CGSpace Notes

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

July, 2020

by Alan Orth in  Notes

2020-07-01

  • A few users noticed that CGSpace wasn’t loading items today, item pages seem blank
    • I looked at the PostgreSQL locks but they don’t seem unusual
    • I guess this is the same “blank item page” issue that we had a few times in 2019 that we never solved
    • 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
  • Also, Linode is alerting that we had high outbound traffic rate early this morning around midnight AND high CPU load later in the morning
  • First looking at the traffic in the morning:
# cat /var/log/nginx/*.log.1 /var/log/nginx/*.log | grep -E "01/Jul/2020:(00|01|02|03|04)" | goaccess --log-format=COMBINED -
...
9659 33.56%    1  0.08% 340.94 MiB 64.39.99.13
3317 11.53%    1  0.08% 871.71 MiB 199.47.87.140
2986 10.38%    1  0.08%  17.39 MiB 199.47.87.144
2286  7.94%    1  0.08%  13.04 MiB 199.47.87.142
  • 64.39.99.13 belongs to Qualys, but I see they are using a normal desktop user agent:
Mozilla/5.0 (Macintosh; Intel Mac OS X 10_14_5) AppleWebKit/605.1.15 (KHTML, like Gecko) Version/12.1.1 Safari/605.1.15
  • I will purge hits from that IP from Solr
  • The 199.47.87.x IPs belong to Turnitin, and apparently they are NOT marked as bots and we have 40,000 hits from them in 2020 statistics alone:
$ curl -s "http://localhost:8081/solr/statistics/select" -d "q=userAgent:/Turnitin.*/&rows=0" | grep -oE 'numFound="[0-9]+"'
numFound="41694"
  • They used to be “TurnitinBot”… hhmmmm, seems they use both: https://turnitin.com/robot/crawlerinfo.html
  • I will add Turnitin to the DSpace bot user agent list, but I see they are reqesting robots.txt and only requesting item pages, so that’s impressive! I don’t need to add them to the “bad bot” rate limit list in nginx
  • While looking at the logs I noticed eighty-one IPs in the range 185.152.250.x making little requests this user agent:
Mozilla/5.0 (Macintosh; Intel Mac OS X 10.14; rv:76.0) Gecko/20100101 Firefox/76.0
  • The IPs all belong to HostRoyale:
# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep '01/Jul/2020' | awk '{print $1}' | grep 185.152.250. | sort | uniq | wc -l
81
# cat /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep '01/Jul/2020' | awk '{print $1}' | grep 185.152.250. | sort | uniq | sort -h
185.152.250.1
185.152.250.101
185.152.250.103
185.152.250.105
185.152.250.107
185.152.250.111
185.152.250.115
185.152.250.119
185.152.250.121
185.152.250.123
185.152.250.125
185.152.250.129
185.152.250.13
185.152.250.131
185.152.250.133
185.152.250.135
185.152.250.137
185.152.250.141
185.152.250.145
185.152.250.149
185.152.250.153
185.152.250.155
185.152.250.157
185.152.250.159
185.152.250.161
185.152.250.163
185.152.250.165
185.152.250.167
185.152.250.17
185.152.250.171
185.152.250.183
185.152.250.189
185.152.250.191
185.152.250.197
185.152.250.201
185.152.250.205
185.152.250.209
185.152.250.21
185.152.250.213
185.152.250.217
185.152.250.219
185.152.250.221
185.152.250.223
185.152.250.225
185.152.250.227
185.152.250.229
185.152.250.231
185.152.250.233
185.152.250.235
185.152.250.239
185.152.250.243
185.152.250.247
185.152.250.249
185.152.250.25
185.152.250.251
185.152.250.253
185.152.250.255
185.152.250.27
185.152.250.29
185.152.250.3
185.152.250.31
185.152.250.39
185.152.250.41
185.152.250.47
185.152.250.5
185.152.250.59
185.152.250.63
185.152.250.65
185.152.250.67
185.152.250.7
185.152.250.71
185.152.250.73
185.152.250.77
185.152.250.81
185.152.250.85
185.152.250.89
185.152.250.9
185.152.250.93
185.152.250.95
185.152.250.97
185.152.250.99
  • It’s only a few hundred requests each, but I am very suspicious so I will record it here and purge their IPs from Solr
  • Then I see 185.187.30.14 and 185.187.30.13 making requests also, with several different “normal” user agents
    • They are both apparently in France, belonging to Scalair FR hosting
    • I will purge their requests from Solr too
  • Now I see some other new bots I hadn’t noticed before:
    • Mozilla/5.0 (compatible; MSIE 10.0; Windows NT 6.1; Trident/6.0) LinkCheck by Siteimprove.com
    • Consilio (WebHare Platform 4.28.2-dev); LinkChecker), which appears to be a university CMS
    • I will add LinkCheck, Consilio, and WebHare to the list of DSpace bot agents and purge them from Solr stats
    • COUNTER-Robots list already has link.?check but for some reason DSpace didn’t match that and I see hits for some of these…
    • Maybe I should add [Ll]ink.?[Cc]heck.? to a custom list for now?
    • For now I added Turnitin to the new bots pull request on COUNTER-Robots
  • I purged 20,000 hits from IPs and 45,000 hits from user agents
  • I will revert the default “example” agents file back to the upstream master branch of COUNTER-Robots, and then add all my custom ones that are pending in pull requests they haven’t merged yet:
$ diff --unchanged-line-format= --old-line-format= --new-line-format='%L' dspace/config/spiders/agents/example ~/src/git/COUNTER-Robots/COUNTER_Robots_list.txt
Citoid
ecointernet
GigablastOpenSource
Jersey\/\d
MarcEdit
OgScrper
okhttp
^Pattern\/\d
ReactorNetty\/\d
sqlmap
Typhoeus
7siters
  • Just a note that I still can’t deploy the 6_x-dev-atmire-modules branch as it fails at ant update:
     [java] java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'DefaultStorageUpdateConfig': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire method: public void com.atmire.statistics.util.StorageReportsUpdater.setStorageReportServices(java.util.List); nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'cuaEPersonStorageReportService': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.dspace.cua.dao.storage.CUAEPersonStorageReportDAO com.atmire.dspace.cua.CUAStorageReportServiceImpl$CUAEPersonStorageReportServiceImpl.CUAEPersonStorageReportDAO; nested exception is org.springframework.beans.factory.NoUniqueBeanDefinitionException: No qualifying bean of type [com.atmire.dspace.cua.dao.storage.CUAEPersonStorageReportDAO] is defined: expected single matching bean but found 2: com.atmire.dspace.cua.dao.impl.CUAStorageReportDAOImpl$CUAEPersonStorageReportDAOImpl#0,com.atmire.dspace.cua.dao.impl.CUAStorageReportDAOImpl$CUAEPersonStorageReportDAOImpl#1
  • I had told Atmire about this several weeks ago… but I reminded them again in the ticket
    • Atmire says they are able to build fine, so I tried again and noticed that I had been building with -Denv=dspacetest.cgiar.org, which is not necessary for DSpace 6 of course
    • Once I removed that it builds fine
  • I quickly re-applied the Font Awesome 5 changes to use SVG+JS instead of web fonts (from 2020-04) and things are looking good!
  • Run all system updates on DSpace Test (linode26), deploy latest 6_x-dev-atmire-modules branch, and reboot it

2020-07-02

  • I need to export some Solr statistics data from CGSpace to test Salem’s modifications to the dspace-statistics-api
    • He modified it to query Solr on the fly instead of indexing it, which will be heavier and slower, but allows us to get more granular stats and countries/cities
    • Because have so many records I want to use solr-import-export-json to get several months at a time with a date range, but it seems there are first issues with curl (need to disable globbing with -g and URL encode the range)
    • For reference, the Solr 4.10.x DateField docs
    • This range works in Solr UI: [2019-01-01T00:00:00Z TO 2019-06-30T23:59:59Z]
    • As well in curl:
$ curl -g -s 'http://localhost:8081/solr/statistics-2019/select?q=*:*&fq=time:%5B2019-01-01T00%3A00%3A00Z%20TO%202019-06-30T23%3A59%3A59Z%5D&rows=0&wt=json&indent=true'
{
  "responseHeader":{
    "status":0,
    "QTime":0,
    "params":{
      "q":"*:*",
      "indent":"true",
      "fq":"time:[2019-01-01T00:00:00Z TO 2019-06-30T23:59:59Z]",
      "rows":"0",
      "wt":"json"}},
  "response":{"numFound":7784285,"start":0,"docs":[]
  }}
  • But not in solr-import-export-json… hmmm… seems we need to URL encode only the date range itself, but not the brackets:
$ ./run.sh -s http://localhost:8081/solr/statistics-2019 -a export -o /tmp/statistics-2019-1.json -f 'time:%5B2019-01-01T00%3A00%3A00Z%20TO%202019-06-30T23%3A59%3A59Z]' -k uid
$ zstd /tmp/statistics-2019-1.json
  • Then import it on my local dev environment:
$ zstd -d statistics-2019-1.json.zst
$ ./run.sh -s http://localhost:8080/solr/statistics -a import -o ~/Downloads/statistics-2019-1.json -k uid

2020-07-05

  • Import twelve items into the CRP Livestock multimedia collection for Peter Ballantyne
    • I ran the data through csv-metadata-quality first to validate and fix some common mistakes
    • Interesting to check the data with csvstat to see if there are any duplicates
  • Peter recently asked me to add Target audience (cg.targetaudience) to the CGSpace sidebar facets and AReS filters
    • I added it on my local DSpace test instance, but I’m waiting for him to tell me what he wants the header to be “Audiences” or “Target audience” etc…
  • Peter also asked me to increase the size of links in the CGSpace “Welcome” text
    • I suggested using the CSS font-size: larger property to just bump it up one relative to what it already is
    • He said it looks good, but that actually now the links seem OK (I told him to refresh, as I had made them bold a few days ago) so we don’t need to adjust it actually
  • Mohammed Salem modified my dspace-statistics-api to query Solr directly so I started writing a script to benchmark it today
    • I will monitor the JVM memory and CPU usage in visualvm, just like I did in 2019-04
    • I noticed an issue with his limit parameter so I sent him some feedback on that in the meantime
  • I noticed that we have 20,000 distinct values for dc.subject, but there are at least 500 that are lower or mixed case that we should simply uppercase without further thought:
dspace=# UPDATE metadatavalue SET text_value=UPPER(text_value) WHERE resource_type_id=2 AND metadata_field_id=57 AND text_value ~ '[[:lower:]]';
  • DSpace Test needs a different query because it is running DSpace 6 with UUIDs for everything:
dspace63=# UPDATE metadatavalue SET text_value=UPPER(text_value) WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=57 AND text_value ~ '[[:lower:]]';
  • Note the use of the POSIX character class :)
  • I suggest that we generate a list of the top 5,000 values that don’t match AGROVOC so that Sisay can correct them
    • Start by getting the top 6,500 subjects (assuming that the top ~1,500 are valid from our previous work):
dspace=# \COPY (SELECT DISTINCT text_value, count(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=57 GROUP BY text_value ORDER BY count DESC) TO /tmp/2020-07-05-subjects.csv WITH CSV;
COPY 19640
dspace=# \q
$ csvcut -c1 /tmp/2020-07-05-subjects-upper.csv | head -n 6500 > 2020-07-05-cgspace-subjects.txt
  • Then start looking them up using agrovoc-lookup.py:
$ ./agrovoc-lookup.py -i 2020-07-05-cgspace-subjects.txt -om 2020-07-05-cgspace-subjects-matched.txt -or 2020-07-05-cgspace-subjects-rejected.txt -d

2020-07-06

  • I made some optimizations to the suite of Python utility scripts in our DSpace directory as well as the csv-metadata-quality script
    • Mostly to make more efficient usage of the requests cache and to use parameterized requests instead of building the request URL by concatenating the URL with query parameters
  • I modified the agrovoc-lookup.py script to save its results as a CSV, with the subject, language, type of match (preferred, alternate, and total number of matches) rather than save two separate files
    • Note that I see prefLabel, matchedPrefLabel, and altLabel in the REST API responses and I’m not sure what the second one means
    • I emailed FAO’s AGROVOC contact to ask them
    • They responded to say that matchedPrefLabel is not a property in SKOS/SKOSXL vocabulary, but their SKOSMOS system seems to use it to hint that the search terms matched a prefLabel in another language
    • I will treat the matchedPrefLabel values as if they were prefLabel values for the indicated language then

2020-07-07

  • Peter asked me to send him a list of sponsors on CGSpace
dspace=# \COPY (SELECT DISTINCT text_value as "dc.description.sponsorship", count(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=29 GROUP BY "dc.description.sponsorship" ORDER BY count DESC) TO /tmp/2020-07-07-sponsors.csv WITH CSV HEADER;
COPY 707
  • I ran it quickly through my csv-metadata-quality tool and found two issues that I will correct with fix-metadata-values.py on CGSpace immediately:
$ cat 2020-07-07-fix-sponsors.csv
dc.description.sponsorship,correct
"Ministe`re des Affaires Etrange`res et Européennes, France","Ministère des Affaires Étrangères et Européennes, France"
"Global Food Security Programme,  United Kingdom","Global Food Security Programme, United Kingdom"
$ ./fix-metadata-values.py -i 2020-07-07-fix-sponsors.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -t correct -m 29
  • Upload the Capacity Development July newsletter to CGSpace for Ben Hack because Abenet and Bizu usually do it, but they are currently offline due to the Internet being turned off in Ethiopia
  • I implemented the Dimensions.ai badge on DSpace Test for Peter to see, as he’s been asking me for awhile:

Dimensions.ai badge

  • It was easy once I figured out how to do the XSLT in the DSpace theme (need to get the DOI link and remove the “https://doi.org/" from the string)
    • Actually this raised an issue that the Altmetric badges weren’t enabled in our DSpace 6 branch yet because I had forgotten to copy the config
    • Also, I noticed a big issue in both our DSpace 5 and DSpace 6 branches related to the $identifier_doi variable being defined incorrectly and thus never getting set (has to do with DRI)
    • I fixed both and now the Altmetric badge and the Dimensions badge both appear… nice

Altmetric and Dimensions.ai badge

2020-07-08

  • Generate a CSV of all the AGROVOC subjects that didn’t match from the top 6500 I exported earlier this week:
$ csvgrep -c 'number of matches' -r "^0$" 2020-07-05-cgspace-subjects.csv | csvcut -c 1 > 2020-07-05-cgspace-invalid-subjects.csv
  • Yesterday Gabriela from CIP emailed to say that she was removing the accents from her authors’ names because of “funny character” issues with reports generated from CGSpace
    • I told her that it’s probably her Windows / Excel that is messing up the data, and she figured out how to open them correctly!
    • Now she says she doesn’t want to remove the accents after all and she sent me a new list of corrections
    • I used csvgrep and found a few where she is still removing accents:
$ csvgrep -c 2 -r "^.+$" ~/Downloads/cip-authors-GH-20200706.csv | csvgrep -c 1 -r "^.*[À-ú].*$" | csvgrep -c 2 -r "^.*[À-ú].*$" -i | csvcut -c 1,2
dc.contributor.author,correction
"López, G.","Lopez, G."
"Gómez, R.","Gomez, R."
"García, M.","Garcia, M."
"Mejía, A.","Mejia, A."
"Quiróz, Roberto A.","Quiroz, R."

  • csvgrep from the csvkit suite is so cool:

    • Select lines with column two (the correction) having a value
    • Select lines with column one (the original author name) having an accent / diacritic
    • Select lines with column two (the correction) NOT having an accent (ie, she’s not removing an accent)
    • Select columns one and two

  • Peter said he liked the work I didn on the badges yesterday so I put some finishing touches on it to detect more DOI URI styles and pushed it to the 5_x-prod branch

    • I will port it to DSpace 6 soon

Altmetric and Dimensions badges

  • I wrote a quick script to lookup organizations (affiliations) in the Research Organization Repository (ROR) JSON data release v5
    • I want to use this to evaluate ROR as a controlled vocabulary for CGSpace and MELSpace
    • I exported a list of affiliations from CGSpace:
dspace=# \COPY (SELECT DISTINCT text_value as "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 GROUP BY text_value ORDER BY count DESC) to /tmp/2020-07-08-affiliations.csv WITH CSV HEADER;
  • Then I stripped the CSV header and quotes to make it a plain text file and ran ror-lookup.py:
$ ./ror-lookup.py -i /tmp/2020-07-08-affiliations.txt -r ror.json -o 2020-07-08-affiliations-ror.csv -d
$ wc -l /tmp/2020-07-08-affiliations.txt 
5866 /tmp/2020-07-08-affiliations.txt
$ csvgrep -c matched -m true 2020-07-08-affiliations-ror.csv | wc -l 
1406
$ csvgrep -c matched -m false 2020-07-08-affiliations-ror.csv | wc -l
4462
  • So, minus the CSV header, we have 1405 case-insensitive matches out of 5866 (23.9%)

2020-07-09

  • Atmire responded to the ticket about DSpace 6 and Solr yesterday
    • They said that the CUA issue is due to the “unmigrated” Solr records and that we should delete them
    • I told them that the “unmigrated” IDs are a known issue in DSpace 6 and we should rather figure out why they are unmigrated
    • I didn’t see any discussion on the dspace-tech mailing list or on DSpace Jira about unmigrated IDs, so I sent a mail to the mailing list to ask
  • I updated ror-lookup.py to check aliases and acronyms as well and now the results are better for CGSpace’s affiliation list:
$ wc -l /tmp/2020-07-08-affiliations.txt 
5866 /tmp/2020-07-08-affiliations.txt
$ csvgrep -c matched -m true 2020-07-08-affiliations-ror.csv | wc -l 
1516
$ csvgrep -c matched -m false 2020-07-08-affiliations-ror.csv | wc -l
4352
  • So now our matching improves to 1515 out of 5866 (25.8%)
  • Gabriela from CIP said that I should run the author corrections minus those that remove accent characters so I will run it on CGSpace:
$ ./fix-metadata-values.py -i /tmp/2020-07-09-fix-90-cip-authors.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correction -m 3
  • Apply 110 fixes and 90 deletions to sponsorships that Peter sent me a few days ago:
$ ./fix-metadata-values.py -i /tmp/2020-07-07-fix-110-sponsors.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -t 'correct/action' -m 29
$ ./delete-metadata-values.py -i /tmp/2020-07-07-delete-90-sponsors.csv -db dspace -u dspace -p 'fuuu' -f dc.description.sponsorship -m 29
  • Start a full Discovery re-index on CGSpace:
$ time chrt -b 0 dspace index-discovery -b

real    94m21.413s
user    9m40.364s
sys     2m37.246s
  • I modified crossref-funders-lookup.py to be case insensitive and now CGSpace’s sponsors match 173 out of 534 (32.4%):
$ ./crossref-funders-lookup.py -i 2020-07-09-cgspace-sponsors.txt -o 2020-07-09-cgspace-sponsors-crossref.csv -d -e a.orth@cgiar.org
$ wc -l 2020-07-09-cgspace-sponsors.txt
534 2020-07-09-cgspace-sponsors.txt
$ csvgrep -c matched -m true 2020-07-09-cgspace-sponsors-crossref.csv | wc -l 
174

2020-07-12

  • On 2020-07-10 Macaroni Bros emailed to ask if there are issues with CGSpace because they are getting HTTP 504 on the REST API
    • First, I looked in Munin and I see high number of DSpace sessions and threads on Friday evening around midnight, though that was much later than his email:

DSpace sessions Threads PostgreSQL locks PostgreSQL transactions

  • CPU load and memory were not high then, but there was some load on the database and firewall…
    • Looking in the nginx logs I see a few IPs we’ve seen recently, like those 199.47.x.x IPs from Turnitin (which I need to remember to purge from Solr again because I didn’t update the spider agents on CGSpace yet) and some new one 186.112.8.167
    • Also, the Turnitin bot doesn’t re-use its Tomcat JSESSIONID, I see this from today:
# grep 199.47.87 dspace.log.2020-07-12 | grep -o -E 'session_id=[A-Z0-9]{32}' | sort | uniq | wc -l
2815
  • So I need to add this alternative user-agent to the Tomcat Crawler Session Manager valve to force it to re-use a common bot session
  • There are around 9,000 requests from 186.112.8.167 in Colombia and has the user agent Java/1.8.0_241, but those were mostly to REST API and I don’t see any hits in Solr
  • Earlier in the day Linode had alerted that there was high outgoing bandwidth
    • I see some new bot from 134.155.96.78 made ~10,000 requests with the user agent… but it appears to already be in our DSpace user agent list via COUNTER-Robots:
Mozilla/5.0 (compatible; heritrix/3.4.0-SNAPSHOT-2019-02-07T13:53:20Z +http://ifm.uni-mannheim.de)
  • Generate a list of sponsors to update our controlled vocabulary:
dspace=# \COPY (SELECT DISTINCT text_value as "dc.description.sponsorship", count(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=29 GROUP BY "dc.description.sponsorship" ORDER BY count DESC LIMIT 125) TO /tmp/2020-07-12-sponsors.csv;
COPY 125
dspace=# \q
$ csvcut -c 1 --tabs /tmp/2020-07-12-sponsors.csv > dspace/config/controlled-vocabularies/dc-description-sponsorship.xml
# add XML formatting
$ dspace/config/controlled-vocabularies/dc-description-sponsorship.xml
$ tidy -xml -utf8 -m -iq -w 0 dspace/config/controlled-vocabularies/dc-description-sponsorship.xml
  • Deploy latest 5_x-prod branch on CGSpace (linode18), run all system updates, and reboot the server
    • After rebooting it I had to restart Tomcat 7 once to get all Solr statistics cores to come up properly