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Add notes for 2017-01-10 and add some <!--more--> tags

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Alan Orth 2017-01-10 16:21:47 +02:00
parent b580f14896
commit 085b5e1b57
Signed by: alanorth
GPG Key ID: 0FB860CC9C45B1B9
14 changed files with 422 additions and 76 deletions
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2
content/post/2016-10.md
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@ -17,6 +17,8 @@ tags = ["Notes"]
0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
```
<!--more-->
- 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

2
content/post/2016-11.md
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@ -11,6 +11,8 @@ tags = ["Notes"]
![Listings and Reports with output type](/cgspace-notes/2016/11/listings-and-reports.png)
<!--more-->
## 2016-11-02
- Migrate DSpace Test to DSpace 5.5 ([notes](https://gist.github.com/alanorth/61013895c6efe7095d7f81000953d1cf))

2
content/post/2016-12.md
View File

@ -22,6 +22,8 @@ tags = ["Notes"]
- I've raised a ticket with Atmire to ask
- Another worrying error from dspace.log is:
<!--more-->
```
org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)

16
content/post/2017-01.md
View File

@ -103,3 +103,19 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
- I tried to clean up the duplicate mappings by exporting the item's metadata to CSV, editing, and re-importing, but DSpace said "no changes were detected"
- I've asked on the dspace-tech mailing list to see if anyone can help
- I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help
- For example, this shows 186 mappings for the item, the first three of which are real:
```
dspace=# select * from collection2item where item_id = '80596';
```
- Then I deleted the others:
```
dspace=# delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
```
- And in the item view it now shows the correct mappings
- I will have to ask the DSpace people if this is a valid approach
- Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it

61
public/2016-10/index.html
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@ -6,7 +6,23 @@
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="October, 2016" />
<meta property="og:description" content="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&rsquo;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." />
<meta property="og:description" content="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&rsquo;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
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-10/" />
@ -24,7 +40,23 @@
<meta itemprop="name" content="October, 2016">
<meta itemprop="description" content="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&rsquo;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.">
<meta itemprop="description" content="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&rsquo;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
">
<meta itemprop="dateModified" content="2016-10-03T15:53:00&#43;03:00" />
@ -41,7 +73,23 @@
<meta name="twitter:title" content="October, 2016"/>
<meta name="twitter:description" content="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&rsquo;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."/>
<meta name="twitter:description" content="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&rsquo;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
"/>
@ -108,9 +156,7 @@
</p>
</header>
<h2 id="2016-10-03">2016-10-03</h2>
<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>
@ -126,6 +172,8 @@
<pre><code>0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
</code></pre>
<p></p>
<ul>
<li>Hmm, with the <code>dc.contributor.author</code> column removed, DSpace doesn&rsquo;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>
@ -421,7 +469,6 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http:
<li>I skipped metadata fields like citation and description</li>
</ul>

37
public/2016-11/index.html
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@ -6,7 +6,15 @@
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="November, 2016" />
<meta property="og:description" content="2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com." />
<meta property="og:description" content="2016-11-01
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-11/" />
@ -24,7 +32,15 @@
<meta itemprop="name" content="November, 2016">
<meta itemprop="description" content="2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com.">
<meta itemprop="description" content="2016-11-01
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
">
<meta itemprop="dateModified" content="2016-11-01T09:21:00&#43;03:00" />
@ -41,7 +57,15 @@
<meta name="twitter:title" content="November, 2016"/>
<meta name="twitter:description" content="2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com."/>
<meta name="twitter:description" content="2016-11-01
Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286)
"/>
@ -108,9 +132,7 @@
</p>
</header>
<h2 id="2016-11-01">2016-11-01</h2>
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
@ -118,6 +140,8 @@
<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
<p></p>
<h2 id="2016-11-02">2016-11-02</h2>
<ul>
@ -653,7 +677,6 @@ org.dspace.discovery.SearchServiceException: Error executing query
<li>More work on the KM4Dev Journal article</li>
</ul>

73
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@ -6,7 +6,27 @@
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta property="og:title" content="December, 2016" />
<meta property="og:description" content="2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org." />
<meta property="og:description" content="2016-12-02
CGSpace was down for five hours in the morning while I was sleeping
While looking in the logs for errors, I see tons of warnings about Atmire MQM:
2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
" />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://alanorth.github.io/cgspace-notes/2016-12/" />
@ -24,7 +44,27 @@
<meta itemprop="name" content="December, 2016">
<meta itemprop="description" content="2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.">
<meta itemprop="description" content="2016-12-02
CGSpace was down for five hours in the morning while I was sleeping
While looking in the logs for errors, I see tons of warnings about Atmire MQM:
2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
">
<meta itemprop="dateModified" content="2016-12-02T10:43:00&#43;03:00" />
@ -41,7 +81,27 @@
<meta name="twitter:title" content="December, 2016"/>
<meta name="twitter:description" content="2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org."/>
<meta name="twitter:description" content="2016-12-02
CGSpace was down for five hours in the morning while I was sleeping
While looking in the logs for errors, I see tons of warnings about Atmire MQM:
2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade
I&rsquo;ve raised a ticket with Atmire to ask
Another worrying error from dspace.log is:
"/>
@ -108,9 +168,7 @@
</p>
</header>
<h2 id="2016-12-02">2016-12-02</h2>
<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
@ -130,6 +188,8 @@
<li>Another worrying error from dspace.log is:</li>
</ul>
<p></p>
<pre><code>org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
@ -865,7 +925,6 @@ $ exit
<li>I will have to check later why the size keeps increasing</li>
</ul>

20
public/2017-01/index.html
View File

@ -28,7 +28,7 @@
<meta itemprop="dateModified" content="2017-01-02T10:43:00&#43;03:00" />
<meta itemprop="wordCount" content="492">
<meta itemprop="wordCount" content="605">
@ -220,6 +220,24 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
<ul>
<li>I tried to clean up the duplicate mappings by exporting the item&rsquo;s metadata to CSV, editing, and re-importing, but DSpace said &ldquo;no changes were detected&rdquo;</li>
<li>I&rsquo;ve asked on the dspace-tech mailing list to see if anyone can help</li>
<li>I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help</li>
<li>For example, this shows 186 mappings for the item, the first three of which are real:</li>
</ul>
<pre><code>dspace=# select * from collection2item where item_id = '80596';
</code></pre>
<ul>
<li>Then I deleted the others:</li>
</ul>
<pre><code>dspace=# delete from collection2item where item_id = '80596' and id not in (90792, 90806, 90807);
</code></pre>
<ul>
<li>And in the item view it now shows the correct mappings</li>
<li>I will have to ask the DSpace people if this is a valid approach</li>
<li>Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it</li>
</ul>

50
public/index.html
View File

@ -112,7 +112,27 @@
</p>
</header>
2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.
<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
</code></pre>
<ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
</article>
@ -128,7 +148,15 @@
</p>
</header>
2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com.
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
</ul>
<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a>
</article>
@ -144,7 +172,23 @@
</p>
</header>
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&rsquo;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.
<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&rsquo;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>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>

45
public/index.xml
View File

@ -127,6 +127,24 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;ul&gt;
&lt;li&gt;I tried to clean up the duplicate mappings by exporting the item&amp;rsquo;s metadata to CSV, editing, and re-importing, but DSpace said &amp;ldquo;no changes were detected&amp;rdquo;&lt;/li&gt;
&lt;li&gt;I&amp;rsquo;ve asked on the dspace-tech mailing list to see if anyone can help&lt;/li&gt;
&lt;li&gt;I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help&lt;/li&gt;
&lt;li&gt;For example, this shows 186 mappings for the item, the first three of which are real:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# select * from collection2item where item_id = &#39;80596&#39;;
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Then I deleted the others:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# delete from collection2item where item_id = &#39;80596&#39; and id not in (90792, 90806, 90807);
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;And in the item view it now shows the correct mappings&lt;/li&gt;
&lt;li&gt;I will have to ask the DSpace people if this is a valid approach&lt;/li&gt;
&lt;li&gt;Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
@ -137,9 +155,7 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
<description>
&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace was down for five hours in the morning while I was sleeping&lt;/li&gt;
@ -159,6 +175,8 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;li&gt;Another worrying error from dspace.log is:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
@ -892,8 +910,7 @@ $ exit
&lt;ul&gt;
&lt;li&gt;I will have to check later why the size keeps increasing&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -902,9 +919,7 @@ $ exit
<pubDate>Tue, 01 Nov 2016 09:21:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-11/</guid>
<description>
&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.type&lt;/code&gt; to the output options for Atmire&amp;rsquo;s Listings and Reports module (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/286&#34;&gt;#286&lt;/a&gt;)&lt;/li&gt;
@ -912,6 +927,8 @@ $ exit
&lt;p&gt;&lt;img src=&#34;https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/11/listings-and-reports.png&#34; alt=&#34;Listings and Reports with output type&#34; /&gt;&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-11-02&#34;&gt;2016-11-02&lt;/h2&gt;
&lt;ul&gt;
@ -1445,8 +1462,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;li&gt;The &lt;code&gt;maxHttpHeaderSize&lt;/code&gt; fix worked on CGSpace (user is able to see the community list on the homepage)&lt;/li&gt;
&lt;li&gt;The &amp;ldquo;take task&amp;rdquo; cache fix worked on DSpace Test but it&amp;rsquo;s not an official patch, so I&amp;rsquo;ll have to report the bug to DSpace people and try to get advice&lt;/li&gt;
&lt;li&gt;More work on the KM4Dev Journal article&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1455,9 +1471,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
@ -1473,6 +1487,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
@ -1766,8 +1782,7 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, &#39;h
&lt;ul&gt;
&lt;li&gt;I skipped metadata fields like citation and description&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>

50
public/post/index.html
View File

@ -112,7 +112,27 @@
</p>
</header>
2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.
<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
</code></pre>
<ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
</article>
@ -128,7 +148,15 @@
</p>
</header>
2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com.
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
</ul>
<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a>
</article>
@ -144,7 +172,23 @@
</p>
</header>
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&rsquo;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.
<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&rsquo;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>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>

45
public/post/index.xml
View File

@ -127,6 +127,24 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;ul&gt;
&lt;li&gt;I tried to clean up the duplicate mappings by exporting the item&amp;rsquo;s metadata to CSV, editing, and re-importing, but DSpace said &amp;ldquo;no changes were detected&amp;rdquo;&lt;/li&gt;
&lt;li&gt;I&amp;rsquo;ve asked on the dspace-tech mailing list to see if anyone can help&lt;/li&gt;
&lt;li&gt;I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help&lt;/li&gt;
&lt;li&gt;For example, this shows 186 mappings for the item, the first three of which are real:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# select * from collection2item where item_id = &#39;80596&#39;;
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Then I deleted the others:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# delete from collection2item where item_id = &#39;80596&#39; and id not in (90792, 90806, 90807);
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;And in the item view it now shows the correct mappings&lt;/li&gt;
&lt;li&gt;I will have to ask the DSpace people if this is a valid approach&lt;/li&gt;
&lt;li&gt;Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
@ -137,9 +155,7 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
<description>
&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace was down for five hours in the morning while I was sleeping&lt;/li&gt;
@ -159,6 +175,8 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;li&gt;Another worrying error from dspace.log is:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
@ -892,8 +910,7 @@ $ exit
&lt;ul&gt;
&lt;li&gt;I will have to check later why the size keeps increasing&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -902,9 +919,7 @@ $ exit
<pubDate>Tue, 01 Nov 2016 09:21:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-11/</guid>
<description>
&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.type&lt;/code&gt; to the output options for Atmire&amp;rsquo;s Listings and Reports module (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/286&#34;&gt;#286&lt;/a&gt;)&lt;/li&gt;
@ -912,6 +927,8 @@ $ exit
&lt;p&gt;&lt;img src=&#34;https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/11/listings-and-reports.png&#34; alt=&#34;Listings and Reports with output type&#34; /&gt;&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-11-02&#34;&gt;2016-11-02&lt;/h2&gt;
&lt;ul&gt;
@ -1445,8 +1462,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;li&gt;The &lt;code&gt;maxHttpHeaderSize&lt;/code&gt; fix worked on CGSpace (user is able to see the community list on the homepage)&lt;/li&gt;
&lt;li&gt;The &amp;ldquo;take task&amp;rdquo; cache fix worked on DSpace Test but it&amp;rsquo;s not an official patch, so I&amp;rsquo;ll have to report the bug to DSpace people and try to get advice&lt;/li&gt;
&lt;li&gt;More work on the KM4Dev Journal article&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1455,9 +1471,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
@ -1473,6 +1487,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
@ -1766,8 +1782,7 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, &#39;h
&lt;ul&gt;
&lt;li&gt;I skipped metadata fields like citation and description&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>

50
public/tags/notes/index.html
View File

@ -112,7 +112,27 @@
</p>
</header>
2016-12-02 CGSpace was down for five hours in the morning while I was sleeping While looking in the logs for errors, I see tons of warnings about Atmire MQM: 2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;) 2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.
<h2 id="2016-12-02">2016-12-02</h2>
<ul>
<li>CGSpace was down for five hours in the morning while I was sleeping</li>
<li>While looking in the logs for errors, I see tons of warnings about Atmire MQM:</li>
</ul>
<pre><code>2016-12-02 03:00:32,352 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=CREATE, SubjectType=BUNDLE, SubjectID=70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632305, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY_METADATA, SubjectType=BUNDLE, SubjectID =70316, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632309, dispatcher=1544803905, detail=&quot;dc.title&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=ITEM, SubjectID=80044, Object Type=BUNDLE, ObjectID=70316, TimeStamp=1480647632311, dispatcher=1544803905, detail=&quot;THUMBNAIL&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=ADD, SubjectType=BUNDLE, SubjectID=70316, Obje ctType=BITSTREAM, ObjectID=86715, TimeStamp=1480647632318, dispatcher=1544803905, detail=&quot;-1&quot;, transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
2016-12-02 03:00:32,353 WARN com.atmire.metadataquality.batchedit.BatchEditConsumer @ BatchEditConsumer should not have been given this kind of Subject in an event, skipping: org.dspace.event.Event(eventType=MODIFY, SubjectType=ITEM, SubjectID=80044, ObjectType=(Unknown), ObjectID=-1, TimeStamp=1480647632351, dispatcher=1544803905, detail=[null], transactionID=&quot;TX157907838689377964651674089851855413607&quot;)
</code></pre>
<ul>
<li>I see thousands of them in the logs for the last few months, so it&rsquo;s not related to the DSpace 5.5 upgrade</li>
<li>I&rsquo;ve raised a ticket with Atmire to ask</li>
<li>Another worrying error from dspace.log is:</li>
</ul>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-12/'>Read more →</a>
</article>
@ -128,7 +148,15 @@
</p>
</header>
2016-11-01 Add dc.type to the output options for Atmire&rsquo;s Listings and Reports module (#286) 2016-11-02 Migrate DSpace Test to DSpace 5.5 (notes) Run all updates on DSpace Test and reboot the server Looks like the OAI bug from DSpace 5.1 that caused validation at Base Search to fail is now fixed and DSpace Test passes validation! (#63) Indexing Discovery on DSpace Test took 332 minutes, which is like five times as long as it usually takes At the end it appeared to finish correctly but there were lots of errors right after it finished: 2016-11-02 15:09:48,578 INFO com.
<h2 id="2016-11-01">2016-11-01</h2>
<ul>
<li>Add <code>dc.type</code> to the output options for Atmire&rsquo;s Listings and Reports module (<a href="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
</ul>
<p><img src="/cgspace-notes/2016/11/listings-and-reports.png" alt="Listings and Reports with output type" /></p>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-11/'>Read more →</a>
</article>
@ -144,7 +172,23 @@
</p>
</header>
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&rsquo;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.
<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&rsquo;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>
<p></p>
<a href='https://alanorth.github.io/cgspace-notes/2016-10/'>Read more →</a>
</article>

45
public/tags/notes/index.xml
View File

@ -126,6 +126,24 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;ul&gt;
&lt;li&gt;I tried to clean up the duplicate mappings by exporting the item&amp;rsquo;s metadata to CSV, editing, and re-importing, but DSpace said &amp;ldquo;no changes were detected&amp;rdquo;&lt;/li&gt;
&lt;li&gt;I&amp;rsquo;ve asked on the dspace-tech mailing list to see if anyone can help&lt;/li&gt;
&lt;li&gt;I found an old post on the mailing list discussing a similar issue, and listing some SQL commands that might help&lt;/li&gt;
&lt;li&gt;For example, this shows 186 mappings for the item, the first three of which are real:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# select * from collection2item where item_id = &#39;80596&#39;;
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;Then I deleted the others:&lt;/li&gt;
&lt;/ul&gt;
&lt;pre&gt;&lt;code&gt;dspace=# delete from collection2item where item_id = &#39;80596&#39; and id not in (90792, 90806, 90807);
&lt;/code&gt;&lt;/pre&gt;
&lt;ul&gt;
&lt;li&gt;And in the item view it now shows the correct mappings&lt;/li&gt;
&lt;li&gt;I will have to ask the DSpace people if this is a valid approach&lt;/li&gt;
&lt;li&gt;Finish looking at the Journal Title corrections of the top 500 Journal Titles so we can make a controlled vocabulary from it&lt;/li&gt;
&lt;/ul&gt;
</description>
</item>
@ -136,9 +154,7 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
<pubDate>Fri, 02 Dec 2016 10:43:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-12/</guid>
<description>
&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-12-02&#34;&gt;2016-12-02&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;CGSpace was down for five hours in the morning while I was sleeping&lt;/li&gt;
@ -158,6 +174,8 @@ Caused by: java.net.SocketException: Broken pipe (Write failed)
&lt;li&gt;Another worrying error from dspace.log is:&lt;/li&gt;
&lt;/ul&gt;
&lt;p&gt;&lt;/p&gt;
&lt;pre&gt;&lt;code&gt;org.springframework.web.util.NestedServletException: Handler processing failed; nested exception is java.lang.NoSuchMethodError: com.atmire.statistics.generator.DSpaceObjectDatasetGenerator.toDatasetQuery(Lorg/dspace/core/Context;)Lcom/atmire/statistics/content/DatasetQuery;
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:972)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:852)
@ -891,8 +909,7 @@ $ exit
&lt;ul&gt;
&lt;li&gt;I will have to check later why the size keeps increasing&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -901,9 +918,7 @@ $ exit
<pubDate>Tue, 01 Nov 2016 09:21:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-11/</guid>
<description>
&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-11-01&#34;&gt;2016-11-01&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Add &lt;code&gt;dc.type&lt;/code&gt; to the output options for Atmire&amp;rsquo;s Listings and Reports module (&lt;a href=&#34;https://github.com/ilri/DSpace/pull/286&#34;&gt;#286&lt;/a&gt;)&lt;/li&gt;
@ -911,6 +926,8 @@ $ exit
&lt;p&gt;&lt;img src=&#34;https://alanorth.github.io/cgspace-notes/cgspace-notes/2016/11/listings-and-reports.png&#34; alt=&#34;Listings and Reports with output type&#34; /&gt;&lt;/p&gt;
&lt;p&gt;&lt;/p&gt;
&lt;h2 id=&#34;2016-11-02&#34;&gt;2016-11-02&lt;/h2&gt;
&lt;ul&gt;
@ -1444,8 +1461,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;li&gt;The &lt;code&gt;maxHttpHeaderSize&lt;/code&gt; fix worked on CGSpace (user is able to see the community list on the homepage)&lt;/li&gt;
&lt;li&gt;The &amp;ldquo;take task&amp;rdquo; cache fix worked on DSpace Test but it&amp;rsquo;s not an official patch, so I&amp;rsquo;ll have to report the bug to DSpace people and try to get advice&lt;/li&gt;
&lt;li&gt;More work on the KM4Dev Journal article&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>
@ -1454,9 +1470,7 @@ org.dspace.discovery.SearchServiceException: Error executing query
<pubDate>Mon, 03 Oct 2016 15:53:00 +0300</pubDate>
<guid>https://alanorth.github.io/cgspace-notes/2016-10/</guid>
<description>
&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
<description>&lt;h2 id=&#34;2016-10-03&#34;&gt;2016-10-03&lt;/h2&gt;
&lt;ul&gt;
&lt;li&gt;Testing adding &lt;a href=&#34;https://wiki.duraspace.org/display/DSDOC5x/ORCID+Integration#ORCIDIntegration-EditingexistingitemsusingBatchCSVEditing&#34;&gt;ORCIDs to a CSV&lt;/a&gt; file for a single item to see if the author orders get messed up&lt;/li&gt;
@ -1472,6 +1486,8 @@ org.dspace.discovery.SearchServiceException: Error executing query
&lt;pre&gt;&lt;code&gt;0000-0002-6115-0956||0000-0002-3812-8793||0000-0001-7462-405X
&lt;/code&gt;&lt;/pre&gt;
&lt;p&gt;&lt;/p&gt;
&lt;ul&gt;
&lt;li&gt;Hmm, with the &lt;code&gt;dc.contributor.author&lt;/code&gt; column removed, DSpace doesn&amp;rsquo;t detect any changes&lt;/li&gt;
&lt;li&gt;With a blank &lt;code&gt;dc.contributor.author&lt;/code&gt; column, DSpace wants to remove all non-ORCID authors and add the new ORCID authors&lt;/li&gt;
@ -1765,8 +1781,7 @@ dspace=# update metadatavalue set text_value = regexp_replace(text_value, &#39;h
&lt;ul&gt;
&lt;li&gt;I skipped metadata fields like citation and description&lt;/li&gt;
&lt;/ul&gt;
</description>
&lt;/ul&gt;</description>
</item>
<item>