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Update notes for 2017-09-19
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@ -6,7 +6,7 @@ categories = ["Notes"]
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slug = "cgiar-library-migration"
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+++
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_Temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in `config.toml`_
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_Note: I'm temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in `config.toml`_
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Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called _CGIAR System Organization_.
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@ -19,15 +19,14 @@ Things that need to happen before the migration:
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- Set up nginx redirects for URLs like:
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- [x] https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf
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- [x] https://library.cgiar.org/handle/10947/4258
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- [ ] Merge [#339](https://github.com/ilri/DSpace/pull/339) to `5_x-prod` branch and rebuild DSpace
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- [x] Merge [#339](https://github.com/ilri/DSpace/pull/339) to `5_x-prod` branch and rebuild DSpace
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- [x] Increase `max_connections` in `/etc/postgresql/9.5/main/postgresql.conf` by ~10
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- `SELECT * FROM pg_stat_activity;` seems to show ~6 extra connections used by the command line tools during import
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- [x] Temporarily disable nightly `index-discovery` cron job because the import process will be taking place during some of this time and I don't want them to be competing to update the Solr index
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## Migration
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Process for the actual migration:
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## Migration Process
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- Export all top-level communities and collections from DSpace Test:
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**Export all top-level communities and collections from DSpace Test:**
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```
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$ export PATH=$PATH:/home/dspacetest.cgiar.org/bin
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@ -45,7 +44,8 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/105
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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```
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- Import to CGSpace (also see [notes from 2017-05-10](http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10))
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**Import to CGSpace (also see [notes from 2017-05-10](http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10)):**
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- [x] Copy all exports from DSpace Test
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- [x] Add ingestion overrides to `dspace.cfg` before import:
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@ -75,9 +75,10 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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```
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- This submits AIP hierarchies recursively (-r) and suppresses errors when an item's parent collection hasn't been created yet—for example, if the item is mapped
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- The large historic archive (10947/1) is created in several steps because it requires a lot of memory and often crashes
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- Create new subcommunities and collections for content we reorganized into new hierarchies from the original:
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This submits AIP hierarchies recursively (-r) and suppresses errors when an item's parent collection hasn't been created yet—for example, if the item is mapped. The large historic archive (10947/1) is created in several steps because it requires a lot of memory and often crashes.
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**Create new subcommunities and collections for content we reorganized into new hierarchies from the original:**
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- [x] Create _CGIAR System Management Board_ sub-community: 10568/83536
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- [x] Content from _CGIAR System Management Board documents_ collection (10947/4561) goes here
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- Import collection hierarchy first and then the items:
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@ -95,7 +96,7 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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$ for item in 10568-93759/ITEM@10947-46*; do dspace packager -r -t AIP -o ignoreHandle=false -o ignoreParent=true -e aorth@mjanja.ch -p 10568/83538 $item; done
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```
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- Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:
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**Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:**
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```
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dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
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@ -113,12 +114,11 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
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```
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- [ ] Shut down Tomcat and run `update-sequences.sql` as the system's `postgres` user
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## Post Migration
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- [ ] Shut down Tomcat and run `update-sequences.sql` as the system's `postgres` user
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- [x] Remove ingestion overrides from `dspace.cfg`
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- [ ] Reset PostgreSQL `max_connections` to 183
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- [x] Reset PostgreSQL `max_connections` to 183
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- [x] Enable nightly `index-discovery` cron job
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- HTTPS certificates:
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- [x] Install current certificates from their Tomcat keystore
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@ -135,16 +135,15 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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- [ ] Update DNS records:
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- CNAME: cgspace.cgiar.org
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- [ ] Re-deploy DSpace from freshly built `5_x-prod` branch
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- [ ] Merge `cgiar-library` branch to `master` and re-run ansible nginx templates
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- [ ] Run system updates and reboot server
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- [ ] Switch to Let's Encrypt HTTPS certificates (after DNS is updated and server isn't busy)
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- [ ] Switch to Let's Encrypt HTTPS certificates (after DNS is updated and server isn't busy):
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```
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$ sudo systemctl stop tomcat7
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$ ./letsencrypt-auto certonly --standalone -d library.cgiar.org
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```
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- [ ] Merge `cgiar-library` branch to `master` and re-run ansible nginx templates
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## Troubleshooting
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### Foreign Key Error in `dspace cleanup`
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@ -398,3 +398,19 @@ $ for item in 10568-93759/ITEM@10947-46*; do ~/dspace/bin/dspace packager -r -t
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- Moved the CGIAR Library Migration notes to a page — [cgiar-library-migration]({{< relref "cgiar-library-migration.md" >}}) — as there seems to be a bug with post slugs defined in frontmatter when you have a permalink scheme defined in `config.toml` (happens currently in Hugo 0.27.1 at least)
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## 2017-09-19
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- Nightly Solr indexing is working again, and it appears to be pretty quick actually:
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```
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2017-09-19 00:00:14,953 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (0 of 65808): 17607
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...
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2017-09-19 00:04:18,017 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (65807 of 65808): 83753
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```
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- Sisay asked if he could import 50 items for IITA that have already been checked by Bosede and Bizuwork
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- I had a look at the collection and noticed a bunch of issues with item types and donors, so I asked him to fix those and import it to DSpace Test again first
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- Abenet wants to be able to filter by ISI Journal in advanced search on queries like this: https://cgspace.cgiar.org/discover?filtertype_0=dateIssued&filtertype_1=dateIssued&filter_relational_operator_1=equals&filter_relational_operator_0=equals&filter_1=%5B2010+TO+2017%5D&filter_0=2017&filtertype=type&filter_relational_operator=equals&filter=Journal+Article
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- I opened an issue to track this ([#340](https://github.com/ilri/DSpace/issues/340)) and will test it on DSpace Test soon
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@ -61,7 +61,7 @@ Ask Sisay to clean up the WLE approvers a bit, as Marianne’s user account
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"@type": "BlogPosting",
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"headline": "September, 2017",
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"url": "https://alanorth.github.io/cgspace-notes/2017-09/",
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"wordCount": "2764",
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"wordCount": "2886",
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"datePublished": "2017-09-07T16:54:52+07:00",
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"dateModified": "2017-09-18T18:18:09+03:00",
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"author": {
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@ -569,6 +569,24 @@ DELETE 207
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<li>Moved the CGIAR Library Migration notes to a page — <a href="/cgspace-notes/cgiar-library-migration/">cgiar-library-migration</a> — as there seems to be a bug with post slugs defined in frontmatter when you have a permalink scheme defined in <code>config.toml</code> (happens currently in Hugo 0.27.1 at least)</li>
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</ul>
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<h2 id="2017-09-19">2017-09-19</h2>
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<ul>
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<li>Nightly Solr indexing is working again, and it appears to be pretty quick actually:</li>
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</ul>
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<pre><code>2017-09-19 00:00:14,953 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (0 of 65808): 17607
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...
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2017-09-19 00:04:18,017 INFO com.atmire.dspace.discovery.AtmireSolrService @ Processing (65807 of 65808): 83753
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</code></pre>
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<ul>
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<li>Sisay asked if he could import 50 items for IITA that have already been checked by Bosede and Bizuwork</li>
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<li>I had a look at the collection and noticed a bunch of issues with item types and donors, so I asked him to fix those and import it to DSpace Test again first</li>
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<li>Abenet wants to be able to filter by ISI Journal in advanced search on queries like this: <a href="https://cgspace.cgiar.org/discover?filtertype_0=dateIssued&filtertype_1=dateIssued&filter_relational_operator_1=equals&filter_relational_operator_0=equals&filter_1=%5B2010+TO+2017%5D&filter_0=2017&filtertype=type&filter_relational_operator=equals&filter=Journal+Article">https://cgspace.cgiar.org/discover?filtertype_0=dateIssued&filtertype_1=dateIssued&filter_relational_operator_1=equals&filter_relational_operator_0=equals&filter_1=%5B2010+TO+2017%5D&filter_0=2017&filtertype=type&filter_relational_operator=equals&filter=Journal+Article</a></li>
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<li>I opened an issue to track this (<a href="https://github.com/ilri/DSpace/issues/340">#340</a>) and will test it on DSpace Test soon</li>
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</ul>
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@ -17,7 +17,7 @@
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<pubDate>Mon, 18 Sep 2017 16:38:35 +0300</pubDate>
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<guid>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</guid>
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<description>Temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in config.toml
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<description>Note: I&rsquo;m temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in config.toml
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Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.
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Pre-migration Technical TODOs Things that need to happen before the migration:
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Create top-level community on CGSpace to hold the CGIAR Library content: 10568&frasl;83389 Update nginx redirects in ansible templates Update handle in DSpace XMLUI config Set up nginx redirects for URLs like: https://library.</description>
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@ -13,7 +13,7 @@
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<meta property="article:published_time" content="2017-09-18T16:38:35+03:00"/>
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<meta property="article:modified_time" content="2017-09-18T18:05:57+03:00"/>
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<meta property="article:modified_time" content="2017-09-18T21:24:27+03:00"/>
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@ -37,9 +37,9 @@
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"@type": "BlogPosting",
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"headline": "CGIAR Library Migration",
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"url": "https://alanorth.github.io/cgspace-notes/cgiar-library-migration/",
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"wordCount": "1169",
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"wordCount": "1167",
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"datePublished": "2017-09-18T16:38:35+03:00",
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"dateModified": "2017-09-18T18:05:57+03:00",
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"dateModified": "2017-09-18T21:24:27+03:00",
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"author": {
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"@type": "Person",
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"name": "Alan Orth"
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@ -108,7 +108,7 @@
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</header>
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<p><em>Temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in <code>config.toml</code></em></p>
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<p><em>Note: I’m temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in <code>config.toml</code></em></p>
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<p>Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called <em>CGIAR System Organization</em>.</p>
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@ -129,7 +129,7 @@
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<li><label><input type="checkbox" checked disabled class="task-list-item"> <a href="https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf">https://library.cgiar.org/bitstream/handle/10947/2699/CGIAR_Branding_Guidelines_and_Toolkit.pdf</a></label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> <a href="https://library.cgiar.org/handle/10947/4258">https://library.cgiar.org/handle/10947/4258</a></label></li>
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</ul></li>
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<li><label><input type="checkbox" disabled class="task-list-item"> Merge <a href="https://github.com/ilri/DSpace/pull/339">#339</a> to <code>5_x-prod</code> branch and rebuild DSpace</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Merge <a href="https://github.com/ilri/DSpace/pull/339">#339</a> to <code>5_x-prod</code> branch and rebuild DSpace</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Increase <code>max_connections</code> in <code>/etc/postgresql/9.5/main/postgresql.conf</code> by ~10
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<ul>
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@ -138,13 +138,9 @@
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Temporarily disable nightly <code>index-discovery</code> cron job because the import process will be taking place during some of this time and I don’t want them to be competing to update the Solr index</label></li>
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</ul>
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<h2 id="migration">Migration</h2>
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<h2 id="migration-process">Migration Process</h2>
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<p>Process for the actual migration:</p>
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<ul>
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<li>Export all top-level communities and collections from DSpace Test:</li>
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</ul>
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<p><strong>Export all top-level communities and collections from DSpace Test:</strong></p>
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<pre><code>$ export PATH=$PATH:/home/dspacetest.cgiar.org/bin
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/2515 10947-2515/10947-2515.zip
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@ -161,13 +157,11 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10568/93760 10568-93760/105
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$ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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</code></pre>
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<ul class="task-list">
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<li>Import to CGSpace (also see <a href="http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10">notes from 2017-05-10</a>)
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<p><strong>Import to CGSpace (also see <a href="http://alanorth.github.io/cgspace-notes/2017-05/#2017-05-10">notes from 2017-05-10</a>):</strong></p>
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Copy all exports from DSpace Test</label></li>
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Add ingestion overrides to <code>dspace.cfg</code> before import:</label></li>
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</ul></li>
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</ul>
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<pre><code>mets.dspaceAIP.ingest.crosswalk.METSRIGHTS = NIL
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@ -196,16 +190,17 @@ $ dspace packager -d -a -t AIP -e aorth@mjanja.ch -i 10947/1 10947-1/10947-1.zip
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$ for item in 10947-1/ITEM@10947-*; do dspace packager -r -f -u -t AIP -e aorth@mjanja.ch $item; done
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</code></pre>
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<ul class="task-list">
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<li>This submits AIP hierarchies recursively (-r) and suppresses errors when an item’s parent collection hasn’t been created yet—for example, if the item is mapped</li>
|
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<li>The large historic archive (<sup>10947</sup>⁄<sub>1</sub>) is created in several steps because it requires a lot of memory and often crashes</li>
|
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<p>This submits AIP hierarchies recursively (-r) and suppresses errors when an item’s parent collection hasn’t been created yet—for example, if the item is mapped. The large historic archive (<sup>10947</sup>⁄<sub>1</sub>) is created in several steps because it requires a lot of memory and often crashes.</p>
|
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|
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<li><p>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</p>
|
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<p><strong>Create new subcommunities and collections for content we reorganized into new hierarchies from the original:</strong></p>
|
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|
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<ul class="task-list">
|
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Board</em> sub-community: <sup>10568</sup>⁄<sub>83536</sub>
|
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<ul class="task-list">
|
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Board</em> sub-community: <sup>10568</sup>⁄<sub>83536</sub></label></li>
|
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Content from <em>CGIAR System Management Board documents</em> collection (<sup>10947</sup>⁄<sub>4561</sub>) goes here</label></li>
|
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<li>Import collection hierarchy first and then the items:</li>
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</ul></label></li>
|
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</ul>
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<pre><code>$ dspace packager -r -t AIP -o ignoreHandle=false -e aorth@mjanja.ch -p 10568/83536 10568-93760/COLLECTION@10947-4651.zip
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@ -213,18 +208,18 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
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</code></pre>
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|
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<ul class="task-list">
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office</em> sub-community: <sup>10568</sup>⁄<sub>83537</sub></label></li>
|
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office</em> sub-community: <sup>10568</sup>⁄<sub>83537</sub>
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|
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<ul class="task-list">
|
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<li><label><input type="checkbox" checked disabled class="task-list-item"> Create <em>CGIAR System Management Office documents</em> collection: <sup>10568</sup>⁄<sub>83538</sub></label></li>
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<li>Import items to collection individually in replace mode (-r) while explicitly preserving handles and ignoring parents:</li>
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</ul></label></li>
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</ul>
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<pre><code>$ for item in 10568-93759/ITEM@10947-46*; do dspace packager -r -t AIP -o ignoreHandle=false -o ignoreParent=true -e aorth@mjanja.ch -p 10568/83538 $item; done
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</code></pre>
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|
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<ul>
|
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<li>Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:</li>
|
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</ul></li>
|
||||
</ul>
|
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<p><strong>Get the handles for the last few items from CGIAR Library that were created since we did the migration to DSpace Test in May:</strong></p>
|
||||
|
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<pre><code>dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
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</code></pre>
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@ -243,15 +238,12 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
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||||
<pre><code>$ for item in 10947-latest/*.zip; do dspace packager -r -u -t AIP -e aorth@mjanja.ch $item; done
|
||||
</code></pre>
|
||||
|
||||
<ul class="task-list">
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system’s <code>postgres</code> user</label></li>
|
||||
</ul>
|
||||
|
||||
<h2 id="post-migration">Post Migration</h2>
|
||||
|
||||
<ul class="task-list">
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Shut down Tomcat and run <code>update-sequences.sql</code> as the system’s <code>postgres</code> user</label></li>
|
||||
<li><label><input type="checkbox" checked disabled class="task-list-item"> Remove ingestion overrides from <code>dspace.cfg</code></label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Reset PostgreSQL <code>max_connections</code> to 183</label></li>
|
||||
<li><label><input type="checkbox" checked disabled class="task-list-item"> Reset PostgreSQL <code>max_connections</code> to 183</label></li>
|
||||
<li><label><input type="checkbox" checked disabled class="task-list-item"> Enable nightly <code>index-discovery</code> cron job</label></li>
|
||||
<li>HTTPS certificates:
|
||||
|
||||
@ -275,18 +267,15 @@ $ for item in 10568-93760/ITEM@10947-465*; do dspace packager -r -f -u -t AIP -e
|
||||
<li>CNAME: cgspace.cgiar.org</li>
|
||||
</ul></label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Re-deploy DSpace from freshly built <code>5_x-prod</code> branch</label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Run system updates and reboot server</label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Switch to Let’s Encrypt HTTPS certificates (after DNS is updated and server isn’t busy)</label></li>
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Switch to Let’s Encrypt HTTPS certificates (after DNS is updated and server isn’t busy):</label></li>
|
||||
</ul>
|
||||
|
||||
<pre><code>$ sudo systemctl stop tomcat7
|
||||
$ ./letsencrypt-auto certonly --standalone -d library.cgiar.org
|
||||
</code></pre>
|
||||
|
||||
<ul class="task-list">
|
||||
<li><label><input type="checkbox" disabled class="task-list-item"> Merge <code>cgiar-library</code> branch to <code>master</code> and re-run ansible nginx templates</label></li>
|
||||
</ul>
|
||||
|
||||
<h2 id="troubleshooting">Troubleshooting</h2>
|
||||
|
||||
<h3 id="foreign-key-error-in-dspace-cleanup">Foreign Key Error in <code>dspace cleanup</code></h3>
|
||||
|
||||
@ -17,7 +17,7 @@
|
||||
<pubDate>Mon, 18 Sep 2017 16:38:35 +0300</pubDate>
|
||||
|
||||
<guid>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</guid>
|
||||
<description>Temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in config.toml
|
||||
<description>Note: I&rsquo;m temporarily making this a page because it seems Hugo (currently 0.27.1) cannot use a custom slug for a post when there is a permalink defined in config.toml
|
||||
Rough notes for importing the CGIAR Library content. It was decided that this content would go to a new top-level community called CGIAR System Organization.
|
||||
Pre-migration Technical TODOs Things that need to happen before the migration:
|
||||
Create top-level community on CGSpace to hold the CGIAR Library content: 10568&frasl;83389 Update nginx redirects in ansible templates Update handle in DSpace XMLUI config Set up nginx redirects for URLs like: https://library.</description>
|
||||
|
||||
@ -4,7 +4,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/cgiar-library-migration/</loc>
|
||||
<lastmod>2017-09-18T18:05:57+03:00</lastmod>
|
||||
<lastmod>2017-09-18T21:24:27+03:00</lastmod>
|
||||
</url>
|
||||
|
||||
<url>
|
||||
@ -124,7 +124,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/</loc>
|
||||
<lastmod>2017-09-18T18:05:57+03:00</lastmod>
|
||||
<lastmod>2017-09-18T21:24:27+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
@ -141,7 +141,7 @@
|
||||
|
||||
<url>
|
||||
<loc>https://alanorth.github.io/cgspace-notes/categories/notes/</loc>
|
||||
<lastmod>2017-09-18T18:05:57+03:00</lastmod>
|
||||
<lastmod>2017-09-18T21:24:27+03:00</lastmod>
|
||||
<priority>0</priority>
|
||||
</url>
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user