--- title: "March, 2018" date: 2018-03-02T16:07:54+02:00 author: "Alan Orth" categories: ["Notes"] --- ## 2018-03-02 - Export a CSV of the IITA community metadata for Martin Mueller ## 2018-03-06 - Add three new CCAFS project tags to `input-forms.xml` ([#357](https://github.com/ilri/DSpace/pull/357)) - Andrea from Macaroni Bros had sent me an email that CCAFS needs them - Give Udana more feedback on his WLE records from last month - There were some records using a non-breaking space in their AGROVOC subject field - I checked and tested some author corrections from Peter from last week, and then applied them on CGSpace ``` $ ./fix-metadata-values.py -i Correct-309-authors-2018-03-06.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 $ ./delete-metadata-values.py -i Delete-3-Authors-2018-03-06.csv -db dspace -u dspace-p 'fuuu' -f dc.contributor.author -m 3 ``` - This time there were no errors in whitespace but I did have to correct one incorrectly encoded accent character - Add new CRP subject "GRAIN LEGUMES AND DRYLAND CEREALS" to `input-forms.xml` ([#358](https://github.com/ilri/DSpace/pull/358)) - Merge the ORCID integration stuff in to `5_x-prod` for deployment on CGSpace soon ([#359](https://github.com/ilri/DSpace/pull/359)) - Deploy ORCID changes on CGSpace (linode18), run all system updates, and reboot the server - Run all system updates on DSpace Test and reboot server - I ran the [orcid-authority-to-item.py](https://gist.github.com/alanorth/24d8081a5dc25e2a4e27e548e7e2389c) script on CGSpace and mapped 2,864 ORCID identifiers from Solr to item metadata ``` $ ./orcid-authority-to-item.py -db dspace -u dspace -p 'fuuu' -s http://localhost:8081/solr -d ``` - I ran the DSpace cleanup script on CGSpace and it threw an error (as always): ``` Error: ERROR: update or delete on table "bitstream" violates foreign key constraint "bundle_primary_bitstream_id_fkey" on table "bundle" Detail: Key (bitstream_id)=(150659) is still referenced from table "bundle". ``` - The solution is, as always: ``` $ psql dspace -c 'update bundle set primary_bitstream_id=NULL where primary_bitstream_id in (150659);' UPDATE 1 ``` - Apply the proposed PostgreSQL indexes from DS-3636 (pull request [#1791](https://github.com/DSpace/DSpace/pull/1791/) on CGSpace (linode18) ## 2018-03-07 - Add CIAT author Mauricio Efren Sotelo Cabrera to controlled vocabulary for ORCID identifiers ([#360](https://github.com/ilri/DSpace/pull/360)) - Help Sisay proof 200 IITA records on DSpace Test - Finally import Udana's 24 items to [IWMI Journal Articles](https://cgspace.cgiar.org/handle/10568/36185) on CGSpace - Skype with James Stapleton to discuss CGSpace, ILRI website, CKM staff issues, etc ## 2018-03-08 - Looking at a CSV dump of the CIAT community I see there are tons of stupid text languages people add for their metadata - This makes the CSV have tons of columns, for example `dc.title`, `dc.title[]`, `dc.title[en]`, `dc.title[eng]`, `dc.title[en_US]` and so on! - I think I can fix — or at least normalize — them in the database: ``` dspace=# select distinct text_lang from metadatavalue where resource_type_id=2; text_lang ----------- ethnob en spa EN En en_ en_US E. EN_US en_U eng fr es_ES es (16 rows) dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and text_lang in ('en','EN','En','en_','EN_US','en_U','eng'); UPDATE 122227 dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2; text_lang ----------- ethnob en_US spa E. fr es_ES es (9 rows) ``` - On second inspection it looks like `dc.description.provenance` fields use the text_lang "en" so that's probably why there are over 100,000 fields changed... - If I skip that, there are about 2,000, which seems more reasonably like the amount of fields users have edited manually, or fucked up during CSV import, etc: ``` dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and text_lang in ('EN','En','en_','EN_US','en_U','eng'); UPDATE 2309 ``` - I will apply this on CGSpace right now - In other news, I was playing with adding ORCID identifiers to a dump of CIAT's community via CSV in OpenRefine - Using a series of filters, flags, and GREL expressions to isolate items for a certain author, I figured out how to add ORCID identifiers to the `cg.creator.id` field - For example, a GREL expression in a custom text facet to get all items with `dc.contributor.author[en_US]` of a certain author with several name variations (this is how you use a logical OR in OpenRefine): ``` or(value.contains('Ceballos, Hern'), value.contains('Hernández Ceballos')) ``` - Then you can flag or star matching items and then use a conditional to either set the value directly or add it to an existing value: ``` if(isBlank(value), "Hernan Ceballos: 0000-0002-8744-7918", value + "||Hernan Ceballos: 0000-0002-8744-7918") ``` - One thing that bothers me is that this won't honor author order - It might be better to do batches of these in PostgreSQL with a script that takes the `place` column of an author into account when setting the `cg.creator.id` - I wrote a Python script to read the author names and ORCID identifiers from CSV and create matching `cg.creator.id` fields: [add-orcid-identifiers-csv.py ](https://gist.github.com/alanorth/a49d85cd9c5dea89cddbe809813a7050) - The CSV should have two columns: author name and ORCID identifier: ``` dc.contributor.author,cg.creator.id "Orth, Alan",Alan S. Orth: 0000-0002-1735-7458 "Orth, A.",Alan S. Orth: 0000-0002-1735-7458 ``` - I didn't integrate the ORCID API lookup for author names in this script for now because I was only interested in "tagging" old items for a few given authors - I added ORCID identifers for 187 items by CIAT's Hernan Ceballos, because that is what Elizabeth was trying to do manually! - Also, I decided to add ORCID identifiers for all records from Peter, Abenet, and Sisay as well ## 2018-03-09 - Give James Stapleton input on Sisay's KRAs - Create a pull request to disable ORCID authority integration for `dc.contributor.author` in the submission forms and XMLUI display ([#363](https://github.com/ilri/DSpace/pull/363)) ## 2018-03-11 - Peter also wrote to say he is having issues with the Atmire Listings and Reports module - When I logged in to try it I get a blank white page after continuing and I see this in dspace.log.2018-03-11: ``` 2018-03-11 11:38:15,592 WARN org.dspace.app.webui.servlet.InternalErrorServlet @ :session_id=91C2C0C59669B33A7683570F6010603A:internal_error:-- URL Was: https://cgspace.cgiar.or g/jspui/listings-and-reports -- Method: POST -- Parameters were: -- selected_admin_preset: "ilri authors2" -- load: "normal" -- next: "NEXT STEP >>" -- step: "1" org.apache.jasper.JasperException: java.lang.NullPointerException ``` - Looks like I needed to remove the Humidtropics subject from Listings and Reports because it was looking for the terms and couldn't find them - I made a quick fix and it's working now ([#364](https://github.com/ilri/DSpace/pull/364)) ## 2018-03-12 - Increase upload size on CGSpace's nginx config to 85MB so Sisay can upload some data ## 2018-03-13 - I created a new Linode server for DSpace Test (linode6623840) so I could try the block storage stuff, but when I went to add a 300GB volume it said that block storage capacity was exceeded in that datacenter (Newark, NJ) - I deleted the Linode and created another one (linode6624164) in the Fremont, CA region - After that I deployed the Ubuntu 16.04 image and attached a 300GB block storage volume to the image - Magdalena wrote to ask why there was no Altmetric donut for an item on CGSpace, but there was one on the related CCAFS publication page - It looks the the CCAFS publications page fetches the donut using its DOI, whereas CGSpace queries via Handle - I will write to Altmetric support and ask them, as perhaps its part of a larger issue - CGSpace item: https://cgspace.cgiar.org/handle/10568/89643 - CCAFS publication page: https://ccafs.cgiar.org/publications/can-scenario-planning-catalyse-transformational-change-evaluating-climate-change-policy - Peter tweeted the Handle link and now Altmetric shows the donut for both the DOI and the Handle ## 2018-03-14 - Help Abenet with a troublesome Listings and Report question for CIAT author Steve Beebe - Continue migrating DSpace Test to the new server (linode6624164) - I emailed ILRI service desk to update the DNS records for dspacetest.cgiar.org - Abenet was having problems saving Listings and Reports configurations or layouts but I tested it and it works ## 2018-03-15 - Help Abenet troubleshoot the Listings and Reports issue again - It looks like it's an issue with the layouts, if you create a new layout that only has one type (`dc.identifier.citation`): ![Listing and Reports layout](/cgspace-notes/2018/03/layout-only-citation.png) - The error in the DSpace log is: ``` org.apache.jasper.JasperException: java.lang.ArrayIndexOutOfBoundsException: -1 ``` - The full error is here: https://gist.github.com/alanorth/ea47c092725960e39610db9b0c13f6ca - If I do a report for "Orth, Alan" with the same custom layout it works! - I submitted a ticket to Atmire: https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589 - Small fix to the example citation text in Listings and Reports ([#365](https://github.com/ilri/DSpace/pull/365)) ## 2018-03-16 - ICT made the DNS updates for dspacetest.cgiar.org late last night - I have removed the old server (linode02 aka linode578611) in favor of linode19 aka linode6624164 - Looking at the CRP subjects on CGSpace I see there is one blank one so I'll just fix it: ``` dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=230 and text_value=''; ``` - Copy all CRP subjects to a CSV to do the mass updates: ``` dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=230 group by text_value order by count desc) to /tmp/crps.csv with csv header; COPY 21 ``` - Once I prepare the new input forms ([#362](https://github.com/ilri/DSpace/issues/362)) I will need to do the batch corrections: ``` $ ./fix-metadata-values.py -i Correct-21-CRPs-2018-03-16.csv -db dspace -u dspace -p 'fuuu' -f cg.contributor.crp -t correct -m 230 -n -d ``` - Create a pull request to update the input forms for the new CRP subject style ([#366](https://github.com/ilri/DSpace/pull/366)) ## 2018-03-19 - Tezira has been having problems accessing CGSpace from the ILRI Nairobi campus since last week - She is getting an HTTPS error apparently - It's working outside, and Ethiopian users seem to be having no issues so I've asked ICT to have a look - CGSpace crashed this morning for about seven minutes and Dani restarted Tomcat - Around that time there were an increase of SQL errors: ``` 2018-03-19 09:10:54,856 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error - ... 2018-03-19 09:10:54,862 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL query singleTable Error - ``` - But these errors, I don't even know what they mean, because a handful of them happen every day: ``` $ grep -c 'ERROR org.dspace.storage.rdbms.DatabaseManager' dspace.log.2018-03-1* dspace.log.2018-03-10:13 dspace.log.2018-03-11:15 dspace.log.2018-03-12:13 dspace.log.2018-03-13:13 dspace.log.2018-03-14:14 dspace.log.2018-03-15:13 dspace.log.2018-03-16:13 dspace.log.2018-03-17:13 dspace.log.2018-03-18:15 dspace.log.2018-03-19:90 ``` - There wasn't even a lot of traffic at the time (8–9 AM): ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "19/Mar/2018:0[89]:" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 92 40.77.167.197 92 83.103.94.48 96 40.77.167.175 116 207.46.13.178 122 66.249.66.153 140 95.108.181.88 196 213.55.99.121 206 197.210.168.174 207 104.196.152.243 294 54.198.169.202 ``` - Well there is a hint in Tomcat's `catalina.out`: ``` Mon Mar 19 09:05:28 UTC 2018 | Query:id: 92032 AND type:2 Exception in thread "http-bio-127.0.0.1-8081-exec-280" java.lang.OutOfMemoryError: Java heap space ``` - So someone was doing something heavy somehow... my guess is content and usage stats! - ICT responded that they "fixed" the CGSpace connectivity issue in Nairobi without telling me the problem - When I asked, Robert Okal said CGNET messed up when updating the DNS for cgspace.cgiar.org last week - I told him that my request last week was for dspacetest.cgiar.org, not cgspace.cgiar.org! - So they updated the wrong fucking DNS records - Magdalena from CCAFS wrote to ask about one record that has a bunch of metadata missing in her Listings and Reports export - It appears to be this one: https://cgspace.cgiar.org/handle/10568/83473?show=full - The title is "Untitled" and there is some metadata but indeed the citation is missing - I don't know what would cause that ## 2018-03-20 - DSpace Test has been down for a few hours with SQL and memory errors starting this morning: ``` 2018-03-20 08:47:10,177 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error - ... 2018-03-20 08:53:11,624 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request! org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space ``` - I have no idea why it crashed - I ran all system updates and rebooted it - Abenet told me that one of Lance Robinson's ORCID iDs on CGSpace is incorrect - I will remove it from the controlled vocabulary ([#367](https://github.com/ilri/DSpace/pull/367)) and update any items using the old one: ``` dspace=# update metadatavalue set text_value='Lance W. Robinson: 0000-0002-5224-8644' where resource_type_id=2 and metadata_field_id=240 and text_value like '%0000-0002-6344-195X%'; UPDATE 1 ``` - Communicate with DSpace editors on Yammer about being more careful about spaces and character editing when doing manual metadata edits - Merge the changes to CRP names to the `5_x-prod` branch and deploy on CGSpace ([#363](https://github.com/ilri/DSpace/pull/363)) - Run corrections for CRP names in the database: ``` $ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db dspace -u dspace -p 'fuuu' ``` - Run all system updates on CGSpace (linode18) and reboot the server - I started a full Discovery re-index on CGSpace because of the updated CRPs - I see this error in the DSpace log: ``` 2018-03-20 19:03:14,844 ERROR com.atmire.dspace.discovery.AtmireSolrService @ No choices plugin was configured for field "dc_contributor_author". java.lang.IllegalArgumentException: No choices plugin was configured for field "dc_contributor_author". at org.dspace.content.authority.ChoiceAuthorityManager.getLabel(ChoiceAuthorityManager.java:261) at org.dspace.content.authority.ChoiceAuthorityManager.getLabel(ChoiceAuthorityManager.java:249) at org.dspace.browse.SolrBrowseCreateDAO.additionalIndex(SolrBrowseCreateDAO.java:215) at com.atmire.dspace.discovery.AtmireSolrService.buildDocument(AtmireSolrService.java:662) at com.atmire.dspace.discovery.AtmireSolrService.indexContent(AtmireSolrService.java:807) at com.atmire.dspace.discovery.AtmireSolrService.updateIndex(AtmireSolrService.java:876) at org.dspace.discovery.SolrServiceImpl.createIndex(SolrServiceImpl.java:370) at org.dspace.discovery.IndexClient.main(IndexClient.java:117) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.dspace.app.launcher.ScriptLauncher.runOneCommand(ScriptLauncher.java:226) at org.dspace.app.launcher.ScriptLauncher.main(ScriptLauncher.java:78) ``` - I have to figure that one out... ## 2018-03-21 - Looks like the indexing gets confused that there is still data in the `authority` column - Unfortunately this causes those items to simply not be indexed, which users noticed because item counts were cut in half and old items showed up in RSS! - Since we've migrated the ORCID identifiers associated with the authority data to the `cg.creator.id` field we can nullify the authorities remaining in the database: ```sql dspace=# UPDATE metadatavalue SET authority=NULL WHERE resource_type_id=2 AND metadata_field_id=3 AND authority IS NOT NULL; UPDATE 195463 ``` - After this the indexing works as usual and item counts and facets are back to normal - Send Peter a list of all authors to correct: ```sql dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/authors.csv with csv header; COPY 56156 ``` - Afterwards we'll want to do some batch tagging of ORCID identifiers to these names - CGSpace crashed again this afternoon, I'm not sure of the cause but there are a lot of SQL errors in the DSpace log: ``` 2018-03-21 15:11:08,166 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL QueryTable Error - java.sql.SQLException: Connection has already been closed. ``` - I have no idea why so many connections were abandoned this afternoon: ``` # grep 'Mar 21, 2018' /var/log/tomcat7/catalina.out | grep -c 'org.apache.tomcat.jdbc.pool.ConnectionPool abandon' 268 ``` - DSpace Test crashed again due to Java heap space, this is from the DSpace log: ``` 2018-03-21 15:18:48,149 ERROR org.dspace.app.xmlui.cocoon.DSpaceCocoonServletFilter @ Serious Error Occurred Processing Request! org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.OutOfMemoryError: Java heap space ``` - And this is from the Tomcat Catalina log: ``` Mar 21, 2018 11:20:00 AM org.apache.catalina.core.ContainerBase$ContainerBackgroundProcessor run SEVERE: Unexpected death of background thread ContainerBackgroundProcessor[StandardEngine[Catalina]] java.lang.OutOfMemoryError: Java heap space ``` - But there are tons of heap space errors on DSpace Test actually: ``` # grep -c 'java.lang.OutOfMemoryError: Java heap space' /var/log/tomcat7/catalina.out 319 ``` - I guess we need to give it more RAM because it now has CGSpace's large Solr core - I will increase the memory from 3072m to 4096m - Update [Ansible playbooks](https://github.com/ilri/rmg-ansible-public) to use [PostgreSQL JBDC driver](https://jdbc.postgresql.org/) 42.2.2 - Deploy the new JDBC driver on DSpace Test - I'm also curious to see how long the `dspace index-discovery -b` takes on DSpace Test where the DSpace installation directory is on one of Linode's new block storage volumes ``` $ time schedtool -D -e ionice -c2 -n7 nice -n19 dspace index-discovery -b real 208m19.155s user 8m39.138s sys 2m45.135s ``` - So that's about three times as long as it took on CGSpace this morning - I should also check the raw read speed with `hdparm -tT /dev/sdc` - Looking at Peter's author corrections there are some mistakes due to Windows 1252 encoding - I need to find a way to filter these easily with OpenRefine - For example, Peter has inadvertantly introduced Unicode character 0xfffd into several fields - I can search for Unicode values by their hex code in OpenRefine using the following GREL expression: ``` isNotNull(value.match(/.*\ufffd.*/)) ``` - I need to be able to add many common characters though so that it is useful to copy and paste into a new project to find issues ## 2018-03-22 - Add ORCID identifier for Silvia Alonso - Update my Mirage 2 setup notes for Ubuntu 18.04: https://gist.github.com/alanorth/9bfd29feb7d2e836a9d417633319b3f5 ## 2018-03-24 - More work on the Ubuntu 18.04 readiness stuff for the [Ansible playbooks](https://github.com/ilri/rmg-ansible-public) - The playbook now uses the system's Ruby and Node.js so I don't have to manually install RVM and NVM after ## 2018-03-25 - Looking at Peter's author corrections and trying to work out a way to find errors in OpenRefine easily - I can find all names that have acceptable characters using a GREL expression like: ``` isNotNull(value.match(/.*[a-zA-ZáÁéèïíñØøöóúü].*/)) ``` - But it's probably better to just say which characters I know for sure are not valid (like parentheses, pipe, or weird Unicode characters): ``` or( isNotNull(value.match(/.*[(|)].*/)), isNotNull(value.match(/.*\uFFFD.*/)), isNotNull(value.match(/.*\u00A0.*/)), isNotNull(value.match(/.*\u200A.*/)) ) ``` - And here's one combined GREL expression to check for items marked as to delete or check so I can flag them and export them to a separate CSV (though perhaps it's time to add delete support to my `fix-metadata-values.py` script: ``` or( isNotNull(value.match(/.*delete.*/i)), isNotNull(value.match(/.*remove.*/i)), isNotNull(value.match(/.*check.*/i)) ) ``` - So I guess the routine is in OpenRefine is: - Transform: trim leading/trailing whitespace - Transform: collapse consecutive whitespace - Custom text facet for items to delete/check - Custom text facet for illegal characters - Test the corrections and deletions locally, then run them on CGSpace: ``` $ ./fix-metadata-values.py -i /tmp/Correct-2928-Authors-2018-03-21.csv -db dspace -u dspace -p 'fuuu' -f dc.contributor.author -t correct -m 3 $ ./delete-metadata-values.py -i /tmp/Delete-8-Authors-2018-03-21.csv -f dc.contributor.author -m 3 -db dspacetest -u dspace -p 'fuuu' ``` - Afterwards I started a full Discovery reindexing on both CGSpace and DSpace Test - CGSpace took 76m28.292s - DSpace Test took 194m56.048s ## 2018-03-26 - Atmire got back to me about the [Listings and Reports issue](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=589) and said it's caused by items that have missing `dc.identifier.citation` fields - The will send a fix ## 2018-03-27 - Atmire got back with an updated quote about the DSpace 5.8 compatibility so I've forwarded it to Peter ## 2018-03-28 - DSpace Test crashed due to heap space so I've increased it from 4096m to 5120m - The error in Tomcat's `catalina.out` was: ``` Exception in thread "RMI TCP Connection(idle)" java.lang.OutOfMemoryError: Java heap space ``` - Add ISI Journal (cg.isijournal) as an option in Atmire's Listing and Reports layout ([#370](https://github.com/ilri/DSpace/pull/370)) for Abenet - I noticed a few hundred CRPs using the old capitalized formatting so I corrected them: ``` $ ./fix-metadata-values.py -i /tmp/Correct-21-CRPs-2018-03-16.csv -f cg.contributor.crp -t correct -m 230 -db cgspace -u cgspace -p 'fuuu' Fixed 29 occurences of: CLIMATE CHANGE, AGRICULTURE AND FOOD SECURITY Fixed 7 occurences of: WATER, LAND AND ECOSYSTEMS Fixed 19 occurences of: AGRICULTURE FOR NUTRITION AND HEALTH Fixed 100 occurences of: ROOTS, TUBERS AND BANANAS Fixed 31 occurences of: HUMIDTROPICS Fixed 21 occurences of: MAIZE Fixed 11 occurences of: POLICIES, INSTITUTIONS, AND MARKETS Fixed 28 occurences of: GRAIN LEGUMES Fixed 3 occurences of: FORESTS, TREES AND AGROFORESTRY Fixed 5 occurences of: GENEBANKS ``` - That's weird because we just updated them last week... - Create a pull request to enable searching by ORCID identifier (`cg.creator.id`) in Discovery and Listings and Reports ([#371](https://github.com/ilri/DSpace/pull/371)) - I will test it on DSpace Test first! - Fix one missing XMLUI string for "Access Status" (cg.identifier.status) - Run all system updates on DSpace Test and reboot the machine