cgspace-notes/content/2016-09.md

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2016-09-02 10:44:44 +02:00
+++
date = "2016-09-01T15:53:00+03:00"
author = "Alan Orth"
title = "September, 2016"
tags = ["notes"]
image = "../images/bg.jpg"
+++
## 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
```
2016-09-02 16:22:11 +02:00
- Changing the DSpace LDAP config to use `OU=ILRIHUB` seems to work:
![DSpace groups based on LDAP DN](../images/2016/09/ilri-ldap-users.png)
2016-09-02 10:44:44 +02:00
- 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
```
2016-09-02 16:22:11 +02:00
- 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
2016-09-02 22:36:26 +02:00
- Run authority updates on CGSpace
2016-09-06 14:17:40 +02:00
## 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
2016-09-06 16:15:25 +02:00
- 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 13:26:16 +02:00
## 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
2016-09-07 15:31:00 +02:00
- 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 15:56:34 +02:00
## 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)
```