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Add notes for 2022-03-04
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@ -60,7 +60,7 @@ This was due to newline characters in the dc.description.abstract column, which
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I exported a new CSV from the collection on DSpace Test and then manually removed the characters in vim using g/^$/d
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Then I cleaned up the author authorities and HTML characters in OpenRefine and sent the file back to Abenet
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"/>
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<meta name="generator" content="Hugo 0.92.2" />
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<meta name="generator" content="Hugo 0.93.1" />
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@ -215,7 +215,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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<li>I need to get an author list from the database for only the CGIAR Library community to send to Peter</li>
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<li>It turns out that I had already used this SQL query in <a href="/cgspace-notes/2017-05">May, 2017</a> to get the authors from CGIAR Library:</li>
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</ul>
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<pre tabindex="0"><code>dspace#= \copy (select distinct text_value, count(*) 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9'))) group by text_value order by count desc) to /tmp/cgiar-library-authors.csv with csv;
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<pre tabindex="0"><code>dspace#= \copy (select distinct text_value, count(*) 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9'))) group by text_value order by count desc) to /tmp/cgiar-library-authors.csv with csv;
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</code></pre><ul>
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<li>Meeting with Peter and CGSpace team
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<ul>
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@ -242,7 +242,7 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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<li>I sent a message to the mailing list about the duplicate content issue with <code>/rest</code> and <code>/bitstream</code> URLs</li>
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<li>Looking at the logs for the REST API on <code>/rest</code>, it looks like there is someone hammering doing testing or something on it…</li>
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</ul>
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<pre tabindex="0"><code># awk '{print $1}' /var/log/nginx/rest.log.1 | sort -n | uniq -c | sort -h | tail -n 5
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<pre tabindex="0"><code># awk '{print $1}' /var/log/nginx/rest.log.1 | sort -n | uniq -c | sort -h | tail -n 5
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140 66.249.66.91
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404 66.249.66.90
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1479 50.116.102.77
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@ -270,9 +270,9 @@ Then I cleaned up the author authorities and HTML characters in OpenRefine and s
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</code></pre><ul>
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<li>There were only three deletions so I just did them manually:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='C';
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<pre tabindex="0"><code>dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='C';
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DELETE 1
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dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='WSSD';
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dspace=# delete from metadatavalue where resource_type_id=2 and metadata_field_id=3 and text_value='WSSD';
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</code></pre><ul>
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<li>Generate a new list of authors from the CGIAR Library community for Peter to look through now that the initial corrections have been done</li>
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<li>Thinking about resource limits for PostgreSQL again after last week’s CGSpace crash and related to a recently discussion I had in the comments of the <a href="https://wiki.lyrasis.org/display/cmtygp/DCAT+Meeting+April+2017">April, 2017 DCAT meeting notes</a></li>
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@ -324,22 +324,22 @@ $ grep -rsI SQLException dspace-xmlui | wc -l
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</code></pre><ul>
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<li>And actually, we can do it for other generic fields for items in those collections, for example <code>dc.description.abstract</code>:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang='en_US' where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'abstract') 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9')))
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang='en_US' where metadata_field_id = (select metadata_field_id from metadatafieldregistry where element = 'description' and qualifier = 'abstract') 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9')))
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</code></pre><ul>
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<li>And on others like <code>dc.language.iso</code>, <code>dc.relation.ispartofseries</code>, <code>dc.type</code>, <code>dc.title</code>, etc…</li>
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<li>Also, to move fields from <code>dc.identifier.url</code> to <code>cg.identifier.url[en_US]</code> (because we don’t use the Dublin Core one for some reason):</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set metadata_field_id = 219, text_lang = 'en_US' where resource_type_id = 2 AND metadata_field_id = 237;
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<pre tabindex="0"><code>dspace=# update metadatavalue set metadata_field_id = 219, text_lang = 'en_US' where resource_type_id = 2 AND metadata_field_id = 237;
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UPDATE 15
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</code></pre><ul>
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<li>Set the text_lang of all <code>dc.identifier.uri</code> (Handle) fields to be NULL, just like default DSpace does:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang=NULL where resource_type_id = 2 and metadata_field_id = 25 and text_value like 'http://hdl.handle.net/10947/%';
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang=NULL where resource_type_id = 2 and metadata_field_id = 25 and text_value like 'http://hdl.handle.net/10947/%';
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UPDATE 4248
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</code></pre><ul>
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<li>Also update the text_lang of <code>dc.contributor.author</code> fields for metadata in these collections:</li>
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</ul>
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang=NULL 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9')));
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<pre tabindex="0"><code>dspace=# update metadatavalue set text_lang=NULL 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 ('10568/93761', '10947/1', '10947/10', '10947/11', '10947/12', '10947/13', '10947/14', '10947/15', '10947/16', '10947/17', '10947/18', '10947/19', '10947/2', '10947/20', '10947/21', '10947/22', '10947/23', '10947/24', '10947/25', '10947/2512', '10947/2515', '10947/2516', '10947/2517', '10947/2518', '10947/2519', '10947/2520', '10947/2521', '10947/2522', '10947/2523', '10947/2524', '10947/2525', '10947/2526', '10947/2527', '10947/2528', '10947/2529', '10947/2530', '10947/2531', '10947/2532', '10947/2533', '10947/2534', '10947/2535', '10947/2536', '10947/2537', '10947/2538', '10947/2539', '10947/2540', '10947/2541', '10947/2589', '10947/26', '10947/2631', '10947/27', '10947/2708', '10947/2776', '10947/2782', '10947/2784', '10947/2786', '10947/2790', '10947/28', '10947/2805', '10947/2836', '10947/2871', '10947/2878', '10947/29', '10947/2900', '10947/2919', '10947/3', '10947/30', '10947/31', '10947/32', '10947/33', '10947/34', '10947/3457', '10947/35', '10947/36', '10947/37', '10947/38', '10947/39', '10947/4', '10947/40', '10947/4052', '10947/4054', '10947/4056', '10947/4068', '10947/41', '10947/42', '10947/43', '10947/4368', '10947/44', '10947/4467', '10947/45', '10947/4508', '10947/4509', '10947/4510', '10947/4573', '10947/46', '10947/4635', '10947/4636', '10947/4637', '10947/4638', '10947/4639', '10947/4651', '10947/4657', '10947/47', '10947/48', '10947/49', '10947/5', '10947/50', '10947/51', '10947/5308', '10947/5322', '10947/5324', '10947/5326', '10947/6', '10947/7', '10947/8', '10947/9')));
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||||
UPDATE 4899
|
||||
</code></pre><ul>
|
||||
<li>Wow, I just wrote this baller regex facet to find duplicate authors:</li>
|
||||
@ -370,7 +370,7 @@ java.io.StreamCorruptedException: invalid stream header: 00000000
|
||||
</code></pre><ul>
|
||||
<li>Weird that these errors seem to have started on August 11th, the same day we had capacity issues with PostgreSQL:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code># grep -c "ERROR net.sf.ehcache.store.DiskStore" dspace.log.2017-08-*
|
||||
<pre tabindex="0"><code># grep -c "ERROR net.sf.ehcache.store.DiskStore" dspace.log.2017-08-*
|
||||
dspace.log.2017-08-01:0
|
||||
dspace.log.2017-08-02:0
|
||||
dspace.log.2017-08-03:0
|
||||
@ -418,7 +418,7 @@ SELECT
|
||||
?label
|
||||
WHERE {
|
||||
{ ?concept skos:altLabel ?label . } UNION { ?concept skos:prefLabel ?label . }
|
||||
FILTER regex(str(?label), "^fish", "i") .
|
||||
FILTER regex(str(?label), "^fish", "i") .
|
||||
} LIMIT 10;
|
||||
|
||||
┌───────────────────────┐
|
||||
@ -452,7 +452,7 @@ WHERE {
|
||||
<li>Since I cleared the XMLUI cache on 2017-08-17 there haven’t been any more <code>ERROR net.sf.ehcache.store.DiskStore</code> errors</li>
|
||||
<li>Look at the CGIAR Library to see if I can find the items that have been submitted since May:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code>dspace=# select * from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z';
|
||||
<pre tabindex="0"><code>dspace=# select * from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z';
|
||||
metadata_value_id | item_id | metadata_field_id | text_value | text_lang | place | authority | confidence
|
||||
-------------------+---------+-------------------+----------------------+-----------+-------+-----------+------------
|
||||
123117 | 5872 | 11 | 2017-06-28T13:05:18Z | | 1 | | -1
|
||||
@ -465,7 +465,7 @@ WHERE {
|
||||
<li>According to <code>dc.date.accessioned</code> (metadata field id 11) there have only been five items submitted since May</li>
|
||||
<li>These are their handles:</li>
|
||||
</ul>
|
||||
<pre tabindex="0"><code>dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
|
||||
<pre tabindex="0"><code>dspace=# select handle from item, handle where handle.resource_id = item.item_id AND item.item_id in (select item_id from metadatavalue where metadata_field_id=11 and date(text_value) > '2017-05-01T00:00:00Z');
|
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handle
|
||||
------------
|
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10947/4658
|
||||
|
Reference in New Issue
Block a user