From ba0fe49fd6cb85413d835746637571696f418708 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Mon, 28 Oct 2019 13:51:00 +0200 Subject: [PATCH] Regenerate public --- docs/2019-10/index.html | 23 +- docs/categories/notes/page/2/index.html | 462 ++++++++++++++++ docs/categories/notes/page/3/index.html | 404 ++++++++++++++ docs/cgspace-cgcorev2-migration/index.html | 580 +++++++++++++++++++++ docs/sitemap.xml | 16 +- docs/tags/migration/index.html | 185 +++++++ docs/tags/migration/index.xml | 35 ++ docs/tags/migration/page/1/index.html | 1 + 8 files changed, 1695 insertions(+), 11 deletions(-) create mode 100644 docs/categories/notes/page/2/index.html create mode 100644 docs/categories/notes/page/3/index.html create mode 100644 docs/cgspace-cgcorev2-migration/index.html create mode 100644 docs/tags/migration/index.html create mode 100644 docs/tags/migration/index.xml create mode 100644 docs/tags/migration/page/1/index.html diff --git a/docs/2019-10/index.html b/docs/2019-10/index.html index 1309ea574..151067452 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -11,7 +11,7 @@ - + @@ -27,9 +27,9 @@ "@type": "BlogPosting", "headline": "October, 2019", "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2019-10\/", - "wordCount": "1535", + "wordCount": "1593", "datePublished": "2019-10-01T13:20:51+03:00", - "dateModified": "2019-10-28T13:41:08+02:00", + "dateModified": "2019-10-28T13:50:17+02:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -384,6 +384,23 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
  • Create a test user for Mohammad Salem to test depositing from MEL to DSpace Test, as the last one I had created in 2019-08 was cleared when we re-syncronized DSpace Test with CGSpace recently.
  • +

    2019-10-25

    + + + +

    2019-10-28

    + + + diff --git a/docs/categories/notes/page/2/index.html b/docs/categories/notes/page/2/index.html new file mode 100644 index 000000000..43f68ba62 --- /dev/null +++ b/docs/categories/notes/page/2/index.html @@ -0,0 +1,462 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + CGSpace Notes + + + + + + + + + + + + + + + + + + + +
    +
    + +
    +
    + + + + +
    +
    +

    CGSpace Notes

    +

    Documenting day-to-day work on the CGSpace repository.

    +
    +
    + + + + +
    +
    +
    + + + + + + + + +
    +
    +

    January, 2019

    + +
    +

    2019-01-02

    + +
      +
    • Linode alerted that CGSpace (linode18) had a higher outbound traffic rate than normal early this morning
    • + +
    • I don’t see anything interesting in the web server logs around that time though:

      + +
      # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "02/Jan/2019:0(1|2|3)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
      + 92 40.77.167.4
      + 99 210.7.29.100
      +120 38.126.157.45
      +177 35.237.175.180
      +177 40.77.167.32
      +216 66.249.75.219
      +225 18.203.76.93
      +261 46.101.86.248
      +357 207.46.13.1
      +903 54.70.40.11
      +
    • +
    + Read more → +
    + + + + + + +
    +
    +

    December, 2018

    + +
    +

    2018-12-01

    + +
      +
    • Switch CGSpace (linode18) to use OpenJDK instead of Oracle JDK
    • +
    • I manually installed OpenJDK, then removed Oracle JDK, then re-ran the Ansible playbook to update all configuration files, etc
    • +
    • Then I ran all system updates and restarted the server
    • +
    + +

    2018-12-02

    + + + Read more → +
    + + + + + + +
    +
    +

    November, 2018

    + +
    +

    2018-11-01

    + +
      +
    • Finalize AReS Phase I and Phase II ToRs
    • +
    • Send a note about my dspace-statistics-api to the dspace-tech mailing list
    • +
    + +

    2018-11-03

    + +
      +
    • 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:
    • +
    + Read more → +
    + + + + + + +
    +
    +

    October, 2018

    + +
    +

    2018-10-01

    + +
      +
    • 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
    • +
    + Read more → +
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    +
    +

    September, 2018

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    +

    2018-09-02

    + +
      +
    • New PostgreSQL JDBC driver version 42.2.5
    • +
    • I’ll update the DSpace role in our Ansible infrastructure playbooks and run the updated playbooks on CGSpace and DSpace Test
    • +
    • 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
    • +
    • 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:
    • +
    + Read more → +
    + + + + + + +
    +
    +

    August, 2018

    + +
    +

    2018-08-01

    + +
      +
    • DSpace Test had crashed at some point yesterday morning and I see the following in dmesg:

      + +
      [Tue Jul 31 00:00:41 2018] Out of memory: Kill process 1394 (java) score 668 or sacrifice child
      +[Tue Jul 31 00:00:41 2018] Killed process 1394 (java) total-vm:15601860kB, anon-rss:5355528kB, file-rss:0kB, shmem-rss:0kB
      +[Tue Jul 31 00:00:41 2018] oom_reaper: reaped process 1394 (java), now anon-rss:0kB, file-rss:0kB, shmem-rss:0kB
      +
    • + +
    • Judging from the time of the crash it was probably related to the Discovery indexing that starts at midnight

    • + +
    • From the DSpace log I see that eventually Solr stopped responding, so I guess the java process that was OOM killed above was Tomcat’s

    • + +
    • I’m not sure why Tomcat didn’t crash with an OutOfMemoryError…

    • + +
    • Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did a few months ago when we tried to run the whole CGSpace Solr core

    • + +
    • 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

    • + +
    • I ran all system updates on DSpace Test and rebooted it

    • +
    + Read more → +
    + + + + + + +
    +
    +

    July, 2018

    + +
    +

    2018-07-01

    + +
      +
    • I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case:

      + +
      $ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace
      +
    • + +
    • During the mvn package stage on the 5.8 branch I kept getting issues with java running out of memory:

      + +
      There is insufficient memory for the Java Runtime Environment to continue.
      +
    • +
    + Read more → +
    + + + + + + +
    +
    +

    June, 2018

    + +
    +

    2018-06-04

    + +
      +
    • Test the DSpace 5.8 module upgrades from Atmire (#378) + +
        +
      • There seems to be a problem with the CUA and L&R versions in pom.xml because they are using SNAPSHOT and it doesn’t build
      • +
    • +
    • I added the new CCAFS Phase II Project Tag PII-FP1_PACCA2 and merged it into the 5_x-prod branch (#379)
    • + +
    • I proofed and tested the ILRI author corrections that Peter sent back to me this week:

      + +
      $ ./fix-metadata-values.py -i /tmp/2018-05-30-Correct-660-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 -n
      +
    • + +
    • I think a sane proofing workflow in OpenRefine is to apply the custom text facets for check/delete/remove and illegal characters that I developed in March, 2018

    • + +
    • Time to index ~70,000 items on CGSpace:

      + +
      $ time schedtool -D -e ionice -c2 -n7 nice -n19 [dspace]/bin/dspace index-discovery -b                                  
      +
      +real    74m42.646s
      +user    8m5.056s
      +sys     2m7.289s
      +
    • +
    + Read more → +
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    +
    +

    May, 2018

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    +

    2018-05-01

    + + + Read more → +
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    +
    +

    April, 2018

    + +
    +

    2018-04-01

    + +
      +
    • I tried to test something on DSpace Test but noticed that it’s down since god knows when
    • +
    • Catalina logs at least show some memory errors yesterday:
    • +
    + Read more → +
    + + + + + + + + + + + +
    + + + + +
    +
    + + + + + + + + + diff --git a/docs/categories/notes/page/3/index.html b/docs/categories/notes/page/3/index.html new file mode 100644 index 000000000..8ea98c45e --- /dev/null +++ b/docs/categories/notes/page/3/index.html @@ -0,0 +1,404 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + CGSpace Notes + + + + + + + + + + + + + + + + + + + +
    +
    + +
    +
    + + + + +
    +
    +

    CGSpace Notes

    +

    Documenting day-to-day work on the CGSpace repository.

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    +
    + + + + + + + + +
    +
    +

    March, 2018

    + +
    +

    2018-03-02

    + +
      +
    • Export a CSV of the IITA community metadata for Martin Mueller
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    + Read more → +
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    +
    +

    February, 2018

    + +
    +

    2018-02-01

    + +
      +
    • Peter gave feedback on the dc.rights proof of concept that I had sent him last week
    • +
    • We don’t need to distinguish between internal and external works, so that makes it just a simple list
    • +
    • Yesterday I figured out how to monitor DSpace sessions using JMX
    • +
    • 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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    + Read more → +
    + + + + + + +
    +
    +

    January, 2018

    + +
    +

    2018-01-02

    + +
      +
    • Uptime Robot noticed that CGSpace went down and up a few times last night, for a few minutes each time
    • +
    • I didn’t get any load alerts from Linode and the REST and XMLUI logs don’t show anything out of the ordinary
    • +
    • The nginx logs show HTTP 200s until 02/Jan/2018:11:27:17 +0000 when Uptime Robot got an HTTP 500
    • +
    • In dspace.log around that time I see many errors like “Client closed the connection before file download was complete”
    • + +
    • And just before that I see this:

      + +
      Caused by: org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-980] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:50; busy:50; idle:0; lastwait:5000].
      +
    • + +
    • Ah hah! So the pool was actually empty!

    • + +
    • I need to increase that, let’s try to bump it up from 50 to 75

    • + +
    • After that one client got an HTTP 499 but then the rest were HTTP 200, so I don’t know what the hell Uptime Robot saw

    • + +
    • I notice this error quite a few times in dspace.log:

      + +
      2018-01-02 01:21:19,137 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
      +org.dspace.discovery.SearchServiceException: org.apache.solr.search.SyntaxError: Cannot parse 'dateIssued_keyword:[1976+TO+1979]': Encountered " "]" "] "" at line 1, column 32.
      +
    • + +
    • And there are many of these errors every day for the past month:

      + +
      $ grep -c "Error while searching for sidebar facets" dspace.log.*
      +dspace.log.2017-11-21:4
      +dspace.log.2017-11-22:1
      +dspace.log.2017-11-23:4
      +dspace.log.2017-11-24:11
      +dspace.log.2017-11-25:0
      +dspace.log.2017-11-26:1
      +dspace.log.2017-11-27:7
      +dspace.log.2017-11-28:21
      +dspace.log.2017-11-29:31
      +dspace.log.2017-11-30:15
      +dspace.log.2017-12-01:15
      +dspace.log.2017-12-02:20
      +dspace.log.2017-12-03:38
      +dspace.log.2017-12-04:65
      +dspace.log.2017-12-05:43
      +dspace.log.2017-12-06:72
      +dspace.log.2017-12-07:27
      +dspace.log.2017-12-08:15
      +dspace.log.2017-12-09:29
      +dspace.log.2017-12-10:35
      +dspace.log.2017-12-11:20
      +dspace.log.2017-12-12:44
      +dspace.log.2017-12-13:36
      +dspace.log.2017-12-14:59
      +dspace.log.2017-12-15:104
      +dspace.log.2017-12-16:53
      +dspace.log.2017-12-17:66
      +dspace.log.2017-12-18:83
      +dspace.log.2017-12-19:101
      +dspace.log.2017-12-20:74
      +dspace.log.2017-12-21:55
      +dspace.log.2017-12-22:66
      +dspace.log.2017-12-23:50
      +dspace.log.2017-12-24:85
      +dspace.log.2017-12-25:62
      +dspace.log.2017-12-26:49
      +dspace.log.2017-12-27:30
      +dspace.log.2017-12-28:54
      +dspace.log.2017-12-29:68
      +dspace.log.2017-12-30:89
      +dspace.log.2017-12-31:53
      +dspace.log.2018-01-01:45
      +dspace.log.2018-01-02:34
      +
    • + +
    • 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

    • +
    + Read more → +
    + + + + + + +
    +
    +

    December, 2017

    + +
    +

    2017-12-01

    + +
      +
    • Uptime Robot noticed that CGSpace went down
    • +
    • The logs say “Timeout waiting for idle object”
    • +
    • PostgreSQL activity says there are 115 connections currently
    • +
    • The list of connections to XMLUI and REST API for today:
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    + Read more → +
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    +
    +

    November, 2017

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    +

    2017-11-01

    + +
      +
    • The CORE developers responded to say they are looking into their bot not respecting our robots.txt
    • +
    + +

    2017-11-02

    + +
      +
    • Today there have been no hits by CORE and no alerts from Linode (coincidence?)

      + +
      # grep -c "CORE" /var/log/nginx/access.log
      +0
      +
    • + +
    • 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 = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv;
      +COPY 54701
      +
    • +
    + Read more → +
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    +
    +

    October, 2017

    + +
    +

    2017-10-01

    + +
      +
    • Peter emailed to point out that many items in the ILRI archive collection have multiple handles:

      + +
      http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336
      +
    • + +
    • 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

    • + +
    • Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections

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    + Read more → +
    + + + + + + +
    +
    +

    CGIAR Library Migration

    + +
    +

    Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.

    + Read more → +
    + + + + + + + + + + + +
    + + + + +
    +
    + + + + + + + + + diff --git a/docs/cgspace-cgcorev2-migration/index.html b/docs/cgspace-cgcorev2-migration/index.html new file mode 100644 index 000000000..68fd7e3ef --- /dev/null +++ b/docs/cgspace-cgcorev2-migration/index.html @@ -0,0 +1,580 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + CGSpace CG Core v2 Migration | CGSpace Notes + + + + + + + + + + + + + + + + + + +
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    + + + + +
    +
    +

    CGSpace Notes

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    Documenting day-to-day work on the CGSpace repository.

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    + + + + +
    +
    +

    CGSpace CG Core v2 Migration

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    +

    Possible changes to CGSpace metadata fields to align more with DC, QDC, and DCTERMS as well as CG Core v2.

    + +

    With reference to CG Core v2 draft standard by Marie-Angélique as well as DCMI DCTERMS.

    + + + +

    Proposed Changes

    + +

    As of 2019-09-11 the scope of the changes includes the following fields:

    + +
      +
    • dc.contributor.author→dcterms.creator + +
        +
      • for people and institutional authors
      • +
    • +
    • cg.creator.id→cg.creator.identifier + +
        +
      • ORCID identifiers
      • +
    • +
    • dc.title→dcterms.title
    • +
    • dc.format.extent→dcterms.extent
    • +
    • dc.date.issued→dcterms.issued
    • +
    • dc.description.abstract→dcterms.abstract
    • +
    • dc.description→dcterms.description
    • +
    • dc.description.sponsorship→cg.contributor.donor + +
        +
      • values from CrossRef or Grid.ac if possible
      • +
    • +
    • dc.description.version→cg.peer-reviewed
    • +
    • cg.fulltextstatus→cg.howpublished + +
        +
      • CGSpace uses values like “Formally Published” or “Grey Literature”
      • +
    • +
    • dc.identifier.citation→dcterms.bibliographicCitation
    • +
    • cg.identifier.status→dcterms.accessRights + +
        +
      • current values are “Open Access” and “Limited Access”
      • +
      • future values are possibly “Open” and “Restricted”?
      • +
    • +
    • dc.language.iso→dcterms.language + +
        +
      • current values are ISO 639-1 (aka Alpha 2)
      • +
      • future values are possibly ISO 639-3 (aka Alpha 3)?
      • +
    • +
    • cg.link.reference→dcterms.relation
    • +
    • dc.publisher→dcterms.publisher
    • +
    • dc.relation.ispartofseries→dcterms.isPartOf
    • +
    • dc.rights→dcterms.license + +
    • +
    • dc.source→cg.journal
    • +
    • dc.subject→dcterms.subject
    • +
    • dc.type→dcterms.type
    • +
    • dc.identifier.isbn→cg.isbn
    • +
    • dc.identifier.issn→cg.issn
    • +
    • cg.identifier.dataurl→cg.hasMetadata
    • +
    • dc.title.alternative→dcterms.alternative
    • +
    + +

    The following fields are currently out of the scope of this migration because they are used internally by DSpace 5.x/6.x and would be difficult to change without significant modifications to the core of the code:

    + +
      +
    • dc.date.available
    • +
    • dc.date.accessioned
    • +
    • dc.identifier.uri
    • +
    • dc.description.provenance
    • +
    + +

    Fields to Create

    + +

    Make sure the following fields exist:

    + +
      +
    • +
    • +
    • +
    • +
    • +
    • +
    • +
    • +
    + +

    Fields to delete

    + +

    Fields to delete after migration:

    + +
      +
    • +
    • +
    • +
    • +
    • +
    + +

    Implementation Progress

    + +

    Tally of the status of the implementation of the new fields in the CGSpace 5_x-cgcorev2 branch.

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    Field Namemigrate-fields.shInput FormsXMLUI Themes¹dspace.cfgDiscoveryAtmire ModulesCrosswalks
    dcterms.creator?
    cg.creator.identifier-
    dcterms.title
    dcterms.extent----
    dcterms.issued?
    dcterms.abstract-
    dcterms.description
    cg.contributor.donor
    cg.peer-reviewed--
    cg.howpublished----
    dcterms.bibliographicCitation--
    dcterms.accessRights-
    dcterms.language-
    dcterms.relation---
    dcterms.publisher--
    dcterms.isPartOf-
    dcterms.license
    cg.journal--
    dcterms.subject
    dcterms.type
    cg.isbn---
    cg.issn---
    cg.hasMetadata-
    dcterms.alternative-
    + +

    There are a few things that I need to check once I get a deployment of this code up and running:

    + +
      +
    • Assess the XSL changes to see if things like not(@qualifier)] still make sense after we move fields from DC to DCTERMS, as some fields will no longer have qualifiers
    • +
    • Do I need to edit crosswalks that we are not using, like MODS?
    • +
    • There is potentially a lot of work in the OAI metadata formats like DIM, METS, and QDC (see dspace/config/crosswalks/oai/*.xsl)
    • +
    + +
    + +

    ¹ Not committed yet because I don’t want to have to make minor adjustments in multiple commits. Re-apply the gauntlet of fixes with the sed script:

    + +
    $ find dspace/modules/xmlui-mirage2/src/main/webapp/themes -iname "*.xsl" -exec ./cgcore-xsl-replacements.sed {} \;
    +
    + + + + + +
    + + + +
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    CGSpace Notes

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    Documenting day-to-day work on the CGSpace repository.

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    CGIAR Library Migration

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    Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.

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    + + + + + + + + + diff --git a/docs/tags/migration/index.xml b/docs/tags/migration/index.xml new file mode 100644 index 000000000..c3eedaddf --- /dev/null +++ b/docs/tags/migration/index.xml @@ -0,0 +1,35 @@ + + + + Migration on CGSpace Notes + https://alanorth.github.io/cgspace-notes/tags/migration/ + Recent content in Migration on CGSpace Notes + Hugo -- gohugo.io + en-us + Mon, 28 Oct 2019 13:27:35 +0200 + + + + + + CGSpace CG Core v2 Migration + https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ + Mon, 28 Oct 2019 13:27:35 +0200 + + https://alanorth.github.io/cgspace-notes/cgspace-cgcorev2-migration/ + <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> + + + + CGIAR Library Migration + https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ + Mon, 18 Sep 2017 16:38:35 +0300 + + https://alanorth.github.io/cgspace-notes/cgiar-library-migration/ + <p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p> + + + + \ No newline at end of file diff --git a/docs/tags/migration/page/1/index.html b/docs/tags/migration/page/1/index.html new file mode 100644 index 000000000..1a7f2976c --- /dev/null +++ b/docs/tags/migration/page/1/index.html @@ -0,0 +1 @@ +https://alanorth.github.io/cgspace-notes/tags/migration/ \ No newline at end of file