<metaproperty="og:description"content="2016-11-01 Add dc.type to the output options for Atmire’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."/>
<metaitemprop="description"content="2016-11-01 Add dc.type to the output options for Atmire’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.">
<metaname="twitter:description"content="2016-11-01 Add dc.type to the output options for Atmire’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."/>
<li>Add <code>dc.type</code> to the output options for Atmire’s Listings and Reports module (<ahref="https://github.com/ilri/DSpace/pull/286">#286</a>)</li>
<li>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! (<ahref="https://github.com/ilri/DSpace/issues/63">#63</a>)</li>
<li>After re-deploying and re-indexing I didn’t see the same issue, and the indexing completed in 85 minutes, which is about how long it is supposed to take</li>
<li>I noticed some weird CRPs in the database, and they don’t show up in Discovery for some reason, perhaps the <code>:</code></li>
<li>I’ll export these and fix them in batch:</li>
</ul>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=230 group by text_value order by count desc) to /tmp/crp.csv with csv;
<li>Add <code>AMR</code> to ILRI subjects and remove one duplicate instance of IITA in author affiliations controlled vocabulary (<ahref="https://github.com/ilri/DSpace/pull/288">#288</a>)</li>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where metadata_field_id=3 group by text_value order by count desc limit 210) to /tmp/210-authors.csv with csv;
<li>CGSpace crashed so I quickly ran system updates, applied one or two of the waiting changes from the <code>5_x-prod</code> branch, and rebooted the server</li>
<li>The error was <code>Timeout waiting for idle object</code> but I haven’t looked into the Tomcat logs to see what happened</li>
<li>Also, I ran the corrections for CRPs from earlier this week</li>
<li>But the results are deceiving because metadata fields can have text languages and your query must match exactly!</li>
</ul>
<pre><code>dspace=# select distinct text_value, text_lang from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
text_value | text_lang
------------+-----------
SEEDS |
SEEDS |
SEEDS | en_US
(3 rows)
</code></pre>
<ul>
<li>So basically, the text language here could be null, blank, or en_US</li>
<li>To query metadata with these properties, you can do:</li>
<li>The results (55+34=89) don’t seem to match those from the database:</li>
</ul>
<pre><code>dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang is null;
count
-------
15
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='';
count
-------
4
dspace=# select count(text_value) from metadatavalue where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS' and text_lang='en_US';
count
-------
66
</code></pre>
<ul>
<li>So, querying from the API I get 55 + 34 = 89 results, but the database actually only has 85…</li>
<li>And the <code>find-by-metadata-field</code> endpoint doesn’t seem to have a way to get all items with the field, or a wildcard value</li>
<li>I’ll ask a question on the dspace-tech mailing list</li>
<li>And speaking of <code>text_lang</code>, this is interesting:</li>
</ul>
<pre><code>dspacetest=# select distinct text_lang from metadatavalue where resource_type_id=2;
<pre><code>dspace=# \copy (select distinct text_lang, count(*) from metadatavalue where resource_type_id=2 group by text_lang order by count desc) to /tmp/text-langs.csv with csv;
COPY 14
</code></pre>
<ul>
<li>Perhaps we need to fix them all in batch, or experiment with fixing only certain metadatavalues:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_lang='en_US' where resource_type_id=2 and metadata_field_id=203 and text_value='SEEDS';
<li>The <code>fix-metadata.py</code> script I have is meant for specific metadata values, so if I want to update some <code>text_lang</code> values I should just do it directly in the database</li>
<li>For example, on a limited set:</li>
</ul>
<pre><code>dspace=# update metadatavalue set text_lang=NULL where resource_type_id=2 and metadata_field_id=203 and text_value='LIVESTOCK' and text_lang='';
UPDATE 420
</code></pre>
<ul>
<li>And assuming I want to do it for all fields:</li>
</ul>
<pre><code>dspacetest=# update metadatavalue set text_lang=NULL where resource_type_id=2 and text_lang='';
UPDATE 183726
</code></pre>
<ul>
<li>After that restarted Tomcat and PostgreSQL (because I’m superstitious about caches) and now I see the following in REST API query:</li>
<li>I applied Atmire’s suggestions to fix Listings and Reports for DSpace 5.5 and now it works</li>
<li>There were some issues with the <code>dspace/modules/jspui/pom.xml</code>, which is annoying because all I did was rebase our working 5.1 code on top of 5.5, meaning Atmire’s installation procedure must have changed</li>
<li>So there is apparently this Tomcat native way to limit web crawlers to one session: <ahref="https://tomcat.apache.org/tomcat-7.0-doc/config/valve.html#Crawler_Session_Manager_Valve">Crawler Session Manager</a></li>
<li>After adding that to <code>server.xml</code> bots matching the pattern in the configuration will all use ONE session, just like normal users:</li>
</ul>
<pre><code>$ http --print h https://dspacetest.cgiar.org 'User-Agent:Mozilla/5.0 (compatible; Googlebot/2.1; +http://www.google.com/bot.html)'
<li>Generate a list of journal titles for Peter and Abenet to look through so we can make a controlled vocabulary out of them:</li>
</ul>
<pre><code>dspace=# \copy (select distinct text_value, count(*) from metadatavalue where resource_type_id=2 and metadata_field_id=55 group by text_value order by count desc) to /tmp/journal-titles.csv with csv;
COPY 2515
</code></pre>
<ul>
<li>Send a message to users of the CGSpace REST API to notify them of upcoming upgrade so they can test their apps against DSpace Test</li>
<li>Test an update old, non-HTTPS links to the CCAFS website in CGSpace metadata:</li>
</ul>
<pre><code>dspacetest=# update metadatavalue set text_value = regexp_replace(text_value, 'http://ccafs.cgiar.org','https://ccafs.cgiar.org') where resource_type_id=2 and text_value like '%http://ccafs.cgiar.org%';
UPDATE 164
dspace=# update metadatavalue set text_value = regexp_replace(text_value, 'http://ccafs.cgiar.org','https://ccafs.cgiar.org') where resource_type_id=2 and text_value like '%http://ccafs.cgiar.org%';
UPDATE 7
</code></pre>
<ul>
<li>Had to run it twice to get all (not sure about “global” regex in PostgreSQL)</li>
<li>Run the updates on CGSpace as well</li>
<li>Run through some collections and manually regenerate some PDF thumbnails for items from before 2016 on DSpace Test to compare with CGSpace</li>
<li>I’m debating forcing the re-generation of ALL thumbnails, since some come from DSpace 3 and 4 when the thumbnailing wasn’t as good</li>
<li>The results were very good, I think that after we upgrade to 5.5 I will do it, perhaps one community / collection at a time:</li>
</ul>
<pre><code>$ [dspace]/bin/dspace filter-media -f -i 10568/67156 -p "ImageMagick PDF Thumbnail"
</code></pre>
<ul>
<li>In related news, I’m looking at thumbnails of thumbnails (the ones we uploaded manually before, and now DSpace’s media filter has made thumbnails of THEM):</li>
</ul>
<pre><code>dspace=# select text_value from metadatavalue where text_value like '%.jpg.jpg';
</code></pre>
<ul>
<li>I’m not sure if there’s anything we can do, actually, because we would have to remove those from the thumbnail bundles, and replace them with the regular JPGs from the content bundle, and then remove them from the assetstore…</li>
<li>I had started planning the inplace PostgreSQL 9.3→9.5 upgrade but decided that I will have to <code>pg_dump</code> and <code>pg_restore</code> when I move to the new server soon anyways, so there’s no need to upgrade the database right now</li>
<li>Chat with Carlos about CGCore and the CGSpace metadata registry</li>
<li>Dump CGSpace metadata field registry for Carlos: <ahref="https://gist.github.com/alanorth/8cbd0bb2704d4bbec78025b4742f8e70">https://gist.github.com/alanorth/8cbd0bb2704d4bbec78025b4742f8e70</a></li>
<li>Send some feedback to Carlos on CG Core so they can better understand how DSpace/CGSpace uses metadata</li>
<li>Notes about PostgreSQL tuning from James: <ahref="https://paste.fedoraproject.org/488776/14798952/">https://paste.fedoraproject.org/488776/14798952/</a></li>
<li>Play with Creative Commons stuff in DSpace submission step</li>
<li>It seems to work but it doesn’t let you choose a version of CC (like 4.0), and we would need to customize the XMLUI item display so it doesn’t display the gross CC badges</li>
<li>Bizuwork was testing DSpace Test on DSPace 5.5 and noticed that the Listings and Reports module seems to be case sensitive, whereas CGSpace’s Listings and Reports isn’t (ie, a search for “orth, alan” vs “Orth, Alan” returns the same results on CGSpace, but different on DSpace Test)</li>
<li>It says OAI, and seems to start at 3:00 AM, but I only see the <code>filter-media</code> cron job set to start then</li>
<li>Double checking the <ahref="https://wiki.duraspace.org/display/DSDOC5x/Upgrading+DSpace">DSpace 5.x upgrade notes</a> for anything I missed, or troubleshooting tips</li>
<li>Running some manual processes just in case:</li>
<li>Wow, Bram from Atmire pointed out this solution for using multiple handles with one DSpace instance: <ahref="https://wiki.duraspace.org/display/DSDOC5x/Installing+DSpace?focusedCommentId=78163296#comment-78163296">https://wiki.duraspace.org/display/DSDOC5x/Installing+DSpace?focusedCommentId=78163296#comment-78163296</a></li>
<li>We might be able to migrate the <ahref="http://library.cgiar.org/">CGIAR Library</a> now, as they had wanted to keep their handles</li>
<li>Sisay tried deleting and re-creating Goshu’s account but he still can’t see any communities on the homepage after he logs in</li>
<li>Around the time of his login I see this in the DSpace logs:</li>
</ul>
<pre><code>2016-11-29 07:56:36,350 INFO org.dspace.authenticate.LDAPAuthentication @ g.cherinet@cgiar.org:session_id=F628E13AB4EF2BA949198A99EFD8EBE4:ip_addr=213.55.99.121:failed_login:no DN found for user g.cherinet@cgiar.org
2016-11-29 07:56:36,350 INFO org.dspace.authenticate.PasswordAuthentication @ g.cherinet@cgiar.org:session_id=F628E13AB4EF2BA949198A99EFD8EBE4:ip_addr=213.55.99.121:authenticate:attempting password auth of user=g.cherinet@cgiar.org
2016-11-29 07:56:36,352 INFO org.dspace.app.xmlui.utils.AuthenticationUtil @ g.cherinet@cgiar.org:session_id=F628E13AB4EF2BA949198A99EFD8EBE4:ip_addr=213.55.99.121:failed_login:email=g.cherinet@cgiar.org, realm=null, result=2
2016-11-29 07:56:36,545 INFO com.atmire.utils.UpdateSolrStatsMetadata @ Start processing item 10568/50391 id:51744
2016-11-29 07:56:36,545 INFO com.atmire.utils.UpdateSolrStatsMetadata @ Processing item stats
2016-11-29 07:56:36,583 INFO com.atmire.utils.UpdateSolrStatsMetadata @ Solr metadata up-to-date
2016-11-29 07:56:36,583 INFO com.atmire.utils.UpdateSolrStatsMetadata @ Processing item's bitstream stats
2016-11-29 07:56:36,608 INFO com.atmire.utils.UpdateSolrStatsMetadata @ Solr metadata up-to-date
2016-11-29 07:56:36,701 INFO org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ facets for scope, null: 23
2016-11-29 07:56:36,747 ERROR org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer @ Error while searching for sidebar facets
at org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1618)
at org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1600)
at org.dspace.discovery.SolrServiceImpl.search(SolrServiceImpl.java:1583)
at org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.performSearch(SidebarFacetsTransformer.java:165)
at org.dspace.app.xmlui.aspect.discovery.SidebarFacetsTransformer.addOptions(SidebarFacetsTransformer.java:174)
at org.dspace.app.xmlui.wing.AbstractWingTransformer.startElement(AbstractWingTransformer.java:228)
at sun.reflect.GeneratedMethodAccessor277.invoke(Unknown Source)
...
</code></pre>
<ul>
<li>At about the same time in the solr log I see a super long query:</li>
</ul>
<pre><code>2016-11-29 07:56:36,734 INFO org.apache.solr.core.SolrCore @ [search] webapp=/solr path=/select params={q=*:*&fl=dateIssued.year,handle,search.resourcetype,search.resourceid,search.uniqueid&start=0&fq=NOT(withdrawn:true)&fq=NOT(discoverable:false)&fq=dateIssued.year:[*+TO+*]&fq=read:(g0+OR+e574+OR+g0+OR+g3+OR+g9+OR+g10+OR+g14+OR+g16+OR+g18+OR+g20+OR+g23+OR+g24+OR+g2072+OR+g2074+OR+g28+OR+g2076+OR+g29+OR+g2078+OR+g2080+OR+g34+OR+g2082+OR+g2084+OR+g38+OR+g2086+OR+g2088+OR+g2091+OR+g43+OR+g2092+OR+g2093+OR+g2095+OR+g2097+OR+g50+OR+g2099+OR+g51+OR+g2103+OR+g62+OR+g65+OR+g2115+OR+g2117+OR+g2119+OR+g2121+OR+g2123+OR+g2125+OR+g77+OR+g78+OR+g79+OR+g2127+OR+g80+OR+g2129+OR+g2131+OR+g2133+OR+g2134+OR+g2135+OR+g2136+OR+g2137+OR+g2138+OR+g2139+OR+g2140+OR+g2141+OR+g2142+OR+g2148+OR+g2149+OR+g2150+OR+g2151+OR+g2152+OR+g2153+OR+g2154+OR+g2156+OR+g2165+OR+g2167+OR+g2171+OR+g2174+OR+g2175+OR+g129+OR+g2182+OR+g2186+OR+g2189+OR+g153+OR+g158+OR+g166+OR+g167+OR+g168+OR+g169+OR+g2225+OR+g179+OR+g2227+OR+g2229+OR+g183+OR+g2231+OR+g184+OR+g2233+OR+g186+OR+g2235+OR+g2237+OR+g191+OR+g192+OR+g193+OR+g202+OR+g203+OR+g204+OR+g205+OR+g207+OR+g208+OR+g218+OR+g219+OR+g222+OR+g223+OR+g230+OR+g231+OR+g238+OR+g241+OR+g244+OR+g254+OR+g255+OR+g262+OR+g265+OR+g268+OR+g269+OR+g273+OR+g276+OR+g277+OR+g279+OR+g282+OR+g2332+OR+g2335+OR+g2338+OR+g292+OR+g293+OR+g2341+OR+g296+OR+g2344+OR+g297+OR+g2347+OR+g301+OR+g2350+OR+g303+OR+g305+OR+g2356+OR+g310+OR+g311+OR+g2359+OR+g313+OR+g2362+OR+g2365+OR+g2368+OR+g321+OR+g2371+OR+g325+OR+g2374+OR+g328+OR+g2377+OR+g2380+OR+g333+OR+g2383+OR+g2386+OR+g2389+OR+g342+OR+g343+OR+g2392+OR+g345+OR+g2395+OR+g348+OR+g2398+OR+g2401+OR+g2404+OR+g2407+OR+g364+OR+g366+OR+g2425+OR+g2427+OR+g385+OR+g387+OR+g388+OR+g389+OR+g2442+OR+g395+OR+g2443+OR+g2444+OR+g401+OR+g403+OR+g405+OR+g408+OR+g2457+OR+g2458+OR+g411+OR+g2459+OR+g414+OR+g2463+OR+g417+OR+g2465+OR+g2467+OR+g421+OR+g2469+OR+g2471+OR+g424+OR+g2473+OR+g2475+OR+g2476+OR+g429+OR+g433+OR+g2481+OR+g2482+OR+g2483+OR+g443+OR+g444+OR+g445+OR+g446+OR+g448+OR+g453+OR+g455+OR+g456+OR+g457+OR+g458+OR+g459+OR+g461+OR+g462+OR+g463+OR+g464+OR+g465+OR+g467+OR+g468+OR+g469+OR+g474+OR+g476+OR+g477+OR+g480+OR+g483+OR+g484+OR+g493+OR+g496+OR+g497+OR+g498+OR+g500+OR+g502+OR+g504+OR+g505+OR+g2559+OR+g2560+OR+g513+OR+g2561+OR+g515+OR+g516+OR+g518+OR+g519+OR+g2567+OR+g520+OR+g521+OR+g522+OR+g2570+OR+g523+OR+g2571+OR+g524+OR+g525+OR+g2573+OR+g526+OR+g2574+OR+g527+OR+g528+OR+g2576+OR+g529+OR+g531+OR+g2579+OR+g533+OR+g534+OR+g2582+OR+g535+OR+g2584+OR+g538+OR+g2586+OR+g540+OR+g2588+OR+g541+OR+g543+OR+g544+OR+g545+OR+g546+OR+g548+OR+g2596+OR+g549+OR+g551+OR+g555+OR+g556+OR+g558+OR+g561+OR+g569+OR+g570+OR+g571+OR+g2619+OR+g572+OR+g2620+OR+g573+OR+g2621+OR+g2622+OR+g575+OR+g578+OR+g581+OR+g582+OR+g584+OR+g585+OR+g586+OR+g587+OR+g588+OR+g590+OR+g591+OR+g593+OR+g595+OR+g596+OR+g598+OR+g599+OR+g601+OR+g602+OR+g603+OR+g604+OR+g605+OR+g606+OR+g608+OR+g609+OR+g610+OR+g612+OR+g614+OR+g616+OR+g620+OR+g621+OR+g623+OR+g630+OR+g635+OR+g636+OR+g646+OR+g649+OR+g683+OR+g684+OR+g687+OR+g689+OR+g691+OR+g695+OR+g697+OR+g698+OR+g699+OR+g700+OR+g701+OR+g707+OR+g708+OR+g709+OR+g710+OR+g711+OR+g712+OR+g713+OR+g714+OR+g715+OR+g716+OR+g717+OR+g719+OR+g720+OR+g729+OR+g732+OR+g733+OR+g734+OR+g736+OR+g737+OR+g738+OR+g2786+OR+g752+OR+g754+OR+g2804+OR+g757+OR+g2805+OR+g2806+OR+g760+OR+g761+OR+g2810+OR+g2815+OR+g769+OR+g771+OR+g773+OR+g776+OR+g786+OR+g787+OR+g788+OR+g789+OR+g791+OR+g792+OR+g793+OR+g794+OR+g795+OR+g796+OR+g798+OR+g800+OR+g802+OR+g803+OR+g806+OR+g808+OR+g810+OR+g814+OR+g815+OR+g817+OR+g829+OR+g830+OR+g849+OR+g893+OR+g895+OR+g898+OR+g902+OR+g903+OR+g917+OR+g919+OR+g921+OR+g922+OR+g923+OR+g924+OR+g925+OR+g926+OR+g927+OR+g928+OR+g929+OR+g930+OR+g932+OR+g933+OR+g934+OR+g938+OR+g939+OR+g944+OR+g945+OR+g946+OR+g947+OR+g948+OR+g949+OR+g950+OR+g951+OR+g953+OR+g954+OR+g955+OR+g956+OR+g958+OR+g959+OR+g960+OR+g963+OR+g964+OR+g965+OR+g968+OR+g969+OR+g970+OR+g971+OR+g972+OR+g973+OR+g974+OR+g976+OR+g978+OR+g979+OR+g984+OR+g985+OR+g987+OR+g988+OR+g991+OR+g993+OR+g994+OR+g999+OR+g1000+OR+g1003+OR+g1005+OR+
</code></pre>
<ul>
<li>Which, according to some old threads on DSpace Tech, means that the user has a lot of permissions (from groups or on the individual eperson) which increases the Solr query size / query URL</li>
<li>It might be fixed by increasing the Tomcat <code>maxHttpHeaderSize</code>, which is <ahref="http://tomcat.apache.org/tomcat-7.0-doc/config/http.html">8192 (or 8KB) by default</a></li>
<li>I’ve increased the <code>maxHttpHeaderSize</code> to 16384 on DSpace Test and the user said he is now able to see the communities on the homepage</li>
<li>A few users are reporting having issues with their workflows, they get the following message: “You are not allowed to perform this task”</li>
<li>Might be the same as <ahref="https://jira.duraspace.org/browse/DS-2920">DS-2920</a> on the bug tracker</li>
<li>The <code>maxHttpHeaderSize</code> fix worked on CGSpace (user is able to see the community list on the homepage)</li>
<li>The “take task” cache fix worked on DSpace Test but it’s not an official patch, so I’ll have to report the bug to DSpace people and try to get advice</li>
