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52
content/posts/2023-07.md
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@ -154,4 +154,56 @@ $ psql < locks-age.sql | grep -E " (19|18|17|16|12):" | awk -F"|" '{print $10}'
- Export CGSpace tp fix missing Initiative collections
- Start a harvest on AReS
## 2023-07-24
- Test Salem's new JavaScript-based DSpace Statistics API and send him some feedback
- I noticed a few times that the Solr service on my DSpace 7 instance is getting OOM killed
- I had been using a 4g Solr heap, but maybe we don't need that much
- Tomcat is also using 4.6GB, and then there's PostgreSQL... so perhaps it's all a bit much on this system now
## 2023-07-25
- Start testing exporting DSpace 6 Solr cores to import on DSpace 7:
```console
$ chrt -b 0 dspace solr-export-statistics -i statistics
```
- I'm curious how long it takes and how much data there will be
- The size of the Solr data directory is currently 82GB
- The export took about 2.5 hours and created 6,000 individual CSVs, one for each day of Solr stats
- The size of the exported CSVs is about 88GB
- I will copy just a few years to import on the DSpace 7 test server
- So importing these is going to require removing the Atmire custom fields:
```console
$ dspace solr-import-statistics -i statistics
Exception: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field 'containerCommunity'
org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field 'containerCommunity'
at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:681)
at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:266)
at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:248)
at org.apache.solr.client.solrj.SolrClient.request(SolrClient.java:1290)
at org.dspace.util.SolrImportExport.importIndex(SolrImportExport.java:465)
at org.dspace.util.SolrImportExport.main(SolrImportExport.java:148)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:568)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:277)
at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:133)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:98)
```
- I will try using solr-import-export-json, which I've used in the past to skip Atmire custom fields in Solr:
```console
$ chrt -b 0 ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2022.json -f 'time:[2022-01-01T00\:00\:00Z TO 2022-12-31T23\:59\:59Z]' -k uid -S author_mtdt,author_mtdt_search,iso_mtdt_search,iso_mtdt,subject_mtdt,subject_mtdt_search,containerCollection,containerCommunity,containerItem,countryCode_ngram,countryCode_search,cua_version,dateYear,dateYearMonth,geoipcountrycode,geoIpCountryCode,ip_ngram,ip_search,isArchived,isInternal,isWithdrawn,containerBitstream,file_id,referrer_ngram,referrer_search,userAgent_ngram,userAgent_search,version_id,complete_query,complete_query_search,filterquery,ngram_query_search,ngram_simplequery_search,simple_query,simple_query_search,range,rangeDescription,rangeDescription_ngram,rangeDescription_search,range_ngram,range_search,actingGroupId,actorMemberGroupId,bitstreamCount,solr_update_time_stamp,bitstreamId,core_update_run_nb
```
- Some users complained that CGSpace was slow and I found a handful of locks that were hours and days old...
- I killed those and told them to try again
- After importing the Solr statistics into DSpace 7 I realized that my DSpace Statistics API will work fine
- I made some minor modifications to the Ansible infrastructure scripts to make sure it is enabled and then activated it on DSpace 7 Test
<!-- vim: set sw=2 ts=2: -->

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@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now
$ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspace
78
"/>
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@ -36,7 +36,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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@ -28,7 +28,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_
I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
Update GitHub wiki for documentation of maintenance tasks.
"/>
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@ -38,7 +38,7 @@ I noticed we have a very interesting list of countries on CGSpace:
Not only are there 49,000 countries, we have some blanks (25)&hellip;
Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
"/>
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@ -28,7 +28,7 @@ Looking at issues with author authorities on CGSpace
For some reason we still have the index-lucene-update cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module
Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
"/>
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@ -32,7 +32,7 @@ After running DSpace for over five years I&rsquo;ve never needed to look in any
This will save us a few gigs of backup space we&rsquo;re paying for on S3
Also, I noticed the checker log has some errors we should pay attention to:
"/>
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@ -34,7 +34,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
# awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168
"/>
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@ -34,7 +34,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec
You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
"/>
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@ -44,7 +44,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
"/>
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2
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@ -42,7 +42,7 @@ $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
"/>
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@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &#34;dc=cgiarad,dc=org&#34; -D &#34;admigration1@cgiarad.org&#34; -W &#34;(sAMAccountName=admigration1)&#34;
"/>
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@ -478,8 +478,8 @@ $ ./delete-metadata-values.py -f cg.contributor.affiliation -i affiliations_pb-2
</code></pre><ul>
<li>It actually works really well, and search results return much less hits now (before, after):</li>
</ul>
<p><img src="/cgspace-notes/2016/09/cgspace-search.png" alt="CGSpace search with &amp;ldquo;OR&amp;rdquo; boolean logic">
<img src="/cgspace-notes/2016/09/dspacetest-search.png" alt="DSpace Test search with &amp;ldquo;AND&amp;rdquo; boolean logic"></p>
<p><img src="/cgspace-notes/2016/09/cgspace-search.png" alt="CGSpace search with &ldquo;OR&rdquo; boolean logic">
<img src="/cgspace-notes/2016/09/dspacetest-search.png" alt="DSpace Test search with &ldquo;AND&rdquo; boolean logic"></p>
<ul>
<li>Found a way to improve the configuration of Atmire&rsquo;s Content and Usage Analysis (CUA) module for date fields</li>
</ul>

2
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@ -42,7 +42,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
"/>
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@ -26,7 +26,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
"/>
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@ -46,7 +46,7 @@ I see thousands of them in the logs for the last few months, so it&rsquo;s not r
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
"/>
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@ -668,7 +668,7 @@ Caused by: java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceOb
<li>This is how DSpace works, and I need to ask if there is a way to override someone&rsquo;s submission, as the other reviewer seems to not be paying attention, or has perhaps taken the item from the task pool?</li>
<li>Run a batch edit to add &ldquo;RANGELANDS&rdquo; ILRI subject to all items containing the word &ldquo;RANGELANDS&rdquo; in their metadata for Peter Ballantyne</li>
</ul>
<p><img src="/cgspace-notes/2016/12/batch-edit1.png" alt="Select all items with &amp;ldquo;rangelands&amp;rdquo; in metadata">
<p><img src="/cgspace-notes/2016/12/batch-edit1.png" alt="Select all items with &ldquo;rangelands&rdquo; in metadata">
<img src="/cgspace-notes/2016/12/batch-edit2.png" alt="Add RANGELANDS ILRI subject"></p>
<h2 id="2016-12-18">2016-12-18</h2>
<ul>

2
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@ -28,7 +28,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s
I tested on DSpace Test as well and it doesn&rsquo;t work there either
I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years
"/>
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2
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@ -50,7 +50,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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@ -54,7 +54,7 @@ Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing reg
$ identify ~/Desktop/alc_contrastes_desafios.jpg
/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000
"/>
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@ -40,7 +40,7 @@ Testing the CMYK patch on a collection with 650 items:
$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &#34;ImageMagick PDF Thumbnail&#34; -v &gt;&amp; /tmp/filter-media-cmyk.txt
"/>
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@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/>
<meta name="twitter:description" content="2017-05-01 ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items: https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683 2017-05-02 Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request 2017-05-04 Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
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@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/>
<meta name="twitter:description" content="2017-06-01 After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
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@ -36,7 +36,7 @@ Merge changes for WLE Phase II theme rename (#329)
Looking at extracting the metadata registries from ICARDA&rsquo;s MEL DSpace database so we can compare fields with CGSpace
We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
"/>
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@ -60,7 +60,7 @@ This was due to newline characters in the dc.description.abstract column, which
I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
"/>
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2
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@ -32,7 +32,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two
Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account is both in the approvers step as well as the group
"/>
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@ -34,7 +34,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
There appears to be a pattern but I&rsquo;ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
"/>
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2
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@ -48,7 +48,7 @@ Generate list of authors on CGSpace for Peter to go through and correct:
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = &#39;contributor&#39; and qualifier = &#39;author&#39;) AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
COPY 54701
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@ -30,7 +30,7 @@ The logs say &ldquo;Timeout waiting for idle object&rdquo;
PostgreSQL activity says there are 115 connections currently
The list of connections to XMLUI and REST API for today:
"/>
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2
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@ -150,7 +150,7 @@ dspace.log.2018-01-02:34
Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains
"/>
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@ -30,7 +30,7 @@ We don&rsquo;t need to distinguish between internal and external works, so that
Yesterday I figured out how to monitor DSpace sessions using JMX
I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
"/>
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@ -24,7 +24,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
Export a CSV of the IITA community metadata for Martin Mueller
"/>
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@ -26,7 +26,7 @@ Catalina logs at least show some memory errors yesterday:
I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when
Catalina logs at least show some memory errors yesterday:
"/>
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@ -38,7 +38,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
Then I reduced the JVM heap size from 6144 back to 5120m
Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
"/>
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@ -58,7 +58,7 @@ real 74m42.646s
user 8m5.056s
sys 2m7.289s
"/>
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@ -36,7 +36,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
There is insufficient memory for the Java Runtime Environment to continue.
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@ -46,7 +46,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did
The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a larger one because we&rsquo;ll start starving the OS, PostgreSQL, and command line batch processes
I ran all system updates on DSpace Test and rebooted it
"/>
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@ -30,7 +30,7 @@ I&rsquo;ll update the DSpace role in our Ansible infrastructure playbooks and ru
Also, I&rsquo;ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month
I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:
"/>
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@ -26,7 +26,7 @@ I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nai
Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items
I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now
"/>
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@ -36,7 +36,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list
Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
Today these are the top 10 IPs:
"/>
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@ -36,7 +36,7 @@ Then I ran all system updates and restarted the server
I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
"/>
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@ -50,7 +50,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
357 207.46.13.1
903 54.70.40.11
"/>
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@ -72,7 +72,7 @@ real 0m19.873s
user 0m22.203s
sys 0m1.979s
"/>
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@ -46,7 +46,7 @@ Most worryingly, there are encoding errors in the abstracts for eleven items, fo
I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs
"/>
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@ -64,7 +64,7 @@ $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u ds
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
"/>
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2
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@ -48,7 +48,7 @@ DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present&hellip;
"/>
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@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2
"/>
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2
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@ -38,7 +38,7 @@ CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
"/>
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2
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@ -46,7 +46,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck
Run system updates on DSpace Test (linode19) and reboot it
"/>
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2
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@ -72,7 +72,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2
"/>
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2
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@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2019"/>
<meta name="twitter:description" content="2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U&#43;00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c &#39;id,dc."/>
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2
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@ -58,7 +58,7 @@ Let&rsquo;s see how many of the REST API requests were for bitstreams (because t
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E &#34;[0-9]{1,2}/Oct/2019&#34; | grep -c -E &#34;/rest/bitstreams&#34;
106781
"/>
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2
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@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C
# reboot
"/>
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2
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@ -56,7 +56,7 @@ I tweeted the CGSpace repository link
"/>
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2
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@ -38,7 +38,7 @@ The code finally builds and runs with a fresh install
"/>
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2
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@ -42,7 +42,7 @@ You need to download this into the DSpace 6.x source and compile it
"/>
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2
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@ -48,7 +48,7 @@ The third item now has a donut with score 1 since I tweeted it last week
On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week
"/>
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2
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@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
"/>
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2
docs/2020-06/index.html
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@ -36,7 +36,7 @@ I sent Atmire the dspace.log from today and told them to log into the server to
In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working
I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:
"/>
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2
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@ -38,7 +38,7 @@ I restarted Tomcat and PostgreSQL and the issue was gone
Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the 5_x-prod branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter&rsquo;s request
"/>
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2
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@ -36,7 +36,7 @@ It is class based so I can easily add support for other vocabularies, and the te
"/>
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2
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@ -48,7 +48,7 @@ I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
"/>
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2
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@ -44,7 +44,7 @@ During the FlywayDB migration I got an error:
"/>
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2
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@ -32,7 +32,7 @@ So far we&rsquo;ve spent at least fifty hours to process the statistics and stat
"/>
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2
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@ -36,7 +36,7 @@ I started processing those (about 411,000 records):
"/>
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2
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@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS
"/>
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2
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@ -60,7 +60,7 @@ $ curl -s &#39;http://localhost:9200/openrxv-items-temp/_count?q=*&amp;pretty&#3
}
}
"/>
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2
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@ -34,7 +34,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
"/>
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2
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@ -44,7 +44,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
"/>
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2
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@ -36,7 +36,7 @@ I looked at the top user agents and IPs in the Solr statistics for last month an
I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one&hellip; as that&rsquo;s an actual user&hellip;
"/>
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2
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@ -36,7 +36,7 @@ I simply started it and AReS was running again:
"/>
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2
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@ -30,7 +30,7 @@ Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVO
localhost/dspace63= &gt; \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER;
COPY 20994
"/>
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2
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@ -32,7 +32,7 @@ Update Docker images on AReS server (linode20) and reboot the server:
I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
"/>
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2
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@ -48,7 +48,7 @@ The syntax Moayad showed me last month doesn&rsquo;t seem to honor the search qu
"/>
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2
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@ -46,7 +46,7 @@ $ wc -l /tmp/2021-10-01-affiliations.txt
So we have 1879/7100 (26.46%) matching already
"/>
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2
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@ -32,7 +32,7 @@ First I exported all the 2019 stats from CGSpace:
$ ./run.sh -s http://localhost:8081/solr/statistics -f &#39;time:2019-*&#39; -a export -o statistics-2019.json -k uid
$ zstd statistics-2019.json
"/>
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2
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@ -40,7 +40,7 @@ Purging 455 hits from WhatsApp in statistics
Total number of bot hits purged: 3679
"/>
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2
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@ -24,7 +24,7 @@ Start a full harvest on AReS
Start a full harvest on AReS
"/>
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2
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@ -38,7 +38,7 @@ We agreed to try to do more alignment of affiliations/funders with ROR
"/>
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2
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@ -34,7 +34,7 @@ $ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p &#39;fuuu&
$ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv &gt; /tmp/tac4-filenames.csv
$ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv &gt; /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
"/>
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2
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@ -18,7 +18,7 @@
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="April, 2022"/>
<meta name="twitter:description" content="2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia&rsquo;s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54."/>
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2
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@ -66,7 +66,7 @@ If I query Solr for time:2022-04* AND dns:*msnbot* AND dns:*.msn.com. I see a ha
I purged 93,974 hits from these IPs using my check-spider-ip-hits.sh script
"/>
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2
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@ -48,7 +48,7 @@ There seem to be many more of these:
"/>
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2
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@ -34,7 +34,7 @@ Also, the trgm functions I&rsquo;ve used before are case insensitive, but Levens
"/>
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2
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@ -24,7 +24,7 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
"/>
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2
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@ -46,7 +46,7 @@ I also fixed a few bugs and improved the region-matching logic
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2
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@ -36,7 +36,7 @@ I filed an issue to ask about Java 11&#43; support
"/>
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2
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@ -44,7 +44,7 @@ I want to make sure they use groups instead of individuals where possible!
I reverted the Cocoon autosave change because it was more of a nuissance that Peter can&rsquo;t upload CSVs from the web interface and is a very low severity security issue
"/>
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2
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@ -36,7 +36,7 @@ I exported the CCAFS and IITA communities, extracted just the country and region
Add a few more authors to my CSV with author names and ORCID identifiers and tag 283 items!
Replace &ldquo;East Asia&rdquo; with &ldquo;Eastern Asia&rdquo; region on CGSpace (UN M.49 region)
"/>
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2
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@ -34,7 +34,7 @@ I see we have some new ones that aren&rsquo;t in our list if I combine with this
"/>
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2
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@ -32,7 +32,7 @@ I want to try to expand my use of their data to journals, publishers, volumes, i
"/>
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2
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@ -28,7 +28,7 @@ Remove cg.subject.wle and cg.identifier.wletheme from CGSpace input form after c
iso-codes 4.13.0 was released, which incorporates my changes to the common names for Iran, Laos, and Syria
I finally got through with porting the input form from DSpace 6 to DSpace 7
"/>
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2
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@ -36,7 +36,7 @@ I also did a check for missing country/region mappings with csv-metadata-quality
Start a harvest on AReS
"/>
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2
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@ -46,7 +46,7 @@ Also I found at least two spelling mistakes, for example &ldquo;decison support
Work on cleaning, proofing, and uploading twenty-seven records for IFPRI to CGSpace
"/>
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2
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@ -44,7 +44,7 @@ From what I can see we need to upgrade the MODS schema from 3.1 to 3.7 and then
"/>
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66
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@ -11,14 +11,14 @@
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2023-07/" />
<meta property="article:published_time" content="2023-07-01T17:14:36+03:00" />
<meta property="article:modified_time" content="2023-07-20T16:02:38+03:00" />
<meta property="article:modified_time" content="2023-07-22T09:19:48+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="July, 2023"/>
<meta name="twitter:description" content="2023-07-01 Export CGSpace to check for missing Initiative collection mappings Start harvesting on AReS 2023-07-02 Minor edits to the crossref_doi_lookup.py script while running some checks from 22,000 CGSpace DOIs 2023-07-03 I analyzed the licenses declared by Crossref and found with high confidence that ~400 of ours were incorrect I took the more accurate ones from Crossref and updated the items on CGSpace I took a few hundred ISBNs as well for where we were missing them I also tagged ~4,700 items with missing licenses as &ldquo;Copyrighted; all rights reserved&rdquo; based on their Crossref license status being TDM, mostly from Elsevier, Wiley, and Springer Checking a dozen or so manually, I confirmed that if Crossref only has a TDM license then it&rsquo;s usually copyrighted (could still be open access, but we can&rsquo;t tell via Crossref) I would be curious to write a script to check the Unpaywall API for open access status&hellip; In the past I found that their license status was not very accurate, but the open access status might be more reliable More minor work on the DSpace 7 item views I learned some new Angular template syntax I created a custom component to show Creative Commons licenses on the simple item page I also decided that I don&rsquo;t like the Impact Area icons as a component because they don&rsquo;t have any visual meaning 2023-07-04 Focus group meeting with CGSpace partners about DSpace 7 I added a themed file selection component to the CGSpace theme It displays the bistream description instead of the file name, just like we did in DSpace 6 XMLUI I added a custom component to show share icons 2023-07-05 I spent some time trying to update OpenRXV from Angular 9 to 10 to 11 to 12 to 13 Most things work but there are some minor bugs it seems Mishell from CIP emailed me to say she was having problems approving an item on CGSpace Looking at PostgreSQL I saw there were a dozen or so locks that were several hours and even over one day old so I killed those processes and told her to try again 2023-07-06 Types meeting I wrote a Python script to check Unpaywall for some information about DOIs 2023-07-7 Continue exploring Unpaywall data for some of our DOIs In the past I&rsquo;ve found their licensing information to not be very reliable (preferring Crossref), but I think their open access status is more reliable, especially when the provider is listed as being the publisher Even so, sometimes the version can be &ldquo;acceptedVersion&rdquo;, which is presumably the author&rsquo;s version, as opposed to the &ldquo;publishedVersion&rdquo;, which means it&rsquo;s available as open access on the publisher&rsquo;s website I did some quality assurance and found ~100 that were marked as Limited Access, but should have been Open Access, and fixed a handful of licenses Delete duplicate metadata as describe in my DSpace issue from last year: https://github."/>
<meta name="generator" content="Hugo 0.112.3">
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@ -28,9 +28,9 @@
"@type": "BlogPosting",
"headline": "July, 2023",
"url": "https://alanorth.github.io/cgspace-notes/2023-07/",
"wordCount": "1177",
"wordCount": "1503",
"datePublished": "2023-07-01T17:14:36+03:00",
"dateModified": "2023-07-20T16:02:38+03:00",
"dateModified": "2023-07-22T09:19:48+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -279,6 +279,64 @@
<li>Export CGSpace tp fix missing Initiative collections</li>
<li>Start a harvest on AReS</li>
</ul>
<h2 id="2023-07-24">2023-07-24</h2>
<ul>
<li>Test Salem&rsquo;s new JavaScript-based DSpace Statistics API and send him some feedback</li>
<li>I noticed a few times that the Solr service on my DSpace 7 instance is getting OOM killed
<ul>
<li>I had been using a 4g Solr heap, but maybe we don&rsquo;t need that much</li>
<li>Tomcat is also using 4.6GB, and then there&rsquo;s PostgreSQL&hellip; so perhaps it&rsquo;s all a bit much on this system now</li>
</ul>
</li>
</ul>
<h2 id="2023-07-25">2023-07-25</h2>
<ul>
<li>Start testing exporting DSpace 6 Solr cores to import on DSpace 7:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> dspace solr-export-statistics -i statistics
</span></span></code></pre></div><ul>
<li>I&rsquo;m curious how long it takes and how much data there will be
<ul>
<li>The size of the Solr data directory is currently 82GB</li>
<li>The export took about 2.5 hours and created 6,000 individual CSVs, one for each day of Solr stats</li>
<li>The size of the exported CSVs is about 88GB</li>
<li>I will copy just a few years to import on the DSpace 7 test server</li>
<li>So importing these is going to require removing the Atmire custom fields:</li>
</ul>
</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ dspace solr-import-statistics -i statistics
</span></span><span style="display:flex;"><span>Exception: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field &#39;containerCommunity&#39;
</span></span><span style="display:flex;"><span>org.apache.solr.client.solrj.impl.HttpSolrClient$RemoteSolrException: Error from server at http://localhost:8983/solr/statistics: ERROR: [doc=1a92472e-e39d-4602-9b4d-da022df8f233] unknown field &#39;containerCommunity&#39;
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrClient.executeMethod(HttpSolrClient.java:681)
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:266)
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.impl.HttpSolrClient.request(HttpSolrClient.java:248)
</span></span><span style="display:flex;"><span> at org.apache.solr.client.solrj.SolrClient.request(SolrClient.java:1290)
</span></span><span style="display:flex;"><span> at org.dspace.util.SolrImportExport.importIndex(SolrImportExport.java:465)
</span></span><span style="display:flex;"><span> at org.dspace.util.SolrImportExport.main(SolrImportExport.java:148)
</span></span><span style="display:flex;"><span> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
</span></span><span style="display:flex;"><span> at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
</span></span><span style="display:flex;"><span> at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
</span></span><span style="display:flex;"><span> at java.base/java.lang.reflect.Method.invoke(Method.java:568)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:277)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.handleScript(ScriptLauncher.java:133)
</span></span><span style="display:flex;"><span> at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:98)
</span></span></code></pre></div><ul>
<li>I will try using solr-import-export-json, which I&rsquo;ve used in the past to skip Atmire custom fields in Solr:</li>
</ul>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ chrt -b <span style="color:#ae81ff">0</span> ./run.sh -s http://localhost:8081/solr/statistics -a export -o /tmp/statistics-2022.json -f <span style="color:#e6db74">&#39;time:[2022-01-01T00\:00\:00Z TO 2022-12-31T23\:59\:59Z]&#39;</span> -k uid -S author_mtdt,author_mtdt_search,iso_mtdt_search,iso_mtdt,subject_mtdt,subject_mtdt_search,containerCollection,containerCommunity,containerItem,countryCode_ngram,countryCode_search,cua_version,dateYear,dateYearMonth,geoipcountrycode,geoIpCountryCode,ip_ngram,ip_search,isArchived,isInternal,isWithdrawn,containerBitstream,file_id,referrer_ngram,referrer_search,userAgent_ngram,userAgent_search,version_id,complete_query,complete_query_search,filterquery,ngram_query_search,ngram_simplequery_search,simple_query,simple_query_search,range,rangeDescription,rangeDescription_ngram,rangeDescription_search,range_ngram,range_search,actingGroupId,actorMemberGroupId,bitstreamCount,solr_update_time_stamp,bitstreamId,core_update_run_nb
</span></span></code></pre></div><ul>
<li>Some users complained that CGSpace was slow and I found a handful of locks that were hours and days old&hellip;
<ul>
<li>I killed those and told them to try again</li>
</ul>
</li>
<li>After importing the Solr statistics into DSpace 7 I realized that my DSpace Statistics API will work fine
<ul>
<li>I made some minor modifications to the Ansible infrastructure scripts to make sure it is enabled and then activated it on DSpace 7 Test</li>
</ul>
</li>
</ul>
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