cgspace-notes/content/posts/2020-09.md

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2020-09-02 12:39:11 +02:00
---
title: "September, 2020"
date: 2020-09-02T15:35:54+03:00
author: "Alan Orth"
categories: ["Notes"]
---
## 2020-09-02
- Replace Marissa van Epp for Rhys Bucknall in the CCAFS groups on CGSpace because Marissa no longer works at CCAFS
- The AReS Explorer hasn't updated its index since 2020-08-22 when I last forced it
- I restarted it again now and told Moayad that the automatic indexing isn't working
- Add `Alliance of Bioversity International and CIAT` to affiliations on CGSpace
- Abenet told me that the general search text on AReS doesn't get reset when you use the "Reset Filters" button
- I filed a bug on OpenRXV: https://github.com/ilri/OpenRXV/issues/39
- I filed an issue on OpenRXV to make some minor edits to the admin UI: https://github.com/ilri/OpenRXV/issues/40
<!--more-->
- I ran the country code tagger on CGSpace:
```
$ time chrt -b 0 dspace curate -t countrycodetagger -i all -r - -l 500 -s object | tee /tmp/2020-09-02-countrycodetagger.log
...
real 2m10.516s
user 1m43.953s
sys 0m15.192s
$ grep -c added /tmp/2020-09-02-countrycodetagger.log
39
```
- I still need to create a cron job for this...
- Sisay and Abenet said they can't log in with LDAP on DSpace Test (DSpace 6)
- I tried and I can't either... but it is working on CGSpace
- The error on DSpace 6 is:
```
2020-09-02 12:03:10,666 INFO org.dspace.authenticate.LDAPAuthentication @ anonymous:session_id=A629116488DCC467E1EA2062A2E2EFD7:ip_addr=92.220.02.201:failed_login:no DN found for user aorth
```
- I tried to query LDAP directly using the application credentials with ldapsearch and it works:
```
$ ldapsearch -x -H ldaps://AZCGNEROOT2.CGIARAD.ORG:636/ -b "dc=cgiarad,dc=org" -D "applicationaccount@cgiarad.org" -W "(sAMAccountName=me)"
```
- According to the [DSpace 6 docs](https://wiki.lyrasis.org/display/DSDOC6x/Authentication+Plugins#AuthenticationPlugins-LDAPAuthentication) we need to escape commas in our LDAP parameters due to the new configuration system
- I added the commas and restarted DSpace (though technically we shouldn't need to restart due to the new config system hot reloading configs)
- Run all system updates on DSpace Test (linode26) and reboot it
- After the restart LDAP login works...
2020-09-03 12:50:56 +02:00
## 2020-09-03
- Fix some erroneous "review status" fields that Abenet noticed on AReS
- I used my `fix-metadata-values.py` and `delete-metadata-values.py` scripts with the following input files:
```
$ cat 2020-09-03-fix-review-status.csv
dc.description.version,correct
Externally Peer Reviewed,Peer Review
Peer Reviewed,Peer Review
Peer review,Peer Review
Peer reviewed,Peer Review
Peer-Reviewed,Peer Review
Peer-reviewed,Peer Review
peer Review,Peer Review
$ cat 2020-09-03-delete-review-status.csv
dc.description.version
Report
Formally Published
Poster
Unrefereed reprint
$ ./delete-metadata-values.py -i 2020-09-03-delete-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -m 68
$ ./fix-metadata-values.py -i 2020-09-03-fix-review-status.csv -db dspace -u dspace -p 'fuuu' -f dc.description.version -t 'correct' -m 68
```
- Start reviewing 95 items for IITA (20201stbatch)
- I used my [csv-metadata-quality](https://github.com/ilri/csv-metadata-quality) tool to check and fix some low-hanging fruit first
- This fixed a few unnecessary Unicode, excessive whitespace, invalid multi-value separator, and duplicate metadata values
- Then I looked at the data in OpenRefine and noticed some things:
- All issue dates use year only, but some have months in the citation so they could be more specific
- I normalized all the DOIs to use "https://doi.org" format
- I fixed a few AGROVOC subjects with a simple GREL: `value.replace("GRAINS","GRAIN").replace("SOILS","SOIL").replace("CORN","MAIZE")`
- But there are a few more that are invalid that she will have to look at
- I uploaded the items to [DSpace Test](https://dspacetest.cgiar.org/handle/10568/108357) and it was apparently successful but I get these errors to the console:
```
Thu Sep 03 12:26:33 CEST 2020 | Query:containerItem:ea7a2648-180d-4fce-bdc5-c3aa2304fc58
Error while updating
java.lang.NullPointerException
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl$5.visit(SourceFile:1131)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.visitEachStatisticShard(SourceFile:212)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1104)
at com.atmire.dspace.cua.CUASolrLoggerServiceImpl.update(SourceFile:1093)
at org.dspace.statistics.StatisticsLoggingConsumer.consume(SourceFile:104)
at org.dspace.event.BasicDispatcher.consume(BasicDispatcher.java:177)
at org.dspace.event.BasicDispatcher.dispatch(BasicDispatcher.java:123)
at org.dspace.core.Context.dispatchEvents(Context.java:455)
at org.dspace.core.Context.commit(Context.java:424)
at org.dspace.core.Context.complete(Context.java:380)
at org.dspace.app.bulkedit.MetadataImport.main(MetadataImport.java:1399)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:229)
at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:81)
```
- There are more in the DSpace log so I will raise it with Atmire immediately
2020-09-04 12:32:16 +02:00
## 2020-09-04
- I was checking the recent IITA data for duplicates when I noticed that one in CIFOR's Archive and saw that CIFOR has updated a bunch of their website URLs, for example:
- http://www.cifor.org/nc/online-library/browse/view-publication/publication/151.html → https://www.cifor.org/knowledge/publication/151
- https://www.cifor.org/library/4033 → https://www.cifor.org/knowledge/publication/4033
- https://www.cifor.org/pid/5087 → https://www.cifor.org/knowledge/publication/5087
- I will update our nearly 6,000 metadata values for CIFOR in the database accordingly:
```
dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^(http://)?www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/([[:digit:]]+)\.html$', 'https://www.cifor.org/knowledge/publication/\3') WHERE metadata_field_id=219 AND text_value ~ 'www\.cifor\.org/(nc/)?online-library/browse/view-publication/publication/[[:digit:]]+';
dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/library/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/library/[[:digit:]]+/?';
dspace=# UPDATE metadatavalue SET text_value = regexp_replace(text_value, '^https?://www\.cifor\.org/pid/([[:digit:]]+)/?$', 'https://www.cifor.org/knowledge/publication/\1') WHERE metadata_field_id=219 AND text_value ~ 'https?://www\.cifor\.org/pid/[[:digit:]]+';
```
- I did some cleanup on the author affiliations of the IITA data our 2019-04 list using reconcile-csv and OpenRefine:
- `$ lein run ~/src/git/DSpace/2019-04-08-affiliations.csv name id`
- I always forget how to copy the reconciled values in OpenRefine, but you need to make a new column and populate it using this GREL: `if(cell.recon.matched, cell.recon.match.name, value)`
- I mapped one duplicated from the CIFOR Archives and re-uploaded the 94 IITA items to a new collection on [DSpace Test](https://dspacetest.cgiar.org/handle/10568/108453)
2020-09-08 11:10:08 +02:00
## 2020-09-08
- I noticed that the "share" link in AReS wasn't working properly because it excludes the "explorer" part of the URI
![AReS share link broken](/cgspace-notes/2020/09/ares-share-link.png)
- I filed an issue on GitHub: https://github.com/ilri/OpenRXV/issues/41
- I uploaded the 94 IITA items that I had been working on last week to CGSpace
- RTB emailed to ask why they are getting HTTP 503 errors during harvesting to the RTB WordPress website
- From the screenshot I can see they are requesting URLs like this:
```
https://cgspace.cgiar.org/bitstream/handle/10568/82745/Characteristics-Silage.JPG
```
- So they end up getting rate limited due to the XMLUI rate limits
- I told them to use the REST API bitstream retrieve links, because we don't have any rate limits there
2020-09-10 11:18:03 +02:00
## 2020-09-09
- Wire up the systemd service/timer for the CGSpace Country Code Tagger curation task in the [Ansible infrastructure scripts](https://github.com/ilri/rmg-ansible-public)
- ~~For now it won't work on DSpace 6 because the curation task invocation needs to be slightly different (minus the `-l` parameter) and for some reason the task isn't working on DSpace Test (version 6) right now~~
- I added DSpace 6 support to the playbook templates...
- Run system updates on DSpace Test (linode26), re-deploy the DSpace 6 test branch, and reboot the server
- After rebooting I deleted old copies of the cgspace-java-helpers JAR in the DSpace lib directory and then the curation worked
- To my great surprise the curation worked (and completed, albeit a few times slower) on my local DSpace 6 environment as well:
```
$ ~/dspace63/bin/dspace curate -t countrycodetagger -i all -s object
```
## 2020-09-10
- I checked the country code tagger on CGSpace and DSpace Test and it ran fine from the systemd timer last night... w00t
- I started looking at Peter's changes to the CGSpace regions that were proposed in 2020-07
- The changes will be:
```
$ cat 2020-09-10-fix-cgspace-regions.csv
cg.coverage.region,correct
EAST AFRICA,EASTERN AFRICA
WEST AFRICA,WESTERN AFRICA
SOUTHEAST ASIA,SOUTHEASTERN ASIA
SOUTH ASIA,SOUTHERN ASIA
AFRICA SOUTH OF SAHARA,SUB-SAHARAN AFRICA
NORTH AFRICA,NORTHERN AFRICA
WEST ASIA,WESTERN ASIA
SOUTHWEST ASIA,SOUTHWESTERN ASIA
$ ./fix-metadata-values.py -i 2020-09-10-fix-cgspace-regions.csv -db dspace -u dspace -p 'fuuu' -f cg.coverage.region -t 'correct' -m 227 -d -n
Connected to database.
Would fix 12227 occurences of: EAST AFRICA
Would fix 7996 occurences of: WEST AFRICA
Would fix 3515 occurences of: SOUTHEAST ASIA
Would fix 3443 occurences of: SOUTH ASIA
Would fix 1134 occurences of: AFRICA SOUTH OF SAHARA
Would fix 357 occurences of: NORTH AFRICA
Would fix 81 occurences of: WEST ASIA
Would fix 3 occurences of: SOUTHWEST ASIA
```
- I think we need to wait for the web team, though, as they need to update their mappings
- Not to mention that we'll need to give WLE and CCAFS time to update their harvesters as well... hmmm
2020-09-10 14:00:40 +02:00
- Looking at the top user agents active on CGSpace in 2020-08 and I see:
- `Delphi 2009`: 235353 (this is GARDIAN harvester I guess, as the IP is in Greece)
- `Mozilla/4.5 (compatible; HTTrack 3.0x; Windows 98)`: 57004 (IP is 18.196.100.94, and the requests seem to be for CTA's content)
- `RTB website BOT`: 12282
- `ILRI Livestock Website Publications importer BOT`: 9393
- Shit, I meant to add Delphi to the DSpace spider agents list last month but I guess I didn't commit the change
- HTTrack is in the agents list so I'm not sure why DSpace registers a hit from that request
- Also, I am surprised to see the RTB and ILRI bots here because they have "BOT" in the name and that should also be dropped
- I also see hits from `curl` and `Java/1.8.0_66` and `Apache-HttpClient` so WTF... those are supposed to be dropped by the default agents list
- Some IP `2607:f298:5:101d:f816:3eff:fed9:a484` made 9,000 requests with the `RI/1.0` user agent this year...
- That's on DreamHost...?
- I purged 448658 hits from these agents and added `Delphi` to our local agents overload for Solr as well as Tomcat's Crawler Session Manager Valve so that it forces them to re-use a single session
- I made a pull request on the COUNTER-Robots project for the Daum robot: https://github.com/atmire/COUNTER-Robots/pull/38
- This bot made 8,000 requests to CGSpace this year
- I purged about 20,000 total requests from this bot from our Solr stats for the last few years
2020-09-08 11:10:08 +02:00
2020-09-12 18:53:57 +02:00
## 2020-09-11
- Peter noticed that an export from AReS shows some items with zero views and others with zero views/downloads, but on CGSpace and in the statistics API there are views/downloads
- I need to ask Moayad...
## 2020-09-12
- Carlos Tejo from the LandPortal emailed to ask for advice about integrating their [LandVoc](https://landvoc.org/) vocabulary, which is a subset of AGROVOC, into DSpace
- I told him that they could use the DSpace authority control framework and sent an example of the VIAFAuthority from the DSpace-CRIS project: https://github.com/4Science/DSpace/blob/dspace-6_x_x-cris/dspace-api/src/main/java/org/dspace/content/authority/VIAFAuthority.java
- Redeploy the latest `5_x-prod` branch on CGSpace, re-run the latest Ansible DSpace playbook, run all system updates, and reboot the server (linode18)
- This will bring the latest bot lists for Solr and Tomcat
- I had to restart Tomcat 7 three times before all Solr statistics cores came up OK
- Leroy and Carol from CIAT/Bioversity were asking for information about posting to the CGSpace REST API from Sharepoint
- I told them that we don't allow this yet, but that we need to check in the future whether content can be posted to a workflow
2020-09-15 16:32:29 +02:00
## 2020-09-15
- Charlotte from Altmetric said they had issues parsing the XML file I sent them last month
- I told them that it was mimicking the same format that they had sent me (fourteen pages of XML responses concatenated together)!
- A few days ago IWMI asked us if we can add a new field on CGSpace for their library identifier
- The IDs look like this: H049940
- I suggested that we use `cg.identifier.iwmilibrary`
- I added it to the input forms and push it to the `5_x-prod` and 6.x branches and will re-deploy it in the next few days
- Abenet asked me to import sixty-nine (69) CIP Annual Reports to CGSpace
- I looked at the data in OpenRefine and it is very good quality
- I only added descriptions to the filename field so that SAFBuilder will add them to the bitstreams on import:
```
value + "__description:" + cells["dc.type"].value
```
- Then I created a SAF bundle with SAFBuilder:
```
$ ./safbuilder.sh -c ~/Downloads/cip-annual-reports/cip-reports.csv
```
- And imported them into my local test instance of CGSpace:
```
$ ~/dspace/bin/dspace import -a -e y.arrr@cgiar.org -m /tmp/2020-09-15-cip-annual-reports.map -s ~/Downloads/cip-annual-reports/SimpleArchiveFormat
```
- Then I uploaded them to CGSpace
2020-09-17 14:33:37 +02:00
## 2020-09-16
- Looking further into Carlos Tejos's question about integrating LandVoc (the AGROVOC subset) into DSpace
- I see that you can actually get LandVoc concepts directly from AGROVOC's SPARQL, for example with [this query](http://agrovoc.uniroma2.it/sparql#query=PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0APREFIX+skos%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2004%2F02%2Fskos%2Fcore%23%3E%0A%0ASELECT+%3Fconcept%0AWHERE+%7B%0A++%3Fconcept+a+skos%3AConcept+%3B%0A+++++++++++skos%3AinScheme+%3Chttp%3A%2F%2Flandvoc.org%2Flandvoc%3E+.%0A%0A%7D+ORDER+BY+%3Fconcept&contentTypeConstruct=text%2Fturtle&contentTypeSelect=application%2Fsparql-results%2Bjson&endpoint=http%3A%2F%2Fagrovoc.uniroma2.it%2Fsparql&requestMethod=POST&tabTitle=Query&headers=%7B%7D&outputFormat=table)
![AGROVOC LandVoc SPARQL](/cgspace-notes/2020/09/agrovoc-landvoc-sparql.png)
- So maybe we can query AGROVOC directly using a similar method to [DSpace-CRIS's GettyAuthority](https://github.com/4Science/DSpace/blob/dspace-5_x_x-cris/dspace-api/src/main/java/org/dspace/content/authority/TGNAuthority.java)
- I wired up DSpace-CRIS's VIAFAuthority to see how authorities for auto suggested names get stored
- After submission you can see the item's VIAF identifier:
![VIAF authority](/cgspace-notes/2020/09/viaf-authority.png)
- And this identifier is the ID on VIAF, pretty cool!
![VIAF entry for Charles Darwin](/cgspace-notes/2020/09/viaf-darwin.png)
- I did a similar test with the Getty Thesaurus of Geographic Names (TGN) and it stores the concept URI in the authority:
![TGNAuthority](/cgspace-notes/2020/09/tgn-concept-uri.png)
- But the authority values are not exposed anywhere as metadata...
- I need to play with it a bit more I guess...
- The nice thing is that the Getty example from DSpace-CRIS uses SPARQL as well, and the TGN authority extends it
- We could use a similar model for AGROVOC/LandVoc very easily
## 2020-09-17
- Maria from Bioveristy asked about the ORCID identifier for one of her colleagues that seems to have been removed from our list
- I re-added it to our controlled vocabulary and added the identifier to fifty-one of his existing items on CGSpace using my script:
```
$ cat 2020-09-17-add-bioversity-orcids.csv
dc.contributor.author,cg.creator.id
"Etten, Jacob van","Jacob van Etten: 0000-0001-7554-2558"
"van Etten, Jacob","Jacob van Etten: 0000-0001-7554-2558"
$ ./add-orcid-identifiers-csv.py -i 2020-09-17-add-bioversity-orcids.csv -db dspace -u dspace -p 'dom@in34sniper'
```
- I sent a follow-up message to Atmire to look into the two remaining issues with the DSpace 6 upgrade
- First is the fact that we have zero results in our Listings and Reports, for any search
- Second is the error we get during CSV imports
- Help Natalia and Cathy from Bioversity-CIAT with their OpenSearch query on "trade offs" again
- They wanted to build a search query with multiple filters (type, crpsubject, status) and the general query "trade offs"
- I found a great [reference for DSpace's OpenSearch syntax](https://www.kiwi.fi/pages/viewpage.action?pageId=45782169) (albeit in Finnish, but the example URLs show the syntax clearly)
- We can use quotes and `AND` and `OR` and even group search parameters with parenthesis!
- So now I built a query for Natalia which uses these (showing without URL encoding so you can see the syntax):
```
https://cgspace.cgiar.org/open-search/discover?query=type:"Journal Article" AND status:"Open Access" AND crpsubject:"Water, Land and Ecosystems" AND "tradeoffs"&rpp=100
```
- I noticed that my `move-collections.sh` script didn't work on DSpace 6 because of the change from IDs to UUIDs, so I modified it to quote the collection `resource_id` parameters in the PostgreSQL query
2020-09-18 18:25:55 +02:00
## 2020-09-18
- Help Natalia with her WLE "tradeoffs" search query again...
2020-09-22 11:38:53 +02:00
## 2020-09-20
- Deploy latest 5_x-prod branch on CGSpace, run all system updates, and reboot the server
- To my great surprise, all the Solr statistics cores came up correctly after reboot
- Deploy latest 6_x-dev branch on DSpace Test, run all system updates and reboot the server
## 2020-09-22
- Abenet sent some feedback about AReS
- The item views and downloads are still incorrect
- I looked in the server's API logs and there are no errors, and the database has many more views/downloads:
```
dspacestatistics=# SELECT SUM(views) FROM items;
sum
----------
15714024
(1 row)
dspacestatistics=# SELECT SUM(downloads) FROM items;
sum
----------
13979911
(1 row)
```
2020-09-22 13:14:18 +02:00
- I deleted "Report" from twelve items that had it in their peer review field:
```
dspace=# BEGIN;
BEGIN
dspace=# DELETE FROM metadatavalue WHERE text_value='Report' AND resource_type_id=2 AND metadata_field_id=68;
DELETE 12
dspace=# COMMIT;
```
2020-09-22 11:38:53 +02:00
2020-09-23 11:59:10 +02:00
- I added all CG center- and CRP-specific subject fields and mapped them to `dc.subject` in AReS
- After forcing a re-harvesting now the review status is much cleaner and the missing subjects are available
2020-09-22 11:38:53 +02:00
- Last week Natalia from CIAT had asked me to download all the PDFs for a certain query:
- items with status "Open Access"
- items with type "Journal Article"
- items containing any of the following words: water land and ecosystems & trade offs
- The resulting OpenSearch query is: https://cgspace.cgiar.org/open-search/discover?query=type:"Journal Article" AND status:"Open Access" AND Water Land Ecosystems trade offs&rpp=1
- There were 241 results with a total of 208 PDFs, which I downloaded with my `get-wle-pdfs.py` script and shared to her via bashupload.com
2020-09-23 11:59:10 +02:00
## 2020-09-23
- Peter said he was having problems submitting items to CGSpace
- On a hunch I looked at the PostgreSQL locks in Munin and indeed the normal issue with locks is back (though I haven't seen it in a few months?)
![PostgreSQL connections day](/cgspace-notes/2020/09/postgres_connections_ALL-day.png)
- Instead of restarting Tomcat I restarted the PostgreSQL service and then Peter said he was able to submit the item...
- Experiment with doing direct queries for items in the [dspace-statistics-api](https://github.com/ilri/dspace-statistics-api)
- I tested querying a handful of item UUIDs with a date range and returning their hits faceted by `id`
- Assuming a list of item UUIDs was posted to the REST API we could prepare them for a Solr query by joining them into a string with "OR" and escaping the hyphens:
```
...
item_ids = ['0079470a-87a1-4373-beb1-b16e3f0c4d81', '007a9df1-0871-4612-8b28-5335982198cb']
item_ids_str = ' OR '.join(item_ids).replace('-', '\-')
...
solr_query_params = {
"q": f"id:({item_ids_str})",
"fq": "type:2 AND isBot:false AND statistics_type:view AND time:[2020-01-01T00:00:00Z TO 2020-09-02T00:00:00Z]",
"facet": "true",
"facet.field": "id",
"facet.mincount": 1,
"facet.limit": 1,
"facet.offset": 0,
"stats": "true",
"stats.field": "id",
"stats.calcdistinct": "true",
"shards": shards,
"rows": 0,
"wt": "json",
}
```
- The date range format for Solr is important, but it seems we only need to add `T00:00:00Z` to the normal ISO 8601 YYYY-MM-DD strings
2020-09-02 12:39:11 +02:00
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