CGSpace Notes

November, 2016

by Alan Orth in  

2016-11-01

  • Add dc.type to the output options for Atmire’s Listings and Reports module (#286)

Listings and Reports with output type

2016-11-02

  • Migrate DSpace Test to DSpace 5.5 (notes)
  • 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)
  • 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)

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

  • I’ve filed a ticket with Atmire
  • Thinking about batch updates for ORCIDs and authors
  • Playing with 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

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)
  • Generate a list of all these so I can maybe fix them in batch:
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
  • 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

  • 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
  • So there is apparently this Tomcat native way to limit web crawlers to one session: Crawler Session Manager
  • 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
  • The first one gets a session, and any after that — within 60 seconds — will be internally mapped to the same session by Tomcat
  • 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!

2016-11-15

  • The Tomcat JVM heap looks really good after applying the Crawler Session Manager fix on DSpace Test last night:

Tomcat JVM heap (day) after setting up the Crawler Session Manager Tomcat JVM heap (week) after setting up the Crawler Session Manager

  • Seems the default regex doesn’t catch Baidu, though:
$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Baiduspider/2.0; +http://www.baidu.com/search/spider.html)'
HTTP/1.1 200 OK
Connection: keep-alive
Content-Encoding: gzip
Content-Language: en-US
Content-Type: text/html;charset=utf-8
Date: Tue, 15 Nov 2016 08:49:54 GMT
Server: nginx
Set-Cookie: JSESSIONID=131409D143E8C01DE145C50FC748256E; Path=/; Secure; HttpOnly
Transfer-Encoding: chunked
Vary: Accept-Encoding
X-Cocoon-Version: 2.2.0

$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Baiduspider/2.0; +http://www.baidu.com/search/spider.html)'
HTTP/1.1 200 OK
Connection: keep-alive
Content-Encoding: gzip
Content-Language: en-US
Content-Type: text/html;charset=utf-8
Date: Tue, 15 Nov 2016 08:49:59 GMT
Server: nginx
Set-Cookie: JSESSIONID=F6403C084480F765ED787E41D2521903; Path=/; Secure; HttpOnly
Transfer-Encoding: chunked
Vary: Accept-Encoding
X-Cocoon-Version: 2.2.0
  • Adding Baiduspider to the list of user agents seems to work, and the final configuration should be:
<!-- Crawler Session Manager Valve helps mitigate damage done by web crawlers -->
<Valve className="org.apache.catalina.valves.CrawlerSessionManagerValve"
       crawlerUserAgents=".*[bB]ot.*|.*Yahoo! Slurp.*|.*Feedfetcher-Google.*|.*Baiduspider.*" />
  • Looking at the bots that were active yesterday it seems the above regex should be sufficient:
$ grep -o -E 'Mozilla/5\.0 \(compatible;.*\"' /var/log/nginx/access.log | sort | uniq
Mozilla/5.0 (compatible; Baiduspider/2.0; +http://www.baidu.com/search/spider.html)" "-"
Mozilla/5.0 (compatible; bingbot/2.0; +http://www.bing.com/bingbot.htm)" "-"
Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)" "-"
Mozilla/5.0 (compatible; YandexBot/3.0; +http://yandex.com/bots)" "-"
Mozilla/5.0 (compatible; YandexImages/3.0; +http://yandex.com/bots)" "-"
  • Neat maven trick to exclude some modules from being built:
$ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=localhost -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2 clean package
  • We absolutely don’t use those modules, so we shouldn’t build them in the first place

2016-11-17

  • Generate a list of journal titles for Peter and Abenet to look through so we can make a controlled vocabulary out of them:
dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=55 group by text_value order by count desc) to /tmp/journal-titles.csv with csv;
COPY 2515
  • Send a message to users of the CGSpace REST API to notify them of upcoming upgrade so they can test their apps against DSpace Test
  • Test an update old, non-HTTPS links to the CCAFS website in CGSpace metadata:
dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, 'http://ccafs.cgiar.org','https://ccafs.cgiar.org') where resource_type_id=2 and text_value like '%http://ccafs.cgiar.org%';
UPDATE 164
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://ccafs.cgiar.org','https://ccafs.cgiar.org') where resource_type_id=2 and text_value like '%http://ccafs.cgiar.org%';
UPDATE 7
  • Had to run it twice to get all (not sure about “global” regex in PostgreSQL)
  • Run the updates on CGSpace as well
  • Run through some collections and manually regenerate some PDF thumbnails for items from before 2016 on DSpace Test to compare with CGSpace
  • I’m debating forcing the re-generation of ALL thumbnails, since some come from DSpace 3 and 4 when the thumbnailing wasn’t as good
  • The results were very good, I think that after we upgrade to 5.5 I will do it, perhaps one community / collection at a time:
$ [dspace]/bin/dspace filter-media -f -i 10568/67156 -p "ImageMagick PDF Thumbnail"
  • In related news, I’m looking at thumbnails of thumbnails (the ones we uploaded manually before, and now DSpace’s media filter has made thumbnails of THEM):
dspace=# select text_value from metadatavalue where text_value like '%.jpg.jpg';
  • I’m not sure if there’s anything we can do, actually, because we would have to remove those from the thumbnail bundles, and replace them with the regular JPGs from the content bundle, and then remove them from the assetstore…

2016-11-18

  • Enable Tomcat Crawler Session Manager on CGSpace

2016-11-21

  • More work on Ansible playbooks for PostgreSQL 9.3→9.5 and Java 7→8 work
  • CGSpace virtual managers meeting
  • I need to look into making the item thumbnail clickable

2016-11-23

  • Upgrade Java from 7 to 8 on CGSpace
  • I had started planning the inplace PostgreSQL 9.3→9.5 upgrade but decided that I will have to pg_dump and pg_restore when I move to the new server soon anyways, so there’s no need to upgrade the database right now
  • Chat with Carlos about CGCore and the CGSpace metadata registry
  • Dump CGSpace metadata field registry for Carlos: https://gist.github.com/alanorth/8cbd0bb2704d4bbec78025b4742f8e70
  • Send some feedback to Carlos on CG Core so they can better understand how DSpace/CGSpace uses metadata
  • Notes about PostgreSQL tuning from James: https://paste.fedoraproject.org/488776/14798952/