CGSpace Notes

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

February, 2022

in  Notes

2022-02-01

  • Meeting with Peter and Abenet about CGSpace in the One CGIAR
    • We agreed to buy $5,000 worth of credits from Atmire for future upgrades
    • We agreed to move CRPs and non-CGIAR communities off the home page, as well as some other things for the CGIAR System Organization
    • We agreed to make a Discovery facet for CGIAR Action Areas above the existing CGIAR Impact Areas one
    • We agreed to try to do more alignment of affiliations/funders with ROR
  • I moved a bunch of communities:
$ dspace community-filiator --remove --parent=10568/114639 --child=10568/115089
$ dspace community-filiator --remove --parent=10568/114639 --child=10568/115087
$ dspace community-filiator --remove --parent=10568/83389 --child=10568/108598
$ dspace community-filiator --remove --parent=10568/83389 --child=10947/1
$ dspace community-filiator --set --parent=10568/35697 --child=10568/80211
$ dspace community-filiator --remove --parent=10568/83389 --child=10947/2517
$ dspace community-filiator --set --parent=10568/97114 --child=10947/2517
$ dspace community-filiator --set --parent=10568/97114 --child=10568/89416
$ dspace community-filiator --set --parent=10568/97114 --child=10568/3530
$ dspace community-filiator --set --parent=10568/97114 --child=10568/80099
$ dspace community-filiator --set --parent=10568/97114 --child=10568/80100
$ dspace community-filiator --set --parent=10568/97114 --child=10568/34494
$ dspace community-filiator --set --parent=10568/117867 --child=10568/114644
$ dspace community-filiator --set --parent=10568/117867 --child=10568/16573
$ dspace community-filiator --set --parent=10568/117867 --child=10568/42211
$ dspace community-filiator --set --parent=10568/117865 --child=10568/109945
$ dspace community-filiator --set --parent=10568/117865 --child=10568/16498
$ dspace community-filiator --set --parent=10568/117865 --child=10568/99453
$ dspace community-filiator --set --parent=10568/117865 --child=10568/2983
$ dspace community-filiator --set --parent=10568/117865 --child=10568/133
$ dspace community-filiator --remove --parent=10568/83389 --child=10568/1208
$ dspace community-filiator --set --parent=10568/117865 --child=10568/1208
$ dspace community-filiator --remove --parent=10568/83389 --child=10568/56924
$ dspace community-filiator --set --parent=10568/117865 --child=10568/56924
$ dspace community-filiator --remove --parent=10568/83389 --child=10568/91688
$ dspace community-filiator --set --parent=10947/1 --child=10568/91688
$ dspace community-filiator --remove --parent=10568/83389 --child=10947/2515
$ dspace community-filiator --set --parent=10947/1 --child=10947/2515
  • Remove CPWF and CTA subjects from the Discovery facets
  • Start a full Discovery index on CGSpace:
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    275m15.777s
user    182m52.171s
sys     2m51.573s
  • I got a request to confirm validation of CGSpace on openarchives.org, with the requestor’s IP being 128.84.116.66
    • That is at Cornell… hmmmm who could that be?!
    • Oh, the OpenArchives initiative is at Cornell… maybe this is an automated periodic check?

2022-02-02

  • Looking at the top user agents and IP addresses in CGSpace’s Solr statistics for 2022-01
    • 64.39.98.40 made 26,000 requests, owned by Qualys so it’s some kind of security scanning
    • 45.134.26.171 made 8,000 requests and it’s own by some Russian company and makes requests like this hmmmmm:
45.134.26.171 - - [12/Jan/2022:06:25:27 +0100] "GET /bitstream/handle/10568/81964/varietal-2faea58f.pdf?sequence=1 HTTP/1.1" 200 1157807 "https://cgspace.cgiar.org:443/bitstream/handle/10568/81964/varietal-2faea58f.pdf" "Opera/9.64 (Windows NT 6.1; U; MRA 5.5 (build 02842); ru) Presto/2.1.1)) AND 4734=CTXSYS.DRITHSX.SN(4734,(CHR(113)||CHR(120)||CHR(120)||CHR(112)||CHR(113)||(SELECT (CASE WHEN (4734=4734) THEN 1 ELSE 0 END) FROM DUAL)||CHR(113)||CHR(120)||CHR(113)||CHR(122)||CHR(113))) AND ((3917=3917"
  • 3.225.28.105 made 3,000 requests mostly for one CIAT collection on the REST API and it is owned by Amazon
    • The user agent is sometimes a normal user one, and sometimes Apache-HttpClient/4.3.4 (java 1.5)
  • 217.182.21.193 made 2,400 requests and is on OVH
  • I purged these hits
$ ./ilri/check-spider-ip-hits.sh -f /tmp/ips.txt -p
Purging 26817 hits from 64.39.98.40 in statistics
Purging 9446 hits from 45.134.26.171 in statistics
Purging 6490 hits from 3.225.28.105 in statistics
Purging 11949 hits from 217.182.21.193 in statistics

Total number of bot hits purged: 54702
  • Export donors and affiliations from CGSpace database:
localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.donor", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 248 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-donors.csv WITH CSV HEADER;
COPY 1036
localhost/dspace63= ☘ \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2022-02-02-affiliations.csv WITH CSV HEADER;
COPY 7901
  • Then check matches against the latest ROR dump:
$ csvcut -c cg.contributor.donor /tmp/2022-02-02-donors.csv | sed '1d' > /tmp/2022-02-02-donors.txt
$ ./ilri/ror-lookup.py -i /tmp/2022-02-02-donors.txt -r 2021-09-23-ror-data.json -o /tmp/donor-ror-matches.csv
...
  • I see we have 258/1036 (24.9%) of our donors matching ROR (as of the 2021-09-23 ROR dump)
  • I see we have 1986/7901 (25.1%) of our affiliations matching ROR (as of the 2021-09-23 ROR dump)
  • Update the PostgreSQL JDBC driver to 42.3.2 in the Ansible Infrastructure playbooks and deploy on DSpace Test
  • Mishell from CIP sent me a copy of a security scan their ICT had done on CGSpace using QualysGuard
    • The report was very long and generic, highlighting low-severity things like being able to post crap to search forms and have it appear on the results page
    • Also they say we’re using old jQuery and bootstrap, etc (fair enough) but there are no exploits per se
    • At least now I know why all those Qualys IPs are scanning us all the time!!!
  • Mishell also said she’s having issues logging into CGSpace
    • According to the logs her account is failing on LDAP authentication
    • I checked CGSpace’s LDAP credentials using ldapsearch and was able to connect so it’s gotta be something with her account

2022-02-03

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

2022-02-04

  • I found a thread on the dspace-tech mailing list about the media-filter crash above
    • The problem is that the default filter for Word files is outdated, so we need to switch to the PoiWordFilter extractor
    • After changing that I was able to filter the Word file on that item above:
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace filter-media -i 10568/67391 -p "Word Text Extractor" -v
The following MediaFilters are enabled: 
Full Filter Name: org.dspace.app.mediafilter.PoiWordFilter
org.dspace.app.mediafilter.PoiWordFilter
File: Agreement_on_the_Estab_of_ILRI.doc.txt

FILTERED: bitstream 31db7d05-5369-4309-adeb-3b888c80b73d (item: 10568/67391) and created 'Agreement_on_the_Estab_of_ILRI.doc.txt'
  • Meeting with the repositories working group to discuss issues moving forward in the One CGIAR

2022-02-07

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

2022-02-08

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

2022-02-09

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

2022-02-10

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

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

  • I extract the logs from nginx for yesterday so I can analyze the traffic:
# zcat --force /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-access.log
# zcat --force /var/log/nginx/rest.log.1 /var/log/nginx/rest.log.2.gz | grep '09/Feb/2022' > /tmp/feb9-rest.log
# awk '{print $1}' /tmp/feb9-* | less | sort -u > /tmp/feb9-ips.txt
# wc -l /tmp/feb9-ips.txt
11636 /tmp/feb9-ips.tx
  • I started resolving them with my resolve-addresses-geoip2.py script
  • In the mean time I am looking at the requests and I see a new user agent: 1science Resolver 1.0.0
    • Seems to be a defunct project from Elsevier (website down, Twitter account inactive since 2020)
  • I also see 3,400 requests from EyeMonIT_bot_version_0.1_(http://www.eyemon.it/), but because it has “bot” in the name it gets heavily throttled…
    • I wonder who is monitoring CGSpace with that service…
  • Looking at the top twenty or so ASNs for the resolved IPs I see lots of bot traffic, but nothing malicious:
$ csvcut -c asn /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20
     79 24940
     89 36908
    100 9299
    107 2635
    110 44546
    111 16509
    118 7552
    120 4837
    123 50245
    123 55836
    147 45899
    173 33771
    192 39832
    202 32934
    235 29465
    260 15169
    466 14618
    607 24757
    768 714
   1214 8075
  • The same information, but by org name:
$ csvcut -c org /tmp/feb9-ips.csv | sort | uniq -c | sort -h | tail -n 20
     92 Orange
    100 Hetzner Online GmbH
    100 Philippine Long Distance Telephone Company
    107 AUTOMATTIC
    110 ALFA TELECOM s.r.o.
    111 AMAZON-02
    118 Viettel Group
    120 CHINA UNICOM China169 Backbone
    123 Reliance Jio Infocomm Limited
    123 Serverel Inc.
    147 VNPT Corp
    173 SAFARICOM-LIMITED
    192 Opera Software AS
    202 FACEBOOK
    235 MTN NIGERIA Communication limited
    260 GOOGLE
    466 AMAZON-AES
    607 Ethiopian Telecommunication Corporation
    768 APPLE-ENGINEERING
   1214 MICROSOFT-CORP-MSN-AS-BLOCK
  • Most of these are pretty normal except “Serverel” and Hetzner perhaps, but their user agents are pretending to be normal users so who knows…
  • I decided to look in the Solr stats with facet.limit=1000&facet.mincount=1 and found a few more definitely non-human agents:
  • I added them to the ILRI override in the DSpace spider list and ran the check-spider-hits.sh script:
$ ./ilri/check-spider-hits.sh -f dspace/config/spiders/agents/ilri -p
Purging 234 hits from randint in statistics
Purging 337 hits from Koha in statistics
Purging 1164 hits from scalaj-http in statistics
Purging 1528 hits from scpitspi-rs in statistics
Purging 3050 hits from lua-resty-http in statistics
Purging 1683 hits from AHC in statistics
Purging 1129 hits from acebookexternalhit in statistics
Purging 534 hits from Iframely in statistics
Purging 1022 hits from qbhttp in statistics
Purging 330 hits from ^got in statistics
Purging 156 hits from ^colly in statistics
Purging 38 hits from article-parser in statistics
Purging 1148 hits from SomeRandomText in statistics
Purging 3126 hits from adreview in statistics
Purging 217 hits from 1science in statistics

Total number of bot hits purged: 14696
  • I don’t have time right now to add any of these to the COUNTER-Robots list…
  • Peter asked me to add a new item type on CGSpace: Opinion Piece
  • Map an item on CGSpace for Maria since she couldn’t find it in the item mapper

2022-02-11

  • CGSpace is slow and the load has been over 400% for a few hours
    • The number of DSpace sessions seems normal, even lower than a few days ago
    • The number of PostgreSQL connections is low, but I see there are lots of “AccessShare” locks (green on Munin, not blue like usual)
    • I will run all system updates, copy the latest config changes, and restart the server

2022-02-12

  • Install PostgreSQL 12 on my local dev environment to starting DSpace 6.x workflows with it:
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:12-alpine
$ createuser -h localhost -p 5432 -U postgres --pwprompt dspacetest
$ createdb -h localhost -p 5432 -U postgres -O dspacetest --encoding=UNICODE dspacetest
$ psql -h localhost -U postgres -c 'ALTER USER dspacetest SUPERUSER;'
$ pg_restore -h localhost -U postgres -d dspacetest -O --role=dspacetest -h localhost ~/Downloads/dspace-2022-02-12.backup
$ psql -h localhost -U postgres -c 'ALTER USER dspacetest NOSUPERUSER;'
  • Eventually I will updated DSpace Test, then CGSpace (time to start paying off some technical debt!)
  • Start a full Discovery re-index on CGSpace:
$ time chrt -b 0 ionice -c2 -n7 nice -n19 dspace index-discovery -b

real    292m49.263s
user    201m26.097s
sys     3m2.459s
  • Start a full harvest on AReS

2022-02-14

  • Last week Gaia sent me her notes on the second batch of TAC/ICW documents (items 201–400 in the spreadsheet)
    • I created a filter in LibreOffice and selected the IDs for items with the action “delete”, then I created a custom text facet in OpenRefine with this GREL:
or(
isNotNull(value.match('201')),
isNotNull(value.match('203')),
isNotNull(value.match('209')),
isNotNull(value.match('209')),
isNotNull(value.match('215')),
isNotNull(value.match('220')),
isNotNull(value.match('225')),
isNotNull(value.match('226')),
isNotNull(value.match('227')),
...
isNotNull(value.match('396'))
  • Then I flagged all matching records and exported a CSV to use with SAFBuilder
    • Then I imported the SAF bundle on DSpace Test:
$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" dspace import --add --eperson=fuuu@umm.com --source /tmp/SimpleArchiveFormat --mapfile=./2022-02-14-tac-batch2-201to400.map
  • Export the next batch from OpenRefine (items with ID 401 to 700), check duplicates, and then join with the file names:
$ csvcut -c id,dc.title,dcterms.issued,dcterms.type ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv > /tmp/tac3.csv
$ ./ilri/check-duplicates.py -i /tmp/tac3.csv -db dspacetest -u dspacetest -p 'dom@in34sniper' -o /tmp/2022-02-14-tac-batch3-401-700.csv
$ csvcut -c id,filename ~/Downloads/2022-01-21-CGSpace-TAC-ICW-batch3-401to700.csv > /tmp/tac3-filenames.csv
$ csvjoin -c id /tmp/2022-02-14-tac-batch3-401-700.csv /tmp/tac3-filenames.csv > /tmp/2022-02-14-tac-batch3-401-700-filenames.csv
  • I sent these 300 items to Gaia…