Add notes for 2022-09-30

content/posts/2022-09.md

@@ -496,4 +496,79 @@ Fixed 1 occurences of: Amanda De Filippo: 0000-0002-1536-3221
 ...
 ```
 
+## 2022-09-29
+
+- I've been checking the size of the nginx proxy cache the last few days and it always seems to hover around 14,000 entries and 385MB:
+
+```console
+# find /var/cache/nginx/rest_cache/ -type f | wc -l
+14202
+# du -sh /var/cache/nginx/rest_cache
+384M    /var/cache/nginx/rest_cache
+```
+
+- Also on that note I'm trying to implement a workaround for a potential caching issue that causes MEL to not be able to update items on DSpace Test
+  - I *think* we might need to allow requests with a JSESSIONID to bypass the cache, but I have to verify with Salem
+  - We can do this with an nginx map:
+
+```console
+# Check if the JSESSIONID cookie is present and contains a 32-character hex
+# value, which would mean that a user is actively attempting to re-use their
+# Tomcat session. Then we set the $active_user_session variable and use it
+# to bypass the nginx proxy cache in REST requests.
+map $cookie_jsessionid $active_user_session {
+    # requests with an empty key are not evaluated by limit_req
+    # see: http://nginx.org/en/docs/http/ngx_http_limit_req_module.html
+    default '';
+
+    '~[A-Z0-9]{32}' 1;
+}
+```
+
+- Then in the location block where we do the proxy cache:
+
+```console
+            # Don't cache when user Shift-refreshes (Cache-Control: no-cache) or
+            # when a client has an active session (see the $cookie_jsessionid map).
+            proxy_cache_bypass $http_cache_control $active_user_session;
+            proxy_no_cache $http_cache_control $active_user_session;
+```
+
+- I found one client making 10,000 requests using a Windows 98 user agent:
+
+```console
+Mozilla/4.0 (compatible; MSIE 5.00; Windows 98)
+```
+
+- They all come from one IP address (129.227.149.43) in Hong Kong
+  - The IP belongs to a hosting provider called Zenlayer
+  - I will add this IP to the nginx bot networks and purge its hits
+
+```console
+$ ./ilri/check-spider-ip-hits.sh -f /tmp/ip -p
+Purging 33027 hits from 129.227.149.43 in statistics
+
+Total number of bot hits purged: 33027
+```
+
+- So it seems we've seen this bot before and the total number is much higher than the 10,000 this month
+- I had a call with Salem and we verified that the nginx cache bypass for clients who provide a JSESSIONID fixes their issue with updating items/bitstreams from MEL
+  - The issue was that they delete all metadata and bitstreams, then add them again to make sure everything is up to date, and in that process they also re-request the item with all expands to get the bitstreams, which ends up getting cached and then they try to delete the old bitstream
+- I also noticed that someone made a [pull request to enable POSTing bitstreams to a particular bundle](https://github.com/DSpace/DSpace/pull/8343) and it works, so that's awesome!
+
+## 2022-09-30
+
+- I applied [the patch for POSTing bitstreams to other bundles](https://github.com/DSpace/DSpace/pull/8343) on CGSpace
+- Testing a few other DSpace 6.4 patches on DSpace Test:
+  - [DS-3791 Make sure the "yearDifference" takes into account that a gap of 10 year contains 11 years](https://github.com/DSpace/DSpace/pull/1901)
+  - [DS-3873 Limit the usage of PDFBoxThumbnail to PDFs](https://github.com/DSpace/DSpace/pull/2501)
+  - [Reduce itemCounter init](https://github.com/DSpace/DSpace/pull/2161)
+  - [ImageMagick: Only execute "identify" on first page](https://github.com/DSpace/DSpace/pull/2201)
+  - [DS-3881: Show no total results on search-filter](https://github.com/DSpace/DSpace/pull/2371)
+  - [pass value instead of qualifier to method](https://github.com/DSpace/DSpace/pull/2699)
+  - [dspace-api: check for null AND empty qualifier in findByElement()](https://github.com/DSpace/DSpace/pull/7993)
+  - [Avoid exporting mapped Item more than once](https://github.com/DSpace/DSpace/pull/7995)
+  - [[DS-4574] v. 6 - Upgrade DBCP2 dependency](https://github.com/DSpace/DSpace/pull/3162)
+  - [bump up pdfbox version on 6.x to match main branch](https://github.com/DSpace/DSpace/pull/2742)
+
 <!-- vim: set sw=2 ts=2: -->

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
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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
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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.
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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”
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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
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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:
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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
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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
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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
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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
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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)"
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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
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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)
 
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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:
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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
 "/>
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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
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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
 "/>
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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
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docs/2017-05/index.html

@@ -18,7 +18,7 @@
 <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."/>
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docs/2017-06/index.html

@@ -18,7 +18,7 @@
 <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."/>
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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:
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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
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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
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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
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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
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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:
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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
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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
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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
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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:
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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
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docs/2018-06/index.html

@@ -58,7 +58,7 @@ real    74m42.646s
 user    8m5.056s
 sys     2m7.289s
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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.
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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
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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:
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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
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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:
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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
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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
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docs/2019-02/index.html

@@ -72,7 +72,7 @@ real    0m19.873s
 user    0m22.203s
 sys     0m1.979s
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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
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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
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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…
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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
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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
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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
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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
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docs/2019-10/index.html

@@ -18,7 +18,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="October, 2019"/>
 <meta name="twitter:description" content="2019-10-01 Udana from IWMI asked me for a CSV export of their community on CGSpace I exported it, but a quick run through the csv-metadata-quality tool shows that there are some low-hanging fruits we can fix before I send him the data I will limit the scope to the titles, regions, subregions, and river basins for now to manually fix some non-breaking spaces (U&#43;00A0) there that would otherwise be removed by the csv-metadata-quality script&rsquo;s &ldquo;unneccesary Unicode&rdquo; fix: $ csvcut -c &#39;id,dc."/>
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+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-01/index.html

@@ -56,7 +56,7 @@ I tweeted the CGSpace repository link
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-02/index.html

@@ -38,7 +38,7 @@ The code finally builds and runs with a fresh install
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-03/index.html

@@ -42,7 +42,7 @@ You need to download this into the DSpace 6.x source and compile it
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-05/index.html

@@ -34,7 +34,7 @@ I see that CGSpace (linode18) is still using PostgreSQL JDBC driver version 42.2
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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:
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-10/index.html

@@ -44,7 +44,7 @@ During the FlywayDB migration I got an error:
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-11/index.html

@@ -32,7 +32,7 @@ So far we’ve spent at least fifty hours to process the statistics and stat
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2020-12/index.html

@@ -36,7 +36,7 @@ I started processing those (about 411,000 records):
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-01/index.html

@@ -50,7 +50,7 @@ For example, this item has 51 views on CGSpace, but 0 on AReS
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-02/index.html

@@ -60,7 +60,7 @@ $ curl -s 'http://localhost:9200/openrxv-items-temp/_count?q=*&pretty&#3
   }
 }
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-03/index.html

@@ -34,7 +34,7 @@ Also, we found some issues building and running OpenRXV currently due to ecosyst
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-04/index.html

@@ -44,7 +44,7 @@ Perhaps one of the containers crashed, I should have looked closer but I was in
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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…
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-06/index.html

@@ -36,7 +36,7 @@ I simply started it and AReS was running again:
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-09/index.html

@@ -48,7 +48,7 @@ The syntax Moayad showed me last month doesn’t seem to honor the search qu
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

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
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2021-12/index.html

@@ -40,7 +40,7 @@ Purging 455 hits from WhatsApp in statistics
 
 Total number of bot hits purged: 3679
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-01/index.html

@@ -24,7 +24,7 @@ Start a full harvest on AReS
 
 Start a full harvest on AReS
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-02/index.html

@@ -38,7 +38,7 @@ We agreed to try to do more alignment of affiliations/funders with ROR
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-03/index.html

@@ -34,7 +34,7 @@ $ ./ilri/check-duplicates.py -i /tmp/tac4.csv -db dspace -u dspace -p 'fuuu&
 $ csvcut -c id,filename ~/Downloads/2022-03-01-CGSpace-TAC-ICW-batch4-701-980.csv > /tmp/tac4-filenames.csv
 $ csvjoin -c id /tmp/2022-03-01-tac-batch4-701-980.csv /tmp/tac4-filenames.csv > /tmp/2022-03-01-tac-batch4-701-980-filenames.csv
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-04/index.html

@@ -18,7 +18,7 @@
 <meta name="twitter:card" content="summary"/>
 <meta name="twitter:title" content="April, 2022"/>
 <meta name="twitter:description" content="2022-04-01 I did G1GC tests on DSpace Test (linode26) to compliment the CMS tests I did yesterday The Discovery indexing took this long: real 334m33.625s user 227m51.331s sys 3m43.037s 2022-04-04 Start a full harvest on AReS Help Marianne with submit/approve access on a new collection on CGSpace Go back in Gaia&rsquo;s batch reports to find records that she indicated for replacing on CGSpace (ie, those with better new copies, new versions, etc) Looking at the Solr statistics for 2022-03 on CGSpace I see 54."/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-05/index.html

@@ -66,7 +66,7 @@ If I query Solr for time:2022-04* AND dns:*msnbot* AND dns:*.msn.com. I see a ha
 
 I purged 93,974 hits from these IPs using my check-spider-ip-hits.sh script
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-06/index.html

@@ -48,7 +48,7 @@ There seem to be many more of these:
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-07/index.html

@@ -34,7 +34,7 @@ Also, the trgm functions I’ve used before are case insensitive, but Levens
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-08/index.html

@@ -24,7 +24,7 @@ Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
 
 Our request to add CC-BY-3.0-IGO to SPDX was approved a few weeks ago
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/2022-09/index.html

@@ -25,7 +25,7 @@ I also fixed a few bugs and improved the region-matching logic
 <meta property="og:type" content="article" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2022-09/" />
 <meta property="article:published_time" content="2022-09-01T09:41:36+03:00" />
-<meta property="article:modified_time" content="2022-09-28T17:10:23+03:00" />
+<meta property="article:modified_time" content="2022-09-28T21:22:59+03:00" />
 
 
 
@@ -46,7 +46,7 @@ I also fixed a few bugs and improved the region-matching logic
 
 
 "/>
-<meta name="generator" content="Hugo 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     
@@ -56,9 +56,9 @@ I also fixed a few bugs and improved the region-matching logic
   "@type": "BlogPosting",
   "headline": "September, 2022",
   "url": "https://alanorth.github.io/cgspace-notes/2022-09/",
-  "wordCount": "3112",
+  "wordCount": "3621",
   "datePublished": "2022-09-01T09:41:36+03:00",
-  "dateModified": "2022-09-28T17:10:23+03:00",
+  "dateModified": "2022-09-28T21:22:59+03:00",
   "author": {
     "@type": "Person",
     "name": "Alan Orth"
@@ -685,7 +685,84 @@ harvesting of meat from wildlife and not from livestock.</p>
 </span></span><span style="display:flex;"><span>Fixed 3 occurences of: Alessandra Galie: 0000-0001-9868-7733
 </span></span><span style="display:flex;"><span>Fixed 1 occurences of: Amanda De Filippo: 0000-0002-1536-3221
 </span></span><span style="display:flex;"><span>...
-</span></span></code></pre></div><!-- raw HTML omitted -->
+</span></span></code></pre></div><h2 id="2022-09-29">2022-09-29</h2>
+<ul>
+<li>I&rsquo;ve been checking the size of the nginx proxy cache the last few days and it always seems to hover around 14,000 entries and 385MB:</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># find /var/cache/nginx/rest_cache/ -type f | wc -l
+</span></span><span style="display:flex;"><span>14202
+</span></span><span style="display:flex;"><span># du -sh /var/cache/nginx/rest_cache
+</span></span><span style="display:flex;"><span>384M    /var/cache/nginx/rest_cache
+</span></span></code></pre></div><ul>
+<li>Also on that note I&rsquo;m trying to implement a workaround for a potential caching issue that causes MEL to not be able to update items on DSpace Test
+<ul>
+<li>I <em>think</em> we might need to allow requests with a JSESSIONID to bypass the cache, but I have to verify with Salem</li>
+<li>We can do this with an nginx map:</li>
+</ul>
+</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span># Check <span style="color:#66d9ef">if</span> the JSESSIONID cookie is present and contains a 32-character hex
+</span></span><span style="display:flex;"><span># value, which would mean that a user is actively attempting to re-use their
+</span></span><span style="display:flex;"><span># Tomcat session. Then we set the $active_user_session variable and use it
+</span></span><span style="display:flex;"><span># to bypass the nginx proxy cache in REST requests.
+</span></span><span style="display:flex;"><span>map $cookie_jsessionid $active_user_session {
+</span></span><span style="display:flex;"><span>    # requests with an empty key are not evaluated by limit_req
+</span></span><span style="display:flex;"><span>    # see: http://nginx.org/en/docs/http/ngx_http_limit_req_module.html
+</span></span><span style="display:flex;"><span>    default &#39;&#39;;
+</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
+</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>    &#39;~[A-Z0-9]{32}&#39; 1;
+</span></span><span style="display:flex;"><span>}
+</span></span></code></pre></div><ul>
+<li>Then in the location block where we do the proxy cache:</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>            # Don&#39;t cache when user Shift-refreshes (Cache-Control: no-cache) or
+</span></span><span style="display:flex;"><span>            # when a client has an active session (see the $cookie_jsessionid map).
+</span></span><span style="display:flex;"><span>            proxy_cache_bypass $http_cache_control $active_user_session;
+</span></span><span style="display:flex;"><span>            proxy_no_cache $http_cache_control $active_user_session;
+</span></span></code></pre></div><ul>
+<li>I found one client making 10,000 requests using a Windows 98 user agent:</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>Mozilla/4.0 (compatible; MSIE 5.00; Windows 98)
+</span></span></code></pre></div><ul>
+<li>They all come from one IP address (129.227.149.43) in Hong Kong
+<ul>
+<li>The IP belongs to a hosting provider called Zenlayer</li>
+<li>I will add this IP to the nginx bot networks and purge its hits</li>
+</ul>
+</li>
+</ul>
+<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-console" data-lang="console"><span style="display:flex;"><span>$ ./ilri/check-spider-ip-hits.sh -f /tmp/ip -p
+</span></span><span style="display:flex;"><span>Purging 33027 hits from 129.227.149.43 in statistics
+</span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010">
+</span></span></span><span style="display:flex;"><span><span style="color:#960050;background-color:#1e0010"></span>Total number of bot hits purged: 33027
+</span></span></code></pre></div><ul>
+<li>So it seems we&rsquo;ve seen this bot before and the total number is much higher than the 10,000 this month</li>
+<li>I had a call with Salem and we verified that the nginx cache bypass for clients who provide a JSESSIONID fixes their issue with updating items/bitstreams from MEL
+<ul>
+<li>The issue was that they delete all metadata and bitstreams, then add them again to make sure everything is up to date, and in that process they also re-request the item with all expands to get the bitstreams, which ends up getting cached and then they try to delete the old bitstream</li>
+</ul>
+</li>
+<li>I also noticed that someone made a <a href="https://github.com/DSpace/DSpace/pull/8343">pull request to enable POSTing bitstreams to a particular bundle</a> and it works, so that&rsquo;s awesome!</li>
+</ul>
+<h2 id="2022-09-30">2022-09-30</h2>
+<ul>
+<li>I applied <a href="https://github.com/DSpace/DSpace/pull/8343">the patch for POSTing bitstreams to other bundles</a> on CGSpace</li>
+<li>Testing a few other DSpace 6.4 patches on DSpace Test:
+<ul>
+<li><a href="https://github.com/DSpace/DSpace/pull/1901">DS-3791 Make sure the &ldquo;yearDifference&rdquo; takes into account that a gap of 10 year contains 11 years</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2501">DS-3873 Limit the usage of PDFBoxThumbnail to PDFs</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2161">Reduce itemCounter init</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2201">ImageMagick: Only execute &ldquo;identify&rdquo; on first page</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2371">DS-3881: Show no total results on search-filter</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2699">pass value instead of qualifier to method</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/7993">dspace-api: check for null AND empty qualifier in findByElement()</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/7995">Avoid exporting mapped Item more than once</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/3162">[DS-4574] v. 6 - Upgrade DBCP2 dependency</a></li>
+<li><a href="https://github.com/DSpace/DSpace/pull/2742">bump up pdfbox version on 6.x to match main branch</a></li>
+</ul>
+</li>
+</ul>
+<!-- raw HTML omitted -->
 
   
 

docs/404.html

@@ -17,7 +17,7 @@
 <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 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/categories/index.html

@@ -10,14 +10,14 @@
 <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/" />
-<meta property="og:updated_time" content="2022-09-28T17:10:23+03:00" />
+<meta property="og:updated_time" content="2022-09-28T21:22:59+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 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/categories/notes/index.html

@@ -10,14 +10,14 @@
 <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2022-09-28T17:10:23+03:00" />
+<meta property="og:updated_time" content="2022-09-28T21:22:59+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 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/categories/notes/page/2/index.html

@@ -10,14 +10,14 @@
 <meta property="og:description" content="Documenting day-to-day work on the [CGSpace](https://cgspace.cgiar.org) repository." />
 <meta property="og:type" content="website" />
 <meta property="og:url" content="https://alanorth.github.io/cgspace-notes/categories/notes/" />
-<meta property="og:updated_time" content="2022-09-28T17:10:23+03:00" />
+<meta property="og:updated_time" content="2022-09-28T21:22:59+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 0.104.1" />
+<meta name="generator" content="Hugo 0.104.2" />
 
 
     

docs/categories/notes/page/3/index.html

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