cgspace-notes/content/post/2017-07.md

+++
date = "2017-07-01T18:03:52+03:00"
author = "Alan Orth"
title = "July, 2017"
tags = ["Notes"]

+++
## 2017-07-01

- Run system updates and reboot DSpace Test

## 2017-07-04

- Merge changes for WLE Phase II theme rename ([#329](https://github.com/ilri/DSpace/pull/329))
- Looking at extracting the metadata registries from ICARDA's MEL DSpace database so we can compare fields with CGSpace
- We can use PostgreSQL's extended output format (`-x`) plus `sed` to format the output into quasi XML:

<!--more-->

```
$ psql dspacenew -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=5 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*):  <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::'
```

- The `sed` script is from a post on the [PostgreSQL mailing list](https://www.postgresql.org/message-id/437E44A5.508%40ultimeth.com)
- Abenet says the ILRI board wants to be able to have "lead author" for every item, so I've whipped up a WIP test in the `5_x-lead-author` branch
- It works but is still very rough and we haven't thought out the whole lifecycle yet

![Testing lead author in submission form](/cgspace-notes/2017/07/lead-author-test.png)

- I assume that "lead author" would actually be the first question on the item submission form
- We also need to check to see which ORCID authority core this uses, because it seems to be using an entirely new one rather than the one for `dc.contributor.author` (which makes sense of course, but fuck, all the author problems aren't bad enough?!)
- Also would need to edit XMLUI item displays to incorporate this into authors list
- And fuck, then anyone consuming our data via REST / OAI will not notice that we have an author outside of `dc.contributor.authors`... ugh
- What if we modify the item submission form to use [`type-bind` fields to show/hide certain fields depending on the type](https://wiki.duraspace.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection)?

## 2017-07-05

- Adjust WLE Research Theme to include both Phase I and II on the submission form according to editor feedback ([#330](https://github.com/ilri/DSpace/pull/330))
- Generate list of fields in the current CGSpace `cg` scheme so we can record them properly in the metadata registry:

```
$ psql dspace -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=2 order by element, qualifier;' | sed -r 's:^-\[ RECORD (.*) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]*) +\| (.*):  <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' > cg-types.xml
```

- CGSpace was unavailable briefly, and I saw this error in the DSpace log file:

```
2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -
org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections
```

- Looking at the `pg_stat_activity` table I saw there were indeed 98 active connections to PostgreSQL, and at this time the limit is 100, so that makes sense
- Tsega restarted Tomcat and it's working now
- Abenet said she was generating a report with Atmire's CUA module, so it could be due to that?
- Looking in the logs I see this random error again that I should report to DSpace:

```
2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU
```

- Seems to come from `dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java`

## 2017-07-06

- Sisay tried to help by making a [pull request for the RTB flagships](https://github.com/ilri/DSpace/pull/331) but there are formatting errors, unrelated changes, and the flagship names are not in the style I requested
- Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field

## 2017-07-13

- Remove `UKaid` from the controlled vocabulary for `dc.description.sponsorship`, as `Department for International Development, United Kingdom` is the correct form and it is already present ([#334](https://github.com/ilri/DSpace/pull/334))

## 2017-07-14

- Sisay sent me a patch to add "Photo Report" to `dc.type` so I've added it to the `5_x-prod` branch

- Linode shut down our seventeen (17) VMs due to nonpayment of the July 1st invoice
- It took me a few hours to find the ICT/Finance contacts to pay the bill and boot all the servers back up
- Since the server was down anyways, I decided to run all system updates and re-deploy CGSpace so that the latest changes to `input-forms.xml` and the sponsors controlled vocabulary
Add notes for 2017-07-01 2017-07-01 17:03:19 +02:00			`+++`
			`date = "2017-07-01T18:03:52+03:00"`
			`author = "Alan Orth"`
			`title = "July, 2017"`
			`tags = ["Notes"]`

			`+++`
			`## 2017-07-01`

			`- Run system updates and reboot DSpace Test`

Add notes for 2017-07-04 2017-07-04 07:04:46 +02:00			`## 2017-07-04`

			`- Merge changes for WLE Phase II theme rename ([#329](https://github.com/ilri/DSpace/pull/329))`
Update notes for 2017-07-04 2017-07-04 09:53:39 +02:00			`- Looking at extracting the metadata registries from ICARDA's MEL DSpace database so we can compare fields with CGSpace`
			- We can use PostgreSQL's extended output format (`-x`) plus `sed` to format the output into quasi XML:

Update notes for 2017-07-04 2017-07-04 12:49:16 +02:00			`<!--more-->`

Update notes for 2017-07-04 2017-07-04 09:53:39 +02:00			```
Add notes for 2017-07-05 2017-07-05 13:33:20 +02:00			`$ psql dspacenew -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=5 order by element, qualifier;' \| sed -r 's:^-\[ RECORD (.) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]) +\\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::'`
Update notes for 2017-07-04 2017-07-04 09:53:39 +02:00			```

			- The `sed` script is from a post on the [PostgreSQL mailing list](https://www.postgresql.org/message-id/437E44A5.508%40ultimeth.com)
Update notes for 2017-07-04 2017-07-04 12:49:16 +02:00			- Abenet says the ILRI board wants to be able to have "lead author" for every item, so I've whipped up a WIP test in the `5_x-lead-author` branch
			`- It works but is still very rough and we haven't thought out the whole lifecycle yet`

			`![Testing lead author in submission form](/cgspace-notes/2017/07/lead-author-test.png)`

			`- I assume that "lead author" would actually be the first question on the item submission form`
			- We also need to check to see which ORCID authority core this uses, because it seems to be using an entirely new one rather than the one for `dc.contributor.author` (which makes sense of course, but fuck, all the author problems aren't bad enough?!)
			`- Also would need to edit XMLUI item displays to incorporate this into authors list`
			- And fuck, then anyone consuming our data via REST / OAI will not notice that we have an author outside of `dc.contributor.authors`... ugh
Update notes for 2017-07-04 2017-07-04 22:39:47 +02:00			- What if we modify the item submission form to use [`type-bind` fields to show/hide certain fields depending on the type](https://wiki.duraspace.org/display/DSDOC5x/Submission+User+Interface#SubmissionUserInterface-ItemtypeBasedMetadataCollection)?
Add notes for 2017-07-05 2017-07-05 13:33:20 +02:00
			`## 2017-07-05`

			`- Adjust WLE Research Theme to include both Phase I and II on the submission form according to editor feedback ([#330](https://github.com/ilri/DSpace/pull/330))`
			- Generate list of fields in the current CGSpace `cg` scheme so we can record them properly in the metadata registry:

			```
			`$ psql dspace -x -c 'select element, qualifier, scope_note from metadatafieldregistry where metadata_schema_id=2 order by element, qualifier;' \| sed -r 's:^-\[ RECORD (.) \]-+$:</dc-type>\n<dc-type>\n<schema>cg</schema>:;s:([^ ]) +\\| (.*): <\1>\2</\1>:;s:^$:</dc-type>:;1s:</dc-type>\n::' > cg-types.xml`
			```
Update notes for 2017-07-05 2017-07-05 16:27:41 +02:00
			`- CGSpace was unavailable briefly, and I saw this error in the DSpace log file:`

			```
			`2017-07-05 13:05:36,452 ERROR org.dspace.storage.rdbms.DatabaseManager @ SQL connection Error -`
			`org.postgresql.util.PSQLException: FATAL: remaining connection slots are reserved for non-replication superuser connections`
			```

			- Looking at the `pg_stat_activity` table I saw there were indeed 98 active connections to PostgreSQL, and at this time the limit is 100, so that makes sense
			`- Tsega restarted Tomcat and it's working now`
			`- Abenet said she was generating a report with Atmire's CUA module, so it could be due to that?`
			`- Looking in the logs I see this random error again that I should report to DSpace:`

			```
			`2017-07-05 13:50:07,196 ERROR org.dspace.statistics.SolrLogger @ COUNTRY ERROR: EU`
			```

			- Seems to come from `dspace-api/src/main/java/org/dspace/statistics/SolrLogger.java`
Add notes for 2017-07-06 2017-07-06 15:03:28 +02:00
			`## 2017-07-06`

			`- Sisay tried to help by making a [pull request for the RTB flagships](https://github.com/ilri/DSpace/pull/331) but there are formatting errors, unrelated changes, and the flagship names are not in the style I requested`
Update notes for 2017-07-06 2017-07-06 15:59:03 +02:00			`- Abenet talked to CIP and they said they are actually ok with using collection names rather than adding a new metadata field`
Add notes for 2017-07-13 2017-07-13 20:16:25 +02:00
			`## 2017-07-13`

			- Remove `UKaid` from the controlled vocabulary for `dc.description.sponsorship`, as `Department for International Development, United Kingdom` is the correct form and it is already present ([#334](https://github.com/ilri/DSpace/pull/334))
Add notes for 2017-07-14 2017-07-14 14:25:58 +02:00
			`## 2017-07-14`

			- Sisay sent me a patch to add "Photo Report" to `dc.type` so I've added it to the `5_x-prod` branch
Add notes for 2017-07-17 2017-07-17 21:50:33 +02:00
			`- Linode shut down our seventeen (17) VMs due to nonpayment of the July 1st invoice`
			`- It took me a few hours to find the ICT/Finance contacts to pay the bill and boot all the servers back up`
			- Since the server was down anyways, I decided to run all system updates and re-deploy CGSpace so that the latest changes to `input-forms.xml` and the sponsors controlled vocabulary