Add notes for 2019-08-08

2024-11-22 06:35:03 +01:00 · 2019-08-08 18:10:44 +03:00 · 2019-08-08 18:10:44 +03:00 · 0beed6b6df
commit 0beed6b6df
parent 34e488a327
76 changed files with 307 additions and 217 deletions
--- a/content/posts/2019-08.md
+++ b/content/posts/2019-08.md
@ -71,4 +71,42 @@ or(
  - After removing the two duplicates there are now 1427 records
  - Fix one invalid ISSN: 1020-2002→1020-3362

+## 2019-08-07
+
+- Daniel Haile-Michael asked about using a logical OR with the DSpace OpenSearch, but I looked in the DSpace manual and it does not seem to be possible
+
+## 2019-08-08
+
+- Moayad noticed that the HTTPS certificate expired on the AReS dev server (linode20)
+  - The first problem was that there is a Docker container listening on port 80, so it conflicts with the ACME http-01 validation
+  - The second problem was that we only allow access to port 80 from localhost
+  - I adjusted the `renew-letsencrypt` systemd service so it stops/starts the Docker container and firewall:
+
+```
+# /opt/certbot-auto renew --standalone --pre-hook "/usr/bin/docker stop angular_nginx; /bin/systemctl stop firewalld" --post-hook "/bin/systemctl start firewalld; /usr/bin/docker start angular_nginx"
+```
+
+- It is important that the firewall starts back up before the Docker container or else Docker will complain about missing iptables chains
+- Also, I updated to the latest TLS Intermediate settings as appropriate for Ubuntu 18.04's [OpenSSL 1.1.0g with nginx 1.16.0](https://ssl-config.mozilla.org/#server=nginx&server-version=1.16.0&config=intermediate&openssl-version=1.1.0g&hsts=false&ocsp=false)
+- Run all system updates on AReS dev server (linode20) and reboot it
+- Get a list of all PDFs from the Bioversity migration that fail to download and save them so I can try again with a different path in the URL:
+
+```
+$ ./generate-thumbnails.py -i /tmp/2019-08-05-Bioversity-Migration.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs.txt
+$ grep -B1 "Download failed" /tmp/2019-08-08-download-pdfs.txt | grep "Downloading" | sed -e 's/> Downloading //' -e 's/\.\.\.//' | sed -r 's/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g' | csvcut -H -c 1,1 > /tmp/user-upload.csv
+$ ./generate-thumbnails.py -i /tmp/user-upload.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs2.txt
+$ grep -B1 "Download failed" /tmp/2019-08-08-download-pdfs2.txt | grep "Downloading" | sed -e 's/> Downloading //' -e 's/\.\.\.//' | sed -r 's/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g' | csvcut -H -c 1,1 > /tmp/user-upload2.csv
+$ ./generate-thumbnails.py -i /tmp/user-upload2.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs3.txt
+```
+
+- (the weird sed regex removes color codes, because my generate-thumbnails script prints pretty colors)
+- Some PDFs are uploaded in different paths so I have to try a few times to get them all:
+  - `/fileadmin/_migrated/uploads/tx_news/`
+  - `/fileadmin/user_upload/online_library/publications/pdfs/`
+  - `/fileadmin/user_upload/`
+
+- Even so, there are still 52 items with incorrect filenames, so I can't derive their PDF URLs...
+  - For example, `Wild_cherry_Prunus_avium_859.pdf` is here (with double underscore): https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/Wild_cherry__Prunus_avium__859.pdf
+- I will proceed with a metadata-only upload first and then let them know about the missing PDFs
+
 <!-- vim: set sw=2 ts=2: -->
--- a/docs/2015-11/index.html
+++ b/docs/2015-11/index.html
@ -20,8 +20,8 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-11/" />
-<meta property="article:published_time" content="2015-11-23T17:00:57&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2015-11-23T17:00:57+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2015"/>
@ -37,7 +37,7 @@ $ psql -c &#39;SELECT * from pg_stat_activity;&#39; | grep idle | grep -c cgspac
 78

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2015-12/index.html
+++ b/docs/2015-12/index.html
@ -20,8 +20,8 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2015-12/" />
-<meta property="article:published_time" content="2015-12-02T13:18:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2015-12-02T13:18:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="December, 2015"/>
@ -37,7 +37,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less
 -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-01/index.html
+++ b/docs/2016-01/index.html
@ -15,8 +15,8 @@ Update GitHub wiki for documentation of maintenance tasks.
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-01/" />
-<meta property="article:published_time" content="2016-01-13T13:18:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-01-13T13:18:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="January, 2016"/>
@ -27,7 +27,7 @@ Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_
 I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
 Update GitHub wiki for documentation of maintenance tasks.
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-02/index.html
+++ b/docs/2016-02/index.html
@ -22,8 +22,8 @@ Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&r
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-02/" />
-<meta property="article:published_time" content="2016-02-05T13:18:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-02-05T13:18:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="February, 2016"/>
@ -41,7 +41,7 @@ I noticed we have a very interesting list of countries on CGSpace:
 Not only are there 49,000 countries, we have some blanks (25)&hellip;
 Also, lots of things like &ldquo;COTE D`LVOIRE&rdquo; and &ldquo;COTE D IVOIRE&rdquo;
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-03/index.html
+++ b/docs/2016-03/index.html
@ -15,8 +15,8 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-03/" />
-<meta property="article:published_time" content="2016-03-02T16:50:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-03-02T16:50:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="March, 2016"/>
@ -27,7 +27,7 @@ Looking at issues with author authorities on CGSpace
 For some reason we still have the index-lucene-update cron job active on CGSpace, but I&rsquo;m pretty sure we don&rsquo;t need it as of the latest few versions of Atmire&rsquo;s Listings and Reports module
 Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-04/index.html
+++ b/docs/2016-04/index.html
@ -17,8 +17,8 @@ Also, I noticed the checker log has some errors we should pay attention to:
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-04/" />
-<meta property="article:published_time" content="2016-04-04T11:06:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-04-04T11:06:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2016"/>
@ -31,7 +31,7 @@ After running DSpace for over five years I&rsquo;ve never needed to look in any
 This will save us a few gigs of backup space we&rsquo;re paying for on S3
 Also, I noticed the checker log has some errors we should pay attention to:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-05/index.html
+++ b/docs/2016-05/index.html
@ -20,8 +20,8 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-05/" />
-<meta property="article:published_time" content="2016-05-01T23:06:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-05-01T23:06:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2016"/>
@ -37,7 +37,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period!
 3168

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-06/index.html
+++ b/docs/2016-06/index.html
@ -18,8 +18,8 @@ Working on second phase of metadata migration, looks like this will work for mov
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-06/" />
-<meta property="article:published_time" content="2016-06-01T10:53:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-06-01T10:53:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2016"/>
@ -33,7 +33,7 @@ This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRec
 You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
 Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-07/index.html
+++ b/docs/2016-07/index.html
@ -25,8 +25,8 @@ In this case the select query was showing 95 results before the update
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-07/" />
-<meta property="article:published_time" content="2016-07-01T10:53:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-07-01T10:53:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="July, 2016"/>
@ -47,7 +47,7 @@ text_value

 In this case the select query was showing 95 results before the update
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-08/index.html
+++ b/docs/2016-08/index.html
@ -24,8 +24,8 @@ $ git rebase -i dspace-5.5
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-08/" />
-<meta property="article:published_time" content="2016-08-01T15:53:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-08-01T15:53:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="August, 2016"/>
@ -45,7 +45,7 @@ $ git reset --hard ilri/5_x-prod
 $ git rebase -i dspace-5.5

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-09/index.html
+++ b/docs/2016-09/index.html
@ -20,8 +20,8 @@ $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=or
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-09/" />
-<meta property="article:published_time" content="2016-09-01T15:53:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-09-01T15:53:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="September, 2016"/>
@ -37,7 +37,7 @@ It looks like we might be able to use OUs now, instead of DCs:
 $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b &quot;dc=cgiarad,dc=org&quot; -D &quot;admigration1@cgiarad.org&quot; -W &quot;(sAMAccountName=admigration1)&quot;

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-10/index.html
+++ b/docs/2016-10/index.html
@ -24,8 +24,8 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-10/" />
-<meta property="article:published_time" content="2016-10-03T15:53:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-04-04T16:25:57&#43;03:00"/>
+<meta property="article:published_time" content="2016-10-03T15:53:00+03:00" />
+<meta property="article:modified_time" content="2018-04-04T16:25:57+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="October, 2016"/>
@ -45,7 +45,7 @@ I exported a random item&rsquo;s metadata as CSV, deleted all columns except id
 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-11/index.html
+++ b/docs/2016-11/index.html
@ -15,8 +15,8 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-11/" />
-<meta property="article:published_time" content="2016-11-01T09:21:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-11-01T09:21:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2016"/>
@ -27,7 +27,7 @@ Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module


 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2016-12/index.html
+++ b/docs/2016-12/index.html
@ -28,8 +28,8 @@ Another worrying error from dspace.log is:
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-12/" />
-<meta property="article:published_time" content="2016-12-02T10:43:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2016-12-02T10:43:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="December, 2016"/>
@ -53,7 +53,7 @@ I&rsquo;ve raised a ticket with Atmire to ask

 Another worrying error from dspace.log is:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-01/index.html
+++ b/docs/2017-01/index.html
@ -15,8 +15,8 @@ I asked on the dspace-tech mailing list because it seems to be broken, and actua
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-01/" />
-<meta property="article:published_time" content="2017-01-02T10:43:00&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-01-02T10:43:00+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="January, 2017"/>
@ -27,7 +27,7 @@ I checked to see if the Solr sharding task that is supposed to run on January 1s
 I tested on DSpace Test as well and it doesn&rsquo;t work there either
 I asked on the dspace-tech mailing list because it seems to be broken, and actually now I&rsquo;m not sure if we&rsquo;ve ever had the sharding task run successfully over all these years
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-02/index.html
+++ b/docs/2017-02/index.html
@ -28,8 +28,8 @@ Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-02/" />
-<meta property="article:published_time" content="2017-02-07T07:04:52-08:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-02-07T07:04:52-08:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="February, 2017"/>
@ -53,7 +53,7 @@ Create issue on GitHub to track the addition of CCAFS Phase II project tags (#30

 Looks like we&rsquo;ll be using cg.identifier.ccafsprojectpii as the field name
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-03/index.html
+++ b/docs/2017-03/index.html
@ -32,8 +32,8 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-03/" />
-<meta property="article:published_time" content="2017-03-01T17:08:52&#43;02:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-03-01T17:08:52+02:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="March, 2017"/>
@ -61,7 +61,7 @@ $ identify ~/Desktop/alc_contrastes_desafios.jpg
 /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600&#43;0&#43;0 8-bit CMYK 168KB 0.000u 0:00.000

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-04/index.html
+++ b/docs/2017-04/index.html
@ -25,8 +25,8 @@ $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Th
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-04/" />
-<meta property="article:published_time" content="2017-04-02T17:08:52&#43;02:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-04-02T17:08:52+02:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2017"/>
@ -47,7 +47,7 @@ Testing the CMYK patch on a collection with 650 items:
 $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p &quot;ImageMagick PDF Thumbnail&quot; -v &gt;&amp; /tmp/filter-media-cmyk.txt

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-05/index.html
+++ b/docs/2017-05/index.html
@ -9,13 +9,13 @@
 <meta property="og:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace." />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-05/" />
-<meta property="article:published_time" content="2017-05-01T16:21:52&#43;02:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-05-01T16:21:52+02:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2017"/>
 <meta name="twitter:description" content="2017-05-01  ICARDA apparently started working on CG Core on their MEL repository They have done a few cg.* fields, but not very consistent and even copy some of CGSpace items:  https://mel.cgiar.org/xmlui/handle/20.500.11766/6911?show=full https://cgspace.cgiar.org/handle/10568/73683   2017-05-02  Atmire got back about the Workflow Statistics issue, and apparently it&rsquo;s a bug in the CUA module so they will send us a pull request  2017-05-04  Sync DSpace Test with database and assetstore from CGSpace Re-deploy DSpace Test with Atmire&rsquo;s CUA patch for workflow statistics, run system updates, and restart the server Now I can see the workflow statistics and am able to select users, but everything returns 0 items Megan says there are still some mapped items are not appearing since last week, so I forced a full index-discovery -b Need to remember to check if the collection has more items (currently 39 on CGSpace, but 118 on the freshly reindexed DSPace Test) tomorrow: https://cgspace."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-06/index.html
+++ b/docs/2017-06/index.html
@ -9,13 +9,13 @@
 <meta property="og:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg." />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-06/" />
-<meta property="article:published_time" content="2017-06-01T10:14:52&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-06-01T10:14:52+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2017"/>
 <meta name="twitter:description" content="2017-06-01  After discussion with WLE and CGSpace content people, we decided to just add one metadata field for the WLE Research Themes The cg.identifier.wletheme field will be used for both Phase I and Phase II Research Themes Then we&rsquo;ll create a new sub-community for Phase II and create collections for the research themes there The current &ldquo;Research Themes&rdquo; community will be renamed to &ldquo;WLE Phase I Research Themes&rdquo; Tagged all items in the current Phase I collections with their appropriate themes Create pull request to add Phase II research themes to the submission form: #328 Add cg."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-07/index.html
+++ b/docs/2017-07/index.html
@ -21,8 +21,8 @@ We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-07/" />
-<meta property="article:published_time" content="2017-07-01T18:03:52&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-07-01T18:03:52+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="July, 2017"/>
@ -39,7 +39,7 @@ Merge changes for WLE Phase II theme rename (#329)
 Looking at extracting the metadata registries from ICARDA&rsquo;s MEL DSpace database so we can compare fields with CGSpace
 We can use PostgreSQL&rsquo;s extended output format (-x) plus sed to format the output into quasi XML:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-08/index.html
+++ b/docs/2017-08/index.html
@ -31,8 +31,8 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-08/" />
-<meta property="article:published_time" content="2017-08-01T11:51:52&#43;03:00"/>
-<meta property="article:modified_time" content="2019-03-04T02:43:22&#43;02:00"/>
+<meta property="article:published_time" content="2017-08-01T11:51:52+03:00" />
+<meta property="article:modified_time" content="2019-03-04T02:43:22+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="August, 2017"/>
@ -59,7 +59,7 @@ This was due to newline characters in the dc.description.abstract column, which
 I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
 Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-09/index.html
+++ b/docs/2017-09/index.html
@ -19,8 +19,8 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-09/" />
-<meta property="article:published_time" content="2017-09-07T16:54:52&#43;07:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-09-07T16:54:52+07:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="September, 2017"/>
@ -35,7 +35,7 @@ Linode sent an alert that CGSpace (linode18) was using 261% CPU for the past two

 Ask Sisay to clean up the WLE approvers a bit, as Marianne&rsquo;s user account is both in the approvers step as well as the group
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-10/index.html
+++ b/docs/2017-10/index.html
@ -20,8 +20,8 @@ Add Katherine Lutz to the groups for content submission and edit steps of the CG
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-10/" />
-<meta property="article:published_time" content="2017-10-01T08:07:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-10-01T08:07:54+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="October, 2017"/>
@ -37,7 +37,7 @@ There appears to be a pattern but I&rsquo;ll have to look a bit closer and try t

 Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-11/index.html
+++ b/docs/2017-11/index.html
@ -29,8 +29,8 @@ COPY 54701
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-11/" />
-<meta property="article:published_time" content="2017-11-02T09:37:54&#43;02:00"/>
-<meta property="article:modified_time" content="2018-04-10T08:27:55&#43;03:00"/>
+<meta property="article:published_time" content="2017-11-02T09:37:54+02:00" />
+<meta property="article:modified_time" content="2018-04-10T08:27:55+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2017"/>
@ -55,7 +55,7 @@ dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue
 COPY 54701

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2017-12/index.html
+++ b/docs/2017-12/index.html
@ -16,8 +16,8 @@ The list of connections to XMLUI and REST API for today:
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2017-12/" />
-<meta property="article:published_time" content="2017-12-01T13:53:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-12-01T13:53:54+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="December, 2017"/>
@ -29,7 +29,7 @@ The logs say &ldquo;Timeout waiting for idle object&rdquo;
 PostgreSQL activity says there are 115 connections currently
 The list of connections to XMLUI and REST API for today:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-01/index.html
+++ b/docs/2018-01/index.html
@ -83,8 +83,8 @@ Danny wrote to ask for help renewing the wildcard ilri.org certificate and I adv
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-01/" />
-<meta property="article:published_time" content="2018-01-02T08:35:54-08:00"/>
-<meta property="article:modified_time" content="2018-03-28T09:48:08&#43;03:00"/>
+<meta property="article:published_time" content="2018-01-02T08:35:54-08:00" />
+<meta property="article:modified_time" content="2018-03-28T09:48:08+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="January, 2018"/>
@ -163,7 +163,7 @@ dspace.log.2018-01-02:34

 Danny wrote to ask for help renewing the wildcard ilri.org certificate and I advised that we should probably use Let&rsquo;s Encrypt if it&rsquo;s just a handful of domains
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-02/index.html
+++ b/docs/2018-02/index.html
@ -16,8 +16,8 @@ I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-pl
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-02/" />
-<meta property="article:published_time" content="2018-02-01T16:28:54&#43;02:00"/>
-<meta property="article:modified_time" content="2018-08-19T18:42:55&#43;03:00"/>
+<meta property="article:published_time" content="2018-02-01T16:28:54+02:00" />
+<meta property="article:modified_time" content="2018-08-19T18:42:55+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="February, 2018"/>
@ -29,7 +29,7 @@ We don&rsquo;t need to distinguish between internal and external works, so that
 Yesterday I figured out how to monitor DSpace sessions using JMX
 I copied the logic in the jmx_tomcat_dbpools provided by Ubuntu&rsquo;s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-03/index.html
+++ b/docs/2018-03/index.html
@ -13,8 +13,8 @@ Export a CSV of the IITA community metadata for Martin Mueller
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-03/" />
-<meta property="article:published_time" content="2018-03-02T16:07:54&#43;02:00"/>
-<meta property="article:modified_time" content="2019-04-26T12:13:02&#43;03:00"/>
+<meta property="article:published_time" content="2018-03-02T16:07:54+02:00" />
+<meta property="article:modified_time" content="2019-04-26T12:13:02+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="March, 2018"/>
@ -23,7 +23,7 @@ Export a CSV of the IITA community metadata for Martin Mueller

 Export a CSV of the IITA community metadata for Martin Mueller
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
@ -494,24 +494,22 @@ java.lang.IllegalArgumentException: No choices plugin was configured for  field
 <ul>
 <li>Looks like the indexing gets confused that there is still data in the <code>authority</code> column</li>
 <li>Unfortunately this causes those items to simply not be indexed, which users noticed because item counts were cut in half and old items showed up in RSS!</li>
-<li>Since we&rsquo;ve migrated the ORCID identifiers associated with the authority data to the <code>cg.creator.id</code> field we can nullify the authorities remaining in the database:</li>
-</ul>
+
+<li><p>Since we&rsquo;ve migrated the ORCID identifiers associated with the authority data to the <code>cg.creator.id</code> field we can nullify the authorities remaining in the database:</p>

 <pre><code class="language-sql">dspace=# UPDATE metadatavalue SET authority=NULL WHERE resource_type_id=2 AND metadata_field_id=3 AND authority IS NOT NULL;
 UPDATE 195463
-</code></pre>
+</code></pre></li>

-<ul>
-<li>After this the indexing works as usual and item counts and facets are back to normal</li>
-<li>Send Peter a list of all authors to correct:</li>
-</ul>
+<li><p>After this the indexing works as usual and item counts and facets are back to normal</p></li>
+
+<li><p>Send Peter a list of all authors to correct:</p>

 <pre><code class="language-sql">dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv header;
 COPY 56156
-</code></pre>
+</code></pre></li>

-<ul>
-<li>Afterwards we&rsquo;ll want to do some batch tagging of ORCID identifiers to these names</li>
+<li><p>Afterwards we&rsquo;ll want to do some batch tagging of ORCID identifiers to these names</p></li>

 <li><p>CGSpace crashed again this afternoon, I&rsquo;m not sure of the cause but there are a lot of SQL errors in the DSpace log:</p>

--- a/docs/2018-04/index.html
+++ b/docs/2018-04/index.html
@ -14,8 +14,8 @@ Catalina logs at least show some memory errors yesterday:
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-04/" />
-<meta property="article:published_time" content="2018-04-01T16:13:54&#43;02:00"/>
-<meta property="article:modified_time" content="2018-04-30T18:45:30&#43;03:00"/>
+<meta property="article:published_time" content="2018-04-01T16:13:54+02:00" />
+<meta property="article:modified_time" content="2018-04-30T18:45:30+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2018"/>
@ -25,7 +25,7 @@ Catalina logs at least show some memory errors yesterday:
 I tried to test something on DSpace Test but noticed that it&rsquo;s down since god knows when
 Catalina logs at least show some memory errors yesterday:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
@ -154,16 +154,15 @@ sys     2m2.498s
 <pre><code>$ ./add-orcid-identifiers-csv.py -i /tmp/jtohme-2018-04-04.csv -db dspace -u dspace -p 'fuuu'
 </code></pre></li>

-<li><p>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</p></li>
-</ul>
+<li><p>The CSV format of <code>jtohme-2018-04-04.csv</code> was:</p>

 <pre><code class="language-csv">dc.contributor.author,cg.creator.id
 &quot;Tohme, Joseph M.&quot;,Joe Tohme: 0000-0003-2765-7101
-</code></pre>
+</code></pre></li>

-<ul>
-<li>There was a quoting error in my CRP CSV and the replacements for <code>Forests, Trees and Agroforestry</code> got messed up</li>
-<li>So I fixed them and had to re-index again!</li>
+<li><p>There was a quoting error in my CRP CSV and the replacements for <code>Forests, Trees and Agroforestry</code> got messed up</p></li>
+
+<li><p>So I fixed them and had to re-index again!</p></li>

 <li><p>I started preparing the git branch for the the DSpace 5.5→5.8 upgrade:</p>

--- a/docs/2018-05/index.html
+++ b/docs/2018-05/index.html
@ -20,8 +20,8 @@ Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-05/" />
-<meta property="article:published_time" content="2018-05-01T16:43:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-09-04T16:15:26&#43;03:00"/>
+<meta property="article:published_time" content="2018-05-01T16:43:54+03:00" />
+<meta property="article:modified_time" content="2018-09-04T16:15:26+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2018"/>
@ -37,7 +37,7 @@ http://localhost:3000/solr/statistics/update?stream.body=%3Ccommit/%3E
 Then I reduced the JVM heap size from 6144 back to 5120m
 Also, I switched it to use OpenJDK instead of Oracle Java, as well as re-worked the Ansible infrastructure scripts to support hosts choosing which distribution they want to use
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-06/index.html
+++ b/docs/2018-06/index.html
@ -34,8 +34,8 @@ sys     2m7.289s
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-06/" />
-<meta property="article:published_time" content="2018-06-04T19:49:54-07:00"/>
-<meta property="article:modified_time" content="2018-06-28T13:37:35&#43;03:00"/>
+<meta property="article:published_time" content="2018-06-04T19:49:54-07:00" />
+<meta property="article:modified_time" content="2018-06-28T13:37:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2018"/>
@ -65,7 +65,7 @@ user    8m5.056s
 sys     2m7.289s

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-07/index.html
+++ b/docs/2018-07/index.html
@ -21,8 +21,8 @@ There is insufficient memory for the Java Runtime Environment to continue.
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-07/" />
-<meta property="article:published_time" content="2018-07-01T12:56:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-07-28T12:06:56&#43;03:00"/>
+<meta property="article:published_time" content="2018-07-01T12:56:54+03:00" />
+<meta property="article:modified_time" content="2018-07-28T12:06:56+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="July, 2018"/>
@ -39,7 +39,7 @@ During the mvn package stage on the 5.8 branch I kept getting issues with java r
 There is insufficient memory for the Java Runtime Environment to continue.

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-08/index.html
+++ b/docs/2018-08/index.html
@ -30,8 +30,8 @@ I ran all system updates on DSpace Test and rebooted it
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-08/" />
-<meta property="article:published_time" content="2018-08-01T11:52:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-09-10T23:35:46&#43;03:00"/>
+<meta property="article:published_time" content="2018-08-01T11:52:54+03:00" />
+<meta property="article:modified_time" content="2018-09-10T23:35:46+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="August, 2018"/>
@ -57,7 +57,7 @@ The server only has 8GB of RAM so we&rsquo;ll eventually need to upgrade to a la

 I ran all system updates on DSpace Test and rebooted it
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-09/index.html
+++ b/docs/2018-09/index.html
@ -16,8 +16,8 @@ I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-09/" />
-<meta property="article:published_time" content="2018-09-02T09:55:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-09-30T08:23:48&#43;03:00"/>
+<meta property="article:published_time" content="2018-09-02T09:55:54+03:00" />
+<meta property="article:modified_time" content="2018-09-30T08:23:48+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="September, 2018"/>
@ -29,7 +29,7 @@ I&rsquo;ll update the DSpace role in our Ansible infrastructure playbooks and ru
 Also, I&rsquo;ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system&rsquo;s RAM, and we never re-ran them after migrating to larger Linodes last month
 I&rsquo;m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I&rsquo;m getting those autowire errors in Tomcat 8.5.30 again:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-10/index.html
+++ b/docs/2018-10/index.html
@ -14,8 +14,8 @@ I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nai
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-10/" />
-<meta property="article:published_time" content="2018-10-01T22:31:54&#43;03:00"/>
-<meta property="article:modified_time" content="2018-11-01T16:42:20&#43;02:00"/>
+<meta property="article:published_time" content="2018-10-01T22:31:54+03:00" />
+<meta property="article:modified_time" content="2018-11-01T16:42:20+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="October, 2018"/>
@ -25,7 +25,7 @@ I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nai
 Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items
 I created a GitHub issue to track this #389, because I&rsquo;m super busy in Nairobi right now
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-11/index.html
+++ b/docs/2018-11/index.html
@ -21,8 +21,8 @@ Today these are the top 10 IPs:
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-11/" />
-<meta property="article:published_time" content="2018-11-01T16:41:30&#43;02:00"/>
-<meta property="article:modified_time" content="2019-02-07T10:52:23&#43;02:00"/>
+<meta property="article:published_time" content="2018-11-01T16:41:30+02:00" />
+<meta property="article:modified_time" content="2019-02-07T10:52:23+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="November, 2018"/>
@ -39,7 +39,7 @@ Send a note about my dspace-statistics-api to the dspace-tech mailing list
 Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage
 Today these are the top 10 IPs:
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2018-12/index.html
+++ b/docs/2018-12/index.html
@ -21,8 +21,8 @@ I noticed that there is another issue with PDF thumbnails on CGSpace, and I see
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2018-12/" />
-<meta property="article:published_time" content="2018-12-02T02:09:30&#43;02:00"/>
-<meta property="article:modified_time" content="2018-12-30T18:12:18&#43;02:00"/>
+<meta property="article:published_time" content="2018-12-02T02:09:30+02:00" />
+<meta property="article:modified_time" content="2018-12-30T18:12:18+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="December, 2018"/>
@ -39,7 +39,7 @@ Then I ran all system updates and restarted the server

 I noticed that there is another issue with PDF thumbnails on CGSpace, and I see there was another Ghostscript vulnerability last week
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-01/index.html
+++ b/docs/2019-01/index.html
@ -28,8 +28,8 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-01/" />
-<meta property="article:published_time" content="2019-01-02T09:48:30&#43;02:00"/>
-<meta property="article:modified_time" content="2019-02-01T21:45:50&#43;02:00"/>
+<meta property="article:published_time" content="2019-01-02T09:48:30+02:00" />
+<meta property="article:modified_time" content="2019-02-01T21:45:50+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="January, 2019"/>
@ -53,7 +53,7 @@ I don&rsquo;t see anything interesting in the web server logs around that time t
 903 54.70.40.11

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-02/index.html
+++ b/docs/2019-02/index.html
@ -42,8 +42,8 @@ sys     0m1.979s
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-02/" />
-<meta property="article:published_time" content="2019-02-01T21:37:30&#43;02:00"/>
-<meta property="article:modified_time" content="2019-03-18T15:25:49&#43;02:00"/>
+<meta property="article:published_time" content="2019-02-01T21:37:30+02:00" />
+<meta property="article:modified_time" content="2019-03-18T15:25:49+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="February, 2019"/>
@ -81,7 +81,7 @@ user    0m22.203s
 sys     0m1.979s

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-03/index.html
+++ b/docs/2019-03/index.html
@ -24,8 +24,8 @@ I think I will need to ask Udana to re-copy and paste the abstracts with more ca
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-03/" />
-<meta property="article:published_time" content="2019-03-01T12:16:30&#43;01:00"/>
-<meta property="article:modified_time" content="2019-07-12T14:05:21&#43;03:00"/>
+<meta property="article:published_time" content="2019-03-01T12:16:30+01:00" />
+<meta property="article:modified_time" content="2019-07-12T14:05:21+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="March, 2019"/>
@ -45,7 +45,7 @@ Most worryingly, there are encoding errors in the abstracts for eleven items, fo

 I think I will need to ask Udana to re-copy and paste the abstracts with more care using Google Docs
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-04/index.html
+++ b/docs/2019-04/index.html
@ -37,8 +37,8 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-04/" />
-<meta property="article:published_time" content="2019-04-01T09:00:43&#43;03:00"/>
-<meta property="article:modified_time" content="2019-07-04T19:37:10&#43;03:00"/>
+<meta property="article:published_time" content="2019-04-01T09:00:43+03:00" />
+<meta property="article:modified_time" content="2019-07-04T19:37:10+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2019"/>
@ -71,7 +71,7 @@ $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspa
 $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p &#39;fuuu&#39; -m 231 -f cg.coverage.region -d

 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-05/index.html
+++ b/docs/2019-05/index.html
@ -27,8 +27,8 @@ But after this I tried to delete the item from the XMLUI and it is still present
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-05/" />
-<meta property="article:published_time" content="2019-05-01T07:37:43&#43;03:00"/>
-<meta property="article:modified_time" content="2019-07-08T11:18:51&#43;03:00"/>
+<meta property="article:published_time" content="2019-05-01T07:37:43+03:00" />
+<meta property="article:modified_time" content="2019-07-08T11:18:51+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="May, 2019"/>
@ -51,7 +51,7 @@ DELETE 1

 But after this I tried to delete the item from the XMLUI and it is still present&hellip;
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-06/index.html
+++ b/docs/2019-06/index.html
@ -20,8 +20,8 @@ Skype with Marie-Angélique and Abenet about CG Core v2
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-06/" />
-<meta property="article:published_time" content="2019-06-02T10:57:51&#43;03:00"/>
-<meta property="article:modified_time" content="2019-07-01T12:14:35&#43;03:00"/>
+<meta property="article:published_time" content="2019-06-02T10:57:51+03:00" />
+<meta property="article:modified_time" content="2019-07-01T12:14:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="June, 2019"/>
@ -37,7 +37,7 @@ Run system updates on CGSpace (linode18) and reboot it

 Skype with Marie-Angélique and Abenet about CG Core v2
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-07/index.html
+++ b/docs/2019-07/index.html
@ -20,8 +20,8 @@ Abenet had another similar issue a few days ago when trying to find the stats fo
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-07/" />
-<meta property="article:published_time" content="2019-07-01T12:13:51&#43;03:00"/>
-<meta property="article:modified_time" content="2019-07-30T20:15:21&#43;03:00"/>
+<meta property="article:published_time" content="2019-07-01T12:13:51+03:00" />
+<meta property="article:modified_time" content="2019-07-30T20:15:21+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="July, 2019"/>
@ -37,7 +37,7 @@ CGSpace

 Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/2019-08/index.html
+++ b/docs/2019-08/index.html
@ -26,8 +26,8 @@ Run system updates on DSpace Test (linode19) and reboot it
 " />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2019-08/" />
-<meta property="article:published_time" content="2019-08-03T12:39:51&#43;03:00"/>
-<meta property="article:modified_time" content="2019-08-06T20:07:44&#43;03:00"/>
+<meta property="article:published_time" content="2019-08-03T12:39:51+03:00" />
+<meta property="article:modified_time" content="2019-08-06T20:11:27+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="August, 2019"/>
@ -49,7 +49,7 @@ After rebooting, all statistics cores were loaded&hellip; wow, that&rsquo;s luck

 Run system updates on DSpace Test (linode19) and reboot it
 "/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
@ -59,9 +59,9 @@ Run system updates on DSpace Test (linode19) and reboot it
  "@type": "BlogPosting",
  "headline": "August, 2019",
  "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2019-08\/",
-  "wordCount": "433",
+  "wordCount": "793",
  "datePublished": "2019-08-03T12:39:51\x2b03:00",
-  "dateModified": "2019-08-06T20:07:44\x2b03:00",
+  "dateModified": "2019-08-06T20:11:27\x2b03:00",
  "author": {
    "@type": "Person",
    "name": "Alan Orth"
@ -211,6 +211,61 @@ isNotNull(value.match(/^.*û.*$/))
 </ul></li>
 </ul>

+<h2 id="2019-08-07">2019-08-07</h2>
+
+<ul>
+<li>Daniel Haile-Michael asked about using a logical OR with the DSpace OpenSearch, but I looked in the DSpace manual and it does not seem to be possible</li>
+</ul>
+
+<h2 id="2019-08-08">2019-08-08</h2>
+
+<ul>
+<li><p>Moayad noticed that the HTTPS certificate expired on the AReS dev server (linode20)</p>
+
+<ul>
+<li>The first problem was that there is a Docker container listening on port 80, so it conflicts with the ACME http-01 validation</li>
+<li>The second problem was that we only allow access to port 80 from localhost</li>
+
+<li><p>I adjusted the <code>renew-letsencrypt</code> systemd service so it stops/starts the Docker container and firewall:</p>
+
+<pre><code># /opt/certbot-auto renew --standalone --pre-hook &quot;/usr/bin/docker stop angular_nginx; /bin/systemctl stop firewalld&quot; --post-hook &quot;/bin/systemctl start firewalld; /usr/bin/docker start angular_nginx&quot;
+</code></pre></li>
+</ul></li>
+
+<li><p>It is important that the firewall starts back up before the Docker container or else Docker will complain about missing iptables chains</p></li>
+
+<li><p>Also, I updated to the latest TLS Intermediate settings as appropriate for Ubuntu 18.04&rsquo;s <a href="https://ssl-config.mozilla.org/#server=nginx&amp;server-version=1.16.0&amp;config=intermediate&amp;openssl-version=1.1.0g&amp;hsts=false&amp;ocsp=false">OpenSSL 1.1.0g with nginx 1.16.0</a></p></li>
+
+<li><p>Run all system updates on AReS dev server (linode20) and reboot it</p></li>
+
+<li><p>Get a list of all PDFs from the Bioversity migration that fail to download and save them so I can try again with a different path in the URL:</p>
+
+<pre><code>$ ./generate-thumbnails.py -i /tmp/2019-08-05-Bioversity-Migration.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs.txt
+$ grep -B1 &quot;Download failed&quot; /tmp/2019-08-08-download-pdfs.txt | grep &quot;Downloading&quot; | sed -e 's/&gt; Downloading //' -e 's/\.\.\.//' | sed -r 's/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g' | csvcut -H -c 1,1 &gt; /tmp/user-upload.csv
+$ ./generate-thumbnails.py -i /tmp/user-upload.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs2.txt
+$ grep -B1 &quot;Download failed&quot; /tmp/2019-08-08-download-pdfs2.txt | grep &quot;Downloading&quot; | sed -e 's/&gt; Downloading //' -e 's/\.\.\.//' | sed -r 's/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[mGK]//g' | csvcut -H -c 1,1 &gt; /tmp/user-upload2.csv
+$ ./generate-thumbnails.py -i /tmp/user-upload2.csv -w --url-field-name url -d | tee /tmp/2019-08-08-download-pdfs3.txt
+</code></pre></li>
+
+<li><p>(the weird sed regex removes color codes, because my generate-thumbnails script prints pretty colors)</p></li>
+
+<li><p>Some PDFs are uploaded in different paths so I have to try a few times to get them all:</p>
+
+<ul>
+<li><code>/fileadmin/_migrated/uploads/tx_news/</code></li>
+<li><code>/fileadmin/user_upload/online_library/publications/pdfs/</code></li>
+<li><code>/fileadmin/user_upload/</code></li>
+</ul></li>
+
+<li><p>Even so, there are still 52 items with incorrect filenames, so I can&rsquo;t derive their PDF URLs&hellip;</p>
+
+<ul>
+<li>For example, <code>Wild_cherry_Prunus_avium_859.pdf</code> is here (with double underscore): <a href="https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/Wild_cherry__Prunus_avium__859.pdf">https://www.bioversityinternational.org/fileadmin/_migrated/uploads/tx_news/Wild_cherry__Prunus_avium__859.pdf</a></li>
+</ul></li>
+
+<li><p>I will proceed with a metadata-only upload first and then let them know about the missing PDFs</p></li>
+</ul>
+
 <!-- vim: set sw=2 ts=2: -->

  
--- a/docs/404.html
+++ b/docs/404.html
@ -14,7 +14,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="404 Page not found"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/index.html
+++ b/docs/categories/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/notes/index.html
+++ b/docs/categories/notes/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Notes"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/page/2/index.html
+++ b/docs/categories/page/2/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/page/3/index.html
+++ b/docs/categories/page/3/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/page/4/index.html
+++ b/docs/categories/page/4/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/categories/page/5/index.html
+++ b/docs/categories/page/5/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />

-<meta property="og:updated_time" content="2017-09-18T16:38:35&#43;03:00"/>
+<meta property="og:updated_time" content="2017-09-18T16:38:35+03:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="Categories"/>
 <meta name="twitter:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository."/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/cgiar-library-migration/index.html
+++ b/docs/cgiar-library-migration/index.html
@ -9,13 +9,13 @@
 <meta property="og:description" content="Notes on the migration of the CGIAR Library to CGSpace" />
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/cgiar-library-migration/" />
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-<meta property="article:modified_time" content="2018-03-09T22:10:33&#43;02:00"/>
+<meta property="article:published_time" content="2017-09-18T16:38:35+03:00" />
+<meta property="article:modified_time" content="2018-03-09T22:10:33+02:00" />

 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="CGIAR Library Migration"/>
 <meta name="twitter:description" content="Notes on the migration of the CGIAR Library to CGSpace"/>
-<meta name="generator" content="Hugo 0.55.6" />
+<meta name="generator" content="Hugo 0.56.3" />


    
--- a/docs/index.html
+++ b/docs/index.html
@ -10,12 +10,12 @@
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/" />

-<meta property="og:updated_time" content="2019-08-03T12:39:51&#43;03:00"/>
+<meta property="og:updated_time" content="2019-08-03T12:39:51+03:00" />

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