li >
< li > In dspace.log around that time I see many errors like “ Client closed the connection before file download was complete” < / li >
2019-11-28 16:30:45 +01:00
< li > And just before that I see this:< / li >
< / ul >
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< pre > < code > Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Ah hah! So the pool was actually empty!< / li >
2020-01-27 15:20:44 +01:00
< li > I need to increase that, let’ s try to bump it up from 50 to 75< / li >
< li > After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’ t know what the hell Uptime Robot saw< / li >
2019-11-28 16:30:45 +01:00
< li > I notice this error quite a few times in dspace.log:< / li >
< / ul >
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< pre > < code > 2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " " ]" " ] " " at line 1, column 32.
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > And there are many of these errors every day for the past month:< / li >
< / ul >
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< pre > < code > $ grep -c " Error while searching for sidebar facets" dspace.log.*
dspace.log.2017-11-21:4
dspace.log.2017-11-22:1
dspace.log.2017-11-23:4
dspace.log.2017-11-24:11
dspace.log.2017-11-25:0
dspace.log.2017-11-26:1
dspace.log.2017-11-27:7
dspace.log.2017-11-28:21
dspace.log.2017-11-29:31
dspace.log.2017-11-30:15
dspace.log.2017-12-01:15
dspace.log.2017-12-02:20
dspace.log.2017-12-03:38
dspace.log.2017-12-04:65
dspace.log.2017-12-05:43
dspace.log.2017-12-06:72
dspace.log.2017-12-07:27
dspace.log.2017-12-08:15
dspace.log.2017-12-09:29
dspace.log.2017-12-10:35
dspace.log.2017-12-11:20
dspace.log.2017-12-12:44
dspace.log.2017-12-13:36
dspace.log.2017-12-14:59
dspace.log.2017-12-15:104
dspace.log.2017-12-16:53
dspace.log.2017-12-17:66
dspace.log.2017-12-18:83
dspace.log.2017-12-19:101
dspace.log.2017-12-20:74
dspace.log.2017-12-21:55
dspace.log.2017-12-22:66
dspace.log.2017-12-23:50
dspace.log.2017-12-24:85
dspace.log.2017-12-25:62
dspace.log.2017-12-26:49
dspace.log.2017-12-27:30
dspace.log.2017-12-28:54
dspace.log.2017-12-29:68
dspace.log.2017-12-30:89
dspace.log.2017-12-31:53
dspace.log.2018-01-01:45
dspace.log.2018-01-02:34
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
2020-01-27 15:20:44 +01:00
< li > Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’ s Encrypt if it’ s just a handful of domains< / li >
2019-09-01 09:41:30 +02:00
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2018-01/' > Read more →< / a >
< / article >
2019-08-04 21:49:04 +02:00
< article class = "blog-post" >
< header >
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< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2017-12/" > December, 2017< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2017-12-01T13:53:54+03:00" > Fri Dec 01, 2017< / time > by Alan Orth in
2020-01-28 11:01:42 +01:00
< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2017-12-01" > 2017-12-01< / h2 >
2019-08-04 21:49:04 +02:00
< ul >
< li > Uptime Robot noticed that CGSpace went down< / li >
< li > The logs say “ Timeout waiting for idle object” < / li >
< li > PostgreSQL activity says there are 115 connections currently< / li >
< li > The list of connections to XMLUI and REST API for today:< / li >
< / ul >
< a href = 'https://alanorth.github.io/cgspace-notes/2017-12/' > Read more →< / a >
< / article >
2019-07-01 11:22:43 +02:00
< article class = "blog-post" >
< header >
2019-10-11 10:19:42 +02:00
< h2 class = "blog-post-title" dir = "auto" > < a href = "https://alanorth.github.io/cgspace-notes/2017-11/" > November, 2017< / a > < / h2 >
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< p class = "blog-post-meta" > < time datetime = "2017-11-02T09:37:54+02:00" > Thu Nov 02, 2017< / time > by Alan Orth in
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< span class = "fas fa-folder" aria-hidden = "true" > < / span > < a href = "/cgspace-notes/categories/notes/" rel = "category tag" > Notes< / a >
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< / p >
< / header >
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< h2 id = "2017-11-01" > 2017-11-01< / h2 >
2019-07-01 11:22:43 +02:00
< ul >
< li > The CORE developers responded to say they are looking into their bot not respecting our robots.txt< / li >
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2019-12-17 13:49:24 +01:00
< h2 id = "2017-11-02" > 2017-11-02< / h2 >
2019-07-01 11:22:43 +02:00
< ul >
2019-11-28 16:30:45 +01:00
< li > Today there have been no hits by CORE and no alerts from Linode (coincidence?)< / li >
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2019-07-01 11:22:43 +02:00
< pre > < code > # grep -c " CORE" /var/log/nginx/access.log
0
2019-11-28 16:30:45 +01:00
< / code > < / pre > < ul >
< li > Generate list of authors on CGSpace for Peter to go through and correct:< / li >
< / ul >
2019-07-01 11:22:43 +02:00
< pre > < code > dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
2019-11-28 16:30:45 +01:00
< / code > < / pre >
2019-07-01 11:22:43 +02:00
< a href = 'https://alanorth.github.io/cgspace-notes/2017-11/' > Read more →< / a >
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2018-02-11 17:28:23 +01:00
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2018-03-09 21:16:20 +01:00
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2018-02-11 17:28:23 +01:00
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2018-04-23 17:09:26 +02:00
2018-02-11 17:28:23 +01:00
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< h4 > Recent Posts< / h4 >
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2020-03-02 11:38:10 +01:00
< li > < a href = "/cgspace-notes/2020-03/" > March, 2020< / a > < / li >
2020-02-02 16:15:48 +01:00
< li > < a href = "/cgspace-notes/2020-02/" > February, 2020< / a > < / li >
2020-01-14 19:40:41 +01:00
< li > < a href = "/cgspace-notes/2020-01/" > January, 2020< / a > < / li >
2019-12-01 10:29:49 +01:00
< li > < a href = "/cgspace-notes/2019-12/" > December, 2019< / a > < / li >
2019-11-04 15:41:19 +01:00
< li > < a href = "/cgspace-notes/2019-11/" > November, 2019< / a > < / li >
2018-02-11 17:28:23 +01:00
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< h4 > Links< / h4 >
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< 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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2019-10-11 10:19:42 +02:00
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2018-02-11 17:28:23 +01:00
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