From 564bb119847b20121d98f3bb8ec011f904feec41 Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Thu, 10 Feb 2022 20:35:40 +0300 Subject: [PATCH] Add notes for 2022-02-10 --- content/posts/2022-02.md | 121 ++++ docs/2015-11/index.html | 6 +- docs/2015-12/index.html | 6 +- docs/2016-01/index.html | 6 +- docs/2016-02/index.html | 6 +- docs/2016-03/index.html | 6 +- docs/2016-04/index.html | 6 +- docs/2016-05/index.html | 6 +- docs/2016-06/index.html | 6 +- docs/2016-07/index.html | 6 +- docs/2016-08/index.html | 6 +- docs/2016-09/index.html | 6 +- docs/2016-10/index.html | 6 +- docs/2016-11/index.html | 6 +- docs/2016-12/index.html | 6 +- docs/2017-01/index.html | 6 +- docs/2017-02/index.html | 6 +- docs/2017-03/index.html | 6 +- docs/2017-04/index.html | 6 +- docs/2017-05/index.html | 6 +- docs/2017-06/index.html | 6 +- docs/2017-07/index.html | 6 +- docs/2017-08/index.html | 6 +- docs/2017-09/index.html | 6 +- docs/2017-10/index.html | 6 +- docs/2017-11/index.html | 6 +- 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docs/2020-08/index.html | 6 +- docs/2020-09/index.html | 6 +- docs/2020-10/index.html | 6 +- docs/2020-11/index.html | 6 +- docs/2020-12/index.html | 6 +- docs/2021-01/index.html | 6 +- docs/2021-02/index.html | 6 +- docs/2021-03/index.html | 6 +- docs/2021-04/index.html | 6 +- docs/2021-05/index.html | 6 +- docs/2021-06/index.html | 6 +- docs/2021-07/index.html | 6 +- docs/2021-08/index.html | 6 +- docs/2021-09/index.html | 6 +- docs/2021-10/index.html | 6 +- docs/2021-11/index.html | 6 +- docs/2021-12/index.html | 6 +- docs/2022-01/index.html | 14 +- docs/2022-02/index.html | 536 ++++++++++++++++++ docs/2022/02/fw_packets-day-fs8.png | Bin 0 -> 15659 bytes docs/2022/02/jmx_dspace_sessions-day-fs8.png | Bin 0 -> 10620 bytes docs/2022/02/jmx_tomcat_dbpools-day-fs8.png | Bin 0 -> 15089 bytes .../02/postgres_connections_db-day-fs8.png | Bin 0 -> 12345 bytes docs/404.html | 6 +- docs/categories/index.html | 10 +- docs/categories/notes/index.html | 67 ++- 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docs/tags/migration/index.html | 6 +- docs/tags/notes/index.html | 6 +- docs/tags/notes/page/2/index.html | 6 +- docs/tags/notes/page/3/index.html | 6 +- static/2022/02/fw_packets-day-fs8.png | Bin 0 -> 15659 bytes .../2022/02/jmx_dspace_sessions-day-fs8.png | Bin 0 -> 10620 bytes static/2022/02/jmx_tomcat_dbpools-day-fs8.png | Bin 0 -> 15089 bytes .../02/postgres_connections_db-day-fs8.png | Bin 0 -> 12345 bytes 118 files changed, 1590 insertions(+), 849 deletions(-) create mode 100644 docs/2022-02/index.html create mode 100644 docs/2022/02/fw_packets-day-fs8.png create mode 100644 docs/2022/02/jmx_dspace_sessions-day-fs8.png create mode 100644 docs/2022/02/jmx_tomcat_dbpools-day-fs8.png create mode 100644 docs/2022/02/postgres_connections_db-day-fs8.png create mode 100644 static/2022/02/fw_packets-day-fs8.png create mode 100644 static/2022/02/jmx_dspace_sessions-day-fs8.png create mode 100644 static/2022/02/jmx_tomcat_dbpools-day-fs8.png create mode 100644 static/2022/02/postgres_connections_db-day-fs8.png diff --git a/content/posts/2022-02.md b/content/posts/2022-02.md index ce90c41d0..8104a980d 100644 --- a/content/posts/2022-02.md +++ b/content/posts/2022-02.md @@ -219,4 +219,125 @@ $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=bngo - Fix some occurrences of "Hammond, Jim" to be "Hammond, James" on CGSpace - Start a full index on AReS +## 2022-02-09 + +- UptimeRobot said that CGSpace was down yesterday evening, but when I looked it was up and I didn't see a high database load or anything wrong +- Maria from Bioversity wrote to say that CGSpace was very slow also... + +## 2022-02-10 + +- Looking at the Munin graphs on CGSpace I see several metrics showing that there was likely just increased load... + +![Firewall packets day](/cgspace-notes/2022/02/fw_packets-day-fs8.png) +![DSpace sessions day](/cgspace-notes/2022/02/jmx_dspace_sessions-day-fs8.png) +![Tomcat pool day](/cgspace-notes/2022/02/jmx_tomcat_dbpools-day-fs8.png) +![PostgreSQL connections day](/cgspace-notes/2022/02/postgres_connections_db-day-fs8.png) + +- I extract the logs from nginx for yesterday so I can analyze the traffic: + +```console +# zcat --force /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-access.log +# zcat --force /var/log/nginx/rest.log.1 /var/log/nginx/rest.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-rest.log +# awk '{print $1}' /tmp/feb9-* | less | sort -u > /tmp/feb9-ips.txt +# wc -l /tmp/feb9-ips.txt +11636 /tmp/feb9-ips.tx +``` + +- I started resolving them with my `resolve-addresses-geoip2.py` script +- In the mean time I am looking at the requests and I see a new user agent: `1science Resolver 1.0.0` + - Seems to be a defunct project from Elsevier (website down, Twitter account inactive since 2020) +- I also see 3,400 requests from `EyeMonIT_bot_version_0.1_(http://www.eyemon.it/)`, but because it has "bot" in the name it gets heavily throttled... + - I wonder who is monitoring CGSpace with that service... +- Looking at the top twenty or so ASNs for the resolved IPs I see lots of bot traffic, but nothing malicious: + +```console +$ csvcut -c asn /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20 + 79 24940 + 89 36908 + 100 9299 + 107 2635 + 110 44546 + 111 16509 + 118 7552 + 120 4837 + 123 50245 + 123 55836 + 147 45899 + 173 33771 + 192 39832 + 202 32934 + 235 29465 + 260 15169 + 466 14618 + 607 24757 + 768 714 + 1214 8075 +``` + +- The same information, but by org name: + +```console +$ csvcut -c org /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20 + 92 Orange + 100 Hetzner Online GmbH + 100 Philippine Long Distance Telephone Company + 107 AUTOMATTIC + 110 ALFA TELECOM s.r.o. + 111 AMAZON-02 + 118 Viettel Group + 120 CHINA UNICOM China169 Backbone + 123 Reliance Jio Infocomm Limited + 123 Serverel Inc. + 147 VNPT Corp + 173 SAFARICOM-LIMITED + 192 Opera Software AS + 202 FACEBOOK + 235 MTN NIGERIA Communication limited + 260 GOOGLE + 466 AMAZON-AES + 607 Ethiopian Telecommunication Corporation + 768 APPLE-ENGINEERING + 1214 MICROSOFT-CORP-MSN-AS-BLOCK +``` + +- Most of these are pretty normal except "Serverel" and Hetzner perhaps, but their user agents are pretending to be normal users so who knows... +- I decided to look in the Solr stats with `facet.limit=1000&facet.mincount=1` and found a few more definitely non-human agents: + - scalaj-http/2.4.2 + - scpitspi-rs + - lua-resty-http + - AHC/2.1 + - acebookexternalhit <---- typo, but purge it!!! + - Iframely/1.3.1 (+https://iframely.com/docs/about) Atlassian + - qbhttp/1.0.0 + - got (https://github.com/sindresorhus/got) + - colly - https://github.com/gocolly/colly/v2 + - article-parser/4.2.10 + - SomeRandomText + - adreview/1.0 +- I added them to the ILRI override in the DSpace spider list and ran the `check-spider-hits.sh` script: + +```console +$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p +Purging 234 hits from randint in statistics +Purging 337 hits from Koha in statistics +Purging 1164 hits from scalaj-http in statistics +Purging 1528 hits from scpitspi-rs in statistics +Purging 3050 hits from lua-resty-http in statistics +Purging 1683 hits from AHC in statistics +Purging 1129 hits from acebookexternalhit in statistics +Purging 534 hits from Iframely in statistics +Purging 1022 hits from qbhttp in statistics +Purging 330 hits from ^got in statistics +Purging 156 hits from ^colly in statistics +Purging 38 hits from article-parser in statistics +Purging 1148 hits from SomeRandomText in statistics +Purging 3126 hits from adreview in statistics + +Total number of bot hits purged: 14479 +``` + +- I don't have time right now to add any of these to the COUNTER-Robots list... +- Peter asked me to add a new item type on CGSpace: Opinion Piece +- Map an item on CGSpace for Maria since she couldn't find it in the item mapper + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index 987e2fecb..bbd549b75 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -34,7 +34,7 @@ Last week I had increased the limit from 30 to 60, which seemed to help, but now $ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace 78 "/> - + @@ -242,6 +242,8 @@ db.statementpool = true
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -250,8 +252,6 @@ db.statementpool = true
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2015-12/index.html b/docs/2015-12/index.html index ad012ae52..d59c0d6df 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -36,7 +36,7 @@ Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less -rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo -rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz "/> - + @@ -264,6 +264,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
    +
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    2. +
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    4. @@ -272,8 +274,6 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
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    5. -
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    6. -
diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html index 3e914d1f9..94fa6418d 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -28,7 +28,7 @@ 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. "/> - + @@ -200,6 +200,8 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} ; | sor
    +
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    2. +
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  3. December, 2021
    4. @@ -208,8 +210,6 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} ; | sor
  4. October, 2021
    5. -
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    6. -
diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html index 73ad9f77e..3b3cdac2a 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -38,7 +38,7 @@ I noticed we have a very interesting list of countries on CGSpace: Not only are there 49,000 countries, we have some blanks (25)… Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE” "/> - + @@ -378,6 +378,8 @@ Bitstream: tést señora alimentación.pdf
    +
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    2. +
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    4. @@ -386,8 +388,6 @@ Bitstream: tést señora alimentación.pdf
  4. October, 2021
    5. -
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diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html index 5c8015078..a34623126 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -28,7 +28,7 @@ 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’m pretty sure we don’t need it as of the latest few versions of Atmire’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 "/> - + @@ -316,6 +316,8 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
    +
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    2. +
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    4. @@ -324,8 +326,6 @@ Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Ja
  4. October, 2021
    5. -
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    6. -
diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html index b69874ac3..7530b5ab9 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -32,7 +32,7 @@ After running DSpace for over five years I’ve never needed to look in any This will save us a few gigs of backup space we’re paying for on S3 Also, I noticed the checker log has some errors we should pay attention to: "/> - + @@ -495,6 +495,8 @@ dspace.log.2016-04-27:7271
    +
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    2. +
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    4. @@ -503,8 +505,6 @@ dspace.log.2016-04-27:7271
  4. October, 2021
    5. -
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diff --git a/docs/2016-05/index.html b/docs/2016-05/index.html index 0541e268e..3ce9a20ac 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -34,7 +34,7 @@ There are 3,000 IPs accessing the REST API in a 24-hour period! # awk '{print $1}' /var/log/nginx/rest.log | uniq | wc -l 3168 "/> - + @@ -371,6 +371,8 @@ sys 0m20.540s
    +
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    2. +
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    4. @@ -379,8 +381,6 @@ sys 0m20.540s
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diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html index 052eca5b2..1d34a8fdd 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -34,7 +34,7 @@ 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 "/> - + @@ -409,6 +409,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
    +
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    4. @@ -417,8 +419,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
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diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html index bae6af1a3..75556f5ed 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -44,7 +44,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and In this case the select query was showing 95 results before the update "/> - + @@ -325,6 +325,8 @@ discovery.index.authority.ignore-variants=true
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    4. @@ -333,8 +335,6 @@ discovery.index.authority.ignore-variants=true
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diff --git a/docs/2016-08/index.html b/docs/2016-08/index.html index 2cd59c85a..fa9f76116 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -42,7 +42,7 @@ $ git checkout -b 55new 5_x-prod $ git reset --hard ilri/5_x-prod $ git rebase -i dspace-5.5 "/> - + @@ -389,6 +389,8 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/b
    +
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    2. +
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    4. @@ -397,8 +399,6 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/b
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diff --git a/docs/2016-09/index.html b/docs/2016-09/index.html index 16a1016a4..5fa0fb1aa 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -34,7 +34,7 @@ It looks like we might be able to use OUs now, instead of DCs: $ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)" "/> - + @@ -606,6 +606,8 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
    +
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    4. @@ -614,8 +616,6 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
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diff --git a/docs/2016-10/index.html b/docs/2016-10/index.html index 7ba7802eb..2166f70ff 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -42,7 +42,7 @@ I exported a random item’s metadata as CSV, deleted all columns except id 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X "/> - + @@ -372,6 +372,8 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
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    4. @@ -380,8 +382,6 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
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diff --git a/docs/2016-11/index.html b/docs/2016-11/index.html index e3f3404c5..4920849bf 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -26,7 +26,7 @@ Add dc.type to the output options for Atmire’s Listings and Reports module Add dc.type to the output options for Atmire’s Listings and Reports module (#286) "/> - + @@ -548,6 +548,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
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    4. @@ -556,8 +558,6 @@ org.dspace.discovery.SearchServiceException: Error executing query
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diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html index 9df2a668e..0d4d24053 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -46,7 +46,7 @@ I see thousands of them in the logs for the last few months, so it’s not r I’ve raised a ticket with Atmire to ask Another worrying error from dspace.log is: "/> - + @@ -784,6 +784,8 @@ $ exit
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    4. @@ -792,8 +794,6 @@ $ exit
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diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html index af99196b6..87fd1611d 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -28,7 +28,7 @@ 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’t work there either I asked on the dspace-tech mailing list because it seems to be broken, and actually now I’m not sure if we’ve ever had the sharding task run successfully over all these years "/> - + @@ -369,6 +369,8 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
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    4. @@ -377,8 +379,6 @@ $ gs -sDEVICE=pdfwrite -dCompatibilityLevel=1.4 -dPDFSETTINGS=/ebook -dNOPAUSE -
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diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html index 1a2347f4d..63a508a6f 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -50,7 +50,7 @@ DELETE 1 Create issue on GitHub to track the addition of CCAFS Phase II project tags (#301) Looks like we’ll be using cg.identifier.ccafsprojectpii as the field name "/> - + @@ -424,6 +424,8 @@ COPY 1968
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    4. @@ -432,8 +434,6 @@ COPY 1968
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diff --git a/docs/2017-03/index.html b/docs/2017-03/index.html index 3349d43e1..a21f740e4 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -54,7 +54,7 @@ Interestingly, it seems DSpace 4.x’s thumbnails were sRGB, but forcing reg $ identify ~/Desktop/alc_contrastes_desafios.jpg /Users/aorth/Desktop/alc_contrastes_desafios.jpg JPEG 464x600 464x600+0+0 8-bit CMYK 168KB 0.000u 0:00.000 "/> - + @@ -355,6 +355,8 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
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  2. January, 2022
  3. December, 2021
    4. @@ -363,8 +365,6 @@ $ ./delete-metadata-values.py -i Investors-Delete-121.csv -f dc.description.spon
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-04/index.html b/docs/2017-04/index.html index 0f9947d51..06ce024dd 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -40,7 +40,7 @@ Testing the CMYK patch on a collection with 650 items: $ [dspace]/bin/dspace filter-media -f -i 10568/16498 -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media-cmyk.txt "/> - + @@ -585,6 +585,8 @@ $ gem install compass -v 1.0.3
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -593,8 +595,6 @@ $ gem install compass -v 1.0.3
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-05/index.html b/docs/2017-05/index.html index 9a41d9bce..b16fb3c70 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -18,7 +18,7 @@ - + @@ -391,6 +391,8 @@ UPDATE 187
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -399,8 +401,6 @@ UPDATE 187
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index 48f578fec..f9e3f3497 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -18,7 +18,7 @@ - + @@ -270,6 +270,8 @@ $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace impo
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -278,8 +280,6 @@ $ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" [dspace]/bin/dspace impo
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index 8bdd0148b..f0307411c 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -36,7 +36,7 @@ Merge changes for WLE Phase II theme rename (#329) Looking at extracting the metadata registries from ICARDA’s MEL DSpace database so we can compare fields with CGSpace We can use PostgreSQL’s extended output format (-x) plus sed to format the output into quasi XML: "/> - + @@ -275,6 +275,8 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -283,8 +285,6 @@ delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html index aa892f313..f93cbca26 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -60,7 +60,7 @@ 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 "/> - + @@ -517,6 +517,8 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -525,8 +527,6 @@ org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html index 559b6b710..e5e778ebf 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -32,7 +32,7 @@ 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’s user account is both in the approvers step as well as the group "/> - + @@ -659,6 +659,8 @@ Cert Status: good
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -667,8 +669,6 @@ Cert Status: good
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html index 0f49726c5..a8880e74f 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -34,7 +34,7 @@ http://hdl.handle.net/10568/78495||http://hdl.handle.net/10568/79336 There appears to be a pattern but I’ll have to look a bit closer and try to clean them up automatically, either in SQL or in OpenRefine Add Katherine Lutz to the groups for content submission and edit steps of the CGIAR System collections "/> - + @@ -443,6 +443,8 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -451,8 +453,6 @@ session_id=6C30F10B4351A4ED83EC6ED50AFD6B6A
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html index ed0e5f990..d216bc14c 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -48,7 +48,7 @@ Generate list of authors on CGSpace for Peter to go through and correct: dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv; COPY 54701 "/> - + @@ -944,6 +944,8 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -952,8 +954,6 @@ $ cat dspace.log.2017-11-28 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort -n | u
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html index 22154bfdb..3982c1f87 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -30,7 +30,7 @@ The logs say “Timeout waiting for idle object” PostgreSQL activity says there are 115 connections currently The list of connections to XMLUI and REST API for today: "/> - + @@ -783,6 +783,8 @@ DELETE 20
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -791,8 +793,6 @@ DELETE 20
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-01/index.html b/docs/2018-01/index.html index a3e1f558a..66dd46a49 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -150,7 +150,7 @@ 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’s Encrypt if it’s just a handful of domains "/> - + @@ -1452,6 +1452,8 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1460,8 +1462,6 @@ Catalina:type=Manager,context=/,host=localhost activeSessions 8
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html index a31039fa1..7517b9090 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -30,7 +30,7 @@ We don’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’s munin-plugins-java package and used the stuff I discovered about JMX in 2018-01 "/> - + @@ -1039,6 +1039,8 @@ UPDATE 3
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1047,8 +1049,6 @@ UPDATE 3
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html index b8938e1dc..ae0a23de2 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -24,7 +24,7 @@ Export a CSV of the IITA community metadata for Martin Mueller Export a CSV of the IITA community metadata for Martin Mueller "/> - + @@ -585,6 +585,8 @@ Fixed 5 occurences of: GENEBANKS
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -593,8 +595,6 @@ Fixed 5 occurences of: GENEBANKS
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-04/index.html b/docs/2018-04/index.html index 4cf6403c5..85ecbba98 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -26,7 +26,7 @@ Catalina logs at least show some memory errors yesterday: I tried to test something on DSpace Test but noticed that it’s down since god knows when Catalina logs at least show some memory errors yesterday: "/> - + @@ -594,6 +594,8 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -602,8 +604,6 @@ $ pg_restore -O -U dspacetest -d dspacetest -W -h localhost /tmp/dspace_2018-04-
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html index b46420f99..102d52f97 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -38,7 +38,7 @@ 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 "/> - + @@ -523,6 +523,8 @@ $ psql -h localhost -U postgres dspacetest
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -531,8 +533,6 @@ $ psql -h localhost -U postgres dspacetest
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-06/index.html b/docs/2018-06/index.html index 789dd25ac..028947bb8 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -58,7 +58,7 @@ real 74m42.646s user 8m5.056s sys 2m7.289s "/> - + @@ -517,6 +517,8 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 > map-to-cifor-archive.csv
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -525,8 +527,6 @@ $ sed '/^id/d' 10568-*.csv | csvcut -c 1,2 > map-to-cifor-archive.csv
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index 7ddfcfe4e..248504268 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -36,7 +36,7 @@ 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. "/> - + @@ -569,6 +569,8 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -577,8 +579,6 @@ dspace=# select count(text_value) from metadatavalue where resource_type_id=2 an
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-08/index.html b/docs/2018-08/index.html index d18cdec53..cd29eac69 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -46,7 +46,7 @@ Anyways, perhaps I should increase the JVM heap from 5120m to 6144m like we did The server only has 8GB of RAM so we’ll eventually need to upgrade to a larger one because we’ll start starving the OS, PostgreSQL, and command line batch processes I ran all system updates on DSpace Test and rebooted it "/> - + @@ -442,6 +442,8 @@ $ dspace database migrate ignored
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -450,8 +452,6 @@ $ dspace database migrate ignored
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-09/index.html b/docs/2018-09/index.html index e7a230c23..80b061a27 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -30,7 +30,7 @@ I’ll update the DSpace role in our Ansible infrastructure playbooks and ru Also, I’ll re-run the postgresql tasks because the custom PostgreSQL variables are dynamic according to the system’s RAM, and we never re-ran them after migrating to larger Linodes last month I’m testing the new DSpace 5.8 branch in my Ubuntu 18.04 environment and I’m getting those autowire errors in Tomcat 8.5.30 again: "/> - + @@ -748,6 +748,8 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -756,8 +758,6 @@ UPDATE metadatavalue SET text_value='ja' WHERE resource_type_id=2 AND metadata_f
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html index 85812fd71..2122578d0 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -26,7 +26,7 @@ I created a GitHub issue to track this #389, because I’m super busy in Nai Phil Thornton got an ORCID identifier so we need to add it to the list on CGSpace and tag his existing items I created a GitHub issue to track this #389, because I’m super busy in Nairobi right now "/> - + @@ -656,6 +656,8 @@ $ curl -X GET -H "Content-Type: application/json" -H "Accept: app
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -664,8 +666,6 @@ $ curl -X GET -H "Content-Type: application/json" -H "Accept: app
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html index 51c307346..83eade7b4 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -36,7 +36,7 @@ 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: "/> - + @@ -553,6 +553,8 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -561,8 +563,6 @@ $ dspace dsrun org.dspace.eperson.Groomer -a -b 11/27/2016 -d
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html index 1f7ff7edb..cefe2037c 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -36,7 +36,7 @@ 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 "/> - + @@ -594,6 +594,8 @@ UPDATE 1
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -602,8 +604,6 @@ UPDATE 1
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-01/index.html b/docs/2019-01/index.html index 73f94c770..2d3e2010d 100644 --- a/docs/2019-01/index.html +++ b/docs/2019-01/index.html @@ -50,7 +50,7 @@ I don’t see anything interesting in the web server logs around that time t 357 207.46.13.1 903 54.70.40.11 "/> - + @@ -1264,6 +1264,8 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1272,8 +1274,6 @@ identify: CorruptImageProfile `xmp' @ warning/profile.c/SetImageProfileInternal/
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-02/index.html b/docs/2019-02/index.html index ea1243df3..82bebe9b0 100644 --- a/docs/2019-02/index.html +++ b/docs/2019-02/index.html @@ -72,7 +72,7 @@ real 0m19.873s user 0m22.203s sys 0m1.979s "/> - + @@ -1344,6 +1344,8 @@ Please see the DSpace documentation for assistance.
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1352,8 +1354,6 @@ Please see the DSpace documentation for assistance.
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html index 7f31cd44a..07779fca1 100644 --- a/docs/2019-03/index.html +++ b/docs/2019-03/index.html @@ -46,7 +46,7 @@ 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 "/> - + @@ -1208,6 +1208,8 @@ sys 0m2.551s
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1216,8 +1218,6 @@ sys 0m2.551s
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-04/index.html b/docs/2019-04/index.html index 4c83b6404..2857329a6 100644 --- a/docs/2019-04/index.html +++ b/docs/2019-04/index.html @@ -64,7 +64,7 @@ $ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u ds $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d $ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d "/> - + @@ -1299,6 +1299,8 @@ UPDATE 14
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1307,8 +1309,6 @@ UPDATE 14
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-05/index.html b/docs/2019-05/index.html index 33df5a829..32c08b5ce 100644 --- a/docs/2019-05/index.html +++ b/docs/2019-05/index.html @@ -48,7 +48,7 @@ DELETE 1 But after this I tried to delete the item from the XMLUI and it is still present… "/> - + @@ -631,6 +631,8 @@ COPY 64871
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -639,8 +641,6 @@ COPY 64871
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-06/index.html b/docs/2019-06/index.html index 35d6939bc..20a9752df 100644 --- a/docs/2019-06/index.html +++ b/docs/2019-06/index.html @@ -34,7 +34,7 @@ Run system updates on CGSpace (linode18) and reboot it Skype with Marie-Angélique and Abenet about CG Core v2 "/> - + @@ -317,6 +317,8 @@ UPDATE 2
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -325,8 +327,6 @@ UPDATE 2
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-07/index.html b/docs/2019-07/index.html index 08925d18d..97cf4a566 100644 --- a/docs/2019-07/index.html +++ b/docs/2019-07/index.html @@ -38,7 +38,7 @@ CGSpace Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community "/> - + @@ -554,6 +554,8 @@ issn.validate('1020-3362')
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -562,8 +564,6 @@ issn.validate('1020-3362')
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-08/index.html b/docs/2019-08/index.html index a09490595..694796a12 100644 --- a/docs/2019-08/index.html +++ b/docs/2019-08/index.html @@ -46,7 +46,7 @@ After rebooting, all statistics cores were loaded… wow, that’s luck Run system updates on DSpace Test (linode19) and reboot it "/> - + @@ -573,6 +573,8 @@ sys 2m27.496s
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -581,8 +583,6 @@ sys 2m27.496s
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-09/index.html b/docs/2019-09/index.html index 22f4b6afc..61f87920d 100644 --- a/docs/2019-09/index.html +++ b/docs/2019-09/index.html @@ -72,7 +72,7 @@ Here are the top ten IPs in the nginx XMLUI and REST/OAI logs this morning: 7249 2a01:7e00::f03c:91ff:fe18:7396 9124 45.5.186.2 "/> - + @@ -581,6 +581,8 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -589,8 +591,6 @@ $ csv-metadata-quality -i /tmp/clarisa-institutions.csv -o /tmp/clarisa-institut
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-10/index.html b/docs/2019-10/index.html index e66f8402d..b011a0eab 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -18,7 +18,7 @@ - + @@ -385,6 +385,8 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -393,8 +395,6 @@ $ dspace import -a -c 10568/104057 -e fuu@cgiar.org -m 2019-10-15-Bioversity.map
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-11/index.html b/docs/2019-11/index.html index 069a27b05..1e7b17803 100644 --- a/docs/2019-11/index.html +++ b/docs/2019-11/index.html @@ -58,7 +58,7 @@ Let’s see how many of the REST API requests were for bitstreams (because t # zcat --force /var/log/nginx/rest.log.*.gz | grep -E "[0-9]{1,2}/Oct/2019" | grep -c -E "/rest/bitstreams" 106781 "/> - + @@ -692,6 +692,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -700,8 +702,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2019-12/index.html b/docs/2019-12/index.html index cabc0c83e..c3db101ac 100644 --- a/docs/2019-12/index.html +++ b/docs/2019-12/index.html @@ -46,7 +46,7 @@ Make sure all packages are up to date and the package manager is up to date, the # dpkg -C # reboot "/> - + @@ -404,6 +404,8 @@ UPDATE 1
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -412,8 +414,6 @@ UPDATE 1
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-01/index.html b/docs/2020-01/index.html index 65996bd3f..ab909ef77 100644 --- a/docs/2020-01/index.html +++ b/docs/2020-01/index.html @@ -56,7 +56,7 @@ I tweeted the CGSpace repository link "/> - + @@ -604,6 +604,8 @@ COPY 2900
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -612,8 +614,6 @@ COPY 2900
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-02/index.html b/docs/2020-02/index.html index e38e8d3b4..cd8268d5f 100644 --- a/docs/2020-02/index.html +++ b/docs/2020-02/index.html @@ -38,7 +38,7 @@ The code finally builds and runs with a fresh install "/> - + @@ -1275,6 +1275,8 @@ Moving: 21993 into core statistics-2019
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1283,8 +1285,6 @@ Moving: 21993 into core statistics-2019
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-03/index.html b/docs/2020-03/index.html index 610de1cc4..cfac3b7f2 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -42,7 +42,7 @@ You need to download this into the DSpace 6.x source and compile it "/> - + @@ -484,6 +484,8 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -492,8 +494,6 @@ $ tidy -xml -utf8 -iq -m -w 0 dspace/config/controlled-vocabularies/cg-creator-i
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-04/index.html b/docs/2020-04/index.html index 7a1f5801f..d51cd6b61 100644 --- a/docs/2020-04/index.html +++ b/docs/2020-04/index.html @@ -48,7 +48,7 @@ The third item now has a donut with score 1 since I tweeted it last week On the same note, the one item Abenet pointed out last week now has a donut with score of 104 after I tweeted it last week "/> - + @@ -658,6 +658,8 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -666,8 +668,6 @@ $ psql -c 'select * from pg_stat_activity' | wc -l
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-05/index.html b/docs/2020-05/index.html index 63dd780b5..fdb0c1efb 100644 --- a/docs/2020-05/index.html +++ b/docs/2020-05/index.html @@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2 "/> - + @@ -477,6 +477,8 @@ Caused by: java.lang.NullPointerException
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -485,8 +487,6 @@ Caused by: java.lang.NullPointerException
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-06/index.html b/docs/2020-06/index.html index 5ab0000d9..eaf6f3ec8 100644 --- a/docs/2020-06/index.html +++ b/docs/2020-06/index.html @@ -36,7 +36,7 @@ I sent Atmire the dspace.log from today and told them to log into the server to In other news, I checked the statistics API on DSpace 6 and it’s working I tried to build the OAI registry on the freshly migrated DSpace 6 on DSpace Test and I get an error: "/> - + @@ -811,6 +811,8 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -819,8 +821,6 @@ $ csvcut -c 'id,cg.subject.ilri[],cg.subject.ilri[en_US],dc.subject[en_US]' /tmp
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-07/index.html b/docs/2020-07/index.html index dc7f04a2c..de62b61dc 100644 --- a/docs/2020-07/index.html +++ b/docs/2020-07/index.html @@ -38,7 +38,7 @@ I restarted Tomcat and PostgreSQL and the issue was gone Since I was restarting Tomcat anyways I decided to redeploy the latest changes from the 5_x-prod branch and I added a note about COVID-19 items to the CGSpace frontpage at Peter’s request "/> - + @@ -1142,6 +1142,8 @@ Fixed 4 occurences of: Muloi, D.M.
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1150,8 +1152,6 @@ Fixed 4 occurences of: Muloi, D.M.
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-08/index.html b/docs/2020-08/index.html index 3c9202bea..9254f3d83 100644 --- a/docs/2020-08/index.html +++ b/docs/2020-08/index.html @@ -36,7 +36,7 @@ It is class based so I can easily add support for other vocabularies, and the te "/> - + @@ -798,6 +798,8 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -806,8 +808,6 @@ $ grep -c added /tmp/2020-08-27-countrycodetagger.log
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-09/index.html b/docs/2020-09/index.html index 117fd8519..84e79de68 100644 --- a/docs/2020-09/index.html +++ b/docs/2020-09/index.html @@ -48,7 +48,7 @@ I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39 I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40 "/> - + @@ -717,6 +717,8 @@ solr_query_params = {
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -725,8 +727,6 @@ solr_query_params = {
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-10/index.html b/docs/2020-10/index.html index 60d3eb02c..0da1f218a 100644 --- a/docs/2020-10/index.html +++ b/docs/2020-10/index.html @@ -44,7 +44,7 @@ During the FlywayDB migration I got an error: "/> - + @@ -1241,6 +1241,8 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1249,8 +1251,6 @@ $ ./delete-metadata-values.py -i 2020-10-31-delete-74-sponsors.csv -db dspace -u
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-11/index.html b/docs/2020-11/index.html index 94979f3c9..ad60407be 100644 --- a/docs/2020-11/index.html +++ b/docs/2020-11/index.html @@ -32,7 +32,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat "/> - + @@ -731,6 +731,8 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -739,8 +741,6 @@ $ ./fix-metadata-values.py -i 2020-11-30-fix-hung-orcid.csv -db dspace63 -u dspa
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2020-12/index.html b/docs/2020-12/index.html index 3ae376882..44154d928 100644 --- a/docs/2020-12/index.html +++ b/docs/2020-12/index.html @@ -36,7 +36,7 @@ I started processing those (about 411,000 records): "/> - + @@ -869,6 +869,8 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-i
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -877,8 +879,6 @@ $ curl -XDELETE 'http://localhost:9200/openrxv-i
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-01/index.html b/docs/2021-01/index.html index c35ba5853..4ff0abfe3 100644 --- a/docs/2021-01/index.html +++ b/docs/2021-01/index.html @@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS "/> - + @@ -688,6 +688,8 @@ java.lang.IllegalArgumentException: Invalid character found in the request targe
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -696,8 +698,6 @@ java.lang.IllegalArgumentException: Invalid character found in the request targe
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-02/index.html b/docs/2021-02/index.html index 265356b2e..e22d3c4ac 100644 --- a/docs/2021-02/index.html +++ b/docs/2021-02/index.html @@ -60,7 +60,7 @@ $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty } } "/> - + @@ -898,6 +898,8 @@ dspace.log.2021-02-28:0
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -906,8 +908,6 @@ dspace.log.2021-02-28:0
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-03/index.html b/docs/2021-03/index.html index fdf20bbaf..50f0bfe39 100644 --- a/docs/2021-03/index.html +++ b/docs/2021-03/index.html @@ -34,7 +34,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst "/> - + @@ -875,6 +875,8 @@ COPY 3081
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -883,8 +885,6 @@ COPY 3081
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-04/index.html b/docs/2021-04/index.html index ef5181c97..095961bc0 100644 --- a/docs/2021-04/index.html +++ b/docs/2021-04/index.html @@ -44,7 +44,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in "/> - + @@ -1042,6 +1042,8 @@ $ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.csv -db dspace63 -u d
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -1050,8 +1052,6 @@ $ ./ilri/doi-to-handle.py -i /tmp/dois.txt -o /tmp/handles.csv -db dspace63 -u d
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-05/index.html b/docs/2021-05/index.html index 3875ff66e..2c3f1de26 100644 --- a/docs/2021-05/index.html +++ b/docs/2021-05/index.html @@ -36,7 +36,7 @@ I looked at the top user agents and IPs in the Solr statistics for last month an I will add the RI/1.0 pattern to our DSpace agents overload and purge them from Solr (we had previously seen this agent with 9,000 hits or so in 2020-09), but I think I will leave the Microsoft Word one… as that’s an actual user… "/> - + @@ -685,6 +685,8 @@ May 26, 02:57 UTC
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -693,8 +695,6 @@ May 26, 02:57 UTC
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-06/index.html b/docs/2021-06/index.html index 900825807..e0a77016d 100644 --- a/docs/2021-06/index.html +++ b/docs/2021-06/index.html @@ -36,7 +36,7 @@ I simply started it and AReS was running again: "/> - + @@ -693,6 +693,8 @@ COPY 1710
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -701,8 +703,6 @@ COPY 1710
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-07/index.html b/docs/2021-07/index.html index 4cf80d28f..746a9728d 100644 --- a/docs/2021-07/index.html +++ b/docs/2021-07/index.html @@ -30,7 +30,7 @@ Export another list of ALL subjects on CGSpace, including AGROVOC and non-AGROVO localhost/dspace63= > \COPY (SELECT DISTINCT LOWER(text_value) AS subject, count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (119, 120, 127, 122, 128, 125, 135, 203, 208, 210, 215, 123, 236, 242, 187) GROUP BY subject ORDER BY count DESC) to /tmp/2021-07-01-all-subjects.csv WITH CSV HEADER; COPY 20994 "/> - + @@ -715,6 +715,8 @@ $ cat AS* /tmp/ddos-networks-to-block.txt | sed -e &
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -723,8 +725,6 @@ $ cat AS* /tmp/ddos-networks-to-block.txt | sed -e &
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-08/index.html b/docs/2021-08/index.html index 9fb43c180..a9e4490e4 100644 --- a/docs/2021-08/index.html +++ b/docs/2021-08/index.html @@ -32,7 +32,7 @@ Update Docker images on AReS server (linode20) and reboot the server: I decided to upgrade linode20 from Ubuntu 18.04 to 20.04 "/> - + @@ -606,6 +606,8 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-08-25-add-orcids.csv -db dspace -u
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -614,8 +616,6 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-08-25-add-orcids.csv -db dspace -u
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-09/index.html b/docs/2021-09/index.html index ed0408905..b93f25de5 100644 --- a/docs/2021-09/index.html +++ b/docs/2021-09/index.html @@ -48,7 +48,7 @@ The syntax Moayad showed me last month doesn’t seem to honor the search qu "/> - + @@ -588,6 +588,8 @@ $ csvcut -c subject,'match type' /tmp
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -596,8 +598,6 @@ $ csvcut -c subject,'match type' /tmp
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-10/index.html b/docs/2021-10/index.html index 56b14d856..fc4a9fea7 100644 --- a/docs/2021-10/index.html +++ b/docs/2021-10/index.html @@ -46,7 +46,7 @@ $ wc -l /tmp/2021-10-01-affiliations.txt So we have 1879/7100 (26.46%) matching already "/> - + @@ -791,6 +791,8 @@ Purging 3383 hits from 45.155.204.82 in statistics
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -799,8 +801,6 @@ Purging 3383 hits from 45.155.204.82 in statistics
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-11/index.html b/docs/2021-11/index.html index 4cf1f2638..f8f725516 100644 --- a/docs/2021-11/index.html +++ b/docs/2021-11/index.html @@ -32,7 +32,7 @@ First I exported all the 2019 stats from CGSpace: $ ./run.sh -s http://localhost:8081/solr/statistics -f 'time:2019-*' -a export -o statistics-2019.json -k uid $ zstd statistics-2019.json "/> - + @@ -494,6 +494,8 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-11-30-add-orcids.csv -db dspace -u
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -502,8 +504,6 @@ $ ./ilri/add-orcid-identifiers-csv.py -i 2021-11-30-add-orcids.csv -db dspace -u
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2021-12/index.html b/docs/2021-12/index.html index 2b41e22b7..0581fb026 100644 --- a/docs/2021-12/index.html +++ b/docs/2021-12/index.html @@ -40,7 +40,7 @@ Purging 455 hits from WhatsApp in statistics Total number of bot hits purged: 3679 "/> - + @@ -577,6 +577,8 @@ Purging 1822 hits from 2605\:b100\:316\:7f74\:8d67\:5860\:a9f3\:d87c in statisti
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -585,8 +587,6 @@ Purging 1822 hits from 2605\:b100\:316\:7f74\:8d67\:5860\:a9f3\:d87c in statisti
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2022-01/index.html b/docs/2022-01/index.html index d2c1ba1e3..7f82983f0 100644 --- a/docs/2022-01/index.html +++ b/docs/2022-01/index.html @@ -14,7 +14,7 @@ Start a full harvest on AReS - + @@ -24,7 +24,7 @@ Start a full harvest on AReS Start a full harvest on AReS "/> - + @@ -34,9 +34,9 @@ Start a full harvest on AReS "@type": "BlogPosting", "headline": "January, 2022", "url": "https://alanorth.github.io/cgspace-notes/2022-01/", - "wordCount": "1223", + "wordCount": "1224", "datePublished": "2022-01-01T15:20:54+02:00", - "dateModified": "2022-01-28T16:59:40+03:00", + "dateModified": "2022-02-07T09:49:34+03:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -224,7 +224,7 @@ node_modules/@elastic/elasticsearch/api/types.d.ts:3209:13 - error TS2456: Type
  • Spend some time adding months to the CGIAR TAC and IWC records from Gaia
      -
    • Most of the PDFs have months so this is annoying…
      • +
    • Most of the PDFs have only YYYY, so this is annoying…
@@ -380,6 +380,8 @@ cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -388,8 +390,6 @@ cells['dcterms.bibliographicCitation[en_US]'].value.match(/.*:\s?(\d+)(-
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/2022-02/index.html b/docs/2022-02/index.html new file mode 100644 index 000000000..574332e0e --- /dev/null +++ b/docs/2022-02/index.html @@ -0,0 +1,536 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + February, 2022 | CGSpace Notes + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+
+ + + + +
+
+

CGSpace Notes

+

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

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

February, 2022

+

+ + in + Notes + + +

+
+

2022-02-01

+
    +
  • Meeting with Peter and Abenet about CGSpace in the One CGIAR +
      +
    • We agreed to buy $5,000 worth of credits from Atmire for future upgrades
      • +
    • We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization
      • +
    • We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one
      • +
    • We agreed to try to do more alignment of affiliations/funders with ROR
      • +
    +
    • +
+
    +
  • I moved a bunch of communities:
    • +
+
$ dspace community-filiator --remove --parent=10568/114639 --child=10568/115089
+$ dspace community-filiator --remove --parent=10568/114639 --child=10568/115087
+$ dspace community-filiator --remove --parent=10568/83389 --child=10568/108598
+$ dspace community-filiator --remove --parent=10568/83389 --child=10947/1
+$ dspace community-filiator --set --parent=10568/35697 --child=10568/80211
+$ dspace community-filiator --remove --parent=10568/83389 --child=10947/2517
+$ dspace community-filiator --set --parent=10568/97114 --child=10947/2517
+$ dspace community-filiator --set --parent=10568/97114 --child=10568/89416
+$ dspace community-filiator --set --parent=10568/97114 --child=10568/3530
+$ dspace community-filiator --set --parent=10568/97114 --child=10568/80099
+$ dspace community-filiator --set --parent=10568/97114 --child=10568/80100
+$ dspace community-filiator --set --parent=10568/97114 --child=10568/34494
+$ dspace community-filiator --set --parent=10568/117867 --child=10568/114644
+$ dspace community-filiator --set --parent=10568/117867 --child=10568/16573
+$ dspace community-filiator --set --parent=10568/117867 --child=10568/42211
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/109945
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/16498
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/99453
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/2983
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/133
+$ dspace community-filiator --remove --parent=10568/83389 --child=10568/1208
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/1208
+$ dspace community-filiator --remove --parent=10568/83389 --child=10568/56924
+$ dspace community-filiator --set --parent=10568/117865 --child=10568/56924
+$ dspace community-filiator --remove --parent=10568/83389 --child=10568/91688
+$ dspace community-filiator --set --parent=10947/1 --child=10568/91688
+$ dspace community-filiator --remove --parent=10568/83389 --child=10947/2515
+$ dspace community-filiator --set --parent=10947/1 --child=10947/2515
+
    +
  • Remove CPWF and CTA subjects from the Discovery facets
    • +
  • Start a full Discovery index on CGSpace:
    • +
+
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b
+
+real    275m15.777s
+user    182m52.171s
+sys     2m51.573s
+
    +
  • I got a request to confirm validation of CGSpace on openarchives.org, with the requestor’s IP being 128.84.116.66 +
      +
    • That is at Cornell… hmmmm who could that be?!
      • +
    • Oh, the OpenArchives initiative is at Cornell… maybe this is an automated periodic check?
      • +
    +
    • +
+

2022-02-02

+
    +
  • Looking at the top user agents and IP addresses in CGSpace’s Solr statistics for 2022-01 +
      +
    • 64.39.98.40 made 26,000 requests, owned by Qualys so it’s some kind of security scanning
      • +
    • 45.134.26.171 made 8,000 requests and it’s own by some Russian company and makes requests like this hmmmmm:
      • +
    +
    • +
+
45.134.26.171 - - [12/Jan/2022:06:25:27 +0100] "GET /bitstream/handle/10568/81964/varietal-2faea58f.pdf?sequence=1 HTTP/1.1" 200 1157807 "https://cgspace.cgiar.org:443/bitstream/handle/10568/81964/varietal-2faea58f.pdf" "Opera/9.64 (Windows NT 6.1; U; MRA 5.5 (build 02842); ru) Presto/2.1.1)) AND 4734=CTXSYS.DRITHSX.SN(4734,(CHR(113)||CHR(120)||CHR(120)||CHR(112)||CHR(113)||(SELECT (CASE WHEN (4734=4734) THEN 1 ELSE 0 END) FROM DUAL)||CHR(113)||CHR(120)||CHR(113)||CHR(122)||CHR(113))) AND ((3917=3917"
+
    +
  • 3.225.28.105 made 3,000 requests mostly for one CIAT collection on the REST API and it is owned by Amazon +
      +
    • The user agent is sometimes a normal user one, and sometimes Apache-HttpClient/4.3.4 (java 1.5)
      • +
    +
    • +
  • 217.182.21.193 made 2,400 requests and is on OVH
    • +
  • I purged these hits
    • +
+
$ ./ilri/check-spider-ip-hits.sh -f /tmp/ips.txt -p
+Purging 26817 hits from 64.39.98.40 in statistics
+Purging 9446 hits from 45.134.26.171 in statistics
+Purging 6490 hits from 3.225.28.105 in statistics
+Purging 11949 hits from 217.182.21.193 in statistics
+
+Total number of bot hits purged: 54702
+
    +
  • Export donors and affiliations from CGSpace database:
    • +
+
localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.donor", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 248 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-donors.csv WITH CSV HEADER;
+COPY 1036
+localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-affiliations.csv WITH CSV HEADER;
+COPY 7901
+
    +
  • Then check matches against the latest ROR dump:
    • +
+
$ csvcut -c cg.contributor.donor /tmp/2022-02-02-donors.csv | sed '1d' > /tmp/2022-02-02-donors.txt
+$ ./ilri/ror-lookup.py -i /tmp/2022-02-02-donors.txt -r 2021-09-23-ror-data.json -o /tmp/donor-ror-matches.csv
+...
+
    +
  • I see we have 258/1036 (24.9%) of our donors matching ROR (as of the 2021-09-23 ROR dump)
    • +
  • I see we have 1986/7901 (25.1%) of our affiliations matching ROR (as of the 2021-09-23 ROR dump)
    • +
  • Update the PostgreSQL JDBC driver to 42.3.2 in the Ansible Infrastructure playbooks and deploy on DSpace Test
    • +
  • Mishell from CIP sent me a copy of a security scan their ICT had done on CGSpace using QualysGuard +
      +
    • The report was very long and generic, highlighting low-severity things like being able to post crap to search forms and have it appear on the results page
      • +
    • Also they say we’re using old jQuery and bootstrap, etc (fair enough) but there are no exploits per se
      • +
    • At least now I know why all those Qualys IPs are scanning us all the time!!!
      • +
    +
    • +
  • Mishell also said she’s having issues logging into CGSpace +
      +
    • According to the logs her account is failing on LDAP authentication
      • +
    • I checked CGSpace’s LDAP credentials using ldapsearch and was able to connect so it’s gotta be something with her account
      • +
    +
    • +
+

2022-02-03

+
    +
  • I synchronized DSpace Test with a fresh snapshot of CGSpace
    • +
  • I noticed a bunch of thumbnails missing for items submitted in the last week on CGSpace so I ran the dspace filter-media script manually and eventually it crashed:
    • +
+
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media
+...
+SKIPPED: bitstream 48612de7-eec5-4990-8f1b-589a87219a39 (item: 10568/67391) because 'ilri_establishiment.pdf.txt' already exists
+Generated Thumbnail ilri_establishiment.pdf matches pattern and is replacable.
+SKIPPED: bitstream 48612de7-eec5-4990-8f1b-589a87219a39 (item: 10568/67391) because 'ilri_establishiment.pdf.jpg' already exists
+File: Agreement_on_the_Estab_of_ILRI.doc.txt
+Exception: org.apache.poi.util.LittleEndian.getUnsignedByte([BI)I
+java.lang.NoSuchMethodError: org.apache.poi.util.LittleEndian.getUnsignedByte([BI)I
+        at org.textmining.extraction.word.model.FormattedDiskPage.<init>(FormattedDiskPage.java:66)
+        at org.textmining.extraction.word.model.CHPFormattedDiskPage.<init>(CHPFormattedDiskPage.java:62)
+        at org.textmining.extraction.word.model.CHPBinTable.<init>(CHPBinTable.java:70)
+        at org.textmining.extraction.word.Word97TextExtractor.getText(Word97TextExtractor.java:122)
+        at org.textmining.extraction.word.Word97TextExtractor.getText(Word97TextExtractor.java:63)
+        at org.dspace.app.mediafilter.WordFilter.getDestinationStream(WordFilter.java:83)
+        at com.atmire.dspace.app.mediafilter.AtmireMediaFilter.processBitstream(AtmireMediaFilter.java:103)
+        at com.atmire.dspace.app.mediafilter.AtmireMediaFilterServiceImpl.filterBitstream(AtmireMediaFilterServiceImpl.java:61)
+        at org.dspace.app.mediafilter.MediaFilterServiceImpl.filterItem(MediaFilterServiceImpl.java:181)
+        at org.dspace.app.mediafilter.MediaFilterServiceImpl.applyFiltersItem(MediaFilterServiceImpl.java:159)
+        at org.dspace.app.mediafilter.MediaFilterServiceImpl.applyFiltersAllItems(MediaFilterServiceImpl.java:111)
+        at org.dspace.app.mediafilter.MediaFilterCLITool.main(MediaFilterCLITool.java:212)
+        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
+        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
+        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
+        at java.lang.reflect.Method.invoke(Method.java:498)
+        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
+        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
+
    +
  • I should look up that issue and report a bug somewhere perhaps, but for now I just forced the JPG thumbnails with:
    • +
+
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media -p "ImageMagick PDF Thumbnail" -v >& /tmp/filter-media.log
+

2022-02-04

+
    +
  • I found a thread on the dspace-tech mailing list about the media-filter crash above +
      +
    • The problem is that the default filter for Word files is outdated, so we need to switch to the PoiWordFilter extractor
      • +
    • After changing that I was able to filter the Word file on that item above:
      • +
    +
    • +
+
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media -i 10568/67391 -p "Word Text Extractor" -v
+The following MediaFilters are enabled: 
+Full Filter Name: org.dspace.app.mediafilter.PoiWordFilter
+org.dspace.app.mediafilter.PoiWordFilter
+File: Agreement_on_the_Estab_of_ILRI.doc.txt
+
+FILTERED: bitstream 31db7d05-5369-4309-adeb-3b888c80b73d (item: 10568/67391) and created 'Agreement_on_the_Estab_of_ILRI.doc.txt'
+
    +
  • Meeting with the repositories working group to discuss issues moving forward in the One CGIAR
    • +
+

2022-02-07

+
    +
  • Gaia sent me her feedback on the duplicates for the TAC and ICW items for CGSpace a few days ago +
      +
    • I used the IDs marked “delete” in her spreadsheet to create a custom text facet with this GREL in OpenRefine:
      • +
    +
    • +
+
or(
+isNotNull(value.match('1')),
+isNotNull(value.match('4')),
+isNotNull(value.match('5')),
+isNotNull(value.match('6')),
+isNotNull(value.match('8')),
+...
+sNotNull(value.match('178')),
+isNotNull(value.match('186')),
+isNotNull(value.match('188')),
+isNotNull(value.match('189')),
+isNotNull(value.match('197'))
+)
+
    +
  • Then I flagged all of these (seventy-five items)… +
      +
    • I decided to flag the deletes instead of star the keeps because there are some items in the original file that we not marked as duplicates so we have to keep those too
      • +
    +
    • +
  • I generated the next batch of 200 items, from IDs 201 to 400, checked them for duplicates, and then added the PDF file names to the CSV for reference:
    • +
+
$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch201-400.csv > /tmp/tac.csv
+$ ./ilri/check-duplicates.py -i /tmp/tac.csv -db dspace63 -u dspacetest -p 'dom@in34sniper' -o /tmp/2022-02-07-tac-batch2-201-400.csv
+$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch201-400.csv > /tmp/batch2-filenames.csv
+$ csvjoin -c id /tmp/2022-02-07-tac-batch2-201-400.csv /tmp/batch2-filenames.csv > /tmp/2022-02-07-tac-batch2-201-400-filenames.csv
+
    +
  • Then I sent this second batch of items to Gaia to look at
    • +
+

2022-02-08

+
    +
  • Create a SAF archive for the first 200 items (IDs 1 to 200) that were not flagged as duplicates and upload them to a new collection on DSpace Test:
    • +
+
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=bngo@mfin.com --source /tmp/SimpleArchiveFormat --mapfile=./2022-02-08-tac-batch1-1to200.map
+
    +
  • Fix some occurrences of “Hammond, Jim” to be “Hammond, James” on CGSpace
    • +
  • Start a full index on AReS
    • +
+

2022-02-09

+
    +
  • UptimeRobot said that CGSpace was down yesterday evening, but when I looked it was up and I didn’t see a high database load or anything wrong
    • +
  • Maria from Bioversity wrote to say that CGSpace was very slow also…
    • +
+

2022-02-10

+
    +
  • Looking at the Munin graphs on CGSpace I see several metrics showing that there was likely just increased load…
    • +
+

Firewall packets day +DSpace sessions day +Tomcat pool day +PostgreSQL connections day

+
    +
  • I extract the logs from nginx for yesterday so I can analyze the traffic:
    • +
+
# zcat --force /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-access.log
+# zcat --force /var/log/nginx/rest.log.1 /var/log/nginx/rest.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-rest.log
+# awk '{print $1}' /tmp/feb9-* | less | sort -u > /tmp/feb9-ips.txt
+# wc -l /tmp/feb9-ips.txt
+11636 /tmp/feb9-ips.tx
+
    +
  • I started resolving them with my resolve-addresses-geoip2.py script
    • +
  • In the mean time I am looking at the requests and I see a new user agent: 1science Resolver 1.0.0 +
      +
    • Seems to be a defunct project from Elsevier (website down, Twitter account inactive since 2020)
      • +
    +
    • +
  • I also see 3,400 requests from EyeMonIT_bot_version_0.1_(http://www.eyemon.it/), but because it has “bot” in the name it gets heavily throttled… +
      +
    • I wonder who is monitoring CGSpace with that service…
      • +
    +
    • +
  • Looking at the top twenty or so ASNs for the resolved IPs I see lots of bot traffic, but nothing malicious:
    • +
+
$ csvcut -c asn /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20
+     79 24940
+     89 36908
+    100 9299
+    107 2635
+    110 44546
+    111 16509
+    118 7552
+    120 4837
+    123 50245
+    123 55836
+    147 45899
+    173 33771
+    192 39832
+    202 32934
+    235 29465
+    260 15169
+    466 14618
+    607 24757
+    768 714
+   1214 8075
+
    +
  • The same information, but by org name:
    • +
+
$ csvcut -c org /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20
+     92 Orange
+    100 Hetzner Online GmbH
+    100 Philippine Long Distance Telephone Company
+    107 AUTOMATTIC
+    110 ALFA TELECOM s.r.o.
+    111 AMAZON-02
+    118 Viettel Group
+    120 CHINA UNICOM China169 Backbone
+    123 Reliance Jio Infocomm Limited
+    123 Serverel Inc.
+    147 VNPT Corp
+    173 SAFARICOM-LIMITED
+    192 Opera Software AS
+    202 FACEBOOK
+    235 MTN NIGERIA Communication limited
+    260 GOOGLE
+    466 AMAZON-AES
+    607 Ethiopian Telecommunication Corporation
+    768 APPLE-ENGINEERING
+   1214 MICROSOFT-CORP-MSN-AS-BLOCK
+
    +
  • Most of these are pretty normal except “Serverel” and Hetzner perhaps, but their user agents are pretending to be normal users so who knows…
    • +
  • I decided to look in the Solr stats with facet.limit=1000&facet.mincount=1 and found a few more definitely non-human agents: + +
    • +
  • I added them to the ILRI override in the DSpace spider list and ran the check-spider-hits.sh script:
    • +
+
$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p
+Purging 234 hits from randint in statistics
+Purging 337 hits from Koha in statistics
+Purging 1164 hits from scalaj-http in statistics
+Purging 1528 hits from scpitspi-rs in statistics
+Purging 3050 hits from lua-resty-http in statistics
+Purging 1683 hits from AHC in statistics
+Purging 1129 hits from acebookexternalhit in statistics
+Purging 534 hits from Iframely in statistics
+Purging 1022 hits from qbhttp in statistics
+Purging 330 hits from ^got in statistics
+Purging 156 hits from ^colly in statistics
+Purging 38 hits from article-parser in statistics
+Purging 1148 hits from SomeRandomText in statistics
+Purging 3126 hits from adreview in statistics
+
+Total number of bot hits purged: 14479
+
    +
  • I don’t have time right now to add any of these to the COUNTER-Robots list…
    • +
  • Peter asked me to add a new item type on CGSpace: Opinion Piece
    • +
  • Map an item on CGSpace for Maria since she couldn’t find it in the item mapper
    • +
+ + + + + + +
+ + + +
+ + + + +
+
+ + + + + + + + + diff --git a/docs/2022/02/fw_packets-day-fs8.png b/docs/2022/02/fw_packets-day-fs8.png new file mode 100644 index 0000000000000000000000000000000000000000..b73940093ecd124b91e42b30d306ad7a91a8566a GIT binary patch literal 15659 zcmYj&1yCGK)GdVI5L|=1Zg7VX2o@~C-QC?SxGe7O?(PnYySpszi#sph`|E%8s%EOD zdhVP)edhMPT{E}Ce#=RqA`v1%K|!HPN&ZxTf`W$pJE;(0{GKF&cw!9e|%Q4)h1 zhcYoS$t;@O-`~IK?q+Ob{GCN~b#?Xe@v*tN>AUZ{zJ2Fiy5Z~Vdw6&_Jw1JXe!jQ2 zx4XN0a&oe>vjYNwE-x?b?Ccg77lVU?2L}iJ{ry)~R)&U#&d$yp92}gSoaW}{JUl$s zH`eLr=^Gjvy1Kf&y}d_AN2jKyJUu;QVq&bVt>fe4g;#_xE-sO$kfqn8yRW>LxMn*

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z6)n-6&rOQ_vjx8m52@ey`R|7N|J#}Z!P-~&>F|K?sUqy{w_gI_6l7GSt0heW{tu@| B(pCTf literal 0 HcmV?d00001 diff --git a/docs/404.html b/docs/404.html index 0a0b4e2f5..8f682761f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -17,7 +17,7 @@ - + @@ -95,6 +95,8 @@

    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -103,8 +105,6 @@
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/categories/index.html b/docs/categories/index.html index bb9437049..b9d74285d 100644 --- a/docs/categories/index.html +++ b/docs/categories/index.html @@ -10,14 +10,14 @@ - + - + @@ -84,7 +84,7 @@

Notes

-

by Alan Orth

+

by Alan Orth

Read more → @@ -108,6 +108,8 @@
    +
  1. February, 2022
    2. +
  2. January, 2022
  3. December, 2021
    4. @@ -116,8 +118,6 @@
  4. October, 2021
    5. -
  5. September, 2021
    6. -
diff --git a/docs/categories/notes/index.html b/docs/categories/notes/index.html index 8c368ee06..1accbe070 100644 --- a/docs/categories/notes/index.html +++ b/docs/categories/notes/index.html @@ -10,14 +10,14 @@ - + - + @@ -81,6 +81,34 @@ +
+
+

February, 2022

+

by Alan Orth in + Notes + + +

+
+

2022-02-01

+
    +
  • Meeting with Peter and Abenet about CGSpace in the One CGIAR +
      +
    • We agreed to buy $5,000 worth of credits from Atmire for future upgrades
      • +
    • We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization
      • +
    • We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one
      • +
    • We agreed to try to do more alignment of affiliations/funders with ROR
      • +
    +
    • +
+ Read more → +
+ + + + + +

January, 2022

@@ -323,37 +351,6 @@ COPY 20994 - -
-
-

April, 2021

-

by Alan Orth in - Notes - - -

-
-

2021-04-01

-
    -
  • I wrote a script to query Sherpa’s API for our ISSNs: sherpa-issn-lookup.py -
      -
    • I’m curious to see how the results compare with the results from Crossref yesterday
      • -
    -
    • -
  • AReS Explorer was down since this morning, I didn’t see anything in the systemd journal -
      -
    • I simply took everything down with docker-compose and then back up, and then it was OK
      • -
    • Perhaps one of the containers crashed, I should have looked closer but I was in a hurry
      • -
    -
    • -
- Read more → -
- - - - -