diff --git a/content/post/2016-09.md b/content/post/2016-09.md
index f271d5023..5e0a1f2ac 100644
--- a/content/post/2016-09.md
+++ b/content/post/2016-09.md
@@ -540,6 +540,11 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
- Add `cg.identifier.ciatproject` to metadata registry in preparation for CIAT project tag
- Merge changes for CIAT project tag ([#282](https://github.com/ilri/DSpace/pull/282))
- DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console
+- People on DSpace mailing list gave me a query to get authors from certain collections:
+
+```
+dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
+```
## 2016-09-30
diff --git a/content/post/2016-10.md b/content/post/2016-10.md
new file mode 100644
index 000000000..6e7730d44
--- /dev/null
+++ b/content/post/2016-10.md
@@ -0,0 +1,26 @@
++++
+date = "2016-10-03T15:53:00+03:00"
+author = "Alan Orth"
+title = "October, 2016"
+tags = ["Notes"]
+
++++
+## 2016-10-03
+
+- Testing adding [ORCIDs to a CSV](https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing) file for a single item to see if the author orders get messed up
+- Need to test the following scenarios to see how author order is affected:
+ - ORCIDs only
+ - ORCIDs plus normal authors
+- I exported a random item's metadata as CSV, deleted *all columns* except id and collection, and made a new coloum called `ORCID:dc.contributor.author` with the following random ORCIDs from the ORCID registry:
+
+```
+0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
+```
+
+- Hmm, with the `dc.contributor.author` column removed, DSpace doesn't detect any changes
+- With a blank `dc.contributor.author` column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors
+- I added the [disclaimer text](https://github.com/ilri/DSpace/issues/234) to the About page, then added a footer link to the disclaimer's ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: https://github.com/twbs/bootstrap/issues/1768
+
+
+
+- Looks like we'll just have to add the text to the About page (without a link) or add a separate page
diff --git a/public/2015-11/index.html b/public/2015-11/index.html
index b77bf150e..b1d5e1eb8 100644
--- a/public/2015-11/index.html
+++ b/public/2015-11/index.html
@@ -35,7 +35,7 @@
-
+
@@ -82,9 +82,7 @@
-
-
-
2015-11-22
+
2015-11-22
CGSpace went down
@@ -96,6 +94,8 @@
78
+
+
For now I have increased the limit from 60 to 90, run updates, and rebooted the server
@@ -229,7 +229,6 @@ db.statementpool = true
This might help with REST API speed (which I mentioned above and still need to do real tests)
Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit
@@ -94,6 +92,8 @@
Also, I noticed the checker log has some errors we should pay attention to:
+
+
Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@@ -535,7 +535,6 @@ dspace.log.2016-04-27:7271
I will check the logs again in a few days to look for patterns, see who is accessing it, etc
Experimenting with IFPRI OAI (we want to harvest their publications)
@@ -95,6 +93,8 @@
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
+
+
dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@@ -428,7 +428,6 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
# update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console
+
People on DSpace mailing list gave me a query to get authors from certain collections:
+
dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
+
Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up
+
Need to test the following scenarios to see how author order is affected:
+
+
+
ORCIDs only
+
ORCIDs plus normal authors
+
+
I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry:
Hmm, with the dc.contributor.author column removed, DSpace doesn’t detect any changes
+
With a blank dc.contributor.author column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors
+
I added the disclaimer text to the About page, then added a footer link to the disclaimer’s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: https://github.com/twbs/bootstrap/issues/1768
+
+
+
+
+
+
Looks like we’ll just have to add the text to the About page (without a link) or add a separate page
+
+ 2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
+ Read more →
+
+
+
+
Read more →
@@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
+
Read more →
@@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
+
Read more →
@@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
-
diff --git a/public/index.xml b/public/index.xml
index 227650658..9adfdec2c 100644
--- a/public/index.xml
+++ b/public/index.xml
@@ -2,22 +2,58 @@
CGSpace Notes
- https://alanorth.github.io/cgspace-notes/
+ https://alanorth.github.io/cgspace-notes/index.xml
Recent content on CGSpace NotesHugo -- gohugo.ioen-us
- Thu, 01 Sep 2016 15:53:00 +0300
+ Mon, 03 Oct 2016 15:53:00 +0300
+
+ October, 2016
+ https://alanorth.github.io/cgspace-notes/2016-10/
+ Mon, 03 Oct 2016 15:53:00 +0300
+
+ https://alanorth.github.io/cgspace-notes/2016-10/
+
+
+<h2 id="2016-10-03">2016-10-03</h2>
+
+<ul>
+<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
+<li>Need to test the following scenarios to see how author order is affected:
+
+<ul>
+<li>ORCIDs only</li>
+<li>ORCIDs plus normal authors</li>
+</ul></li>
+<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
+</ul>
+
+<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
+</code></pre>
+
+<ul>
+<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn’t detect any changes</li>
+<li>With a blank <code>dc.contributor.author</code> column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors</li>
+<li>I added the <a href="https://github.com/ilri/DSpace/issues/234">disclaimer text</a> to the About page, then added a footer link to the disclaimer’s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: <a href="https://github.com/twbs/bootstrap/issues/1768">https://github.com/twbs/bootstrap/issues/1768</a></li>
+</ul>
+
+<p><img src="2016/10/bootstrap-issue.png" alt="Bootstrap issue with in-page anchors" /></p>
+
+<ul>
+<li>Looks like we’ll just have to add the text to the About page (without a link) or add a separate page</li>
+</ul>
+
+
+
September, 2016
https://alanorth.github.io/cgspace-notes/2016-09/
Thu, 01 Sep 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-09/
-
-
-<h2 id="2016-09-01">2016-09-01</h2>
+ <h2 id="2016-09-01">2016-09-01</h2>
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
@@ -29,6 +65,8 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
</code></pre>
+<p></p>
+
<ul>
<li>User who has been migrated to the root vs user still in the hierarchical structure:</li>
</ul>
@@ -637,15 +675,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li>Add <code>cg.identifier.ciatproject</code> to metadata registry in preparation for CIAT project tag</li>
<li>Merge changes for CIAT project tag (<a href="https://github.com/ilri/DSpace/pull/282">#282</a>)</li>
<li>DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console</li>
+<li>People on DSpace mailing list gave me a query to get authors from certain collections:</li>
</ul>
+<pre><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
+</code></pre>
+
<h2 id="2016-09-30">2016-09-30</h2>
<ul>
<li>Deny access to REST API’s <code>find-by-metadata-field</code> endpoint to protect against an upstream security issue (DS-3250)</li>
<li>There is a patch but it is only for 5.5 and doesn’t apply cleanly to 5.1</li>
-</ul>
-
+</ul>
@@ -654,9 +695,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
Mon, 01 Aug 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-08/
-
-
-<h2 id="2016-08-01">2016-08-01</h2>
+ <h2 id="2016-08-01">2016-08-01</h2>
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
@@ -672,6 +711,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
+<p></p>
+
<ul>
<li>Lots of conflicts that don’t make sense (ie, shouldn’t conflict!)</li>
<li>This file in particular conflicts almost 10 times: <code>dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss</code></li>
@@ -979,8 +1020,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
<ul>
<li>Run corrections for Delia Grace and <code>CONGO, DR</code>, and deploy August changes to CGSpace</li>
<li>Run all system updates and reboot the server</li>
-</ul>
-
+</ul>
@@ -989,9 +1029,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
Fri, 01 Jul 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-07/
-
-
-<h2 id="2016-07-01">2016-07-01</h2>
+ <h2 id="2016-07-01">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
@@ -1010,6 +1048,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
+<p></p>
+
<h2 id="2016-07-02">2016-07-02</h2>
<ul>
@@ -1235,8 +1275,7 @@ discovery.index.authority.ignore-variants=true
<ul>
<li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li>
<li>Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (<a href="https://github.com/ilri/DSpace/issues/257">#257</a>)</li>
-</ul>
-
+</ul>
@@ -1245,9 +1284,7 @@ discovery.index.authority.ignore-variants=true
Wed, 01 Jun 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-06/
-
-
-<h2 id="2016-06-01">2016-06-01</h2>
+ <h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
@@ -1258,6 +1295,8 @@ discovery.index.authority.ignore-variants=true
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
+<p></p>
+
<pre><code>dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@@ -1589,8 +1628,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
</ul>
<pre><code># update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
-</code></pre>
-
+</code></pre>
@@ -1599,9 +1637,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
Sun, 01 May 2016 23:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-05/
-
-
-<h2 id="2016-05-01">2016-05-01</h2>
+ <h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
@@ -1613,6 +1649,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
</code></pre>
+<p></p>
+
<ul>
<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
@@ -1896,8 +1934,7 @@ sys 0m20.540s
<li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li>
<li>Re-sync DSpace Test data with CGSpace</li>
<li>Clean up and import ~65 more CTA items into CGSpace</li>
-</ul>
-
+</ul>
@@ -1906,9 +1943,7 @@ sys 0m20.540s
Mon, 04 Apr 2016 11:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-04/
-
-
-<h2 id="2016-04-04">2016-04-04</h2>
+ <h2 id="2016-04-04">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
@@ -1918,6 +1953,8 @@ sys 0m20.540s
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul>
+<p></p>
+
<pre><code>Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@@ -2357,8 +2394,7 @@ dspace.log.2016-04-27:7271
<ul>
<li>I will check the logs again in a few days to look for patterns, see who is accessing it, etc</li>
-</ul>
-
+</ul>
@@ -2367,9 +2403,7 @@ dspace.log.2016-04-27:7271
Wed, 02 Mar 2016 16:50:00 +0300https://alanorth.github.io/cgspace-notes/2016-03/
-
-
-<h2 id="2016-03-02">2016-03-02</h2>
+ <h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
@@ -2377,6 +2411,8 @@ dspace.log.2016-04-27:7271
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
+<p></p>
+
<h2 id="2016-03-07">2016-03-07</h2>
<ul>
@@ -2605,8 +2641,7 @@ dspace.log.2016-04-27:7271
<li>We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to <code>cg.*</code>, and then worry about broader changes to DC</li>
<li>Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields</li>
<li>After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects</li>
-</ul>
-
+</ul>
@@ -2615,9 +2650,7 @@ dspace.log.2016-04-27:7271
Fri, 05 Feb 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-02/
-
-
-<h2 id="2016-02-05">2016-02-05</h2>
+ <h2 id="2016-02-05">2016-02-05</h2>
<ul>
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
@@ -2632,6 +2665,8 @@ dspace.log.2016-04-27:7271
<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
</ul>
+<p></p>
+
<h2 id="2016-02-06">2016-02-06</h2>
<ul>
@@ -2939,8 +2974,7 @@ Bitstream: tést señora alimentación.pdf
<ul>
<li>Finally import the 1127 CIAT items into CGSpace: <a href="https://cgspace.cgiar.org/handle/10568/35710">https://cgspace.cgiar.org/handle/10568/35710</a></li>
<li>Re-deploy CGSpace with the Google Scholar fix, but I’m waiting on the Atmire fixes for now, as the branch history is ugly</li>
-</ul>
-
+</ul>
@@ -2949,9 +2983,7 @@ Bitstream: tést señora alimentación.pdf
Wed, 13 Jan 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-01/
-
-
-<h2 id="2016-01-13">2016-01-13</h2>
+ <h2 id="2016-01-13">2016-01-13</h2>
<ul>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
@@ -2959,6 +2991,8 @@ Bitstream: tést señora alimentación.pdf
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
</ul>
+<p></p>
+
<h2 id="2016-01-14">2016-01-14</h2>
<ul>
@@ -3034,8 +3068,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
<li>After:</li>
</ul>
-<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
-
+<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
@@ -3044,9 +3077,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
Wed, 02 Dec 2015 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2015-12/
-
-
-<h2 id="2015-12-02">2015-12-02</h2>
+ <h2 id="2015-12-02">2015-12-02</h2>
<ul>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
@@ -3059,6 +3090,8 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre>
+<p></p>
+
<ul>
<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
@@ -3204,8 +3237,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<ul>
<li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn’t as good, but it’s much faster and causes less IO/CPU load</li>
<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot’s crawl rate to the “Let Google optimize” setting</li>
-</ul>
-
+</ul>
@@ -3214,9 +3246,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
Mon, 23 Nov 2015 17:00:57 +0300https://alanorth.github.io/cgspace-notes/2015-11/
-
-
-<h2 id="2015-11-22">2015-11-22</h2>
+ <h2 id="2015-11-22">2015-11-22</h2>
<ul>
<li>CGSpace went down</li>
@@ -3228,6 +3258,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
</code></pre>
+<p></p>
+
<ul>
<li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li>
</ul>
@@ -3359,8 +3391,7 @@ db.statementpool = true
<li>Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace’s thirst can ever be quenched</li>
<li>On another note, SUNScholar’s notes suggest adjusting some other postgres variables: <a href="http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database">http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database</a></li>
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
-</ul>
-
+</ul>
diff --git a/public/post/index.html b/public/post/index.html
index 9562cadbe..e4f70b8c7 100644
--- a/public/post/index.html
+++ b/public/post/index.html
@@ -32,7 +32,7 @@
-
+
@@ -74,6 +74,20 @@
+
+
+
+
+ 2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
+ Read more →
+
+
+
+
Read more →
@@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
+
Read more →
@@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
+
Read more →
@@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
-
diff --git a/public/post/index.xml b/public/post/index.xml
index a5bbcabc7..19376a044 100644
--- a/public/post/index.xml
+++ b/public/post/index.xml
@@ -1,23 +1,59 @@
- Posts on CGSpace Notes
- https://alanorth.github.io/cgspace-notes/post/
- Recent content in Posts on CGSpace Notes
+ Post-rsses on CGSpace Notes
+ https://alanorth.github.io/cgspace-notes/post/index.xml
+ Recent content in Post-rsses on CGSpace NotesHugo -- gohugo.ioen-us
- Thu, 01 Sep 2016 15:53:00 +0300
+ Mon, 03 Oct 2016 15:53:00 +0300
+
+ October, 2016
+ https://alanorth.github.io/cgspace-notes/2016-10/
+ Mon, 03 Oct 2016 15:53:00 +0300
+
+ https://alanorth.github.io/cgspace-notes/2016-10/
+
+
+<h2 id="2016-10-03">2016-10-03</h2>
+
+<ul>
+<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
+<li>Need to test the following scenarios to see how author order is affected:
+
+<ul>
+<li>ORCIDs only</li>
+<li>ORCIDs plus normal authors</li>
+</ul></li>
+<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
+</ul>
+
+<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
+</code></pre>
+
+<ul>
+<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn’t detect any changes</li>
+<li>With a blank <code>dc.contributor.author</code> column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors</li>
+<li>I added the <a href="https://github.com/ilri/DSpace/issues/234">disclaimer text</a> to the About page, then added a footer link to the disclaimer’s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: <a href="https://github.com/twbs/bootstrap/issues/1768">https://github.com/twbs/bootstrap/issues/1768</a></li>
+</ul>
+
+<p><img src="2016/10/bootstrap-issue.png" alt="Bootstrap issue with in-page anchors" /></p>
+
+<ul>
+<li>Looks like we’ll just have to add the text to the About page (without a link) or add a separate page</li>
+</ul>
+
+
+
September, 2016
https://alanorth.github.io/cgspace-notes/2016-09/
Thu, 01 Sep 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-09/
-
-
-<h2 id="2016-09-01">2016-09-01</h2>
+ <h2 id="2016-09-01">2016-09-01</h2>
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
@@ -29,6 +65,8 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
</code></pre>
+<p></p>
+
<ul>
<li>User who has been migrated to the root vs user still in the hierarchical structure:</li>
</ul>
@@ -637,15 +675,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li>Add <code>cg.identifier.ciatproject</code> to metadata registry in preparation for CIAT project tag</li>
<li>Merge changes for CIAT project tag (<a href="https://github.com/ilri/DSpace/pull/282">#282</a>)</li>
<li>DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console</li>
+<li>People on DSpace mailing list gave me a query to get authors from certain collections:</li>
</ul>
+<pre><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
+</code></pre>
+
<h2 id="2016-09-30">2016-09-30</h2>
<ul>
<li>Deny access to REST API’s <code>find-by-metadata-field</code> endpoint to protect against an upstream security issue (DS-3250)</li>
<li>There is a patch but it is only for 5.5 and doesn’t apply cleanly to 5.1</li>
-</ul>
-
+</ul>
@@ -654,9 +695,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
Mon, 01 Aug 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-08/
-
-
-<h2 id="2016-08-01">2016-08-01</h2>
+ <h2 id="2016-08-01">2016-08-01</h2>
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
@@ -672,6 +711,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
+<p></p>
+
<ul>
<li>Lots of conflicts that don’t make sense (ie, shouldn’t conflict!)</li>
<li>This file in particular conflicts almost 10 times: <code>dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss</code></li>
@@ -979,8 +1020,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
<ul>
<li>Run corrections for Delia Grace and <code>CONGO, DR</code>, and deploy August changes to CGSpace</li>
<li>Run all system updates and reboot the server</li>
-</ul>
-
+</ul>
@@ -989,9 +1029,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
Fri, 01 Jul 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-07/
-
-
-<h2 id="2016-07-01">2016-07-01</h2>
+ <h2 id="2016-07-01">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
@@ -1010,6 +1048,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
+<p></p>
+
<h2 id="2016-07-02">2016-07-02</h2>
<ul>
@@ -1235,8 +1275,7 @@ discovery.index.authority.ignore-variants=true
<ul>
<li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li>
<li>Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (<a href="https://github.com/ilri/DSpace/issues/257">#257</a>)</li>
-</ul>
-
+</ul>
@@ -1245,9 +1284,7 @@ discovery.index.authority.ignore-variants=true
Wed, 01 Jun 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-06/
-
-
-<h2 id="2016-06-01">2016-06-01</h2>
+ <h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
@@ -1258,6 +1295,8 @@ discovery.index.authority.ignore-variants=true
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
+<p></p>
+
<pre><code>dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@@ -1589,8 +1628,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
</ul>
<pre><code># update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
-</code></pre>
-
+</code></pre>
@@ -1599,9 +1637,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
Sun, 01 May 2016 23:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-05/
-
-
-<h2 id="2016-05-01">2016-05-01</h2>
+ <h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
@@ -1613,6 +1649,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
</code></pre>
+<p></p>
+
<ul>
<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
@@ -1896,8 +1934,7 @@ sys 0m20.540s
<li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li>
<li>Re-sync DSpace Test data with CGSpace</li>
<li>Clean up and import ~65 more CTA items into CGSpace</li>
-</ul>
-
+</ul>
@@ -1906,9 +1943,7 @@ sys 0m20.540s
Mon, 04 Apr 2016 11:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-04/
-
-
-<h2 id="2016-04-04">2016-04-04</h2>
+ <h2 id="2016-04-04">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
@@ -1918,6 +1953,8 @@ sys 0m20.540s
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul>
+<p></p>
+
<pre><code>Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@@ -2357,8 +2394,7 @@ dspace.log.2016-04-27:7271
<ul>
<li>I will check the logs again in a few days to look for patterns, see who is accessing it, etc</li>
-</ul>
-
+</ul>
@@ -2367,9 +2403,7 @@ dspace.log.2016-04-27:7271
Wed, 02 Mar 2016 16:50:00 +0300https://alanorth.github.io/cgspace-notes/2016-03/
-
-
-<h2 id="2016-03-02">2016-03-02</h2>
+ <h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
@@ -2377,6 +2411,8 @@ dspace.log.2016-04-27:7271
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
+<p></p>
+
<h2 id="2016-03-07">2016-03-07</h2>
<ul>
@@ -2605,8 +2641,7 @@ dspace.log.2016-04-27:7271
<li>We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to <code>cg.*</code>, and then worry about broader changes to DC</li>
<li>Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields</li>
<li>After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects</li>
-</ul>
-
+</ul>
@@ -2615,9 +2650,7 @@ dspace.log.2016-04-27:7271
Fri, 05 Feb 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-02/
-
-
-<h2 id="2016-02-05">2016-02-05</h2>
+ <h2 id="2016-02-05">2016-02-05</h2>
<ul>
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
@@ -2632,6 +2665,8 @@ dspace.log.2016-04-27:7271
<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
</ul>
+<p></p>
+
<h2 id="2016-02-06">2016-02-06</h2>
<ul>
@@ -2939,8 +2974,7 @@ Bitstream: tést señora alimentación.pdf
<ul>
<li>Finally import the 1127 CIAT items into CGSpace: <a href="https://cgspace.cgiar.org/handle/10568/35710">https://cgspace.cgiar.org/handle/10568/35710</a></li>
<li>Re-deploy CGSpace with the Google Scholar fix, but I’m waiting on the Atmire fixes for now, as the branch history is ugly</li>
-</ul>
-
+</ul>
@@ -2949,9 +2983,7 @@ Bitstream: tést señora alimentación.pdf
Wed, 13 Jan 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-01/
-
-
-<h2 id="2016-01-13">2016-01-13</h2>
+ <h2 id="2016-01-13">2016-01-13</h2>
<ul>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
@@ -2959,6 +2991,8 @@ Bitstream: tést señora alimentación.pdf
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
</ul>
+<p></p>
+
<h2 id="2016-01-14">2016-01-14</h2>
<ul>
@@ -3034,8 +3068,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
<li>After:</li>
</ul>
-<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
-
+<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
@@ -3044,9 +3077,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
Wed, 02 Dec 2015 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2015-12/
-
-
-<h2 id="2015-12-02">2015-12-02</h2>
+ <h2 id="2015-12-02">2015-12-02</h2>
<ul>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
@@ -3059,6 +3090,8 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre>
+<p></p>
+
<ul>
<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
@@ -3204,8 +3237,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<ul>
<li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn’t as good, but it’s much faster and causes less IO/CPU load</li>
<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot’s crawl rate to the “Let Google optimize” setting</li>
-</ul>
-
+</ul>
@@ -3214,9 +3246,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
Mon, 23 Nov 2015 17:00:57 +0300https://alanorth.github.io/cgspace-notes/2015-11/
-
-
-<h2 id="2015-11-22">2015-11-22</h2>
+ <h2 id="2015-11-22">2015-11-22</h2>
<ul>
<li>CGSpace went down</li>
@@ -3228,6 +3258,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
</code></pre>
+<p></p>
+
<ul>
<li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li>
</ul>
@@ -3359,8 +3391,7 @@ db.statementpool = true
<li>Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace’s thirst can ever be quenched</li>
<li>On another note, SUNScholar’s notes suggest adjusting some other postgres variables: <a href="http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database">http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database</a></li>
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
-</ul>
-
+</ul>
diff --git a/public/robots.txt b/public/robots.txt
index ba8f32004..c80886374 100644
--- a/public/robots.txt
+++ b/public/robots.txt
@@ -1,6 +1,7 @@
User-agent: *
+Disallow: /cgspace-notes/2016-10/
Disallow: /cgspace-notes/2016-09/
Disallow: /cgspace-notes/2016-08/
Disallow: /cgspace-notes/2016-07/
diff --git a/public/sitemap.xml b/public/sitemap.xml
index 2718875af..10a32b7e9 100644
--- a/public/sitemap.xml
+++ b/public/sitemap.xml
@@ -3,7 +3,12 @@
https://alanorth.github.io/cgspace-notes/
- 2016-09-01T15:53:00+03:00
+ 2016-10-03T15:53:00+03:00
+
+
+
+ https://alanorth.github.io/cgspace-notes/2016-10/
+ 2016-10-03T15:53:00+03:00
diff --git a/public/tags/notes/index.html b/public/tags/notes/index.html
index 7777774c2..11c6f0673 100644
--- a/public/tags/notes/index.html
+++ b/public/tags/notes/index.html
@@ -32,7 +32,7 @@
-
+
@@ -74,6 +74,20 @@
+
+
+
+
+ 2016-10-03 Testing adding ORCIDs to a CSV file for a single item to see if the author orders get messed up Need to test the following scenarios to see how author order is affected: ORCIDs only ORCIDs plus normal authors I exported a random item’s metadata as CSV, deleted all columns except id and collection, and made a new coloum called ORCID:dc.contributor.author with the following random ORCIDs from the ORCID registry: 0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X Hmm, with the dc.
+ Read more →
+
+
+
+
Read more →
@@ -124,6 +139,7 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
+
Read more →
@@ -156,6 +172,7 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
In this case the select query was showing 95 results before the update
+
Read more →
@@ -180,35 +197,11 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in dc.identifier.fund to cg.identifier.cpwfproject and then the rest to dc.description.sponsorship
-
diff --git a/public/tags/notes/index.xml b/public/tags/notes/index.xml
index 58811cdca..d4dd3fd97 100644
--- a/public/tags/notes/index.xml
+++ b/public/tags/notes/index.xml
@@ -1,23 +1,58 @@
- Notes on CGSpace Notes
- https://alanorth.github.io/cgspace-notes/tags/notes/
- Recent content in Notes on CGSpace Notes
+ CGSpace Notes
+ https://alanorth.github.io/cgspace-notes/tags/notes/index.xml
+ Recent content on CGSpace NotesHugo -- gohugo.ioen-us
- Thu, 01 Sep 2016 15:53:00 +0300
+
+ October, 2016
+ https://alanorth.github.io/cgspace-notes/2016-10/
+ Mon, 03 Oct 2016 15:53:00 +0300
+
+ https://alanorth.github.io/cgspace-notes/2016-10/
+
+
+<h2 id="2016-10-03">2016-10-03</h2>
+
+<ul>
+<li>Testing adding <a href="https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing">ORCIDs to a CSV</a> file for a single item to see if the author orders get messed up</li>
+<li>Need to test the following scenarios to see how author order is affected:
+
+<ul>
+<li>ORCIDs only</li>
+<li>ORCIDs plus normal authors</li>
+</ul></li>
+<li>I exported a random item’s metadata as CSV, deleted <em>all columns</em> except id and collection, and made a new coloum called <code>ORCID:dc.contributor.author</code> with the following random ORCIDs from the ORCID registry:</li>
+</ul>
+
+<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
+</code></pre>
+
+<ul>
+<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn’t detect any changes</li>
+<li>With a blank <code>dc.contributor.author</code> column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors</li>
+<li>I added the <a href="https://github.com/ilri/DSpace/issues/234">disclaimer text</a> to the About page, then added a footer link to the disclaimer’s ID, but there is a Bootstrap issue that causes the page content to disappear when using in-page anchors: <a href="https://github.com/twbs/bootstrap/issues/1768">https://github.com/twbs/bootstrap/issues/1768</a></li>
+</ul>
+
+<p><img src="2016/10/bootstrap-issue.png" alt="Bootstrap issue with in-page anchors" /></p>
+
+<ul>
+<li>Looks like we’ll just have to add the text to the About page (without a link) or add a separate page</li>
+</ul>
+
+
+
September, 2016
https://alanorth.github.io/cgspace-notes/2016-09/
Thu, 01 Sep 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-09/
-
-
-<h2 id="2016-09-01">2016-09-01</h2>
+ <h2 id="2016-09-01">2016-09-01</h2>
<ul>
<li>Discuss helping CCAFS with some batch tagging of ORCID IDs for their authors</li>
@@ -29,6 +64,8 @@
<pre><code>$ ldapsearch -x -H ldaps://svcgroot2.cgiarad.org:3269/ -b "dc=cgiarad,dc=org" -D "admigration1@cgiarad.org" -W "(sAMAccountName=admigration1)"
</code></pre>
+<p></p>
+
<ul>
<li>User who has been migrated to the root vs user still in the hierarchical structure:</li>
</ul>
@@ -637,15 +674,18 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
<li>Add <code>cg.identifier.ciatproject</code> to metadata registry in preparation for CIAT project tag</li>
<li>Merge changes for CIAT project tag (<a href="https://github.com/ilri/DSpace/pull/282">#282</a>)</li>
<li>DSpace Test (linode02) became unresponsive for some reason, I had to hard reboot it from the Linode console</li>
+<li>People on DSpace mailing list gave me a query to get authors from certain collections:</li>
</ul>
+<pre><code>dspacetest=# select distinct text_value from metadatavalue where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'contributor' and qualifier = 'author') AND resource_type_id = 2 AND resource_id IN (select item_id from collection2item where collection_id IN (select resource_id from handle where handle in ('10568/5472', '10568/5473')));
+</code></pre>
+
<h2 id="2016-09-30">2016-09-30</h2>
<ul>
<li>Deny access to REST API’s <code>find-by-metadata-field</code> endpoint to protect against an upstream security issue (DS-3250)</li>
<li>There is a patch but it is only for 5.5 and doesn’t apply cleanly to 5.1</li>
-</ul>
-
+</ul>
@@ -654,9 +694,7 @@ $ ./delete-metadata-values.py -i ilrisubjects-delete-13.csv -f cg.subject.ilri -
Mon, 01 Aug 2016 15:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-08/
-
-
-<h2 id="2016-08-01">2016-08-01</h2>
+ <h2 id="2016-08-01">2016-08-01</h2>
<ul>
<li>Add updated distribution license from Sisay (<a href="https://github.com/ilri/DSpace/issues/259">#259</a>)</li>
@@ -672,6 +710,8 @@ $ git reset --hard ilri/5_x-prod
$ git rebase -i dspace-5.5
</code></pre>
+<p></p>
+
<ul>
<li>Lots of conflicts that don’t make sense (ie, shouldn’t conflict!)</li>
<li>This file in particular conflicts almost 10 times: <code>dspace/modules/xmlui-mirage2/src/main/webapp/themes/CGIAR/styles/_style.scss</code></li>
@@ -979,8 +1019,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
<ul>
<li>Run corrections for Delia Grace and <code>CONGO, DR</code>, and deploy August changes to CGSpace</li>
<li>Run all system updates and reboot the server</li>
-</ul>
-
+</ul>
@@ -989,9 +1028,7 @@ $ JAVA_OPTS="-Dfile.encoding=UTF-8 -Xmx512m" /home/cgspace.cgi
Fri, 01 Jul 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-07/
-
-
-<h2 id="2016-07-01">2016-07-01</h2>
+ <h2 id="2016-07-01">2016-07-01</h2>
<ul>
<li>Add <code>dc.description.sponsorship</code> to Discovery sidebar facets and make investors clickable in item view (<a href="https://github.com/ilri/DSpace/issues/232">#232</a>)</li>
@@ -1010,6 +1047,8 @@ dspacetest=# select text_value from metadatavalue where metadata_field_id=3 and
<li>In this case the select query was showing 95 results before the update</li>
</ul>
+<p></p>
+
<h2 id="2016-07-02">2016-07-02</h2>
<ul>
@@ -1235,8 +1274,7 @@ discovery.index.authority.ignore-variants=true
<ul>
<li>Work on removing Dryland Systems and Humidtropics subjects from Discovery sidebar and Browse by</li>
<li>Also change “Subjects” to “AGROVOC keywords” in Discovery sidebar/search and Browse by (<a href="https://github.com/ilri/DSpace/issues/257">#257</a>)</li>
-</ul>
-
+</ul>
@@ -1245,9 +1283,7 @@ discovery.index.authority.ignore-variants=true
Wed, 01 Jun 2016 10:53:00 +0300https://alanorth.github.io/cgspace-notes/2016-06/
-
-
-<h2 id="2016-06-01">2016-06-01</h2>
+ <h2 id="2016-06-01">2016-06-01</h2>
<ul>
<li>Experimenting with IFPRI OAI (we want to harvest their publications)</li>
@@ -1258,6 +1294,8 @@ discovery.index.authority.ignore-variants=true
<li>Working on second phase of metadata migration, looks like this will work for moving CPWF-specific data in <code>dc.identifier.fund</code> to <code>cg.identifier.cpwfproject</code> and then the rest to <code>dc.description.sponsorship</code></li>
</ul>
+<p></p>
+
<pre><code>dspacetest=# update metadatavalue set metadata_field_id=130 where metadata_field_id=75 and (text_value like 'PN%' or text_value like 'PHASE%' or text_value = 'CBA' or text_value = 'IA');
UPDATE 497
dspacetest=# update metadatavalue set metadata_field_id=29 where metadata_field_id=75;
@@ -1589,8 +1627,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
</ul>
<pre><code># update metadatavalue set text_value = regexp_replace(text_value, '(Poole, J),', '\1') where metadata_field_id=3 and text_value = 'Poole, J,';
-</code></pre>
-
+</code></pre>
@@ -1599,9 +1636,7 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
Sun, 01 May 2016 23:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-05/
-
-
-<h2 id="2016-05-01">2016-05-01</h2>
+ <h2 id="2016-05-01">2016-05-01</h2>
<ul>
<li>Since yesterday there have been 10,000 REST errors and the site has been unstable again</li>
@@ -1613,6 +1648,8 @@ $ ./delete-metadata-values.py -f dc.contributor.corporate -i Corporate-Authors-D
3168
</code></pre>
+<p></p>
+
<ul>
<li>The two most often requesters are in Ethiopia and Colombia: 213.55.99.121 and 181.118.144.29</li>
<li>100% of the requests coming from Ethiopia are like this and result in an HTTP 500:</li>
@@ -1896,8 +1933,7 @@ sys 0m20.540s
<li>Manually mapped the authors of a few old CCAFS records to the new CCAFS authority UUID and re-indexed authority indexes to see if it helps correct those items.</li>
<li>Re-sync DSpace Test data with CGSpace</li>
<li>Clean up and import ~65 more CTA items into CGSpace</li>
-</ul>
-
+</ul>
@@ -1906,9 +1942,7 @@ sys 0m20.540s
Mon, 04 Apr 2016 11:06:00 +0300https://alanorth.github.io/cgspace-notes/2016-04/
-
-
-<h2 id="2016-04-04">2016-04-04</h2>
+ <h2 id="2016-04-04">2016-04-04</h2>
<ul>
<li>Looking at log file use on CGSpace and notice that we need to work on our cron setup a bit</li>
@@ -1918,6 +1952,8 @@ sys 0m20.540s
<li>Also, I noticed the <code>checker</code> log has some errors we should pay attention to:</li>
</ul>
+<p></p>
+
<pre><code>Run start time: 03/06/2016 04:00:22
Error retrieving bitstream ID 71274 from asset store.
java.io.FileNotFoundException: /home/cgspace.cgiar.org/assetstore/64/29/06/64290601546459645925328536011917633626 (Too many open files)
@@ -2357,8 +2393,7 @@ dspace.log.2016-04-27:7271
<ul>
<li>I will check the logs again in a few days to look for patterns, see who is accessing it, etc</li>
-</ul>
-
+</ul>
@@ -2367,9 +2402,7 @@ dspace.log.2016-04-27:7271
Wed, 02 Mar 2016 16:50:00 +0300https://alanorth.github.io/cgspace-notes/2016-03/
-
-
-<h2 id="2016-03-02">2016-03-02</h2>
+ <h2 id="2016-03-02">2016-03-02</h2>
<ul>
<li>Looking at issues with author authorities on CGSpace</li>
@@ -2377,6 +2410,8 @@ dspace.log.2016-04-27:7271
<li>Reinstall my local (Mac OS X) DSpace stack with Tomcat 7, PostgreSQL 9.3, and Java JDK 1.7 to match environment on CGSpace server</li>
</ul>
+<p></p>
+
<h2 id="2016-03-07">2016-03-07</h2>
<ul>
@@ -2605,8 +2640,7 @@ dspace.log.2016-04-27:7271
<li>We decided to proceed with some deletes first, then identify CGSpace-specific fields to clean/move to <code>cg.*</code>, and then worry about broader changes to DC</li>
<li>Before we move or rename and fields we need to circulate a list of fields we intend to change to CCAFS, CWPF, etc who might be harvesting the fields</li>
<li>After all of this we need to start implementing controlled vocabularies for fields, either with the Javascript lookup or like existing ILRI subjects</li>
-</ul>
-
+</ul>
@@ -2615,9 +2649,7 @@ dspace.log.2016-04-27:7271
Fri, 05 Feb 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-02/
-
-
-<h2 id="2016-02-05">2016-02-05</h2>
+ <h2 id="2016-02-05">2016-02-05</h2>
<ul>
<li>Looking at some DAGRIS data for Abenet Yabowork</li>
@@ -2632,6 +2664,8 @@ dspace.log.2016-04-27:7271
<li>Also, lots of things like “COTE D`LVOIRE” and “COTE D IVOIRE”</li>
</ul>
+<p></p>
+
<h2 id="2016-02-06">2016-02-06</h2>
<ul>
@@ -2939,8 +2973,7 @@ Bitstream: tést señora alimentación.pdf
<ul>
<li>Finally import the 1127 CIAT items into CGSpace: <a href="https://cgspace.cgiar.org/handle/10568/35710">https://cgspace.cgiar.org/handle/10568/35710</a></li>
<li>Re-deploy CGSpace with the Google Scholar fix, but I’m waiting on the Atmire fixes for now, as the branch history is ugly</li>
-</ul>
-
+</ul>
@@ -2949,9 +2982,7 @@ Bitstream: tést señora alimentación.pdf
Wed, 13 Jan 2016 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2016-01/
-
-
-<h2 id="2016-01-13">2016-01-13</h2>
+ <h2 id="2016-01-13">2016-01-13</h2>
<ul>
<li>Move ILRI collection <code>10568/12503</code> from <code>10568/27869</code> to <code>10568/27629</code> using the <a href="https://gist.github.com/alanorth/392c4660e8b022d99dfa">move_collections.sh</a> script I wrote last year.</li>
@@ -2959,6 +2990,8 @@ Bitstream: tést señora alimentación.pdf
<li>Update GitHub wiki for documentation of <a href="https://github.com/ilri/DSpace/wiki/Maintenance-Tasks">maintenance tasks</a>.</li>
</ul>
+<p></p>
+
<h2 id="2016-01-14">2016-01-14</h2>
<ul>
@@ -3034,8 +3067,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
<li>After:</li>
</ul>
-<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
-
+<p><img src="2016/01/xmlui-subjects-after.png" alt="XMLUI subjects after" /></p>
@@ -3044,9 +3076,7 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
Wed, 02 Dec 2015 13:18:00 +0300https://alanorth.github.io/cgspace-notes/2015-12/
-
-
-<h2 id="2015-12-02">2015-12-02</h2>
+ <h2 id="2015-12-02">2015-12-02</h2>
<ul>
<li>Replace <code>lzop</code> with <code>xz</code> in log compression cron jobs on DSpace Test—it uses less space:</li>
@@ -3059,6 +3089,8 @@ $ find SimpleArchiveForBio/ -iname “*.pdf” -exec basename {}
-rw-rw-r-- 1 tomcat7 tomcat7 169K Nov 18 23:59 dspace.log.2015-11-18.xz
</code></pre>
+<p></p>
+
<ul>
<li>I had used lrzip once, but it needs more memory and is harder to use as it requires the lrztar wrapper</li>
<li>Need to remember to go check if everything is ok in a few days and then change CGSpace</li>
@@ -3204,8 +3236,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
<ul>
<li>Switch CGSpace log compression cron jobs from using lzop to xz—the compression isn’t as good, but it’s much faster and causes less IO/CPU load</li>
<li>Since we figured out (and fixed) the cause of the performance issue, I reverted Google Bot’s crawl rate to the “Let Google optimize” setting</li>
-</ul>
-
+</ul>
@@ -3214,9 +3245,7 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
Mon, 23 Nov 2015 17:00:57 +0300https://alanorth.github.io/cgspace-notes/2015-11/
-
-
-<h2 id="2015-11-22">2015-11-22</h2>
+ <h2 id="2015-11-22">2015-11-22</h2>
<ul>
<li>CGSpace went down</li>
@@ -3228,6 +3257,8 @@ $ curl -o /dev/null -s -w %{time_total}\\n https://cgspace.cgiar.org/rest/handle
78
</code></pre>
+<p></p>
+
<ul>
<li>For now I have increased the limit from 60 to 90, run updates, and rebooted the server</li>
</ul>
@@ -3359,8 +3390,7 @@ db.statementpool = true
<li>Perhaps I need to start drastically increasing the connection limits—like to 300—to see if DSpace’s thirst can ever be quenched</li>
<li>On another note, SUNScholar’s notes suggest adjusting some other postgres variables: <a href="http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database">http://wiki.lib.sun.ac.za/index.php/SUNScholar/Optimisations/Database</a></li>
<li>This might help with REST API speed (which I mentioned above and still need to do real tests)</li>
-</ul>
-
+</ul>
diff --git a/static/2016/10/bootstrap-issue.png b/static/2016/10/bootstrap-issue.png
new file mode 100644
index 000000000..bf8c73b64
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