mirror of
https://github.com/alanorth/cgspace-notes.git
synced 2024-11-16 11:57:03 +01:00
104 lines
5.4 KiB
Markdown
104 lines
5.4 KiB
Markdown
+++
|
|
date = "2016-11-01T09:21:00+03:00"
|
|
author = "Alan Orth"
|
|
title = "November, 2016"
|
|
tags = ["Notes"]
|
|
|
|
+++
|
|
## 2016-11-01
|
|
|
|
- Add `dc.type` to the output options for Atmire's Listings and Reports module ([#286](https://github.com/ilri/DSpace/pull/286))
|
|
|
|
|
|
|
|
## 2016-11-02
|
|
|
|
- Migrate DSpace Test to DSpace 5.5 ([notes](https://gist.github.com/alanorth/61013895c6efe7095d7f81000953d1cf))
|
|
- Run all updates on DSpace Test and reboot the server
|
|
- 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))
|
|
- 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
|
|
|
|
- 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
|
|
|
|
- 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
|
|
|
|
- Atmire's Listings and Reports module seems to be broken on DSpace 5.5
|
|
|
|
|
|
|
|
- I've filed a ticket with Atmire
|
|
- 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
|
|
|
|
- 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
|