From 6b4a2f7091d6ef66f633e8ef487c80dd9b788654 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Wed, 3 Aug 2016 10:09:36 +0300 Subject: [PATCH] Regenerate site --- public/2015-11/index.html | 34 ++--- public/2015-12/index.html | 36 ++--- public/2016-01/index.html | 44 +++--- public/2016-02/index.html | 52 +++---- public/2016-03/index.html | 60 ++++---- public/2016-04/index.html | 64 ++++----- public/2016-05/index.html | 52 +++---- public/2016-06/index.html | 58 ++++---- public/2016-07/index.html | 52 +++---- public/2016-08/index.html | 28 ++-- public/404.html | 22 +-- public/categories/index.html | 22 +-- public/index.html | 62 ++++---- public/index.xml | 268 +++++++++++++++++------------------ public/page/1/index.html | 2 +- public/sitemap.xml | 31 ++-- public/tags/index.html | 24 ++-- public/tags/notes/index.html | 62 ++++---- public/tags/notes/index.xml | 268 +++++++++++++++++------------------ 19 files changed, 620 insertions(+), 621 deletions(-) diff --git a/public/2015-11/index.html b/public/2015-11/index.html index 5f661fbd3..29cc06f61 100644 --- a/public/2015-11/index.html +++ b/public/2015-11/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ November, 2015 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2015-11-22

+

2015-11-22

  • CGSpace went down
    • @@ -95,7 +95,7 @@
  • For now I have increased the limit from 60 to 90, run updates, and rebooted the server
-

2015-11-24

+

2015-11-24

  • CGSpace went down again
    • @@ -111,7 +111,7 @@
  • For some reason the number of idle connections is very high since we upgraded to DSpace 5
-

2015-11-25

+

2015-11-25

  • Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config
    • @@ -171,7 +171,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr
  • Also deploy the nginx fixes for the try_files location block as well as the expires block
-

2015-11-26

+

2015-11-26

  • CGSpace behaving much better since changing db.maxidle yesterday, but still two up/down notices from monitoring this morning (better than 50!)
    • @@ -197,7 +197,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr
  • I reduced the pool back to the default of 30, and reduced the db.maxidle settings from 10 to 8
-

2015-11-29

+

2015-11-29

  • Still more alerts that CGSpace has been up and down all day
    • @@ -244,7 +244,7 @@ db.statementpool = true - +
@@ -269,7 +269,7 @@ db.statementpool = true - + diff --git a/public/2015-12/index.html b/public/2015-12/index.html index 3266379a2..a2520c8de 100644 --- a/public/2015-12/index.html +++ b/public/2015-12/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ December, 2015 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2015-12-02

+

2015-12-02

  • Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less space:
    • @@ -160,7 +160,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
  • I also filed a ticket on Atmire’s issue tracker for the PostgreSQL stuff
-

2015-12-03

+

2015-12-03

  • CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)
    • @@ -192,7 +192,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.854 -

    2015-12-05

    +

    2015-12-05

    • CGSpace has been up and down all day and REST API is completely unresponsive
      • @@ -213,7 +213,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle PostgreSQL locks (year) PostgreSQL scans (year)

      -

      2015-12-07

      +

      2015-12-07

      • Atmire sent some fixes to DSpace’s REST API code that was leaving contexts open (causing the slow performance and database issues)
        • @@ -232,7 +232,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.497 -

        2015-12-08

        +

        2015-12-08

        • Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn’t as good, but it’s much faster and causes less IO/CPU load
          • @@ -256,10 +256,10 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
@@ -284,7 +284,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle - + diff --git a/public/2016-01/index.html b/public/2016-01/index.html index fe923194d..d892e6703 100644 --- a/public/2016-01/index.html +++ b/public/2016-01/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ January, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-01-13

+

2016-01-13

  • Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_collections.sh script I wrote last year.
    • @@ -87,20 +87,20 @@
  • Update GitHub wiki for documentation of maintenance tasks.
-

2016-01-14

+

2016-01-14

  • Update CCAFS project identifiers in input-forms.xml
  • Run system updates and restart the server
-

2016-01-18

+

2016-01-18

  • Change “Extension material” to “Extension Material” in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)
-

2016-01-19

+

2016-01-19

  • Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme’s primary color (#157)
    • @@ -110,7 +110,7 @@
  • Altmetrics’ support for Handles is kinda weak, so they can’t associate our items with DOIs until they are tweeted or blogged, etc first.
-

2016-01-21

+

2016-01-21

  • Still waiting for my IFTTT recipe to fire, two days later
    • @@ -122,21 +122,21 @@
  • Work around a CSS issue with long URLs in the item view (#172)
-

2016-01-25

+

2016-01-25

  • Re-deploy CGSpace and DSpace Test with latest 5_x-prod branch
  • This included the social icon fixes/updates, date-based facet tweaks, reducing the feed cache age, and fixing a layout issue in XMLUI item view when an item had long URLs
-

2016-01-26

+

2016-01-26

  • Run nginx updates on CGSpace and DSpace Test (1.8.1 and 1.9.10, respectively)
  • Run updates on DSpace Test and reboot for new Linode kernel Linux 4.4.0-x86_64-linode63 (first update in months)
-

2016-01-28

+

2016-01-28

  • Start looking at importing some Bioversity data that had been prepared earlier this week
    • @@ -149,7 +149,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} \; | so 8

-

2016-01-29

+

2016-01-29

  • Add five missing center-specific subjects to XMLUI item view (#174)
    • @@ -181,10 +181,10 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} \; | so
@@ -209,7 +209,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} \; | so - + diff --git a/public/2016-02/index.html b/public/2016-02/index.html index 1136c7efa..621bc19eb 100644 --- a/public/2016-02/index.html +++ b/public/2016-02/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ February, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-02-05

+

2016-02-05

  • Looking at some DAGRIS data for Abenet Yabowork
    • @@ -94,7 +94,7 @@
  • Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”
-

2016-02-06

+

2016-02-06

  • Found a way to get items with null/empty metadata values from SQL
    • @@ -135,7 +135,7 @@ DELETE 25
  • Process the empty countries on CGSpace
-

2016-02-07

+

2016-02-07

  • Working on cleaning up Abenet’s DAGRIS data with OpenRefine
    • @@ -189,7 +189,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start 
    $ ~/dspace/bin/dspace index-discovery -b
    -

    2016-02-08

    +

    2016-02-08

    • Finish cleaning up and importing ~400 DAGRIS items into CGSpace
      • @@ -199,7 +199,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start

      ILRI submission buttons Drylands submission buttons

      -

      2016-02-09

      +

      2016-02-09

      • Re-sync DSpace Test with CGSpace
        • @@ -250,7 +250,7 @@ Swap: 255 57 198
      • So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)
      -

      2016-02-11

      +

      2016-02-11

      • Massaging some CIAT data in OpenRefine
        • @@ -274,7 +274,7 @@ Processing 64195.pdf > Creating thumbnail for 64195.pdf -

        2016-02-12

        +

        2016-02-12

        • Looking at CIAT’s records again, there are some problems with a dozen or so files (out of 1200)
          • @@ -285,7 +285,7 @@ Processing 64195.pdf
        • Also, I’m not sure if we import these items, will be remove the dc.identifier.url field from the records?
        -

        2016-02-12

        +

        2016-02-12

        • Looking at CIAT’s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I’m not sure if we can use those
          • @@ -310,7 +310,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_
        • They will be deployed on CGSpace the next time I re-deploy
        -

        2016-02-16

        +

        2016-02-16

        • Turns out OpenRefine has an unescape function!
          • @@ -329,7 +329,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_
        • This also works for records that have multiple URLs (separated by “||”)
        -

        2016-02-17

        +

        2016-02-17

        • Re-deploy CGSpace, run all system updates, and reboot
          • @@ -338,7 +338,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_
        • Need to re-process the filename column to replace multiple underscores with one: value.replace(/_{2,}/, "_")
        -

        2016-02-20

        +

        2016-02-20

        • Turns out the “bug” in SAFBuilder isn’t a bug, it’s a feature that allows you to encode extra information like the destintion bundle in the filename
          • @@ -353,7 +353,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_
        • Useful custom text facet for URLs ending with “.pdf”: value.endsWith(".pdf")
        -

        2016-02-22

        +

        2016-02-22

        • To change Spanish accents to ASCII in OpenRefine:
          • @@ -378,7 +378,7 @@ Bitstream: tést señora alimentación.pdf
        • Running the SAFBuilder on Mac OS X works if you’re going to import the resulting bundle on Mac OS X, but if your DSpace is running on Linux you need to run the SAFBuilder there where the filesystem’s encoding matches
        -

        2016-02-29

        +

        2016-02-29

        • Got notified by some CIFOR colleagues that the Google Scholar team had contacted them about CGSpace’s incorrect ordering of authors in Google Scholar metadata
          • @@ -420,10 +420,10 @@ Bitstream: tést señora alimentación.pdf
@@ -448,7 +448,7 @@ Bitstream: tést señora alimentación.pdf - + diff --git a/public/2016-03/index.html b/public/2016-03/index.html index 2f21a5f20..6972d5652 100644 --- a/public/2016-03/index.html +++ b/public/2016-03/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ March, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-03-02

+

2016-03-02

  • Looking at issues with author authorities on CGSpace
    • @@ -87,7 +87,7 @@
  • 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
-

2016-03-07

+

2016-03-07

  • Troubleshooting the issues with the slew of commits for Atmire modules in #182
    • @@ -100,14 +100,14 @@ 
    Exception in thread "Lucene Merge Thread #19" org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device
    -

    2016-03-08

    +

    2016-03-08

    • Add a few new filters to Atmire’s Listings and Reports module (#180)
    • We had also wanted to add a few to the Content and Usage module but I have to ask the editors which ones they were
    -

    2016-03-10

    +

    2016-03-10

    • Disable the lucene cron job on CGSpace as it shouldn’t be needed anymore
      • @@ -124,7 +124,7 @@
    • Update documentation for Atmire modules
    -

    2016-03-11

    +

    2016-03-11

    • As I was looking at the CUA config I realized our Discovery config is all messed up and confusing
      • @@ -134,7 +134,7 @@
    • There is still some more work to be done to remove references to old outputtype and output
    -

    2016-03-14

    +

    2016-03-14

    • Fix some items that had invalid dates (I noticed them in the log during a re-indexing)
      • @@ -145,13 +145,13 @@

      Missing XMLUI string

      -

      2016-03-15

      +

      2016-03-15

      • Create simple theme for new AVCD community just for a unique Google Tracking ID (#191)
      -

      2016-03-16

      +

      2016-03-16

      • Still having problems deploying Atmire’s CUA updates and fixes from January!
        • @@ -182,7 +182,7 @@
      • Also, dc.language.iso has some weird values, like “En” and “English”
      -

      2016-03-17

      +

      2016-03-17

      • It turns out hi is the ISO 639 language code for Hindi, but these should be in dc.language.iso instead of dc.language
        • @@ -192,7 +192,7 @@
      • The patches work fine with a clean database, so the error was caused by some mismatch in CUA versions and the database during my testing
      -

      2016-03-18

      +

      2016-03-18

      • Merge Atmire fixes into 5_x-prod
        • @@ -219,7 +219,7 @@
      • Also, it looks like adding -sharpen 0x1.0 really improves the quality of the image for only a few KB
      -

      2016-03-21

      +

      2016-03-21

      • Fix 66 site errors in Google’s webmaster tools
        • @@ -259,13 +259,13 @@
      • Deploy Let’s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks
      -

      2016-03-22

      +

      2016-03-22

      • Merge robots.txt patch and disallow indexing of browse pages as our sitemap is consumed correctly (#198)
      -

      2016-03-23

      +

      2016-03-23

      -

      2016-03-24

      +

      2016-03-24

      -

      2016-03-25

      +

      2016-03-25

      • Having problems with Listings and Reports, seems to be caused by a rogue reference to dc.type.output
        • @@ -294,7 +294,7 @@
      • Commenting out the line works, but I haven’t figured out the proper syntax for referring to dc.type.*
      -

      2016-03-28

      +

      2016-03-28

      -

      2016-03-29

      +

      2016-03-29

      • Skype meeting with Peter and Addis team to discuss metadata changes for Dublin Core, CGcore, and CGSpace-specific fields
        • @@ -334,10 +334,10 @@
@@ -362,7 +362,7 @@ - + diff --git a/public/2016-04/index.html b/public/2016-04/index.html index 21cc9ff38..066f9a623 100644 --- a/public/2016-04/index.html +++ b/public/2016-04/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ April, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-04-04

+

2016-04-04

  • Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit
    • @@ -120,7 +120,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290
  • Submit pull request for Tomcat 7 limits in Ansible dspace role (#30)
-

2016-04-05

+

2016-04-05

  • Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don’t need!
    • @@ -138,7 +138,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290
  • Try to do some metadata field migrations using the Atmire batch UI (dc.Species → cg.species) but it took several hours and even missed a few records
-

2016-04-06

+

2016-04-06

  • A better way to move metadata on this scale is via SQL, for example dc.type.output → dc.type (their IDs in the metadatafieldregistry are 66 and 109, respectively):
    • @@ -153,7 +153,7 @@ UPDATE 40852
  • Start working on metadata migrations, add 25 or so new metadata fields to CGSpace
-

2016-04-07

+

2016-04-07

  • Write shell script to do the migration of fields: https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b
    • @@ -169,14 +169,14 @@ UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76 UPDATE 51258 -

    2016-04-08

    +

    2016-04-08

    • Discuss metadata renaming with Abenet, we decided it’s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF
    • I’ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change
    -

    2016-04-10

    +

    2016-04-10

    • Looking at the DOI issue reported by Leroy from CIAT a few weeks ago
      • @@ -199,14 +199,14 @@ dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and t
    • I will manually edit the dc.identifier.doi in 10568⁄72509 and tweet the link, then check back in a week to see if the donut gets updated
    -

    2016-04-11

    +

    2016-04-11

    • The donut is already updated and shows the correct number now
    • CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we’d do it tentatively on Monday the 18th.
    -

    2016-04-12

    +

    2016-04-12

    • Looking at quality of WLE data (cg.subject.iwmi) in SQL:
      • @@ -243,7 +243,7 @@ DELETE 226
    • We want to do the dc.type.output move on CGSpace anyways, but we should wait as it might affect other external people!
    -

    2016-04-14

    +

    2016-04-14

    • Communicate with Macaroni Bros again about dc.type
      • @@ -251,13 +251,13 @@ DELETE 226
    • Notify CIAT people of metadata changes (I had forgotten them last week)
    -

    2016-04-15

    +

    2016-04-15

    • DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code
    -

    2016-04-18

    +

    2016-04-18

    • Talk to CIAT people about their portal again
      • @@ -336,7 +336,7 @@ javax.ws.rs.WebApplicationException
    • After restarting Tomcat a few more of these errors were logged but the application was up
    -

    2016-04-19

    +

    2016-04-19

    • Get handles for items that are using a given metadata field, ie dc.Species.animal (105):
      • @@ -392,7 +392,7 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
    • And then remove them from the metadata registry
    -

    2016-04-20

    +

    2016-04-20

    • Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server
      • @@ -431,20 +431,20 @@ UPDATE 46075
    • I’ve sent a message to Atmire asking about compatibility with DSpace 5.5
    -

    2016-04-21

    +

    2016-04-21

    • Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)
    • Atmire responded with DSpace 5.5 compatible versions for their modules, so I’ll start testing those in a few weeks
    -

    2016-04-22

    +

    2016-04-22

    -

    2016-04-26

    +

    2016-04-26

    • Test embargo during item upload
      • @@ -460,7 +460,7 @@ UPDATE 46075
-

2016-04-27

+

2016-04-27

  • I woke up to ten or fifteen “up” and “down” emails from the monitoring website
    • @@ -507,14 +507,14 @@ dspace.log.2016-04-27:7271
  • CGSpace down, restarted tomcat and it’s back up
-

2016-04-28

+

2016-04-28

  • Problems with stability again. I’ve blocked access to /rest for now to see if the number of errors in the log files drop
  • Later we could maybe start logging access to /rest and perhaps whitelist some IPs…
-

2016-04-30

+

2016-04-30

  • Logs for today and yesterday have zero references to this REST error, so I’m going to open back up the REST API but log all requests
    • @@ -547,10 +547,10 @@ dspace.log.2016-04-27:7271
@@ -575,7 +575,7 @@ dspace.log.2016-04-27:7271 - + diff --git a/public/2016-05/index.html b/public/2016-05/index.html index 029f6b7d2..8ae2b599b 100644 --- a/public/2016-05/index.html +++ b/public/2016-05/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ May, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-05-01

+

2016-05-01

  • Since yesterday there have been 10,000 REST errors and the site has been unstable again
    • @@ -104,7 +104,7 @@
  • The owner of that application has said that the NaN (not a number) is an error in his code and he’ll fix it
-

2016-05-03

+

2016-05-03

  • Update nginx to 1.10.x branch on CGSpace
    • @@ -113,7 +113,7 @@

    Item type in Discovery results

    -

    2016-05-06

    +

    2016-05-06

    • DSpace Test is down, catalina.out has lots of messages about heap space from some time yesterday (!)
      • @@ -151,7 +151,7 @@ fi
    • Seems to work well
    -

    2016-05-10

    +

    2016-05-10

    • Start looking at more metadata migrations
      • @@ -166,7 +166,7 @@ fi
    • CGSpace’s dc registry has 96 items, and the default DSpace one has 73.
    -

    2016-05-11

    +

    2016-05-11

    • Identify and propose the next phase of CGSpace fields to migrate:

      @@ -199,7 +199,7 @@ fi
    • Turns out she was able to decrease the size of the PDF so we didn’t have to do anything
    -

    2016-05-12

    +

    2016-05-12

    • Looks like the issue that Abenet was having a few days ago with “Connection Reset” in Firefox might be due to a Firefox 46 issue: https://bugzilla.mozilla.org/show_bug.cgi?id=1268775
      • @@ -223,7 +223,7 @@ fi 
      # select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "%  %";
      -

      2016-05-13

      +

      2016-05-13

      • More theorizing about CGcore
        • @@ -237,7 +237,7 @@ fi
      • I’ve removed dc.title.jtitle from the list for now because there’s no use moving it out of DC until we know where it will go (see discussion yesterday)
      -

      2016-05-18

      +

      2016-05-18

      • Work on 707 CCAFS records
        • @@ -254,7 +254,7 @@ fi
      • Before importing with SAFBuilder I tested adding “__bundle:THUMBNAIL” to the filename column and it works fine
      -

      2016-05-19

      +

      2016-05-19

      • More quality control on filename field of CCAFS records to make processing in shell and SAFBuilder more reliable:
        • @@ -278,7 +278,7 @@ fi 
        # select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
        -

        2016-05-20

        +

        2016-05-20

        • More work on CCAFS Video and Images records
          • @@ -303,7 +303,7 @@ fi
        • Work on configuration changes for Phase 2 metadata migrations
        -

        2016-05-23

        +

        2016-05-23

        • Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine
          • @@ -312,7 +312,7 @@ fi
        • I will have to try later
        -

        2016-05-30

        +

        2016-05-30

        • Export CCAFS video and image records from DSpace Test using the migrate option (-m):
          • @@ -348,7 +348,7 @@ $ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA 
          $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority
          -

          2016-05-31

          +

          2016-05-31

          • The index-authority script ran over night and was finished in the morning
            • @@ -393,10 +393,10 @@ sys 0m20.540s
@@ -421,7 +421,7 @@ sys 0m20.540s - + diff --git a/public/2016-06/index.html b/public/2016-06/index.html index 22bb6c75a..39bd320a5 100644 --- a/public/2016-06/index.html +++ b/public/2016-06/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ June, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-06-01

+

2016-06-01

  • Experimenting with IFPRI OAI (we want to harvest their publications)
    • @@ -100,7 +100,7 @@ UPDATE 14
  • Fix a few minor miscellaneous issues in dspace.cfg (#227)
-

2016-06-02

+

2016-06-02

  • Testing the configuration and theme changes for the upcoming metadata migration and I found some issues with cg.coverage.admin-unit
    • @@ -118,7 +118,7 @@ UPDATE 14
  • The patch applies successfully on DSpace 5.1 so I will try it later
-

2016-06-03

+

2016-06-03

  • Investigating the CCAFS authority issue, I exported the metadata for the Videos collection
    • @@ -191,7 +191,7 @@ UPDATE 960
  • That would only be for the “Browse by” function… so we’ll have to see what effect that has later
-

2016-06-04

+

2016-06-04

  • Re-sync DSpace Test with CGSpace and perform test of metadata migration again
    • @@ -199,7 +199,7 @@ UPDATE 960
  • Run all system updates and reboot CGSpace server
-

2016-06-07

+

2016-06-07

  • Figured out how to export a list of the unique values from a metadata field ordered by count:
    • @@ -228,7 +228,7 @@ UPDATE 960

  • Looks like OAI is kinda obtuse for this, and if we use ContentDM’s API we’ll be able to access their internal field names (rather than trying to figure out how they stuffed them into various, repeated Dublin Core fields)

-

2016-06-08

+

2016-06-08

-

2016-06-09

+

2016-06-09

  • Atmire explained that the atmire.orcid.id field doesn’t exist in the schema, as it actually comes from the authority cache during XMLUI run time
    • @@ -254,7 +254,7 @@ UPDATE 960
  • They opened a feature ticket on the DSpace tracker to ask for support of this: https://jira.duraspace.org/browse/DS-3239
-

2016-06-10

+

2016-06-10

  • Investigating authority confidences
    • @@ -279,20 +279,20 @@ UPDATE 960
  • Merge controlled vocabulary functionality for subregions (#238)
-

2016-06-11

+

2016-06-11

  • Merge controlled vocabulary for sponsorship field (#239)
  • Fix character encoding issues for animal breed lookup that I merged yesterday
-

2016-06-17

+

2016-06-17

  • Linode has free RAM upgrades for their 13th birthday so I migrated DSpace Test (4→8GB of RAM)
-

2016-06-18

+

2016-06-18

  • Clean up titles and hints in input-forms.xml to use title/sentence case and a few more consistency things (#241)
    • @@ -319,7 +319,7 @@ UPDATE 960

  • Need to run fix-metadata-values.py and then fix-metadata-values.py

-

2016-06-20

+

2016-06-20

  • CGSpace’s HTTPS certificate expired last night and I didn’t notice, had to renew:
    • @@ -332,7 +332,7 @@ UPDATE 960
  • I really need to fix that cron job…
-

2016-06-24

+

2016-06-24

  • Run the replacements/deletes for dc.description.sponsorship (investors) on CGSpace:
    • @@ -353,7 +353,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons
  • Refine submission form labels and hints
-

2016-06-28

+

2016-06-28

  • Testing the cleanup of dc.contributor.corporate with 13 deletions and 121 replacements
    • @@ -368,7 +368,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons
  • Re-evaluate dc.contributor.corporate and it seems we will move it to dc.contributor.author as this is more in line with how editors are actually using it
-

2016-06-29

+

2016-06-29

  • Test run of migrate-fields.sh with the following re-mappings:
    • @@ -407,7 +407,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
  • Start working on config changes for phase three of the metadata migrations
-

2016-06-30

+

2016-06-30

  • Wow, there are 95 authors in the database who have ‘,’ at the end of their name:
    • @@ -440,10 +440,10 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
@@ -468,7 +468,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D - + diff --git a/public/2016-07/index.html b/public/2016-07/index.html index a179e575e..07be66f0c 100644 --- a/public/2016-07/index.html +++ b/public/2016-07/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ July, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-07-01

+

2016-07-01

  • Add dc.description.sponsorship to Discovery sidebar facets and make investors clickable in item view (#232)
    • @@ -98,19 +98,19 @@ 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
-

2016-07-02

+

2016-07-02

  • Comment on DSpace Jira ticket about author lookup search text (DS-2329)
-

2016-07-04

+

2016-07-04

  • Seems the database’s author authority values mean nothing without the authority Solr core from the host where they were created!
-

2016-07-05

+

2016-07-05

  • Amend backup-solr.sh script so it backs up the entire Solr folder
    • @@ -128,7 +128,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
  • I will merge it to 5_x-prod
-

2016-07-06

+

2016-07-06

  • Delete 23 blank metadata values from CGSpace:
    • @@ -165,7 +165,7 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele
  • I then ran all server updates and rebooted the server
-

2016-07-11

+

2016-07-11

  • Doing some author cleanups from Peter and Abenet:
    • @@ -175,20 +175,20 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele $ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu -

    2016-07-13

    +

    2016-07-13

    • Run the author cleanups on CGSpace and start a full Discovery re-index
    -

    2016-07-14

    +

    2016-07-14

    • Test LDAP settings for new root LDAP
    • Seems to work when binding as a top-level user
    -

    2016-07-18

    +

    2016-07-18

    • Adjust identifiers in XMLUI item display to be more prominent
      • @@ -223,14 +223,14 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error } -

      2016-07-21

      +

      2016-07-21

      -

      2016-07-22

      +

      2016-07-22

      • Help Paola from CCAFS with thumbnails for batch uploads
        • @@ -284,7 +284,7 @@ index.authority.ignore-variants=true
      • After re-indexing and clearing the XMLUI cache nothing has changed
      -

      2016-07-25

      +

      2016-07-25

      • Trying a few more settings (plus reindex) for Discovery on DSpace Test:
        • @@ -318,7 +318,7 @@ discovery.index.authority.ignore-variants=true
      • I noticed that our backup scripts don’t send Solr cores to S3 so I amended the script
      -

      2016-07-31

      +

      2016-07-31

      • Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by
        • @@ -342,10 +342,10 @@ discovery.index.authority.ignore-variants=true
@@ -370,7 +370,7 @@ discovery.index.authority.ignore-variants=true - + diff --git a/public/2016-08/index.html b/public/2016-08/index.html index e43f97270..0b2c70b6f 100644 --- a/public/2016-08/index.html +++ b/public/2016-08/index.html @@ -6,7 +6,7 @@ - + @@ -21,19 +21,19 @@ August, 2016 · CGSpace Notes - - - - + + + + - - + +
-

CGSpace Notes

+

CGSpace Notes

@@ -48,7 +48,7 @@
- @@ -71,7 +71,7 @@
- #notes + #notes
@@ -79,7 +79,7 @@
-

2016-08-01

+

2016-08-01

  • Add updated distribution license from Sisay (#259)
    • @@ -105,7 +105,7 @@ $ git rebase -i dspace-5.5
  • The 5.5 code now builds but doesn’t run (white page in Tomcat)
-

2016-08-02

+

2016-08-02

  • Ask Atmire for help with DSpace 5.5 issue
    • @@ -131,7 +131,7 @@ $ git rebase -i dspace-5.5
    - + @@ -159,7 +159,7 @@ $ git rebase -i dspace-5.5 - + diff --git a/public/404.html b/public/404.html index 5bf3f8568..ebae2729c 100644 --- a/public/404.html +++ b/public/404.html @@ -6,7 +6,7 @@ - + @@ -16,19 +16,19 @@ 404 Page not found · CGSpace Notes - - - - + + + + - - + +
    -

    CGSpace Notes

    +

    CGSpace Notes

    @@ -43,13 +43,13 @@
    - - @@ -81,7 +81,7 @@ - + diff --git a/public/categories/index.html b/public/categories/index.html index 41b7e6324..185a4f387 100644 --- a/public/categories/index.html +++ b/public/categories/index.html @@ -6,7 +6,7 @@ - + @@ -16,19 +16,19 @@ Categories · CGSpace Notes - - - - + + + + - - + +
    -

    CGSpace Notes

    +

    CGSpace Notes

    @@ -43,13 +43,13 @@
    - - @@ -85,7 +85,7 @@ - + diff --git a/public/index.html b/public/index.html index fb31d03eb..794319e3e 100644 --- a/public/index.html +++ b/public/index.html @@ -6,7 +6,7 @@ - + @@ -16,21 +16,21 @@ CGSpace Notes - - - - + + + + - - + + - +
    -

    CGSpace Notes

    +

    CGSpace Notes

    @@ -46,7 +46,7 @@ - @@ -60,7 +60,7 @@
    -

    August, 2016

    +

    August, 2016

    Posted on @@ -76,7 +76,7 @@ @@ -88,7 +88,7 @@
    -

    July, 2016

    +

    July, 2016

    Posted on @@ -104,7 +104,7 @@ @@ -116,7 +116,7 @@
    -

    June, 2016

    +

    June, 2016

    Posted on @@ -132,7 +132,7 @@ @@ -144,7 +144,7 @@
    -

    May, 2016

    +

    May, 2016

    Posted on @@ -160,7 +160,7 @@ @@ -172,7 +172,7 @@
    -

    April, 2016

    +

    April, 2016

    Posted on @@ -188,7 +188,7 @@ @@ -200,7 +200,7 @@
    -

    March, 2016

    +

    March, 2016

    Posted on @@ -216,7 +216,7 @@ @@ -228,7 +228,7 @@
    -

    February, 2016

    +

    February, 2016

    Posted on @@ -244,7 +244,7 @@ @@ -256,7 +256,7 @@
    -

    January, 2016

    +

    January, 2016

    Posted on @@ -272,7 +272,7 @@ @@ -284,7 +284,7 @@
    -

    December, 2015

    +

    December, 2015

    Posted on @@ -300,7 +300,7 @@ @@ -312,7 +312,7 @@
    -

    November, 2015

    +

    November, 2015

    Posted on @@ -328,7 +328,7 @@ @@ -362,7 +362,7 @@ - + diff --git a/public/index.xml b/public/index.xml index f7c0a44fa..877282382 100644 --- a/public/index.xml +++ b/public/index.xml @@ -2,22 +2,22 @@ CGSpace Notes - /cgspace-notes/ + https://alanorth.github.io/cgspace-notes/ Recent content on CGSpace Notes Hugo -- gohugo.io en-us Mon, 01 Aug 2016 15:53:00 +0300 - + August, 2016 - /cgspace-notes/2016-08/ + https://alanorth.github.io/cgspace-notes/2016-08/ Mon, 01 Aug 2016 15:53:00 +0300 - /cgspace-notes/2016-08/ + https://alanorth.github.io/cgspace-notes/2016-08/ -<h2 id="2016-08-01:e34bd801c7748b7746ad4364bbdb5eb5">2016-08-01</h2> +<h2 id="2016-08-01">2016-08-01</h2> <ul> <li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li> @@ -43,7 +43,7 @@ $ git rebase -i dspace-5.5 <li>The 5.5 code now builds but doesn&rsquo;t run (white page in Tomcat)</li> </ul> -<h2 id="2016-08-02:e34bd801c7748b7746ad4364bbdb5eb5">2016-08-02</h2> +<h2 id="2016-08-02">2016-08-02</h2> <ul> <li>Ask Atmire for help with DSpace 5.5 issue</li> @@ -56,13 +56,13 @@ $ git rebase -i dspace-5.5 July, 2016 - /cgspace-notes/2016-07/ + https://alanorth.github.io/cgspace-notes/2016-07/ Fri, 01 Jul 2016 10:53:00 +0300 - /cgspace-notes/2016-07/ + https://alanorth.github.io/cgspace-notes/2016-07/ -<h2 id="2016-07-01:edc14796891c14dec087b4bb89c38aa9">2016-07-01</h2> +<h2 id="2016-07-01">2016-07-01</h2> <ul> <li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li> @@ -81,19 +81,19 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and <li>In this case the select query was showing 95 results before the update</li> </ul> -<h2 id="2016-07-02:edc14796891c14dec087b4bb89c38aa9">2016-07-02</h2> +<h2 id="2016-07-02">2016-07-02</h2> <ul> <li>Comment on DSpace Jira ticket about author lookup search text (<a href="https://jira.duraspace.org/browse/DS-2329">DS-2329</a>)</li> </ul> -<h2 id="2016-07-04:edc14796891c14dec087b4bb89c38aa9">2016-07-04</h2> +<h2 id="2016-07-04">2016-07-04</h2> <ul> <li>Seems the database&rsquo;s author authority values mean nothing without the <code>authority</code> Solr core from the host where they were created!</li> </ul> -<h2 id="2016-07-05:edc14796891c14dec087b4bb89c38aa9">2016-07-05</h2> +<h2 id="2016-07-05">2016-07-05</h2> <ul> <li>Amend <code>backup-solr.sh</code> script so it backs up the entire Solr folder</li> @@ -111,7 +111,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and <li>I will merge it to <code>5_x-prod</code></li> </ul> -<h2 id="2016-07-06:edc14796891c14dec087b4bb89c38aa9">2016-07-06</h2> +<h2 id="2016-07-06">2016-07-06</h2> <ul> <li>Delete 23 blank metadata values from CGSpace:</li> @@ -148,7 +148,7 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele <li>I then ran all server updates and rebooted the server</li> </ul> -<h2 id="2016-07-11:edc14796891c14dec087b4bb89c38aa9">2016-07-11</h2> +<h2 id="2016-07-11">2016-07-11</h2> <ul> <li>Doing some author cleanups from Peter and Abenet:</li> @@ -158,20 +158,20 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele $ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu </code></pre> -<h2 id="2016-07-13:edc14796891c14dec087b4bb89c38aa9">2016-07-13</h2> +<h2 id="2016-07-13">2016-07-13</h2> <ul> <li>Run the author cleanups on CGSpace and start a full Discovery re-index</li> </ul> -<h2 id="2016-07-14:edc14796891c14dec087b4bb89c38aa9">2016-07-14</h2> +<h2 id="2016-07-14">2016-07-14</h2> <ul> <li>Test LDAP settings for new root LDAP</li> <li>Seems to work when binding as a top-level user</li> </ul> -<h2 id="2016-07-18:edc14796891c14dec087b4bb89c38aa9">2016-07-18</h2> +<h2 id="2016-07-18">2016-07-18</h2> <ul> <li>Adjust identifiers in XMLUI item display to be more prominent</li> @@ -206,14 +206,14 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error } </code></pre> -<h2 id="2016-07-21:edc14796891c14dec087b4bb89c38aa9">2016-07-21</h2> +<h2 id="2016-07-21">2016-07-21</h2> <ul> <li>Mitigate the <a href="https://httpoxy.org">HTTPoxy</a> vulnerability for Tomcat etc in nginx: <a href="https://github.com/ilri/rmg-ansible-public/pull/38">https://github.com/ilri/rmg-ansible-public/pull/38</a></li> <li>Unblock 70.32.99.142 from <code>/rest</code> as it has been blocked for a few days</li> </ul> -<h2 id="2016-07-22:edc14796891c14dec087b4bb89c38aa9">2016-07-22</h2> +<h2 id="2016-07-22">2016-07-22</h2> <ul> <li>Help Paola from CCAFS with thumbnails for batch uploads</li> @@ -267,7 +267,7 @@ index.authority.ignore-variants=true <li>After re-indexing and clearing the XMLUI cache nothing has changed</li> </ul> -<h2 id="2016-07-25:edc14796891c14dec087b4bb89c38aa9">2016-07-25</h2> +<h2 id="2016-07-25">2016-07-25</h2> <ul> <li>Trying a few more settings (plus reindex) for Discovery on DSpace Test:</li> @@ -301,7 +301,7 @@ discovery.index.authority.ignore-variants=true <li>I noticed that our backup scripts don&rsquo;t send Solr cores to S3 so I amended the script</li> </ul> -<h2 id="2016-07-31:edc14796891c14dec087b4bb89c38aa9">2016-07-31</h2> +<h2 id="2016-07-31">2016-07-31</h2> <ul> <li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li> @@ -312,13 +312,13 @@ discovery.index.authority.ignore-variants=true June, 2016 - /cgspace-notes/2016-06/ + https://alanorth.github.io/cgspace-notes/2016-06/ Wed, 01 Jun 2016 10:53:00 +0300 - /cgspace-notes/2016-06/ + https://alanorth.github.io/cgspace-notes/2016-06/ -<h2 id="2016-06-01:6783872e82b68b1517e00f494e6b6504">2016-06-01</h2> +<h2 id="2016-06-01">2016-06-01</h2> <ul> <li>Experimenting with IFPRI OAI (we want to harvest their publications)</li> @@ -339,7 +339,7 @@ UPDATE 14 <li>Fix a few minor miscellaneous issues in <code>dspace.cfg</code> (<a href="https://github.com/ilri/DSpace/pull/227">#227</a>)</li> </ul> -<h2 id="2016-06-02:6783872e82b68b1517e00f494e6b6504">2016-06-02</h2> +<h2 id="2016-06-02">2016-06-02</h2> <ul> <li>Testing the configuration and theme changes for the upcoming metadata migration and I found some issues with <code>cg.coverage.admin-unit</code></li> @@ -357,7 +357,7 @@ UPDATE 14 <li>The patch applies successfully on DSpace 5.1 so I will try it later</li> </ul> -<h2 id="2016-06-03:6783872e82b68b1517e00f494e6b6504">2016-06-03</h2> +<h2 id="2016-06-03">2016-06-03</h2> <ul> <li>Investigating the CCAFS authority issue, I exported the metadata for the Videos collection</li> @@ -430,7 +430,7 @@ UPDATE 960 <li>That would only be for the &ldquo;Browse by&rdquo; function&hellip; so we&rsquo;ll have to see what effect that has later</li> </ul> -<h2 id="2016-06-04:6783872e82b68b1517e00f494e6b6504">2016-06-04</h2> +<h2 id="2016-06-04">2016-06-04</h2> <ul> <li>Re-sync DSpace Test with CGSpace and perform test of metadata migration again</li> @@ -438,7 +438,7 @@ UPDATE 960 <li>Run all system updates and reboot CGSpace server</li> </ul> -<h2 id="2016-06-07:6783872e82b68b1517e00f494e6b6504">2016-06-07</h2> +<h2 id="2016-06-07">2016-06-07</h2> <ul> <li>Figured out how to export a list of the unique values from a metadata field ordered by count:</li> @@ -467,7 +467,7 @@ UPDATE 960 <li><p>Looks like OAI is kinda obtuse for this, and if we use ContentDM&rsquo;s API we&rsquo;ll be able to access their internal field names (rather than trying to figure out how they stuffed them into various, repeated Dublin Core fields)</p></li> </ul> -<h2 id="2016-06-08:6783872e82b68b1517e00f494e6b6504">2016-06-08</h2> +<h2 id="2016-06-08">2016-06-08</h2> <ul> <li>Discuss controlled vocabularies for ~28 fields</li> @@ -485,7 +485,7 @@ UPDATE 960 <li>File bug about <code>closed=&quot;true&quot;</code> attribute of controlled vocabularies not working: <a href="https://jira.duraspace.org/browse/DS-3238">https://jira.duraspace.org/browse/DS-3238</a></li> </ul> -<h2 id="2016-06-09:6783872e82b68b1517e00f494e6b6504">2016-06-09</h2> +<h2 id="2016-06-09">2016-06-09</h2> <ul> <li>Atmire explained that the <code>atmire.orcid.id</code> field doesn&rsquo;t exist in the schema, as it actually comes from the authority cache during XMLUI run time</li> @@ -493,7 +493,7 @@ UPDATE 960 <li>They opened a feature ticket on the DSpace tracker to ask for support of this: <a href="https://jira.duraspace.org/browse/DS-3239">https://jira.duraspace.org/browse/DS-3239</a></li> </ul> -<h2 id="2016-06-10:6783872e82b68b1517e00f494e6b6504">2016-06-10</h2> +<h2 id="2016-06-10">2016-06-10</h2> <ul> <li>Investigating authority confidences</li> @@ -518,20 +518,20 @@ UPDATE 960 <li>Merge controlled vocabulary functionality for subregions (<a href="https://github.com/ilri/DSpace/pull/238">#238</a>)</li> </ul> -<h2 id="2016-06-11:6783872e82b68b1517e00f494e6b6504">2016-06-11</h2> +<h2 id="2016-06-11">2016-06-11</h2> <ul> <li>Merge controlled vocabulary for sponsorship field (<a href="https://github.com/ilri/DSpace/pull/239">#239</a>)</li> <li>Fix character encoding issues for animal breed lookup that I merged yesterday</li> </ul> -<h2 id="2016-06-17:6783872e82b68b1517e00f494e6b6504">2016-06-17</h2> +<h2 id="2016-06-17">2016-06-17</h2> <ul> <li>Linode has free RAM upgrades for their 13th birthday so I migrated DSpace Test (4→8GB of RAM)</li> </ul> -<h2 id="2016-06-18:6783872e82b68b1517e00f494e6b6504">2016-06-18</h2> +<h2 id="2016-06-18">2016-06-18</h2> <ul> <li>Clean up titles and hints in <code>input-forms.xml</code> to use title/sentence case and a few more consistency things (<a href="https://github.com/ilri/DSpace/pull/241">#241</a>)</li> @@ -558,7 +558,7 @@ UPDATE 960 <li><p>Need to run <code>fix-metadata-values.py</code> and then <code>fix-metadata-values.py</code></p></li> </ul> -<h2 id="2016-06-20:6783872e82b68b1517e00f494e6b6504">2016-06-20</h2> +<h2 id="2016-06-20">2016-06-20</h2> <ul> <li>CGSpace&rsquo;s HTTPS certificate expired last night and I didn&rsquo;t notice, had to renew:</li> @@ -571,7 +571,7 @@ UPDATE 960 <li>I really need to fix that cron job&hellip;</li> </ul> -<h2 id="2016-06-24:6783872e82b68b1517e00f494e6b6504">2016-06-24</h2> +<h2 id="2016-06-24">2016-06-24</h2> <ul> <li>Run the replacements/deletes for <code>dc.description.sponsorship</code> (investors) on CGSpace:</li> @@ -592,7 +592,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons <li>Refine submission form labels and hints</li> </ul> -<h2 id="2016-06-28:6783872e82b68b1517e00f494e6b6504">2016-06-28</h2> +<h2 id="2016-06-28">2016-06-28</h2> <ul> <li>Testing the cleanup of <code>dc.contributor.corporate</code> with 13 deletions and 121 replacements</li> @@ -607,7 +607,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons <li>Re-evaluate <code>dc.contributor.corporate</code> and it seems we will move it to <code>dc.contributor.author</code> as this is more in line with how editors are actually using it</li> </ul> -<h2 id="2016-06-29:6783872e82b68b1517e00f494e6b6504">2016-06-29</h2> +<h2 id="2016-06-29">2016-06-29</h2> <ul> <li>Test run of <code>migrate-fields.sh</code> with the following re-mappings:</li> @@ -646,7 +646,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <li>Start working on config changes for phase three of the metadata migrations</li> </ul> -<h2 id="2016-06-30:6783872e82b68b1517e00f494e6b6504">2016-06-30</h2> +<h2 id="2016-06-30">2016-06-30</h2> <ul> <li>Wow, there are 95 authors in the database who have &lsquo;,&rsquo; at the end of their name:</li> @@ -666,13 +666,13 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D May, 2016 - /cgspace-notes/2016-05/ + https://alanorth.github.io/cgspace-notes/2016-05/ Sun, 01 May 2016 23:06:00 +0300 - /cgspace-notes/2016-05/ + https://alanorth.github.io/cgspace-notes/2016-05/ -<h2 id="2016-05-01:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-01</h2> +<h2 id="2016-05-01">2016-05-01</h2> <ul> <li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li> @@ -697,7 +697,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <li>The owner of that application has said that the <code>NaN</code> (not a number) is an error in his code and he&rsquo;ll fix it</li> </ul> -<h2 id="2016-05-03:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-03</h2> +<h2 id="2016-05-03">2016-05-03</h2> <ul> <li>Update nginx to 1.10.x branch on CGSpace</li> @@ -706,7 +706,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <p><img src="../images/2016/05/discovery-types.png" alt="Item type in Discovery results" /></p> -<h2 id="2016-05-06:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-06</h2> +<h2 id="2016-05-06">2016-05-06</h2> <ul> <li>DSpace Test is down, <code>catalina.out</code> has lots of messages about heap space from some time yesterday (!)</li> @@ -744,7 +744,7 @@ fi <li>Seems to work well</li> </ul> -<h2 id="2016-05-10:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-10</h2> +<h2 id="2016-05-10">2016-05-10</h2> <ul> <li>Start looking at more metadata migrations</li> @@ -759,7 +759,7 @@ fi <li>CGSpace&rsquo;s <code>dc</code> registry has 96 items, and the default DSpace one has 73.</li> </ul> -<h2 id="2016-05-11:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-11</h2> +<h2 id="2016-05-11">2016-05-11</h2> <ul> <li><p>Identify and propose the next phase of CGSpace fields to migrate:</p> @@ -792,7 +792,7 @@ fi <li>Turns out she was able to decrease the size of the PDF so we didn&rsquo;t have to do anything</li> </ul> -<h2 id="2016-05-12:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-12</h2> +<h2 id="2016-05-12">2016-05-12</h2> <ul> <li>Looks like the issue that Abenet was having a few days ago with &ldquo;Connection Reset&rdquo; in Firefox might be due to a Firefox 46 issue: <a href="https://bugzilla.mozilla.org/show_bug.cgi?id=1268775">https://bugzilla.mozilla.org/show_bug.cgi?id=1268775</a></li> @@ -816,7 +816,7 @@ fi <pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to &quot;% %&quot;; </code></pre> -<h2 id="2016-05-13:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-13</h2> +<h2 id="2016-05-13">2016-05-13</h2> <ul> <li>More theorizing about CGcore</li> @@ -830,7 +830,7 @@ fi <li>I&rsquo;ve removed <code>dc.title.jtitle</code> from the list for now because there&rsquo;s no use moving it out of DC until we know where it will go (see discussion yesterday)</li> </ul> -<h2 id="2016-05-18:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-18</h2> +<h2 id="2016-05-18">2016-05-18</h2> <ul> <li>Work on 707 CCAFS records</li> @@ -847,7 +847,7 @@ fi <li>Before importing with SAFBuilder I tested adding &ldquo;__bundle:THUMBNAIL&rdquo; to the <code>filename</code> column and it works fine</li> </ul> -<h2 id="2016-05-19:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-19</h2> +<h2 id="2016-05-19">2016-05-19</h2> <ul> <li>More quality control on <code>filename</code> field of CCAFS records to make processing in shell and SAFBuilder more reliable:</li> @@ -871,7 +871,7 @@ fi <pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA'); </code></pre> -<h2 id="2016-05-20:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-20</h2> +<h2 id="2016-05-20">2016-05-20</h2> <ul> <li>More work on CCAFS Video and Images records</li> @@ -896,7 +896,7 @@ fi <li>Work on configuration changes for Phase 2 metadata migrations</li> </ul> -<h2 id="2016-05-23:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-23</h2> +<h2 id="2016-05-23">2016-05-23</h2> <ul> <li>Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine</li> @@ -905,7 +905,7 @@ fi <li>I will have to try later</li> </ul> -<h2 id="2016-05-30:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-30</h2> +<h2 id="2016-05-30">2016-05-30</h2> <ul> <li>Export CCAFS video and image records from DSpace Test using the migrate option (<code>-m</code>):</li> @@ -941,7 +941,7 @@ $ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA <pre><code>$ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; /home/cgspace.cgiar.org/bin/dspace index-authority </code></pre> -<h2 id="2016-05-31:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-31</h2> +<h2 id="2016-05-31">2016-05-31</h2> <ul> <li>The <code>index-authority</code> script ran over night and was finished in the morning</li> @@ -973,13 +973,13 @@ sys 0m20.540s April, 2016 - /cgspace-notes/2016-04/ + https://alanorth.github.io/cgspace-notes/2016-04/ Mon, 04 Apr 2016 11:06:00 +0300 - /cgspace-notes/2016-04/ + https://alanorth.github.io/cgspace-notes/2016-04/ -<h2 id="2016-04-04:c88be15f5b2f07c85f7742556a955e47">2016-04-04</h2> +<h2 id="2016-04-04">2016-04-04</h2> <ul> <li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li> @@ -1020,7 +1020,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290 <li>Submit pull request for Tomcat 7 limits in Ansible dspace role (<a href="https://github.com/ilri/rmg-ansible-public/pull/30">#30</a>)</li> </ul> -<h2 id="2016-04-05:c88be15f5b2f07c85f7742556a955e47">2016-04-05</h2> +<h2 id="2016-04-05">2016-04-05</h2> <ul> <li>Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don&rsquo;t need!</li> @@ -1038,7 +1038,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290 <li>Try to do some metadata field migrations using the Atmire batch UI (<code>dc.Species</code> → <code>cg.species</code>) but it took several hours and even missed a few records</li> </ul> -<h2 id="2016-04-06:c88be15f5b2f07c85f7742556a955e47">2016-04-06</h2> +<h2 id="2016-04-06">2016-04-06</h2> <ul> <li>A better way to move metadata on this scale is via SQL, for example <code>dc.type.output</code> → <code>dc.type</code> (their IDs in the metadatafieldregistry are 66 and 109, respectively):</li> @@ -1053,7 +1053,7 @@ UPDATE 40852 <li>Start working on metadata migrations, add 25 or so new metadata fields to CGSpace</li> </ul> -<h2 id="2016-04-07:c88be15f5b2f07c85f7742556a955e47">2016-04-07</h2> +<h2 id="2016-04-07">2016-04-07</h2> <ul> <li>Write shell script to do the migration of fields: <a href="https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b">https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b</a></li> @@ -1069,14 +1069,14 @@ UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76 UPDATE 51258 </code></pre> -<h2 id="2016-04-08:c88be15f5b2f07c85f7742556a955e47">2016-04-08</h2> +<h2 id="2016-04-08">2016-04-08</h2> <ul> <li>Discuss metadata renaming with Abenet, we decided it&rsquo;s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF</li> <li>I&rsquo;ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change</li> </ul> -<h2 id="2016-04-10:c88be15f5b2f07c85f7742556a955e47">2016-04-10</h2> +<h2 id="2016-04-10">2016-04-10</h2> <ul> <li>Looking at the DOI issue <a href="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=678507860">reported by Leroy from CIAT a few weeks ago</a></li> @@ -1099,14 +1099,14 @@ dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and t <li>I will manually edit the <code>dc.identifier.doi</code> in <a href="https://cgspace.cgiar.org/handle/10568/72509?show=full"><sup>10568</sup>&frasl;<sub>72509</sub></a> and tweet the link, then check back in a week to see if the donut gets updated</li> </ul> -<h2 id="2016-04-11:c88be15f5b2f07c85f7742556a955e47">2016-04-11</h2> +<h2 id="2016-04-11">2016-04-11</h2> <ul> <li>The donut is already updated and shows the correct number now</li> <li>CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we&rsquo;d do it tentatively on Monday the 18th.</li> </ul> -<h2 id="2016-04-12:c88be15f5b2f07c85f7742556a955e47">2016-04-12</h2> +<h2 id="2016-04-12">2016-04-12</h2> <ul> <li>Looking at quality of WLE data (<code>cg.subject.iwmi</code>) in SQL:</li> @@ -1143,7 +1143,7 @@ DELETE 226 <li>We want to do the <code>dc.type.output</code> move on CGSpace anyways, but we should wait as it might affect other external people!</li> </ul> -<h2 id="2016-04-14:c88be15f5b2f07c85f7742556a955e47">2016-04-14</h2> +<h2 id="2016-04-14">2016-04-14</h2> <ul> <li>Communicate with Macaroni Bros again about <code>dc.type</code></li> @@ -1151,13 +1151,13 @@ DELETE 226 <li>Notify CIAT people of metadata changes (I had forgotten them last week)</li> </ul> -<h2 id="2016-04-15:c88be15f5b2f07c85f7742556a955e47">2016-04-15</h2> +<h2 id="2016-04-15">2016-04-15</h2> <ul> <li>DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code</li> </ul> -<h2 id="2016-04-18:c88be15f5b2f07c85f7742556a955e47">2016-04-18</h2> +<h2 id="2016-04-18">2016-04-18</h2> <ul> <li>Talk to CIAT people about their portal again</li> @@ -1236,7 +1236,7 @@ javax.ws.rs.WebApplicationException <li>After restarting Tomcat a few more of these errors were logged but the application was up</li> </ul> -<h2 id="2016-04-19:c88be15f5b2f07c85f7742556a955e47">2016-04-19</h2> +<h2 id="2016-04-19">2016-04-19</h2> <ul> <li>Get handles for items that are using a given metadata field, ie <code>dc.Species.animal</code> (105):</li> @@ -1292,7 +1292,7 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error <li>And then remove them from the metadata registry</li> </ul> -<h2 id="2016-04-20:c88be15f5b2f07c85f7742556a955e47">2016-04-20</h2> +<h2 id="2016-04-20">2016-04-20</h2> <ul> <li>Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server</li> @@ -1331,20 +1331,20 @@ UPDATE 46075 <li>I&rsquo;ve sent a message to Atmire asking about compatibility with DSpace 5.5</li> </ul> -<h2 id="2016-04-21:c88be15f5b2f07c85f7742556a955e47">2016-04-21</h2> +<h2 id="2016-04-21">2016-04-21</h2> <ul> <li>Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)</li> <li>Atmire responded with DSpace 5.5 compatible versions for their modules, so I&rsquo;ll start testing those in a few weeks</li> </ul> -<h2 id="2016-04-22:c88be15f5b2f07c85f7742556a955e47">2016-04-22</h2> +<h2 id="2016-04-22">2016-04-22</h2> <ul> <li>Import 95 records into <a href="https://cgspace.cgiar.org/handle/10568/42219">CTA&rsquo;s Agrodok collection</a></li> </ul> -<h2 id="2016-04-26:c88be15f5b2f07c85f7742556a955e47">2016-04-26</h2> +<h2 id="2016-04-26">2016-04-26</h2> <ul> <li>Test embargo during item upload</li> @@ -1360,7 +1360,7 @@ UPDATE 46075 </ul></li> </ul> -<h2 id="2016-04-27:c88be15f5b2f07c85f7742556a955e47">2016-04-27</h2> +<h2 id="2016-04-27">2016-04-27</h2> <ul> <li>I woke up to ten or fifteen &ldquo;up&rdquo; and &ldquo;down&rdquo; emails from the monitoring website</li> @@ -1407,14 +1407,14 @@ dspace.log.2016-04-27:7271 <li>CGSpace down, restarted tomcat and it&rsquo;s back up</li> </ul> -<h2 id="2016-04-28:c88be15f5b2f07c85f7742556a955e47">2016-04-28</h2> +<h2 id="2016-04-28">2016-04-28</h2> <ul> <li>Problems with stability again. I&rsquo;ve blocked access to <code>/rest</code> for now to see if the number of errors in the log files drop</li> <li>Later we could maybe start logging access to <code>/rest</code> and perhaps whitelist some IPs&hellip;</li> </ul> -<h2 id="2016-04-30:c88be15f5b2f07c85f7742556a955e47">2016-04-30</h2> +<h2 id="2016-04-30">2016-04-30</h2> <ul> <li>Logs for today and yesterday have zero references to this REST error, so I&rsquo;m going to open back up the REST API but log all requests</li> @@ -1434,13 +1434,13 @@ dspace.log.2016-04-27:7271 March, 2016 - /cgspace-notes/2016-03/ + https://alanorth.github.io/cgspace-notes/2016-03/ Wed, 02 Mar 2016 16:50:00 +0300 - /cgspace-notes/2016-03/ + https://alanorth.github.io/cgspace-notes/2016-03/ -<h2 id="2016-03-02:5a28ddf3ee658c043c064ccddb151717">2016-03-02</h2> +<h2 id="2016-03-02">2016-03-02</h2> <ul> <li>Looking at issues with author authorities on CGSpace</li> @@ -1448,7 +1448,7 @@ dspace.log.2016-04-27:7271 <li>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</li> </ul> -<h2 id="2016-03-07:5a28ddf3ee658c043c064ccddb151717">2016-03-07</h2> +<h2 id="2016-03-07">2016-03-07</h2> <ul> <li>Troubleshooting the issues with the slew of commits for Atmire modules in <a href="https://github.com/ilri/DSpace/pull/182">#182</a></li> @@ -1461,14 +1461,14 @@ dspace.log.2016-04-27:7271 <pre><code>Exception in thread &quot;Lucene Merge Thread #19&quot; org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device </code></pre> -<h2 id="2016-03-08:5a28ddf3ee658c043c064ccddb151717">2016-03-08</h2> +<h2 id="2016-03-08">2016-03-08</h2> <ul> <li>Add a few new filters to Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/issues/180">#180</a>)</li> <li>We had also wanted to add a few to the Content and Usage module but I have to ask the editors which ones they were</li> </ul> -<h2 id="2016-03-10:5a28ddf3ee658c043c064ccddb151717">2016-03-10</h2> +<h2 id="2016-03-10">2016-03-10</h2> <ul> <li>Disable the lucene cron job on CGSpace as it shouldn&rsquo;t be needed anymore</li> @@ -1485,7 +1485,7 @@ dspace.log.2016-04-27:7271 <li>Update documentation for Atmire modules</li> </ul> -<h2 id="2016-03-11:5a28ddf3ee658c043c064ccddb151717">2016-03-11</h2> +<h2 id="2016-03-11">2016-03-11</h2> <ul> <li>As I was looking at the CUA config I realized our Discovery config is all messed up and confusing</li> @@ -1495,7 +1495,7 @@ dspace.log.2016-04-27:7271 <li>There is still some more work to be done to remove references to old <code>outputtype</code> and <code>output</code></li> </ul> -<h2 id="2016-03-14:5a28ddf3ee658c043c064ccddb151717">2016-03-14</h2> +<h2 id="2016-03-14">2016-03-14</h2> <ul> <li>Fix some items that had invalid dates (I noticed them in the log during a re-indexing)</li> @@ -1506,13 +1506,13 @@ dspace.log.2016-04-27:7271 <p><img src="../images/2016/03/missing-xmlui-string.png" alt="Missing XMLUI string" /></p> -<h2 id="2016-03-15:5a28ddf3ee658c043c064ccddb151717">2016-03-15</h2> +<h2 id="2016-03-15">2016-03-15</h2> <ul> <li>Create simple theme for new AVCD community just for a unique Google Tracking ID (<a href="https://github.com/ilri/DSpace/pull/191">#191</a>)</li> </ul> -<h2 id="2016-03-16:5a28ddf3ee658c043c064ccddb151717">2016-03-16</h2> +<h2 id="2016-03-16">2016-03-16</h2> <ul> <li>Still having problems deploying Atmire&rsquo;s CUA updates and fixes from January!</li> @@ -1543,7 +1543,7 @@ dspace.log.2016-04-27:7271 <li>Also, <code>dc.language.iso</code> has some weird values, like &ldquo;En&rdquo; and &ldquo;English&rdquo;</li> </ul> -<h2 id="2016-03-17:5a28ddf3ee658c043c064ccddb151717">2016-03-17</h2> +<h2 id="2016-03-17">2016-03-17</h2> <ul> <li>It turns out <code>hi</code> is the ISO 639 language code for Hindi, but these should be in <code>dc.language.iso</code> instead of <code>dc.language</code></li> @@ -1553,7 +1553,7 @@ dspace.log.2016-04-27:7271 <li>The patches work fine with a clean database, so the error was caused by some mismatch in CUA versions and the database during my testing</li> </ul> -<h2 id="2016-03-18:5a28ddf3ee658c043c064ccddb151717">2016-03-18</h2> +<h2 id="2016-03-18">2016-03-18</h2> <ul> <li>Merge Atmire fixes into <code>5_x-prod</code></li> @@ -1580,7 +1580,7 @@ dspace.log.2016-04-27:7271 <li>Also, it looks like adding <code>-sharpen 0x1.0</code> really improves the quality of the image for only a few KB</li> </ul> -<h2 id="2016-03-21:5a28ddf3ee658c043c064ccddb151717">2016-03-21</h2> +<h2 id="2016-03-21">2016-03-21</h2> <ul> <li>Fix 66 site errors in Google&rsquo;s webmaster tools</li> @@ -1620,13 +1620,13 @@ dspace.log.2016-04-27:7271 <li>Deploy Let&rsquo;s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks</li> </ul> -<h2 id="2016-03-22:5a28ddf3ee658c043c064ccddb151717">2016-03-22</h2> +<h2 id="2016-03-22">2016-03-22</h2> <ul> <li>Merge robots.txt patch and disallow indexing of browse pages as our sitemap is consumed correctly (<a href="https://github.com/ilri/DSpace/issues/198">#198</a>)</li> </ul> -<h2 id="2016-03-23:5a28ddf3ee658c043c064ccddb151717">2016-03-23</h2> +<h2 id="2016-03-23">2016-03-23</h2> <ul> <li>Abenet is having problems saving group memberships, and she gets this error: <a href="https://gist.github.com/alanorth/87281c061c2de57b773e">https://gist.github.com/alanorth/87281c061c2de57b773e</a></li> @@ -1640,14 +1640,14 @@ dspace.log.2016-04-27:7271 <li>Looks to be an issue with the Atmire modules, I&rsquo;ve submitted a ticket to their tracker.</li> </ul> -<h2 id="2016-03-24:5a28ddf3ee658c043c064ccddb151717">2016-03-24</h2> +<h2 id="2016-03-24">2016-03-24</h2> <ul> <li>Atmire sent a patch for the group saving issue: <a href="https://github.com/ilri/DSpace/pull/201">https://github.com/ilri/DSpace/pull/201</a></li> <li>I tested it locally and it works, so I merged it to <code>5_x-prod</code> and will deploy on CGSpace this week</li> </ul> -<h2 id="2016-03-25:5a28ddf3ee658c043c064ccddb151717">2016-03-25</h2> +<h2 id="2016-03-25">2016-03-25</h2> <ul> <li>Having problems with Listings and Reports, seems to be caused by a rogue reference to <code>dc.type.output</code></li> @@ -1655,7 +1655,7 @@ dspace.log.2016-04-27:7271 <li>Commenting out the line works, but I haven&rsquo;t figured out the proper syntax for referring to <code>dc.type.*</code></li> </ul> -<h2 id="2016-03-28:5a28ddf3ee658c043c064ccddb151717">2016-03-28</h2> +<h2 id="2016-03-28">2016-03-28</h2> <ul> <li>Look into enabling the embargo during item submission, see: <a href="https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess">https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess</a></li> @@ -1669,7 +1669,7 @@ dspace.log.2016-04-27:7271 <li>Deploy robots.txt fix, embargo for item submissions, and listings and reports fix on CGSpace</li> </ul> -<h2 id="2016-03-29:5a28ddf3ee658c043c064ccddb151717">2016-03-29</h2> +<h2 id="2016-03-29">2016-03-29</h2> <ul> <li>Skype meeting with Peter and Addis team to discuss metadata changes for Dublin Core, CGcore, and CGSpace-specific fields</li> @@ -1682,13 +1682,13 @@ dspace.log.2016-04-27:7271 February, 2016 - /cgspace-notes/2016-02/ + https://alanorth.github.io/cgspace-notes/2016-02/ Fri, 05 Feb 2016 13:18:00 +0300 - /cgspace-notes/2016-02/ + https://alanorth.github.io/cgspace-notes/2016-02/ -<h2 id="2016-02-05:124a59adbaa8ef13e1518d003fc03981">2016-02-05</h2> +<h2 id="2016-02-05">2016-02-05</h2> <ul> <li>Looking at some DAGRIS data for Abenet Yabowork</li> @@ -1703,7 +1703,7 @@ dspace.log.2016-04-27:7271 <li>Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;</li> </ul> -<h2 id="2016-02-06:124a59adbaa8ef13e1518d003fc03981">2016-02-06</h2> +<h2 id="2016-02-06">2016-02-06</h2> <ul> <li>Found a way to get items with null/empty metadata values from SQL</li> @@ -1744,7 +1744,7 @@ DELETE 25 <li>Process the empty countries on CGSpace</li> </ul> -<h2 id="2016-02-07:124a59adbaa8ef13e1518d003fc03981">2016-02-07</h2> +<h2 id="2016-02-07">2016-02-07</h2> <ul> <li>Working on cleaning up Abenet&rsquo;s DAGRIS data with OpenRefine</li> @@ -1798,7 +1798,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start <pre><code>$ ~/dspace/bin/dspace index-discovery -b </code></pre> -<h2 id="2016-02-08:124a59adbaa8ef13e1518d003fc03981">2016-02-08</h2> +<h2 id="2016-02-08">2016-02-08</h2> <ul> <li>Finish cleaning up and importing ~400 DAGRIS items into CGSpace</li> @@ -1808,7 +1808,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start <p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" /> <img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p> -<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2> +<h2 id="2016-02-09">2016-02-09</h2> <ul> <li>Re-sync DSpace Test with CGSpace</li> @@ -1859,7 +1859,7 @@ Swap: 255 57 198 <li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li> </ul> -<h2 id="2016-02-11:124a59adbaa8ef13e1518d003fc03981">2016-02-11</h2> +<h2 id="2016-02-11">2016-02-11</h2> <ul> <li>Massaging some CIAT data in OpenRefine</li> @@ -1883,7 +1883,7 @@ Processing 64195.pdf &gt; Creating thumbnail for 64195.pdf </code></pre> -<h2 id="2016-02-12:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2> +<h2 id="2016-02-12">2016-02-12</h2> <ul> <li>Looking at CIAT&rsquo;s records again, there are some problems with a dozen or so files (out of 1200)</li> @@ -1894,7 +1894,7 @@ Processing 64195.pdf <li>Also, I&rsquo;m not sure if we import these items, will be remove the <code>dc.identifier.url</code> field from the records?</li> </ul> -<h2 id="2016-02-12-1:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2> +<h2 id="2016-02-12-1">2016-02-12</h2> <ul> <li>Looking at CIAT&rsquo;s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I&rsquo;m not sure if we can use those</li> @@ -1919,7 +1919,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>They will be deployed on CGSpace the next time I re-deploy</li> </ul> -<h2 id="2016-02-16:124a59adbaa8ef13e1518d003fc03981">2016-02-16</h2> +<h2 id="2016-02-16">2016-02-16</h2> <ul> <li>Turns out OpenRefine has an unescape function!</li> @@ -1938,7 +1938,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>This also works for records that have multiple URLs (separated by &ldquo;||&rdquo;)</li> </ul> -<h2 id="2016-02-17:124a59adbaa8ef13e1518d003fc03981">2016-02-17</h2> +<h2 id="2016-02-17">2016-02-17</h2> <ul> <li>Re-deploy CGSpace, run all system updates, and reboot</li> @@ -1947,7 +1947,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>Need to re-process the filename column to replace multiple underscores with one: <code>value.replace(/_{2,}/, &quot;_&quot;)</code></li> </ul> -<h2 id="2016-02-20:124a59adbaa8ef13e1518d003fc03981">2016-02-20</h2> +<h2 id="2016-02-20">2016-02-20</h2> <ul> <li>Turns out the &ldquo;bug&rdquo; in SAFBuilder isn&rsquo;t a bug, it&rsquo;s a feature that allows you to encode extra information like the destintion bundle in the filename</li> @@ -1962,7 +1962,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>Useful custom text facet for URLs ending with &ldquo;.pdf&rdquo;: <code>value.endsWith(&quot;.pdf&quot;)</code></li> </ul> -<h2 id="2016-02-22:124a59adbaa8ef13e1518d003fc03981">2016-02-22</h2> +<h2 id="2016-02-22">2016-02-22</h2> <ul> <li>To change Spanish accents to ASCII in OpenRefine:</li> @@ -1987,7 +1987,7 @@ Bitstream: tést señora alimentación.pdf <li>Running the SAFBuilder on Mac OS X works if you&rsquo;re going to import the resulting bundle on Mac OS X, but if your DSpace is running on Linux you need to run the SAFBuilder there where the filesystem&rsquo;s encoding matches</li> </ul> -<h2 id="2016-02-29:124a59adbaa8ef13e1518d003fc03981">2016-02-29</h2> +<h2 id="2016-02-29">2016-02-29</h2> <ul> <li>Got notified by some CIFOR colleagues that the Google Scholar team had contacted them about CGSpace&rsquo;s incorrect ordering of authors in Google Scholar metadata</li> @@ -2016,13 +2016,13 @@ Bitstream: tést señora alimentación.pdf January, 2016 - /cgspace-notes/2016-01/ + https://alanorth.github.io/cgspace-notes/2016-01/ Wed, 13 Jan 2016 13:18:00 +0300 - /cgspace-notes/2016-01/ + https://alanorth.github.io/cgspace-notes/2016-01/ -<h2 id="2016-01-13:3846b7fcbca60cdedafd373cb39cd76d">2016-01-13</h2> +<h2 id="2016-01-13">2016-01-13</h2> <ul> <li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li> @@ -2030,20 +2030,20 @@ Bitstream: tést señora alimentación.pdf <li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li> </ul> -<h2 id="2016-01-14:3846b7fcbca60cdedafd373cb39cd76d">2016-01-14</h2> +<h2 id="2016-01-14">2016-01-14</h2> <ul> <li>Update CCAFS project identifiers in input-forms.xml</li> <li>Run system updates and restart the server</li> </ul> -<h2 id="2016-01-18:3846b7fcbca60cdedafd373cb39cd76d">2016-01-18</h2> +<h2 id="2016-01-18">2016-01-18</h2> <ul> <li>Change &ldquo;Extension material&rdquo; to &ldquo;Extension Material&rdquo; in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)</li> </ul> -<h2 id="2016-01-19:3846b7fcbca60cdedafd373cb39cd76d">2016-01-19</h2> +<h2 id="2016-01-19">2016-01-19</h2> <ul> <li>Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme&rsquo;s primary color (<a href="https://github.com/ilri/DSpace/issues/157">#157</a>)</li> @@ -2053,7 +2053,7 @@ Bitstream: tést señora alimentación.pdf <li>Altmetrics&rsquo; support for Handles is kinda weak, so they can&rsquo;t associate our items with DOIs until they are tweeted or blogged, etc first.</li> </ul> -<h2 id="2016-01-21:3846b7fcbca60cdedafd373cb39cd76d">2016-01-21</h2> +<h2 id="2016-01-21">2016-01-21</h2> <ul> <li>Still waiting for my IFTTT recipe to fire, two days later</li> @@ -2065,21 +2065,21 @@ Bitstream: tést señora alimentación.pdf <li>Work around a CSS issue with long URLs in the item view (<a href="https://github.com/ilri/DSpace/issues/172">#172</a>)</li> </ul> -<h2 id="2016-01-25:3846b7fcbca60cdedafd373cb39cd76d">2016-01-25</h2> +<h2 id="2016-01-25">2016-01-25</h2> <ul> <li>Re-deploy CGSpace and DSpace Test with latest <code>5_x-prod</code> branch</li> <li>This included the social icon fixes/updates, date-based facet tweaks, reducing the feed cache age, and fixing a layout issue in XMLUI item view when an item had long URLs</li> </ul> -<h2 id="2016-01-26:3846b7fcbca60cdedafd373cb39cd76d">2016-01-26</h2> +<h2 id="2016-01-26">2016-01-26</h2> <ul> <li>Run nginx updates on CGSpace and DSpace Test (<a href="http://mailman.nginx.org/pipermail/nginx/2016-January/049700.html">1.8.1 and 1.9.10, respectively</a>)</li> <li>Run updates on DSpace Test and reboot for new Linode kernel <code>Linux 4.4.0-x86_64-linode63</code> (first update in months)</li> </ul> -<h2 id="2016-01-28:3846b7fcbca60cdedafd373cb39cd76d">2016-01-28</h2> +<h2 id="2016-01-28">2016-01-28</h2> <ul> <li>Start looking at importing some Bioversity data that had been prepared earlier this week</li> @@ -2092,7 +2092,7 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} 8</p></li> </ul> -<h2 id="2016-01-29:3846b7fcbca60cdedafd373cb39cd76d">2016-01-29</h2> +<h2 id="2016-01-29">2016-01-29</h2> <ul> <li>Add five missing center-specific subjects to XMLUI item view (<a href="https://github.com/ilri/DSpace/issues/174">#174</a>)</li> @@ -2111,13 +2111,13 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} December, 2015 - /cgspace-notes/2015-12/ + https://alanorth.github.io/cgspace-notes/2015-12/ Wed, 02 Dec 2015 13:18:00 +0300 - /cgspace-notes/2015-12/ + https://alanorth.github.io/cgspace-notes/2015-12/ -<h2 id="2015-12-02:012a628feed6d64ae1151cbd6151ccd6">2015-12-02</h2> +<h2 id="2015-12-02">2015-12-02</h2> <ul> <li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li> @@ -2198,7 +2198,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>I also filed a ticket on Atmire&rsquo;s issue tracker for the PostgreSQL stuff</li> </ul> -<h2 id="2015-12-03:012a628feed6d64ae1151cbd6151ccd6">2015-12-03</h2> +<h2 id="2015-12-03">2015-12-03</h2> <ul> <li>CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)</li> @@ -2230,7 +2230,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.854 </code></pre> -<h2 id="2015-12-05:012a628feed6d64ae1151cbd6151ccd6">2015-12-05</h2> +<h2 id="2015-12-05">2015-12-05</h2> <ul> <li>CGSpace has been up and down all day and REST API is completely unresponsive</li> @@ -2251,7 +2251,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <img src="../images/2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" /> <img src="../images/2015/12/postgres_scans_cgspace-year.png" alt="PostgreSQL scans (year)" /></p> -<h2 id="2015-12-07:012a628feed6d64ae1151cbd6151ccd6">2015-12-07</h2> +<h2 id="2015-12-07">2015-12-07</h2> <ul> <li>Atmire sent <a href="https://github.com/ilri/DSpace/pull/161">some fixes</a> to DSpace&rsquo;s REST API code that was leaving contexts open (causing the slow performance and database issues)</li> @@ -2270,7 +2270,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.497 </code></pre> -<h2 id="2015-12-08:012a628feed6d64ae1151cbd6151ccd6">2015-12-08</h2> +<h2 id="2015-12-08">2015-12-08</h2> <ul> <li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&rsquo;t as good, but it&rsquo;s much faster and causes less IO/CPU load</li> @@ -2281,13 +2281,13 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle November, 2015 - /cgspace-notes/2015-11/ + https://alanorth.github.io/cgspace-notes/2015-11/ Mon, 23 Nov 2015 17:00:57 +0300 - /cgspace-notes/2015-11/ + https://alanorth.github.io/cgspace-notes/2015-11/ -<h2 id="2015-11-22:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-22</h2> +<h2 id="2015-11-22">2015-11-22</h2> <ul> <li>CGSpace went down</li> @@ -2303,7 +2303,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li> </ul> -<h2 id="2015-11-24:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-24</h2> +<h2 id="2015-11-24">2015-11-24</h2> <ul> <li>CGSpace went down again</li> @@ -2319,7 +2319,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>For some reason the number of idle connections is very high since we upgraded to DSpace 5</li> </ul> -<h2 id="2015-11-25:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-25</h2> +<h2 id="2015-11-25">2015-11-25</h2> <ul> <li>Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config</li> @@ -2379,7 +2379,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr <li>Also deploy the nginx fixes for the <code>try_files</code> location block as well as the expires block</li> </ul> -<h2 id="2015-11-26:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-26</h2> +<h2 id="2015-11-26">2015-11-26</h2> <ul> <li>CGSpace behaving much better since changing <code>db.maxidle</code> yesterday, but still two up/down notices from monitoring this morning (better than 50!)</li> @@ -2405,7 +2405,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr <li>I reduced the pool back to the default of 30, and reduced the <code>db.maxidle</code> settings from 10 to 8</li> </ul> -<h2 id="2015-11-29:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-29</h2> +<h2 id="2015-11-29">2015-11-29</h2> <ul> <li>Still more alerts that CGSpace has been up and down all day</li> diff --git a/public/page/1/index.html b/public/page/1/index.html index f96cf8533..04196b592 100644 --- a/public/page/1/index.html +++ b/public/page/1/index.html @@ -1 +1 @@ - \ No newline at end of file +https://alanorth.github.io/cgspace-notes/ \ No newline at end of file diff --git a/public/sitemap.xml b/public/sitemap.xml index af833753c..067868458 100644 --- a/public/sitemap.xml +++ b/public/sitemap.xml @@ -2,58 +2,57 @@ - /cgspace-notes/ - 2016-08-01T15:53:00+03:00 - 0 - - - - /cgspace-notes/2016-08/ + https://alanorth.github.io/cgspace-notes/ 2016-08-01T15:53:00+03:00 - /cgspace-notes/2016-07/ + https://alanorth.github.io/cgspace-notes/2016-08/ + 2016-08-01T15:53:00+03:00 + + + + https://alanorth.github.io/cgspace-notes/2016-07/ 2016-07-01T10:53:00+03:00 - /cgspace-notes/2016-06/ + https://alanorth.github.io/cgspace-notes/2016-06/ 2016-06-01T10:53:00+03:00 - /cgspace-notes/2016-05/ + https://alanorth.github.io/cgspace-notes/2016-05/ 2016-05-01T23:06:00+03:00 - /cgspace-notes/2016-04/ + https://alanorth.github.io/cgspace-notes/2016-04/ 2016-04-04T11:06:00+03:00 - /cgspace-notes/2016-03/ + https://alanorth.github.io/cgspace-notes/2016-03/ 2016-03-02T16:50:00+03:00 - /cgspace-notes/2016-02/ + https://alanorth.github.io/cgspace-notes/2016-02/ 2016-02-05T13:18:00+03:00 - /cgspace-notes/2016-01/ + https://alanorth.github.io/cgspace-notes/2016-01/ 2016-01-13T13:18:00+03:00 - /cgspace-notes/2015-12/ + https://alanorth.github.io/cgspace-notes/2015-12/ 2015-12-02T13:18:00+03:00 - /cgspace-notes/2015-11/ + https://alanorth.github.io/cgspace-notes/2015-11/ 2015-11-23T17:00:57+03:00 diff --git a/public/tags/index.html b/public/tags/index.html index d488edddb..718ba4d2d 100644 --- a/public/tags/index.html +++ b/public/tags/index.html @@ -6,7 +6,7 @@ - + @@ -16,19 +16,19 @@ Tags · CGSpace Notes - - - - + + + + - - + +
    -

    CGSpace Notes

    +

    CGSpace Notes

    @@ -43,13 +43,13 @@
    - - @@ -64,7 +64,7 @@
    @@ -87,7 +87,7 @@ - + diff --git a/public/tags/notes/index.html b/public/tags/notes/index.html index f1f06d86c..9adc77e58 100644 --- a/public/tags/notes/index.html +++ b/public/tags/notes/index.html @@ -6,7 +6,7 @@ - + @@ -16,19 +16,19 @@ Notes · CGSpace Notes - - - - + + + + - - + +
    -

    CGSpace Notes

    +

    CGSpace Notes

    @@ -43,13 +43,13 @@
    - - @@ -64,7 +64,7 @@
    -

    August, 2016

    +

    August, 2016

    Posted on @@ -80,7 +80,7 @@ @@ -90,7 +90,7 @@
    -

    July, 2016

    +

    July, 2016

    Posted on @@ -106,7 +106,7 @@ @@ -116,7 +116,7 @@
    -

    June, 2016

    +

    June, 2016

    Posted on @@ -132,7 +132,7 @@ @@ -142,7 +142,7 @@
    -

    May, 2016

    +

    May, 2016

    Posted on @@ -158,7 +158,7 @@ @@ -168,7 +168,7 @@
    -

    April, 2016

    +

    April, 2016

    Posted on @@ -184,7 +184,7 @@ @@ -194,7 +194,7 @@
    -

    March, 2016

    +

    March, 2016

    Posted on @@ -210,7 +210,7 @@ @@ -220,7 +220,7 @@
    -

    February, 2016

    +

    February, 2016

    Posted on @@ -236,7 +236,7 @@ @@ -246,7 +246,7 @@
    -

    January, 2016

    +

    January, 2016

    Posted on @@ -262,7 +262,7 @@ @@ -272,7 +272,7 @@
    -

    December, 2015

    +

    December, 2015

    Posted on @@ -288,7 +288,7 @@ @@ -298,7 +298,7 @@
    -

    November, 2015

    +

    November, 2015

    Posted on @@ -314,7 +314,7 @@ @@ -341,7 +341,7 @@ - + diff --git a/public/tags/notes/index.xml b/public/tags/notes/index.xml index 02bf33d54..d9d8d5444 100644 --- a/public/tags/notes/index.xml +++ b/public/tags/notes/index.xml @@ -2,22 +2,22 @@ Notes on CGSpace Notes - /cgspace-notes/tags/notes/ + https://alanorth.github.io/cgspace-notes/tags/notes/ Recent content in Notes on CGSpace Notes Hugo -- gohugo.io en-us Mon, 01 Aug 2016 15:53:00 +0300 - + August, 2016 - /cgspace-notes/2016-08/ + https://alanorth.github.io/cgspace-notes/2016-08/ Mon, 01 Aug 2016 15:53:00 +0300 - /cgspace-notes/2016-08/ + https://alanorth.github.io/cgspace-notes/2016-08/ -<h2 id="2016-08-01:e34bd801c7748b7746ad4364bbdb5eb5">2016-08-01</h2> +<h2 id="2016-08-01">2016-08-01</h2> <ul> <li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li> @@ -43,7 +43,7 @@ $ git rebase -i dspace-5.5 <li>The 5.5 code now builds but doesn&rsquo;t run (white page in Tomcat)</li> </ul> -<h2 id="2016-08-02:e34bd801c7748b7746ad4364bbdb5eb5">2016-08-02</h2> +<h2 id="2016-08-02">2016-08-02</h2> <ul> <li>Ask Atmire for help with DSpace 5.5 issue</li> @@ -56,13 +56,13 @@ $ git rebase -i dspace-5.5 July, 2016 - /cgspace-notes/2016-07/ + https://alanorth.github.io/cgspace-notes/2016-07/ Fri, 01 Jul 2016 10:53:00 +0300 - /cgspace-notes/2016-07/ + https://alanorth.github.io/cgspace-notes/2016-07/ -<h2 id="2016-07-01:edc14796891c14dec087b4bb89c38aa9">2016-07-01</h2> +<h2 id="2016-07-01">2016-07-01</h2> <ul> <li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li> @@ -81,19 +81,19 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and <li>In this case the select query was showing 95 results before the update</li> </ul> -<h2 id="2016-07-02:edc14796891c14dec087b4bb89c38aa9">2016-07-02</h2> +<h2 id="2016-07-02">2016-07-02</h2> <ul> <li>Comment on DSpace Jira ticket about author lookup search text (<a href="https://jira.duraspace.org/browse/DS-2329">DS-2329</a>)</li> </ul> -<h2 id="2016-07-04:edc14796891c14dec087b4bb89c38aa9">2016-07-04</h2> +<h2 id="2016-07-04">2016-07-04</h2> <ul> <li>Seems the database&rsquo;s author authority values mean nothing without the <code>authority</code> Solr core from the host where they were created!</li> </ul> -<h2 id="2016-07-05:edc14796891c14dec087b4bb89c38aa9">2016-07-05</h2> +<h2 id="2016-07-05">2016-07-05</h2> <ul> <li>Amend <code>backup-solr.sh</code> script so it backs up the entire Solr folder</li> @@ -111,7 +111,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and <li>I will merge it to <code>5_x-prod</code></li> </ul> -<h2 id="2016-07-06:edc14796891c14dec087b4bb89c38aa9">2016-07-06</h2> +<h2 id="2016-07-06">2016-07-06</h2> <ul> <li>Delete 23 blank metadata values from CGSpace:</li> @@ -148,7 +148,7 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele <li>I then ran all server updates and rebooted the server</li> </ul> -<h2 id="2016-07-11:edc14796891c14dec087b4bb89c38aa9">2016-07-11</h2> +<h2 id="2016-07-11">2016-07-11</h2> <ul> <li>Doing some author cleanups from Peter and Abenet:</li> @@ -158,20 +158,20 @@ $ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Dele $ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu </code></pre> -<h2 id="2016-07-13:edc14796891c14dec087b4bb89c38aa9">2016-07-13</h2> +<h2 id="2016-07-13">2016-07-13</h2> <ul> <li>Run the author cleanups on CGSpace and start a full Discovery re-index</li> </ul> -<h2 id="2016-07-14:edc14796891c14dec087b4bb89c38aa9">2016-07-14</h2> +<h2 id="2016-07-14">2016-07-14</h2> <ul> <li>Test LDAP settings for new root LDAP</li> <li>Seems to work when binding as a top-level user</li> </ul> -<h2 id="2016-07-18:edc14796891c14dec087b4bb89c38aa9">2016-07-18</h2> +<h2 id="2016-07-18">2016-07-18</h2> <ul> <li>Adjust identifiers in XMLUI item display to be more prominent</li> @@ -206,14 +206,14 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error } </code></pre> -<h2 id="2016-07-21:edc14796891c14dec087b4bb89c38aa9">2016-07-21</h2> +<h2 id="2016-07-21">2016-07-21</h2> <ul> <li>Mitigate the <a href="https://httpoxy.org">HTTPoxy</a> vulnerability for Tomcat etc in nginx: <a href="https://github.com/ilri/rmg-ansible-public/pull/38">https://github.com/ilri/rmg-ansible-public/pull/38</a></li> <li>Unblock 70.32.99.142 from <code>/rest</code> as it has been blocked for a few days</li> </ul> -<h2 id="2016-07-22:edc14796891c14dec087b4bb89c38aa9">2016-07-22</h2> +<h2 id="2016-07-22">2016-07-22</h2> <ul> <li>Help Paola from CCAFS with thumbnails for batch uploads</li> @@ -267,7 +267,7 @@ index.authority.ignore-variants=true <li>After re-indexing and clearing the XMLUI cache nothing has changed</li> </ul> -<h2 id="2016-07-25:edc14796891c14dec087b4bb89c38aa9">2016-07-25</h2> +<h2 id="2016-07-25">2016-07-25</h2> <ul> <li>Trying a few more settings (plus reindex) for Discovery on DSpace Test:</li> @@ -301,7 +301,7 @@ discovery.index.authority.ignore-variants=true <li>I noticed that our backup scripts don&rsquo;t send Solr cores to S3 so I amended the script</li> </ul> -<h2 id="2016-07-31:edc14796891c14dec087b4bb89c38aa9">2016-07-31</h2> +<h2 id="2016-07-31">2016-07-31</h2> <ul> <li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li> @@ -312,13 +312,13 @@ discovery.index.authority.ignore-variants=true June, 2016 - /cgspace-notes/2016-06/ + https://alanorth.github.io/cgspace-notes/2016-06/ Wed, 01 Jun 2016 10:53:00 +0300 - /cgspace-notes/2016-06/ + https://alanorth.github.io/cgspace-notes/2016-06/ -<h2 id="2016-06-01:6783872e82b68b1517e00f494e6b6504">2016-06-01</h2> +<h2 id="2016-06-01">2016-06-01</h2> <ul> <li>Experimenting with IFPRI OAI (we want to harvest their publications)</li> @@ -339,7 +339,7 @@ UPDATE 14 <li>Fix a few minor miscellaneous issues in <code>dspace.cfg</code> (<a href="https://github.com/ilri/DSpace/pull/227">#227</a>)</li> </ul> -<h2 id="2016-06-02:6783872e82b68b1517e00f494e6b6504">2016-06-02</h2> +<h2 id="2016-06-02">2016-06-02</h2> <ul> <li>Testing the configuration and theme changes for the upcoming metadata migration and I found some issues with <code>cg.coverage.admin-unit</code></li> @@ -357,7 +357,7 @@ UPDATE 14 <li>The patch applies successfully on DSpace 5.1 so I will try it later</li> </ul> -<h2 id="2016-06-03:6783872e82b68b1517e00f494e6b6504">2016-06-03</h2> +<h2 id="2016-06-03">2016-06-03</h2> <ul> <li>Investigating the CCAFS authority issue, I exported the metadata for the Videos collection</li> @@ -430,7 +430,7 @@ UPDATE 960 <li>That would only be for the &ldquo;Browse by&rdquo; function&hellip; so we&rsquo;ll have to see what effect that has later</li> </ul> -<h2 id="2016-06-04:6783872e82b68b1517e00f494e6b6504">2016-06-04</h2> +<h2 id="2016-06-04">2016-06-04</h2> <ul> <li>Re-sync DSpace Test with CGSpace and perform test of metadata migration again</li> @@ -438,7 +438,7 @@ UPDATE 960 <li>Run all system updates and reboot CGSpace server</li> </ul> -<h2 id="2016-06-07:6783872e82b68b1517e00f494e6b6504">2016-06-07</h2> +<h2 id="2016-06-07">2016-06-07</h2> <ul> <li>Figured out how to export a list of the unique values from a metadata field ordered by count:</li> @@ -467,7 +467,7 @@ UPDATE 960 <li><p>Looks like OAI is kinda obtuse for this, and if we use ContentDM&rsquo;s API we&rsquo;ll be able to access their internal field names (rather than trying to figure out how they stuffed them into various, repeated Dublin Core fields)</p></li> </ul> -<h2 id="2016-06-08:6783872e82b68b1517e00f494e6b6504">2016-06-08</h2> +<h2 id="2016-06-08">2016-06-08</h2> <ul> <li>Discuss controlled vocabularies for ~28 fields</li> @@ -485,7 +485,7 @@ UPDATE 960 <li>File bug about <code>closed=&quot;true&quot;</code> attribute of controlled vocabularies not working: <a href="https://jira.duraspace.org/browse/DS-3238">https://jira.duraspace.org/browse/DS-3238</a></li> </ul> -<h2 id="2016-06-09:6783872e82b68b1517e00f494e6b6504">2016-06-09</h2> +<h2 id="2016-06-09">2016-06-09</h2> <ul> <li>Atmire explained that the <code>atmire.orcid.id</code> field doesn&rsquo;t exist in the schema, as it actually comes from the authority cache during XMLUI run time</li> @@ -493,7 +493,7 @@ UPDATE 960 <li>They opened a feature ticket on the DSpace tracker to ask for support of this: <a href="https://jira.duraspace.org/browse/DS-3239">https://jira.duraspace.org/browse/DS-3239</a></li> </ul> -<h2 id="2016-06-10:6783872e82b68b1517e00f494e6b6504">2016-06-10</h2> +<h2 id="2016-06-10">2016-06-10</h2> <ul> <li>Investigating authority confidences</li> @@ -518,20 +518,20 @@ UPDATE 960 <li>Merge controlled vocabulary functionality for subregions (<a href="https://github.com/ilri/DSpace/pull/238">#238</a>)</li> </ul> -<h2 id="2016-06-11:6783872e82b68b1517e00f494e6b6504">2016-06-11</h2> +<h2 id="2016-06-11">2016-06-11</h2> <ul> <li>Merge controlled vocabulary for sponsorship field (<a href="https://github.com/ilri/DSpace/pull/239">#239</a>)</li> <li>Fix character encoding issues for animal breed lookup that I merged yesterday</li> </ul> -<h2 id="2016-06-17:6783872e82b68b1517e00f494e6b6504">2016-06-17</h2> +<h2 id="2016-06-17">2016-06-17</h2> <ul> <li>Linode has free RAM upgrades for their 13th birthday so I migrated DSpace Test (4→8GB of RAM)</li> </ul> -<h2 id="2016-06-18:6783872e82b68b1517e00f494e6b6504">2016-06-18</h2> +<h2 id="2016-06-18">2016-06-18</h2> <ul> <li>Clean up titles and hints in <code>input-forms.xml</code> to use title/sentence case and a few more consistency things (<a href="https://github.com/ilri/DSpace/pull/241">#241</a>)</li> @@ -558,7 +558,7 @@ UPDATE 960 <li><p>Need to run <code>fix-metadata-values.py</code> and then <code>fix-metadata-values.py</code></p></li> </ul> -<h2 id="2016-06-20:6783872e82b68b1517e00f494e6b6504">2016-06-20</h2> +<h2 id="2016-06-20">2016-06-20</h2> <ul> <li>CGSpace&rsquo;s HTTPS certificate expired last night and I didn&rsquo;t notice, had to renew:</li> @@ -571,7 +571,7 @@ UPDATE 960 <li>I really need to fix that cron job&hellip;</li> </ul> -<h2 id="2016-06-24:6783872e82b68b1517e00f494e6b6504">2016-06-24</h2> +<h2 id="2016-06-24">2016-06-24</h2> <ul> <li>Run the replacements/deletes for <code>dc.description.sponsorship</code> (investors) on CGSpace:</li> @@ -592,7 +592,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons <li>Refine submission form labels and hints</li> </ul> -<h2 id="2016-06-28:6783872e82b68b1517e00f494e6b6504">2016-06-28</h2> +<h2 id="2016-06-28">2016-06-28</h2> <ul> <li>Testing the cleanup of <code>dc.contributor.corporate</code> with 13 deletions and 121 replacements</li> @@ -607,7 +607,7 @@ $ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.spons <li>Re-evaluate <code>dc.contributor.corporate</code> and it seems we will move it to <code>dc.contributor.author</code> as this is more in line with how editors are actually using it</li> </ul> -<h2 id="2016-06-29:6783872e82b68b1517e00f494e6b6504">2016-06-29</h2> +<h2 id="2016-06-29">2016-06-29</h2> <ul> <li>Test run of <code>migrate-fields.sh</code> with the following re-mappings:</li> @@ -646,7 +646,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <li>Start working on config changes for phase three of the metadata migrations</li> </ul> -<h2 id="2016-06-30:6783872e82b68b1517e00f494e6b6504">2016-06-30</h2> +<h2 id="2016-06-30">2016-06-30</h2> <ul> <li>Wow, there are 95 authors in the database who have &lsquo;,&rsquo; at the end of their name:</li> @@ -666,13 +666,13 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D May, 2016 - /cgspace-notes/2016-05/ + https://alanorth.github.io/cgspace-notes/2016-05/ Sun, 01 May 2016 23:06:00 +0300 - /cgspace-notes/2016-05/ + https://alanorth.github.io/cgspace-notes/2016-05/ -<h2 id="2016-05-01:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-01</h2> +<h2 id="2016-05-01">2016-05-01</h2> <ul> <li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li> @@ -697,7 +697,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <li>The owner of that application has said that the <code>NaN</code> (not a number) is an error in his code and he&rsquo;ll fix it</li> </ul> -<h2 id="2016-05-03:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-03</h2> +<h2 id="2016-05-03">2016-05-03</h2> <ul> <li>Update nginx to 1.10.x branch on CGSpace</li> @@ -706,7 +706,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D <p><img src="../images/2016/05/discovery-types.png" alt="Item type in Discovery results" /></p> -<h2 id="2016-05-06:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-06</h2> +<h2 id="2016-05-06">2016-05-06</h2> <ul> <li>DSpace Test is down, <code>catalina.out</code> has lots of messages about heap space from some time yesterday (!)</li> @@ -744,7 +744,7 @@ fi <li>Seems to work well</li> </ul> -<h2 id="2016-05-10:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-10</h2> +<h2 id="2016-05-10">2016-05-10</h2> <ul> <li>Start looking at more metadata migrations</li> @@ -759,7 +759,7 @@ fi <li>CGSpace&rsquo;s <code>dc</code> registry has 96 items, and the default DSpace one has 73.</li> </ul> -<h2 id="2016-05-11:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-11</h2> +<h2 id="2016-05-11">2016-05-11</h2> <ul> <li><p>Identify and propose the next phase of CGSpace fields to migrate:</p> @@ -792,7 +792,7 @@ fi <li>Turns out she was able to decrease the size of the PDF so we didn&rsquo;t have to do anything</li> </ul> -<h2 id="2016-05-12:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-12</h2> +<h2 id="2016-05-12">2016-05-12</h2> <ul> <li>Looks like the issue that Abenet was having a few days ago with &ldquo;Connection Reset&rdquo; in Firefox might be due to a Firefox 46 issue: <a href="https://bugzilla.mozilla.org/show_bug.cgi?id=1268775">https://bugzilla.mozilla.org/show_bug.cgi?id=1268775</a></li> @@ -816,7 +816,7 @@ fi <pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to &quot;% %&quot;; </code></pre> -<h2 id="2016-05-13:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-13</h2> +<h2 id="2016-05-13">2016-05-13</h2> <ul> <li>More theorizing about CGcore</li> @@ -830,7 +830,7 @@ fi <li>I&rsquo;ve removed <code>dc.title.jtitle</code> from the list for now because there&rsquo;s no use moving it out of DC until we know where it will go (see discussion yesterday)</li> </ul> -<h2 id="2016-05-18:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-18</h2> +<h2 id="2016-05-18">2016-05-18</h2> <ul> <li>Work on 707 CCAFS records</li> @@ -847,7 +847,7 @@ fi <li>Before importing with SAFBuilder I tested adding &ldquo;__bundle:THUMBNAIL&rdquo; to the <code>filename</code> column and it works fine</li> </ul> -<h2 id="2016-05-19:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-19</h2> +<h2 id="2016-05-19">2016-05-19</h2> <ul> <li>More quality control on <code>filename</code> field of CCAFS records to make processing in shell and SAFBuilder more reliable:</li> @@ -871,7 +871,7 @@ fi <pre><code># select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA'); </code></pre> -<h2 id="2016-05-20:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-20</h2> +<h2 id="2016-05-20">2016-05-20</h2> <ul> <li>More work on CCAFS Video and Images records</li> @@ -896,7 +896,7 @@ fi <li>Work on configuration changes for Phase 2 metadata migrations</li> </ul> -<h2 id="2016-05-23:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-23</h2> +<h2 id="2016-05-23">2016-05-23</h2> <ul> <li>Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine</li> @@ -905,7 +905,7 @@ fi <li>I will have to try later</li> </ul> -<h2 id="2016-05-30:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-30</h2> +<h2 id="2016-05-30">2016-05-30</h2> <ul> <li>Export CCAFS video and image records from DSpace Test using the migrate option (<code>-m</code>):</li> @@ -941,7 +941,7 @@ $ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA <pre><code>$ JAVA_OPTS=&quot;-Xmx1024m -Dfile.encoding=UTF-8&quot; /home/cgspace.cgiar.org/bin/dspace index-authority </code></pre> -<h2 id="2016-05-31:b7bf1a0f8f2415a40e1e11e343b04c0d">2016-05-31</h2> +<h2 id="2016-05-31">2016-05-31</h2> <ul> <li>The <code>index-authority</code> script ran over night and was finished in the morning</li> @@ -973,13 +973,13 @@ sys 0m20.540s April, 2016 - /cgspace-notes/2016-04/ + https://alanorth.github.io/cgspace-notes/2016-04/ Mon, 04 Apr 2016 11:06:00 +0300 - /cgspace-notes/2016-04/ + https://alanorth.github.io/cgspace-notes/2016-04/ -<h2 id="2016-04-04:c88be15f5b2f07c85f7742556a955e47">2016-04-04</h2> +<h2 id="2016-04-04">2016-04-04</h2> <ul> <li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li> @@ -1020,7 +1020,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290 <li>Submit pull request for Tomcat 7 limits in Ansible dspace role (<a href="https://github.com/ilri/rmg-ansible-public/pull/30">#30</a>)</li> </ul> -<h2 id="2016-04-05:c88be15f5b2f07c85f7742556a955e47">2016-04-05</h2> +<h2 id="2016-04-05">2016-04-05</h2> <ul> <li>Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don&rsquo;t need!</li> @@ -1038,7 +1038,7 @@ java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290 <li>Try to do some metadata field migrations using the Atmire batch UI (<code>dc.Species</code> → <code>cg.species</code>) but it took several hours and even missed a few records</li> </ul> -<h2 id="2016-04-06:c88be15f5b2f07c85f7742556a955e47">2016-04-06</h2> +<h2 id="2016-04-06">2016-04-06</h2> <ul> <li>A better way to move metadata on this scale is via SQL, for example <code>dc.type.output</code> → <code>dc.type</code> (their IDs in the metadatafieldregistry are 66 and 109, respectively):</li> @@ -1053,7 +1053,7 @@ UPDATE 40852 <li>Start working on metadata migrations, add 25 or so new metadata fields to CGSpace</li> </ul> -<h2 id="2016-04-07:c88be15f5b2f07c85f7742556a955e47">2016-04-07</h2> +<h2 id="2016-04-07">2016-04-07</h2> <ul> <li>Write shell script to do the migration of fields: <a href="https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b">https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b</a></li> @@ -1069,14 +1069,14 @@ UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76 UPDATE 51258 </code></pre> -<h2 id="2016-04-08:c88be15f5b2f07c85f7742556a955e47">2016-04-08</h2> +<h2 id="2016-04-08">2016-04-08</h2> <ul> <li>Discuss metadata renaming with Abenet, we decided it&rsquo;s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF</li> <li>I&rsquo;ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change</li> </ul> -<h2 id="2016-04-10:c88be15f5b2f07c85f7742556a955e47">2016-04-10</h2> +<h2 id="2016-04-10">2016-04-10</h2> <ul> <li>Looking at the DOI issue <a href="https://www.yammer.com/dspacedevelopers/#/Threads/show?threadId=678507860">reported by Leroy from CIAT a few weeks ago</a></li> @@ -1099,14 +1099,14 @@ dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and t <li>I will manually edit the <code>dc.identifier.doi</code> in <a href="https://cgspace.cgiar.org/handle/10568/72509?show=full"><sup>10568</sup>&frasl;<sub>72509</sub></a> and tweet the link, then check back in a week to see if the donut gets updated</li> </ul> -<h2 id="2016-04-11:c88be15f5b2f07c85f7742556a955e47">2016-04-11</h2> +<h2 id="2016-04-11">2016-04-11</h2> <ul> <li>The donut is already updated and shows the correct number now</li> <li>CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we&rsquo;d do it tentatively on Monday the 18th.</li> </ul> -<h2 id="2016-04-12:c88be15f5b2f07c85f7742556a955e47">2016-04-12</h2> +<h2 id="2016-04-12">2016-04-12</h2> <ul> <li>Looking at quality of WLE data (<code>cg.subject.iwmi</code>) in SQL:</li> @@ -1143,7 +1143,7 @@ DELETE 226 <li>We want to do the <code>dc.type.output</code> move on CGSpace anyways, but we should wait as it might affect other external people!</li> </ul> -<h2 id="2016-04-14:c88be15f5b2f07c85f7742556a955e47">2016-04-14</h2> +<h2 id="2016-04-14">2016-04-14</h2> <ul> <li>Communicate with Macaroni Bros again about <code>dc.type</code></li> @@ -1151,13 +1151,13 @@ DELETE 226 <li>Notify CIAT people of metadata changes (I had forgotten them last week)</li> </ul> -<h2 id="2016-04-15:c88be15f5b2f07c85f7742556a955e47">2016-04-15</h2> +<h2 id="2016-04-15">2016-04-15</h2> <ul> <li>DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code</li> </ul> -<h2 id="2016-04-18:c88be15f5b2f07c85f7742556a955e47">2016-04-18</h2> +<h2 id="2016-04-18">2016-04-18</h2> <ul> <li>Talk to CIAT people about their portal again</li> @@ -1236,7 +1236,7 @@ javax.ws.rs.WebApplicationException <li>After restarting Tomcat a few more of these errors were logged but the application was up</li> </ul> -<h2 id="2016-04-19:c88be15f5b2f07c85f7742556a955e47">2016-04-19</h2> +<h2 id="2016-04-19">2016-04-19</h2> <ul> <li>Get handles for items that are using a given metadata field, ie <code>dc.Species.animal</code> (105):</li> @@ -1292,7 +1292,7 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error <li>And then remove them from the metadata registry</li> </ul> -<h2 id="2016-04-20:c88be15f5b2f07c85f7742556a955e47">2016-04-20</h2> +<h2 id="2016-04-20">2016-04-20</h2> <ul> <li>Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server</li> @@ -1331,20 +1331,20 @@ UPDATE 46075 <li>I&rsquo;ve sent a message to Atmire asking about compatibility with DSpace 5.5</li> </ul> -<h2 id="2016-04-21:c88be15f5b2f07c85f7742556a955e47">2016-04-21</h2> +<h2 id="2016-04-21">2016-04-21</h2> <ul> <li>Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)</li> <li>Atmire responded with DSpace 5.5 compatible versions for their modules, so I&rsquo;ll start testing those in a few weeks</li> </ul> -<h2 id="2016-04-22:c88be15f5b2f07c85f7742556a955e47">2016-04-22</h2> +<h2 id="2016-04-22">2016-04-22</h2> <ul> <li>Import 95 records into <a href="https://cgspace.cgiar.org/handle/10568/42219">CTA&rsquo;s Agrodok collection</a></li> </ul> -<h2 id="2016-04-26:c88be15f5b2f07c85f7742556a955e47">2016-04-26</h2> +<h2 id="2016-04-26">2016-04-26</h2> <ul> <li>Test embargo during item upload</li> @@ -1360,7 +1360,7 @@ UPDATE 46075 </ul></li> </ul> -<h2 id="2016-04-27:c88be15f5b2f07c85f7742556a955e47">2016-04-27</h2> +<h2 id="2016-04-27">2016-04-27</h2> <ul> <li>I woke up to ten or fifteen &ldquo;up&rdquo; and &ldquo;down&rdquo; emails from the monitoring website</li> @@ -1407,14 +1407,14 @@ dspace.log.2016-04-27:7271 <li>CGSpace down, restarted tomcat and it&rsquo;s back up</li> </ul> -<h2 id="2016-04-28:c88be15f5b2f07c85f7742556a955e47">2016-04-28</h2> +<h2 id="2016-04-28">2016-04-28</h2> <ul> <li>Problems with stability again. I&rsquo;ve blocked access to <code>/rest</code> for now to see if the number of errors in the log files drop</li> <li>Later we could maybe start logging access to <code>/rest</code> and perhaps whitelist some IPs&hellip;</li> </ul> -<h2 id="2016-04-30:c88be15f5b2f07c85f7742556a955e47">2016-04-30</h2> +<h2 id="2016-04-30">2016-04-30</h2> <ul> <li>Logs for today and yesterday have zero references to this REST error, so I&rsquo;m going to open back up the REST API but log all requests</li> @@ -1434,13 +1434,13 @@ dspace.log.2016-04-27:7271 March, 2016 - /cgspace-notes/2016-03/ + https://alanorth.github.io/cgspace-notes/2016-03/ Wed, 02 Mar 2016 16:50:00 +0300 - /cgspace-notes/2016-03/ + https://alanorth.github.io/cgspace-notes/2016-03/ -<h2 id="2016-03-02:5a28ddf3ee658c043c064ccddb151717">2016-03-02</h2> +<h2 id="2016-03-02">2016-03-02</h2> <ul> <li>Looking at issues with author authorities on CGSpace</li> @@ -1448,7 +1448,7 @@ dspace.log.2016-04-27:7271 <li>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</li> </ul> -<h2 id="2016-03-07:5a28ddf3ee658c043c064ccddb151717">2016-03-07</h2> +<h2 id="2016-03-07">2016-03-07</h2> <ul> <li>Troubleshooting the issues with the slew of commits for Atmire modules in <a href="https://github.com/ilri/DSpace/pull/182">#182</a></li> @@ -1461,14 +1461,14 @@ dspace.log.2016-04-27:7271 <pre><code>Exception in thread &quot;Lucene Merge Thread #19&quot; org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device </code></pre> -<h2 id="2016-03-08:5a28ddf3ee658c043c064ccddb151717">2016-03-08</h2> +<h2 id="2016-03-08">2016-03-08</h2> <ul> <li>Add a few new filters to Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/issues/180">#180</a>)</li> <li>We had also wanted to add a few to the Content and Usage module but I have to ask the editors which ones they were</li> </ul> -<h2 id="2016-03-10:5a28ddf3ee658c043c064ccddb151717">2016-03-10</h2> +<h2 id="2016-03-10">2016-03-10</h2> <ul> <li>Disable the lucene cron job on CGSpace as it shouldn&rsquo;t be needed anymore</li> @@ -1485,7 +1485,7 @@ dspace.log.2016-04-27:7271 <li>Update documentation for Atmire modules</li> </ul> -<h2 id="2016-03-11:5a28ddf3ee658c043c064ccddb151717">2016-03-11</h2> +<h2 id="2016-03-11">2016-03-11</h2> <ul> <li>As I was looking at the CUA config I realized our Discovery config is all messed up and confusing</li> @@ -1495,7 +1495,7 @@ dspace.log.2016-04-27:7271 <li>There is still some more work to be done to remove references to old <code>outputtype</code> and <code>output</code></li> </ul> -<h2 id="2016-03-14:5a28ddf3ee658c043c064ccddb151717">2016-03-14</h2> +<h2 id="2016-03-14">2016-03-14</h2> <ul> <li>Fix some items that had invalid dates (I noticed them in the log during a re-indexing)</li> @@ -1506,13 +1506,13 @@ dspace.log.2016-04-27:7271 <p><img src="../images/2016/03/missing-xmlui-string.png" alt="Missing XMLUI string" /></p> -<h2 id="2016-03-15:5a28ddf3ee658c043c064ccddb151717">2016-03-15</h2> +<h2 id="2016-03-15">2016-03-15</h2> <ul> <li>Create simple theme for new AVCD community just for a unique Google Tracking ID (<a href="https://github.com/ilri/DSpace/pull/191">#191</a>)</li> </ul> -<h2 id="2016-03-16:5a28ddf3ee658c043c064ccddb151717">2016-03-16</h2> +<h2 id="2016-03-16">2016-03-16</h2> <ul> <li>Still having problems deploying Atmire&rsquo;s CUA updates and fixes from January!</li> @@ -1543,7 +1543,7 @@ dspace.log.2016-04-27:7271 <li>Also, <code>dc.language.iso</code> has some weird values, like &ldquo;En&rdquo; and &ldquo;English&rdquo;</li> </ul> -<h2 id="2016-03-17:5a28ddf3ee658c043c064ccddb151717">2016-03-17</h2> +<h2 id="2016-03-17">2016-03-17</h2> <ul> <li>It turns out <code>hi</code> is the ISO 639 language code for Hindi, but these should be in <code>dc.language.iso</code> instead of <code>dc.language</code></li> @@ -1553,7 +1553,7 @@ dspace.log.2016-04-27:7271 <li>The patches work fine with a clean database, so the error was caused by some mismatch in CUA versions and the database during my testing</li> </ul> -<h2 id="2016-03-18:5a28ddf3ee658c043c064ccddb151717">2016-03-18</h2> +<h2 id="2016-03-18">2016-03-18</h2> <ul> <li>Merge Atmire fixes into <code>5_x-prod</code></li> @@ -1580,7 +1580,7 @@ dspace.log.2016-04-27:7271 <li>Also, it looks like adding <code>-sharpen 0x1.0</code> really improves the quality of the image for only a few KB</li> </ul> -<h2 id="2016-03-21:5a28ddf3ee658c043c064ccddb151717">2016-03-21</h2> +<h2 id="2016-03-21">2016-03-21</h2> <ul> <li>Fix 66 site errors in Google&rsquo;s webmaster tools</li> @@ -1620,13 +1620,13 @@ dspace.log.2016-04-27:7271 <li>Deploy Let&rsquo;s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks</li> </ul> -<h2 id="2016-03-22:5a28ddf3ee658c043c064ccddb151717">2016-03-22</h2> +<h2 id="2016-03-22">2016-03-22</h2> <ul> <li>Merge robots.txt patch and disallow indexing of browse pages as our sitemap is consumed correctly (<a href="https://github.com/ilri/DSpace/issues/198">#198</a>)</li> </ul> -<h2 id="2016-03-23:5a28ddf3ee658c043c064ccddb151717">2016-03-23</h2> +<h2 id="2016-03-23">2016-03-23</h2> <ul> <li>Abenet is having problems saving group memberships, and she gets this error: <a href="https://gist.github.com/alanorth/87281c061c2de57b773e">https://gist.github.com/alanorth/87281c061c2de57b773e</a></li> @@ -1640,14 +1640,14 @@ dspace.log.2016-04-27:7271 <li>Looks to be an issue with the Atmire modules, I&rsquo;ve submitted a ticket to their tracker.</li> </ul> -<h2 id="2016-03-24:5a28ddf3ee658c043c064ccddb151717">2016-03-24</h2> +<h2 id="2016-03-24">2016-03-24</h2> <ul> <li>Atmire sent a patch for the group saving issue: <a href="https://github.com/ilri/DSpace/pull/201">https://github.com/ilri/DSpace/pull/201</a></li> <li>I tested it locally and it works, so I merged it to <code>5_x-prod</code> and will deploy on CGSpace this week</li> </ul> -<h2 id="2016-03-25:5a28ddf3ee658c043c064ccddb151717">2016-03-25</h2> +<h2 id="2016-03-25">2016-03-25</h2> <ul> <li>Having problems with Listings and Reports, seems to be caused by a rogue reference to <code>dc.type.output</code></li> @@ -1655,7 +1655,7 @@ dspace.log.2016-04-27:7271 <li>Commenting out the line works, but I haven&rsquo;t figured out the proper syntax for referring to <code>dc.type.*</code></li> </ul> -<h2 id="2016-03-28:5a28ddf3ee658c043c064ccddb151717">2016-03-28</h2> +<h2 id="2016-03-28">2016-03-28</h2> <ul> <li>Look into enabling the embargo during item submission, see: <a href="https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess">https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess</a></li> @@ -1669,7 +1669,7 @@ dspace.log.2016-04-27:7271 <li>Deploy robots.txt fix, embargo for item submissions, and listings and reports fix on CGSpace</li> </ul> -<h2 id="2016-03-29:5a28ddf3ee658c043c064ccddb151717">2016-03-29</h2> +<h2 id="2016-03-29">2016-03-29</h2> <ul> <li>Skype meeting with Peter and Addis team to discuss metadata changes for Dublin Core, CGcore, and CGSpace-specific fields</li> @@ -1682,13 +1682,13 @@ dspace.log.2016-04-27:7271 February, 2016 - /cgspace-notes/2016-02/ + https://alanorth.github.io/cgspace-notes/2016-02/ Fri, 05 Feb 2016 13:18:00 +0300 - /cgspace-notes/2016-02/ + https://alanorth.github.io/cgspace-notes/2016-02/ -<h2 id="2016-02-05:124a59adbaa8ef13e1518d003fc03981">2016-02-05</h2> +<h2 id="2016-02-05">2016-02-05</h2> <ul> <li>Looking at some DAGRIS data for Abenet Yabowork</li> @@ -1703,7 +1703,7 @@ dspace.log.2016-04-27:7271 <li>Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;</li> </ul> -<h2 id="2016-02-06:124a59adbaa8ef13e1518d003fc03981">2016-02-06</h2> +<h2 id="2016-02-06">2016-02-06</h2> <ul> <li>Found a way to get items with null/empty metadata values from SQL</li> @@ -1744,7 +1744,7 @@ DELETE 25 <li>Process the empty countries on CGSpace</li> </ul> -<h2 id="2016-02-07:124a59adbaa8ef13e1518d003fc03981">2016-02-07</h2> +<h2 id="2016-02-07">2016-02-07</h2> <ul> <li>Working on cleaning up Abenet&rsquo;s DAGRIS data with OpenRefine</li> @@ -1798,7 +1798,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start <pre><code>$ ~/dspace/bin/dspace index-discovery -b </code></pre> -<h2 id="2016-02-08:124a59adbaa8ef13e1518d003fc03981">2016-02-08</h2> +<h2 id="2016-02-08">2016-02-08</h2> <ul> <li>Finish cleaning up and importing ~400 DAGRIS items into CGSpace</li> @@ -1808,7 +1808,7 @@ $ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start <p><img src="../images/2016/02/submit-button-ilri.png" alt="ILRI submission buttons" /> <img src="../images/2016/02/submit-button-drylands.png" alt="Drylands submission buttons" /></p> -<h2 id="2016-02-09:124a59adbaa8ef13e1518d003fc03981">2016-02-09</h2> +<h2 id="2016-02-09">2016-02-09</h2> <ul> <li>Re-sync DSpace Test with CGSpace</li> @@ -1859,7 +1859,7 @@ Swap: 255 57 198 <li>So I&rsquo;ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)</li> </ul> -<h2 id="2016-02-11:124a59adbaa8ef13e1518d003fc03981">2016-02-11</h2> +<h2 id="2016-02-11">2016-02-11</h2> <ul> <li>Massaging some CIAT data in OpenRefine</li> @@ -1883,7 +1883,7 @@ Processing 64195.pdf &gt; Creating thumbnail for 64195.pdf </code></pre> -<h2 id="2016-02-12:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2> +<h2 id="2016-02-12">2016-02-12</h2> <ul> <li>Looking at CIAT&rsquo;s records again, there are some problems with a dozen or so files (out of 1200)</li> @@ -1894,7 +1894,7 @@ Processing 64195.pdf <li>Also, I&rsquo;m not sure if we import these items, will be remove the <code>dc.identifier.url</code> field from the records?</li> </ul> -<h2 id="2016-02-12-1:124a59adbaa8ef13e1518d003fc03981">2016-02-12</h2> +<h2 id="2016-02-12-1">2016-02-12</h2> <ul> <li>Looking at CIAT&rsquo;s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I&rsquo;m not sure if we can use those</li> @@ -1919,7 +1919,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>They will be deployed on CGSpace the next time I re-deploy</li> </ul> -<h2 id="2016-02-16:124a59adbaa8ef13e1518d003fc03981">2016-02-16</h2> +<h2 id="2016-02-16">2016-02-16</h2> <ul> <li>Turns out OpenRefine has an unescape function!</li> @@ -1938,7 +1938,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>This also works for records that have multiple URLs (separated by &ldquo;||&rdquo;)</li> </ul> -<h2 id="2016-02-17:124a59adbaa8ef13e1518d003fc03981">2016-02-17</h2> +<h2 id="2016-02-17">2016-02-17</h2> <ul> <li>Re-deploy CGSpace, run all system updates, and reboot</li> @@ -1947,7 +1947,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>Need to re-process the filename column to replace multiple underscores with one: <code>value.replace(/_{2,}/, &quot;_&quot;)</code></li> </ul> -<h2 id="2016-02-20:124a59adbaa8ef13e1518d003fc03981">2016-02-20</h2> +<h2 id="2016-02-20">2016-02-20</h2> <ul> <li>Turns out the &ldquo;bug&rdquo; in SAFBuilder isn&rsquo;t a bug, it&rsquo;s a feature that allows you to encode extra information like the destintion bundle in the filename</li> @@ -1962,7 +1962,7 @@ CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_ <li>Useful custom text facet for URLs ending with &ldquo;.pdf&rdquo;: <code>value.endsWith(&quot;.pdf&quot;)</code></li> </ul> -<h2 id="2016-02-22:124a59adbaa8ef13e1518d003fc03981">2016-02-22</h2> +<h2 id="2016-02-22">2016-02-22</h2> <ul> <li>To change Spanish accents to ASCII in OpenRefine:</li> @@ -1987,7 +1987,7 @@ Bitstream: tést señora alimentación.pdf <li>Running the SAFBuilder on Mac OS X works if you&rsquo;re going to import the resulting bundle on Mac OS X, but if your DSpace is running on Linux you need to run the SAFBuilder there where the filesystem&rsquo;s encoding matches</li> </ul> -<h2 id="2016-02-29:124a59adbaa8ef13e1518d003fc03981">2016-02-29</h2> +<h2 id="2016-02-29">2016-02-29</h2> <ul> <li>Got notified by some CIFOR colleagues that the Google Scholar team had contacted them about CGSpace&rsquo;s incorrect ordering of authors in Google Scholar metadata</li> @@ -2016,13 +2016,13 @@ Bitstream: tést señora alimentación.pdf January, 2016 - /cgspace-notes/2016-01/ + https://alanorth.github.io/cgspace-notes/2016-01/ Wed, 13 Jan 2016 13:18:00 +0300 - /cgspace-notes/2016-01/ + https://alanorth.github.io/cgspace-notes/2016-01/ -<h2 id="2016-01-13:3846b7fcbca60cdedafd373cb39cd76d">2016-01-13</h2> +<h2 id="2016-01-13">2016-01-13</h2> <ul> <li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li> @@ -2030,20 +2030,20 @@ Bitstream: tést señora alimentación.pdf <li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li> </ul> -<h2 id="2016-01-14:3846b7fcbca60cdedafd373cb39cd76d">2016-01-14</h2> +<h2 id="2016-01-14">2016-01-14</h2> <ul> <li>Update CCAFS project identifiers in input-forms.xml</li> <li>Run system updates and restart the server</li> </ul> -<h2 id="2016-01-18:3846b7fcbca60cdedafd373cb39cd76d">2016-01-18</h2> +<h2 id="2016-01-18">2016-01-18</h2> <ul> <li>Change &ldquo;Extension material&rdquo; to &ldquo;Extension Material&rdquo; in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)</li> </ul> -<h2 id="2016-01-19:3846b7fcbca60cdedafd373cb39cd76d">2016-01-19</h2> +<h2 id="2016-01-19">2016-01-19</h2> <ul> <li>Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme&rsquo;s primary color (<a href="https://github.com/ilri/DSpace/issues/157">#157</a>)</li> @@ -2053,7 +2053,7 @@ Bitstream: tést señora alimentación.pdf <li>Altmetrics&rsquo; support for Handles is kinda weak, so they can&rsquo;t associate our items with DOIs until they are tweeted or blogged, etc first.</li> </ul> -<h2 id="2016-01-21:3846b7fcbca60cdedafd373cb39cd76d">2016-01-21</h2> +<h2 id="2016-01-21">2016-01-21</h2> <ul> <li>Still waiting for my IFTTT recipe to fire, two days later</li> @@ -2065,21 +2065,21 @@ Bitstream: tést señora alimentación.pdf <li>Work around a CSS issue with long URLs in the item view (<a href="https://github.com/ilri/DSpace/issues/172">#172</a>)</li> </ul> -<h2 id="2016-01-25:3846b7fcbca60cdedafd373cb39cd76d">2016-01-25</h2> +<h2 id="2016-01-25">2016-01-25</h2> <ul> <li>Re-deploy CGSpace and DSpace Test with latest <code>5_x-prod</code> branch</li> <li>This included the social icon fixes/updates, date-based facet tweaks, reducing the feed cache age, and fixing a layout issue in XMLUI item view when an item had long URLs</li> </ul> -<h2 id="2016-01-26:3846b7fcbca60cdedafd373cb39cd76d">2016-01-26</h2> +<h2 id="2016-01-26">2016-01-26</h2> <ul> <li>Run nginx updates on CGSpace and DSpace Test (<a href="http://mailman.nginx.org/pipermail/nginx/2016-January/049700.html">1.8.1 and 1.9.10, respectively</a>)</li> <li>Run updates on DSpace Test and reboot for new Linode kernel <code>Linux 4.4.0-x86_64-linode63</code> (first update in months)</li> </ul> -<h2 id="2016-01-28:3846b7fcbca60cdedafd373cb39cd76d">2016-01-28</h2> +<h2 id="2016-01-28">2016-01-28</h2> <ul> <li>Start looking at importing some Bioversity data that had been prepared earlier this week</li> @@ -2092,7 +2092,7 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} 8</p></li> </ul> -<h2 id="2016-01-29:3846b7fcbca60cdedafd373cb39cd76d">2016-01-29</h2> +<h2 id="2016-01-29">2016-01-29</h2> <ul> <li>Add five missing center-specific subjects to XMLUI item view (<a href="https://github.com/ilri/DSpace/issues/174">#174</a>)</li> @@ -2111,13 +2111,13 @@ $ find SimpleArchiveForBio/ -iname &ldquo;*.pdf&rdquo; -exec basename {} December, 2015 - /cgspace-notes/2015-12/ + https://alanorth.github.io/cgspace-notes/2015-12/ Wed, 02 Dec 2015 13:18:00 +0300 - /cgspace-notes/2015-12/ + https://alanorth.github.io/cgspace-notes/2015-12/ -<h2 id="2015-12-02:012a628feed6d64ae1151cbd6151ccd6">2015-12-02</h2> +<h2 id="2015-12-02">2015-12-02</h2> <ul> <li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li> @@ -2198,7 +2198,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>I also filed a ticket on Atmire&rsquo;s issue tracker for the PostgreSQL stuff</li> </ul> -<h2 id="2015-12-03:012a628feed6d64ae1151cbd6151ccd6">2015-12-03</h2> +<h2 id="2015-12-03">2015-12-03</h2> <ul> <li>CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)</li> @@ -2230,7 +2230,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.854 </code></pre> -<h2 id="2015-12-05:012a628feed6d64ae1151cbd6151ccd6">2015-12-05</h2> +<h2 id="2015-12-05">2015-12-05</h2> <ul> <li>CGSpace has been up and down all day and REST API is completely unresponsive</li> @@ -2251,7 +2251,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <img src="../images/2015/12/postgres_locks_cgspace-year.png" alt="PostgreSQL locks (year)" /> <img src="../images/2015/12/postgres_scans_cgspace-year.png" alt="PostgreSQL scans (year)" /></p> -<h2 id="2015-12-07:012a628feed6d64ae1151cbd6151ccd6">2015-12-07</h2> +<h2 id="2015-12-07">2015-12-07</h2> <ul> <li>Atmire sent <a href="https://github.com/ilri/DSpace/pull/161">some fixes</a> to DSpace&rsquo;s REST API code that was leaving contexts open (causing the slow performance and database issues)</li> @@ -2270,7 +2270,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle 0.497 </code></pre> -<h2 id="2015-12-08:012a628feed6d64ae1151cbd6151ccd6">2015-12-08</h2> +<h2 id="2015-12-08">2015-12-08</h2> <ul> <li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn&rsquo;t as good, but it&rsquo;s much faster and causes less IO/CPU load</li> @@ -2281,13 +2281,13 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle November, 2015 - /cgspace-notes/2015-11/ + https://alanorth.github.io/cgspace-notes/2015-11/ Mon, 23 Nov 2015 17:00:57 +0300 - /cgspace-notes/2015-11/ + https://alanorth.github.io/cgspace-notes/2015-11/ -<h2 id="2015-11-22:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-22</h2> +<h2 id="2015-11-22">2015-11-22</h2> <ul> <li>CGSpace went down</li> @@ -2303,7 +2303,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li> </ul> -<h2 id="2015-11-24:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-24</h2> +<h2 id="2015-11-24">2015-11-24</h2> <ul> <li>CGSpace went down again</li> @@ -2319,7 +2319,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle <li>For some reason the number of idle connections is very high since we upgraded to DSpace 5</li> </ul> -<h2 id="2015-11-25:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-25</h2> +<h2 id="2015-11-25">2015-11-25</h2> <ul> <li>Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config</li> @@ -2379,7 +2379,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr <li>Also deploy the nginx fixes for the <code>try_files</code> location block as well as the expires block</li> </ul> -<h2 id="2015-11-26:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-26</h2> +<h2 id="2015-11-26">2015-11-26</h2> <ul> <li>CGSpace behaving much better since changing <code>db.maxidle</code> yesterday, but still two up/down notices from monitoring this morning (better than 50!)</li> @@ -2405,7 +2405,7 @@ datid | datname | pid | usesysid | usename | application_name | client_addr <li>I reduced the pool back to the default of 30, and reduced the <code>db.maxidle</code> settings from 10 to 8</li> </ul> -<h2 id="2015-11-29:3d03b850f8126f80d8144c2e17ea0ae7">2015-11-29</h2> +<h2 id="2015-11-29">2015-11-29</h2> <ul> <li>Still more alerts that CGSpace has been up and down all day</li>