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Finalize AReS Phase I and Phase II ToRs
Send a note about my dspace-statistics-api to the dspace-tech mailing list
2018-11-03 17:13:49 +01:00
2018-11-03
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:
2018-11-01 15:43:37 +01:00
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Finalize AReS Phase I and Phase II ToRs
Send a note about my dspace-statistics-api to the dspace-tech mailing list
2018-11-03 17:13:49 +01:00
2018-11-03
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:
2018-11-01 15:43:37 +01:00
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< h1 class = "blog-title" > < a href = "https://alanorth.github.io/cgspace-notes/" rel = "home" > CGSpace Notes< / a > < / h1 >
< p class = "lead blog-description" > Documenting day-to-day work on the < a href = "https://cgspace.cgiar.org" > CGSpace< / a > repository.< / p >
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< h2 class = "blog-post-title" > < a href = "https://alanorth.github.io/cgspace-notes/2018-11/" > November, 2018< / a > < / h2 >
< p class = "blog-post-meta" > < time datetime = "2018-11-01T16:41:30+02:00" > Thu Nov 01, 2018< / time > by Alan Orth in
< i class = "fa fa-tag" aria-hidden = "true" > < / i > < a href = "/cgspace-notes/tags/notes" rel = "tag" > Notes< / a >
< / p >
< / header >
< h2 id = "2018-11-01" > 2018-11-01< / h2 >
< ul >
< li > Finalize AReS Phase I and Phase II ToRs< / li >
< li > Send a note about my < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > to the dspace-tech mailing list< / li >
< / ul >
2018-11-03 17:13:49 +01:00
< h2 id = "2018-11-03" > 2018-11-03< / h2 >
< ul >
< li > Linode has been sending mails a few times a day recently that CGSpace (linode18) has had high CPU usage< / li >
< li > Today these are the top 10 IPs:< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 03/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
1300 66.249.64.63
1384 35.237.175.180
1430 138.201.52.218
1455 207.46.13.156
1500 40.77.167.175
1979 50.116.102.77
2790 66.249.64.61
3367 84.38.130.177
4537 70.32.83.92
22508 66.249.64.59
< / code > < / pre >
< ul >
< li > The < code > 66.249.64.x< / code > are definitely Google< / li >
< li > < code > 70.32.83.92< / code > is well known, probably CCAFS or something, as it’ s only a few thousand requests and always to REST API< / li >
< li > < code > 84.38.130.177< / code > is some new IP in Latvia that is only hitting the XMLUI, using the following user agent:< / li >
< / ul >
< pre > < code > Mozilla/5.0 (Windows NT 5.1) AppleWebKit/535.1 (KHTML, like Gecko) Chrome/14.0.792.0 Safari/535.1
< / code > < / pre >
< ul >
< li > They at least seem to be re-using their Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=84.38.130.177' dspace.log.2018-11-03 | sort | uniq
342
< / code > < / pre >
< ul >
< li > < code > 50.116.102.77< / code > is also a regular REST API user< / li >
< li > < code > 40.77.167.175< / code > and < code > 207.46.13.156< / code > seem to be Bing< / li >
< li > < code > 138.201.52.218< / code > seems to be on Hetzner in Germany, but is using this user agent:< / li >
< / ul >
< pre > < code > Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0
< / code > < / pre >
< ul >
< li > And it doesn’ t seem they are re-using their Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=138.201.52.218' dspace.log.2018-11-03 | sort | uniq
1243
< / code > < / pre >
< ul >
< li > Ah, we’ ve apparently seen this server exactly a year ago in 2017-11, making 40,000 requests in one day… < / li >
< li > I wonder if it’ s worth adding them to the list of bots in the nginx config?< / li >
2018-11-04 00:02:29 +01:00
< li > Linode sent a mail that CGSpace (linode18) is using high outgoing bandwidth< / li >
< li > Looking at the nginx logs again I see the following top ten IPs:< / li >
2018-11-03 17:13:49 +01:00
< / ul >
2018-11-04 00:02:29 +01:00
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 03/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
1979 50.116.102.77
1980 35.237.175.180
2186 207.46.13.156
2208 40.77.167.175
2843 66.249.64.63
4220 84.38.130.177
4537 70.32.83.92
5593 66.249.64.61
12557 78.46.89.18
32152 66.249.64.59
< / code > < / pre >
< ul >
< li > < code > 78.46.89.18< / code > is new since I last checked a few hours ago, and it’ s from Hetzner with the following user agent:< / li >
< / ul >
< pre > < code > Mozilla/5.0 (Macintosh; Intel Mac OS X 10.12; rv:62.0) Gecko/20100101 Firefox/62.0
< / code > < / pre >
< ul >
< li > It’ s making lots of requests and using quite a number of Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.89.18' /home/cgspace.cgiar.org/log/dspace.log.2018-11-03 | sort | uniq
8449
< / code > < / pre >
< ul >
< li > I could add this IP to the list of bot IPs in nginx, but it seems like a futile effort when some new IP could come along and do the same thing< / li >
< li > Perhaps I should think about adding rate limits to dynamic pages like < code > /discover< / code > and < code > /browse< / code > < / li >
< li > I think it’ s reasonable for a human to click one of those links five or ten times a minute… < / li >
< li > To contrast, < code > 78.46.89.18< / code > made about 300 requests per minute for a few hours today:< / li >
< / ul >
< pre > < code > # grep 78.46.89.18 /var/log/nginx/access.log | grep -o -E '03/Nov/2018:[0-9][0-9]:[0-9][0-9]' | sort | uniq -c | sort -n | tail -n 20
286 03/Nov/2018:18:02
287 03/Nov/2018:18:21
289 03/Nov/2018:18:23
291 03/Nov/2018:18:27
293 03/Nov/2018:18:34
300 03/Nov/2018:17:58
300 03/Nov/2018:18:22
300 03/Nov/2018:18:32
304 03/Nov/2018:18:12
305 03/Nov/2018:18:13
305 03/Nov/2018:18:24
312 03/Nov/2018:18:39
322 03/Nov/2018:18:17
326 03/Nov/2018:18:38
327 03/Nov/2018:18:16
330 03/Nov/2018:17:57
332 03/Nov/2018:18:19
336 03/Nov/2018:17:56
340 03/Nov/2018:18:14
341 03/Nov/2018:18:18
< / code > < / pre >
< ul >
< li > If they want to download all our metadata and PDFs they should use an API rather than scraping the XMLUI< / li >
< li > I will add them to the list of bot IPs in nginx for now and think about enforcing rate limits in XMLUI later< / li >
2018-11-04 11:18:52 +01:00
< li > Also, this is the third (?) time a mysterious IP on Hetzner has done this… who is this?< / li >
< / ul >
< h2 id = "2018-11-04" > 2018-11-04< / h2 >
< ul >
< li > Forward Peter’ s information about CGSpace financials to Modi from ICRISAT< / li >
< li > Linode emailed about the CPU load and outgoing bandwidth on CGSpace (linode18) again< / li >
< li > Here are the top ten IPs active so far this morning:< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 04/Nov/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
1083 2a03:2880:11ff:2::face:b00c
1105 2a03:2880:11ff:d::face:b00c
1111 2a03:2880:11ff:f::face:b00c
1134 84.38.130.177
1893 50.116.102.77
2040 66.249.64.63
4210 66.249.64.61
4534 70.32.83.92
13036 78.46.89.18
20407 66.249.64.59
< / code > < / pre >
< ul >
< li > < code > 78.46.89.18< / code > is back… and still making tons of Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=78.46.89.18' dspace.log.2018-11-04 | sort | uniq
8765
< / code > < / pre >
< ul >
< li > Also, now we have a ton of Facebook crawlers:< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 04/Nov/2018" | grep " 2a03:2880:11ff:" | awk '{print $1}' | sort | uniq -c | sort -n
905 2a03:2880:11ff:b::face:b00c
955 2a03:2880:11ff:5::face:b00c
965 2a03:2880:11ff:e::face:b00c
984 2a03:2880:11ff:8::face:b00c
993 2a03:2880:11ff:3::face:b00c
994 2a03:2880:11ff:7::face:b00c
1006 2a03:2880:11ff:10::face:b00c
1011 2a03:2880:11ff:4::face:b00c
1023 2a03:2880:11ff:6::face:b00c
1026 2a03:2880:11ff:9::face:b00c
1039 2a03:2880:11ff:1::face:b00c
1043 2a03:2880:11ff:c::face:b00c
1070 2a03:2880:11ff::face:b00c
1075 2a03:2880:11ff:a::face:b00c
1093 2a03:2880:11ff:2::face:b00c
1107 2a03:2880:11ff:d::face:b00c
1116 2a03:2880:11ff:f::face:b00c
< / code > < / pre >
< ul >
< li > They are really making shit tons of Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-04 | sort | uniq
14368
< / code > < / pre >
< ul >
< li > Their user agent is:< / li >
< / ul >
< pre > < code > facebookexternalhit/1.1 (+http://www.facebook.com/externalhit_uatext.php)
< / code > < / pre >
< ul >
< li > I will add it to the Tomcat Crawler Session Manager valve< / li >
2018-11-04 21:45:00 +01:00
< li > Later in the evening… ok, this Facebook bot is getting super annoying:< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 04/Nov/2018" | grep " 2a03:2880:11ff:" | awk '{print $1}' | sort | uniq -c | sort -n
1871 2a03:2880:11ff:3::face:b00c
1885 2a03:2880:11ff:b::face:b00c
1941 2a03:2880:11ff:8::face:b00c
1942 2a03:2880:11ff:e::face:b00c
1987 2a03:2880:11ff:1::face:b00c
2023 2a03:2880:11ff:2::face:b00c
2027 2a03:2880:11ff:4::face:b00c
2032 2a03:2880:11ff:9::face:b00c
2034 2a03:2880:11ff:10::face:b00c
2050 2a03:2880:11ff:5::face:b00c
2061 2a03:2880:11ff:c::face:b00c
2076 2a03:2880:11ff:6::face:b00c
2093 2a03:2880:11ff:7::face:b00c
2107 2a03:2880:11ff::face:b00c
2118 2a03:2880:11ff:d::face:b00c
2164 2a03:2880:11ff:a::face:b00c
2178 2a03:2880:11ff:f::face:b00c
< / code > < / pre >
< ul >
< li > And still making shit tons of Tomcat sessions:< / li >
< / ul >
< pre > < code > $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-04 | sort | uniq
28470
< / code > < / pre >
< ul >
< li > And that’ s even using the Tomcat Crawler Session Manager valve!< / li >
< li > Maybe we need to limit more dynamic pages, like the “ most popular” country, item, and author pages< / li >
< li > It seems these are popular too, and there is no fucking way Facebook needs that information, yet they are requesting thousands of them!< / li >
< / ul >
< pre > < code > # grep 'face:b00c' /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep -c 'most-popular/'
7033
< / code > < / pre >
< ul >
< li > I added the “ most-popular” pages to the list that return < code > X-Robots-Tag: none< / code > to try to inform bots not to index or follow those pages< / li >
< li > Also, I implemented an nginx rate limit of twelve requests per minute on all dynamic pages… I figure a human user might legitimately request one every five seconds< / li >
2018-11-06 10:36:04 +01:00
< / ul >
< h2 id = "2018-11-05" > 2018-11-05< / h2 >
< ul >
2018-11-05 16:45:39 +01:00
< li > I wrote a small Python script < a href = "https://gist.github.com/alanorth/4ff81d5f65613814a66cb6f84fdf1fc5" > add-dc-rights.py< / a > to add usage rights (< code > dc.rights< / code > ) to CGSpace items based on the CSV Hector gave me from MARLO:< / li >
< / ul >
< pre > < code > $ ./add-dc-rights.py -i /tmp/marlo.csv -db dspace -u dspace -p 'fuuu'
< / code > < / pre >
< ul >
< li > The file < code > marlo.csv< / code > was cleaned up and formatted in Open Refine< / li >
< li > 165 of the items in their 2017 data are from CGSpace!< / li >
2018-11-05 23:04:18 +01:00
< li > I will add the data to CGSpace this week (done!)< / li >
< li > Jesus, is Facebook < em > trying< / em > to be annoying?< / li >
< / ul >
< pre > < code > # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 05/Nov/2018" | grep -c " 2a03:2880:11ff:"
29889
# grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=2a03:2880:11ff' dspace.log.2018-11-05 | sort | uniq
29156
# zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E " 05/Nov/2018" | grep " 2a03:2880:11ff:" | grep -c -E " (handle|bitstream)"
29896
< / code > < / pre >
< ul >
< li > 29,000 requests from Facebook, 29,000 Tomcat sessions, and none of the requests are to the dynamic pages I rate limited yesterday!< / li >
2018-11-04 00:02:29 +01:00
< / ul >
2018-11-01 15:43:37 +01:00
2018-11-06 10:36:04 +01:00
< h2 id = "2018-11-06" > 2018-11-06< / h2 >
< ul >
< li > I updated all the < a href = "https://github.com/ilri/DSpace/wiki/Scripts" > DSpace helper Python scripts< / a > to validate against PEP 8 using Flake8< / li >
2018-11-06 17:03:44 +01:00
< li > While I was updating the < a href = "https://gist.github.com/alanorth/ddd7f555f0e487fe0e9d3eb4ff26ce50" > rest-find-collections.py< / a > script I noticed it was using < code > expand=all< / code > to get the collection and community IDs< / li >
< li > I realized I actually only need < code > expand=collections,subCommunities< / code > , and I wanted to see how much overhead the extra expands created so I did three runs of each:< / li >
< / ul >
< pre > < code > $ time ./rest-find-collections.py 10568/27629 --rest-url https://dspacetest.cgiar.org/rest
< / code > < / pre >
< ul >
< li > Average time with all expands was 14.3 seconds, and 12.8 seconds with < code > collections,subCommunities< / code > , so < strong > 1.5 seconds difference< / strong > !< / li >
2018-11-06 10:36:04 +01:00
< / ul >
2018-11-07 18:20:25 +01:00
< h2 id = "2018-11-07" > 2018-11-07< / h2 >
< ul >
< li > Update my < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > to use a database management class with Python contexts so that connections and cursors are automatically opened and closed< / li >
< li > Tag version 0.7.0 of the dspace-statistics-api< / li >
< / ul >
2018-11-08 08:02:20 +01:00
< h2 id = "2018-11-08" > 2018-11-08< / h2 >
< ul >
< li > I deployed verison 0.7.0 of the dspace-statistics-api on DSpace Test (linode19) so I can test it for a few days (and check the Munin stats to see the change in database connections) before deploying on CGSpace< / li >
< li > I also enabled systemd’ s persistent journal by setting < a href = "https://www.freedesktop.org/software/systemd/man/journald.conf.html" > < code > Storage=persistent< / code > in < em > journald.conf< / em > < / a > < / li >
< li > Apparently < a href = "https://www.freedesktop.org/software/systemd/man/journald.conf.html" > Ubuntu 16.04 defaulted to using rsyslog for boot records until early 2018< / a > , so I removed < code > rsyslog< / code > too< / li >
2018-11-08 16:13:55 +01:00
< li > Proof 277 IITA records on DSpace Test: < a href = "https://dspacetest.cgiar.org/handle/10568/107871" > IITA_ ALIZZY1802-csv_oct23< / a >
< ul >
< li > There were a few issues with countries, a few language erorrs, a few whitespace errors, and then a handful of ISSNs in the ISBN field< / li >
< / ul > < / li >
2018-11-08 08:02:20 +01:00
< / ul >
2018-11-11 16:15:54 +01:00
< h2 id = "2018-11-11" > 2018-11-11< / h2 >
< ul >
< li > I added tests to the < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > !< / li >
< li > It runs with Python 3.5, 3.6, and 3.7 using pytest, including automatically on Travis CI!< / li >
< / ul >
2018-11-13 11:20:42 +01:00
< h2 id = "2018-11-13" > 2018-11-13< / h2 >
< ul >
< li > Help troubleshoot an issue with Judy Kimani submitting to the < em > ILRI project reports, papers and documents< / em > collection on CGSpace< / li >
< li > For some reason there is an existing group for the “ Accept/Reject” workflow step, but it’ s empty< / li >
< li > I added Judy to the group and told her to try again< / li >
2018-11-13 16:42:55 +01:00
< li > Sisay changed his leave to be full days until December so I need to finish the IITA records that he was working on (< a href = "https://dspacetest.cgiar.org/handle/10568/107871" > IITA_ ALIZZY1802-csv_oct23< / a > < / li >
< li > Sisay had said there were a few PDFs missing and Bosede sent them this week, so I had to find those items on DSpace Test and add the bitstreams to the items manually< / li >
< li > As for the collection mappings I think I need to export the CSV from DSpace Test, add mappings for each type (ie Books go to IITA books collection, etc), then re-import to DSpace Test, then export from DSpace command line in “ migrate” mode… < / li >
< li > From there I should be able to script the removal of the old DSpace Test collection so they just go to the correct IITA collections on import into CGSpace< / li >
2018-11-13 11:20:42 +01:00
< / ul >
2018-11-14 09:00:25 +01:00
< h2 id = "2018-11-14" > 2018-11-14< / h2 >
< ul >
< li > Finally import the 277 IITA (ALIZZY1802) records to CGSpace< / li >
< li > I had to export them from DSpace Test and import them into a temporary collection on CGSpace first, then export the collection as CSV to map them to new owning collections (IITA books, IITA posters, etc) with OpenRefine because DSpace’ s < code > dspace export< / code > command doesn’ t include the collections for the items!< / li >
< li > Delete all old IITA collections on DSpace Test and run < code > dspace cleanup< / code > to get rid of all the bitstreams< / li >
< / ul >
2018-11-15 08:09:39 +01:00
< h2 id = "2018-11-15" > 2018-11-15< / h2 >
< ul >
< li > Deploy version 0.8.1 of the < a href = "https://github.com/ilri/dspace-statistics-api" > dspace-statistics-api< / a > to CGSpace (linode18)< / li >
< / ul >
2018-11-18 16:35:32 +01:00
< h2 id = "2018-11-18" > 2018-11-18< / h2 >
< ul >
< li > Request invoice from Wild Jordan for their meeting venue in January< / li >
< / ul >
2018-11-19 16:17:04 +01:00
< h2 id = "2018-11-19" > 2018-11-19< / h2 >
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< li > Testing corrections and deletions for AGROVOC (< code > dc.subject< / code > ) that Sisay and Peter were working on earlier this month:< / li >
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< pre > < code > $ ./fix-metadata-values.py -i 2018-11-19-correct-agrovoc.csv -f dc.subject -t correct -m 57 -db dspace -u dspace -p 'fuu' -d
$ ./delete-metadata-values.py -i 2018-11-19-delete-agrovoc.csv -f dc.subject -m 57 -db dspace -u dspace -p 'fuu' -d
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< li > Then I ran them on both CGSpace and DSpace Test, and started a full Discovery re-index on CGSpace:< / li >
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< pre > < code > $ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
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2018-11-19 16:25:08 +01:00
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< li > Generate a new list of the top 1500 AGROVOC subjects on CGSpace to send to Peter and Sisay:< / li >
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< pre > < code > dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 57 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2018-11-19-top-1500-subject.csv WITH CSV HEADER;
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2018-11-01 15:43:37 +01:00
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< h4 > Recent Posts< / h4 >
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< li > < a href = "/cgspace-notes/2018-11/" > November, 2018< / a > < / li >
< li > < a href = "/cgspace-notes/2018-10/" > October, 2018< / a > < / li >
< li > < a href = "/cgspace-notes/2018-09/" > September, 2018< / a > < / li >
< li > < a href = "/cgspace-notes/2018-08/" > August, 2018< / a > < / li >
< li > < a href = "/cgspace-notes/2018-07/" > July, 2018< / a > < / li >
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< h4 > Links< / h4 >
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< li > < a href = "https://cgspace.cgiar.org" > CGSpace< / a > < / li >
< li > < a href = "https://dspacetest.cgiar.org" > DSpace Test< / a > < / li >
< li > < a href = "https://github.com/ilri/DSpace" > CGSpace @ GitHub< / a > < / li >
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