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Add notes for 2020-01-29
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@ -324,4 +324,46 @@ COPY 77
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- I did some metadata enrichment by searching for the items and copying relevant data from journal pages
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- I asked Bosede to try to do the same for the rest of the journal articles
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## 2020-01-29
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- Normalize about 4,500 DOI, YouTube, and SlideShare links on CGSpace that are missing HTTPS or using old format:
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```
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://www.doi.org%';
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://doi.org%';
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://dx.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://dx.doi.org%';
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'https://dx.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'https://dx.doi.org%';
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.youtube.com', 'https://www.youtube.com') WHERE resource_type_id = 2 AND metadata_field_id = 219 AND text_value LIKE 'http://www.youtube.com%';
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UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.slideshare.net', 'https://www.slideshare.net') WHERE resource_type_id = 2 AND metadata_field_id = 219 AND text_value LIKE 'http://www.slideshare.net%';
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```
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- I exported a list of all of our ISSNs with item IDs so that I could fix them in OpenRefine and submit them with multi-value separators to DSpace metadata import:
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```
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dspace=# \COPY (SELECT resource_id as "id", text_value as "dc.identifier.issn" FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 21) to /tmp/2020-01-29-issn.csv WITH CSV HEADER;
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COPY 23339
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```
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- Then, after spending two hours correcting 1,000 ISSNs I realized that I need to normalize the `text_lang` fields in the database first or else these will all look like changes due to the "en_US" and NULL, etc (for both ISSN and ISBN):
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```
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dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id = 2 AND metadata_field_id IN (20,21);
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UPDATE 30454
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```
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- Then I realized that my initial PostgreSQL query wasn't so genius because if a field already has multiple values it will appear on separate lines with the same ID, so when `dspace metadata-import` sees it, the change will be removed and added, or added and removed, depending on the order it is seen!
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- A better course of action is to select the distinct ones and then correct them using `fix-metadata-values.py`...
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```
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dspace=# \COPY (SELECT DISTINCT text_value as "dc.identifier.issn[en_US]", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 21 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-29-issn-distinct.csv WITH CSV HEADER;
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COPY 2900
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```
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- I re-applied all my corrections, filtering out things like multi-value separators and values that are actually ISBNs so I can fix them later
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- Then I applied 181 fixes for ISSNs using `fix-metadata-values.py` on DSpace Test and CGSpace (after testing locally):
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``
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$ ./fix-metadata-values.py -i /tmp/2020-01-29-ISSNs-Distinct.csv -db dspace -u dspace -p 'fuuu' -f 'dc.identifier.issn[en_US]' -m 21 -t correct -d
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```
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<!-- vim: set sw=2 ts=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
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$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
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78
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -33,7 +33,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
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-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
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-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -25,7 +25,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_
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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.
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Update GitHub wiki for documentation of maintenance tasks.
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -35,7 +35,7 @@ I noticed we have a very interesting list of countries on CGSpace:
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Not only are there 49,000 countries, we have some blanks (25)…
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Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -25,7 +25,7 @@ Looking at issues with author authorities on CGSpace
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For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
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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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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -29,7 +29,7 @@ After running DSpace for over five years I’ve never needed to look in any
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This will save us a few gigs of backup space we’re paying for on S3
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Also, I noticed the checker log has some errors we should pay attention to:
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -31,7 +31,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
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# awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l
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3168
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -31,7 +31,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec
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You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
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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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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -41,7 +41,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
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In this case the select query was showing 95 results before the update
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -39,7 +39,7 @@ $ git checkout -b 55new 5_x-prod
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$ git reset --hard ilri/5_x-prod
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$ git rebase -i dspace-5.5
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -31,7 +31,7 @@ It looks like we might be able to use OUs now, instead of DCs:
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$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -39,7 +39,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id
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0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -23,7 +23,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module
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Add dc.type to the output options for Atmire’s Listings and Reports module (#286)
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -43,7 +43,7 @@ I see thousands of them in the logs for the last few months, so it’s not r
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I’ve raised a ticket with Atmire to ask
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Another worrying error from dspace.log is:
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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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
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I tested on DSpace Test as well and it doesn’t work there either
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I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -47,7 +47,7 @@ DELETE 1
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Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301)
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Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -51,7 +51,7 @@ Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing reg
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$ identify ~/Desktop/alc_contrastes_desafios.jpg
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/Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -37,7 +37,7 @@ Testing the CMYK patch on a collection with 650 items:
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$ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt
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"/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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@ -15,7 +15,7 @@
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="May, 2017"/>
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<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’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’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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<meta name="generator" content="Hugo 0.63.2" />
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@ -15,7 +15,7 @@
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="June, 2017"/>
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<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’ll create a new sub-community for Phase II and create collections for the research themes there The current “Research Themes” community will be renamed to “WLE Phase I Research Themes” 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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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace
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We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML:
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
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Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -29,7 +29,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two
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Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account is both in the approvers step as well as the group
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -31,7 +31,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
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There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine
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Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
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COPY 54701
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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PostgreSQL activity says there are 115 connections currently
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The list of connections to XMLUI and REST API for today:
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -147,7 +147,7 @@ dspace.log.2018-01-02:34
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Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let’s Encrypt if it’s just a handful of domains
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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Yesterday I figured out how to monitor DSpace sessions using JMX
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I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -21,7 +21,7 @@ Export a CSV of the IITA community metadata for Martin Mueller
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Export a CSV of the IITA community metadata for Martin Mueller
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -23,7 +23,7 @@ Catalina logs at least show some memory errors yesterday:
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I tried to test something on DSpace Test but noticed that it’s down since god knows when
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Catalina logs at least show some memory errors yesterday:
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -35,7 +35,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
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Then I reduced the JVM heap size from 6144 back to 5120m
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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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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -55,7 +55,7 @@ real 74m42.646s
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user 8m5.056s
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sys 2m7.289s
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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There is insufficient memory for the Java Runtime Environment to continue.
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes
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I ran all system updates on DSpace Test and rebooted it
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"/>
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<meta name="generator" content="Hugo 0.63.2" />
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Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month
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I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again:
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -23,7 +23,7 @@ I created a GitHub issue to track this #389, because I’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’m super busy in Nairobi right now
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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:
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -47,7 +47,7 @@ I don’t see anything interesting in the web server logs around that time t
|
||||
357 207.46.13.1
|
||||
903 54.70.40.11
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -69,7 +69,7 @@ real 0m19.873s
|
||||
user 0m22.203s
|
||||
sys 0m1.979s
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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 'fuuu' -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 'fuuu' -m 231 -f cg.coverage.region -d
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -45,7 +45,7 @@ DELETE 1
|
||||
|
||||
But after this I tried to delete the item from the XMLUI and it is still present…
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -31,7 +31,7 @@ Run system updates on CGSpace (linode18) and reboot it
|
||||
|
||||
Skype with Marie-Angélique and Abenet about CG Core v2
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -43,7 +43,7 @@ After rebooting, all statistics cores were loaded… wow, that’s luck
|
||||
|
||||
Run system updates on DSpace Test (linode19) and reboot it
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -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+00A0) there that would otherwise be removed by the csv-metadata-quality script’s “unneccesary Unicode” fix: $ csvcut -c 'id,dc."/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -55,7 +55,7 @@ Let’s see how many of the REST API requests were for bitstreams (because t
|
||||
# zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams"
|
||||
106781
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -43,7 +43,7 @@ Make sure all packages are up to date and the package manager is up to date, the
|
||||
# dpkg -C
|
||||
# reboot
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -29,7 +29,7 @@ I tweeted the CGSpace repository link
|
||||
<meta property="og:type" content="article" />
|
||||
<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:modified_time" content="2020-01-27T16:20:44+02:00" />
|
||||
<meta property="article:modified_time" content="2020-01-28T17:37:27+02:00" />
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="January, 2020"/>
|
||||
@ -53,7 +53,7 @@ I tweeted the CGSpace repository link
|
||||
|
||||
|
||||
"/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
@ -63,9 +63,9 @@ I tweeted the CGSpace repository link
|
||||
"@type": "BlogPosting",
|
||||
"headline": "January, 2020",
|
||||
"url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-01\/",
|
||||
"wordCount": "2910",
|
||||
"wordCount": "3328",
|
||||
"datePublished": "2020-01-06T10:48:30+02:00",
|
||||
"dateModified": "2020-01-27T16:20:44+02:00",
|
||||
"dateModified": "2020-01-28T17:37:27+02:00",
|
||||
"author": {
|
||||
"@type": "Person",
|
||||
"name": "Alan Orth"
|
||||
@ -476,7 +476,41 @@ COPY 77
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<!-- raw HTML omitted -->
|
||||
<h2 id="2020-01-29">2020-01-29</h2>
|
||||
<ul>
|
||||
<li>Normalize about 4,500 DOI, YouTube, and SlideShare links on CGSpace that are missing HTTPS or using old format:</li>
|
||||
</ul>
|
||||
<pre><code>UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://www.doi.org%';
|
||||
UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://doi.org%';
|
||||
UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://dx.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'http://dx.doi.org%';
|
||||
UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'https://dx.doi.org', 'https://doi.org') WHERE resource_type_id = 2 AND metadata_field_id = 220 AND text_value LIKE 'https://dx.doi.org%';
|
||||
UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.youtube.com', 'https://www.youtube.com') WHERE resource_type_id = 2 AND metadata_field_id = 219 AND text_value LIKE 'http://www.youtube.com%';
|
||||
UPDATE metadatavalue SET text_value = regexp_replace(text_value, 'http://www.slideshare.net', 'https://www.slideshare.net') WHERE resource_type_id = 2 AND metadata_field_id = 219 AND text_value LIKE 'http://www.slideshare.net%';
|
||||
</code></pre><ul>
|
||||
<li>I exported a list of all of our ISSNs with item IDs so that I could fix them in OpenRefine and submit them with multi-value separators to DSpace metadata import:</li>
|
||||
</ul>
|
||||
<pre><code>dspace=# \COPY (SELECT resource_id as "id", text_value as "dc.identifier.issn" FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 21) to /tmp/2020-01-29-issn.csv WITH CSV HEADER;
|
||||
COPY 23339
|
||||
</code></pre><ul>
|
||||
<li>Then, after spending two hours correcting 1,000 ISSNs I realized that I need to normalize the <code>text_lang</code> fields in the database first or else these will all look like changes due to the “en_US” and NULL, etc (for both ISSN and ISBN):</li>
|
||||
</ul>
|
||||
<pre><code>dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id = 2 AND metadata_field_id IN (20,21);
|
||||
UPDATE 30454
|
||||
</code></pre><ul>
|
||||
<li>Then I realized that my initial PostgreSQL query wasn’t so genius because if a field already has multiple values it will appear on separate lines with the same ID, so when <code>dspace metadata-import</code> sees it, the change will be removed and added, or added and removed, depending on the order it is seen!</li>
|
||||
<li>A better course of action is to select the distinct ones and then correct them using <code>fix-metadata-values.py</code>…</li>
|
||||
</ul>
|
||||
<pre><code>dspace=# \COPY (SELECT DISTINCT text_value as "dc.identifier.issn[en_US]", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 21 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-01-29-issn-distinct.csv WITH CSV HEADER;
|
||||
COPY 2900
|
||||
</code></pre><ul>
|
||||
<li>I re-applied all my corrections, filtering out things like multi-value separators and values that are actually ISBNs so I can fix them later</li>
|
||||
<li>Then I applied 181 fixes for ISSNs using <code>fix-metadata-values.py</code> on DSpace Test and CGSpace (after testing locally):</li>
|
||||
</ul>
|
||||
<p>``
|
||||
$ ./fix-metadata-values.py -i /tmp/2020-01-29-ISSNs-Distinct.csv -db dspace -u dspace -p ‘fuuu’ -f ‘dc.identifier.issn[en_US]’ -m 21 -t correct -d</p>
|
||||
<pre><code>
|
||||
<!-- vim: set sw=2 ts=2: -->
|
||||
</code></pre>
|
||||
|
||||
|
||||
|
||||
|
148
docs/404.html
Normal file
148
docs/404.html
Normal file
@ -0,0 +1,148 @@
|
||||
<!DOCTYPE html>
|
||||
<html lang="en" >
|
||||
|
||||
<head>
|
||||
<meta charset="utf-8">
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
|
||||
|
||||
<meta property="og:title" content="404 Page not found" />
|
||||
<meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
|
||||
<meta property="og:type" content="website" />
|
||||
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/404.html" />
|
||||
|
||||
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="404 Page not found"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<link rel="canonical" href="https://alanorth.github.io/cgspace-notes/404.html">
|
||||
|
||||
<title>CGSpace Notes</title>
|
||||
|
||||
|
||||
<!-- combined, minified CSS -->
|
||||
|
||||
<link href="https://alanorth.github.io/cgspace-notes/css/style.6da5c906cc7a8fbb93f31cd2316c5dbe3f19ac4aa6bfb066f1243045b8f6061e.css" rel="stylesheet" integrity="sha256-baXJBsx6j7uT8xzSMWxdvj8ZrEqmv7Bm8SQwRbj2Bh4=" crossorigin="anonymous">
|
||||
|
||||
|
||||
<!-- minified Font Awesome for SVG icons -->
|
||||
|
||||
<script defer src="https://alanorth.github.io/cgspace-notes/js/fontawesome.min.90e14c13cee52929ac33e1c21694a3cc95063a194eb22aad9f7976434e1a9125.js" integrity="sha256-kOFME87lKSmsM+HCFpSjzJUGOhlOsiqtn3l2Q04akSU=" crossorigin="anonymous"></script>
|
||||
|
||||
<!-- RSS 2.0 feed -->
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="blog-masthead">
|
||||
<div class="container">
|
||||
<nav class="nav blog-nav">
|
||||
<a class="nav-link " href="https://alanorth.github.io/cgspace-notes/">Home</a>
|
||||
</nav>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
|
||||
<header class="blog-header">
|
||||
<div class="container">
|
||||
<h1 class="blog-title" dir="auto"><a href="https://alanorth.github.io/cgspace-notes/" rel="home">CGSpace Notes</a></h1>
|
||||
<p class="lead blog-description" dir="auto">Documenting day-to-day work on the <a href="https://cgspace.cgiar.org">CGSpace</a> repository.</p>
|
||||
</div>
|
||||
</header>
|
||||
|
||||
|
||||
|
||||
|
||||
<div class="container">
|
||||
<div class="row">
|
||||
<div class="col-sm-8 blog-main">
|
||||
|
||||
|
||||
|
||||
<article class="blog-post">
|
||||
<header>
|
||||
<h2 class="blog-post-title">Page Not Found</h2>
|
||||
</header>
|
||||
<p>Page not found. Go back <a href="/cgspace-notes/">home</a>.</p>
|
||||
</article>
|
||||
|
||||
|
||||
|
||||
</div> <!-- /.blog-main -->
|
||||
|
||||
<aside class="col-sm-3 ml-auto blog-sidebar">
|
||||
|
||||
|
||||
|
||||
<section class="sidebar-module">
|
||||
<h4>Recent Posts</h4>
|
||||
<ol class="list-unstyled">
|
||||
|
||||
|
||||
<li><a href="/cgspace-notes/2020-01/">January, 2020</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2019-12/">December, 2019</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2019-11/">November, 2019</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/cgspace-cgcorev2-migration/">CGSpace CG Core v2 Migration</a></li>
|
||||
|
||||
<li><a href="/cgspace-notes/2019-10/">October, 2019</a></li>
|
||||
|
||||
</ol>
|
||||
</section>
|
||||
|
||||
|
||||
|
||||
|
||||
<section class="sidebar-module">
|
||||
<h4>Links</h4>
|
||||
<ol class="list-unstyled">
|
||||
|
||||
<li><a href="https://cgspace.cgiar.org">CGSpace</a></li>
|
||||
|
||||
<li><a href="https://dspacetest.cgiar.org">DSpace Test</a></li>
|
||||
|
||||
<li><a href="https://github.com/ilri/DSpace">CGSpace @ GitHub</a></li>
|
||||
|
||||
</ol>
|
||||
</section>
|
||||
|
||||
</aside>
|
||||
|
||||
|
||||
</div> <!-- /.row -->
|
||||
</div> <!-- /.container -->
|
||||
|
||||
|
||||
|
||||
<footer class="blog-footer">
|
||||
<p dir="auto">
|
||||
|
||||
Blog template created by <a href="https://twitter.com/mdo">@mdo</a>, ported to Hugo by <a href='https://twitter.com/mralanorth'>@mralanorth</a>.
|
||||
|
||||
</p>
|
||||
<p>
|
||||
<a href="#">Back to top</a>
|
||||
</p>
|
||||
</footer>
|
||||
|
||||
|
||||
</body>
|
||||
|
||||
</html>
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Categories"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Notes"/>
|
||||
<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
|
||||
<meta name="generator" content="Hugo 0.63.1" />
|
||||
<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Categories"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="Categories"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="Categories"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="Categories"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="Categories"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -15,7 +15,7 @@
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<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGIAR Library Migration"/>
|
||||
<meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
|
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<meta name="generator" content="Hugo 0.63.2" />
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@ -15,7 +15,7 @@
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<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGSpace CG Core v2 Migration"/>
|
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<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="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -14,7 +14,7 @@
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -14,7 +14,7 @@
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<meta name="twitter:card" content="summary"/>
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<meta name="twitter:title" content="CGSpace Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
|
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|
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||||
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@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
|
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|
||||
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|
||||
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@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
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@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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|
||||
|
||||
|
||||
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@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Posts"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Posts"/>
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|
||||
|
||||
|
||||
|
@ -4,27 +4,27 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/</loc>
|
||||
<lastmod>2020-01-27T16:20:44+02:00</lastmod>
|
||||
<lastmod>2020-01-28T17:37:27+02:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2020-01-27T16:20:44+02:00</lastmod>
|
||||
<lastmod>2020-01-28T17:37:27+02:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/2020-01/</loc>
|
||||
<lastmod>2020-01-27T16:20:44+02:00</lastmod>
|
||||
<lastmod>2020-01-28T17:37:27+02:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2020-01-27T16:20:44+02:00</lastmod>
|
||||
<lastmod>2020-01-28T17:37:27+02:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/posts/</loc>
|
||||
<lastmod>2020-01-27T16:20:44+02:00</lastmod>
|
||||
<lastmod>2020-01-28T17:37:27+02:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Tags"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
|
||||
|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
||||
<meta name="twitter:title" content="Migration"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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|
||||
|
||||
|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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|
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|
||||
|
@ -14,7 +14,7 @@
|
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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|
||||
|
||||
|
@ -14,7 +14,7 @@
|
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Notes"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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|
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|
||||
|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Tags"/>
|
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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|
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|
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|
@ -14,7 +14,7 @@
|
||||
<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Tags"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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|
@ -14,7 +14,7 @@
|
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Tags"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.2" />
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|
@ -14,7 +14,7 @@
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Tags"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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|
@ -14,7 +14,7 @@
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<meta name="twitter:card" content="summary"/>
|
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<meta name="twitter:title" content="Tags"/>
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<meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
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<meta name="generator" content="Hugo 0.63.1" />
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<meta name="generator" content="Hugo 0.63.2" />
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||||
|
||||
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user