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@ -437,5 +437,167 @@ COPY 3917
- Email GRID.ac to ask them about where old names for institutes are stores, as I see them in the "Disambiguate" search function online, but not in the standalone data
- For example, both "International Laboratory for Research on Animal Diseases" (ILRAD) and "International Livestock Centre for Africa" (ILCA) correctly return a hit for "International Livestock Research Institute", but it's nowhere in the data
- I discovered two interesting OpenRefine reconciliation services:
- [OpenRefine reconciler for the Research Organization Registry](https://github.com/ror-community/ror-reconciler)
- [Getty Vocabularies OpenRefine Reconciliation](https://www.getty.edu/research/tools/vocabularies/obtain/openrefine.html) (see the Getty Thesaurus of Geographic Names ® (TGN))
## 2020-06-29
- I stumbled upon a sort of [standard for rights statements](https://rightsstatements.org/page/1.0/) that we might want to use for `dc.rights` eventually
- I'm trying to understand the difference between `dcterms.coverage`, `dcterms.spatial`, and `dcterms.temporal`
- According to the [Dublin Core specification for coverage](https://www.dublincore.org/specifications/dublin-core/dcmi-terms/terms/coverage/) the more specific spatial and temporal subproperties:
> Because coverage is so broadly defined, it is preferable to use the more specific subproperties Temporal Coverage and Spatial Coverage.
- So I guess we should be using this for countries... but then all regions, countries, etc get merged together into this when you use DCTERMS
- Perhaps better to use `cg.coverage.country` and crosswalk to `dcterms.spatial`
- Another thing is that these values are not literals—you are supposed to embed classes...
- I also notice that there is a [CrossRef funders registry](https://www.crossref.org/services/funder-registry/) with 23,000+ funders that you can [download as RDF](https://gitlab.com/crossref/open_funder_registry) or [access via an API](https://www.crossref.org/education/funder-registry/accessing-the-funder-registry/)
```
$ http 'https://api.crossref.org/funders?query=Bill+and+Melinda+Gates&mailto=a.orth@cgiar.org'
```
- Searching for "Bill and Melinda Gates" we can see the `name` literal and a list of `alt-names` literals
- This could be good for checking our funders
- The API currently returns pages for each funder in the vocabulary, but they are giving HTTP 404 right now: https://data.crossref.org/fundingdata/vocabulary/Label-599174
- I sent an email to the CrossRef Funders Registry team
- See the [CrossRef API docs](https://github.com/CrossRef/rest-api-doc) (specifically the parameters and filters)
- I made a pull request on CG Core v2 to recommend using persistent identifiers for DOIs and ORCID iDs ([#26](https://github.com/AgriculturalSemantics/cg-core/pull/26))
- I exported sponsors/funders from CGSpace and wrote a script to query the CrossRef API for matches:
```
dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=29) TO /tmp/2020-06-29-sponsors.csv;
COPY 682
```
- The script is `crossref-funders-lookup.py` and it is based on `agrovoc-lookup.py`
- On that note, I realized I need to URL encode the funder before making the search request with requests because, while the requests library *does* do URL encoding, it seems that it interprets characters like `&` as indicative query parameters and this causes searches for funders like `Bill & Melinda Gates Foundation` to get misinterpreted
- So then I noticed that I had worked around this in `agrovoc-lookup.py` a few years ago by just ignoring subjects with special characters like apostrophes and accents!
- I tested the script on our funders:
```
$ ./crossref-funders-lookup.py -i /tmp/2020-06-29-sponsors.csv -om /tmp/sponsors-matched.txt -or /tmp/sponsors-rejected.txt -d -e blah@blah.com
$ wc -l /tmp/2020-06-29-sponsors.csv
682 /tmp/2020-06-29-sponsors.csv
$ wc -l /tmp/sponsors-*
180 /tmp/sponsors-matched.txt
502 /tmp/sponsors-rejected.txt
682 total
```
- It seems that 35% of our funders already match... I bet a few more will match if I check for simple errors
- Interesting, I found a few funders that we have correct, but can't figure out how to match them in the API:
- `Claussen-Simon-Stiftung`
- `H2020 Marie Skłodowska-Curie Actions`
## 2020-06-30
- GRID responded to my question about historical names
- They said the information is not part of the public GRID or ROR lists, but you can access it with a license to the Dimensions API
- Gabriela from CIP sent me a list of erroneously added CIP subjects to remove from CGSpace:
```
$ cat /tmp/2020-06-30-remove-cip-subjects.csv
cg.subject.cip
INTEGRATED PEST MANAGEMENT
ORANGE FLESH SWEET POTATOES
AEROPONICS
FOOD SUPPLY
SASHA
SPHI
INSECT LIFE CYCLE MODELLING
SUSTAIN
AGRICULTURAL INNOVATIONS
NATIVE VARIETIES
PHYTOPHTHORA INFESTANS
$ ./delete-metadata-values.py -i /tmp/2020-06-30-remove-cip-subjects.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.cip -m 127 -d
```
- She also wants to change their `SWEET POTATOES` term to `SWEETPOTATOES`, both in the CIP subject list and existing items so I updated those too:
```
$ cat /tmp/2020-06-30-fix-cip-subjects.csv
cg.subject.cip,correct
SWEET POTATOES,SWEETPOTATOES
$ ./fix-metadata-values.py -i /tmp/2020-06-30-fix-cip-subjects.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.cip -t correct -m 127 -d
```
- She also finished doing all the corrections to authors that I had sent her last week, but many of the changes are removing Spanish accents from authors names so I asked if she's really should she wants to do that
- I ran the fixes and deletes on CGSpace, but not on DSpace Test yet because those scripts need updating for DSpace 6 UUIDs
- I spent about two hours manually checking our sponsors that were rejected from CrossRef and found about fifty-five corrections that I ran on CGSpace:
```
$ cat 2020-06-29-fix-sponsors.csv
dc.description.sponsorship,correct
"Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil","Conselho Nacional de Desenvolvimento Científico e Tecnológico"
"Claussen Simon Stiftung","Claussen-Simon-Stiftung"
"Fonds pour la formation á la Recherche dans l'Industrie et dans l'Agriculture, Belgium","Fonds pour la Formation à la Recherche dans l’Industrie et dans l’Agriculture"
"Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil","Fundação de Amparo à Pesquisa do Estado de São Paulo"
"Schlumberger Foundation Faculty for the Future","Schlumberger Foundation"
"Wildlife Conservation Society, United States","Wildlife Conservation Society"
"Portuguese Foundation for Science and Technology","Portuguese Science and Technology Foundation"
"Wageningen University and Research","Wageningen University and Research Centre"
"Leverhulme Centre for Integrative Research in Agriculture and Health","Leverhulme Centre for Integrative Research on Agriculture and Health"
"Natural Science and Engineering Research Council of Canada","Natural Sciences and Engineering Research Council of Canada"
"Biotechnology and Biological Sciences Research Council, United Kingdom","Biotechnology and Biological Sciences Research Council"
"Home Grown Ceraels Authority United Kingdom","Home-Grown Cereals Authority"
"Fiat Panis Foundation","Foundation fiat panis"
"Defence Science and Technology Laboratory, United Kingdom","Defence Science and Technology Laboratory"
"African Development Bank","African Development Bank Group"
"Ministry of Health, Labour, and Welfare, Japan","Ministry of Health, Labour and Welfare"
"World Academy of Sciences","The World Academy of Sciences"
"Agricultural Research Council, South Africa","Agricultural Research Council"
"Department of Homeland Security, USA","U.S. Department of Homeland Security"
"Quadram Institute","Quadram Institute Bioscience"
"Google.org","Google"
"Department for Environment, Food and Rural Affairs, United Kingdom","Department for Environment, Food and Rural Affairs, UK Government"
"National Commission for Science, Technology and Innovation, Kenya","National Commission for Science, Technology and Innovation"
"Hainan Province Natural Science Foundation of China","Natural Science Foundation of Hainan Province"
"German Society for International Cooperation (GIZ)","GIZ"
"German Federal Ministry of Food and Agriculture","Federal Ministry of Food and Agriculture"
"State Key Laboratory of Environmental Geochemistry, China","State Key Laboratory of Environmental Geochemistry"
"QUT student scholarship","Queensland University of Technology"
"Australia Centre for International Agricultural Research","Australian Centre for International Agricultural Research"
"Belgian Science Policy","Belgian Federal Science Policy Office"
"U.S. Department of Agriculture USDA","U.S. Department of Agriculture"
"U.S.. Department of Agriculture (USDA)","U.S. Department of Agriculture"
"Fundação de Amparo à Pesquisa do Estado de São Paulo ( FAPESP)","Fundação de Amparo à Pesquisa do Estado de São Paulo"
"Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul, Brazil","Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul"
"Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Brazil","Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro"
"Swedish University of Agricultural Sciences (SLU)","Swedish University of Agricultural Sciences"
"U.S. Department of Agriculture (USDA)","U.S. Department of Agriculture"
"Swedish International Development Cooperation Agency (Sida)","Sida"
"Swedish International Development Agency","Sida"
"Federal Ministry for Economic Cooperation and Development, Germany","Federal Ministry for Economic Cooperation and Development"
"Natural Environment Research Council, United Kingdom","Natural Environment Research Council"
"Economic and Social Research Council, United Kingdom","Economic and Social Research Council"
"Medical Research Council, United Kingdom","Medical Research Council"
"Federal Ministry for Education and Research, Germany","Federal Ministry for Education, Science, Research and Technology"
"UK Government’s Department for International Development","Department for International Development, UK Government"
"Department for International Development, United Kingdom","Department for International Development, UK Government"
"United Nations Children's Fund","United Nations Children's Emergency Fund"
"Swedish Research Council for Environment, Agricultural Science and Spatial Planning","Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning"
"Agence Nationale de la Recherche, France","French National Research Agency"
"Fondation pour la recherche sur la biodiversité","Foundation for Research on Biodiversity"
"Programa Nacional de Innovacion Agraria, Peru","Programa Nacional de Innovación Agraria, Peru"
"United States Agency for International Development (USAID)","United States Agency for International Development"
"West Africa Agricultural Productivity Programme","West Africa Agricultural Productivity Program"
"West African Agricultural Productivity Project","West Africa Agricultural Productivity Program"
"Rural Development Administration, Republic of Korea","Rural Development Administration"
"UK’s Biotechnology and Biological Sciences Research Council (BBSRC)","Biotechnology and Biological Sciences Research Council"
$ ./fix-metadata-values.py -i /tmp/2020-06-29-fix-sponsors.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -t correct -m 29
```
- Peter wants me to add "CORONAVIRUS DISEASE" to all ILRI items that have ILRI subject "COVID19"
- I exported the ILRI community and cut the columns I needed, then opened the file in OpenRefine:
```
$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
$ dspace metadata-export -i 10568/1 -f /tmp/ilri.cs
$ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp/ilri.csv > /tmp/ilri-covid19.csv
```
- I see that all items with "COVID19" already have "CORONAVIRUS DISEASE" so I don't need to do anything
<!-- vim: set sw=2 ts=2: -->

2
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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
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 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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2
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.
Update GitHub wiki for documentation of maintenance tasks.
"/>
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2
docs/2016-02/index.html
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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;
Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
"/>
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2
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
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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2
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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
Also, I noticed the checker log has some errors we should pay attention to:
"/>
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2
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
3168
"/>
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2
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
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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2
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
"/>
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2
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 rebase -i dspace-5.5
"/>
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2
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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;
"/>
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2
docs/2016-10/index.html
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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
"/>
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2
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)
"/>
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2
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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
Another worrying error from dspace.log is:
"/>
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2
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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 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
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)
Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
"/>
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2
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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
/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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2
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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
"/>
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2
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@ -15,7 +15,7 @@
<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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@ -15,7 +15,7 @@
<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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@ -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
We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
"/>
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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
Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
"/>
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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
"/>
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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
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;
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
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
"/>
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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
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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@ -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
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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
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
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
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.
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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
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
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
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
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
"/>
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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
903 54.70.40.11
"/>
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@ -69,7 +69,7 @@ real 0m19.873s
user 0m22.203s
sys 0m1.979s
"/>
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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
"/>
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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-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d
"/>
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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;
"/>
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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
"/>
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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
"/>
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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
"/>
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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
9124 45.5.186.2
"/>
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@ -15,7 +15,7 @@
<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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@ -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;
106781
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2
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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
# reboot
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@ -53,7 +53,7 @@ I tweeted the CGSpace repository link
"/>
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@ -35,7 +35,7 @@ The code finally builds and runs with a fresh install
"/>
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@ -39,7 +39,7 @@ You need to download this into the DSpace 6.x source and compile it
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2
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@ -45,7 +45,7 @@ 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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@ -31,7 +31,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
"/>
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@ -19,7 +19,7 @@ I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Tes
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2020-06/" />
<meta property="article:published_time" content="2020-06-01T13:55:39+03:00" />
<meta property="article:modified_time" content="2020-06-23T16:13:27+03:00" />
<meta property="article:modified_time" content="2020-06-28T18:13:44+03:00" />
<meta name="twitter:card" content="summary"/>
<meta name="twitter:title" content="June, 2020"/>
@ -33,7 +33,7 @@ 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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@ -43,9 +43,9 @@ I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Tes
"@type": "BlogPosting",
"headline": "June, 2020",
"url": "https://alanorth.github.io/cgspace-notes/2020-06/",
"wordCount": "3319",
"wordCount": "4764",
"datePublished": "2020-06-01T13:55:39+03:00",
"dateModified": "2020-06-23T16:13:27+03:00",
"dateModified": "2020-06-28T18:13:44+03:00",
"author": {
"@type": "Person",
"name": "Alan Orth"
@ -594,6 +594,191 @@ COPY 3917
</ul>
</li>
</ul>
<h2 id="2020-06-28">2020-06-28</h2>
<ul>
<li>Email GRID.ac to ask them about where old names for institutes are stores, as I see them in the &ldquo;Disambiguate&rdquo; search function online, but not in the standalone data
<ul>
<li>For example, both &ldquo;International Laboratory for Research on Animal Diseases&rdquo; (ILRAD) and &ldquo;International Livestock Centre for Africa&rdquo; (ILCA) correctly return a hit for &ldquo;International Livestock Research Institute&rdquo;, but it&rsquo;s nowhere in the data</li>
</ul>
</li>
<li>I discovered two interesting OpenRefine reconciliation services:
<ul>
<li><a href="https://github.com/ror-community/ror-reconciler">OpenRefine reconciler for the Research Organization Registry</a></li>
<li><a href="https://www.getty.edu/research/tools/vocabularies/obtain/openrefine.html">Getty Vocabularies OpenRefine Reconciliation</a> (see the Getty Thesaurus of Geographic Names ® (TGN))</li>
</ul>
</li>
</ul>
<h2 id="2020-06-29">2020-06-29</h2>
<ul>
<li>I stumbled upon a sort of <a href="https://rightsstatements.org/page/1.0/">standard for rights statements</a> that we might want to use for <code>dc.rights</code> eventually</li>
<li>I&rsquo;m trying to understand the difference between <code>dcterms.coverage</code>, <code>dcterms.spatial</code>, and <code>dcterms.temporal</code>
<ul>
<li>According to the <a href="https://www.dublincore.org/specifications/dublin-core/dcmi-terms/terms/coverage/">Dublin Core specification for coverage</a> the more specific spatial and temporal subproperties:</li>
</ul>
</li>
</ul>
<blockquote>
<p>Because coverage is so broadly defined, it is preferable to use the more specific subproperties Temporal Coverage and Spatial Coverage.</p>
</blockquote>
<ul>
<li>So I guess we should be using this for countries&hellip; but then all regions, countries, etc get merged together into this when you use DCTERMS
<ul>
<li>Perhaps better to use <code>cg.coverage.country</code> and crosswalk to <code>dcterms.spatial</code></li>
<li>Another thing is that these values are not literals—you are supposed to embed classes&hellip;</li>
</ul>
</li>
<li>I also notice that there is a <a href="https://www.crossref.org/services/funder-registry/">CrossRef funders registry</a> with 23,000+ funders that you can <a href="https://gitlab.com/crossref/open_funder_registry">download as RDF</a> or <a href="https://www.crossref.org/education/funder-registry/accessing-the-funder-registry/">access via an API</a></li>
</ul>
<pre><code>$ http 'https://api.crossref.org/funders?query=Bill+and+Melinda+Gates&amp;mailto=a.orth@cgiar.org'
</code></pre><ul>
<li>Searching for &ldquo;Bill and Melinda Gates&rdquo; we can see the <code>name</code> literal and a list of <code>alt-names</code> literals
<ul>
<li>This could be good for checking our funders</li>
<li>The API currently returns pages for each funder in the vocabulary, but they are giving HTTP 404 right now: <a href="https://data.crossref.org/fundingdata/vocabulary/Label-599174">https://data.crossref.org/fundingdata/vocabulary/Label-599174</a></li>
<li>I sent an email to the CrossRef Funders Registry team</li>
</ul>
</li>
<li>See the <a href="https://github.com/CrossRef/rest-api-doc">CrossRef API docs</a> (specifically the parameters and filters)</li>
<li>I made a pull request on CG Core v2 to recommend using persistent identifiers for DOIs and ORCID iDs (<a href="https://github.com/AgriculturalSemantics/cg-core/pull/26">#26</a>)</li>
<li>I exported sponsors/funders from CGSpace and wrote a script to query the CrossRef API for matches:</li>
</ul>
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=29) TO /tmp/2020-06-29-sponsors.csv;
COPY 682
</code></pre><ul>
<li>The script is <code>crossref-funders-lookup.py</code> and it is based on <code>agrovoc-lookup.py</code>
<ul>
<li>On that note, I realized I need to URL encode the funder before making the search request with requests because, while the requests library <em>does</em> do URL encoding, it seems that it interprets characters like <code>&amp;</code> as indicative query parameters and this causes searches for funders like <code>Bill &amp; Melinda Gates Foundation</code> to get misinterpreted</li>
<li>So then I noticed that I had worked around this in <code>agrovoc-lookup.py</code> a few years ago by just ignoring subjects with special characters like apostrophes and accents!</li>
</ul>
</li>
<li>I tested the script on our funders:</li>
</ul>
<pre><code>$ ./crossref-funders-lookup.py -i /tmp/2020-06-29-sponsors.csv -om /tmp/sponsors-matched.txt -or /tmp/sponsors-rejected.txt -d -e blah@blah.com
$ wc -l /tmp/2020-06-29-sponsors.csv
682 /tmp/2020-06-29-sponsors.csv
$ wc -l /tmp/sponsors-*
180 /tmp/sponsors-matched.txt
502 /tmp/sponsors-rejected.txt
682 total
</code></pre><ul>
<li>It seems that 35% of our funders already match&hellip; I bet a few more will match if I check for simple errors
<ul>
<li>Interesting, I found a few funders that we have correct, but can&rsquo;t figure out how to match them in the API:
<ul>
<li><code>Claussen-Simon-Stiftung</code></li>
<li><code>H2020 Marie Skłodowska-Curie Actions</code></li>
</ul>
</li>
</ul>
</li>
</ul>
<h2 id="2020-06-30">2020-06-30</h2>
<ul>
<li>GRID responded to my question about historical names
<ul>
<li>They said the information is not part of the public GRID or ROR lists, but you can access it with a license to the Dimensions API</li>
</ul>
</li>
<li>Gabriela from CIP sent me a list of erroneously added CIP subjects to remove from CGSpace:</li>
</ul>
<pre><code>$ cat /tmp/2020-06-30-remove-cip-subjects.csv
cg.subject.cip
INTEGRATED PEST MANAGEMENT
ORANGE FLESH SWEET POTATOES
AEROPONICS
FOOD SUPPLY
SASHA
SPHI
INSECT LIFE CYCLE MODELLING
SUSTAIN
AGRICULTURAL INNOVATIONS
NATIVE VARIETIES
PHYTOPHTHORA INFESTANS
$ ./delete-metadata-values.py -i /tmp/2020-06-30-remove-cip-subjects.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.cip -m 127 -d
</code></pre><ul>
<li>She also wants to change their <code>SWEET POTATOES</code> term to <code>SWEETPOTATOES</code>, both in the CIP subject list and existing items so I updated those too:</li>
</ul>
<pre><code>$ cat /tmp/2020-06-30-fix-cip-subjects.csv
cg.subject.cip,correct
SWEET POTATOES,SWEETPOTATOES
$ ./fix-metadata-values.py -i /tmp/2020-06-30-fix-cip-subjects.csv -db dspace -u dspace -p 'fuuu' -f cg.subject.cip -t correct -m 127 -d
</code></pre><ul>
<li>She also finished doing all the corrections to authors that I had sent her last week, but many of the changes are removing Spanish accents from authors names so I asked if she&rsquo;s really should she wants to do that</li>
<li>I ran the fixes and deletes on CGSpace, but not on DSpace Test yet because those scripts need updating for DSpace 6 UUIDs</li>
<li>I spent about two hours manually checking our sponsors that were rejected from CrossRef and found about fifty-five corrections that I ran on CGSpace:</li>
</ul>
<pre><code>$ cat 2020-06-29-fix-sponsors.csv
dc.description.sponsorship,correct
&quot;Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil&quot;,&quot;Conselho Nacional de Desenvolvimento Científico e Tecnológico&quot;
&quot;Claussen Simon Stiftung&quot;,&quot;Claussen-Simon-Stiftung&quot;
&quot;Fonds pour la formation á la Recherche dans l'Industrie et dans l'Agriculture, Belgium&quot;,&quot;Fonds pour la Formation à la Recherche dans l’Industrie et dans l’Agriculture&quot;
&quot;Fundação de Amparo à Pesquisa do Estado de São Paulo, Brazil&quot;,&quot;Fundação de Amparo à Pesquisa do Estado de São Paulo&quot;
&quot;Schlumberger Foundation Faculty for the Future&quot;,&quot;Schlumberger Foundation&quot;
&quot;Wildlife Conservation Society, United States&quot;,&quot;Wildlife Conservation Society&quot;
&quot;Portuguese Foundation for Science and Technology&quot;,&quot;Portuguese Science and Technology Foundation&quot;
&quot;Wageningen University and Research&quot;,&quot;Wageningen University and Research Centre&quot;
&quot;Leverhulme Centre for Integrative Research in Agriculture and Health&quot;,&quot;Leverhulme Centre for Integrative Research on Agriculture and Health&quot;
&quot;Natural Science and Engineering Research Council of Canada&quot;,&quot;Natural Sciences and Engineering Research Council of Canada&quot;
&quot;Biotechnology and Biological Sciences Research Council, United Kingdom&quot;,&quot;Biotechnology and Biological Sciences Research Council&quot;
&quot;Home Grown Ceraels Authority United Kingdom&quot;,&quot;Home-Grown Cereals Authority&quot;
&quot;Fiat Panis Foundation&quot;,&quot;Foundation fiat panis&quot;
&quot;Defence Science and Technology Laboratory, United Kingdom&quot;,&quot;Defence Science and Technology Laboratory&quot;
&quot;African Development Bank&quot;,&quot;African Development Bank Group&quot;
&quot;Ministry of Health, Labour, and Welfare, Japan&quot;,&quot;Ministry of Health, Labour and Welfare&quot;
&quot;World Academy of Sciences&quot;,&quot;The World Academy of Sciences&quot;
&quot;Agricultural Research Council, South Africa&quot;,&quot;Agricultural Research Council&quot;
&quot;Department of Homeland Security, USA&quot;,&quot;U.S. Department of Homeland Security&quot;
&quot;Quadram Institute&quot;,&quot;Quadram Institute Bioscience&quot;
&quot;Google.org&quot;,&quot;Google&quot;
&quot;Department for Environment, Food and Rural Affairs, United Kingdom&quot;,&quot;Department for Environment, Food and Rural Affairs, UK Government&quot;
&quot;National Commission for Science, Technology and Innovation, Kenya&quot;,&quot;National Commission for Science, Technology and Innovation&quot;
&quot;Hainan Province Natural Science Foundation of China&quot;,&quot;Natural Science Foundation of Hainan Province&quot;
&quot;German Society for International Cooperation (GIZ)&quot;,&quot;GIZ&quot;
&quot;German Federal Ministry of Food and Agriculture&quot;,&quot;Federal Ministry of Food and Agriculture&quot;
&quot;State Key Laboratory of Environmental Geochemistry, China&quot;,&quot;State Key Laboratory of Environmental Geochemistry&quot;
&quot;QUT student scholarship&quot;,&quot;Queensland University of Technology&quot;
&quot;Australia Centre for International Agricultural Research&quot;,&quot;Australian Centre for International Agricultural Research&quot;
&quot;Belgian Science Policy&quot;,&quot;Belgian Federal Science Policy Office&quot;
&quot;U.S. Department of Agriculture USDA&quot;,&quot;U.S. Department of Agriculture&quot;
&quot;U.S.. Department of Agriculture (USDA)&quot;,&quot;U.S. Department of Agriculture&quot;
&quot;Fundação de Amparo à Pesquisa do Estado de São Paulo ( FAPESP)&quot;,&quot;Fundação de Amparo à Pesquisa do Estado de São Paulo&quot;
&quot;Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul, Brazil&quot;,&quot;Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul&quot;
&quot;Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro, Brazil&quot;,&quot;Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro&quot;
&quot;Swedish University of Agricultural Sciences (SLU)&quot;,&quot;Swedish University of Agricultural Sciences&quot;
&quot;U.S. Department of Agriculture (USDA)&quot;,&quot;U.S. Department of Agriculture&quot;
&quot;Swedish International Development Cooperation Agency (Sida)&quot;,&quot;Sida&quot;
&quot;Swedish International Development Agency&quot;,&quot;Sida&quot;
&quot;Federal Ministry for Economic Cooperation and Development, Germany&quot;,&quot;Federal Ministry for Economic Cooperation and Development&quot;
&quot;Natural Environment Research Council, United Kingdom&quot;,&quot;Natural Environment Research Council&quot;
&quot;Economic and Social Research Council, United Kingdom&quot;,&quot;Economic and Social Research Council&quot;
&quot;Medical Research Council, United Kingdom&quot;,&quot;Medical Research Council&quot;
&quot;Federal Ministry for Education and Research, Germany&quot;,&quot;Federal Ministry for Education, Science, Research and Technology&quot;
&quot;UK Government’s Department for International Development&quot;,&quot;Department for International Development, UK Government&quot;
&quot;Department for International Development, United Kingdom&quot;,&quot;Department for International Development, UK Government&quot;
&quot;United Nations Children's Fund&quot;,&quot;United Nations Children's Emergency Fund&quot;
&quot;Swedish Research Council for Environment, Agricultural Science and Spatial Planning&quot;,&quot;Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning&quot;
&quot;Agence Nationale de la Recherche, France&quot;,&quot;French National Research Agency&quot;
&quot;Fondation pour la recherche sur la biodiversité&quot;,&quot;Foundation for Research on Biodiversity&quot;
&quot;Programa Nacional de Innovacion Agraria, Peru&quot;,&quot;Programa Nacional de Innovación Agraria, Peru&quot;
&quot;United States Agency for International Development (USAID)&quot;,&quot;United States Agency for International Development&quot;
&quot;West Africa Agricultural Productivity Programme&quot;,&quot;West Africa Agricultural Productivity Program&quot;
&quot;West African Agricultural Productivity Project&quot;,&quot;West Africa Agricultural Productivity Program&quot;
&quot;Rural Development Administration, Republic of Korea&quot;,&quot;Rural Development Administration&quot;
&quot;UK’s Biotechnology and Biological Sciences Research Council (BBSRC)&quot;,&quot;Biotechnology and Biological Sciences Research Council&quot;
$ ./fix-metadata-values.py -i /tmp/2020-06-29-fix-sponsors.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -t correct -m 29
</code></pre><ul>
<li>Peter wants me to add &ldquo;CORONAVIRUS DISEASE&rdquo; to all ILRI items that have ILRI subject &ldquo;COVID19&rdquo;
<ul>
<li>I exported the ILRI community and cut the columns I needed, then opened the file in OpenRefine:</li>
</ul>
</li>
</ul>
<pre><code>$ export JAVA_OPTS=&quot;-Xmx512m -Dfile.encoding=UTF-8&quot;
$ dspace metadata-export -i 10568/1 -f /tmp/ilri.cs
$ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp/ilri.csv &gt; /tmp/ilri-covid19.csv
</code></pre><ul>
<li>I see that all items with &ldquo;COVID19&rdquo; already have &ldquo;CORONAVIRUS DISEASE&rdquo; so I don&rsquo;t need to do anything</li>
</ul>
<!-- raw HTML omitted -->

2
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<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/categories/notes/">Notes</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
<a href='https://alanorth.github.io/cgspace-notes/categories/notes/'>Read more →</a>
</article>
@ -122,279 +94,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-05-02">2020-05-02</h2>
<ul>
<li>Peter said that CTA is having problems submitting an item to CGSpace
<ul>
<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; state are increasing again</li>
<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-04-02T10:53:24+03:00">Thu Apr 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-04-02">2020-04-02</h2>
<ul>
<li>Maria asked me to update Charles Staver&rsquo;s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
<ul>
<li>I updated the fifty-eight existing items on CGSpace</li>
</ul>
</li>
<li>Looking into the items Udana had asked about last week that were missing Altmetric donuts:
<ul>
<li><a href="https://hdl.handle.net/10568/103225">The first</a> is still missing its DOI, so I added it and <a href="https://twitter.com/mralanorth/status/1245632619661766657">tweeted its handle</a> (after a few hours there was a donut with score 222)</li>
<li><a href="https://hdl.handle.net/10568/106899">The second item</a> now has a donut with score 2 since I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a> last week</li>
<li><a href="https://hdl.handle.net/10568/107258">The third item</a> now has a donut with score 1 since I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> last week</li>
</ul>
</li>
<li>On the same note, the <a href="https://hdl.handle.net/10568/106573">one item</a> Abenet pointed out last week now has a donut with score of 104 after I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> last week</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-04/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-02-02T11:56:30+02:00">Sun Feb 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-02-02">2020-02-02</h2>
<ul>
<li>Continue working on porting CGSpace&rsquo;s DSpace 5 code to DSpace 6.3 that I started yesterday
<ul>
<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
<li>The code finally builds and runs with a fresh install</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-02/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-01/">January, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-01-06T10:48:30+02:00">Mon Jan 06, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-01-06">2020-01-06</h2>
<ul>
<li>Open <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706">a ticket</a> with Atmire to request a quote for the upgrade to DSpace 6</li>
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>
</ul>
<h2 id="2020-01-07">2020-01-07</h2>
<ul>
<li>Peter Ballantyne highlighted one more WLE <a href="https://hdl.handle.net/10568/101286">item</a> that is missing the Altmetric score that its DOI has
<ul>
<li>The DOI has a score of 259, but the Handle has no score at all</li>
<li>I <a href="https://twitter.com/mralanorth/status/1214471427157626881">tweeted</a> the CGSpace repository link</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-12/">December, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-12-01T11:22:30+02:00">Sun Dec 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-12-01">2019-12-01</h2>
<ul>
<li>Upgrade CGSpace (linode18) to Ubuntu 18.04:
<ul>
<li>Check any packages that have residual configs and purge them:</li>
<li><!-- raw HTML omitted --># dpkg -l | grep -E &lsquo;^rc&rsquo; | awk &lsquo;{print $2}&rsquo; | xargs dpkg -P<!-- raw HTML omitted --></li>
<li>Make sure all packages are up to date and the package manager is up to date, then reboot:</li>
</ul>
</li>
</ul>
<pre><code># apt update &amp;&amp; apt full-upgrade
# apt-get autoremove &amp;&amp; apt-get autoclean
# dpkg -C
# reboot
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-12/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-11/">November, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-11-04T12:20:30+02:00">Mon Nov 04, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-11-04">2019-11-04</h2>
<ul>
<li>Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
<ul>
<li>I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:</li>
</ul>
</li>
</ul>
<pre><code># zcat --force /var/log/nginx/*access.log.*.gz | grep -cE &quot;[0-9]{1,2}/Oct/2019&quot;
4671942
# zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE &quot;[0-9]{1,2}/Oct/2019&quot;
1277694
</code></pre><ul>
<li>So 4.6 million from XMLUI and another 1.2 million from API requests</li>
<li>Let&rsquo;s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):</li>
</ul>
<pre><code># zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E &quot;[0-9]{1,2}/Oct/2019&quot;
1183456
# 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
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></h2>
<p class="blog-post-meta"><time datetime="2019-10-28T13:27:35+02:00">Mon Oct 28, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a>
</p>
</header>
<p>Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2.</p>
<p>With reference to <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2 draft standard</a> by Marie-Angélique as well as <a href="http://www.dublincore.org/specifications/dublin-core/dcmi-terms/">DCMI DCTERMS</a>.</p>
<a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-10/">October, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-10-01T13:20:51+03:00">Tue Oct 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
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+00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c 'id,dc.
<a href='https://alanorth.github.io/cgspace-notes/2019-10/'>Read more →</a>
</article>
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<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-06/">June, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-06-01T13:55:39+03:00">Mon Jun 01, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/tags/migration/">Migration</a></h2>
<p class="blog-post-meta"><time datetime="2019-10-28T13:27:35+02:00">Mon Oct 28, 2019</time> by Alan Orth</p>
</header>
<h2 id="2020-06-01">2020-06-01</h2>
<ul>
<li>I tried to run the <code>AtomicStatisticsUpdateCLI</code> CUA migration script on DSpace Test (linode26) again and it is still going very slowly and has tons of errors like I noticed yesterday
<ul>
<li>I sent Atmire the dspace.log from today and told them to log into the server to debug the process</li>
</ul>
</li>
<li>In other news, I checked the statistics API on DSpace 6 and it&rsquo;s working</li>
<li>I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error:</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-06/'>Read more →</a>
<a href='https://alanorth.github.io/cgspace-notes/tags/migration/'>Read more →</a>
</article>
@ -124,23 +96,11 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-05/">May, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-05-02T09:52:04+03:00">Sat May 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/tags/notes/">Notes</a></h2>
<p class="blog-post-meta"><time datetime="2017-09-07T16:54:52+07:00">Thu Sep 07, 2017</time> by Alan Orth</p>
</header>
<h2 id="2020-05-02">2020-05-02</h2>
<ul>
<li>Peter said that CTA is having problems submitting an item to CGSpace
<ul>
<li>Looking at the PostgreSQL stats it seems to be the same issue that Tezira was having last week, as I see the number of connections in &lsquo;idle in transaction&rsquo; and &lsquo;waiting for lock&rsquo; state are increasing again</li>
<li>I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2.11, and there were some bugs related to transactions fixed in 42.2.12 (which I had updated in the Ansible playbooks, but not deployed yet)</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-05/'>Read more →</a>
<a href='https://alanorth.github.io/cgspace-notes/tags/notes/'>Read more →</a>
</article>
@ -148,253 +108,6 @@
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-04/">April, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-04-02T10:53:24+03:00">Thu Apr 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-04-02">2020-04-02</h2>
<ul>
<li>Maria asked me to update Charles Staver&rsquo;s ORCID iD in the submission template and on CGSpace, as his name was lower case before, and now he has corrected it
<ul>
<li>I updated the fifty-eight existing items on CGSpace</li>
</ul>
</li>
<li>Looking into the items Udana had asked about last week that were missing Altmetric donuts:
<ul>
<li><a href="https://hdl.handle.net/10568/103225">The first</a> is still missing its DOI, so I added it and <a href="https://twitter.com/mralanorth/status/1245632619661766657">tweeted its handle</a> (after a few hours there was a donut with score 222)</li>
<li><a href="https://hdl.handle.net/10568/106899">The second item</a> now has a donut with score 2 since I <a href="https://twitter.com/mralanorth/status/1243158045540134913">tweeted its handle</a> last week</li>
<li><a href="https://hdl.handle.net/10568/107258">The third item</a> now has a donut with score 1 since I <a href="https://twitter.com/mralanorth/status/1243158786392625153">tweeted it</a> last week</li>
</ul>
</li>
<li>On the same note, the <a href="https://hdl.handle.net/10568/106573">one item</a> Abenet pointed out last week now has a donut with score of 104 after I <a href="https://twitter.com/mralanorth/status/1243163710241345536">tweeted it</a> last week</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-04/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-03/">March, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-03-02T12:31:30+02:00">Mon Mar 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-03-02">2020-03-02</h2>
<ul>
<li>Update <a href="https://github.com/ilri/dspace-statistics-api">dspace-statistics-api</a> for DSpace 6+ UUIDs
<ul>
<li>Tag version 1.2.0 on GitHub</li>
</ul>
</li>
<li>Test migrating legacy Solr statistics to UUIDs with the as-of-yet unreleased <a href="https://github.com/DSpace/DSpace/commit/184f2b2153479045fba6239342c63e7f8564b8b6#diff-0350ce2e13b28d5d61252b7a8f50a059">SolrUpgradePre6xStatistics.java</a>
<ul>
<li>You need to download this into the DSpace 6.x source and compile it</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-03/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-02/">February, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-02-02T11:56:30+02:00">Sun Feb 02, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-02-02">2020-02-02</h2>
<ul>
<li>Continue working on porting CGSpace&rsquo;s DSpace 5 code to DSpace 6.3 that I started yesterday
<ul>
<li>Sign up for an account with MaxMind so I can get the GeoLite2-City.mmdb database</li>
<li>I still need to wire up the API credentials and cron job into the Ansible infrastructure playbooks</li>
<li>Fix some minor issues in the config and XMLUI themes, like removing Atmire stuff</li>
<li>The code finally builds and runs with a fresh install</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-02/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2020-01/">January, 2020</a></h2>
<p class="blog-post-meta"><time datetime="2020-01-06T10:48:30+02:00">Mon Jan 06, 2020</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2020-01-06">2020-01-06</h2>
<ul>
<li>Open <a href="https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=706">a ticket</a> with Atmire to request a quote for the upgrade to DSpace 6</li>
<li>Last week Altmetric responded about the <a href="https://hdl.handle.net/10568/97087">item</a> that had a lower score than than its DOI
<ul>
<li>The score is now linked to the DOI</li>
<li>Another <a href="https://handle.hdl.net/10568/91278">item</a> that had the same problem in 2019 has now also linked to the score for its DOI</li>
<li>Another <a href="https://hdl.handle.net/10568/81236">item</a> that had the same problem in 2019 has also been fixed</li>
</ul>
</li>
</ul>
<h2 id="2020-01-07">2020-01-07</h2>
<ul>
<li>Peter Ballantyne highlighted one more WLE <a href="https://hdl.handle.net/10568/101286">item</a> that is missing the Altmetric score that its DOI has
<ul>
<li>The DOI has a score of 259, but the Handle has no score at all</li>
<li>I <a href="https://twitter.com/mralanorth/status/1214471427157626881">tweeted</a> the CGSpace repository link</li>
</ul>
</li>
</ul>
<a href='https://alanorth.github.io/cgspace-notes/2020-01/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-12/">December, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-12-01T11:22:30+02:00">Sun Dec 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-12-01">2019-12-01</h2>
<ul>
<li>Upgrade CGSpace (linode18) to Ubuntu 18.04:
<ul>
<li>Check any packages that have residual configs and purge them:</li>
<li><!-- raw HTML omitted --># dpkg -l | grep -E &lsquo;^rc&rsquo; | awk &lsquo;{print $2}&rsquo; | xargs dpkg -P<!-- raw HTML omitted --></li>
<li>Make sure all packages are up to date and the package manager is up to date, then reboot:</li>
</ul>
</li>
</ul>
<pre><code># apt update &amp;&amp; apt full-upgrade
# apt-get autoremove &amp;&amp; apt-get autoclean
# dpkg -C
# reboot
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-12/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-11/">November, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-11-04T12:20:30+02:00">Mon Nov 04, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
<h2 id="2019-11-04">2019-11-04</h2>
<ul>
<li>Peter noticed that there were 5.2 million hits on CGSpace in 2019-10 according to the Atmire usage statistics
<ul>
<li>I looked in the nginx logs and see 4.6 million in the access logs, and 1.2 million in the API logs:</li>
</ul>
</li>
</ul>
<pre><code># zcat --force /var/log/nginx/*access.log.*.gz | grep -cE &quot;[0-9]{1,2}/Oct/2019&quot;
4671942
# zcat --force /var/log/nginx/{rest,oai,statistics}.log.*.gz | grep -cE &quot;[0-9]{1,2}/Oct/2019&quot;
1277694
</code></pre><ul>
<li>So 4.6 million from XMLUI and another 1.2 million from API requests</li>
<li>Let&rsquo;s see how many of the REST API requests were for bitstreams (because they are counted in Solr stats):</li>
</ul>
<pre><code># zcat --force /var/log/nginx/rest.log.*.gz | grep -c -E &quot;[0-9]{1,2}/Oct/2019&quot;
1183456
# 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
</code></pre>
<a href='https://alanorth.github.io/cgspace-notes/2019-11/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></h2>
<p class="blog-post-meta"><time datetime="2019-10-28T13:27:35+02:00">Mon Oct 28, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
<span class="fas fa-tag" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/tags/migration/" rel="tag">Migration</a>
</p>
</header>
<p>Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2.</p>
<p>With reference to <a href="https://agriculturalsemantics.github.io/cg-core/cgcore.html">CG Core v2 draft standard</a> by Marie-Angélique as well as <a href="http://www.dublincore.org/specifications/dublin-core/dcmi-terms/">DCMI DCTERMS</a>.</p>
<a href='https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/'>Read more →</a>
</article>
<article class="blog-post">
<header>
<h2 class="blog-post-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/2019-10/">October, 2019</a></h2>
<p class="blog-post-meta"><time datetime="2019-10-01T13:20:51+03:00">Tue Oct 01, 2019</time> by Alan Orth in
<span class="fas fa-folder" aria-hidden="true"></span>&nbsp;<a href="/cgspace-notes/categories/notes/" rel="category tag">Notes</a>
</p>
</header>
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+00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c 'id,dc.
<a href='https://alanorth.github.io/cgspace-notes/2019-10/'>Read more →</a>
</article>
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