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Add notes for 2020-02-11

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Alan Orth 2020-02-11 12:52:11 +02:00
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47
content/posts/2020-02.md
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@ -389,4 +389,51 @@ $ cat out.dspace510-1 | ../FlameGraph/stackcollapse-perf.pl | grep -E '^java' |
- He uploaded them here: https://cgspace.cgiar.org/handle/10568/105926 - He uploaded them here: https://cgspace.cgiar.org/handle/10568/105926
- On a whim I checked and found five duplicates there, which means Sisay didn't even check - On a whim I checked and found five duplicates there, which means Sisay didn't even check
## 2020-02-10
- Follow up with [Atmire about DSpace 6.x upgrade](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706)
- I raised the issue of targetting 6.4-SNAPSHOT as well as the Discovery indexing performance issues in 6.x
## 2020-02-11
- Maria from Bioversity asked me to add some ORCID iDs to our controlled vocabulary so I combined them with our existing ones and updated the names from the ORCID API:
```
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcid-ids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq > /tmp/2020-02-11-combined-orcids.txt
$ ./resolve-orcids.py -i /tmp/2020-02-11-combined-orcids.txt -o /tmp/2020-02-11-combined-names.txt -d
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
```
- Then I noticed some author names had changed, so I captured the old and new names in a CSV file and fixed them using `fix-metadata-values.py`:
```
$ ./fix-metadata-values.py -i 2020-02-11-correct-orcid-ids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -t correct -m 240 -d
```
- On a hunch I decided to try to add these ORCID iDs to existing items that might not have them yet
- I checked the database for likely matches to the author name and then created a CSV with the author names and ORCID iDs:
```
dc.contributor.author,cg.creator.id
"Staver, Charles",charles staver: 0000-0002-4532-6077
"Staver, C.",charles staver: 0000-0002-4532-6077
"Fungo, R.",Robert Fungo: 0000-0002-4264-6905
"Remans, R.",Roseline Remans: 0000-0003-3659-8529
"Remans, Roseline",Roseline Remans: 0000-0003-3659-8529
"Rietveld A.",Anne Rietveld: 0000-0002-9400-9473
"Rietveld, A.",Anne Rietveld: 0000-0002-9400-9473
"Rietveld, A.M.",Anne Rietveld: 0000-0002-9400-9473
"Rietveld, Anne M.",Anne Rietveld: 0000-0002-9400-9473
"Fongar, A.",Andrea Fongar: 0000-0003-2084-1571
"Müller, Anna",Anna Müller: 0000-0003-3120-8560
"Müller, A.",Anna Müller: 0000-0003-3120-8560
```
- Running the `add-orcid-identifiers-csv.py` script I added 144 ORCID iDs to items!
```
$ ./add-orcid-identifiers-csv.py -i /tmp/2020-02-11-add-orcid-ids.csv -db dspace -u dspace -p 'fuuu'
```
<!-- vim: set sw=2 ts=2: --> <!-- vim: set sw=2 ts=2: -->

2
docs/2015-11/index.html
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@ -31,7 +31,7 @@ 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 $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspace
78 78
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@ -33,7 +33,7 @@ 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 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 -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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docs/2016-01/index.html
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@ -25,7 +25,7 @@ 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. 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. Update GitHub wiki for documentation of maintenance tasks.
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@ -35,7 +35,7 @@ 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; 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; Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
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docs/2016-03/index.html
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@ -25,7 +25,7 @@ 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 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 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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@ -29,7 +29,7 @@ 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 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: Also, I noticed the checker log has some errors we should pay attention to:
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docs/2016-05/index.html
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@ -31,7 +31,7 @@ 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 # awk &#39;{print $1}&#39; /var/log/nginx/rest.log | uniq | wc -l
3168 3168
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docs/2016-06/index.html
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@ -31,7 +31,7 @@ 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 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 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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docs/2016-07/index.html
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@ -41,7 +41,7 @@ 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 In this case the select query was showing 95 results before the update
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docs/2016-08/index.html
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@ -39,7 +39,7 @@ $ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5 $ git rebase -i dspace-5.5
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2
docs/2016-09/index.html
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@ -31,7 +31,7 @@ It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot; $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;
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@ -39,7 +39,7 @@ 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 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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docs/2016-11/index.html
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@ -23,7 +23,7 @@ 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) Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
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docs/2016-12/index.html
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@ -43,7 +43,7 @@ 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 I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is: Another worrying error from dspace.log is:
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docs/2017-01/index.html
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@ -25,7 +25,7 @@ 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 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 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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docs/2017-02/index.html
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@ -47,7 +47,7 @@ DELETE 1
Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301) 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 Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
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docs/2017-03/index.html
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@ -51,7 +51,7 @@ Interestingly, it seems DSpace 4.x&rsquo;s thumbnails were sRGB, but forcing reg
$ identify ~/Desktop/alc_contrastes_desafios.jpg $ 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 /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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docs/2017-04/index.html
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@ -37,7 +37,7 @@ Testing the CMYK patch on a collection with 650 items:
$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="May, 2017"/> <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."/> <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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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2017"/> <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."/> <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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@ -33,7 +33,7 @@ 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 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: We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
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docs/2017-08/index.html
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@ -57,7 +57,7 @@ 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/^$/d I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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docs/2017-09/index.html
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@ -29,7 +29,7 @@ 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 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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@ -31,7 +31,7 @@ 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 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 Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
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@ -45,7 +45,7 @@ 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; 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 COPY 54701
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@ -27,7 +27,7 @@ The logs say &ldquo;Timeout waiting for idle object&rdquo;
PostgreSQL activity says there are 115 connections currently PostgreSQL activity says there are 115 connections currently
The list of connections to XMLUI and REST API for today: The list of connections to XMLUI and REST API for today:
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@ -147,7 +147,7 @@ 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 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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@ -27,7 +27,7 @@ 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 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 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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docs/2018-03/index.html
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@ -21,7 +21,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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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docs/2018-04/index.html
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@ -23,7 +23,7 @@ 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 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: Catalina logs at least show some memory errors yesterday:
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@ -35,7 +35,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
Then I reduced the JVM heap size from 6144 back to 5120m 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 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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@ -55,7 +55,7 @@ real 74m42.646s
user 8m5.056s user 8m5.056s
sys 2m7.289s sys 2m7.289s
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@ -33,7 +33,7 @@ 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. There is insufficient memory for the Java Runtime Environment to continue.
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@ -43,7 +43,7 @@ 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 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 I ran all system updates on DSpace Test and rebooted it
"/> "/>
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@ -27,7 +27,7 @@ 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 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: 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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@ -23,7 +23,7 @@ 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 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 I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now
"/> "/>
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@ -33,7 +33,7 @@ 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 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: Today these are the top 10 IPs:
"/> "/>
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@ -33,7 +33,7 @@ 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 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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2
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@ -47,7 +47,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
357 207.46.13.1 357 207.46.13.1
903 54.70.40.11 903 54.70.40.11
"/> "/>
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2
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@ -69,7 +69,7 @@ real 0m19.873s
user 0m22.203s user 0m22.203s
sys 0m1.979s sys 0m1.979s
"/> "/>
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2
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@ -43,7 +43,7 @@ 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 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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2
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@ -61,7 +61,7 @@ $ ./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-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 $ ./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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@ -45,7 +45,7 @@ DELETE 1
But after this I tried to delete the item from the XMLUI and it is still present&hellip; But after this I tried to delete the item from the XMLUI and it is still present&hellip;
"/> "/>
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2
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@ -31,7 +31,7 @@ Run system updates on CGSpace (linode18) and reboot it
Skype with Marie-Angélique and Abenet about CG Core v2 Skype with Marie-Angélique and Abenet about CG Core v2
"/> "/>
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2
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@ -35,7 +35,7 @@ CGSpace
Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community 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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@ -43,7 +43,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck
Run system updates on DSpace Test (linode19) and reboot it Run system updates on DSpace Test (linode19) and reboot it
"/> "/>
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2
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@ -69,7 +69,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning:
7249 2a01:7e00::f03c:91ff:fe18:7396 7249 2a01:7e00::f03c:91ff:fe18:7396
9124 45.5.186.2 9124 45.5.186.2
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="October, 2019"/> <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."/> <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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@ -55,7 +55,7 @@ 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 &quot;[0-9]{1,2}/Oct/2019&quot; | grep -c -E &quot;/rest/bitstreams&quot; # zcat --force /var/log/nginx/rest.log.*.gz | grep -E &quot;[0-9]{1,2}/Oct/2019&quot; | grep -c -E &quot;/rest/bitstreams&quot;
106781 106781
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@ -43,7 +43,7 @@ Make sure all packages are up to date and the package manager is up to date, the
# dpkg -C # dpkg -C
# reboot # reboot
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6
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@ -29,7 +29,7 @@ I tweeted the CGSpace repository link
<meta property="og:type" content="article" /> <meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-01/" /> <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-01/" />
<meta property="article:published_time" content="2020-01-06T10:48:30+02:00" /> <meta property="article:published_time" content="2020-01-06T10:48:30+02:00" />
<meta property="article:modified_time" content="2020-02-04T13:06:23+02:00" /> <meta property="article:modified_time" content="2020-02-10T10:34:19+02:00" />
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="January, 2020"/> <meta name="twitter:title" content="January, 2020"/>
@ -53,7 +53,7 @@ I tweeted the CGSpace repository link
"/> "/>
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@ -65,7 +65,7 @@ I tweeted the CGSpace repository link
"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-01\/", "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-01\/",
"wordCount": "3523", "wordCount": "3523",
"datePublished": "2020-01-06T10:48:30+02:00", "datePublished": "2020-01-06T10:48:30+02:00",
"dateModified": "2020-02-04T13:06:23+02:00", "dateModified": "2020-02-10T10:34:19+02:00",
"author": { "author": {
"@type": "Person", "@type": "Person",
"name": "Alan Orth" "name": "Alan Orth"

50
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@ -35,7 +35,7 @@ The code finally builds and runs with a fresh install
"/> "/>
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@ -45,7 +45,7 @@ The code finally builds and runs with a fresh install
"@type": "BlogPosting", "@type": "BlogPosting",
"headline": "February, 2020", "headline": "February, 2020",
"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-02\/", "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-02\/",
"wordCount": "2551", "wordCount": "2811",
"datePublished": "2020-02-02T11:56:30+02:00", "datePublished": "2020-02-02T11:56:30+02:00",
"dateModified": "2020-02-09T17:34:12+02:00", "dateModified": "2020-02-09T17:34:12+02:00",
"author": { "author": {
@ -510,7 +510,51 @@ $ cat out.dspace510-1 | ../FlameGraph/stackcollapse-perf.pl | grep -E '^java' |
</ul> </ul>
</li> </li>
</ul> </ul>
<!-- raw HTML omitted --> <h2 id="2020-02-10">2020-02-10</h2>
<ul>
<li>Follow up with <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706">Atmire about DSpace 6.x upgrade</a>
<ul>
<li>I raised the issue of targetting 6.4-SNAPSHOT as well as the Discovery indexing performance issues in 6.x</li>
</ul>
</li>
</ul>
<h2 id="2020-02-11">2020-02-11</h2>
<ul>
<li>Maria from Bioversity asked me to add some ORCID iDs to our controlled vocabulary so I combined them with our existing ones and updated the names from the ORCID API:</li>
</ul>
<pre><code>$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity-orcid-ids.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort | uniq &gt; /tmp/2020-02-11-combined-orcids.txt
$ ./resolve-orcids.py -i /tmp/2020-02-11-combined-orcids.txt -o /tmp/2020-02-11-combined-names.txt -d
# sort names, copy to cg-creator-id.xml, add XML formatting, and then format with tidy (preserving accents)
$ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-id.xml
</code></pre><ul>
<li>Then I noticed some author names had changed, so I captured the old and new names in a CSV file and fixed them using <code>fix-metadata-values.py</code>:</li>
</ul>
<pre><code>$ ./fix-metadata-values.py -i 2020-02-11-correct-orcid-ids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -t correct -m 240 -d
</code></pre><ul>
<li>On a hunch I decided to try to add these ORCID iDs to existing items that might not have them yet
<ul>
<li>I checked the database for likely matches to the author name and then created a CSV with the author names and ORCID iDs:</li>
</ul>
</li>
</ul>
<pre><code>dc.contributor.author,cg.creator.id
&quot;Staver, Charles&quot;,charles staver: 0000-0002-4532-6077
&quot;Staver, C.&quot;,charles staver: 0000-0002-4532-6077
&quot;Fungo, R.&quot;,Robert Fungo: 0000-0002-4264-6905
&quot;Remans, R.&quot;,Roseline Remans: 0000-0003-3659-8529
&quot;Remans, Roseline&quot;,Roseline Remans: 0000-0003-3659-8529
&quot;Rietveld A.&quot;,Anne Rietveld: 0000-0002-9400-9473
&quot;Rietveld, A.&quot;,Anne Rietveld: 0000-0002-9400-9473
&quot;Rietveld, A.M.&quot;,Anne Rietveld: 0000-0002-9400-9473
&quot;Rietveld, Anne M.&quot;,Anne Rietveld: 0000-0002-9400-9473
&quot;Fongar, A.&quot;,Andrea Fongar: 0000-0003-2084-1571
&quot;Müller, Anna&quot;,Anna Müller: 0000-0003-3120-8560
&quot;Müller, A.&quot;,Anna Müller: 0000-0003-3120-8560
</code></pre><ul>
<li>Running the <code>add-orcid-identifiers-csv.py</code> script I added 144 ORCID iDs to items!</li>
</ul>
<pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/2020-02-11-add-orcid-ids.csv -db dspace -u dspace -p 'fuuu'
</code></pre><!-- raw HTML omitted -->

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@ -14,7 +14,7 @@
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@ -14,7 +14,7 @@
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGIAR Library Migration"/> <meta name="twitter:title" content="CGIAR Library Migration"/>
<meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/> <meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
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@ -15,7 +15,7 @@
<meta name="twitter:card" content="summary"/> <meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="CGSpace CG Core v2 Migration"/> <meta name="twitter:title" content="CGSpace CG Core v2 Migration"/>
<meta name="twitter:description" content="Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2."/> <meta name="twitter:description" content="Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2."/>
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<meta name="twitter:title" content="CGSpace Notes"/> <meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:title" content="CGSpace Notes"/> <meta name="twitter:title" content="CGSpace Notes"/>
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