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

## 2017-07-17

- 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

## 2017-07-20

- Skype chat with Addis team about the status of the CGIAR Library migration
- Need to add the CGIAR System Organization subjects to Discovery Facets (test first)
- Tentative list of dates for the migration:
  - August 4: aim to finish data cleanup and then give Peter a list of authors
  - August 18: ready to show System Office
  - September 4: all feedback and decisions (including workflows) from System Office
  - September 10/11: go live?
- Talk to Tsega and Danny about exporting/injesting the blog posts from Drupal into DSpace?
- Followup meeting on August 8/9?
- Sent Abenet the 2415 records from CGIAR Library's Historical Archive (10947/1) after cleaning up the author authorities and HTML entities in `dc.contributor.author` and `dc.description.abstract` using OpenRefine:
  - Authors: `value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")`
  - Abstracts: `replace(value,/<\/?\w+((\s+\w+(\s*=\s*(?:".*?"|'.*?'|[^'">\s]+))?)+\s*|\s*)\/?>/,'')`

## 2017-07-24

- Move two top-level communities to be sub-communities of ILRI Projects

```
$ for community in 10568/2347 10568/25209; do /home/cgspace.cgiar.org/bin/dspace community-filiator --set --parent=10568/27629 --child="$community"; done
```

- Discuss CGIAR Library data cleanup with Sisay and Abenet

## 2017-07-27

- Help Sisay with some transforms to add descriptions to the `filename` column of some CIAT Presentations he's working on in OpenRefine
- Marianne emailed a few days ago to ask why "Integrating Ecosystem Solutions" was not in the list of WLE Phase I Research Themes on the input form
- I told her that I only added the themes that I saw in the [WLE Phase I Research Themes](https://cgspace.cgiar.org/handle/10568/34508) community
- Then Mia from WLE also emailed to ask where some WLE focal regions went, and I said I didn't understand what she was talking about, as all we did in our previous work was rename the old "Research Themes" subcommunity to "WLE Phase I Research Themes" and add a new subcommunity for "WLE Phase II Research Themes".
- Discuss some modifications to the CCAFS project tags in CGSpace submission form and in the database

## 2017-07-28

- Discuss updates to the Phase II CCAFS project tags with Andrea from Macaroni Bros
- I will do the renaming and untagging of items in CGSpace database, and he will update his webservice with the latest project tags and I will get the XML from here for our `input-forms.xml`: https://ccafs.cgiar.org/export/ccafsproject

## 2017-07-29

- Move some WLE items into appropriate Phase I Research Themes communities and delete some empty collections in WLE Regions community

## 2017-07-30

- Start working on CCAFS project tag cleanup
- More questions about inconsistencies and spelling mistakes in their tags, so I've sent some questions for followup

## 2017-07-31

- Looks like the final list of metadata corrections for CCAFS project tags will be:

```
delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-FP4_CRMWestAfrica';
update metadatavalue set text_value='FP3_VietnamLED' where resource_type_id=2 and metadata_field_id=134 and text_value='FP3_VeitnamLED';
update metadatavalue set text_value='PII-FP1_PIRCCA' where resource_type_id=2 and metadata_field_id=235 and text_value='PII-SEA_PIRCCA';
delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-WA_IntegratedInterventions';
```

- Now just waiting to run them on CGSpace, and then apply the modified input forms after Macaroni Bros give me an updated list
- Temporarily increase the nginx upload limit to 200MB for Sisay to upload the CIAT presentations
- Looking at CGSpace activity page, there are 52 Baidu bots concurrently crawling our website (I copied the activity page to a text file and grep it)!

```
$ grep 180.76. /tmp/status | awk '{print $5}' | sort | uniq | wc -l
52
```

- From looking at the `dspace.log` I see they are all using the same session, which means our Crawler Session Manager Valve is working
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
Add notes for 2017-07-20 2017-07-20 11:53:02 +02:00			`## 2017-07-17`

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
Add notes for 2017-07-20 2017-07-20 11:53:02 +02:00
			`## 2017-07-20`

			`- Skype chat with Addis team about the status of the CGIAR Library migration`
			`- Need to add the CGIAR System Organization subjects to Discovery Facets (test first)`
			`- Tentative list of dates for the migration:`
			`- August 4: aim to finish data cleanup and then give Peter a list of authors`
			`- August 18: ready to show System Office`
			`- September 4: all feedback and decisions (including workflows) from System Office`
			`- September 10/11: go live?`
			`- Talk to Tsega and Danny about exporting/injesting the blog posts from Drupal into DSpace?`
			`- Followup meeting on August 8/9?`
Update notes for 2017-07-20 2017-07-20 16:11:41 +02:00			- Sent Abenet the 2415 records from CGIAR Library's Historical Archive (10947/1) after cleaning up the author authorities and HTML entities in `dc.contributor.author` and `dc.description.abstract` using OpenRefine:
			- Authors: `value.replace(/::\w{8}-\w{4}-\w{4}-\w{4}-\w{12}::600/,"")`
			- Abstracts: `replace(value,/<\/?\w+((\s+\w+(\s=\s(?:".?"\|'.?'\|[^'">\s]+))?)+\s\|\s)\/?>/,'')`
Add notes for 2017-07-24 2017-07-24 14:39:20 +02:00
			`## 2017-07-24`

			`- Move two top-level communities to be sub-communities of ILRI Projects`

			```
			`$ for community in 10568/2347 10568/25209; do /home/cgspace.cgiar.org/bin/dspace community-filiator --set --parent=10568/27629 --child="$community"; done`
			```

			`- Discuss CGIAR Library data cleanup with Sisay and Abenet`
Add notes for 2017-07-27 2017-07-27 14:06:04 +02:00
			`## 2017-07-27`

			- Help Sisay with some transforms to add descriptions to the `filename` column of some CIAT Presentations he's working on in OpenRefine
			`- Marianne emailed a few days ago to ask why "Integrating Ecosystem Solutions" was not in the list of WLE Phase I Research Themes on the input form`
			`- I told her that I only added the themes that I saw in the [WLE Phase I Research Themes](https://cgspace.cgiar.org/handle/10568/34508) community`
			`- Then Mia from WLE also emailed to ask where some WLE focal regions went, and I said I didn't understand what she was talking about, as all we did in our previous work was rename the old "Research Themes" subcommunity to "WLE Phase I Research Themes" and add a new subcommunity for "WLE Phase II Research Themes".`
			`- Discuss some modifications to the CCAFS project tags in CGSpace submission form and in the database`
Add notes for 2017-07-28 2017-07-28 14:48:11 +02:00
			`## 2017-07-28`

			`- Discuss updates to the Phase II CCAFS project tags with Andrea from Macaroni Bros`
			- I will do the renaming and untagging of items in CGSpace database, and he will update his webservice with the latest project tags and I will get the XML from here for our `input-forms.xml`: https://ccafs.cgiar.org/export/ccafsproject
Add notes for 2017-07-29 2017-07-29 13:14:41 +02:00
			`## 2017-07-29`

			`- Move some WLE items into appropriate Phase I Research Themes communities and delete some empty collections in WLE Regions community`
Add notes for 2017-07-30 2017-07-30 13:18:23 +02:00
			`## 2017-07-30`

			`- Start working on CCAFS project tag cleanup`
			`- More questions about inconsistencies and spelling mistakes in their tags, so I've sent some questions for followup`
Add notes for 2017-07-31 2017-07-31 11:06:21 +02:00
			`## 2017-07-31`

			`- Looks like the final list of metadata corrections for CCAFS project tags will be:`

			```
			`delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-FP4_CRMWestAfrica';`
			`update metadatavalue set text_value='FP3_VietnamLED' where resource_type_id=2 and metadata_field_id=134 and text_value='FP3_VeitnamLED';`
			`update metadatavalue set text_value='PII-FP1_PIRCCA' where resource_type_id=2 and metadata_field_id=235 and text_value='PII-SEA_PIRCCA';`
			`delete from metadatavalue where resource_type_id=2 and metadata_field_id=235 and text_value='PII-WA_IntegratedInterventions';`
			```

			`- Now just waiting to run them on CGSpace, and then apply the modified input forms after Macaroni Bros give me an updated list`
			`- Temporarily increase the nginx upload limit to 200MB for Sisay to upload the CIAT presentations`
Add notes for 2017-07-31 2017-08-01 07:55:37 +02:00			`- Looking at CGSpace activity page, there are 52 Baidu bots concurrently crawling our website (I copied the activity page to a text file and grep it)!`

			```
			`$ grep 180.76. /tmp/status \| awk '{print $5}' \| sort \| uniq \| wc -l`
			`52`
			```

			- From looking at the `dspace.log` I see they are all using the same session, which means our Crawler Session Manager Valve is working