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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Thanks guys.
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<div>There are details on how to build in the README.md, but the build the steps to make a full executable are in the ansible scripts (see the role nameindexer [1]).</div>
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<div>Dave</div>
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<div>[1] https://github.com/AtlasOfLivingAustralia/ala-install/tree/master/ansible/roles/nameindexer</div>
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<div id="divRpF440431" style="direction: ltr;"><font face="Tahoma" size="2" color="#000000"><b>From:</b> ala-portal-bounces@lists.gbif.org [ala-portal-bounces@lists.gbif.org] on behalf of Tim Robertson [trobertson@gbif.org]<br>
<b>Sent:</b> 04 September 2014 23:25<br>
<b>To:</b> Santiago Martinez de la Riva<br>
<b>Cc:</b> ala-portal@lists.gbif.org<br>
<b>Subject:</b> Re: [Ala-portal] Problem generating a new name index<br>
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<div>Hi Santiago
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<div>This is likely to need ALA folks, but since they are asleep, this might give you some ideas to explore before they come online.</div>
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<div>I’ve logged the issue with a proposed fix: </div>
<div> <a href="https://github.com/AtlasOfLivingAustralia/ala-name-matching/issues/4" target="_blank">https://github.com/AtlasOfLivingAustralia/ala-name-matching/issues/4</a> </div>
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<div>What it fails on though is that it is getting NULL names. Perhaps you can modify your input checklist to not have null names ever?</div>
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<div>You might for example use this kind of SQL or similar for whatever you are using to generate the names list:</div>
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<div>SELECT</div>
<div> kingdom, phylum, class, order, family, genus, </div>
<div> COALESCE (name, genus, family, order, class, phylum, kingdom) AS scientificName</div>
<div>FROM ...</div>
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<div>The COALESCE function will then set the name to be the first non NULL value.</div>
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<div>I tried to build the project the fix myself, but “mvn:assembly:single” did not produce me a fat jar, and the project read me doesn’t tell me how they did it… sorry.</div>
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<div>I hope this helps,</div>
<div>Tim</div>
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<div>On 04 Sep 2014, at 14:50, Santiago Martinez de la Riva <<a href="mailto:sama@gbif.es" target="_blank">sama@gbif.es</a>> wrote:</div>
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<blockquote type="cite">Hi all,<br>
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I'm trying to create our own name index. I'm following the steps of the wiki in GitHub:
<a href="https://github.com/AtlasOfLivingAustralia/documentation/wiki/Creating-a-name-index" target="_blank">
https://github.com/AtlasOfLivingAustralia/documentation/wiki/Creating-a-name-index</a><br>
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Our dwca has the same estructura that dwca-col-mammals, but the problem is that when I try to generate the name index with the command: sudo nameindexer -dwca /...<br>
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I get the next exception:<br>
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vagrant@ala:/data/lucene/sources/dwca-spe2000-plantae$ sudo nameindexer -dwca /data/lucene/sources/dwca-spe2000-plantae<br>
2014-09-04 12:04:26,093 INFO : [DwcaNameIndexer] - Generating loading index: true<br>
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Generating searching index: true<br>
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Using the DwCA name file: /data/lucene/sources/dwca-spe2000-plantae<br>
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Using the default IRMNG name file: /data/lucene/sources/IRMNG_DWC_HOMONYMS<br>
2014-09-04 12:04:26,095 INFO : [DwcaNameIndexer] - Using the default common name file: /data/lucene/sources/col_vernacular.txt<br>
2014-09-04 12:04:26,182 INFO : [DwcaNameIndexer] - Starting to create the temporary loading index.<br>
2014-09-04 12:08:10,283 INFO : [DwcaNameIndexer] - Finished creating the temporary load index with 1070805 concepts<br>
java.lang.NullPointerException<br>
at au.org.ala.names.search.ALANameIndexer.isBlacklisted(ALANameIndexer.java:778)<br>
at au.org.ala.names.search.ALANameIndexer.createALAIndexDocument(ALANameIndexer.java:788)<br>
at au.org.ala.names.search.ALANameIndexer.createALAIndexDocument(ALANameIndexer.java:757)<br>
at au.org.ala.names.search.DwcaNameIndexer.addIndex(DwcaNameIndexer.java:350)<br>
at au.org.ala.names.search.DwcaNameIndexer.generateIndex(DwcaNameIndexer.java:281)<br>
at au.org.ala.names.search.DwcaNameIndexer.create(DwcaNameIndexer.java:101)<br>
at au.org.ala.names.search.DwcaNameIndexer.main(DwcaNameIndexer.java:527)<br>
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And when I try to search some name, I get this other one expection:<br>
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vagrant@ala:/data/lucene$ sudo nameindexer -testSearch "Nepeta Catarea"<br>
Search for name<br>
org.apache.lucene.index.IndexNotFoundException: no segments* file found in org.apache.lucene.store.NIOFSDirectory@/data/lucene/namematching/cb lockFactory=org.apache.lucene.store.NativeFSLockFactory@c22530: files: [write.lock]<br>
at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:741)<br>
at org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:52)<br>
at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:65)<br>
at au.org.ala.names.search.ALANameSearcher.<init>(ALANameSearcher.java:122)<br>
at au.org.ala.names.search.DwcaNameIndexer.main(DwcaNameIndexer.java:465)<br>
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Because the nameindexer didn't generate the necessary files:<br>
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Help meee!! xD<br>
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Cheers,<br>
SaMa<br>
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---------------------------------------------------------------------------------------<br>
Santiago Martínez de la Riva<br>
GBIF.ES, Unidad de Coordinación Tel. +34 91 4203017 x 273<br>
Real Jardín Botánico - CSIC Fax +34 91 429 2405<br>
Plaza de Murillo, 2 <a href="mailto:sama@gbif.es" target="_blank">sama@gbif.es</a><br>
28014 Madrid, Spain <a href="http://www.gbif.es" target="_blank">www.gbif.es</a><br>
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