From 34eae0cbebf598cc91cb79e7acc54bafa52fc19c Mon Sep 17 00:00:00 2001 From: Alan Orth Date: Thu, 12 Mar 2020 12:58:21 +0200 Subject: [PATCH] Add notes for 2020-03-12 --- content/posts/2020-01.md | 2 +- content/posts/2020-03.md | 29 ++++++++++++++++ docs/2015-11/index.html | 2 +- docs/2015-12/index.html | 2 +- docs/2016-01/index.html | 2 +- docs/2016-02/index.html | 2 +- docs/2016-03/index.html | 2 +- docs/2016-04/index.html | 2 +- docs/2016-05/index.html | 2 +- docs/2016-06/index.html | 2 +- docs/2016-07/index.html | 2 +- docs/2016-08/index.html | 2 +- docs/2016-09/index.html | 2 +- docs/2016-10/index.html | 2 +- docs/2016-11/index.html | 2 +- docs/2016-12/index.html | 2 +- docs/2017-01/index.html | 2 +- docs/2017-02/index.html | 2 +- docs/2017-03/index.html | 2 +- docs/2017-04/index.html | 2 +- docs/2017-05/index.html | 2 +- docs/2017-06/index.html | 2 +- docs/2017-07/index.html | 2 +- docs/2017-08/index.html | 2 +- docs/2017-09/index.html | 2 +- docs/2017-10/index.html | 2 +- docs/2017-11/index.html | 2 +- docs/2017-12/index.html | 2 +- docs/2018-01/index.html | 2 +- docs/2018-02/index.html | 2 +- docs/2018-03/index.html | 2 +- docs/2018-04/index.html | 2 +- docs/2018-05/index.html | 2 +- docs/2018-06/index.html | 2 +- docs/2018-07/index.html | 2 +- docs/2018-08/index.html | 2 +- docs/2018-09/index.html | 2 +- docs/2018-10/index.html | 2 +- docs/2018-11/index.html | 2 +- docs/2018-12/index.html | 2 +- docs/2019-01/index.html | 2 +- docs/2019-02/index.html | 2 +- docs/2019-03/index.html | 2 +- docs/2019-04/index.html | 2 +- docs/2019-05/index.html | 2 +- docs/2019-06/index.html | 2 +- docs/2019-07/index.html | 2 +- docs/2019-08/index.html | 2 +- docs/2019-09/index.html | 2 +- docs/2019-10/index.html | 2 +- docs/2019-11/index.html | 2 +- docs/2019-12/index.html | 2 +- docs/2020-01/index.html | 4 +-- docs/2020-02/index.html | 2 +- docs/2020-03/index.html | 40 +++++++++++++++++++--- docs/404.html | 2 +- docs/categories/index.html | 2 +- docs/categories/notes/index.html | 2 +- docs/categories/notes/page/2/index.html | 2 +- docs/categories/notes/page/3/index.html | 2 +- docs/categories/notes/page/4/index.html | 2 +- docs/categories/page/2/index.html | 2 +- docs/categories/page/3/index.html | 2 +- docs/categories/page/4/index.html | 2 +- docs/categories/page/5/index.html | 2 +- docs/categories/page/6/index.html | 2 +- docs/cgiar-library-migration/index.html | 2 +- docs/cgspace-cgcorev2-migration/index.html | 2 +- docs/index.html | 2 +- docs/page/2/index.html | 2 +- docs/page/3/index.html | 2 +- docs/page/4/index.html | 2 +- docs/page/5/index.html | 2 +- docs/page/6/index.html | 2 +- docs/posts/index.html | 2 +- docs/posts/page/2/index.html | 2 +- docs/posts/page/3/index.html | 2 +- docs/posts/page/4/index.html | 2 +- docs/posts/page/5/index.html | 2 +- docs/posts/page/6/index.html | 2 +- docs/sitemap.xml | 10 +++--- docs/tags/index.html | 2 +- docs/tags/migration/index.html | 2 +- docs/tags/notes/index.html | 2 +- docs/tags/notes/page/2/index.html | 2 +- docs/tags/notes/page/3/index.html | 2 +- docs/tags/page/2/index.html | 2 +- docs/tags/page/3/index.html | 2 +- docs/tags/page/4/index.html | 2 +- docs/tags/page/5/index.html | 2 +- docs/tags/page/6/index.html | 2 +- 91 files changed, 158 insertions(+), 99 deletions(-) diff --git a/content/posts/2020-01.md b/content/posts/2020-01.md index 80df3f834..305a77ecc 100644 --- a/content/posts/2020-01.md +++ b/content/posts/2020-01.md @@ -128,7 +128,7 @@ COPY 35 - I corrected one invalid AGROVOC subject - Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine: - `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id` - - I always forget how to copy the reconciled values in OpenRefine, but you need to make a new colum and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)` + - I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)` ## 2020-01-20 diff --git a/content/posts/2020-03.md b/content/posts/2020-03.md index 3974ebc86..0e9029ce9 100644 --- a/content/posts/2020-03.md +++ b/content/posts/2020-03.md @@ -203,4 +203,33 @@ Purging 62 hits from [Ss]pider in statistics (DEBUG) Checking for hits from spider: Apache-HttpClient ``` +## 2020-03-11 + +- Ask Michael Victor for permission to create a new Linode server for DSpace Test + +## 2020-3-12 + +- I'm working on the 170 IITA records on [DSpace Test](https://dspacetest.cgiar.org/handle/10568/106567) from January finally + - It's been two months since I last looked and I want to do a thorough check to make sure Bosede didn't introduce any new issues, but I want to consolidate all the text languages for these records so it's easier to check them in OpenRefine + - First I got a list of IDs from `csvcut` and then I updated the text languages for only those records: + +``` +dspace=# SELECT DISTINCT text_lang, COUNT(*) FROM metadatavalue WHERE resource_type_id=2 AND resource_id in (111295,111294,111293,111292,111291,111290,111288,111286,111285,111284,111283,111282,111281,111280,111279,111278,111277,111276,111275,111274,111273,111272,111271,111270,111269,111268,111267,111266,111265,111264,111263,111262,111261,111260,111259,111258,111257,111256,111255,111254,111253,111252,111251,111250,111249,111248,111247,111246,111245,111244,111243,111242,111241,111240,111238,111237,111236,111235,111234,111233,111232,111231,111230,111229,111228,111227,111226,111225,111224,111223,111222,111221,111220,111219,111218,111217,111216,111215,111214,111213,111212,111211,111209,111208,111207,111206,111205,111204,111203,111202,111201,111200,111199,111198,111197,111196,111195,111194,111193,111192,111191,111190,111189,111188,111187,111186,111185,111184,111183,111182,111181,111180,111179,111178,111177,111176,111175,111174,111173,111172,111171,111170,111169,111168,111299,111298,111297,111296,111167,111166,111165,111164,111163,111162,111161,111160,111159,111158,111157,111156,111155,111154,111153,111152,111151,111150,111149,111148,111147,111146,111145,111144,111143,111142,111141,111140,111139,111138,111137,111136,111135,111134,111133,111132,111131,111129,111128,111127,111126,111125) GROUP BY text_lang ORDER BY count; +``` + +- Then I exported the metadata from DSpace Test and imported it into OpenRefine + - I corrected one invalid AGROVOC subject using my `csv-metadata-quality` script +- I exported a new list of affiliations from the database, added line numbers with `csvcut`, and then validated them in OpenRefine using `reconcile-csv`: + + +``` +dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2020-03-12-affiliations.csv WITH CSV HEADER;` +dspace=# \q +$ csvcut -l -c 0 /tmp/2020-03-12-affiliations.csv | sed -e 's/^line_number/id/' -e 's/text_value/name/' > /tmp/affiliations.csv +$ lein run /tmp/affiliations.csv name id +``` + +- I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)` +- I mapped all 170 items to their appropriate collections based on type and uploaded them to CGSpace + diff --git a/docs/2015-11/index.html b/docs/2015-11/index.html index 6c8bbfa72..2e22d2390 100644 --- a/docs/2015-11/index.html +++ b/docs/2015-11/index.html @@ -31,7 +31,7 @@ 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 "/> - + diff --git a/docs/2015-12/index.html b/docs/2015-12/index.html index 45af0d442..15bc4b266 100644 --- a/docs/2015-12/index.html +++ b/docs/2015-12/index.html @@ -33,7 +33,7 @@ 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 "/> - + diff --git a/docs/2016-01/index.html b/docs/2016-01/index.html index 1d23d5b67..4d7934aa3 100644 --- a/docs/2016-01/index.html +++ b/docs/2016-01/index.html @@ -25,7 +25,7 @@ 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. "/> - + diff --git a/docs/2016-02/index.html b/docs/2016-02/index.html index 179fc732c..c6349785b 100644 --- a/docs/2016-02/index.html +++ b/docs/2016-02/index.html @@ -35,7 +35,7 @@ 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” "/> - + diff --git a/docs/2016-03/index.html b/docs/2016-03/index.html index 9b1130d08..e408a39ed 100644 --- a/docs/2016-03/index.html +++ b/docs/2016-03/index.html @@ -25,7 +25,7 @@ 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 "/> - + diff --git a/docs/2016-04/index.html b/docs/2016-04/index.html index 11a185b96..ee7677290 100644 --- a/docs/2016-04/index.html +++ b/docs/2016-04/index.html @@ -29,7 +29,7 @@ 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: "/> - + diff --git a/docs/2016-05/index.html b/docs/2016-05/index.html index 3b91cf455..6cbf4ad4e 100644 --- a/docs/2016-05/index.html +++ b/docs/2016-05/index.html @@ -31,7 +31,7 @@ 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 "/> - + diff --git a/docs/2016-06/index.html b/docs/2016-06/index.html index e83686ace..2107a8efd 100644 --- a/docs/2016-06/index.html +++ b/docs/2016-06/index.html @@ -31,7 +31,7 @@ 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 "/> - + diff --git a/docs/2016-07/index.html b/docs/2016-07/index.html index 067c7f063..4060b69b1 100644 --- a/docs/2016-07/index.html +++ b/docs/2016-07/index.html @@ -41,7 +41,7 @@ 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 "/> - + diff --git a/docs/2016-08/index.html b/docs/2016-08/index.html index 47ba66ad7..765b95af5 100644 --- a/docs/2016-08/index.html +++ b/docs/2016-08/index.html @@ -39,7 +39,7 @@ $ git checkout -b 55new 5_x-prod $ git reset --hard ilri/5_x-prod $ git rebase -i dspace-5.5 "/> - + diff --git a/docs/2016-09/index.html b/docs/2016-09/index.html index 0150c57ea..f04a1664a 100644 --- a/docs/2016-09/index.html +++ b/docs/2016-09/index.html @@ -31,7 +31,7 @@ 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)" "/> - + diff --git a/docs/2016-10/index.html b/docs/2016-10/index.html index b5df5b23d..67025f15e 100644 --- a/docs/2016-10/index.html +++ b/docs/2016-10/index.html @@ -39,7 +39,7 @@ 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 "/> - + diff --git a/docs/2016-11/index.html b/docs/2016-11/index.html index 5a0ddf24b..b39e8438c 100644 --- a/docs/2016-11/index.html +++ b/docs/2016-11/index.html @@ -23,7 +23,7 @@ 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) "/> - + diff --git a/docs/2016-12/index.html b/docs/2016-12/index.html index 376e6e0e3..ae6fc1103 100644 --- a/docs/2016-12/index.html +++ b/docs/2016-12/index.html @@ -43,7 +43,7 @@ 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: "/> - + diff --git a/docs/2017-01/index.html b/docs/2017-01/index.html index b314645df..4efd93196 100644 --- a/docs/2017-01/index.html +++ b/docs/2017-01/index.html @@ -25,7 +25,7 @@ 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 "/> - + diff --git a/docs/2017-02/index.html b/docs/2017-02/index.html index 75656e2c2..ee7d5907d 100644 --- a/docs/2017-02/index.html +++ b/docs/2017-02/index.html @@ -47,7 +47,7 @@ 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 "/> - + diff --git a/docs/2017-03/index.html b/docs/2017-03/index.html index 820b7c2c0..743f3399b 100644 --- a/docs/2017-03/index.html +++ b/docs/2017-03/index.html @@ -51,7 +51,7 @@ 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 "/> - + diff --git a/docs/2017-04/index.html b/docs/2017-04/index.html index 724d75c1e..b5134b7c9 100644 --- a/docs/2017-04/index.html +++ b/docs/2017-04/index.html @@ -37,7 +37,7 @@ 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 "/> - + diff --git a/docs/2017-05/index.html b/docs/2017-05/index.html index 6aafff040..fd7ff1150 100644 --- a/docs/2017-05/index.html +++ b/docs/2017-05/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2017-06/index.html b/docs/2017-06/index.html index 00ec9c32e..df18ef880 100644 --- a/docs/2017-06/index.html +++ b/docs/2017-06/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2017-07/index.html b/docs/2017-07/index.html index f3a83c9c0..38b940899 100644 --- a/docs/2017-07/index.html +++ b/docs/2017-07/index.html @@ -33,7 +33,7 @@ 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: "/> - + diff --git a/docs/2017-08/index.html b/docs/2017-08/index.html index 0f6e562f1..02ac95370 100644 --- a/docs/2017-08/index.html +++ b/docs/2017-08/index.html @@ -57,7 +57,7 @@ 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 "/> - + diff --git a/docs/2017-09/index.html b/docs/2017-09/index.html index 195d693fd..f7446364e 100644 --- a/docs/2017-09/index.html +++ b/docs/2017-09/index.html @@ -29,7 +29,7 @@ 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 "/> - + diff --git a/docs/2017-10/index.html b/docs/2017-10/index.html index 87cdede3d..3cfa8e1a7 100644 --- a/docs/2017-10/index.html +++ b/docs/2017-10/index.html @@ -31,7 +31,7 @@ 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 "/> - + diff --git a/docs/2017-11/index.html b/docs/2017-11/index.html index 5f6c8071d..d398c951c 100644 --- a/docs/2017-11/index.html +++ b/docs/2017-11/index.html @@ -45,7 +45,7 @@ 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 "/> - + diff --git a/docs/2017-12/index.html b/docs/2017-12/index.html index 6f37869ab..fa835ea8a 100644 --- a/docs/2017-12/index.html +++ b/docs/2017-12/index.html @@ -27,7 +27,7 @@ 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: "/> - + diff --git a/docs/2018-01/index.html b/docs/2018-01/index.html index 162402ed3..2d374b8b2 100644 --- a/docs/2018-01/index.html +++ b/docs/2018-01/index.html @@ -147,7 +147,7 @@ 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 "/> - + diff --git a/docs/2018-02/index.html b/docs/2018-02/index.html index 94359022d..e70c47361 100644 --- a/docs/2018-02/index.html +++ b/docs/2018-02/index.html @@ -27,7 +27,7 @@ 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 "/> - + diff --git a/docs/2018-03/index.html b/docs/2018-03/index.html index 0de1e4014..28b30104e 100644 --- a/docs/2018-03/index.html +++ b/docs/2018-03/index.html @@ -21,7 +21,7 @@ Export a CSV of the IITA community metadata for Martin Mueller Export a CSV of the IITA community metadata for Martin Mueller "/> - + diff --git a/docs/2018-04/index.html b/docs/2018-04/index.html index d3346ff99..ebea64aed 100644 --- a/docs/2018-04/index.html +++ b/docs/2018-04/index.html @@ -23,7 +23,7 @@ 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: "/> - + diff --git a/docs/2018-05/index.html b/docs/2018-05/index.html index 9c21436cb..ba5757314 100644 --- a/docs/2018-05/index.html +++ b/docs/2018-05/index.html @@ -35,7 +35,7 @@ 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 "/> - + diff --git a/docs/2018-06/index.html b/docs/2018-06/index.html index 27afbb4bb..d7d8fd343 100644 --- a/docs/2018-06/index.html +++ b/docs/2018-06/index.html @@ -55,7 +55,7 @@ real 74m42.646s user 8m5.056s sys 2m7.289s "/> - + diff --git a/docs/2018-07/index.html b/docs/2018-07/index.html index 7dc2a779a..bb791391d 100644 --- a/docs/2018-07/index.html +++ b/docs/2018-07/index.html @@ -33,7 +33,7 @@ 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. "/> - + diff --git a/docs/2018-08/index.html b/docs/2018-08/index.html index ec5b44d6f..d4dc4497f 100644 --- a/docs/2018-08/index.html +++ b/docs/2018-08/index.html @@ -43,7 +43,7 @@ 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 "/> - + diff --git a/docs/2018-09/index.html b/docs/2018-09/index.html index ac9869b22..375f20229 100644 --- a/docs/2018-09/index.html +++ b/docs/2018-09/index.html @@ -27,7 +27,7 @@ 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: "/> - + diff --git a/docs/2018-10/index.html b/docs/2018-10/index.html index 3d756690a..e995c0e89 100644 --- a/docs/2018-10/index.html +++ b/docs/2018-10/index.html @@ -23,7 +23,7 @@ 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 "/> - + diff --git a/docs/2018-11/index.html b/docs/2018-11/index.html index d3ba8b9ba..3b948e55f 100644 --- a/docs/2018-11/index.html +++ b/docs/2018-11/index.html @@ -33,7 +33,7 @@ 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: "/> - + diff --git a/docs/2018-12/index.html b/docs/2018-12/index.html index 93a3d7bb9..0386eff0c 100644 --- a/docs/2018-12/index.html +++ b/docs/2018-12/index.html @@ -33,7 +33,7 @@ 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 "/> - + diff --git a/docs/2019-01/index.html b/docs/2019-01/index.html index e7eabc715..a1e221046 100644 --- a/docs/2019-01/index.html +++ b/docs/2019-01/index.html @@ -47,7 +47,7 @@ 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 "/> - + diff --git a/docs/2019-02/index.html b/docs/2019-02/index.html index cd967c050..9d2543cec 100644 --- a/docs/2019-02/index.html +++ b/docs/2019-02/index.html @@ -69,7 +69,7 @@ real 0m19.873s user 0m22.203s sys 0m1.979s "/> - + diff --git a/docs/2019-03/index.html b/docs/2019-03/index.html index 05a2f26de..9f1a3a452 100644 --- a/docs/2019-03/index.html +++ b/docs/2019-03/index.html @@ -43,7 +43,7 @@ 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 "/> - + diff --git a/docs/2019-04/index.html b/docs/2019-04/index.html index b0247114a..bde203dde 100644 --- a/docs/2019-04/index.html +++ b/docs/2019-04/index.html @@ -61,7 +61,7 @@ $ ./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 "/> - + diff --git a/docs/2019-05/index.html b/docs/2019-05/index.html index d25d61007..f5ae145c6 100644 --- a/docs/2019-05/index.html +++ b/docs/2019-05/index.html @@ -45,7 +45,7 @@ DELETE 1 But after this I tried to delete the item from the XMLUI and it is still present… "/> - + diff --git a/docs/2019-06/index.html b/docs/2019-06/index.html index 790c6ec31..5bd53a151 100644 --- a/docs/2019-06/index.html +++ b/docs/2019-06/index.html @@ -31,7 +31,7 @@ Run system updates on CGSpace (linode18) and reboot it Skype with Marie-Angélique and Abenet about CG Core v2 "/> - + diff --git a/docs/2019-07/index.html b/docs/2019-07/index.html index 92c3f24dc..25b0d3d8d 100644 --- a/docs/2019-07/index.html +++ b/docs/2019-07/index.html @@ -35,7 +35,7 @@ CGSpace Abenet had another similar issue a few days ago when trying to find the stats for 2018 in the RTB community "/> - + diff --git a/docs/2019-08/index.html b/docs/2019-08/index.html index 727414d36..c1cc11b43 100644 --- a/docs/2019-08/index.html +++ b/docs/2019-08/index.html @@ -43,7 +43,7 @@ After rebooting, all statistics cores were loaded… wow, that’s luck Run system updates on DSpace Test (linode19) and reboot it "/> - + diff --git a/docs/2019-09/index.html b/docs/2019-09/index.html index 086c75bda..a697233f3 100644 --- a/docs/2019-09/index.html +++ b/docs/2019-09/index.html @@ -69,7 +69,7 @@ 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 "/> - + diff --git a/docs/2019-10/index.html b/docs/2019-10/index.html index b0427b8fb..87b483bac 100644 --- a/docs/2019-10/index.html +++ b/docs/2019-10/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/2019-11/index.html b/docs/2019-11/index.html index db91d1fa6..59e1d6da7 100644 --- a/docs/2019-11/index.html +++ b/docs/2019-11/index.html @@ -55,7 +55,7 @@ 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 "/> - + diff --git a/docs/2019-12/index.html b/docs/2019-12/index.html index 01742ddaa..e8b96ac1d 100644 --- a/docs/2019-12/index.html +++ b/docs/2019-12/index.html @@ -43,7 +43,7 @@ Make sure all packages are up to date and the package manager is up to date, the # dpkg -C # reboot "/> - + diff --git a/docs/2020-01/index.html b/docs/2020-01/index.html index 4b601729c..edff90279 100644 --- a/docs/2020-01/index.html +++ b/docs/2020-01/index.html @@ -53,7 +53,7 @@ I tweeted the CGSpace repository link "/> - + @@ -257,7 +257,7 @@ COPY 35
  • Validate and normalize affiliations against our 2019-04 list using reconcile-csv and OpenRefine:
    • diff --git a/docs/2020-02/index.html b/docs/2020-02/index.html index 59c18ccaa..5e118a278 100644 --- a/docs/2020-02/index.html +++ b/docs/2020-02/index.html @@ -35,7 +35,7 @@ The code finally builds and runs with a fresh install "/> - + diff --git a/docs/2020-03/index.html b/docs/2020-03/index.html index 2b7012c48..cbba247c1 100644 --- a/docs/2020-03/index.html +++ b/docs/2020-03/index.html @@ -22,7 +22,7 @@ You need to download this into the DSpace 6.x source and compile it - + @@ -39,7 +39,7 @@ You need to download this into the DSpace 6.x source and compile it "/> - + @@ -49,9 +49,9 @@ You need to download this into the DSpace 6.x source and compile it "@type": "BlogPosting", "headline": "March, 2020", "url": "https:\/\/alanorth.github.io\/cgspace-notes\/2020-03\/", - "wordCount": "1102", + "wordCount": "1358", "datePublished": "2020-03-02T12:31:30+02:00", - "dateModified": "2020-03-08T15:53:34+02:00", + "dateModified": "2020-03-10T16:18:20+02:00", "author": { "@type": "Person", "name": "Alan Orth" @@ -321,7 +321,37 @@ Purging 62 hits from [Ss]pider in statistics (DEBUG) Checking for hits from spider: Typhoeus (DEBUG) Checking for hits from spider: 7siters (DEBUG) Checking for hits from spider: Apache-HttpClient - +

    2020-03-11

    + +

    2020-3-12

    + +
    dspace=# SELECT DISTINCT text_lang, COUNT(*) FROM metadatavalue WHERE resource_type_id=2 AND resource_id in (111295,111294,111293,111292,111291,111290,111288,111286,111285,111284,111283,111282,111281,111280,111279,111278,111277,111276,111275,111274,111273,111272,111271,111270,111269,111268,111267,111266,111265,111264,111263,111262,111261,111260,111259,111258,111257,111256,111255,111254,111253,111252,111251,111250,111249,111248,111247,111246,111245,111244,111243,111242,111241,111240,111238,111237,111236,111235,111234,111233,111232,111231,111230,111229,111228,111227,111226,111225,111224,111223,111222,111221,111220,111219,111218,111217,111216,111215,111214,111213,111212,111211,111209,111208,111207,111206,111205,111204,111203,111202,111201,111200,111199,111198,111197,111196,111195,111194,111193,111192,111191,111190,111189,111188,111187,111186,111185,111184,111183,111182,111181,111180,111179,111178,111177,111176,111175,111174,111173,111172,111171,111170,111169,111168,111299,111298,111297,111296,111167,111166,111165,111164,111163,111162,111161,111160,111159,111158,111157,111156,111155,111154,111153,111152,111151,111150,111149,111148,111147,111146,111145,111144,111143,111142,111141,111140,111139,111138,111137,111136,111135,111134,111133,111132,111131,111129,111128,111127,111126,111125) GROUP BY text_lang ORDER BY count;
+
    +
    dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2020-03-12-affiliations.csv WITH CSV HEADER;`
+dspace=# \q
+$ csvcut -l -c 0 /tmp/2020-03-12-affiliations.csv | sed -e 's/^line_number/id/' -e 's/text_value/name/' > /tmp/affiliations.csv
+$ lein run /tmp/affiliations.csv name id
+
    + diff --git a/docs/404.html b/docs/404.html index 188f36f9e..5ff5f2a9f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/index.html b/docs/categories/index.html index 3ee6fc3a5..6c848c9f2 100644 --- a/docs/categories/index.html +++ b/docs/categories/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/index.html b/docs/categories/notes/index.html index c24ab46d6..0e6da737f 100644 --- a/docs/categories/notes/index.html +++ b/docs/categories/notes/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/2/index.html b/docs/categories/notes/page/2/index.html index f62933283..e28bd5de5 100644 --- a/docs/categories/notes/page/2/index.html +++ b/docs/categories/notes/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/3/index.html b/docs/categories/notes/page/3/index.html index 49f498169..773d11ce2 100644 --- a/docs/categories/notes/page/3/index.html +++ b/docs/categories/notes/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/notes/page/4/index.html b/docs/categories/notes/page/4/index.html index c96f8e2a4..c2cf9eb2f 100644 --- a/docs/categories/notes/page/4/index.html +++ b/docs/categories/notes/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/2/index.html b/docs/categories/page/2/index.html index 1c9c15353..61e6bd5aa 100644 --- a/docs/categories/page/2/index.html +++ b/docs/categories/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/3/index.html b/docs/categories/page/3/index.html index 20a64e363..7df72ad87 100644 --- a/docs/categories/page/3/index.html +++ b/docs/categories/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/4/index.html b/docs/categories/page/4/index.html index d312afacf..0b67d7a90 100644 --- a/docs/categories/page/4/index.html +++ b/docs/categories/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/5/index.html b/docs/categories/page/5/index.html index 12970a022..0dc63c987 100644 --- a/docs/categories/page/5/index.html +++ b/docs/categories/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/categories/page/6/index.html b/docs/categories/page/6/index.html index 95a68118c..f6a34a5fa 100644 --- a/docs/categories/page/6/index.html +++ b/docs/categories/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/cgiar-library-migration/index.html b/docs/cgiar-library-migration/index.html index c9791012e..2f590b73f 100644 --- a/docs/cgiar-library-migration/index.html +++ b/docs/cgiar-library-migration/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/cgspace-cgcorev2-migration/index.html b/docs/cgspace-cgcorev2-migration/index.html index 500348773..120866abb 100644 --- a/docs/cgspace-cgcorev2-migration/index.html +++ b/docs/cgspace-cgcorev2-migration/index.html @@ -15,7 +15,7 @@ - + diff --git a/docs/index.html b/docs/index.html index db2786dca..213235052 100644 --- a/docs/index.html +++ b/docs/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/2/index.html b/docs/page/2/index.html index 52a4607cb..b1285deaf 100644 --- a/docs/page/2/index.html +++ b/docs/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/3/index.html b/docs/page/3/index.html index 9d5d59225..36e716c5c 100644 --- a/docs/page/3/index.html +++ b/docs/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/4/index.html b/docs/page/4/index.html index fcd321b35..625d2c35c 100644 --- a/docs/page/4/index.html +++ b/docs/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/5/index.html b/docs/page/5/index.html index 74603cd53..3a4a3cbc5 100644 --- a/docs/page/5/index.html +++ b/docs/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/page/6/index.html b/docs/page/6/index.html index 12574113b..0335bf70a 100644 --- a/docs/page/6/index.html +++ b/docs/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/index.html b/docs/posts/index.html index d82d1e50d..c89939ad8 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/2/index.html b/docs/posts/page/2/index.html index 38c05219b..ca6fcbc8c 100644 --- a/docs/posts/page/2/index.html +++ b/docs/posts/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/3/index.html b/docs/posts/page/3/index.html index cb8410614..1fcbb7f26 100644 --- a/docs/posts/page/3/index.html +++ b/docs/posts/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/4/index.html b/docs/posts/page/4/index.html index 5ab5a940e..de5ad2893 100644 --- a/docs/posts/page/4/index.html +++ b/docs/posts/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/5/index.html b/docs/posts/page/5/index.html index 78e712fbf..132586af0 100644 --- a/docs/posts/page/5/index.html +++ b/docs/posts/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/posts/page/6/index.html b/docs/posts/page/6/index.html index b0a381df2..463cb325f 100644 --- a/docs/posts/page/6/index.html +++ b/docs/posts/page/6/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 222869ee5..ecfd0c90f 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -4,27 +4,27 @@ https://alanorth.github.io/cgspace-notes/categories/ - 2020-03-08T15:53:34+02:00 + 2020-03-10T16:18:20+02:00 https://alanorth.github.io/cgspace-notes/ - 2020-03-08T15:53:34+02:00 + 2020-03-10T16:18:20+02:00 https://alanorth.github.io/cgspace-notes/2020-03/ - 2020-03-08T15:53:34+02:00 + 2020-03-10T16:18:20+02:00 https://alanorth.github.io/cgspace-notes/categories/notes/ - 2020-03-08T15:53:34+02:00 + 2020-03-10T16:18:20+02:00 https://alanorth.github.io/cgspace-notes/posts/ - 2020-03-08T15:53:34+02:00 + 2020-03-10T16:18:20+02:00 diff --git a/docs/tags/index.html b/docs/tags/index.html index 56e73c4fd..c025e86eb 100644 --- a/docs/tags/index.html +++ b/docs/tags/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/migration/index.html b/docs/tags/migration/index.html index 064890370..9978ff0e9 100644 --- a/docs/tags/migration/index.html +++ b/docs/tags/migration/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/index.html b/docs/tags/notes/index.html index 1ab7ee995..16de8ef3a 100644 --- a/docs/tags/notes/index.html +++ b/docs/tags/notes/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/page/2/index.html b/docs/tags/notes/page/2/index.html index 597b58930..beda050d0 100644 --- a/docs/tags/notes/page/2/index.html +++ b/docs/tags/notes/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/notes/page/3/index.html b/docs/tags/notes/page/3/index.html index f626a6ed7..72ea96b67 100644 --- a/docs/tags/notes/page/3/index.html +++ b/docs/tags/notes/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/2/index.html b/docs/tags/page/2/index.html index 95f6c56e0..06d04ea93 100644 --- a/docs/tags/page/2/index.html +++ b/docs/tags/page/2/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/3/index.html b/docs/tags/page/3/index.html index 474c14bf1..c2b6b674e 100644 --- a/docs/tags/page/3/index.html +++ b/docs/tags/page/3/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/4/index.html b/docs/tags/page/4/index.html index b872806df..5d3825554 100644 --- a/docs/tags/page/4/index.html +++ b/docs/tags/page/4/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/5/index.html b/docs/tags/page/5/index.html index 0c0c614df..81ec4ef72 100644 --- a/docs/tags/page/5/index.html +++ b/docs/tags/page/5/index.html @@ -14,7 +14,7 @@ - + diff --git a/docs/tags/page/6/index.html b/docs/tags/page/6/index.html index 6e9bcf83e..f0a94f5e0 100644 --- a/docs/tags/page/6/index.html +++ b/docs/tags/page/6/index.html @@ -14,7 +14,7 @@ - +