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230 lines
12 KiB
Markdown
230 lines
12 KiB
Markdown
---
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title: "August, 2021"
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date: 2021-08-01T09:01:07+03:00
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author: "Alan Orth"
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categories: ["Notes"]
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---
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## 2021-08-01
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- Update Docker images on AReS server (linode20) and reboot the server:
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```console
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# docker images | grep -v ^REPO | sed 's/ \+/:/g' | cut -d: -f1,2 | grep -v none | xargs -L1 docker pull
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```
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- I decided to upgrade linode20 from Ubuntu 18.04 to 20.04
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<!--more-->
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- First running all existing updates, taking some backups, checking for broken packages, and then rebooting:
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```console
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# apt update && apt dist-upgrade
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# apt autoremove && apt autoclean
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# check for any packages with residual configs we can purge
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# dpkg -l | grep -E '^rc' | awk '{print $2}'
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# dpkg -l | grep -E '^rc' | awk '{print $2}' | xargs dpkg -P
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# dpkg -C
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# dpkg -l > 2021-08-01-linode20-dpkg.txt
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# tar -I zstd -cvf 2021-08-01-etc.tar.zst /etc
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# reboot
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# sed -i 's/bionic/focal/' /etc/apt/sources.list.d/*.list
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# do-release-upgrade
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```
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- ... but of course it hit [the libxcrypt bug](https://bugs.launchpad.net/ubuntu/+source/libxcrypt/+bug/1903838)
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- I had to get a copy of libcrypt.so.1.1.0 from a working Ubuntu 20.04 system and finish the upgrade manually
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```console
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# apt install -f
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# apt dist-upgrade
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# reboot
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```
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- After rebooting I purged all packages with residual configs and cleaned up again:
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```console
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# dpkg -l | grep -E '^rc' | awk '{print $2}' | xargs dpkg -P
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# apt autoremove && apt autoclean
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```
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- Then I cleared my local Ansible fact cache and re-ran the [infrastructure playbooks](https://github.com/ilri/rmg-ansible-public)
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- Open [an issue for the value mappings global replacement bug in OpenRXV](https://github.com/ilri/OpenRXV/issues/111)
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- Advise Peter and Abenet on expected CGSpace budget for 2022
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- Start a fresh harvesting on AReS (linode20)
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## 2021-08-02
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- Help Udana with OAI validation on CGSpace
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- He was checking the OAI base URL on OpenArchives and I had to verify the results in order to proceed to Step 2
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- Now it seems to be verified (all green): https://www.openarchives.org/Register/ValidateSite?log=R23ZWX85
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- We are listed in the OpenArchives list of databases conforming to OAI 2.0
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## 2021-08-03
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- Run fresh re-harvest on AReS
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## 2021-08-05
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- Have a quick call with Mishell Portilla from CIP about a journal article that was flagged as being in a predatory journal (Beall's List)
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- We agreed to unmap it from RTB's collection for now, and I asked for advice from Peter and Abenet for what to do in the future
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- A developer from the Alliance asked for access to the CGSpace database so they can make some integration with PowerBI
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- I told them we don't allow direct database access, and that it would be tricky anyways (that's what APIs are for!)
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- I'm curious if there are still any requests coming in to CGSpace from the abusive Russian networks
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- I extracted all the unique IPs that nginx processed in the last week:
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```console
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# zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2 /var/log/nginx/access.log.3 /var/log/nginx/access.log.4 /var/log/nginx/access.log.5 /var/log/nginx/access.log.6 /var/log/nginx/access.log.7 /var/log/nginx/access.log.8 | grep -E " (200|499) " | grep -v -E "(mahider|Googlebot|Turnitin|Grammarly|Unpaywall|UptimeRobot|bot)" | awk '{print $1}' | sort | uniq > /tmp/2021-08-05-all-ips.txt
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# wc -l /tmp/2021-08-05-all-ips.txt
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43428 /tmp/2021-08-05-all-ips.txt
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```
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- Already I can see that the total is much less than during the attack on one weekend last month (over 50,000!)
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- Indeed, now I see that there are no IPs from those networks coming in now:
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```console
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$ ./ilri/resolve-addresses-geoip2.py -i /tmp/2021-08-05-all-ips.txt -o /tmp/2021-08-05-all-ips.csv
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$ csvgrep -c asn -r '^(49453|46844|206485|62282|36352|35913|35624|8100)$' /tmp/2021-08-05-all-ips.csv | csvcut -c ip | sed 1d | sort | uniq > /tmp/2021-08-05-all-ips-to-purge.csv
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$ wc -l /tmp/2021-08-05-all-ips-to-purge.csv
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0 /tmp/2021-08-05-all-ips-to-purge.csv
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```
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## 2021-08-08
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- Advise IWMI colleagues on best practices for thumbnails
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- Add a handful of mappings for incorrect countries, regions, and licenses on AReS and start a new harvest
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- I sent a message to Jacquie from WorldFish to ask if I can help her clean up the incorrect countries and regions in their repository, for example:
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- WorldFish countries: Aegean, Euboea, Caribbean Sea, Caspian Sea, Chilwa Lake, Imo River, Indian Ocean, Indo-pacific
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- WorldFish regions: Black Sea, Arabian Sea, Caribbean Sea, California Gulf, Mediterranean Sea, North Sea, Red Sea
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- Looking at the July Solr statistics to find the top IP and user agents, looking for anything strange
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- 35.174.144.154 made 11,000 requests last month with the following user agent:
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```console
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Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_3) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/78.0.3904.97 Safari/537.36
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```
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- That IP is on Amazon, and from looking at the DSpace logs I don't see them logging in at all, only scraping... so I will purge hits from that IP
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- I see 93.158.90.30 is some Swedish IP that also has a normal-looking user agent, but never logs in and requests thousands of XMLUI pages, I will purge their hits too
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- Same deal with 130.255.162.173, which is also in Sweden and makes requests every five seconds or so
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- Same deal with 93.158.90.91, also in Sweden
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- 3.225.28.105 uses a normal-looking user agent but makes thousands of request to the REST API a few seconds apart
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- 61.143.40.50 is in China and uses this hilarious user agent:
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```console
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Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/79.0.3945.{random.randint(0, 9999)} Safari/537.{random.randint(0, 99)}"
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```
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- 47.252.80.214 is owned by Alibaba in the US and has the same user agent
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- 159.138.131.15 is in Hong Kong and also seems to be a bot because I never see it log in and it downloads 4,300 PDFs over the course of a few hours
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- 95.87.154.12 seems to be a new bot with the following user agent:
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```console
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Mozilla/5.0 (compatible; MaCoCu; +https://www.clarin.si/info/macocu-massive-collection-and-curation-of-monolingual-and-bilingual-data/
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```
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- They have a legitimate EU-funded project to enrich data for under-resourced languages in the EU
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- I will purge the hits and add them to our list of bot overrides in the mean time before I submit it to COUNTER-Robots
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- I see a new bot using this user agent:
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```console
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nettle (+https://www.nettle.sk)
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```
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- 129.0.211.251 is in Cameroon and uses a normal-looking user agent, but seems to be a bot of some sort, as it downloaded 900 PDFs over a short period.
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- 217.182.21.193 is on OVH in France and uses a Linux user agent, but never logs in and makes several requests per minute, over 1,000 in a day
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- 103.135.104.139 is in Hong Kong and also seems to be making real requests, but makes way too many to be a human
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- There are probably more but that's most of them over 1,000 hits last month, so I will purge them:
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```console
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$ ./ilri/check-spider-ip-hits.sh -f /tmp/ips.txt -p
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Purging 10796 hits from 35.174.144.154 in statistics
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Purging 9993 hits from 93.158.90.30 in statistics
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Purging 6092 hits from 130.255.162.173 in statistics
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Purging 24863 hits from 3.225.28.105 in statistics
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Purging 2988 hits from 93.158.90.91 in statistics
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Purging 2497 hits from 61.143.40.50 in statistics
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Purging 13866 hits from 159.138.131.15 in statistics
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Purging 2721 hits from 95.87.154.12 in statistics
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Purging 2786 hits from 47.252.80.214 in statistics
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Purging 1485 hits from 129.0.211.251 in statistics
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Purging 8952 hits from 217.182.21.193 in statistics
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Purging 3446 hits from 103.135.104.139 in statistics
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Total number of bot hits purged: 90485
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```
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- Then I purged a few thousand more by user agent:
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```console
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$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri
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Found 2707 hits from MaCoCu in statistics
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Found 1785 hits from nettle in statistics
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Total number of hits from bots: 4492
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```
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- I found some CGSpace metadata in the wrong fields
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- Seven metadata in dc.subject (57) should be in dcterms.subject (187)
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- Twelve metadata in cg.title.journal (202) should be in cg.journal (251)
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- Three dc.identifier.isbn (20) should be in cg.isbn (252)
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- Three dc.identifier.issn (21) should be in cg.issn (253)
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- I re-ran the `migrate-fields.sh` script on CGSpace
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- I exported the entire CGSpace repository as a CSV to do some work on ISSNs and ISBNs:
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```console
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$ csvcut -c 'id,cg.issn,cg.issn[],cg.issn[en],cg.issn[en_US],cg.isbn,cg.isbn[],cg.isbn[en_US]' /tmp/2021-08-08-cgspace.csv > /tmp/2021-08-08-issn-isbn.csv
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```
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- Then in OpenRefine I merged all null, blank, and en fields into the `en_US` one for each, removed all spaces, fixed invalid multi-value separators, removed everything other than ISSN/ISBNs themselves
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- In total it was a few thousand metadata entries or so so I had to split the CSV with `xsv split` in order to process it
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- I was reminded again how DSpace 6 is very fucking slow when it comes to any database-related operations, as it takes over an hour to process 200 metadata changes...
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- In total it was 1,195 changes to ISSN and ISBN metadata fields
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## 2021-08-09
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- Extract all unique ISSNs to look up on Sherpa Romeo and Crossref
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```console
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$ csvcut -c 'cg.issn[en_US]' ~/Downloads/2021-08-08-CGSpace-ISBN-ISSN.csv | csvgrep -c 1 -r '^[0-9]{4}' | sed 1d | sort | uniq > /tmp/2021-08-09-issns.txt
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$ ./ilri/sherpa-issn-lookup.py -a mehhhhhhhhhhhhh -i /tmp/2021-08-09-issns.txt -o /tmp/2021-08-09-journals-sherpa-romeo.csv
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$ ./ilri/crossref-issn-lookup.py -e me@cgiar.org -i /tmp/2021-08-09-issns.txt -o /tmp/2021-08-09-journals-crossref.csv
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```
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- Then I updated the CSV headers for each and joined the CSVs on the issn column:
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```console
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$ sed -i '1s/journal title/sherpa romeo journal title/' /tmp/2021-08-09-journals-sherpa-romeo.csv
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$ sed -i '1s/journal title/crossref journal title/' /tmp/2021-08-09-journals-crossref.csv
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$ csvjoin -c issn /tmp/2021-08-09-journals-sherpa-romeo.csv /tmp/2021-08-09-journals-crossref.csv > /tmp/2021-08-09-journals-all.csv
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```
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- In OpenRefine I faceted by blank in each column and copied the values from the other, then created a new column to indicate whether the values were the same with this GREL:
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```console
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if(cells['sherpa romeo journal title'].value == cells['crossref journal title'].value,"same","different")
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```
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- Then I exported the list of journals that differ and sent it to Peter for comments and corrections
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- I want to build an updated controlled vocabulary so I can update CGSpace and reconcile our existing metadata against it
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- Convert my `generate-thumbnails.py` script to use libvips instead of Graphicsmagick
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- It is faster and uses less memory than GraphicsMagick (and ImageMagick), and produces nice thumbnails from PDFs
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- One drawback is that libvips uses Poppler instead of Graphicsmagick, which apparently means that it can't work in CMYK
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- I tested one item (10568/51999) that uses CMYK and the thumbnail looked OK (closer to the original than GraphicsMagick), so I'm not sure...
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- I did some tests of the memory used and time elapsed with libvips, GraphicsMagick, and ImageMagick:
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```console
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$ /usr/bin/time -f %M:%e vipsthumbnail IPCC.pdf -s 600 -o '%s-vips.jpg[Q=85,optimize_coding,strip]'
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39004:0.08
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$ /usr/bin/time -f %M:%e gm convert IPCC.pdf\[0\] -quality 85 -thumbnail x600 -flatten IPCC-gm.jpg
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40932:0.53
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$ /usr/bin/time -f %M:%e convert IPCC.pdf\[0\] -flatten -profile /usr/share/ghostscript/9.54.0/iccprofiles/default_cmyk.icc -profile /usr/share/ghostscript/9.54.0/iccprofiles/default_rgb.icc /tmp/impdfthumb2862933674765647409.pdf.jpg
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41724:0.59
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$ /usr/bin/time -f %M:%e convert -auto-orient /tmp/impdfthumb2862933674765647409.pdf.jpg -quality 85 -thumbnail 600x600 IPCC-im.jpg
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24736:0.04
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```
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- The ImageMagick way is the same as how DSpace does it (first creating an intermediary image, then getting a thumbnail)
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- libvips does use less time and memory... I should do more tests!
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<!-- vim: set sw=2 ts=2: -->
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