cgspace-notes/content/post/2016-11.md

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2016-11-01 08:23:34 +01:00
+++
date = "2016-11-01T09:21:00+03:00"
author = "Alan Orth"
title = "November, 2016"
tags = ["Notes"]
+++
2016-11-02 11:27:37 +01:00
## 2016-11-01
2016-11-01 08:23:34 +01:00
2016-11-01 08:35:09 +01:00
- Add `dc.type` to the output options for Atmire's Listings and Reports module ([#286](https://github.com/ilri/DSpace/pull/286))
2016-11-01 08:23:34 +01:00
![Listings and Reports with output type](2016/11/listings-and-reports.png)
2016-11-02 11:27:37 +01:00
## 2016-11-02
2016-11-06 12:47:08 +01:00
- Migrate DSpace Test to DSpace 5.5 ([notes](https://gist.github.com/alanorth/61013895c6efe7095d7f81000953d1cf))
2016-11-02 11:27:37 +01:00
- Run all updates on DSpace Test and reboot the server
2016-11-02 12:51:42 +01:00
- Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! ([#63](https://github.com/ilri/DSpace/issues/63))
2016-11-02 16:19:02 +01:00
- Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes
- At the end it appeared to finish correctly but there were lots of errors right after it finished:
```
2016-11-02 15:09:48,578 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76454 to Index
2016-11-02 15:09:48,584 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/3202 to Index
2016-11-02 15:09:48,589 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76455 to Index
2016-11-02 15:09:48,590 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Community: 10568/51693 to Index
2016-11-02 15:09:48,590 INFO org.dspace.discovery.IndexClient @ Done with indexing
2016-11-02 15:09:48,600 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76456 to Index
2016-11-02 15:09:48,613 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/55536 to Index
2016-11-02 15:09:48,616 INFO com.atmire.dspace.discovery.AtmireSolrService @ Wrote Collection: 10568/76457 to Index
2016-11-02 15:09:48,634 ERROR com.atmire.dspace.discovery.AtmireSolrService @
java.lang.NullPointerException
at org.dspace.discovery.SearchUtils.getDiscoveryConfiguration(SourceFile:57)
at org.dspace.discovery.SolrServiceImpl.buildDocument(SolrServiceImpl.java:824)
at com.atmire.dspace.discovery.AtmireSolrService.indexContent(AtmireSolrService.java:821)
at com.atmire.dspace.discovery.AtmireSolrService.updateIndex(AtmireSolrService.java:898)
at org.dspace.discovery.SolrServiceImpl.createIndex(SolrServiceImpl.java:370)
at org.dspace.storage.rdbms.DatabaseUtils$ReindexerThread.run(DatabaseUtils.java:945)
```
- DSpace is still up, and a few minutes later I see the default DSpace indexer is still running
- Sure enough, looking back before the first one finished, I see output from both indexers interleaved in the log:
```
2016-11-02 15:09:28,545 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/47242 to Index
2016-11-02 15:09:28,633 INFO org.dspace.discovery.SolrServiceImpl @ Wrote Item: 10568/60785 to Index
2016-11-02 15:09:28,678 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55695 of 55722): 43557
2016-11-02 15:09:28,688 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (55703 of 55722): 34476
```
- I will raise a ticket with Atmire to ask them
2016-11-06 12:47:08 +01:00
## 2016-11-06
- After re-deploying and re-indexing I didn't see the same issue, and the indexing completed in 85 minutes, which is about how long it is supposed to take
2016-11-07 15:46:42 +01:00
## 2016-11-07
- Horrible one liner to get Linode ID from certain Ansible host vars:
```
$ grep -A 3 contact_info * | grep -E "(Orth|Sisay|Peter|Daniel|Tsega)" | awk -F'-' '{print $1}' | grep linode | uniq | xargs grep linode_id
```
- I noticed some weird CRPs in the database, and they don't show up in Discovery for some reason, perhaps the `:`
- I'll export these and fix them in batch:
```
dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=230 group by text_value order by count desc) to /tmp/crp.csv with csv;
COPY 22
```
- Test running the replacements:
```
$ ./fix-metadata-values.py -i /tmp/CRPs.csv -f cg.contributor.crp -t correct -m 230 -d dspace -u dspace -p 'fuuu'
```
- Add `AMR` to ILRI subjects and remove one duplicate instance of IITA in author affiliations controlled vocabulary ([#288](https://github.com/ilri/DSpace/pull/288))
2016-11-08 10:27:36 +01:00
## 2016-11-08
- Atmire's Listings and Reports module seems to be broken on DSpace 5.5
![Listings and Reports broken in DSpace 5.5](2016/11/listings-and-reports-55.png)
- I've filed a ticket with Atmire
2016-11-08 11:44:29 +01:00
- Thinking about batch updates for ORCIDs and authors
- Playing with [SolrClient](https://github.com/moonlitesolutions/SolrClient) in Python to query Solr
- All records in the authority core are either `authority_type:orcid` or `authority_type:person`
- There is a `deleted` field and all items seem to be `false`, but might be important sanity check to remember
- The way to go is probably to have a CSV of author names and authority IDs, then to batch update them in PostgreSQL
- Dump of the top ~200 authors in CGSpace:
```
dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=3 group by text_value order by count desc limit 210) to /tmp/210-authors.csv with csv;
```
2016-11-09 12:11:16 +01:00
## 2016-11-09
- CGSpace crashed so I quickly ran system updates, applied one or two of the waiting changes from the `5_x-prod` branch, and rebooted the server
- The error was `Timeout waiting for idle object` but I haven't looked into the Tomcat logs to see what happened
- Also, I ran the corrections for CRPs from earlier this week
2016-11-10 13:49:09 +01:00
## 2016-11-10
- Helping Megan Zandstra and CIAT with some questions about the REST API
- Playing with `find-by-metadata-field`, this works:
```
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS"}'
```
- But the results are deceiving because metadata fields can have text languages and your query must match exactly!
```
dspace=# select distinct text_value, text_lang from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
text_value | text_lang
------------+-----------
SEEDS |
SEEDS |
SEEDS | en_US
(3 rows)
```
- So basically, the text language here could be null, blank, or en_US
- To query metadata with these properties, you can do:
```
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS"}' | jq length
55
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":""}' | jq length
34
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":"en_US"}' | jq length
```
- The results (55+34=89) don't seem to match those from the database:
```
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang is null;
count
-------
15
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='';
count
-------
4
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='en_US';
count
-------
66
```
- So, querying from the API I get 55 + 34 = 89 results, but the database actually only has 85...
- And the `find-by-metadata-field` endpoint doesn't seem to have a way to get all items with the field, or a wildcard value
- I'll ask a question on the dspace-tech mailing list
- And speaking of `text_lang`, this is interesting:
```
dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2;
text_lang
-----------
ethnob
en
spa
EN
es
frn
en_
en_US
EN_US
eng
en_U
fr
(14 rows)
```
2016-11-10 17:32:16 +01:00
- Generate a list of all these so I can maybe fix them in batch:
2016-11-10 13:49:09 +01:00
```
dspace=# \copy (select distinct text_lang, count(*) from metadatavalue where resource_type_id=2 group by text_lang order by count desc) to /tmp/text-langs.csv with csv;
COPY 14
```
- Perhaps we need to fix them all in batch, or experiment with fixing only certain metadatavalues:
```
dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
UPDATE 85
```
2016-11-10 17:32:16 +01:00
- The `fix-metadata.py` script I have is meant for specific metadata values, so if I want to update some `text_lang` values I should just do it directly in the database
- For example, on a limited set:
```
dspace=# update metadatavalue set text_lang=NULL where resource_type_id=2 and metadata_field_id=203 and text_value='LIVESTOCK' and text_lang='';
UPDATE 420
```
- And assuming I want to do it for all fields:
```
dspacetest=# update metadatavalue set text_lang=NULL where resource_type_id=2 and text_lang='';
UPDATE 183726
```
- After that restarted Tomcat and PostgreSQL (because I'm superstitious about caches) and now I see the following in REST API query:
```
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS"}' | jq length
71
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":""}' | jq length
0
$ curl -s -H "accept: application/json" -H "Content-Type: application/json" -X POST "http://localhost:8080/rest/items/find-by-metadata-field" -d '{"key": "cg.subject.ilri","value": "SEEDS", "language":"en_US"}' | jq length
```
- Not sure what's going on, but Discovery shows 83 values, and database shows 85, so I'm going to reindex Discovery just in case
2016-11-14 11:57:45 +01:00
## 2016-11-14
- I applied Atmire's suggestions to fix Listings and Reports for DSpace 5.5 and now it works
- There were some issues with the `dspace/modules/jspui/pom.xml`, which is annoying because all I did was rebase our working 5.1 code on top of 5.5, meaning Atmire's installation procedure must have changed
2016-11-14 20:48:55 +01:00
- So there is apparently this Tomcat native way to limit web crawlers to one session: [Crawler Session Manager](https://tomcat.apache.org/tomcat-7.0-doc/config/valve.html#Crawler_Session_Manager_Valve)
- After adding that to `server.xml` bots matching the pattern in the configuration will all use ONE session, just like normal users:
```
$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)'
HTTP/1.1 200 OK
Connection: keep-alive
Content-Encoding: gzip
Content-Language: en-US
Content-Type: text/html;charset=utf-8
Date: Mon, 14 Nov 2016 19:47:29 GMT
Server: nginx
Set-Cookie: JSESSIONID=323694E079A53D5D024F839290EDD7E8; Path=/; Secure; HttpOnly
Transfer-Encoding: chunked
Vary: Accept-Encoding
X-Cocoon-Version: 2.2.0
X-Robots-Tag: none
$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)'
HTTP/1.1 200 OK
Connection: keep-alive
Content-Encoding: gzip
Content-Language: en-US
Content-Type: text/html;charset=utf-8
Date: Mon, 14 Nov 2016 19:47:35 GMT
Server: nginx
Transfer-Encoding: chunked
Vary: Accept-Encoding
X-Cocoon-Version: 2.2.0
```
- This means that when Google or Baidu slam you with tens of concurrent connections they will all map to ONE internal session, which saves RAM!