CGSpace Notes

September, 2016

Posted on
#notes

2016-09-01

  • Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors
  • Discuss how the migration of CGIAR’s Active Directory to a flat structure will break our LDAP groups in DSpace
  • We had been using DC=ILRI to determine whether a user was ILRI or not
  • It looks like we might be able to use OUs now, instead of DCs:
$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
  • User who has been migrated to the root vs user still in the hierarchical structure:
distinguishedName: CN=Last\, First (ILRI),OU=ILRI Kenya Employees,OU=ILRI Kenya,OU=ILRIHUB,DC=CGIARAD,DC=ORG
distinguishedName: CN=Last\, First (ILRI),OU=ILRI Ethiopia Employees,OU=ILRI Ethiopia,DC=ILRI,DC=CGIARAD,DC=ORG
  • Changing the DSpace LDAP config to use OU=ILRIHUB seems to work:

DSpace groups based on LDAP DN

  • Notes for local PostgreSQL database recreation from production snapshot:
$ dropdb dspacetest
$ createdb -O dspacetest --encoding=UNICODE dspacetest
$ psql dspacetest -c 'alter user dspacetest createuser;'
$ pg_restore -O -U dspacetest -d dspacetest ~/Downloads/cgspace_2016-09-01.backup
$ psql dspacetest -c 'alter user dspacetest nocreateuser;'
$ psql -U dspacetest -f ~/src/git/DSpace/dspace/etc/postgres/update-sequences.sql dspacetest -h localhost
$ vacuumdb dspacetest
  • Some names that I thought I fixed in July seem not to be:
dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Poole, %';
      text_value       |              authority               | confidence
-----------------------+--------------------------------------+------------
 Poole, Elizabeth Jane | b6efa27f-8829-4b92-80fe-bc63e03e3ccb |        600
 Poole, Elizabeth Jane | 41628f42-fc38-4b38-b473-93aec9196326 |        600
 Poole, Elizabeth Jane | 83b82da0-f652-4ebc-babc-591af1697919 |        600
 Poole, Elizabeth Jane | c3a22456-8d6a-41f9-bba0-de51ef564d45 |        600
 Poole, E.J.           | c3a22456-8d6a-41f9-bba0-de51ef564d45 |        600
 Poole, E.J.           | 0fbd91b9-1b71-4504-8828-e26885bf8b84 |        600
(6 rows)
  • At least a few of these actually have the correct ORCID, but I will unify the authority to be c3a22456-8d6a-41f9-bba0-de51ef564d45
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, %';
UPDATE 69
  • And for Peter Ballantyne:
dspacetest=# select distinct text_value, authority, confidence from metadatavalue where metadata_field_id=3 and resource_type_id=2 and text_value like 'Ballantyne, %';
    text_value     |              authority               | confidence
-------------------+--------------------------------------+------------
 Ballantyne, Peter | 2dcbcc7b-47b0-4fd7-bef9-39d554494081 |        600
 Ballantyne, Peter | 4f04ca06-9a76-4206-bd9c-917ca75d278e |        600
 Ballantyne, P.G.  | 4f04ca06-9a76-4206-bd9c-917ca75d278e |        600
 Ballantyne, Peter | ba5f205b-b78b-43e5-8e80-0c9a1e1ad2ca |        600
 Ballantyne, Peter | 20f21160-414c-4ecf-89ca-5f2cb64e75c1 |        600
(5 rows)
  • Again, a few have the correct ORCID, but there should only be one authority…
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, %';
UPDATE 58
  • And for me:
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%';
 text_value |              authority               | confidence
------------+--------------------------------------+------------
 Orth, Alan | 4884def0-4d7e-4256-9dd4-018cd60a5871 |        600
 Orth, A.   | 4884def0-4d7e-4256-9dd4-018cd60a5871 |        600
 Orth, A.   | 1a1943a0-3f87-402f-9afe-e52fb46a513e |        600
(3 rows)
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, %';
UPDATE 11
  • And for CCAFS author Bruce Campbell that I had discussed with CCAFS earlier this week:
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%';
UPDATE 166
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%';
       text_value       |              authority               | confidence
------------------------+--------------------------------------+------------
 Campbell, Bruce        | 0e414b4c-4671-4a23-b570-6077aca647d8 |        600
 Campbell, Bruce Morgan | 0e414b4c-4671-4a23-b570-6077aca647d8 |        600
 Campbell, B.           | 0e414b4c-4671-4a23-b570-6077aca647d8 |        600
 Campbell, B.M.         | 0e414b4c-4671-4a23-b570-6077aca647d8 |        600
(4 rows)
  • After updating the Authority indexes (bin/dspace index-authority) everything looks good
  • Run authority updates on CGSpace

2016-09-05

  • After one week of logging TLS connections on CGSpace:
# zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
217
# zcat -f -- /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | wc -l
1164376
# zgrep "DES-CBC3" /var/log/nginx/cgspace.cgiar.org-access-ssl.log* | awk '{print $6}' | sort | uniq
TLSv1/DES-CBC3-SHA
TLSv1/EDH-RSA-DES-CBC3-SHA
  • So this represents 0.02% of 1.16M connections over a one-week period
  • Transforming some filenames in OpenRefine so they can have a useful description for SAFBuilder:
value + "__description:" + cells["dc.type"].value
  • This gives you, for example: Mainstreaming gender in agricultural R&D.pdf__description:Brief

2016-09-06

  • Trying to import the records for CIAT from yesterday, but having filename encoding issues from their zip file
  • Create a zip on Mac OS X from a SAF bundle containing only one record with one PDF:
    • Filename: Complementing Farmers Genetic Knowledge Farmer Breeding Workshop in Turipaná, Colombia.pdf
    • Imports fine on DSpace running on Mac OS X
    • Fails to import on DSpace running on Linux with error No such file or directory
  • Change diacritic in file name from á to a and re-create SAF bundle and zip
    • Success on both Mac OS X and Linux…
  • Looks like on the Mac OS X file system the file names represent á as: a (U+0061) + ́ (U+0301)
  • See: http://www.fileformat.info/info/unicode/char/e1/index.htm
  • See: http://demo.icu-project.org/icu-bin/nbrowser?t=%C3%A1&s=&uv=0
  • 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
  • We should definitely clean filenames so they don’t use characters that are tricky to process in CSV and shell scripts, like: ,, ', and "
value.replace("'","").replace(",","").replace('"','')
  • I need to write a Python script to match that for renaming files in the file system
  • 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
  • Seems that the latter method causes a null pointer exception, so I will just have to use the former method
  • In the end I was able to import the files after unzipping them ONLY on Linux
    • 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
  • 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:
$ ./safbuilder.sh -c /home/aorth/ciat-gender-2016-09-06/66601.csv
$ 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
$ rm -rf ~/ciat-gender-2016-09-06/SimpleArchiveFormat/

2016-09-07

  • Erase and rebuild DSpace Test based on latest Ubuntu 16.04, PostgreSQL 9.5, and Java 8 stuff
  • Reading about PostgreSQL maintenance and it seems manual vacuuming is only for certain workloads, such as heavy update/write loads
  • 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
  • See: https://www.postgresql.org/docs/9.3/static/routine-vacuuming.html
  • CGSpace went down and the error seems to be the same as always (lately):
2016-09-07 11:39:23,162 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
...
  • Since CGSpace had crashed I quickly deployed the new LDAP settings before restarting Tomcat

2016-09-13

  • CGSpace crashed twice today, errors from catalina.out:
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)
  • I enabled logging of requests to /rest again

2016-09-14

  • CGSpace crashed again, errors from catalina.out:
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)
  • I restarted Tomcat and it was ok again
  • CGSpace crashed a few hours later, errors from catalina.out:
Exception in thread "http-bio-127.0.0.1-8081-exec-25" java.lang.OutOfMemoryError: Java heap space
        at java.lang.StringCoding.decode(StringCoding.java:215)
  • We haven’t seen that in quite a while…
  • Indeed, in a month of logs it only occurs 15 times:
# grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
15
  • I also see a bunch of errors from dspace.log:
2016-09-14 12:23:07,981 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
  • Looking at REST requests, it seems there is one IP hitting us nonstop:
# awk '{print $1}' /var/log/nginx/rest.log  | sort -n | uniq -c | sort -h | tail -n 3
    820 50.87.54.15
  12872 70.32.99.142
  25744 70.32.83.92
# awk '{print $1}' /var/log/nginx/rest.log.1  | sort -n | uniq -c | sort -h | tail -n 3
   7966 181.118.144.29
  54706 70.32.99.142
 109412 70.32.83.92
  • Those are the same IPs that were hitting us heavily in July, 2016 as well…
  • I think the stability issues are definitely from REST
  • Crashed AGAIN, errors from dspace.log:
2016-09-14 14:31:43,069 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
  • And more heap space errors:
# grep -rsI "OutOfMemoryError" /var/log/tomcat7/catalina.* | wc -l
19
  • There are no more rest requests since the last crash, so maybe there are other things causing this.
  • 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!)
  • They seem to be coming from Baidu, and so far during today alone account for 1⁄6 of every connection:
# grep -c ip_addr= /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
29084
# grep -c ip_addr=180.76.15 /home/cgspace.cgiar.org/log/dspace.log.2016-09-14
5192
  • Other recent days are the same… hmmm.
  • From the activity control panel I can see 58 unique IPs hitting the site concurrently, which has GOT to hurt our stability
  • A list of all 2000 unique IPs from CGSpace logs today:
# 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
  • Looking at the top 20 IPs or so, most are Yahoo, MSN, Google, Baidu, TurnitIn (iParadigm), etc… do we have any real users?
  • Generate a list of all Affiliations for Peter Ballantyne to go through, make corrections, and create a lookup list from:
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)
 to /tmp/affiliations.csv with csv;