alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-14 02:47:05 +01:00
Code Issues Projects Releases Wiki Activity
c3436ea6c2
cgspace-notes/content/posts/2019-04.md

1062 lines
52 KiB
Markdown
Raw Blame History

This file contains ambiguous Unicode characters

This file contains Unicode characters that might be confused with other characters. If you think that this is intentional, you can safely ignore this warning. Use the Escape button to reveal them.

---
title: "April, 2019"
date: 2019-04-01T09:00:43+03:00
author: "Alan Orth"
categories: ["Notes"]
---
## 2019-04-01
- Meeting with AgroKnow to discuss CGSpace, ILRI data, AReS, GARDIAN, etc
- They asked if we had plans to enable RDF support in CGSpace
- There have been 4,400 more downloads of the CTA Spore publication from those strange Amazon IP addresses today
- I suspected that some might not be successful, because the stats show less, but today they were all HTTP 200!
```
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep 'Spore-192-EN-web.pdf' | grep -E '(18.196.196.108|18.195.78.144|18.195.218.6)' | awk '{print $9}' | sort | uniq -c | sort -n | tail -n 5
4432 200
```
- In the last two weeks there have been 47,000 downloads of this *same exact PDF* by these three IP addresses
- Apply country and region corrections and deletions on DSpace Test and CGSpace:
```
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-9-countries.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.country -m 228 -t ACTION -d
$ ./fix-metadata-values.py -i /tmp/2019-02-21-fix-4-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -m 231 -t action -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-2-countries.csv -db dspace -u dspace -p 'fuuu' -m 228 -f cg.coverage.country -d
$ ./delete-metadata-values.py -i /tmp/2019-02-21-delete-1-region.csv -db dspace -u dspace -p 'fuuu' -m 231 -f cg.coverage.region -d
```
<!--more-->
## 2019-04-02
- CTA says the Amazon IPs are AWS gateways for real user traffic
- I was trying to add Felix Shaw's account back to the Administrators group on DSpace Test, but I couldn't find his name in the user search of the groups page
- If I searched for "Felix" or "Shaw" I saw other matches, included one for his personal email address!
- I ended up finding him via searching for his email address
## 2019-04-03
- Maria from Bioversity emailed me a list of new ORCID identifiers for their researchers so I will add them to our controlled vocabulary
- First I need to extract the ones that are unique from their list compared to our existing one:
```
$ cat dspace/config/controlled-vocabularies/cg-creator-id.xml /tmp/bioversity.txt | grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' | sort -u > /tmp/2019-04-03-orcid-ids.txt
```
- We currently have 1177 unique ORCID identifiers, and this brings our total to 1237!
- Next I will resolve all their names using my `resolve-orcids.py` script:
```
$ ./resolve-orcids.py -i /tmp/2019-04-03-orcid-ids.txt -o 2019-04-03-orcid-ids.txt -d
```
- After that I added the XML formatting, formatted the file with tidy, and sorted the names in vim
- One user's name has changed so I will update those using my `fix-metadata-values.py` script:
```
$ ./fix-metadata-values.py -i 2019-04-03-update-orcids.csv -db dspace -u dspace -p 'fuuu' -f cg.creator.id -m 240 -t correct -d
```
- I created a pull request and merged the changes to the `5_x-prod` branch ([#417](https://github.com/ilri/DSpace/pull/417))
- A few days ago I noticed some weird update process for the statistics-2018 Solr core and I see it's still going:
```
2019-04-03 16:34:02,262 INFO org.dspace.statistics.SolrLogger @ Updating : 1754500/21701 docs in http://localhost:8081/solr//statistics-2018
```
- Interestingly, there are 5666 occurences, and they are mostly for the 2018 core:
```
$ grep 'org.dspace.statistics.SolrLogger @ Updating' /home/cgspace.cgiar.org/log/dspace.log.2019-04-03 | awk '{print $11}' | sort | uniq -c
1
3 http://localhost:8081/solr//statistics-2017
5662 http://localhost:8081/solr//statistics-2018
```
- I will have to keep an eye on it because nothing should be updating 2018 stats in 2019...
## 2019-04-05
- Uptime Robot reported that CGSpace (linode18) went down tonight
- I see there are lots of PostgreSQL connections:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
10 dspaceCli
250 dspaceWeb
```
- I still see those weird messages about updating the statistics-2018 Solr core:
```
2019-04-05 21:06:53,770 INFO org.dspace.statistics.SolrLogger @ Updating : 2444600/21697 docs in http://localhost:8081/solr//statistics-2018
```
- Looking at `iostat 1 10` I also see some CPU steal has come back, and I can confirm it by looking at the Munin graphs:
![CPU usage week](/cgspace-notes/2019/04/cpu-week.png)
- The other thing visible there is that the past few days the load has spiked to 500% and I don't think it's a coincidence that the Solr updating thing is happening...
- I ran all system updates and rebooted the server
- The load was lower on the server after reboot, but Solr didn't come back up properly according to the Solr Admin UI:
```
statistics-2017: org.apache.solr.common.SolrException:org.apache.solr.common.SolrException: Error opening new searcher
```
- I restarted it again and all the Solr cores came up properly...
## 2019-04-06
- Udana asked why item [10568/91278](https://cgspace.cgiar.org/handle/10568/91278) didn't have an Altmetric badge on CGSpace, but on the [WLE website](https://wle.cgiar.org/food-and-agricultural-innovation-pathways-prosperity) it does
- I looked and saw that the WLE website is using the Altmetric score associated with the DOI, and that the Handle has no score at all
- I tweeted the item and I assume this will link the Handle with the DOI in the system
- Twenty minutes later I see the same Altmetric score (9) on CGSpace
- Linode sent an alert that there was high CPU usage this morning on CGSpace (linode18) and these were the top IPs in the webserver access logs around the time:
```
# zcat --force /var/log/nginx/{access,error,library-access}.log /var/log/nginx/{access,error,library-access}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
222 18.195.78.144
245 207.46.13.58
303 207.46.13.194
328 66.249.79.33
564 207.46.13.210
566 66.249.79.62
575 40.77.167.66
1803 66.249.79.59
2834 2a01:4f8:140:3192::2
9623 45.5.184.72
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "06/Apr/2019:(06|07|08|09)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
31 66.249.79.62
41 207.46.13.210
42 40.77.167.66
54 42.113.50.219
132 66.249.79.59
785 2001:41d0:d:1990::
1164 45.5.184.72
2014 50.116.102.77
4267 45.5.186.2
4893 205.186.128.185
```
- `45.5.184.72` is in Colombia so it's probably CIAT, and I see they are indeed trying to get crawl the Discover pages on CIAT's datasets collection:
```
GET /handle/10568/72970/discover?filtertype_0=type&filtertype_1=author&filter_relational_operator_1=contains&filter_relational_operator_0=equals&filter_1=&filter_0=Dataset&filtertype=dateIssued&filter_relational_operator=equals&filter=2014
```
- Their user agent is the one I added to the badbots list in nginx last week: "GuzzleHttp/6.3.3 curl/7.47.0 PHP/7.0.30-0ubuntu0.16.04.1"
- They made 22,000 requests to Discover on this collection today alone (and it's only 11AM):
```
# cat /var/log/nginx/access.log /var/log/nginx/access.log.1 | grep "06/Apr/2019" | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c
22077 /handle/10568/72970/discover
```
- Yesterday they made 43,000 requests and we actually blocked most of them:
```
# zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep "05/Apr/2019" | grep 45.5.184.72 | grep -oE '/handle/[0-9]+/[0-9]+/discover' | sort | uniq -c
43631 /handle/10568/72970/discover
# zcat --force /var/log/nginx/access.log /var/log/nginx/access.log.1 /var/log/nginx/access.log.2.gz | grep "05/Apr/2019" | grep 45.5.184.72 | grep -E '/handle/[0-9]+/[0-9]+/discover' | awk '{print $9}' | sort | uniq -c
142 200
43489 503
```
- I need to find a contact at CIAT to tell them to use the REST API rather than crawling Discover
- Maria from Bioversity recommended that we use the phrase "AGROVOC subject" instead of "Subject" in Listings and Reports
- I made a pull request to update this and merged it to the `5_x-prod` branch ([#418](https://github.com/ilri/DSpace/pull/418))
## 2019-04-07
- Looking into the impact of harvesters like `45.5.184.72`, I see in Solr that this user is not categorized as a bot so it definitely impacts the usage stats by some tens of thousands *per day*
- Last week CTA switched their frontend code to use HEAD requests instead of GET requests for bitstreams
- I am trying to see if these are registered as downloads in Solr or not
- I see 96,925 downloads from their AWS gateway IPs in 2019-03:
```
$ http --print b 'http://localhost:8081/solr/statistics/select?q=type%3A0+AND+(ip%3A18.196.196.108+OR+ip%3A18.195.78.144+OR+ip%3A18.195.218.6)&fq=statistics_type%3Aview&fq=bundleName%3AORIGINAL&fq=dateYearMonth%3A2019-03&rows=0&wt=json&indent=true'
{
"response": {
"docs": [],
"numFound": 96925,
"start": 0
},
"responseHeader": {
"QTime": 1,
"params": {
"fq": [
"statistics_type:view",
"bundleName:ORIGINAL",
"dateYearMonth:2019-03"
],
"indent": "true",
"q": "type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)",
"rows": "0",
"wt": "json"
},
"status": 0
}
}
```
- Strangely I don't see many hits in 2019-04:
```
$ http --print b 'http://localhost:8081/solr/statistics/select?q=type%3A0+AND+(ip%3A18.196.196.108+OR+ip%3A18.195.78.144+OR+ip%3A18.195.218.6)&fq=statistics_type%3Aview&fq=bundleName%3AORIGINAL&fq=dateYearMonth%3A2019-04&rows=0&wt=json&indent=true'
{
"response": {
"docs": [],
"numFound": 38,
"start": 0
},
"responseHeader": {
"QTime": 1,
"params": {
"fq": [
"statistics_type:view",
"bundleName:ORIGINAL",
"dateYearMonth:2019-04"
],
"indent": "true",
"q": "type:0 AND (ip:18.196.196.108 OR ip:18.195.78.144 OR ip:18.195.218.6)",
"rows": "0",
"wt": "json"
},
"status": 0
}
}
```
- Making some tests on GET vs HEAD requests on the [CTA Spore 192 item](https://dspacetest.cgiar.org/handle/10568/100289) on DSpace Test:
```
$ http --print Hh GET https://dspacetest.cgiar.org/bitstream/handle/10568/100289/Spore-192-EN-web.pdf
GET /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: dspacetest.cgiar.org
User-Agent: HTTPie/1.0.2
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2069158
Content-Type: application/pdf;charset=ISO-8859-1
Date: Sun, 07 Apr 2019 08:38:34 GMT
Expires: Sun, 07 Apr 2019 09:38:34 GMT
Last-Modified: Thu, 14 Mar 2019 11:20:05 GMT
Server: nginx
Set-Cookie: JSESSIONID=21A492CC31CA8845278DFA078BD2D9ED; Path=/; Secure; HttpOnly
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-Robots-Tag: none
X-XSS-Protection: 1; mode=block
$ http --print Hh HEAD https://dspacetest.cgiar.org/bitstream/handle/10568/100289/Spore-192-EN-web.pdf
HEAD /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1
Accept: */*
Accept-Encoding: gzip, deflate
Connection: keep-alive
Host: dspacetest.cgiar.org
User-Agent: HTTPie/1.0.2
HTTP/1.1 200 OK
Connection: keep-alive
Content-Language: en-US
Content-Length: 2069158
Content-Type: application/pdf;charset=ISO-8859-1
Date: Sun, 07 Apr 2019 08:39:01 GMT
Expires: Sun, 07 Apr 2019 09:39:01 GMT
Last-Modified: Thu, 14 Mar 2019 11:20:05 GMT
Server: nginx
Set-Cookie: JSESSIONID=36C8502257CC6C72FD3BC9EBF91C4A0E; Path=/; Secure; HttpOnly
Vary: User-Agent
X-Cocoon-Version: 2.2.0
X-Content-Type-Options: nosniff
X-Frame-Options: SAMEORIGIN
X-Robots-Tag: none
X-XSS-Protection: 1; mode=block
```
- And from the server side, the nginx logs show:
```
78.x.x.x - - [07/Apr/2019:01:38:35 -0700] "GET /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1" 200 68078 "-" "HTTPie/1.0.2"
78.x.x.x - - [07/Apr/2019:01:39:01 -0700] "HEAD /bitstream/handle/10568/100289/Spore-192-EN-web.pdf HTTP/1.1" 200 0 "-" "HTTPie/1.0.2"
```
- So definitely the *size* of the transfer is more efficient with a HEAD, but I need to wait to see if these requests show up in Solr
- After twenty minutes of waiting I still don't see any new requests in the statistics core, but when I try the requests from the command line again I see the following in the DSpace log:
```
2019-04-07 02:05:30,966 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous:session_id=EF2DB6E4F69926C5555B3492BB0071A8:ip_addr=78.x.x.x:view_bitstream:bitstream_id=165818
2019-04-07 02:05:39,265 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous:session_id=B6381FC590A5160D84930102D068C7A3:ip_addr=78.x.x.x:view_bitstream:bitstream_id=165818
```
- So my inclination is that both HEAD and GET requests are registered as views as far as Solr and DSpace are concerned
- Strangely, the statistics Solr core says it hasn't been modified in 24 hours, so I tried to start the "optimize" process from the Admin UI and I see this in the Solr log:
```
2019-04-07 02:08:44,186 INFO org.apache.solr.update.UpdateHandler @ start commit{,optimize=true,openSearcher=true,waitSearcher=true,expungeDeletes=false,softCommit=false,prepareCommit=false}
```
- Ugh, even after optimizing there are no Solr results for requests from my IP, and actually I only see 18 results from 2019-04 so far and none of them are `statistics_type:view`... very weird
- I don't even see many hits for days after 2019-03-17, when I migrated the server to Ubuntu 18.04 and copied the statistics core from CGSpace (linode18)
- I will try to re-deploy the `5_x-dev` branch and test again
- According to the [DSpace 5.x Solr documentation](https://wiki.lyrasis.org/display/DSDOC5x/SOLR+Statistics) the default commit time is after 15 minutes or 10,000 documents (see `solrconfig.xml`)
- I looped some GET and HEAD requests to a bitstream on my local instance and after some time I see that they *do* register as downloads (even though they are internal):
```
$ http --print b 'http://localhost:8080/solr/statistics/select?q=type%3A0+AND+time%3A2019-04-07*&fq=statistics_type%3Aview&fq=isInternal%3Atrue&rows=0&wt=json&indent=true'
{
"response": {
"docs": [],
"numFound": 909,
"start": 0
},
"responseHeader": {
"QTime": 0,
"params": {
"fq": [
"statistics_type:view",
"isInternal:true"
],
"indent": "true",
"q": "type:0 AND time:2019-04-07*",
"rows": "0",
"wt": "json"
},
"status": 0
}
}
```
- I confirmed the same on CGSpace itself after making one HEAD request
- So I'm pretty sure it's something about DSpace Test using the CGSpace statistics core, and not that I deployed Solr 4.10.4 there last week
- I deployed Solr 4.10.4 locally and ran a bunch of requests for bitstreams and they do show up in the Solr statistics log, so the issue must be with re-using the existing Solr core from CGSpace
- Now this gets more frustrating: I did the same GET and HEAD tests on a local Ubuntu 16.04 VM with Solr 4.10.2 and 4.10.4 and the statistics are recorded
- This leads me to believe there is something specifically wrong with DSpace Test (linode19)
- The only thing I can think of is that the JVM is using G1GC instead of ConcMarkSweepGC
- Holy shit, all this is actually because of the GeoIP1 deprecation and a missing `GeoLiteCity.dat`
- For some reason the missing GeoIP data causes stats to not be recorded whatsoever and there is no error!
- See: [DS-3986](https://jira.duraspace.org/browse/DS-3986)
- See: [DS-4020](https://jira.duraspace.org/browse/DS-4020)
- See: [DS-3832](https://jira.duraspace.org/browse/DS-3832)
- DSpace 5.10 upgraded to use GeoIP2, but we are on 5.8 so I just copied the missing database file from another server because it has been *removed* from MaxMind's server as of 2018-04-01
- Now I made 100 requests and I see them in the Solr statistics... fuck my life for wasting five hours debugging this
- UptimeRobot said CGSpace went down and up a few times tonight, and my first instict was to check `iostat 1 10` and I saw that CPU steal is around 10–30 percent right now...
- The load average is super high right now, as I've noticed the last few times UptimeRobot said that CGSpace went down:
```
$ cat /proc/loadavg
10.70 9.17 8.85 18/633 4198
```
- According to the server logs there is actually not much going on right now:
```
# zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E "07/Apr/2019:(18|19|20)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
118 18.195.78.144
128 207.46.13.219
129 167.114.64.100
159 207.46.13.129
179 207.46.13.33
188 2408:8214:7a00:868f:7c1e:e0f3:20c6:c142
195 66.249.79.59
363 40.77.167.21
740 2a01:4f8:140:3192::2
4823 45.5.184.72
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "07/Apr/2019:(18|19|20)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
3 66.249.79.62
3 66.249.83.196
4 207.46.13.86
5 82.145.222.150
6 2a01:4f9:2b:1263::2
6 41.204.190.40
7 35.174.176.49
10 40.77.167.21
11 194.246.119.6
11 66.249.79.59
```
- `45.5.184.72` is CIAT, who I already blocked and am waiting to hear from
- `2a01:4f8:140:3192::2` is BLEXbot, which should be handled by the Tomcat Crawler Session Manager Valve
- `2408:8214:7a00:868f:7c1e:e0f3:20c6:c142` is some stupid Chinese bot making malicious POST requests
- There are free database connections in the pool:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
23 dspaceWeb
```
- It seems that the issue with CGSpace being "down" is actually because of CPU steal again!!!
- I opened a ticket with support and asked them to migrate the VM to a less busy host
## 2019-04-08
- Start checking IITA's last round of batch uploads from [March on DSpace Test](https://dspacetest.cgiar.org/handle/10568/100333) (20193rd.xls)
- Lots of problems with affiliations, I had to correct about sixty of them
- I used lein to host the latest CSV of our affiliations for OpenRefine to reconcile against:
```
$ lein run ~/src/git/DSpace/2019-02-22-affiliations.csv name id
```
- After matching the values and creating some new matches I had trouble remembering how to copy the reconciled values to a new column
- The matched values can be accessed with `cell.recon.match.name`, but some of the new values don't appear, perhaps because I edited the original cell values?
- I ended up using this GREL expression to copy all values to a new column:
```
if(cell.recon.matched, cell.recon.match.name, value)
```
- See the [OpenRefine variables documentation](https://github.com/OpenRefine/OpenRefine/wiki/Variables#recon) for more notes about the `recon` object
- I also noticed a handful of errors in our current list of affiliations so I corrected them:
```
$ ./fix-metadata-values.py -i 2019-04-08-fix-13-affiliations.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211 -t correct -d
```
- We should create a new list of affiliations to update our controlled vocabulary again
- I dumped a list of the top 1500 affiliations:
```
dspace=# \COPY (SELECT DISTINCT text_value, count(*) FROM metadatavalue WHERE metadata_field_id = 211 AND resource_type_id = 2 GROUP BY text_value ORDER BY count DESC LIMIT 1500) to /tmp/2019-04-08-top-1500-affiliations.csv WITH CSV HEADER;
COPY 1500
```
- Fix a few more messed up affiliations that have return characters in them (use Ctrl-V Ctrl-M to re-create control character):
```
dspace=# UPDATE metadatavalue SET text_value='International Institute for Environment and Development' WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE 'International Institute^M%';
dspace=# UPDATE metadatavalue SET text_value='Kenya Agriculture and Livestock Research Organization' WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE 'Kenya Agricultural and Livestock Research^M%';
```
- I noticed a bunch of subjects and affiliations that use stylized apostrophes so I will export those and then batch update them:
```
dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 211 AND text_value LIKE '%’%') to /tmp/2019-04-08-affiliations-apostrophes.csv WITH CSV HEADER;
COPY 60
dspace=# \COPY (SELECT DISTINCT text_value FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id = 57 AND text_value LIKE '%’%') to /tmp/2019-04-08-subject-apostrophes.csv WITH CSV HEADER;
COPY 20
```
- I cleaned them up in OpenRefine and then applied the fixes on CGSpace and DSpace Test:
```
$ ./fix-metadata-values.py -i /tmp/2019-04-08-fix-60-affiliations-apostrophes.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.affiliation -m 211 -t correct -d
$ ./fix-metadata-values.py -i /tmp/2019-04-08-fix-20-subject-apostrophes.csv -db dspace -u dspace -p 'fuuu' -f dc.subject -m 57 -t correct -d
```
- UptimeRobot said that CGSpace (linode18) went down tonight
- The load average is at `9.42, 8.87, 7.87`
- I looked at PostgreSQL and see shitloads of connections there:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
250 dspaceWeb
```
- On a related note I see connection pool errors in the DSpace log:
```
2019-04-08 19:01:10,472 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.tomcat.jdbc.pool.PoolExhaustedException: [http-bio-127.0.0.1-8443-exec-319] Timeout: Pool empty. Unable to fetch a connection in 5 seconds, none available[size:250; busy:250; idle:0; lastwait:5000].
```
- But still I see 10 to 30% CPU steal in `iostat` that is also reflected in the Munin graphs:
![CPU usage week](/cgspace-notes/2019/04/cpu-week2.png)
- Linode Support still didn't respond to my ticket from yesterday, so I attached a new output of `iostat 1 10` and asked them to move the VM to a less busy host
- The web server logs are not very busy:
```
# zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E "08/Apr/2019:(17|18|19)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
124 40.77.167.135
135 95.108.181.88
139 157.55.39.206
190 66.249.79.133
202 45.5.186.2
284 207.46.13.95
359 18.196.196.108
457 157.55.39.164
457 40.77.167.132
3822 45.5.184.72
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "08/Apr/2019:(17|18|19)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
5 129.0.79.206
5 41.205.240.21
7 207.46.13.95
7 66.249.79.133
7 66.249.79.135
7 95.108.181.88
8 40.77.167.111
19 157.55.39.164
20 40.77.167.132
370 51.254.16.223
```
## 2019-04-09
- Linode sent an alert that CGSpace (linode18) was 440% CPU for the last two hours this morning
- Here are the top IPs in the web server logs around that time:
```
# zcat --force /var/log/nginx/{rest,oai}.log /var/log/nginx/{rest,oai}.log.1 | grep -E "09/Apr/2019:(06|07|08)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
18 66.249.79.139
21 157.55.39.160
29 66.249.79.137
38 66.249.79.135
50 34.200.212.137
54 66.249.79.133
100 102.128.190.18
1166 45.5.184.72
4251 45.5.186.2
4895 205.186.128.185
# zcat --force /var/log/nginx/{access,library-access}.log /var/log/nginx/{access,library-access}.log.1 | grep -E "09/Apr/2019:(06|07|08)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10
200 144.48.242.108
202 207.46.13.185
206 18.194.46.84
239 66.249.79.139
246 18.196.196.108
274 31.6.77.23
289 66.249.79.137
312 157.55.39.160
441 66.249.79.135
856 66.249.79.133
```
- `45.5.186.2` is at CIAT in Colombia and I see they are mostly making requests to the REST API, but also to XMLUI with the following user agent:
```
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/73.0.3683.103 Safari/537.36
```
- Database connection usage looks fine:
```
$ psql -c 'select * from pg_stat_activity' | grep -o -E '(dspaceWeb|dspaceApi|dspaceCli)' | sort | uniq -c
5 dspaceApi
7 dspaceCli
11 dspaceWeb
```
- Ironically I do still see some 2 to 10% of CPU steal in `iostat 1 10`
- Leroy from CIAT contacted me to say he knows the team who is making all those requests to CGSpace
- I told them how to use the REST API to get the CIAT Datasets collection and enumerate its items
- In other news, Linode staff identified a noisy neighbor sharing our host and migrated it elsewhere last night
## 2019-04-10
- Abenet pointed out a possibility of validating funders against the [CrossRef API](https://support.crossref.org/hc/en-us/articles/215788143-Funder-data-via-the-API)
- Note that if you use HTTPS and specify a contact address in the API request you have less likelihood of being blocked
```
$ http 'https://api.crossref.org/funders?query=mercator&mailto=me@cgiar.org'
```
- Otherwise, they provide the funder data in [CSV and RDF format](https://www.crossref.org/services/funder-registry/)
- I did a quick test with the recent IITA records against reconcile-csv in OpenRefine and it matched a few, but the ones that didn't match will need a human to go and do some manual checking and informed decision making...
- If I want to write a script for this I could use the Python [habanero library](https://habanero.readthedocs.io/en/latest/modules/crossref.html):
```
from habanero import Crossref
cr = Crossref(mailto="me@cgiar.org")
x = cr.funders(query = "mercator")
```
## 2019-04-11
- Continue proofing IITA's last round of batch uploads from [March on DSpace Test](https://dspacetest.cgiar.org/handle/10568/100333) (20193rd.xls)
- One misspelled country
- Three incorrect regions
- Potential duplicates (same DOI, similar title, same authors):
- [10568/100580](https://dspacetest.cgiar.org/handle/10568/100580) and [10568/100579](https://dspacetest.cgiar.org/handle/10568/100579)
- [10568/100444](https://dspacetest.cgiar.org/handle/10568/100444) and [10568/100423](https://dspacetest.cgiar.org/handle/10568/100423)
- Two DOIs with incorrect URL formatting
- Two misspelled IITA subjects
- Two authors with smart quotes
- Lots of issues with sponsors
- One misspelled "Peer review"
- One invalid ISBN that I fixed by Googling the title
- Lots of issues with sponsors (German Aid Agency, Swiss Aid Agency, Italian Aid Agency, Dutch Aid Agency, etc)
- I validated all the AGROVOC subjects against our latest list with reconcile-csv
- About 720 of the 900 terms were matched, then I checked and fixed or deleted the rest manually
- I captured a few general corrections and deletions for AGROVOC subjects while looking at IITA's records, so I applied them to DSpace Test and CGSpace:
```
$ ./fix-metadata-values.py -i /tmp/2019-04-11-fix-14-subjects.csv -db dspace -u dspace -p 'fuuu' -f dc.subject -m 57 -t correct -d
$ ./delete-metadata-values.py -i /tmp/2019-04-11-delete-6-subjects.csv -db dspace -u dspace -p 'fuuu' -m 57 -f dc.subject -d
```
- Answer more questions about DOIs and Altmetric scores from WLE
- Answer more questions about DOIs and Altmetric scores from IWMI
- They can't seem to understand the Altmetric + Twitter flow for associating Handles and DOIs
- To make things worse, many of their items DON'T have DOIs, so when Altmetric harvests them of course there is no link! - Then, a bunch of their items don't have scores because they never tweeted them!
- They added a DOI to this old item [10567/97087](https://cgspace.cgiar.org/handle/10568/97087) this morning and wonder why Altmetric's score hasn't linked with the DOI magically
- We should check in a week to see if Altmetric will make the association after one week when they harvest again
## 2019-04-13
- I copied the `statistics` and `statistics-2018` Solr cores from CGSpace to my local machine and watched the Java process in VisualVM while indexing item views and downloads with my [dspace-statistics-api](https://github.com/ilri/dspace-statistics-api):
![Java GC during Solr indexing with CMS](/cgspace-notes/2019/04/visualvm-solr-indexing.png)
- It took about eight minutes to index 784 pages of item views and 268 of downloads, and you can see a clear "sawtooth" pattern in the garbage collection
- I am curious if the GC pattern would be different if I switched from the `-XX:+UseConcMarkSweepGC` to G1GC
- I switched to G1GC and restarted Tomcat but for some reason I couldn't see the Tomcat PID in VisualVM...
- Anyways, the indexing process took much longer, perhaps twice as long!
- I tried again with the GC tuning settings from the Solr 4.10.4 release:
![Java GC during Solr indexing Solr 4.10.4 settings](/cgspace-notes/2019/04/visualvm-solr-indexing-solr-settings.png)
## 2019-04-14
- Change DSpace Test (linode19) to use the Java GC tuning from the Solr 4.10.4 startup script:
```
GC_TUNE="-XX:NewRatio=3 \
-XX:SurvivorRatio=4 \
-XX:TargetSurvivorRatio=90 \
-XX:MaxTenuringThreshold=8 \
-XX:+UseConcMarkSweepGC \
-XX:+UseParNewGC \
-XX:ConcGCThreads=4 -XX:ParallelGCThreads=4 \
-XX:+CMSScavengeBeforeRemark \
-XX:PretenureSizeThreshold=64m \
-XX:+UseCMSInitiatingOccupancyOnly \
-XX:CMSInitiatingOccupancyFraction=50 \
-XX:CMSMaxAbortablePrecleanTime=6000 \
-XX:+CMSParallelRemarkEnabled \
-XX:+ParallelRefProcEnabled"
```
- I need to remember to check the Munin JVM graphs in a few days
- It might be placebo, but the site *does* feel snappier...
## 2019-04-15
- Rework the dspace-statistics-api to use the vanilla Python requests library instead of Solr client
- [Tag version 1.0.0](https://github.com/ilri/dspace-statistics-api/releases/tag/v1.0.0) and deploy it on DSpace Test
- Pretty annoying to see CGSpace (linode18) with 20–50% CPU steal according to `iostat 1 10`, though I haven't had any Linode alerts in a few days
- Abenet sent me a list of ILRI items that don't have CRPs added to them
- The spreadsheet only had Handles (no IDs), so I'm experimenting with using Python in OpenRefine to get the IDs
- I cloned the handle column and then did a transform to get the IDs from the CGSpace REST API:
```
import json
import re
import urllib
import urllib2
handle = re.findall('[0-9]+/[0-9]+', value)
url = 'https://cgspace.cgiar.org/rest/handle/' + handle[0]
req = urllib2.Request(url)
req.add_header('User-agent', 'Alan Python bot')
res = urllib2.urlopen(req)
data = json.load(res)
item_id = data['id']
return item_id
```
- Luckily none of the items already had CRPs, so I didn't have to worry about them getting removed
- It would have been much trickier if I had to get the CRPs for the items first, then add the CRPs...
- I ran a full Discovery indexing on CGSpace because I didn't do it after all the metadata updates last week:
```
$ time schedtool -B -e ionice -c2 -n7 nice -n19 dspace index-discovery -b
real 82m45.324s
user 7m33.446s
sys 2m13.463s
```
## 2019-04-16
- Export IITA's community from CGSpace because they want to experiment with importing it into their internal DSpace for some testing or something
## 2019-04-17
- Reading an interesting [blog post about Solr caching](https://teaspoon-consulting.com/articles/solr-cache-tuning.html)
- Did some tests of the dspace-statistics-api on my local DSpace instance with 28 million documents in a sharded statistics core (`statistics` and `statistics-2018`) and monitored the memory usage of Tomcat in VisualVM
- 4GB heap, CMS GC, 512 filter cache, 512 query cache, with 28 million documents in two shards
- Run 1:
- Time: 3.11s user 0.44s system 0% cpu 13:45.07 total
- Tomcat (not Solr) max JVM heap usage: 2.04 GiB
- Run 2:
- Time: 3.23s user 0.43s system 0% cpu 13:46.10 total
- Tomcat (not Solr) max JVM heap usage: 2.06 GiB
- Run 3:
- Time: 3.23s user 0.42s system 0% cpu 13:14.70 total
- Tomcat (not Solr) max JVM heap usage: 2.13 GiB
- `filterCache` size: 482, `cumulative_lookups`: 7062712, `cumulative_hits`: 167903, `cumulative_hitratio`: 0.02
- queryResultCache size: 2
- 4GB heap, CMS GC, 1024 filter cache, 512 query cache, with 28 million documents in two shards
- Run 1:
- Time: 2.92s user 0.39s system 0% cpu 12:33.08 total
- Tomcat (not Solr) max JVM heap usage: 2.16 GiB
- Run 2:
- Time: 3.10s user 0.39s system 0% cpu 12:25.32 total
- Tomcat (not Solr) max JVM heap usage: 2.07 GiB
- Run 3:
- Time: 3.29s user 0.36s system 0% cpu 11:53.47 total
- Tomcat (not Solr) max JVM heap usage: 2.08 GiB
- `filterCache` size: 951, `cumulative_lookups`: 7062712, `cumulative_hits`: 254379, `cumulative_hitratio`: 0.04
- 4GB heap, CMS GC, 2048 filter cache, 512 query cache, with 28 million documents in two shards
- Run 1:
- Time: 2.90s user 0.48s system 0% cpu 10:37.31 total
- Tomcat max JVM heap usage: 1.96 GiB
- `filterCache` size: 1901, `cumulative_lookups`: 2354237, `cumulative_hits`: 180111, `cumulative_hitratio`: 0.08
- Run 2:
- Time: 2.97s user 0.39s system 0% cpu 10:40.06 total
- Tomcat max JVM heap usage: 2.09 GiB
- `filterCache` size: 1901, `cumulative_lookups`: 4708473, `cumulative_hits`: 360068, `cumulative_hitratio`: 0.08
- Run 3:
- Time: 3.28s user 0.37s system 0% cpu 10:49.56 total
- Tomcat max JVM heap usage: 2.05 GiB
- `filterCache` size: 1901, `cumulative_lookups`: 7062712, `cumulative_hits`: 540020, `cumulative_hitratio`: 0.08
- 4GB heap, CMS GC, 4096 filter cache, 512 query cache, with 28 million documents in two shards
- Run 1:
- Time: 2.88s user 0.35s system 0% cpu 8:29.55 total
- Tomcat max JVM heap usage: 2.15 GiB
- `filterCache` size: 3770, `cumulative_lookups`: 2354237, `cumulative_hits`: 414512, `cumulative_hitratio`: 0.18
- Run 2:
- Time: 3.01s user 0.38s system 0% cpu 9:15.65 total
- Tomcat max JVM heap usage: 2.17 GiB
- `filterCache` size: 3945, `cumulative_lookups`: 4708473, `cumulative_hits`: 829093, `cumulative_hitratio`: 0.18
- Run 3:
- Time: 3.01s user 0.40s system 0% cpu 9:01.31 total
- Tomcat max JVM heap usage: 2.07 GiB
- `filterCache` size: 3770, `cumulative_lookups`: 7062712, `cumulative_hits`: 1243632, `cumulative_hitratio`: 0.18
- The biggest takeaway I have is that this workload benefits from a larger `filterCache` (for Solr fq parameter), but barely uses the `queryResultCache` (for Solr q parameter) at all
- The number of hits goes up and the time taken decreases when we increase the `filterCache`, and total JVM heap memory doesn't seem to increase much at all
- I guess the `queryResultCache` size is always 2 because I'm only doing two queries: `type:0` and `type:2` (downloads and views, respectively)
- Here is the general pattern of running three sequential indexing runs as seen in VisualVM while monitoring the Tomcat process:
![VisualVM Tomcat 4096 filterCache](/cgspace-notes/2019/04/visualvm-solr-indexing-4096-filterCache.png)
- I ran one test with a `filterCache` of 16384 to try to see if I could make the Tomcat JVM memory balloon, but actually it *drastically* increased the performance and memory usage of the dspace-statistics-api indexer
- 4GB heap, CMS GC, 16384 filter cache, 512 query cache, with 28 million documents in two shards
- Run 1:
- Time: 2.85s user 0.42s system 2% cpu 2:28.92 total
- Tomcat max JVM heap usage: 1.90 GiB
- `filterCache` size: 14851, `cumulative_lookups`: 2354237, `cumulative_hits`: 2331186, `cumulative_hitratio`: 0.99
- Run 2:
- Time: 2.90s user 0.37s system 2% cpu 2:23.50 total
- Tomcat max JVM heap usage: 1.27 GiB
- `filterCache` size: 15834, `cumulative_lookups`: 4708476, `cumulative_hits`: 4664762, `cumulative_hitratio`: 0.99
- Run 3:
- Time: 2.93s user 0.39s system 2% cpu 2:26.17 total
- Tomcat max JVM heap usage: 1.05 GiB
- `filterCache` size: 15248, `cumulative_lookups`: 7062715, `cumulative_hits`: 6998267, `cumulative_hitratio`: 0.99
- The JVM garbage collection graph is MUCH flatter, and memory usage is much lower (not to mention a drop in GC-related CPU usage)!
![VisualVM Tomcat 16384 filterCache](/cgspace-notes/2019/04/visualvm-solr-indexing-16384-filterCache.png)
- I will deploy this `filterCache` setting on DSpace Test (linode19)
- Run all system updates on DSpace Test (linode19) and reboot it
- Lots of CPU steal going on still on CGSpace (linode18):
![CPU usage week](/cgspace-notes/2019/04/cpu-week3.png)
## 2019-04-18
- I've been trying to copy the `statistics-2018` Solr core from CGSpace to DSpace Test since yesterday, but the network speed is like 20KiB/sec
- I opened a support ticket to ask Linode to investigate
- They asked me to send an `mtr` report from Fremont to Frankfurt and vice versa
- Deploy Tomcat 7.0.94 on DSpace Test (linode19)
- Also, I realized that the CMS GC changes I deployed a few days ago were ignored by Tomcat because of something with how Ansible formatted the options string
- I needed to use the "folded" YAML variable format `>-` (with the dash so it doesn't add a return at the end)
- UptimeRobot says that CGSpace went "down" this afternoon, but I looked at the CPU steal with `iostat 1 10` and it's in the 50s and 60s
- The munin graph shows a lot of CPU steal (red) currently (and over all during the week):
![CPU usage week](/cgspace-notes/2019/04/cpu-week4.png)
- I opened a ticket with Linode to migrate us somewhere
- They agreed to migrate us to a quieter host
## 2019-04-20
- Linode agreed to move CGSpace (linode18) to a new machine shortly after I filed my ticket about CPU steal two days ago and now the load is much more sane:
![CPU usage week](/cgspace-notes/2019/04/cpu-week5.png)
- For future reference, Linode mentioned that they consider CPU steal above 8% to be significant
- Regarding the other Linode issue about speed, I did a test with `iperf` between linode18 and linode19:
```
# iperf -s
------------------------------------------------------------
Server listening on TCP port 5001
TCP window size: 85.3 KByte (default)
------------------------------------------------------------
[ 4] local 45.79.x.x port 5001 connected with 139.162.x.x port 51378
------------------------------------------------------------
Client connecting to 139.162.x.x, TCP port 5001
TCP window size: 85.0 KByte (default)
------------------------------------------------------------
[ 5] local 45.79.x.x port 36440 connected with 139.162.x.x port 5001
[ ID] Interval Transfer Bandwidth
[ 5] 0.0-10.2 sec 172 MBytes 142 Mbits/sec
[ 4] 0.0-10.5 sec 202 MBytes 162 Mbits/sec
```
- Even with the software firewalls disabled the rsync speed was low, so it's not a rate limiting issue
- I also tried to download a file over HTTPS from CGSpace to DSpace Test, but it was capped at 20KiB/sec
- I updated the Linode issue with this information
- I'm going to try to switch the kernel to the latest upstream (5.0.8) instead of Linode's latest x86_64
- Nope, still 20KiB/sec
## 2019-04-21
- Deploy Solr 4.10.4 on CGSpace (linode18)
- Deploy Tomcat 7.0.94 on CGSpace
- Deploy dspace-statistics-api v1.0.0 on CGSpace
- Linode support replicated the results I had from the network speed testing and said they don't know why it's so slow
- They offered to live migrate the instance to another host to see if that helps
## 2019-04-22
- Abenet pointed out [an item](https://hdl.handle.net/10568/97912) that doesn't have an Altmetric score on CGSpace, but has a score of 343 in the CGSpace Altmetric dashboard
- I tweeted the Handle to see if it will pick it up...
- Like clockwork, after fifteen minutes there was a donut showing on CGSpace
- I want to get rid of this annoying warning that is constantly in our DSpace logs:
```
2019-04-08 19:02:31,770 WARN org.dspace.xoai.services.impl.xoai.DSpaceRepositoryConfiguration @ { OAI 2.0 :: DSpace } Not able to retrieve the dspace.oai.url property from oai.cfg. Falling back to request address
```
- Apparently it happens once per request, which can be at least 1,500 times per day according to the DSpace logs on CGSpace (linode18):
```
$ grep -c 'Falling back to request address' dspace.log.2019-04-20
dspace.log.2019-04-20:1515
```
- I will fix it in `dspace/config/modules/oai.cfg`
- Linode says that it is likely that the host CGSpace (linode18) is on is showing signs of hardware failure and they recommended that I migrate the VM to a new host
- I told them to migrate it at 04:00:00AM Frankfurt time, when nobody in East Africa, Europe, or South America should be using the server
## 2019-04-23
- One blog post says that there is [no overprovisioning in Azure](https://kvaes.wordpress.com/2017/07/01/what-azure-virtual-machine-size-should-i-pick/):
<blockquote cite="https://kvaes.wordpress.com/2017/07/01/what-azure-virtual-machine-size-should-i-pick/">In Azure, with one exception being the A0, there is no overprovisioning… Each physical cores is only supporting one virtual core.</blockquote>
- Perhaps that's why the [Azure pricing](https://azure.microsoft.com/en-us/pricing/details/virtual-machines/linux/) is so expensive!
- Add a privacy page to CGSpace
- The work was mostly similar to the About page at `/page/about`, but in addition to adding i18n strings etc, I had to add the logic for the trail to `dspace-xmlui-mirage2/src/main/webapp/xsl/preprocess/general.xsl`
## 2019-04-24
- Linode migrated CGSpace (linode18) to a new host, but I am still getting poor performance when copying data to DSpace Test (linode19)
- I asked them if we can migrate DSpace Test to a new host
- They migrated DSpace Test to a new host and the rsync speed from Frankfurt was still capped at 20KiB/sec...
- I booted DSpace Test to a rescue CD and tried the rsync from CGSpace there too, but it was still capped at 20KiB/sec...
- I copied the 18GB `statistics-2018` Solr core from Frankfurt to a Linode in London at 15MiB/sec, then from the London one to DSpace Test in Fremont at 15MiB/sec... so WTF us up with Frankfurt→Fremont?!
- Finally upload the 218 IITA items from March to CGSpace
- Abenet and I had to do a little bit more work to correct the metadata of one item that appeared to be a duplicate, but really just had the wrong DOI
- While I was uploading the IITA records I noticed that twenty of the records Sisay uploaded in 2018-09 had double Handles (`dc.identifier.uri`)
- According to my notes in 2018-09 I had noticed this when he uploaded the records and told him to remove them, but he didn't...
- I exported the IITA community as a CSV then used `csvcut` to extract the two URI columns and identify and fix the records:
```
$ csvcut -c id,dc.identifier.uri,'dc.identifier.uri[]' ~/Downloads/2019-04-24-IITA.csv > /tmp/iita.csv
```
- Carlos Tejo from the Land Portal had been emailing me this week to ask about the old REST API that Tsega was building in 2017
- I told him we never finished it, and that he should try to use the `/items/find-by-metadata-field` endpoint, with the caveat that you need to match the language attribute exactly (ie "en", "en_US", null, etc)
- I asked him how many terms they are interested in, as we could probably make it easier by normalizing the language attributes of these fields (it would help us anyways)
- He says he's getting HTTP 401 errors when trying to search for CPWF subject terms, which I can reproduce:
```
$ curl -f -H "accept: application/json" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": "en_US"}'
curl: (22) The requested URL returned error: 401
```
- Note that curl only shows the HTTP 401 error if you use `-f` (fail), and only then if you *don't* include `-s`
- I see there are about 1,000 items using CPWF subject "WATER MANAGEMENT" in the database, so there should definitely be results
- The breakdown of `text_lang` fields used in those items is 942:
```
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang='en_US';
count
-------
376
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang='';
count
-------
149
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT' AND text_lang IS NULL;
count
-------
417
(1 row)
```
- I see that the HTTP 401 issue seems to be a bug due to an item that the user doesn't have permission to access... from the DSpace log:
```
2019-04-24 08:11:51,129 INFO org.dspace.rest.ItemsResource @ Looking for item with metadata(key=cg.subject.cpwf,value=WATER MANAGEMENT, language=en_US).
2019-04-24 08:11:51,231 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/72448
2019-04-24 08:11:51,238 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/72491
2019-04-24 08:11:51,243 INFO org.dspace.usage.LoggerUsageEventListener @ anonymous::view_item:handle=10568/75703
2019-04-24 08:11:51,252 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item!
```
- Nevertheless, if I request using the `null` language I get 1020 results, plus 179 for a blank language attribute:
```
$ curl -s -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": null}' | jq length
1020
$ curl -s -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": ""}' | jq length
179
```
- This is weird because I see 942–1156 items with "WATER MANAGEMENT" (depending on wildcard matching for errors in subject spelling):
```
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value='WATER MANAGEMENT';
count
-------
942
(1 row)
dspace=# SELECT COUNT(text_value) FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=208 AND text_value LIKE '%WATER MANAGEMENT%';
count
-------
1156
(1 row)
```
- I sent a message to the dspace-tech mailing list to ask for help
## 2019-04-25
- Peter pointed out that we need to remove Delicious and Google+ from our social sharing links
- Also, it would be nice if we could include the item title in the shared link
- I created an issue on GitHub to track this ([#419](https://github.com/ilri/DSpace/issues/419))
- I tested the REST API after logging in with my super admin account and I was able to get results for the problematic query:
```
$ curl -f -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/login" -d '{"email":"example@me.com","password":"fuuuuu"}'
$ curl -f -H "Content-Type: application/json" -H "rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b" -X GET "https://dspacetest.cgiar.org/rest/status"
$ curl -f -H "rest-dspace-token: b43d41a6-5ac1-455d-b49a-616b8debc25b" -H "Content-Type: application/json" -X POST "https://dspacetest.cgiar.org/rest/items/find-by-metadata-field" -d '{"key":"cg.subject.cpwf", "value":"WATER MANAGEMENT","language": "en_US"}'
```
- I created a normal user for Carlos to try as an unprivileged user:
```
$ dspace user --add --givenname Carlos --surname Tejo --email blah@blah.com --password 'ddmmdd'
```
- But still I get the HTTP 401 and I have no idea which item is causing it
- I enabled more verbose logging in `ItemsResource.java` and now I can at least see the item ID that causes the failure...
- The item is not even in the archive, but somehow it is discoverable
```
dspace=# SELECT * FROM item WHERE item_id=74648;
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
74648 | 113 | f | f | 2016-03-30 09:00:52.131+00 | | t
(1 row)
```
- I tried to delete the item in the web interface, and it seems successful, but I can still access the item in the admin interface, and nothing changes in PostgreSQL
- Meet with CodeObia to see progress on AReS version 2
- Marissa Van Epp asked me to add a few new metadata values to their Phase II Project Tags field (cg.identifier.ccafsprojectpii)
- I created a [pull request](https://github.com/ilri/DSpace/pull/420) for it and will do it the next time I run updates on CGSpace
- Communicate with Carlos Tejo from the Land Portal about the `/items/find-by-metadata-value` endpoint
- Run all system updates on DSpace Test (linode19) and reboot it
## 2019-04-26
- Export a list of authors for Peter to look through:
```
dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/2019-04-26-all-authors.csv with csv header;
COPY 65752
```
## 2019-04-28
- Still trying to figure out the issue with the items that cause the REST API's `/items/find-by-metadata-value` endpoint to throw an exception
- I made the item private in the UI and then I see in the UI and PostgreSQL that it is no longer discoverable:
```
dspace=# SELECT * FROM item WHERE item_id=74648;
item_id | submitter_id | in_archive | withdrawn | last_modified | owning_collection | discoverable
---------+--------------+------------+-----------+----------------------------+-------------------+--------------
74648 | 113 | f | f | 2019-04-28 08:48:52.114-07 | | f
(1 row)
```
- And I tried the `curl` command from above again, but I still get the HTTP 401 and and the same error in the DSpace log:
```
2019-04-28 08:53:07,170 ERROR org.dspace.rest.ItemsResource @ User(anonymous) has not permission to read item(id=74648)!
```
- I even tried to "expunge" the item using an [action in CSV](https://wiki.lyrasis.org/display/DSDOC5x/Batch+Metadata+Editing#BatchMetadataEditing-Performing'actions'onitems), and it said "EXPUNGED!" but the item is still there...
## 2019-04-30
- Send mail to the dspace-tech mailing list to ask about the item expunge issue
- Delete and re-create Podman container for dspacedb after pulling a new PostgreSQL container:
```
$ podman run --name dspacedb -v dspacedb_data:/var/lib/postgresql/data -e POSTGRES_PASSWORD=postgres -p 5432:5432 -d postgres:9.6-alpine
```
- Carlos from LandPortal asked if I could export CGSpace in a machine-readable format so I think I'll try to do a CSV
- In order to make it easier for him to understand the CSV I will normalize the text languages (minus the provenance field) on my local development instance before exporting:
```
dspace=# SELECT DISTINCT text_lang, count(*) FROM metadatavalue WHERE resource_type_id = 2 AND metadata_field_id != 28 GROUP BY text_lang;
text_lang | count
-----------+---------
| 358647
* | 11
E. | 1
en | 1635
en_US | 602312
es | 12
es_ES | 2
ethnob | 1
fr | 2
spa | 2
| 1074345
(11 rows)
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('ethnob', 'en', '*', 'E.', '');
UPDATE 360295
dspace=# UPDATE metadatavalue SET text_lang='en_US' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IS NULL;
UPDATE 1074345
dspace=# UPDATE metadatavalue SET text_lang='es_ES' WHERE resource_type_id=2 AND metadata_field_id != 28 AND text_lang IN ('es', 'spa');
UPDATE 14
```
- Then I exported the whole repository as CSV, imported it into OpenRefine, removed a few unneeded columns, exported it, zipped it down to 36MB, and emailed a link to Carlos
- In other news, while I was looking through the CSV in OpenRefine I saw lots of weird values in some fields... we should check, for example:
- issue dates
- items missing handles
- authorship types
<!-- vim: set sw=2 ts=2: -->
Reference in New Issue View Git Blame Copy Permalink