--- title: "July, 2018" date: 2018-07-01T12:56:54+03:00 author: "Alan Orth" tags: ["Notes"] --- ## 2018-07-01 - I want to upgrade DSpace Test to DSpace 5.8 so I took a backup of its current database just in case: ``` $ pg_dump -b -v -o --format=custom -U dspace -f dspace-2018-07-01.backup dspace ``` - During the `mvn package` stage on the 5.8 branch I kept getting issues with java running out of memory: ``` There is insufficient memory for the Java Runtime Environment to continue. ``` - As the machine only has 8GB of RAM, I reduced the Tomcat memory heap from 5120m to 4096m so I could try to allocate more to the build process: ``` $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m" $ mvn -U -Dmirage2.on=true -Dmirage2.deps.included=false -Denv=dspacetest.cgiar.org -P \!dspace-lni,\!dspace-rdf,\!dspace-sword,\!dspace-swordv2 clean package ``` - Then I stopped the Tomcat 7 service, ran the ant update, and manually ran the old and ignored SQL migrations: ``` $ sudo su - postgres $ psql dspace ... dspace=# begin; BEGIN dspace=# \i Atmire-DSpace-5.8-Schema-Migration.sql DELETE 0 UPDATE 1 DELETE 1 dspace=# commit dspace=# \q $ exit $ dspace database migrate ignored ``` - After that I started Tomcat 7 and DSpace seems to be working, now I need to tell our colleagues to try stuff and report issues they have ## 2018-07-02 - Discuss AgriKnowledge including our Handle identifier on their harvested items from CGSpace - They seem to be only interested in Gates-funded outputs, for example: https://www.agriknowledge.org/files/tm70mv21t ## 2018-07-03 - Finally finish with the CIFOR Archive records (a total of 2448): - I mapped the 50 items that were duplicates from elsewhere in CGSpace into [CIFOR Archive](https://cgspace.cgiar.org/handle/10568/16702) - I did one last check of the remaining 2398 items and found eight who have a `cg.identifier.doi` that links to some URL other than a DOI so I moved those to `cg.identifier.url` and `cg.identifier.googleurl` as appropriate - Also, thirteen items had a DOI in their citation, but did not have a `cg.identifier.doi` field, so I added those - Then I imported those 2398 items in two batches (to deal with memory issues): ``` $ export JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx1024m" $ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive.csv $ dspace metadata-import -e aorth@mjanja.ch -f /tmp/2018-06-27-New-CIFOR-Archive2.csv ``` - I noticed there are many items that use HTTP instead of HTTPS for their Google Books URL, and some missing HTTP entirely: ``` dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%'; count ------- 785 dspace=# select count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*'; count ------- 4 ``` - I think I should fix that as well as some other garbage values like "test" and "dspace.ilri.org" etc: ``` dspace=# begin; dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value like 'http://books.google.%'; UPDATE 785 dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'books.google', 'https://books.google') where resource_type_id=2 and metadata_field_id=222 and text_value ~ '^books\.google\..*'; UPDATE 4 dspace=# update metadatavalue set text_value='https://books.google.com/books?id=meF1CLdPSF4C' where resource_type_id=2 and metadata_field_id=222 and text_value='meF1CLdPSF4C'; UPDATE 1 dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=222 and metadata_value_id in (2299312, 10684, 10700, 996403); DELETE 4 dspace=# commit; ``` - Testing DSpace 5.8 with PostgreSQL 9.6 and Tomcat 8.5.32 (instead of my usual 7.0.88) and for some reason I get autowire errors on Catalina startup with 8.5.32: ``` 03-Jul-2018 19:51:37.272 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.listenerStart Exception sending context initialized event to listener instance of class [org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener] java.lang.RuntimeException: Failure during filter init: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)} at org.dspace.servicemanager.servlet.DSpaceKernelServletContextListener.contextInitialized(DSpaceKernelServletContextListener.java:92) at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4792) at org.apache.catalina.core.StandardContext.startInternal(StandardContext.java:5256) at org.apache.catalina.util.LifecycleBase.start(LifecycleBase.java:150) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:754) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:730) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:734) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:629) at org.apache.catalina.startup.HostConfig$DeployDescriptor.run(HostConfig.java:1839) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748) Caused by: java.lang.RuntimeException: Failed to startup the DSpace Service Manager: failure starting up spring service manager: Error creating bean with name 'conversionService' defined in file [/home/aorth/dspace/config/spring/xmlui/spring-dspace-addon-cua-services.xml]: Cannot create inner bean 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a' of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter] while setting bean property 'converters' with key [1]; nested exception is org.springframework.beans.factory.BeanCreationException: Error creating bean with name 'com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter#3f6c3e6a': Injection of autowired dependencies failed; nested exception is org.springframework.beans.factory.BeanCreationException: Could not autowire field: private com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$ColumnsConverter.filterConverter; nested exception is org.springframework.beans.factory.NoSuchBeanDefinitionException: No matching bean of type [com.atmire.app.xmlui.aspect.statistics.mostpopular.MostPopularConfig$FilterConverter] found for dependency: expected at least 1 bean which qualifies as autowire candidate for this dependency. Dependency annotations: {@org.springframework.beans.factory.annotation.Autowired(required=true)} ``` - Gotta check that out later... ## 2018-07-04 - I verified that the autowire error indeed only occurs on Tomcat 8.5, but the application works fine on Tomcat 7 - I have raised this in the [DSpace 5.8 compatibility ticket on Atmire's tracker](https://tracker.atmire.com/tickets-cgiar-ilri/view-ticket?id=560) - Abenet wants me to add "United Kingdom government" to the sponsors on CGSpace so I created a ticket to track it ([#381](https://github.com/ilri/DSpace/issues/381)) - Also, Udana wants me to add "Enhancing Sustainability Across Agricultural Systems" to the WLE Phase II research themes so I created a ticket to track that ([#382](https://github.com/ilri/DSpace/issues/382) - I need to try to finish this DSpace 5.8 business first because I have too many branches with cherry-picks going on right now! ## 2018-07-06 - CCAFS want me to add "PII-FP2_MSCCCAFS" to their Phase II project tags on CGSpace ([#383](https://github.com/ilri/DSpace/issues/383) - I'll do it in a batch with all the other metadata updates next week ## 2018-07-08 - I was tempted to do the Linode instance upgrade on CGSpace (linode18), but after looking closely at the system backups I noticed that Solr isn't being backed up to S3 - I apparently noticed this—and fixed it!—in [2016-07]({{< relref "2016-07.md" >}}), but it doesn't look like the backup has been updated since then! - It looks like I added Solr to the `backup_to_s3.sh` script, but that script is not even being used (`s3cmd` is run directly from root's crontab) - For now I have just initiated a manual S3 backup of the Solr data: ``` # s3cmd sync --delete-removed /home/backup/solr/ s3://cgspace.cgiar.org/solr/ ``` - But I need to add this to cron! - I wonder if I should convert some of the cron jobs to systemd services / timers... - I sent a note to all our users on Yammer to ask them about possible maintenance on Sunday, July 14th - Abenet wants to be able to search by journal title (dc.source) in the advanced Discovery search so I opened an issue for it ([#384](https://github.com/ilri/DSpace/issues/384)) - I regenerated the list of names for all our ORCID iDs using my [resolve-orcids.py](https://gist.github.com/alanorth/57a88379126d844563c1410bd7b8d12b) script: ``` $ grep -oE '[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}-[A-Z0-9]{4}' ~/src/git/DSpace/dspace/config/controlled-vocabularies/cg-creator-id.xml | sort | uniq > /tmp/2018-07-08-orcids.txt $ ./resolve-orcids.py -i /tmp/2018-07-08-orcids.txt -o /tmp/2018-07-08-names.txt -d ``` - But after comparing to the existing list of names I didn't see much change, so I just ignored it ## 2018-07-09 - Uptime Robot said that CGSpace was down for two minutes early this morning but I don't see anything in Tomcat logs or dmesg - Uptime Robot said that CGSpace was down for two minutes again later in the day, and this time I saw a memory error in Tomcat's `catalina.out`: ``` Exception in thread "http-bio-127.0.0.1-8081-exec-557" java.lang.OutOfMemoryError: Java heap space ``` - I'm not sure if it's the same error, but I see this in DSpace's `solr.log`: ``` 2018-07-09 06:25:09,913 ERROR org.apache.solr.servlet.SolrDispatchFilter @ null:java.lang.RuntimeException: java.lang.OutOfMemoryError: Java heap space ``` - I see a strange error around that time in `dspace.log.2018-07-08`: ``` 2018-07-09 06:23:43,510 ERROR com.atmire.statistics.SolrLogThread @ IOException occured when talking to server at: http://localhost:8081/solr/statistics org.apache.solr.client.solrj.SolrServerException: IOException occured when talking to server at: http://localhost:8081/solr/statistics ``` - But not sure what caused that... - I got a message from Linode tonight that CPU usage was high on CGSpace for the past few hours around 8PM GMT - Looking in the nginx logs I see the top ten IP addresses active today: ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "09/Jul/2018" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 1691 40.77.167.84 1701 40.77.167.69 1718 50.116.102.77 1872 137.108.70.6 2172 157.55.39.234 2190 207.46.13.47 2848 178.154.200.38 4367 35.227.26.162 4387 70.32.83.92 4738 95.108.181.88 ``` - Of those, *all* except `70.32.83.92` and `50.116.102.77` are *NOT* re-using their Tomcat sessions, for example from the XMLUI logs: ``` $ grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=95.108.181.88' dspace.log.2018-07-09 4435 ``` - `95.108.181.88` appears to be Yandex, so I dunno why it's creating so many sessions, as its user agent should match Tomcat's Crawler Session Manager Valve - `70.32.83.92` is on MediaTemple but I'm not sure who it is. They are mostly hitting REST so I guess that's fine - `35.227.26.162` doesn't declare a user agent and is on Google Cloud, so I should probably mark them as a bot in nginx - `178.154.200.38` is Yandex again - `207.46.13.47` is Bing - `157.55.39.234` is Bing - `137.108.70.6` is our old friend CORE bot - `50.116.102.77` doesn't declare a user agent and lives on HostGator, but mostly just hits the REST API so I guess that's fine - `40.77.167.84` is Bing again - Interestingly, the first time that I see `35.227.26.162` was on 2018-06-08 - I've added `35.227.26.162` to the bot tagging logic in the nginx vhost ## 2018-07-10 - Add "United Kingdom government" to sponsors ([#381](https://github.com/ilri/DSpace/issues/381)) - Add "Enhancing Sustainability Across Agricultural Systems" to WLE Phase II Research Themes ([#382](https://github.com/ilri/DSpace/issues/382)) - Add "PII-FP2_MSCCCAFS" to CCAFS Phase II Project Tags ([#383](https://github.com/ilri/DSpace/issues/383)) - Add journal title (dc.source) to Discovery search filters ([#384](https://github.com/ilri/DSpace/issues/384)) - All were tested and merged to the `5_x-prod` branch and will be deployed on CGSpace this coming weekend when I do the Linode server upgrade - I need to get them onto the 5.8 testing branch too, either via cherry-picking or by rebasing after we finish testing Atmire's 5.8 pull request ([#378](https://github.com/ilri/DSpace/pull/378)) - Linode sent an alert about CPU usage on CGSpace again, about 13:00UTC - These are the top ten users in the last two hours: ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "10/Jul/2018:(11|12|13)" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 81 193.95.22.113 82 50.116.102.77 112 40.77.167.90 117 196.190.95.98 120 178.154.200.38 215 40.77.167.96 243 41.204.190.40 415 95.108.181.88 695 35.227.26.162 697 213.139.52.250 ``` - Looks like `213.139.52.250` is Moayad testing his new CGSpace vizualization thing: ``` 213.139.52.250 - - [10/Jul/2018:13:39:41 +0000] "GET /bitstream/handle/10568/75668/dryad.png HTTP/2.0" 200 53750 "http://localhost:4200/" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_13_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/67.0.3396.87 Safari/537.36" ``` - He said there was a bug that caused his app to request a bunch of invalid URLs - I'll have to keep and eye on this and see how their platform evolves ## 2018-07-11 - Skype meeting with Peter and Addis CGSpace team - We need to look at doing the `dc.rights` stuff again, which we last worked on in 2018-01 and 2018-02 - Abenet suggested that we do a controlled vocabulary for the authors, perhaps with the top 1,500 or so on CGSpace? - Peter told Sisay to test this controlled vocabulary - Discuss meeting in Nairobi in October ## 2018-07-12 - Uptime Robot said that CGSpace went down a few times last night, around 10:45 PM and 12:30 AM - Here are the top ten IPs from last night and this morning: ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "11/Jul/2018:22" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 48 66.249.64.91 50 35.227.26.162 57 157.55.39.234 59 157.55.39.71 62 147.99.27.190 82 95.108.181.88 92 40.77.167.90 97 183.128.40.185 97 240e:f0:44:fa53:745a:8afe:d221:1232 3634 208.110.72.10 # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "12/Jul/2018:00" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 25 216.244.66.198 38 40.77.167.185 46 66.249.64.93 56 157.55.39.71 60 35.227.26.162 65 157.55.39.234 83 95.108.181.88 87 66.249.64.91 96 40.77.167.90 7075 208.110.72.10 ``` - We have never seen `208.110.72.10` before... so that's interesting! - The user agent for these requests is: Pcore-HTTP/v0.44.0 - A brief Google search doesn't turn up any information about what this bot is, but lots of users complaining about it - This bot does make a lot of requests all through the day, although it seems to re-use its Tomcat session: ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "Pcore-HTTP" | awk '{print $1}' | sort | uniq -c | sort -n | tail -n 10 17098 208.110.72.10 # grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10' dspace.log.2018-07-11 1161 # grep -c -E 'session_id=[A-Z0-9]{32}:ip_addr=208.110.72.10' dspace.log.2018-07-12 1885 ``` - I think the problem is that, despite the bot requesting `robots.txt`, it almost exlusively requests dynamic pages from `/discover`: ``` # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "Pcore-HTTP" | grep -o -E "GET /(browse|discover|search-filter)" | sort -n | uniq -c | sort -rn 13364 GET /discover 993 GET /search-filter 804 GET /browse # zcat --force /var/log/nginx/*.log /var/log/nginx/*.log.1 | grep -E "Pcore-HTTP" | grep robots 208.110.72.10 - - [12/Jul/2018:00:22:28 +0000] "GET /robots.txt HTTP/1.1" 200 1301 "https://cgspace.cgiar.org/robots.txt" "Pcore-HTTP/v0.44.0" ``` - So this bot is just like Baiduspider, and I need to add it to the nginx rate limiting - I'll also add it to Tomcat's Crawler Session Manager Valve to force the re-use of a common Tomcat sesssion for all crawlers just in case - Generate a list of all affiliations in CGSpace to send to Mohamed Salem to compare with the list on MEL (sorting the list by most occurrences): ``` dspace=# \copy (select distinct text_value, count(*) as count from metadatavalue where resource_type_id=2 and metadata_field_id=211 group by text_value order by count desc) to /tmp/affiliations.csv with csv header COPY 4518 dspace=# \q $ csvcut -c 1 < /tmp/affiliations.csv > /tmp/affiliations-1.csv ``` - We also need to discuss standardizing our countries and comparing our ORCID iDs ## 2018-07-13 - Generate a list of affiliations for Peter and Abenet to go over so we can batch correct them before we deploy the new data visualization dashboard: ``` 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 = 'affiliation') AND resource_type_id = 2 group by text_value order by count desc) to /tmp/affiliations.csv with csv header; COPY 4518 ```