2024-01-02
- Work on preparation of new server for DSpace 7 migration
- I’m not quite sure what we need to do for the Handle server
- For now I just ran the
dspace make-handle-config script and diffed it with the one from DSpace 6
- I sent the bundle to the Handle admins to make sure it’s OK before we do the migration
- Continue testing and debugging the cgspace-java-helpers on DSpace 7
- Work on IFPRI ISNAR archive cleanup
2024-01-03
- I haven’t heard from the Handle admins so I’m preparing a backup solution using nginx streams
- This seems to work in my simple tests (this must be outside the
http {} block):
stream {
upstream handle_tcp_9000 {
server 188.34.177.10:9000;
}
server {
listen 9000;
proxy_connect_timeout 1s;
proxy_timeout 3s;
proxy_pass handle_tcp_9000;
}
}
- Here I forwarded a test TCP port 9000 from one server to another and was able to retrieve a test HTML that was running on the target
- I will have to do TCP and UDP on port 2641, and TCP/HTTP on port 8000.
- I did some more minor work on the IFPRI ISNAR archive
- I got some PDFs from the UMN AgEcon search and fixed some metadata
- Then I did some duplicate checking and found five items already on CGSpace
2024-01-04
- Upload 692 items for the ISNAR archive to CGSpace: https://cgspace.cgiar.org/handle/10568/136192
- Help Peter proof and upload 252 items from the 2023 Gender conference to CGSpace
- Meeting with IFPRI to discuss their migration to CGSpace
- We agreed to add two new fields, one for IFPRI project and one for IFPRI publication ranking
- Most likely we will use
cg.identifier.project as a general field and consolidate other project fields there
- Not sure which field to use for the publication rank…
2024-01-05
- Proof and upload 51 items in bulk for IFPRI
- I did a big cleanup of user groups in anticipation of complaints about slow workflow tasks etc in DSpace 7
- I removed ILRI editors from all the dozens of CCAFS community and collection groups, and I should do the same for other CRPs since they are closed for two years now
2024-01-06
- Migrate CGSpace to DSpace 7
2024-01-07
- High load on the server and UptimeRobot saying the frontend is flapping
- I noticed tons of logs from pm2 in the systemd journal, so I disabled those in the systemd unit because they are available from pm2’s log directory anyway
- I also noticed the same for Solr, so I disabled stdout for that systemd unit as well
- I spent a lot of time bringing back the nginx rate limits we used in DSpace 6 and it seems to have helped
- I see some client doing weird HEAD requests to search pages:
47.76.35.19 - - [07/Jan/2024:00:00:02 +0100] "HEAD /search/?f.accessRights=Open+Access%2Cequals&f.actionArea=Resilient+Agrifood+Systems%2Cequals&f.author=Burkart%2C+Stefan%2Cequals&f.country=Kenya%2Cequals&f.impactArea=Climate+adaptation+and+mitigation%2Cequals&f.itemtype=Brief%2Cequals&f.publisher=CGIAR+System+Organization%2Cequals&f.region=Asia%2Cequals&f.sdg=SDG+12+-+Responsible+consumption+and+production%2Cequals&f.sponsorship=CGIAR+Trust+Fund%2Cequals&f.subject=environmental+factors%2Cequals&spc.page=1 HTTP/1.1" 499 0 "-" "Mozilla/5.0 (Windows NT 6.1; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/74.0.2504.63 Safari/537.36"
- I will add their network blocks (AS45102) and regenerate my list of bot networks:
$ wget https://asn.ipinfo.app/api/text/list/AS16276 \
https://asn.ipinfo.app/api/text/list/AS23576 \
https://asn.ipinfo.app/api/text/list/AS24940 \
https://asn.ipinfo.app/api/text/list/AS13238 \
https://asn.ipinfo.app/api/text/list/AS14061 \
https://asn.ipinfo.app/api/text/list/AS12876 \
https://asn.ipinfo.app/api/text/list/AS55286 \
https://asn.ipinfo.app/api/text/list/AS203020 \
https://asn.ipinfo.app/api/text/list/AS204287 \
https://asn.ipinfo.app/api/text/list/AS50245 \
https://asn.ipinfo.app/api/text/list/AS6939 \
https://asn.ipinfo.app/api/text/list/AS45102 \
https://asn.ipinfo.app/api/text/list/AS21859
$ cat AS* | sort | uniq | wc -l
4897
$ cat AS* | ~/go/bin/mapcidr -a > /tmp/networks.txt
$ wc -l /tmp/networks.txt
2017 /tmp/networks.txt
- I’m surprised to see the number of networks reduced from my current ones… hmmm.
- I will also update my list of Bing networks:
$ ./ilri/bing-networks-to-ips.sh
$ ~/go/bin/mapcidr -a < /tmp/bing-ips.txt > /tmp/bing-networks.txt
$ wc -l /tmp/bing-networks.txt
250 /tmp/bing-networks.txt
2024-01-08
- Export list of publishers for Peter to select some amount to use as a controlled vocabulary:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "dcterms.publisher", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 178 GROUP BY "dcterms.publisher" ORDER BY count DESC) to /tmp/2024-01-publishers.csv WITH CSV HEADER;
COPY 4332
- Address some feedback on DSpace 7 from users, including fileing some issues on GitHub
- The Alliance TIP team was having issues posting to one collection via the legacy DSpace 6 REST API
- In the DSpace logs I see the same issue that they had last month:
ERROR unknown unknown org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.
2024-01-09
- I restarted Tomcat to see if it helps the REST issue
- After talking with Peter about publishers we decided to get a clean list of the top ~100 publishers and then make sure all CGIAR centers, Initiatives, and Impact Platforms are there as well
- I exported a list from PostgreSQL and then filtered by count > 40 in OpenRefine and then extracted the metadata values:
$ csvcut -c dcterms.publisher ~/Downloads/2024-01-09-publishers4.csv | sed -e 1d -e 's/"//g' > /tmp/top-publishers.txt
- Export a list of ORCID identifiers from PostgreSQL to look them up on ORCID and update our controlled vocabulary:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT(text_value) FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND metadata_field_id=247) to /tmp/2024-01-09-orcid-identifiers.txt;
localhost/dspace7= ☘ \q
$ cat ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-identifier.xml /tmp/2024-01-09-orcid-identifiers.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2024-01-09-orcids.txt
$ ./ilri/resolve_orcids.py -i /tmp/2024-01-09-orcids.txt -o /tmp/2024-01-09-orcids-names.txt -d
- Then I updated existing ORCID identifiers in CGSpace:
$ ./ilri/update_orcids.py -i /tmp/2024-01-09-orcids-names.txt -db dspace -u dspace -p bahhhh
- Bizu seems to be having issues due to belonging to too many groups
- I see some messages from Solr in the DSpace log:
2024-01-09 06:23:35,893 ERROR unknown unknown org.dspace.authorize.AuthorizeServiceImpl @ Failed getting getting community/collection admin status for bahhhhh@cgiar.org The search error is: Error from server at http://localhost:8983/solr/search: org.apache.solr.search.SyntaxError: Cannot parse 'search.resourcetype:Community AND (admin:eef481147-daf3-4fd2-bb8d-e18af8131d8c OR admin:g80199ef9-bcd6-4961-9512-501dea076607 OR admin:g4ac29263-cf0c-48d0-8be7-7f09317d50ec OR admin:g0e594148-a0f6-4f00-970d-6b7812f89540 OR admin:g0265b87a-2183-4357-a971-7a5b0c7add3a OR admin:g371ae807-f014-4305-b4ec-f2a8f6f0dcfa OR admin:gdc5cb27c-4a5a-45c2-b656-a399fded70de OR admin:ge36d0ece-7a52-4925-afeb-6641d6a348cc OR admin:g15dc1173-7ddf-43cf-a89a-77a7f81c4cfc OR admin:gc3a599d3-c758-46cd-9855-c98f6ab58ae4 OR admin:g3d648c3e-58c3-4342-b500-07cba10ba52d OR admin:g82bf5168-65c1-4627-8eb4-724fa0ea51a7 OR admin:ge751e973-697d-419c-b59b-5a5644702874 OR admin:g44dd0a80-c1e6-4274-9be4-9f342d74928c OR admin:g4842f9c2-73ed-476a-a81a-7167d8aa7946 OR admin:g5f279b3f-c2ce-4c75-b151-1de52c1a540e OR admin:ga6df8adc-2e1d-40f2-8f1e-f77796d0eecd OR admin:gfdfc1621-382e-437a-8674-c9007627565c OR admin:g15cd114a-0b89-442b-a1b4-1febb6959571 OR admin:g12aede99-d018-4c00-b4d4-a732541d0017 OR admin:gc59529d7-002a-4216-b2e1-d909afd2d4a9 OR admin:gd0806714-bc13-460d-bedd-121bdd5436a4 OR admin:gce70739a-8820-4d56-b19c-f191855479e4 OR admin:g7d3409eb-81e3-4156-afb1-7f02de22065f OR admin:g54bc009e-2954-4dad-8c30-be6a09dc5093 OR admin:gc5e1d6b7-4603-40d7-852f-6654c159dec9 OR admin:g0046214d-c85b-4f12-a5e6-2f57a2c3abb0 OR admin:g4c7b4fd0-938f-40e9-ab3e-447c317296c1 OR admin:gcfae9b69-d8dd-4cf3-9a4e-d6e31ff68731 OR ... admin:g20f366c0-96c0-4416-ad0b-46884010925f)': too many boolean clauses The search resourceType filter was: search.resourcetype:Community
- There are 1,805 OR clauses in the full log!
- We previous had this issue in 2020-01 and 2020-02 with DSpace 5 and DSpace 6
- At the time the solution was to increase the
maxBooleanClauses in Solr and to disable access rights awareness, but I don’t think we want to do the second one now
- I saw many users of Solr in other applications increasing this to obscenely high numbers, so I think we should be OK to increase it from 1024 to 2048
- Re-visiting the DSpace user groomer to delete inactive users
- In 2023-08 I noticed that this was now possible in DSpace 7
- As a test I tried to delete all users who have been inactive since six years ago (Janury 9, 2018):
$ dspace dsrun org.dspace.eperson.Groomer -a -b 01/09/2018 -d
- I tested it on DSpace 7 Test and it worked… I am debating running it on CGSpace…
- I see we have almost 9,000 users:
$ dspace user -L > /tmp/users-before.txt
$ wc -l /tmp/users-before.txt
8943 /tmp/users-before.txt
- I decided to do the same on CGSpace and it worked without errors
- I finished working on the controlled vocabulary for publishers
2024-01-10
- I spent some time deleting old groups on CGSpace
- I looked into the use of the
cg.identifier.ciatproject field and found there are only a handful of uses, with some even seeming to be a mistake:
localhost/dspace7= ☘ SELECT DISTINCT text_value AS "cg.identifier.ciatproject", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata
_field_id = 232 GROUP BY "cg.identifier.ciatproject" ORDER BY count DESC;
cg.identifier.ciatproject │ count
───────────────────────────┼───────
D145 │ 4
LAM_LivestockPlus │ 2
A215 │ 1
A217 │ 1
A220 │ 1
A223 │ 1
A224 │ 1
A227 │ 1
A229 │ 1
A230 │ 1
CLIMATE CHANGE MITIGATION │ 1
LIVESTOCK │ 1
(12 rows)
Time: 240.041 ms
- I think we can move those to a new
cg.identifier.project if we create one
- The
cg.identifier.cpwfproject field is similarly sparse, but the CCAFS ones are widely used
2024-01-12
- Export a list of affiliations to do some cleanup:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT text_value AS "cg.contributor.affiliation", count(*) FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id = 211 GROUP BY "cg.contributor.affiliation" ORDER BY count DESC) to /tmp/2024-01-affiliations.csv WITH CSV HEADER;
COPY 11719
- I first did some clustering and editing in OpenRefine, then I’ll import those back into CGSpace and then do another export
- Troubleshooting the statistics pages that aren’t working on DSpace 7
- On a hunch, I queried for for Solr statistics documents that did not have an
id matching the 36-character UUID pattern:
$ curl 'http://localhost:8983/solr/statistics/select?q=-id%3A%2F.\{36\}%2F&rows=0'
{
"responseHeader":{
"status":0,
"QTime":0,
"params":{
"q":"-id:/.{36}/",
"rows":"0"}},
"response":{"numFound":800167,"start":0,"numFoundExact":true,"docs":[]
}}
- They seem to come mostly from 2020, 2023, and 2024:
$ curl 'http://localhost:8983/solr/statistics/select?q=-id%3A%2F.\{36\}%2F&facet.range=time&facet=true&facet.range.start=2010-01-01T00:00:00Z&facet.range.end=NOW&facet.range.gap=%2B1YEAR&rows=0'
{
"responseHeader":{
"status":0,
"QTime":13,
"params":{
"facet.range":"time",
"q":"-id:/.{36}/",
"facet.range.gap":"+1YEAR",
"rows":"0",
"facet":"true",
"facet.range.start":"2010-01-01T00:00:00Z",
"facet.range.end":"NOW"}},
"response":{"numFound":800168,"start":0,"numFoundExact":true,"docs":[]
},
"facet_counts":{
"facet_queries":{},
"facet_fields":{},
"facet_ranges":{
"time":{
"counts":[
"2010-01-01T00:00:00Z",0,
"2011-01-01T00:00:00Z",0,
"2012-01-01T00:00:00Z",0,
"2013-01-01T00:00:00Z",0,
"2014-01-01T00:00:00Z",0,
"2015-01-01T00:00:00Z",89,
"2016-01-01T00:00:00Z",11,
"2017-01-01T00:00:00Z",0,
"2018-01-01T00:00:00Z",0,
"2019-01-01T00:00:00Z",0,
"2020-01-01T00:00:00Z",1339,
"2021-01-01T00:00:00Z",0,
"2022-01-01T00:00:00Z",0,
"2023-01-01T00:00:00Z",653736,
"2024-01-01T00:00:00Z",144993],
"gap":"+1YEAR",
"start":"2010-01-01T00:00:00Z",
"end":"2025-01-01T00:00:00Z"}},
"facet_intervals":{},
"facet_heatmaps":{}}}
- They seem to come from 2023-08 until now (so way before we migrated to DSpace 7):
$ curl 'http://localhost:8983/solr/statistics/select?q=-id%3A%2F.\{36\}%2F&facet.range=time&facet=true&facet.range.start=2023-01-01T00:00:00Z&facet.range.end=NOW&facet.range.gap=%2B1MONTH&rows=0'
{
"responseHeader":{
"status":0,
"QTime":196,
"params":{
"facet.range":"time",
"q":"-id:/.{36}/",
"facet.range.gap":"+1MONTH",
"rows":"0",
"facet":"true",
"facet.range.start":"2023-01-01T00:00:00Z",
"facet.range.end":"NOW"}},
"response":{"numFound":800168,"start":0,"numFoundExact":true,"docs":[]
},
"facet_counts":{
"facet_queries":{},
"facet_fields":{},
"facet_ranges":{
"time":{
"counts":[
"2023-01-01T00:00:00Z",1,
"2023-02-01T00:00:00Z",0,
"2023-03-01T00:00:00Z",0,
"2023-04-01T00:00:00Z",0,
"2023-05-01T00:00:00Z",0,
"2023-06-01T00:00:00Z",0,
"2023-07-01T00:00:00Z",0,
"2023-08-01T00:00:00Z",27621,
"2023-09-01T00:00:00Z",59165,
"2023-10-01T00:00:00Z",115338,
"2023-11-01T00:00:00Z",96147,
"2023-12-01T00:00:00Z",355464,
"2024-01-01T00:00:00Z",125429],
"gap":"+1MONTH",
"start":"2023-01-01T00:00:00Z",
"end":"2024-02-01T00:00:00Z"}},
"facet_intervals":{},
"facet_heatmaps":{}}}
- I see that we had 31,744 statistic events yesterday, and 799 have no
id!
- I asked about this on Slack and will file an issue on GitHub if someone else also finds such records
- Several people said they have them, so it’s a bug of some sort in DSpace, not our configuration
2024-01-13
- Yesterday alone we had 37,000 unique IPs making requests to nginx
- I looked up the ASNs and found 6,000 IPs from this network in Amazon Singapore: 47.128.0.0/14
2024-01-15
- Investigating the CSS selector warning that I’ve seen in PM2 logs:
0|dspace-ui | 1 rules skipped due to selector errors:
0|dspace-ui | .custom-file-input:lang(en)~.custom-file-label -> unmatched pseudo-class :lang
- It seems to be a bug in Angular, as this selector comes from Bootstrap 4.6.x and is not invalid
- Since the production site was flapping a lot I decided to try disabling inlineCriticalCss
- There have been on and off load issues with the Angular frontend today
- I think I will just block all data center network blocks for now
- In the last week I see almost 200,000 unique IPs:
# zcat -f /var/log/nginx/*access.log /var/log/nginx/*access.log.1 /var/log/nginx/*access.log.2.gz /var/log/nginx/*access.log.3.gz /var/log/nginx/*access.log.4.gz /var/log/nginx/*access.log.5.gz /var/log/nginx/*access.log.6.gz | awk '{print $1}' | sort -u |
tee /tmp/ips.txt | wc -l
196493
- Looking these IPs up I see there are 18,000 coming from Comcast, 10,000 from AT&T, 4110 from Charter, 3500 from Cox and dozens of other residential IPs
- I highly doubt these are home users browsing CGSpace… seems super fishy
- Also, over 1,000 IPs from SpaceX Starlink in the last week. RIGHT
- I will temporarily add a few new datacenter ISP network blocks to our rate limit:
- 16509 Amazon-02
- 701 UUNET
- 8075 Microsoft
- 15169 Google
- 14618 Amazon-AES
- 396982 Google Cloud
- The load on the server immediately dropped