CGSpace Notes

August, 2016

Mon, 01 Aug 2016 15:53:00 +0300

2016-08-01

Add updated distribution license from Sisay (#259)
Play with upgrading Mirage 2 dependencies in bower.json because most are several versions of out date
Bootstrap is at 3.3.0 but upstream is at 3.3.7, and upgrading to anything beyond 3.3.1 breaks glyphicons and probably more
bower stuff is a dead end, waste of time, too many issues
Anything after Bootstrap 3.3.1 makes glyphicons disappear (HTTP 404 trying to access from incorrect path of fonts)
Start working on DSpace 5.1 → 5.5 port:

$ git checkout -b 55new 5_x-prod
$ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5

Lots of conflicts that don’t make sense (ie, shouldn’t conflict!)
This file in particular conflicts almost 10 times: dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss
Checking out a clean branch at 5.5 and cherry-picking our commits works where that file would normally have a conflict
Seems to be related to merge commits
git rebase --preserve-merges doesn’t seem to help
Eventually I just turned on git rerere and solved the conflicts and completed the 403 commit rebase
The 5.5 code now builds but doesn’t run (white page in Tomcat)

2016-08-02

Ask Atmire for help with DSpace 5.5 issue
Vanilla DSpace 5.5 deploys and runs fine
Playing with DSpace in Ubuntu 16.04 and Tomcat 7
Everything is still fucked up, even vanilla DSpace 5.5

2016-08-04

Ask on DSpace mailing list about duplicate authors, Discovery and author text values
Atmire responded with some new DSpace 5.5 ready versions to try for their modules

2016-08-05

Fix item display incorrectly displaying Species when Breeds were present (#260)
Experiment with fixing more authors, like Delia Grace:

dspacetest=# update metadatavalue set authority='0b4fcbc1-d930-4319-9b4d-ea1553cca70b', confidence=600 where metadata_field_id=3 and text_value='Grace, D.';

2016-08-06

Finally figured out how to remove “View/Open” and “Bitstreams” from the item view

2016-08-07

Start working on Ubuntu 16.04 Ansible playbook for Tomcat 8, PostgreSQL 9.5, Oracle 8, etc

2016-08-08

Still troubleshooting Atmire modules on DSpace 5.5
Vanilla DSpace 5.5 works on Tomcat 7…
Ooh, and vanilla DSpace 5.5 works on Tomcat 8 with Java 8!
Some notes about setting up Tomcat 8, since it’s new on this machine…
Install latest Oracle Java 8 JDK
Create setenv.sh in Tomcat 8 libexec/bin directory:

CATALINA_OPTS="-Djava.awt.headless=true -Xms3072m -Xmx3072m -XX:+UseConcMarkSweepGC -XX:+CMSIncrementalMode -Dfile.encoding=UTF-8"
CATALINA_OPTS="$CATALINA_OPTS -Djava.library.path=/opt/brew/Cellar/tomcat-native/1.2.8/lib"

JRE_HOME=/Library/Java/JavaVirtualMachines/jdk1.8.0_102.jdk/Contents/Home

Edit Tomcat 8 server.xml to add regular HTTP listener for solr
Symlink webapps:

$ rm -rf /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/ROOT
$ ln -sv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/oai
$ ln -sv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/jspui
$ ln -sv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/rest
$ ln -sv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.5.4/libexec/webapps/solr

2016-08-09

More tests of Atmire’s 5.5 modules on a clean, working instance of 5_x-prod
Still fails, though perhaps differently than before (Flyway): https://gist.github.com/alanorth/5d49c45a16efd7c6bc1e6642e66118b2
More work on Tomcat 8 and Java 8 stuff for Ansible playbooks

2016-08-10

Turns out DSpace 5.x isn’t ready for Tomcat 8: https://jira.duraspace.org/browse/DS-3092
So we’ll need to use Tomcat 7 + Java 8 on Ubuntu 16.04
More work on the Ansible stuff for this, allowing Tomcat 7 to use Java 8
Merge pull request for fixing the type Discovery index to use dc.type (#262)
Merge pull request for removing “Bitstream” text from item display, as it confuses users and isn’t necessary (#263)

2016-08-11

Finally got DSpace (5.5) running on Ubuntu 16.04, Tomcat 7, Java 8, PostgreSQL 9.5 via the updated Ansible stuff

2016-08-14

Update Mirage 2 build notes for Ubuntu 16.04: https://gist.github.com/alanorth/2cf9c15834dc68a514262fcb04004cb0

2016-08-15

Notes on NodeJS + nginx + systemd: https://gist.github.com/alanorth/51acd476891c67dfe27725848cf5ace1

2016-08-16

Troubleshoot Paramiko connection issues with Ansible on ILRI servers: #37
Turns out we need to add some MACs to our sshd_config: hmac-sha2-512,hmac-sha2-256
Update DSpace Test’s Java to version 8 to start testing this configuration (seeing as Solr recommends it)

2016-08-17

More work on Let’s Encrypt stuff for Ansible roles
Yesterday Atmire responded about DSpace 5.5 issues and asked me to try the dspace database repair command to fix Flyway issues
The dspace database command doesn’t even run: https://gist.github.com/alanorth/c43c8d89e8df346d32c0ee938be90cd5
Oops, it looks like the missing classes causing dspace database to fail were coming from the old ~/dspace/config/spring folder
After removing the spring folder and running ant install again, dspace database works
I see there are missing and pending Flyway migrations, but running dspace database repair and dspace database migrate does nothing: https://gist.github.com/alanorth/41ed5abf2ff32d8ac9eedd1c3d015d70

2016-08-18

Fix “CONGO,DR” country name in input-forms.xml (#264)
Also need to fix existing records using the incorrect form in the database:

dspace=# update metadatavalue set text_value='CONGO, DR' where resource_type_id=2 and metadata_field_id=228 and text_value='CONGO,DR';

July, 2016

Fri, 01 Jul 2016 10:53:00 +0300

2016-07-01

Add dc.description.sponsorship to Discovery sidebar facets and make investors clickable in item view (#232)
I think this query should find and replace all authors that have “,” at the end of their names:

dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, '(^.+?),$', '\1') where metadata_field_id=3 and text_value ~ '^.+?,$';
UPDATE 95
dspacetest=# select text_value from  metadatavalue where metadata_field_id=3 and text_value ~ '^.+?,$';
 text_value
------------
(0 rows)

In this case the select query was showing 95 results before the update

2016-07-02

Comment on DSpace Jira ticket about author lookup search text (DS-2329)

2016-07-04

Seems the database’s author authority values mean nothing without the authority Solr core from the host where they were created!

2016-07-05

Amend backup-solr.sh script so it backs up the entire Solr folder
We really only need statistics and authority but meh
Fix metadata for species on DSpace Test:

$ ./fix-metadata-values.py -i /tmp/Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 94 -d dspacetest -u dspacetest -p 'fuuu'

Will run later on CGSpace
A user is still having problems with Sherpa/Romeo causing crashes during the submission process when the journal is “ungraded”
I tested the patch for DS-2740 that I had found last month and it seems to work
I will merge it to 5_x-prod

2016-07-06

Delete 23 blank metadata values from CGSpace:

cgspace=# delete from metadatavalue where resource_type_id=2 and text_value='';
DELETE 23

Complete phase three of metadata migration, for the following fields:
- dc.title.jtitle → dc.source
- dc.crsubject.crpsubject → cg.contributor.crp
- dc.contributor.affiliation → cg.contributor.affiliation
- dc.Species → cg.species
- dc.srplace.subregion → cg.coverage.subregion
- dc.contributor.corporate → dc.contributor.author
- dc.identifier.url → cg.identifier.url
- dc.identifier.doi → cg.identifier.doi
- dc.identifier.googleurl → cg.identifier.googleurl
- dc.identifier.dataurl → cg.identifier.dataurl
Also, run fixes and deletes for species and author affiliations (over 1000 corrections!)

$ ./fix-metadata-values.py -i Species-Peter-Fix.csv -f dc.Species -t CORRECT -m 212 -d dspace -u dspace -p 'fuuu'
$ ./fix-metadata-values.py -i Affiliations-Fix-1045-Peter-Abenet.csv -f dc.contributor.affiliation -t Correct -m 211 -d dspace -u dspace -p 'fuuu'
$ ./delete-metadata-values.py -f dc.contributor.affiliation -i Affiliations-Delete-Peter-Abenet.csv -m 211 -u dspace -d dspace -p 'fuuu'

I then ran all server updates and rebooted the server

2016-07-11

Doing some author cleanups from Peter and Abenet:

$ ./fix-metadata-values.py -i /tmp/Authors-Fix-205-UTF8.csv -f dc.contributor.author -t correct -m 3 -d dspacetest -u dspacetest -p fuuu
$ ./delete-metadata-values.py -f dc.contributor.author -i /tmp/Authors-Delete-UTF8.csv -m 3 -u dspacetest -d dspacetest -p fuuu

2016-07-13

Run the author cleanups on CGSpace and start a full Discovery re-index

2016-07-14

Test LDAP settings for new root LDAP
Seems to work when binding as a top-level user

2016-07-18

Adjust identifiers in XMLUI item display to be more prominent
Add species and breed to the XMLUI item display
CGSpace crashed late at night and the DSpace logs were showing:

2016-07-18 20:26:30,941 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error - 
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
...

I suspect it’s someone hitting REST too much:

# awk '{print $1}' /var/log/nginx/rest.log  | sort -n | uniq -c | sort -h | tail -n 3
    710 66.249.78.38
   1781 181.118.144.29
  24904 70.32.99.142

I just blocked access to /rest for that last IP for now:

     # log rest requests
     location /rest {
         access_log /var/log/nginx/rest.log;
         proxy_pass http://127.0.0.1:8443;
         deny 70.32.99.142;
     }

2016-07-21

Mitigate the HTTPoxy vulnerability for Tomcat etc in nginx: https://github.com/ilri/rmg-ansible-public/pull/38
Unblock 70.32.99.142 from /rest as it has been blocked for a few days

2016-07-22

Help Paola from CCAFS with thumbnails for batch uploads
She has been struggling to get the dimensions right, and manually enlarging smaller thumbnails, renaming PNGs to JPG, etc
Altmetric reports having an issue with some of our authors being doubled…
This is related to authority and confidence!
We might need to use index.authority.ignore-prefered=true to tell the Discovery index to prefer the variation that exists in the metadatavalue rather than what it finds in the authority cache.
Trying these on DSpace Test after a discussion by Daniel Scharon on the dspace-tech mailing list:

index.authority.ignore-prefered.dc.contributor.author=true
index.authority.ignore-variants.dc.contributor.author=false

After reindexing I don’t see any change in Discovery’s display of authors, and still have entries like:

Grace, D. (464)
Grace, D. (62)

I asked for clarification of the following options on the DSpace mailing list:

index.authority.ignore
index.authority.ignore-prefered
index.authority.ignore-variants

In the mean time, I will try these on DSpace Test (plus a reindex):

index.authority.ignore=true
index.authority.ignore-prefered=true
index.authority.ignore-variants=true

Enabled usage of X-Forwarded-For in DSpace admin control panel (#255
It was misconfigured and disabled, but already working for some reason sigh
… no luck. Trying with just:

index.authority.ignore=true

After re-indexing and clearing the XMLUI cache nothing has changed

2016-07-25

Trying a few more settings (plus reindex) for Discovery on DSpace Test:

index.authority.ignore-prefered.dc.contributor.author=true
index.authority.ignore-variants=true

Run all OS updates and reboot DSpace Test server
No changes to Discovery after reindexing… hmm.
Integrate and massively clean up About page (#256)

The DSpace source code mentions the configuration key discovery.index.authority.ignore-prefered.* (with prefix of discovery, despite the docs saying otherwise), so I’m trying the following on DSpace Test:

discovery.index.authority.ignore-prefered.dc.contributor.author=true
discovery.index.authority.ignore-variants=true

Still no change!
Deploy species, breed, and identifier changes to CGSpace, as well as About page
Run Linode RAM upgrade (8→12GB)
Re-sync DSpace Test with CGSpace
I noticed that our backup scripts don’t send Solr cores to S3 so I amended the script

2016-07-31

Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by
Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (#257)

June, 2016

Wed, 01 Jun 2016 10:53:00 +0300

2016-06-01

Experimenting with IFPRI OAI (we want to harvest their publications)
After reading the ContentDM documentation I found IFPRI’s OAI endpoint: http://ebrary.ifpri.org/oai/oai.php
After reading the OAI documentation and testing with an OAI validator I found out how to get their publications
This is their publications set: http://ebrary.ifpri.org/oai/oai.php?verb=ListRecords&from=2016-01-01&set=p15738coll2&metadataPrefix=oai_dc
You can see the others by using the OAI ListSets verb: http://ebrary.ifpri.org/oai/oai.php?verb=ListSets
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship

dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
UPDATE 14

Fix a few minor miscellaneous issues in dspace.cfg (#227)

2016-06-02

Testing the configuration and theme changes for the upcoming metadata migration and I found some issues with cg.coverage.admin-unit
Seems that the Browse configuration in dspace.cfg can’t handle the ‘-’ in the field name:

webui.browse.index.12 = subregion:metadata:cg.coverage.admin-unit:text

But actually, I think since DSpace 4 or 5 (we are 5.1) the Browse indexes come from Discovery (defined in discovery.xml) so this is really just a parsing error
I’ve sent a message to the DSpace mailing list to ask about the Browse index definition
A user was having problems with submission and from the stacktrace it looks like a Sherpa/Romeo issue
I found a thread on the mailing list talking about it and there is bug report and a patch: https://jira.duraspace.org/browse/DS-2740
The patch applies successfully on DSpace 5.1 so I will try it later

2016-06-03

Investigating the CCAFS authority issue, I exported the metadata for the Videos collection
The top two authors are:

CGIAR Research Program on Climate Change, Agriculture and Food Security::acd00765-02f1-4b5b-92fa-bfa3877229ce::500
CGIAR Research Program on Climate Change, Agriculture and Food Security::acd00765-02f1-4b5b-92fa-bfa3877229ce::600

So the only difference is the “confidence”
Ok, well THAT is interesting:

dspacetest=# select text_value, authority, confidence from metadatavalue where metadata_field_id=3 and text_value like '%Orth, %';
 text_value |              authority               | confidence
------------+--------------------------------------+------------
 Orth, A.   | ab606e3a-2b04-4c7d-9423-14beccf54257 |         -1
 Orth, A.   | ab606e3a-2b04-4c7d-9423-14beccf54257 |         -1
 Orth, A.   | ab606e3a-2b04-4c7d-9423-14beccf54257 |         -1
 Orth, Alan |                                      |         -1
 Orth, Alan |                                      |         -1
 Orth, Alan |                                      |         -1
 Orth, Alan |                                      |         -1
 Orth, A.   | 05c2c622-d252-4efb-b9ed-95a07d3adf11 |         -1
 Orth, A.   | 05c2c622-d252-4efb-b9ed-95a07d3adf11 |         -1
 Orth, A.   | ab606e3a-2b04-4c7d-9423-14beccf54257 |         -1
 Orth, A.   | ab606e3a-2b04-4c7d-9423-14beccf54257 |         -1
 Orth, Alan | ad281dbf-ef81-4007-96c3-a7f5d2eaa6d9 |        600
 Orth, Alan | ad281dbf-ef81-4007-96c3-a7f5d2eaa6d9 |        600
(13 rows)

And now an actually relevent example:

dspacetest=# select count(*) from metadatavalue where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security' and confidence = 500;
 count
-------
   707
(1 row)

dspacetest=# select count(*) from metadatavalue where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security' and confidence != 500;
 count
-------
   253
(1 row)

Trying something experimental:

dspacetest=# update metadatavalue set confidence=500 where metadata_field_id=3 and text_value like 'CGIAR Research Program on Climate Change, Agriculture and Food Security';
UPDATE 960

And then re-indexing authority and Discovery…?
After Discovery reindex the CCAFS authors are all together in the Authors sidebar facet
The docs for the ORCiD and Authority stuff for DSpace 5 mention changing the browse indexes to use the Authority as well:

webui.browse.index.2 = author:metadataAuthority:dc.contributor.author:authority

That would only be for the “Browse by” function… so we’ll have to see what effect that has later

2016-06-04

Re-sync DSpace Test with CGSpace and perform test of metadata migration again
Run phase two of metadata migrations on CGSpace (see the migration notes)
Run all system updates and reboot CGSpace server

2016-06-07

Figured out how to export a list of the unique values from a metadata field ordered by count:

dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=29 group by text_value order by count desc) to /tmp/sponsorship.csv with csv;

Identified the next round of fields to migrate:
- dc.title.jtitle → dc.source
- dc.crsubject.crpsubject → cg.contributor.crp
- dc.contributor.affiliation → cg.contributor.affiliation
- dc.Species → cg.species
- dc.contributor.corporate → dc.contributor
- dc.identifier.url → cg.identifier.url
- dc.identifier.doi → cg.identifier.doi
- dc.identifier.googleurl → cg.identifier.googleurl
- dc.identifier.dataurl → cg.identifier.dataurl
Discuss pulling data from IFPRI’s ContentDM with Ryan Miller
Looks like OAI is kinda obtuse for this, and if we use ContentDM’s API we’ll be able to access their internal field names (rather than trying to figure out how they stuffed them into various, repeated Dublin Core fields)

2016-06-08

Discuss controlled vocabularies for ~28 fields
Looks like this is all we need: https://wiki.duraspace.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ConfiguringControlledVocabularies
I wrote an XPath expression to extract the ILRI subjects from input-forms.xml (uses xmlstartlet):

$ xml sel -t -m '//value-pairs[@value-pairs-name="ilrisubject"]/pair/displayed-value/text()' -c '.' -n dspace/config/input-forms.xml

Write to Atmire about the use of atmire.orcid.id to see if we can change it
Seems to be a virtual field that is queried from the authority cache… hmm
In other news, I found out that the About page that we haven’t been using lives in dspace/config/about.xml, so now we can update the text
File bug about closed="true" attribute of controlled vocabularies not working: https://jira.duraspace.org/browse/DS-3238

2016-06-09

Atmire explained that the atmire.orcid.id field doesn’t exist in the schema, as it actually comes from the authority cache during XMLUI run time
This means we don’t see it when harvesting via OAI or REST, for example
They opened a feature ticket on the DSpace tracker to ask for support of this: https://jira.duraspace.org/browse/DS-3239

2016-06-10

Investigating authority confidences
It looks like the values are documented in Choices.java
Experiment with setting all 960 CCAFS author values to be 500:

dspacetest=# SELECT authority, confidence FROM metadatavalue WHERE resource_type_id=2 AND metadata_field_id=3 AND text_value = 'CGIAR Research Program on Climate Change, Agriculture and Food Security';

dspacetest=# UPDATE metadatavalue set confidence = 500 where resource_type_id=2 AND metadata_field_id=3 AND text_value = 'CGIAR Research Program on Climate Change, Agriculture and Food Security';
UPDATE 960

After the database edit, I did a full Discovery re-index
And now there are exactly 960 items in the authors facet for ‘CGIAR Research Program on Climate Change, Agriculture and Food Security’
Now I ran the same on CGSpace
Merge controlled vocabulary functionality for animal breeds to 5_x-prod (#236)
Write python script to update metadata values in batch via PostgreSQL: fix-metadata-values.py
We need to use this to correct some pretty ugly values in fields like dc.description.sponsorship
Merge item display tweaks from earlier this week (#231)
Merge controlled vocabulary functionality for subregions (#238)

2016-06-11

Merge controlled vocabulary for sponsorship field (#239)
Fix character encoding issues for animal breed lookup that I merged yesterday

2016-06-17

Linode has free RAM upgrades for their 13th birthday so I migrated DSpace Test (4→8GB of RAM)

2016-06-18

Clean up titles and hints in input-forms.xml to use title/sentence case and a few more consistency things (#241)
The final list of fields to migrate in the third phase of metadata migrations is:
- dc.title.jtitle → dc.source
- dc.crsubject.crpsubject → cg.contributor.crp
- dc.contributor.affiliation → cg.contributor.affiliation
- dc.srplace.subregion → cg.coverage.subregion
- dc.Species → cg.species
- dc.contributor.corporate → dc.contributor
- dc.identifier.url → cg.identifier.url
- dc.identifier.doi → cg.identifier.doi
- dc.identifier.googleurl → cg.identifier.googleurl
- dc.identifier.dataurl → cg.identifier.dataurl
Interesting “Sunburst” visualization on a Digital Commons page: http://www.repository.law.indiana.edu/sunburst.html
Final testing on metadata fix/delete for dc.description.sponsorship cleanup
Need to run fix-metadata-values.py and then fix-metadata-values.py

2016-06-20

CGSpace’s HTTPS certificate expired last night and I didn’t notice, had to renew:

# /opt/letsencrypt/letsencrypt-auto renew --standalone --pre-hook "/usr/bin/service nginx stop" --post-hook "/usr/bin/service nginx start"

I really need to fix that cron job…

2016-06-24

Run the replacements/deletes for dc.description.sponsorship (investors) on CGSpace:

$ ./fix-metadata-values.py -i investors-not-blank-not-delete-85.csv -f dc.description.sponsorship -t 'correct investor' -m 29 -d cgspace -p 'fuuu' -u cgspace
$ ./delete-metadata-values.py -i investors-delete-82.csv -f dc.description.sponsorship -m 29 -d cgspace -p 'fuuu' -u cgspace

The scripts for this are here:
- fix-metadata-values.py
- delete-metadata-values.py
Add new sponsors to controlled vocabulary (#244)
Refine submission form labels and hints

2016-06-28

Testing the cleanup of dc.contributor.corporate with 13 deletions and 121 replacements
There are still ~97 fields that weren’t indicated to do anything
After the above deletions and replacements I regenerated a CSV and sent it to Peter et al to have a look

dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=126 group by text_value order by count desc) to /tmp/contributors-june28.csv with csv;

Re-evaluate dc.contributor.corporate and it seems we will move it to dc.contributor.author as this is more in line with how editors are actually using it

2016-06-29

Test run of migrate-fields.sh with the following re-mappings:

72  55  #dc.source
86  230 #cg.contributor.crp
91  211 #cg.contributor.affiliation
94  212 #cg.species
107 231 #cg.coverage.subregion
126 3   #dc.contributor.author
73  219 #cg.identifier.url
74  220 #cg.identifier.doi
79  222 #cg.identifier.googleurl
89  223 #cg.identifier.dataurl

Run all cleanups and deletions of dc.contributor.corporate on CGSpace:

$ ./fix-metadata-values.py -i Corporate-Authors-Fix-121.csv -f dc.contributor.corporate -t 'Correct style' -m 126 -d cgspace -u cgspace -p 'fuuu'
$ ./fix-metadata-values.py -i Corporate-Authors-Fix-PB.csv -f dc.contributor.corporate -t 'should be' -m 126 -d cgspace -u cgspace -p 'fuuu'
$ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-Delete-13.csv -m 126 -u cgspace -d cgspace -p 'fuuu'

Re-deploy CGSpace and DSpace Test with latest June changes
Now the sharing and Altmetric bits are more prominent:

Run all system updates on the servers and reboot
Start working on config changes for phase three of the metadata migrations

2016-06-30

Wow, there are 95 authors in the database who have ‘,’ at the end of their name:

# select text_value from  metadatavalue where metadata_field_id=3 and text_value like '%,';

We need to use something like this to fix them, need to write a proper regex later:

# update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';

May, 2016

Sun, 01 May 2016 23:06:00 +0300

2016-05-01

Since yesterday there have been 10,000 REST errors and the site has been unstable again
I have blocked access to the API now
There are 3,000 IPs accessing the REST API in a 24-hour period!

# awk '{print $1}' /var/log/nginx/rest.log  | uniq | wc -l
3168

The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29
100% of the requests coming from Ethiopia are like this and result in an HTTP 500:

GET /rest/handle/10568/NaN?expand=parentCommunityList,metadata HTTP/1.1

For now I’ll block just the Ethiopian IP
The owner of that application has said that the NaN (not a number) is an error in his code and he’ll fix it

2016-05-03

Update nginx to 1.10.x branch on CGSpace
Fix a reference to dc.type.output in Discovery that I had missed when we migrated to dc.type last month (#223)

2016-05-06

DSpace Test is down, catalina.out has lots of messages about heap space from some time yesterday (!)
It looks like Sisay was doing some batch imports
Hmm, also disk space is full
I decided to blow away the solr indexes, since they are 50GB and we don’t really need all the Atmire stuff there right now
I will re-generate the Discovery indexes after re-deploying
Testing renew-letsencrypt.sh script for nginx

#!/usr/bin/env bash

readonly SERVICE_BIN=/usr/sbin/service
readonly LETSENCRYPT_BIN=/opt/letsencrypt/letsencrypt-auto

# stop nginx so LE can listen on port 443
$SERVICE_BIN nginx stop

$LETSENCRYPT_BIN renew -nvv --standalone --standalone-supported-challenges tls-sni-01 > /var/log/letsencrypt/renew.log 2>&1

LE_RESULT=$?

$SERVICE_BIN nginx start

if [[ "$LE_RESULT" != 0 ]]; then
    echo 'Automated renewal failed:'

    cat /var/log/letsencrypt/renew.log

    exit 1
fi

Seems to work well

2016-05-10

Start looking at more metadata migrations
There are lots of fields in dcterms namespace that look interesting, like:
- dcterms.type
- dcterms.spatial
Not sure what dcterms is…
Looks like these were added in DSpace 4 to allow for future work to make DSpace more flexible
CGSpace’s dc registry has 96 items, and the default DSpace one has 73.

2016-05-11

Identify and propose the next phase of CGSpace fields to migrate:
- dc.title.jtitle → cg.title.journal
- dc.identifier.status → cg.identifier.status
- dc.river.basin → cg.river.basin
- dc.Species → cg.species
- dc.targetaudience → cg.targetaudience
- dc.fulltextstatus → cg.fulltextstatus
- dc.editon → cg.edition
- dc.isijournal → cg.isijournal
Start a test rebase of the 5_x-prod branch on top of the dspace-5.5 tag
There were a handful of conflicts that I didn’t understand
After completing the rebase I tried to build with the module versions Atmire had indicated as being 5.5 ready but I got this error:

[ERROR] Failed to execute goal on project additions: Could not resolve dependencies for project org.dspace.modules:additions:jar:5.5: Could not find artifact com.atmire:atmire-metadata-quality-api:jar:5.5-2.10.1-0 in sonatype-releases (https://oss.sonatype.org/content/repositories/releases/) -> [Help 1]

I’ve sent them a question about it
A user mentioned having problems with uploading a 33 MB PDF
I told her I would increase the limit temporarily tomorrow morning
Turns out she was able to decrease the size of the PDF so we didn’t have to do anything

2016-05-12

Looks like the issue that Abenet was having a few days ago with “Connection Reset” in Firefox might be due to a Firefox 46 issue: https://bugzilla.mozilla.org/show_bug.cgi?id=1268775
I finally found a copy of the latest CG Core metadata guidelines and it looks like we can add a few more fields to our next migration:
- dc.rplace.region → cg.coverage.region
- dc.cplace.country → cg.coverage.country
Questions for CG people:
- Our dc.place and dc.srplace.subregion could both map to cg.coverage.admin-unit?
- Should we use dc.contributor.crp or cg.contributor.crp for the CRP (ours is dc.crsubject.crpsubject)?
- Our dc.contributor.affiliation and dc.contributor.corporate could both map to dc.contributor and possibly dc.contributor.center depending on if it’s a CG center or not
- dc.title.jtitle could either map to dc.publisher or dc.source depending on how you read things
Found ~200 messed up CIAT values in dc.publisher:

# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=39 and text_value similar to "%  %";

2016-05-13

More theorizing about CGcore
Add two new fields:
- dc.srplace.subregion → cg.coverage.admin-unit
- dc.place → cg.place
dc.place is our own field, so it’s easy to move
I’ve removed dc.title.jtitle from the list for now because there’s no use moving it out of DC until we know where it will go (see discussion yesterday)

2016-05-18

Work on 707 CCAFS records
They have thumbnails on Flickr and elsewhere
In OpenRefine I created a new filename column based on the thumbnail column with the following GREL:

if(cells['thumbnails'].value.contains('hqdefault'), cells['thumbnails'].value.split('/')[-2] + '.jpg', cells['thumbnails'].value.split('/')[-1])

Because ~400 records had the same filename on Flickr (hqdefault.jpg) but different UUIDs in the URL
So for the hqdefault.jpg ones I just take the UUID (-2) and use it as the filename
Before importing with SAFBuilder I tested adding “__bundle:THUMBNAIL” to the filename column and it works fine

2016-05-19

More quality control on filename field of CCAFS records to make processing in shell and SAFBuilder more reliable:

value.replace('_','').replace('-','')

We need to hold off on moving dc.Species to cg.species because it is only used for plants, and might be better to move it to something like cg.species.plant
And dc.identifier.fund is MOSTLY used for CPWF project identifier but has some other sponsorship things
- We should move PN, SG, CBA, IA, and PHASE* values to cg.identifier.cpwfproject
- The rest, like BMGF and USAID etc, might have to go to either dc.description.sponsorship or cg.identifier.fund (not sure yet)
- There are also some mistakes in CPWF’s things, like “PN 47”
- This ought to catch all the CPWF values (there don’t appear to be and SG* values):

# select text_value from metadatavalue where resource_type_id=2 and metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');

2016-05-20

More work on CCAFS Video and Images records
For SAFBuilder we need to modify filename column to have the thumbnail bundle:

value + "__bundle:THUMBNAIL"

Also, I fixed some weird characters using OpenRefine’s transform with the following GREL:

value.replace(/\u0081/,'')

Write shell script to resize thumbnails with height larger than 400: https://gist.github.com/alanorth/131401dcd39d00e0ce12e1be3ed13256
Upload 707 CCAFS records to DSpace Test
A few miscellaneous fixes for XMLUI display niggles (spaces in item lists and link target _black): #224
Work on configuration changes for Phase 2 metadata migrations

2016-05-23

Try to import the CCAFS Images and Videos to CGSpace but had some issues with LibreOffice and OpenRefine
LibreOffice excludes empty cells when it exports and all the fields shift over to the left and cause URLs to go to Subjects, etc.
Google Docs does this better, but somehow reorders the rows and when I paste the thumbnail/filename row in they don’t match!
I will have to try later

2016-05-30

Export CCAFS video and image records from DSpace Test using the migrate option (-m):

$ mkdir ~/ccafs-images
$ /home/dspacetest.cgiar.org/bin/dspace export -t COLLECTION -i 10568/79355 -d ~/ccafs-images -n 0 -m

And then import to CGSpace:

$ JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace import --add --eperson=aorth@mjanja.ch --collection=10568/70974 --source /tmp/ccafs-images --mapfile=/tmp/ccafs-images-may30.map &> /tmp/ccafs-images-may30.log

But now we have double authors for “CGIAR Research Program on Climate Change, Agriculture and Food Security” in the authority
I’m trying to do a Discovery index before messing with the authority index
Looks like we are missing the index-authority cron job, so who knows what’s up with our authority index
Run system updates on DSpace Test, re-deploy code, and reboot the server
Clean up and import ~200 CTA records to CGSpace via CSV like:

$ export JAVA_OPTS="-Xmx512m -Dfile.encoding=UTF-8"
$ /home/cgspace.cgiar.org/bin/dspace metadata-import -e aorth@mjanja.ch -f ~/CTA-May30/CTA-42229.csv &> ~/CTA-May30/CTA-42229.log

Discovery indexing took a few hours for some reason, and after that I started the index-authority script

$ JAVA_OPTS="-Xmx1024m -Dfile.encoding=UTF-8" /home/cgspace.cgiar.org/bin/dspace index-authority

2016-05-31

The index-authority script ran over night and was finished in the morning
Hopefully this was because we haven’t been running it regularly and it will speed up next time
I am running it again with a timer to see:

$ time /home/cgspace.cgiar.org/bin/dspace index-authority
Retrieving all data
Initialize org.dspace.authority.indexer.DSpaceAuthorityIndexer
Cleaning the old index
Writing new data
All done !

real    37m26.538s
user    2m24.627s
sys     0m20.540s

Update tomcat7 crontab on CGSpace and DSpace Test to have the index-authority script that we were missing
Add new ILRI subject and CCAFS project tags to input-forms.xml (#226, #225)
Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.
Re-sync DSpace Test data with CGSpace
Clean up and import ~65 more CTA items into CGSpace

April, 2016

Mon, 04 Apr 2016 11:06:00 +0300

2016-04-04

Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit
We are backing up all logs in the log folder, including useless stuff like solr, cocoon, handle-plugin, etc
After running DSpace for over five years I’ve never needed to look in any other log file than dspace.log, leave alone one from last year!
This will save us a few gigs of backup space we’re paying for on S3
Also, I noticed the checker log has some errors we should pay attention to:

Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
        at java.io.FileInputStream.open(Native Method)
        at java.io.FileInputStream.<init>(FileInputStream.java:146)
        at edu.sdsc.grid.io.local.LocalFileInputStream.open(LocalFileInputStream.java:171)
        at edu.sdsc.grid.io.GeneralFileInputStream.<init>(GeneralFileInputStream.java:145)
        at edu.sdsc.grid.io.local.LocalFileInputStream.<init>(LocalFileInputStream.java:139)
        at edu.sdsc.grid.io.FileFactory.newFileInputStream(FileFactory.java:630)
        at org.dspace.storage.bitstore.BitstreamStorageManager.retrieve(BitstreamStorageManager.java:525)
        at org.dspace.checker.BitstreamDAO.getBitstream(BitstreamDAO.java:60)
        at org.dspace.checker.CheckerCommand.processBitstream(CheckerCommand.java:303)
        at org.dspace.checker.CheckerCommand.checkBitstream(CheckerCommand.java:171)
        at org.dspace.checker.CheckerCommand.process(CheckerCommand.java:120)
        at org.dspace.app.checker.ChecksumChecker.main(ChecksumChecker.java:236)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:225)
        at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:77)
******************************************************

So this would be the tomcat7 Unix user, who seems to have a default limit of 1024 files in its shell
For what it’s worth, we have been setting the actual Tomcat 7 process’ limit to 16384 for a few years (in /etc/default/tomcat7)
Looks like cron will read limits from /etc/security/limits.* so we can do something for the tomcat7 user there
Submit pull request for Tomcat 7 limits in Ansible dspace role (#30)

2016-04-05

Reduce Amazon S3 storage used for logs from 46 GB to 6GB by deleting a bunch of logs we don’t need!

# s3cmd ls s3://cgspace.cgiar.org/log/ > /tmp/s3-logs.txt
# grep checker.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep cocoon.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep handle-plugin.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del
# grep solr.log /tmp/s3-logs.txt | awk '{print $4}' | xargs s3cmd del

Also, adjust the cron jobs for backups so they only backup dspace.log and some stats files (.dat)
Try to do some metadata field migrations using the Atmire batch UI (dc.Species → cg.species) but it took several hours and even missed a few records

2016-04-06

A better way to move metadata on this scale is via SQL, for example dc.type.output → dc.type (their IDs in the metadatafieldregistry are 66 and 109, respectively):

dspacetest=# update metadatavalue set metadata_field_id=109 where metadata_field_id=66;
UPDATE 40852

After that an index-discovery -bf is required
Start working on metadata migrations, add 25 or so new metadata fields to CGSpace

2016-04-07

Write shell script to do the migration of fields: https://gist.github.com/alanorth/72a70aca856d76f24c127a6e67b3342b
Testing with a few fields it seems to work well:

$ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40883
UPDATE metadatavalue SET metadata_field_id=202 WHERE metadata_field_id=72
UPDATE 21420
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51258

2016-04-08

Discuss metadata renaming with Abenet, we decided it’s better to start with the center-specific subjects like ILRI, CIFOR, CCAFS, IWMI, and CPWF
I’ve e-mailed CCAFS and CPWF people to ask them how much time it will take for them to update their systems to cope with this change

2016-04-10

Looking at the DOI issue reported by Leroy from CIAT a few weeks ago
It seems the dx.doi.org URLs are much more proper in our repository!

dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://dx.doi.org%';
 count
-------
  5638
(1 row)

dspacetest=# select count(*) from metadatavalue where metadata_field_id=74 and text_value like 'http://doi.org%';
 count
-------
     3

I will manually edit the dc.identifier.doi in ¹⁰⁵⁶⁸⁄₇₂₅₀₉ and tweet the link, then check back in a week to see if the donut gets updated

2016-04-11

The donut is already updated and shows the correct number now
CCAFS people say it will only take them an hour to update their code for the metadata renames, so I proposed we’d do it tentatively on Monday the 18th.

2016-04-12

Looking at quality of WLE data (cg.subject.iwmi) in SQL:

dspacetest=# select text_value, count(*) from metadatavalue where metadata_field_id=217 group by text_value order by count(*) desc;

Listings and Reports is still not returning reliable data for dc.type
I think we need to ask Atmire, as their documentation isn’t too clear on the format of the filter configs
Alternatively, I want to see if I move all the data from dc.type.output to dc.type and then re-index, if it behaves better
Looking at our input-forms.xml I see we have two sets of ILRI subjects, but one has a few extra subjects
Remove one set of ILRI subjects and remove duplicate VALUE CHAINS from existing list (#216)
I decided to keep the set of subjects that had FMD and RANGELANDS added, as it appears to have been requested to have been added, and might be the newer list
I found 226 blank metadatavalues:

dspacetest# select * from metadatavalue where resource_type_id=2 and text_value='';

I think we should delete them and do a full re-index:

dspacetest=# delete from metadatavalue where resource_type_id=2 and text_value='';
DELETE 226

I deleted them on CGSpace but I’ll wait to do the re-index as we’re going to be doing one in a few days for the metadata changes anyways
In other news, moving the dc.type.output to dc.type and re-indexing seems to have fixed the Listings and Reports issue from above
Unfortunately this isn’t a very good solution, because Listings and Reports config should allow us to filter on dc.type.* but the documentation isn’t very clear and I couldn’t reach Atmire today
We want to do the dc.type.output move on CGSpace anyways, but we should wait as it might affect other external people!

2016-04-14

Communicate with Macaroni Bros again about dc.type
Help Sisay with some rsync and Linux stuff
Notify CIAT people of metadata changes (I had forgotten them last week)

2016-04-15

DSpace Test had crashed, so I ran all system updates, rebooted, and re-deployed DSpace code

2016-04-18

Talk to CIAT people about their portal again
Start looking more at the fields we want to delete
The following metadata fields have 0 items using them, so we can just remove them from the registry and any references in XMLUI, input forms, etc:
- dc.description.abstractother
- dc.whatwasknown
- dc.whatisnew
- dc.description.nationalpartners
- dc.peerreviewprocess
- cg.species.animal
Deleted!
The following fields have some items using them and I have to decide what to do with them (delete or move):
- dc.icsubject.icrafsubject: 6 items, mostly in CPWF collections
- dc.type.journal: 11 items, mostly in ILRI collections
- dc.publicationcategory: 1 item, in CPWF
- dc.GRP: 2 items, CPWF
- dc.Species.animal: 6 items, in ILRI and AnGR
- cg.livestock.agegroup: 9 items, in ILRI collections
- cg.livestock.function: 20 items, mostly in EADD
Test metadata migration on local instance again:

$ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40885
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51330
UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
UPDATE 5986
UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
UPDATE 2456
UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
UPDATE 3872
UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
UPDATE 46075
$ JAVA_OPTS="-Xms512m -Xmx512m -Dfile.encoding=UTF-8" ~/dspace/bin/dspace index-discovery -bf

CGSpace was down but I’m not sure why, this was in catalina.out:

Apr 18, 2016 7:32:26 PM com.sun.jersey.spi.container.ContainerResponse logException
SEVERE: Mapped exception to response: 500 (Internal Server Error)
javax.ws.rs.WebApplicationException
        at org.dspace.rest.Resource.processFinally(Resource.java:163)
        at org.dspace.rest.HandleResource.getObject(HandleResource.java:81)
        at sun.reflect.GeneratedMethodAccessor198.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at com.sun.jersey.spi.container.JavaMethodInvokerFactory$1.invoke(JavaMethodInvokerFactory.java:60)
        at com.sun.jersey.server.impl.model.method.dispatch.AbstractResourceMethodDispatchProvider$TypeOutInvoker._dispatch(AbstractResourceMethodDispatchProvider.java:185)
        at com.sun.jersey.server.impl.model.method.dispatch.ResourceJavaMethodDispatcher.dispatch(ResourceJavaMethodDispatcher.java:75)
        at com.sun.jersey.server.impl.uri.rules.HttpMethodRule.accept(HttpMethodRule.java:302)
        at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
        at com.sun.jersey.server.impl.uri.rules.ResourceClassRule.accept(ResourceClassRule.java:108)
        at com.sun.jersey.server.impl.uri.rules.RightHandPathRule.accept(RightHandPathRule.java:147)
        at com.sun.jersey.server.impl.uri.rules.RootResourceClassesRule.accept(RootResourceClassesRule.java:84)
        at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1511)
        at com.sun.jersey.server.impl.application.WebApplicationImpl._handleRequest(WebApplicationImpl.java:1442)
        at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1391)
        at com.sun.jersey.server.impl.application.WebApplicationImpl.handleRequest(WebApplicationImpl.java:1381)
        at com.sun.jersey.spi.container.servlet.WebComponent.service(WebComponent.java:416)
...

Everything else in the system looked normal (50GB disk space available, nothing weird in dmesg, etc)
After restarting Tomcat a few more of these errors were logged but the application was up

2016-04-19

Get handles for items that are using a given metadata field, ie dc.Species.animal (105):

# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=105);
   handle
-------------
 10568/10298
 10568/16413
 10568/16774
 10568/34487

Delete metadata values for dc.GRP and dc.icsubject.icrafsubject:

# delete from metadatavalue where resource_type_id=2 and metadata_field_id=96;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=83;

They are old ICRAF fields and we haven’t used them since 2011 or so
Also delete them from the metadata registry
CGSpace went down again, dspace.log had this:

2016-04-19 15:02:17,025 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object

I restarted Tomcat and PostgreSQL and now it’s back up
I bet this is the same crash as yesterday, but I only saw the errors in catalina.out
Looks to be related to this, from dspace.log:

2016-04-19 15:16:34,670 ERROR org.dspace.rest.Resource @ Something get wrong. Aborting context in finally statement.

We have 18,000 of these errors right now…
Delete a few more old metadata values: dc.Species.animal, dc.type.journal, and dc.publicationcategory:

# delete from metadatavalue where resource_type_id=2 and metadata_field_id=105;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=85;
# delete from metadatavalue where resource_type_id=2 and metadata_field_id=95;

And then remove them from the metadata registry

2016-04-20

Re-deploy DSpace Test with the new subject and type fields, run all system updates, and reboot the server
Migrate fields and re-deploy CGSpace with the new subject and type fields, run all system updates, and reboot the server
Field migration went well:

$ ./migrate-fields.sh
UPDATE metadatavalue SET metadata_field_id=109 WHERE metadata_field_id=66
UPDATE 40909
UPDATE metadatavalue SET metadata_field_id=203 WHERE metadata_field_id=76
UPDATE 51419
UPDATE metadatavalue SET metadata_field_id=208 WHERE metadata_field_id=82
UPDATE 5986
UPDATE metadatavalue SET metadata_field_id=210 WHERE metadata_field_id=88
UPDATE 2458
UPDATE metadatavalue SET metadata_field_id=215 WHERE metadata_field_id=106
UPDATE 3872
UPDATE metadatavalue SET metadata_field_id=217 WHERE metadata_field_id=108
UPDATE 46075

Also, I migrated CGSpace to using the PGDG PostgreSQL repo as the infrastructure playbooks had been using it for a while and it seemed to be working well
Basically, this gives us the ability to use the latest upstream stable 9.3.x release (currently 9.3.12)
Looking into the REST API errors again, it looks like these started appearing a few days ago in the tens of thousands:

$ grep -c "Aborting context in finally statement" dspace.log.2016-04-20
21252

I found a recent discussion on the DSpace mailing list and I’ve asked for advice there
Looks like this issue was noted and fixed in DSpace 5.5 (we’re on 5.1): https://jira.duraspace.org/browse/DS-2936
I’ve sent a message to Atmire asking about compatibility with DSpace 5.5

2016-04-21

Fix a bunch of metadata consistency issues with IITA Journal Articles (Peer review, Formally published, messed up DOIs, etc)
Atmire responded with DSpace 5.5 compatible versions for their modules, so I’ll start testing those in a few weeks

2016-04-22

Import 95 records into CTA’s Agrodok collection

2016-04-26

Test embargo during item upload
Seems to be working but the help text is misleading as to the date format
It turns out the robots.txt issue we thought we solved last month isn’t solved because you can’t use wildcards in URL patterns: https://jira.duraspace.org/browse/DS-2962
Write some nginx rules to add X-Robots-Tag HTTP headers to the dynamic requests from robots.txt instead
A few URLs to test with:

2016-04-27

I woke up to ten or fifteen “up” and “down” emails from the monitoring website
Looks like the last one was “down” from about four hours ago
I think there must be something with this REST stuff:

# grep -c "Aborting context in finally statement" dspace.log.2016-04-*
dspace.log.2016-04-01:0
dspace.log.2016-04-02:0
dspace.log.2016-04-03:0
dspace.log.2016-04-04:0
dspace.log.2016-04-05:0
dspace.log.2016-04-06:0
dspace.log.2016-04-07:0
dspace.log.2016-04-08:0
dspace.log.2016-04-09:0
dspace.log.2016-04-10:0
dspace.log.2016-04-11:0
dspace.log.2016-04-12:235
dspace.log.2016-04-13:44
dspace.log.2016-04-14:0
dspace.log.2016-04-15:35
dspace.log.2016-04-16:0
dspace.log.2016-04-17:0
dspace.log.2016-04-18:11942
dspace.log.2016-04-19:28496
dspace.log.2016-04-20:28474
dspace.log.2016-04-21:28654
dspace.log.2016-04-22:28763
dspace.log.2016-04-23:28773
dspace.log.2016-04-24:28775
dspace.log.2016-04-25:28626
dspace.log.2016-04-26:28655
dspace.log.2016-04-27:7271

I restarted tomcat and it is back up
Add Spanish XMLUI strings so those users see “CGSpace” instead of “DSpace” in the user interface (#222)
Submit patch to upstream DSpace for the misleading help text in the embargo step of the item submission: https://jira.duraspace.org/browse/DS-3172
Update infrastructure playbooks for nginx 1.10.x (stable) release: https://github.com/ilri/rmg-ansible-public/issues/32
Currently running on DSpace Test, we’ll give it a few days before we adjust CGSpace
CGSpace down, restarted tomcat and it’s back up

2016-04-28

Problems with stability again. I’ve blocked access to /rest for now to see if the number of errors in the log files drop
Later we could maybe start logging access to /rest and perhaps whitelist some IPs…

2016-04-30

Logs for today and yesterday have zero references to this REST error, so I’m going to open back up the REST API but log all requests

location /rest {
	access_log /var/log/nginx/rest.log;
	proxy_pass http://127.0.0.1:8443;
}

I will check the logs again in a few days to look for patterns, see who is accessing it, etc

March, 2016

Wed, 02 Mar 2016 16:50:00 +0300

2016-03-02

Looking at issues with author authorities on CGSpace
For some reason we still have the index-lucene-update cron job active on CGSpace, but I’m pretty sure we don’t need it as of the latest few versions of Atmire’s Listings and Reports module
Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server

2016-03-07

Troubleshooting the issues with the slew of commits for Atmire modules in #182
Their changes on 5_x-dev branch work, but it is messy as hell with merge commits and old branch base
When I rebase their branch on the latest 5_x-prod I get blank white pages
I identified one commit that causes the issue and let them know
Restart DSpace Test, as it seems to have crashed after Sisay tried to import some CSV or zip or something:

Exception in thread "Lucene Merge Thread #19" org.apache.lucene.index.MergePolicy$MergeException: java.io.IOException: No space left on device

2016-03-08

Add a few new filters to Atmire’s Listings and Reports module (#180)
We had also wanted to add a few to the Content and Usage module but I have to ask the editors which ones they were

2016-03-10

Disable the lucene cron job on CGSpace as it shouldn’t be needed anymore
Discuss ORCiD and duplicate authors on Yammer
Request new documentation for Atmire CUA and L&R modules, as ours are from 2013
Walk Sisay through some data cleaning workflows in OpenRefine
Start cleaning up the configuration for Atmire’s CUA module (#184)
It is very messed up because some labels are incorrect, fields are missing, etc

Update documentation for Atmire modules

2016-03-11

As I was looking at the CUA config I realized our Discovery config is all messed up and confusing
I’ve opened an issue to track some of that work (#186)
I did some major cleanup work on Discovery and XMLUI stuff related to the dc.type indexes (#187)
We had been confusing dc.type (a Dublin Core value) with dc.type.output (a value we invented) for a few years and it had permeated all aspects of our data, indexes, item displays, etc.
There is still some more work to be done to remove references to old outputtype and output

2016-03-14

Fix some items that had invalid dates (I noticed them in the log during a re-indexing)
Reset search.index.* to the default, as it is only used by Lucene (deprecated by Discovery in DSpace 5.x): #188
Make titles in Discovery and Browse by more consistent (singular, sentence case, etc) (#186)
Also four or so center-specific subject strings were missing for Discovery

2016-03-15

Create simple theme for new AVCD community just for a unique Google Tracking ID (#191)

2016-03-16

Still having problems deploying Atmire’s CUA updates and fixes from January!
More discussion on the GitHub issue here: https://github.com/ilri/DSpace/pull/182
Clean up Atmire CUA config (#193)
Help Sisay with some PostgreSQL queries to clean up the incorrect dc.contributor.corporateauthor field
I noticed that we have some weird values in dc.language:

# select * from metadatavalue where metadata_field_id=37;
 metadata_value_id | resource_id | metadata_field_id | text_value | text_lang | place | authority | confidence | resource_type_id
-------------------+-------------+-------------------+------------+-----------+-------+-----------+------------+------------------
           1942571 |       35342 |                37 | hi         |           |     1 |           |         -1 |                2
           1942468 |       35345 |                37 | hi         |           |     1 |           |         -1 |                2
           1942479 |       35337 |                37 | hi         |           |     1 |           |         -1 |                2
           1942505 |       35336 |                37 | hi         |           |     1 |           |         -1 |                2
           1942519 |       35338 |                37 | hi         |           |     1 |           |         -1 |                2
           1942535 |       35340 |                37 | hi         |           |     1 |           |         -1 |                2
           1942555 |       35341 |                37 | hi         |           |     1 |           |         -1 |                2
           1942588 |       35343 |                37 | hi         |           |     1 |           |         -1 |                2
           1942610 |       35346 |                37 | hi         |           |     1 |           |         -1 |                2
           1942624 |       35347 |                37 | hi         |           |     1 |           |         -1 |                2
           1942639 |       35339 |                37 | hi         |           |     1 |           |         -1 |                2

It seems this dc.language field isn’t really used, but we should delete these values
Also, dc.language.iso has some weird values, like “En” and “English”

2016-03-17

It turns out hi is the ISO 639 language code for Hindi, but these should be in dc.language.iso instead of dc.language
I fixed the eleven items with hi as well as some using the incorrect vn for Vietnamese
Start discussing CG core with Abenet and Sisay
Re-sync CGSpace database to DSpace Test for Atmire to do some tests about the problematic CUA patches
The patches work fine with a clean database, so the error was caused by some mismatch in CUA versions and the database during my testing

2016-03-18

Merge Atmire fixes into 5_x-prod
Discuss thumbnails with Francesca from Bioversity
Some of their items end up with thumbnails that have a big white border around them:

Turns out we can add -trim to the GraphicsMagick options to trim the whitespace

Command used:

$ gm convert -trim -quality 82 -thumbnail x300 -flatten Descriptor\ for\ Butia_EN-2015_2021.pdf\[0\] cover.jpg

Also, it looks like adding -sharpen 0x1.0 really improves the quality of the image for only a few KB

2016-03-21

Fix 66 site errors in Google’s webmaster tools
I looked at a bunch of them and they were old URLs, weird things linked from non-existent items, etc, so I just marked them all as fixed
We also have 1,300 “soft 404” errors for URLs like: https://cgspace.cgiar.org/handle/10568/440/browse?type=bioversity
I’ve marked them as fixed as well since the ones I tested were working fine
This raises another question, as many of these pages are linked from Discovery search results and might create a duplicate content problem…
Results pages like this give items that Google already knows from the sitemap: https://cgspace.cgiar.org/discover?filtertype=author&filter_relational_operator=equals&filter=Orth%2C+A.
There are some access denied errors on JSPUI links (of course! we forbid them!), but I’m not sure why Google is trying to index them…
For example:
- This: https://cgspace.cgiar.org/jspui/bitstream/10568/809/1/main-page.pdf
- Linked from: https://cgspace.cgiar.org/jspui/handle/10568/809
I will mark these errors as resolved because they are returning HTTP 403 on purpose, for a long time!
Google says the first time it saw this particular error was September 29, 2015… so maybe it accidentally saw it somehow…
On a related note, we have 51,000 items indexed from the sitemap, but 500,000 items in the Google index, so we DEFINITELY have a problem with duplicate content

Turns out this is a problem with DSpace’s robots.txt, and there’s a Jira ticket since December, 2015: https://jira.duraspace.org/browse/DS-2962
I am not sure if I want to apply it yet
For now I’ve just set a bunch of these dynamic pages to not appear in search results by using the URL Parameters tool in Webmaster Tools

Move AVCD collection to new community and update move_collection.sh script: https://gist.github.com/alanorth/392c4660e8b022d99dfa
It seems Feedburner can do HTTPS now, so we might be able to update our feeds and simplify the nginx configs
De-deploy CGSpace with latest 5_x-prod branch
Run updates on CGSpace and reboot server (new kernel, 4.5.0)
Deploy Let’s Encrypt certificate for cgspace.cgiar.org, but still need to work it into the ansible playbooks

2016-03-22

Merge robots.txt patch and disallow indexing of browse pages as our sitemap is consumed correctly (#198)

2016-03-23

Abenet is having problems saving group memberships, and she gets this error: https://gist.github.com/alanorth/87281c061c2de57b773e

Can't find method org.dspace.app.xmlui.aspect.administrative.FlowGroupUtils.processSaveGroup(org.dspace.core.Context,number,string,[Ljava.lang.String;,[Ljava.lang.String;,org.apache.cocoon.environment.wrapper.RequestWrapper). (resource://aspects/Administrative/administrative.js#967)

I can reproduce the same error on DSpace Test and on my Mac
Looks to be an issue with the Atmire modules, I’ve submitted a ticket to their tracker.

2016-03-24

Atmire sent a patch for the group saving issue: https://github.com/ilri/DSpace/pull/201
I tested it locally and it works, so I merged it to 5_x-prod and will deploy on CGSpace this week

2016-03-25

Having problems with Listings and Reports, seems to be caused by a rogue reference to dc.type.output
This is the error we get when we proceed to the second page of Listings and Reports: https://gist.github.com/alanorth/b2d7fb5b82f94898caaf
Commenting out the line works, but I haven’t figured out the proper syntax for referring to dc.type.*

2016-03-28

Look into enabling the embargo during item submission, see: https://wiki.duraspace.org/display/DSDOC5x/Embargo#Embargo-SubmissionProcess
Seems we only want AccessStep because UploadWithEmbargoStep disables the ability to edit embargos at the item level
This pull request enables the ability to set an item-level embargo during submission: https://github.com/ilri/DSpace/pull/203
I figured out that the problem with Listings and Reports was because I disabled the search.index.* last week, and they are still used by JSPUI apparently
This pull request re-enables them: https://github.com/ilri/DSpace/pull/202
Re-deploy DSpace Test, run all system updates, and restart the server
Looks like the Listings and Reports fix was NOT due to the search indexes (which are actually not used), and rather due to the filter configuration in the Listings and Reports config
This pull request simply updates the config for the dc.type.output → dc.type change that was made last week: https://github.com/ilri/DSpace/pull/204
Deploy robots.txt fix, embargo for item submissions, and listings and reports fix on CGSpace

2016-03-29

Skype meeting with Peter and Addis team to discuss metadata changes for Dublin Core, CGcore, and CGSpace-specific fields
We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to cg.*, and then worry about broader changes to DC
Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields
After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects

February, 2016

Fri, 05 Feb 2016 13:18:00 +0300

2016-02-05

Looking at some DAGRIS data for Abenet Yabowork
Lots of issues with spaces, newlines, etc causing the import to fail
I noticed we have a very interesting list of countries on CGSpace:

Not only are there 49,000 countries, we have some blanks (25)…
Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”

2016-02-06

Found a way to get items with null/empty metadata values from SQL
First, find the metadata_field_id for the field you want from the metadatafieldregistry table:

dspacetest=# select * from metadatafieldregistry;

In this case our country field is 78
Now find all resources with type 2 (item) that have null/empty values for that field:

dspacetest=# select resource_id from metadatavalue where resource_type_id=2 and metadata_field_id=78 and (text_value='' OR text_value IS NULL);

Then you can find the handle that owns it from its resource_id:

dspacetest=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id = '22678';

It’s 25 items so editing in the web UI is annoying, let’s try SQL!

dspacetest=# delete from metadatavalue where metadata_field_id=78 and text_value='';
DELETE 25

After that perhaps a regular dspace index-discovery (no -b) should suffice…
Hmm, I indexed, cleared the Cocoon cache, and restarted Tomcat but the 25 “|||” countries are still there
Maybe I need to do a full re-index…
Yep! The full re-index seems to work.
Process the empty countries on CGSpace

2016-02-07

Working on cleaning up Abenet’s DAGRIS data with OpenRefine
I discovered two really nice functions in OpenRefine: value.trim() and value.escape("javascript") which shows whitespace characters like \r\n!
For some reason when you import an Excel file into OpenRefine it exports dates like 1949 to 1949.0 in the CSV
I re-import the resulting CSV and run a GREL on the date issued column: value.replace("\.0", "")
I need to start running DSpace in Mac OS X instead of a Linux VM
Install PostgreSQL from homebrew, then configure and import CGSpace database dump:

$ postgres -D /opt/brew/var/postgres
$ createuser --superuser postgres
$ createuser --pwprompt dspacetest
$ createdb -O dspacetest --encoding=UNICODE dspacetest
$ psql postgres
postgres=# alter user dspacetest createuser;
postgres=# \q
$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-02-07.backup 
$ psql postgres
postgres=# alter user dspacetest nocreateuser;
postgres=# \q
$ vacuumdb dspacetest
$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost

After building and running a fresh_install I symlinked the webapps into Tomcat’s webapps folder:

$ mv /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT.orig
$ ln -sfv ~/dspace/webapps/xmlui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/ROOT
$ ln -sfv ~/dspace/webapps/rest /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/rest
$ ln -sfv ~/dspace/webapps/jspui /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/jspui
$ ln -sfv ~/dspace/webapps/oai /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/oai
$ ln -sfv ~/dspace/webapps/solr /opt/brew/Cellar/tomcat/8.0.30/libexec/webapps/solr
$ /opt/brew/Cellar/tomcat/8.0.30/bin/catalina start

Add CATALINA_OPTS in /opt/brew/Cellar/tomcat/8.0.30/libexec/bin/setenv.sh, as this script is sourced by the catalina startup script
For example:

CATALINA_OPTS="-Djava.awt.headless=true -Xms2048m -Xmx2048m -XX:MaxPermSize=256m -XX:+UseConcMarkSweepGC -Dfile.encoding=UTF-8"

After verifying that the site is working, start a full index:

$ ~/dspace/bin/dspace index-discovery -b

2016-02-08

Finish cleaning up and importing ~400 DAGRIS items into CGSpace
Whip up some quick CSS to make the button in the submission workflow use the XMLUI theme’s brand colors (#154)

2016-02-09

Re-sync DSpace Test with CGSpace
Help Sisay with OpenRefine
Enable HTTPS on DSpace Test using Let’s Encrypt:

$ cd ~/src/git
$ git clone https://github.com/letsencrypt/letsencrypt
$ cd letsencrypt
$ sudo service nginx stop
# add port 443 to firewall rules
$ ./letsencrypt-auto certonly --standalone -d dspacetest.cgiar.org
$ sudo service nginx start
$ ansible-playbook dspace.yml -l linode02 -t nginx,firewall -u aorth --ask-become-pass

We should install it in /opt/letsencrypt and then script the renewal script, but first we have to wire up some variables and template stuff based on the script here: https://letsencrypt.org/howitworks/
I had to export some CIAT items that were being cleaned up on the test server and I noticed their dc.contributor.author fields have DSpace 5 authority index UUIDs…
To clean those up in OpenRefine I used this GREL expression: value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")
Getting more and more hangs on DSpace Test, seemingly random but also during CSV import
Logs don’t always show anything right when it fails, but eventually one of these appears:

org.dspace.discovery.SearchServiceException: Error while processing facet fields: java.lang.OutOfMemoryError: Java heap space

Caused by: java.util.NoSuchElementException: Timeout waiting for idle object

Right now DSpace Test’s Tomcat heap is set to 1536m and we have quite a bit of free RAM:

# free -m
             total       used       free     shared    buffers     cached
Mem:          3950       3902         48          9         37       1311
-/+ buffers/cache:       2552       1397
Swap:          255         57        198

So I’ll bump up the Tomcat heap to 2048 (CGSpace production server is using 3GB)

2016-02-11

Massaging some CIAT data in OpenRefine
There are 1200 records that have PDFs, and will need to be imported into CGSpace
I created a filename column based on the dc.identifier.url column using the following transform:

value.split('/')[-1]

Then I wrote a tool called generate-thumbnails.py to download the PDFs and generate thumbnails for them, for example:

$ ./generate-thumbnails.py ciat-reports.csv
Processing 64661.pdf
> Downloading 64661.pdf
> Creating thumbnail for 64661.pdf
Processing 64195.pdf
> Downloading 64195.pdf
> Creating thumbnail for 64195.pdf

2016-02-12

Looking at CIAT’s records again, there are some problems with a dozen or so files (out of 1200)
A few items are using the same exact PDF
A few items are using HTM or DOC files
A few items link to PDFs on IFPRI’s e-Library or Research Gate
A few items have no item
Also, I’m not sure if we import these items, will be remove the dc.identifier.url field from the records?

2016-02-12

Looking at CIAT’s records again, there are some files linking to PDFs on Slide Share, Embrapa, UEA UK, and Condesan, so I’m not sure if we can use those
265 items have dirty, URL-encoded filenames:

$ ls | grep -c -E "%"
265

I suggest that we import ~850 or so of the clean ones first, then do the rest after I can find a clean/reliable way to decode the filenames
This python2 snippet seems to work in the CLI, but not so well in OpenRefine:

$ python -c "import urllib, sys; print urllib.unquote(sys.argv[1])" CIAT_COLOMBIA_000169_T%C3%A9cnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf
CIAT_COLOMBIA_000169_Técnicas_para_el_aislamiento_y_cultivo_de_protoplastos_de_yuca.pdf

Merge pull requests for submission form theming (#178) and missing center subjects in XMLUI item views (#176)
They will be deployed on CGSpace the next time I re-deploy

2016-02-16

Turns out OpenRefine has an unescape function!

value.unescape("url")

This turns the URLs into human-readable versions that we can use as proper filenames
Run web server and system updates on DSpace Test and reboot
To merge dc.identifier.url and dc.identifier.url[], rename the second column so it doesn’t have the brackets, like dc.identifier.url2
Then you create a facet for blank values on each column, show the rows that have values for one and not the other, then transform each independently to have the contents of the other, with “||” in between
Work on Python script for parsing and downloading PDF records from dc.identifier.url
To get filenames from dc.identifier.url, create a new column based on this transform: forEach(value.split('||'), v, v.split('/')[-1]).join('||')
This also works for records that have multiple URLs (separated by “||”)

2016-02-17

Re-deploy CGSpace, run all system updates, and reboot
More work on CIAT data, cleaning and doing a last metadata-only import into DSpace Test
SAFBuilder has a bug preventing it from processing filenames containing more than one underscore
Need to re-process the filename column to replace multiple underscores with one: value.replace(/_{2,}/, "_")

2016-02-20

Turns out the “bug” in SAFBuilder isn’t a bug, it’s a feature that allows you to encode extra information like the destintion bundle in the filename
Also, it seems DSpace’s SAF import tool doesn’t like importing filenames that have accents in them:

java.io.FileNotFoundException: /usr/share/tomcat7/SimpleArchiveFormat/item_1021/CIAT_COLOMBIA_000075_Medición_de_palatabilidad_en_forrajes.pdf (No such file or directory)

Need to rename files to have no accents or umlauts, etc…
Useful custom text facet for URLs ending with “.pdf”: value.endsWith(".pdf")

2016-02-22

To change Spanish accents to ASCII in OpenRefine:

value.replace('ó','o').replace('í','i').replace('á','a').replace('é','e').replace('ñ','n')

But actually, the accents might not be an issue, as I can successfully import files containing Spanish accents on my Mac
On closer inspection, I can import files with the following names on Linux (DSpace Test):

Bitstream: tést.pdf
Bitstream: tést señora.pdf
Bitstream: tést señora alimentación.pdf

Seems it could be something with the HFS+ filesystem actually, as it’s not UTF-8 (it’s something like UCS-2)
HFS+ stores filenames as a string, and filenames with accents get stored as character+accent whereas Linux’s ext4 stores them as an array of bytes
Running the SAFBuilder on Mac OS X works if you’re going to import the resulting bundle on Mac OS X, but if your DSpace is running on Linux you need to run the SAFBuilder there where the filesystem’s encoding matches

2016-02-29

Got notified by some CIFOR colleagues that the Google Scholar team had contacted them about CGSpace’s incorrect ordering of authors in Google Scholar metadata
Turns out there is a patch, and it was merged in DSpace 5.4: https://jira.duraspace.org/browse/DS-2679
I’ve merged it into our 5_x-prod branch that is currently based on DSpace 5.1
We found a bug when a user searches from the homepage, sorts the results, and then tries to click “View More” in a sidebar facet
I am not sure what causes it yet, but I opened an issue for it: https://github.com/ilri/DSpace/issues/179
Have more problems with SAFBuilder on Mac OS X
Now it doesn’t recognize description hints in the filename column, like: test.pdf__description:Blah
But on Linux it works fine
Trying to test Atmire’s series of stats and CUA fixes from January and February, but their branch history is really messy and it’s hard to see what’s going on
Rebasing their branch on top of our production branch results in a broken Tomcat, so I’m going to tell them to fix their history and make a proper pull request
Looking at the filenames for the CIAT Reports, some have some really ugly characters, like: ' or , or = or [ or ] or ( or ) or _.pdf or ._ etc
It’s tricky to parse those things in some programming languages so I’d rather just get rid of the weird stuff now in OpenRefine:

value.replace("'",'').replace('_=_','_').replace(',','').replace('[','').replace(']','').replace('(','').replace(')','').replace('_.pdf','.pdf').replace('._','_')

Finally import the 1127 CIAT items into CGSpace: https://cgspace.cgiar.org/handle/10568/35710
Re-deploy CGSpace with the Google Scholar fix, but I’m waiting on the Atmire fixes for now, as the branch history is ugly

January, 2016

Wed, 13 Jan 2016 13:18:00 +0300

2016-01-13

Move ILRI collection 10568/12503 from 10568/27869 to 10568/27629 using the move_collections.sh script I wrote last year.
I realized it is only necessary to clear the Cocoon cache after moving collections—rather than reindexing—as no metadata has changed, and therefore no search or browse indexes need to be updated.
Update GitHub wiki for documentation of maintenance tasks.

2016-01-14

Update CCAFS project identifiers in input-forms.xml
Run system updates and restart the server

2016-01-18

Change “Extension material” to “Extension Material” in input-forms.xml (a mistake that fell through the cracks when we fixed the others in DSpace 4 era)

2016-01-19

Work on tweaks and updates for the social sharing icons on item pages: add Delicious and Mendeley (from Academicons), make links open in new windows, and set the icon color to the theme’s primary color (#157)
Tweak date-based facets to show more values in drill-down ranges (#162)
Need to remember to clear the Cocoon cache after deployment or else you don’t see the new ranges immediately
Set up recipe on IFTTT to tweet new items from the CGSpace Atom feed to my twitter account
Altmetrics’ support for Handles is kinda weak, so they can’t associate our items with DOIs until they are tweeted or blogged, etc first.

2016-01-21

Still waiting for my IFTTT recipe to fire, two days later
It looks like the Atom feed on CGSpace hasn’t changed in two days, but there have definitely been new items
The RSS feed is nearly as old, but has different old items there
On a hunch I cleared the Cocoon cache and now the feeds are fresh
Looks like there is configuration option related to this, webui.feed.cache.age, which defaults to 48 hours, though I’m not sure what relation it has to the Cocoon cache
In any case, we should change this cache to be something more like 6 hours, as we publish new items several times per day.
Work around a CSS issue with long URLs in the item view (#172)

2016-01-25

Re-deploy CGSpace and DSpace Test with latest 5_x-prod branch
This included the social icon fixes/updates, date-based facet tweaks, reducing the feed cache age, and fixing a layout issue in XMLUI item view when an item had long URLs

2016-01-26

Run nginx updates on CGSpace and DSpace Test (1.8.1 and 1.9.10, respectively)
Run updates on DSpace Test and reboot for new Linode kernel Linux 4.4.0-x86_64-linode63 (first update in months)

2016-01-28

Start looking at importing some Bioversity data that had been prepared earlier this week
While checking the data I noticed something strange, there are 79 items but only 8 unique PDFs:

$ ls SimpleArchiveForBio/ | wc -l 79 $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {} \; | sort -u | wc -l 8

2016-01-29

Add five missing center-specific subjects to XMLUI item view (#174)
This CCAFS item Before:

After:

December, 2015

Wed, 02 Dec 2015 13:18:00 +0300

2015-12-02

Replace lzop with xz in log compression cron jobs on DSpace Test—it uses less space:

# cd /home/dspacetest.cgiar.org/log
# ls -lh dspace.log.2015-11-18*
-rw-rw-r-- 1 tomcat7 tomcat7 2.0M Nov 18 23:59 dspace.log.2015-11-18
-rw-rw-r-- 1 tomcat7 tomcat7 387K Nov 18 23:59 dspace.log.2015-11-18.lzo
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz

I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper
Need to remember to go check if everything is ok in a few days and then change CGSpace
CGSpace went down again (due to PostgreSQL idle connections of course)
Current database settings for DSpace are db.maxconnections = 30 and db.maxidle = 8, yet idle connections are exceeding this:

$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
39

I restarted PostgreSQL and Tomcat and it’s back
On a related note of why CGSpace is so slow, I decided to finally try the pgtune script to tune the postgres settings:

# apt-get install pgtune
# pgtune -i /etc/postgresql/9.3/main/postgresql.conf -o postgresql.conf-pgtune
# mv /etc/postgresql/9.3/main/postgresql.conf /etc/postgresql/9.3/main/postgresql.conf.orig 
# mv postgresql.conf-pgtune /etc/postgresql/9.3/main/postgresql.conf

It introduced the following new settings:

default_statistics_target = 50
maintenance_work_mem = 480MB
constraint_exclusion = on
checkpoint_completion_target = 0.9
effective_cache_size = 5632MB
work_mem = 48MB
wal_buffers = 8MB
checkpoint_segments = 16
shared_buffers = 1920MB
max_connections = 80

Now I need to go read PostgreSQL docs about these options, and watch memory settings in munin etc
For what it’s worth, now the REST API should be faster (because of these PostgreSQL tweaks):

$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.474
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
2.141
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.685
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.995
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.786

Last week it was an average of 8 seconds… now this is ¹⁄₄ of that
CCAFS noticed that one of their items displays only the Atmire statlets: https://cgspace.cgiar.org/handle/10568/42445

The authorizations for the item are all public READ, and I don’t see any errors in dspace.log when browsing that item
I filed a ticket on Atmire’s issue tracker
I also filed a ticket on Atmire’s issue tracker for the PostgreSQL stuff

2015-12-03

CGSpace very slow, and monitoring emailing me to say its down, even though I can load the page (very slowly)
Idle postgres connections look like this (with no change in DSpace db settings lately):

$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
29

I restarted Tomcat and postgres…
Atmire commented that we should raise the JVM heap size by ~500M, so it is now -Xms3584m -Xmx3584m
We weren’t out of heap yet, but it’s probably fair enough that the DSpace 5 upgrade (and new Atmire modules) requires more memory so it’s ok
A possible side effect is that I see that the REST API is twice as fast for the request above now:

$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.368
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.968
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
1.006
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.849
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.806
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.854

2015-12-05

CGSpace has been up and down all day and REST API is completely unresponsive
PostgreSQL idle connections are currently:

postgres@linode01:~$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
28

I have reverted all the pgtune tweaks from the other day, as they didn’t fix the stability issues, so I’d rather not have them introducing more variables into the equation
The PostgreSQL stats from Munin all point to something database-related with the DSpace 5 upgrade around mid–late November

2015-12-07

Atmire sent some fixes to DSpace’s REST API code that was leaving contexts open (causing the slow performance and database issues)
After deploying the fix to CGSpace the REST API is consistently faster:

$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.675
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.599
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.588
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.566
$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
0.497

2015-12-08

Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn’t as good, but it’s much faster and causes less IO/CPU load
Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot’s crawl rate to the “Let Google optimize” setting

November, 2015

Mon, 23 Nov 2015 17:00:57 +0300

2015-11-22

CGSpace went down
Looks like DSpace exhausted its PostgreSQL connection pool
Last week I had increased the limit from 30 to 60, which seemed to help, but now there are many more idle connections:

$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
78

For now I have increased the limit from 60 to 90, run updates, and rebooted the server

2015-11-24

CGSpace went down again
Getting emails from uptimeRobot and uptimeButler that it’s down, and Google Webmaster Tools is sending emails that there is an increase in crawl errors
Looks like there are still a bunch of idle PostgreSQL connections:

$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
96

For some reason the number of idle connections is very high since we upgraded to DSpace 5

2015-11-25

Troubleshoot the DSpace 5 OAI breakage caused by nginx routing config
The OAI application requests stylesheets and javascript files with the path /oai/static/css, which gets matched here:

# static assets we can load from the file system directly with nginx
location ~ /(themes|static|aspects/ReportingSuite) {
    try_files $uri @tomcat;
...

The document root is relative to the xmlui app, so this gets a 404—I’m not sure why it doesn’t pass to @tomcat
Anyways, I can’t find any URIs with path /static, and the more important point is to handle all the static theme assets, so we can just remove static from the regex for now (who cares if we can’t use nginx to send Etags for OAI CSS!)
Also, I noticed we aren’t setting CSP headers on the static assets, because in nginx headers are inherited in child blocks, but if you use add_header in a child block it doesn’t inherit the others
We simply need to add include extra-security.conf; to the above location block (but research and test first)
We should add WOFF assets to the list of things to set expires for:

location ~* \.(?:ico|css|js|gif|jpe?g|png|woff)$ {

We should also add aspects/Statistics to the location block for static assets (minus static from above):

location ~ /(themes|aspects/ReportingSuite|aspects/Statistics) {

Need to check /about on CGSpace, as it’s blank on my local test server and we might need to add something there
CGSpace has been up and down all day due to PostgreSQL idle connections (current DSpace pool is 90):

$ psql -c 'SELECT * from pg_stat_activity;' | grep idle | grep -c cgspace
93

I looked closer at the idle connections and saw that many have been idle for hours (current time on server is 2015-11-25T20:20:42+0000):

$ psql -c 'SELECT * from pg_stat_activity;' | less -S
datid | datname  |  pid  | usesysid | usename  | application_name | client_addr | client_hostname | client_port |         backend_start         |          xact_start           |
-------+----------+-------+----------+----------+------------------+-------------+-----------------+-------------+-------------------------------+-------------------------------+---
20951 | cgspace  | 10966 |    18205 | cgspace  |                  | 127.0.0.1   |                 |       37731 | 2015-11-25 13:13:02.837624+00 |                               | 20
20951 | cgspace  | 10967 |    18205 | cgspace  |                  | 127.0.0.1   |                 |       37737 | 2015-11-25 13:13:03.069421+00 |                               | 20
...

There is a relevant Jira issue about this: https://jira.duraspace.org/browse/DS-1458
It seems there is some sense changing DSpace’s default db.maxidle from unlimited (-1) to something like 8 (Tomcat default) or 10 (Confluence default)
Change db.maxidle from -1 to 10, reduce db.maxconnections from 90 to 50, and restart postgres and tomcat7
Also redeploy DSpace Test with a clean sync of CGSpace and mirror these database settings there as well
Also deploy the nginx fixes for the try_files location block as well as the expires block

2015-11-26

CGSpace behaving much better since changing db.maxidle yesterday, but still two up/down notices from monitoring this morning (better than 50!)
CCAFS colleagues mentioned that the REST API is very slow, 24 seconds for one item
Not as bad for me, but still unsustainable if you have to get many:

$ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle/10568/32802?expand=all
8.415

Monitoring e-mailed in the evening to say CGSpace was down
Idle connections in PostgreSQL again:

$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
66

At the time, the current DSpace pool size was 50…
I reduced the pool back to the default of 30, and reduced the db.maxidle settings from 10 to 8

2015-11-29

Still more alerts that CGSpace has been up and down all day
Current database settings for DSpace:

db.maxconnections = 30
db.maxwait = 5000
db.maxidle = 8
db.statementpool = true

And idle connections:

$ psql -c 'SELECT * from pg_stat_activity;' | grep cgspace | grep -c idle
49

Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace’s thirst can ever be quenched
On another note, SUNScholar’s notes suggest adjusting some other postgres variables: http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database
This might help with REST API speed (which I mentioned above and still need to do real tests)