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283 lines
13 KiB
Markdown
283 lines
13 KiB
Markdown
+++
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date = "2016-09-01T15:53:00+03:00"
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author = "Alan Orth"
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title = "September, 2016"
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tags = ["notes"]
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image = "../images/bg.jpg"
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+++
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## 2016-09-01
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- Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors
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- Discuss how the migration of CGIAR's Active Directory to a flat structure will break our LDAP groups in DSpace
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- We had been using `DC=ILRI` to determine whether a user was ILRI or not
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- It looks like we might be able to use OUs now, instead of DCs:
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```
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$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
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```
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- User who has been migrated to the root vs user still in the hierarchical structure:
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```
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distinguishedName: CN=Last\, First (ILRI),OU=ILRI Kenya Employees,OU=ILRI Kenya,OU=ILRIHUB,DC=CGIARAD,DC=ORG
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distinguishedName: CN=Last\, First (ILRI),OU=ILRI Ethiopia Employees,OU=ILRI Ethiopia,DC=ILRI,DC=CGIARAD,DC=ORG
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```
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- Changing the DSpace LDAP config to use `OU=ILRIHUB` seems to work:
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- Notes for local PostgreSQL database recreation from production snapshot:
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```
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$ dropdb dspacetest
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$ createdb -O dspacetest --encoding=UNICODE dspacetest
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$ psql dspacetest -c 'alter user dspacetest createuser;'
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$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-09-01.backup
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$ psql dspacetest -c 'alter user dspacetest nocreateuser;'
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$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost
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$ vacuumdb dspacetest
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```
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- Some names that I thought I fixed in July seem not to be:
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```
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dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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text_value | authority | confidence
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-----------------------+--------------------------------------+------------
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Poole, Elizabeth Jane | b6efa27f-8829-4b92-80fe-bc63e03e3ccb | 600
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Poole, Elizabeth Jane | 41628f42-fc38-4b38-b473-93aec9196326 | 600
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Poole, Elizabeth Jane | 83b82da0-f652-4ebc-babc-591af1697919 | 600
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Poole, Elizabeth Jane | c3a22456-8d6a-41f9-bba0-de51ef564d45 | 600
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Poole, E.J. | c3a22456-8d6a-41f9-bba0-de51ef564d45 | 600
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Poole, E.J. | 0fbd91b9-1b71-4504-8828-e26885bf8b84 | 600
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(6 rows)
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```
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- At least a few of these actually have the correct ORCID, but I will unify the authority to be c3a22456-8d6a-41f9-bba0-de51ef564d45
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```
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dspacetest=# update metadatavalue set authority='c3a22456-8d6a-41f9-bba0-de51ef564d45', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
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UPDATE 69
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```
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- And for Peter Ballantyne:
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```
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dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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text_value | authority | confidence
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-------------------+--------------------------------------+------------
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Ballantyne, Peter | 2dcbcc7b-47b0-4fd7-bef9-39d554494081 | 600
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Ballantyne, Peter | 4f04ca06-9a76-4206-bd9c-917ca75d278e | 600
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Ballantyne, P.G. | 4f04ca06-9a76-4206-bd9c-917ca75d278e | 600
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Ballantyne, Peter | ba5f205b-b78b-43e5-8e80-0c9a1e1ad2ca | 600
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Ballantyne, Peter | 20f21160-414c-4ecf-89ca-5f2cb64e75c1 | 600
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(5 rows)
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```
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- Again, a few have the correct ORCID, but there should only be one authority...
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```
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dspacetest=# update metadatavalue set authority='4f04ca06-9a76-4206-bd9c-917ca75d278e', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
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UPDATE 58
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```
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- And for me:
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```
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dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Orth, A%';
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text_value | authority | confidence
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------------+--------------------------------------+------------
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Orth, Alan | 4884def0-4d7e-4256-9dd4-018cd60a5871 | 600
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Orth, A. | 4884def0-4d7e-4256-9dd4-018cd60a5871 | 600
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Orth, A. | 1a1943a0-3f87-402f-9afe-e52fb46a513e | 600
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(3 rows)
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dspacetest=# update metadatavalue set authority='1a1943a0-3f87-402f-9afe-e52fb46a513e', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Orth, %';
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UPDATE 11
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```
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- And for CCAFS author Bruce Campbell that I had discussed with CCAFS earlier this week:
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```
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dspacetest=# update metadatavalue set authority='0e414b4c-4671-4a23-b570-6077aca647d8', confidence=600 where metadata_field_id=3 and resource_type_id=2 and text_value like 'Campbell, B%';
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UPDATE 166
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dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Campbell, B%';
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text_value | authority | confidence
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------------------------+--------------------------------------+------------
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Campbell, Bruce | 0e414b4c-4671-4a23-b570-6077aca647d8 | 600
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Campbell, Bruce Morgan | 0e414b4c-4671-4a23-b570-6077aca647d8 | 600
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Campbell, B. | 0e414b4c-4671-4a23-b570-6077aca647d8 | 600
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Campbell, B.M. | 0e414b4c-4671-4a23-b570-6077aca647d8 | 600
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(4 rows)
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```
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- After updating the Authority indexes (`bin/dspace index-authority`) everything looks good
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- Run authority updates on CGSpace
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## 2016-09-05
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- After one week of logging TLS connections on CGSpace:
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```
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# zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
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217
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# zcat -f -- /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
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1164376
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# zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | awk '{print $6}' | sort | uniq
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TLSv1/DES-CBC3-SHA
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TLSv1/EDH-RSA-DES-CBC3-SHA
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```
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- So this represents `0.02%` of 1.16M connections over a one-week period
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- Transforming some filenames in OpenRefine so they can have a useful description for SAFBuilder:
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```
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value + "__description:" + cells["dc.type"].value
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```
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- This gives you, for example: `Mainstreaming gender in agricultural R&D.pdf__description:Brief`
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## 2016-09-06
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- Trying to import the records for CIAT from yesterday, but having filename encoding issues from their zip file
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- Create a zip on Mac OS X from a SAF bundle containing only one record with one PDF:
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- Filename: Complementing Farmers Genetic Knowledge Farmer Breeding Workshop in Turipaná, Colombia.pdf
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- Imports fine on DSpace running on Mac OS X
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- Fails to import on DSpace running on Linux with error `No such file or directory`
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- Change diacritic in file name from á to a and re-create SAF bundle and zip
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- Success on both Mac OS X and Linux...
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- Looks like on the Mac OS X file system the file names represent á as: a (U+0061) + ́ (U+0301)
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- See: http://www.fileformat.info/info/unicode/char/e1/index.htm
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- See: http://demo.icu-project.org/icu-bin/nbrowser?t=%C3%A1&s=&uv=0
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- If I unzip the original zip from CIAT on Windows, re-zip it with 7zip on Windows, and then unzip it on Linux directly, the file names seem to be proper UTF-8
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- We should definitely clean filenames so they don't use characters that are tricky to process in CSV and shell scripts, like: `,`, `'`, and `"`
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```
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value.replace("'","").replace(",","").replace('"','')
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```
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- I need to write a Python script to match that for renaming files in the file system
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- When importing SAF bundles it seems you can specify the target collection on the command line using `-c 10568/4003` or in the `collections` file inside each item in the bundle
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- Seems that the latter method causes a null pointer exception, so I will just have to use the former method
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- In the end I was able to import the files after unzipping them ONLY on Linux
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- The CSV file was giving file names in UTF-8, and unzipping the zip on Mac OS X and transferring it was converting the file names to Unicode equivalence like I saw above
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- Import CIAT Gender Network records to CGSpace, first creating the SAF bundles as my user, then importing as the `tomcat7` user, and deleting the bundle, for each collection's items:
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```
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$ ./safbuilder.sh -c /home/aorth/ciat-gender-2016-09-06/66601.csv
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$ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgiar.org/bin/dspace import -a -e aorth@mjanja.ch -c 10568/66601 -s /home/aorth/ciat-gender-2016-09-06/SimpleArchiveFormat -m 66601.map
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$ rm -rf ~/ciat-gender-2016-09-06/SimpleArchiveFormat/
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```
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## 2016-09-07
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- Erase and rebuild DSpace Test based on latest Ubuntu 16.04, PostgreSQL 9.5, and Java 8 stuff
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- Reading about PostgreSQL maintenance and it seems manual vacuuming is only for certain workloads, such as heavy update/write loads
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- I suggest we disable our nightly manual vacuum task, as we're a mostly read workload, and I'd rather stick as close to the documentation as possible since we haven't done any testing/observation of PostgreSQL
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- See: https://www.postgresql.org/docs/9.3/static/routine-vacuuming.html
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- CGSpace went down and the error seems to be the same as always (lately):
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```
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2016-09-07 11:39:23,162 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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...
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```
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- Since CGSpace had crashed I quickly deployed the new LDAP settings before restarting Tomcat
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## 2016-09-13
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- CGSpace crashed twice today, errors from `catalina.out`:
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```
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:114)
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```
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- I enabled logging of requests to `/rest` again
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## 2016-09-14
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- CGSpace crashed again, errors from `catalina.out`:
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```
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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at org.apache.commons.dbcp.PoolingDataSource.getConnection(PoolingDataSource.java:114)
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```
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- I restarted Tomcat and it was ok again
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- CGSpace crashed a few hours later, errors from `catalina.out`:
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```
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Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
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at java.lang.StringCoding.decode(StringCoding.java:215)
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```
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- We haven't seen that in quite a while...
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- Indeed, in a month of logs it only occurs 15 times:
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```
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# grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
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15
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```
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- I also see a bunch of errors from dspace.log:
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```
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2016-09-14 12:23:07,981 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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```
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- Looking at REST requests, it seems there is one IP hitting us nonstop:
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```
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# awk '{print $1}' /var/log/nginx/rest.log | sort -n | uniq -c | sort -h | tail -n 3
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820 50.87.54.15
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12872 70.32.99.142
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25744 70.32.83.92
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# awk '{print $1}' /var/log/nginx/rest.log.1 | sort -n | uniq -c | sort -h | tail -n 3
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7966 181.118.144.29
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54706 70.32.99.142
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109412 70.32.83.92
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```
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- Those are the same IPs that were hitting us heavily in July, 2016 as well...
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- I think the stability issues are definitely from REST
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- Crashed AGAIN, errors from dspace.log:
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```
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2016-09-14 14:31:43,069 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
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org.apache.commons.dbcp.SQLNestedException: Cannot get a connection, pool error Timeout waiting for idle object
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```
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- And more heap space errors:
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```
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# grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
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19
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```
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- There are no more rest requests since the last crash, so maybe there are other things causing this.
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- Hmm, I noticed a shitload of IPs from 180.76.0.0/16 are connecting to both CGSpace and DSpace Test (58 unique IPs concurrently!)
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- They seem to be coming from Baidu, and so far during today alone account for 1/6 of every connection:
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```
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# grep -c ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
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29084
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# grep -c ip_addr=180.76.15 /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
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5192
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```
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- Other recent days are the same... hmmm.
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- From the activity control panel I can see 58 unique IPs hitting the site *concurrently*, which has GOT to hurt our stability
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- A list of all 2000 unique IPs from CGSpace logs today:
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```
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# grep ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-11 | awk -F: '{print $5}' | sort -n | uniq -c | sort -h | tail -n 100
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```
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- Looking at the top 20 IPs or so, most are Yahoo, MSN, Google, Baidu, TurnitIn (iParadigm), etc... do we have any real users?
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- Generate a list of all Affiliations for Peter Ballantyne to go through, make corrections, and create a lookup list from:
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```
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dspacetest=# \copy (select text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=211 group by text_value order by count desc)
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to /tmp/affiliations.csv with csv;
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```
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