alanorth/cgspace-notes
1
0
Fork 0
mirror of https://github.com/alanorth/cgspace-notes.git synced 2024-11-18 12:47:04 +01:00
Code Issues Projects Releases Wiki Activity
c22acbb22e
cgspace-notes/content/post/2017-02.md

170 lines
9.7 KiB
Markdown
Raw Normal View History

Add notes for 2017-02-07
2017-02-07 16:07:44 +01:00
+++
date = "2017-02-07T07:04:52-08:00"
author = "Alan Orth"
title = "February, 2017"
tags = ["Notes"]
+++
## 2017-02-07
- An item was mapped twice erroneously again, so I had to remove one of the mappings manually:
```
dspace=# select * from collection2item where item_id = '80278';
id | collection_id | item_id
-------+---------------+---------
92551 | 313 | 80278
92550 | 313 | 80278
90774 | 1051 | 80278
(3 rows)
dspace=# delete from collection2item where id = 92551 and item_id = 80278;
DELETE 1
```
Update notes for 2017-02-07
2017-02-08 07:11:37 +01:00
- Create issue on GitHub to track the addition of CCAFS Phase II project tags ([#301](https://github.com/ilri/DSpace/issues/301))
- Looks like we'll be using `cg.identifier.ccafsprojectpii` as the field name
Add notes for 2017-02-07
2017-02-07 16:07:44 +01:00
<!--more-->
Add notes for 2017-02-08
2017-02-08 18:31:52 +01:00
## 2017-02-08
- We also need to rename some of the CCAFS Phase I flagships:
- CLIMATE-SMART AGRICULTURAL PRACTICES → CLIMATE-SMART TECHNOLOGIES AND PRACTICES
- CLIMATE RISK MANAGEMENT → CLIMATE SERVICES AND SAFETY NETS
- LOW EMISSIONS AGRICULTURE → LOW EMISSIONS DEVELOPMENT
- POLICIES AND INSTITUTIONS → PRIORITIES AND POLICIES FOR CSA
- The climate risk management one doesn't exist, so I will have to ask Magdalena if they want me to add it to the input forms
Update notes for 2017-02-08
2017-02-09 07:27:37 +01:00
- Start testing some nearly 500 author corrections that CCAFS sent me:
```
$ ./fix-metadata-values.py -i /tmp/CCAFS-Authors-Feb-7.csv -f dc.contributor.author -t 'correct name' -m 3 -d dspace -u dspace -p fuuu
```
Update notes for 2017-02-09
2017-02-10 07:36:23 +01:00
## 2017-02-09
- More work on CCAFS Phase II stuff
- Looks like simply adding a new metadata field to `dspace/config/registries/cgiar-types.xml` and restarting DSpace causes the field to get added to the rregistry
- It requires a restart but at least it allows you to manage the registry programmatically
- It's not a very good way to manage the registry, though, as removing one there doesn't cause it to be removed from the registry, and we always restore from database backups so there would never be a scenario when we needed these to be created
- Testing some corrections on CCAFS Phase II flagships (`cg.subject.ccafs`):
```
$ ./fix-metadata-values.py -i ccafs-flagships-feb7.csv -f cg.subject.ccafs -t correct -m 210 -d dspace -u dspace -p fuuu
```
Update notes for 2017-02-10
2017-02-11 00:28:56 +01:00
## 2017-02-10
- CCAFS said they want to wait on the flagship updates (`cg.subject.ccafs`) on CGSpace, perhaps for a month or so
- Help Marianne Gadeberg (WLE) with some user permissions as it seems she had previously been using a personal email account, and is now on a CGIAR one
- I manually added her new account to ~25 authorizations that her hold user was on
Add notes for 2017-02-14
2017-02-14 12:03:09 +01:00
## 2017-02-14
- Add `SCALING` to ILRI subjects ([#304](https://github.com/ilri/DSpace/pull/304)), as Sisay's attempts were all sloppy
- Cherry pick some patches from the DSpace 5.7 branch:
- DS-3363 CSV import error says "row", means "column": f7b6c83e991db099003ee4e28ca33d3c7bab48c0
- DS-3479 avoid adding empty metadata values during import: 329f3b48a6de7fad074d825fd12118f7e181e151
- [DS-3456] 5x Clarify command line options for statisics import/export tools (#1623): 567ec083c8a94eb2bcc1189816eb4f767745b278
- [DS-3458]5x Allow Shard Process to Append to an existing repo: 3c8ecb5d1fd69a1dcfee01feed259e80abbb7749
- I still need to test these, especially as the last two which change some stuff with Solr maintenance
Add notes for 2017-02-15
2017-02-15 15:04:55 +01:00
## 2017-02-15
Add notes for 2017-02-16
2017-02-16 10:46:05 +01:00
- Update rvm on DSpace Test and CGSpace as there was a [security disclosure about versions less than 1.28.0](https://github.com/justinsteven/advisories/blob/master/2017_rvm_cd_command_execution.md)
## 2017-02-16
- Looking at memory info from munin on CGSpace:
![CGSpace meminfo](/cgspace-notes/2017/02/meminfo_phisical-week.png)
- We are using only ~8GB of RAM for applications, and 16GB for caches!
- The Linode machine we're on has 24GB of RAM but only because that's the only instance that had enough disk space for us (384GB)...
- We should probably look into Google Compute Engine or Digital Ocean where we can get more storage without having to follow a linear increase in instance pricing for CPU/memory as well
- Especially because we only use 2 out of 8 CPUs basically:
![CGSpace CPU](/cgspace-notes/2017/02/cpu-week.png)
Update notes for 2017-02-16
2017-02-16 13:20:22 +01:00
- Fix issue with duplicate declaration of in atmire-dspace-xmlui `pom.xml` (causing non-fatal warnings during the maven build)
- Experiment with making DSpace generate HTTPS handle links, first a change in dspace.cfg or the site's properties file:
```
handle.canonical.prefix = https://hdl.handle.net/
```
- And then a SQL command to update existing records:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://hdl.handle.net', 'https://hdl.handle.net') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'uri');
UPDATE 58193
```
- Seems to work fine!
Update notes for 2017-02-16
2017-02-16 18:31:01 +01:00
- I noticed a few items that have incorrect DOI links (`dc.identifier.doi`), and after looking in the database I see there are over 100 that are missing the scheme or are just plain wrong:
```
Update notes for 2017-02-16
2017-02-16 18:41:58 +01:00
dspace=# select distinct text_value from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value not like 'http%://%';
Update notes for 2017-02-16
2017-02-16 18:31:01 +01:00
```
Update notes for 2017-02-16
2017-02-16 18:41:58 +01:00
- This will replace any that begin with `10.` and change them to `https://dx.doi.org/10.`:
Update notes for 2017-02-16
2017-02-16 18:31:01 +01:00
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^10\..+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like '10.%';
```
Update notes for 2017-02-16
2017-02-16 18:41:58 +01:00
- This will get any that begin with `doi:10.` and change them to `https://dx.doi.org/10.x`:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^doi:(10\..+$)', 'https://dx.doi.org/\1') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'doi:10%';
```
Update notes for 2017-02-16
2017-02-16 22:11:20 +01:00
- Fix DOIs like `dx.doi.org/10.` to be `https://dx.doi.org/10.`:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org/%';
```
- Fix DOIs like `http//`:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, '^http//(dx.doi.org/.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http//%';
```
- Fix DOIs like `dx.doi.org./`:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, '(^dx.doi.org\./.+$)', 'https://dx.doi.org/\1') where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'dx.doi.org./%'
```
- Delete some invalid DOIs:
```
dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value in ('DOI','CPWF Mekong','Bulawayo, Zimbabwe','bb');
```
- Fix some other random outliers:
```
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.1016/j.aquaculture.2015.09.003' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'http:/dx.doi.org/10.1016/j.aquaculture.2015.09.003';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.5337/2016.200' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'doi: https://dx.doi.org/10.5337/2016.200';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/doi:10.1371/journal.pone.0062898' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'Http://dx.doi.org/doi:10.1371/journal.pone.0062898';
dspace=# update metadatavalue set text_value = 'https://dx.doi.10.1016/j.cosust.2013.11.012' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'http:dx.doi.10.1016/j.cosust.2013.11.012';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.1080/03632415.2014.883570' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'org/10.1080/03632415.2014.883570';
dspace=# update metadatavalue set text_value = 'https://dx.doi.org/10.15446/agron.colomb.v32n3.46052' where metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value = 'Doi: 10.15446/agron.colomb.v32n3.46052';
```
- And do another round of `http://` → `https://` cleanups:
```
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://dx.doi.org', 'https://dx.doi.org') where resource_type_id=2 and metadata_field_id IN (select metadata_field_id from metadatafieldregistry where element = 'identifier' and qualifier = 'doi') and text_value like 'http://dx.doi.org%';
```
- Run all DOI corrections on CGSpace
Update notes for 2017-02-16
2017-02-16 22:27:34 +01:00
- Something to think about here is to write a [Curation Task](https://wiki.duraspace.org/display/DSDOC5x/Curation+System#CurationSystem-ScriptedTasks) in Java to do these sanity checks / corrections every night
- Then we could add a cron job for them and run them from the command line like:
```
[dspace]/bin/dspace curate -t noop -i 10568/79891
```
Reference in New Issue Copy Permalink