[Ala-portal] Problem generating a new name index

[Santiago Martinez de la Riva]

Solved. The problem was that the values in dwc-spe2000-plantae were separated by ";" and not by "tab". But my problem now is that when I try to search a scientific name, I never find it and I only have 2 scientific names. mmm Thinkinggg

Do i only have to do sudo: nameindexer -testSearch "Tasmaphena sinclairi" after: sudo nameindexer -dwca /data/lucene/sources/dwca-spe2000-plantae? don't i need to execute other command??

Cheers.
SaMa
---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama at gbif.es
28014 Madrid, Spain                                 www.gbif.es

________________________________________
De: ala-portal-bounces at lists.gbif.org [ala-portal-bounces at lists.gbif.org] En nombre de Santiago Martinez de la Riva [sama at gbif.es]
Enviado el: jueves, 04 de septiembre de 2014 14:50
Para: ala-portal at lists.gbif.org
Asunto: [Ala-portal] Problem generating a new name index

Hi all,


I'm trying to create our own name index. I'm following the steps of the wiki in GitHub: https://github.com/AtlasOfLivingAustralia/documentation/wiki/Creating-a-name-index

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 /...

I get the next exception:

vagrant at ala:/data/lucene/sources/dwca-spe2000-plantae$ sudo nameindexer -dwca /data/lucene/sources/dwca-spe2000-plantae
2014-09-04 12:04:26,093 INFO : [DwcaNameIndexer] - Generating loading index: true
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Generating searching index: true
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Using the  DwCA name file: /data/lucene/sources/dwca-spe2000-plantae
2014-09-04 12:04:26,094 INFO : [DwcaNameIndexer] - Using the default IRMNG name file: /data/lucene/sources/IRMNG_DWC_HOMONYMS
2014-09-04 12:04:26,095 INFO : [DwcaNameIndexer] - Using the default common name file: /data/lucene/sources/col_vernacular.txt
2014-09-04 12:04:26,182 INFO : [DwcaNameIndexer] - Starting to create the temporary loading index.
2014-09-04 12:08:10,283 INFO : [DwcaNameIndexer] - Finished creating the temporary load index with 1070805 concepts
java.lang.NullPointerException
        at au.org.ala.names.search.ALANameIndexer.isBlacklisted(ALANameIndexer.java:778)
        at au.org.ala.names.search.ALANameIndexer.createALAIndexDocument(ALANameIndexer.java:788)
        at au.org.ala.names.search.ALANameIndexer.createALAIndexDocument(ALANameIndexer.java:757)
        at au.org.ala.names.search.DwcaNameIndexer.addIndex(DwcaNameIndexer.java:350)
        at au.org.ala.names.search.DwcaNameIndexer.generateIndex(DwcaNameIndexer.java:281)
        at au.org.ala.names.search.DwcaNameIndexer.create(DwcaNameIndexer.java:101)
        at au.org.ala.names.search.DwcaNameIndexer.main(DwcaNameIndexer.java:527)

And when I try to search some name, I get this other one expection:

vagrant at ala:/data/lucene$ sudo nameindexer -testSearch "Nepeta Catarea"
Search for name
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 at c22530: files: [write.lock]
        at org.apache.lucene.index.SegmentInfos$FindSegmentsFile.run(SegmentInfos.java:741)
        at org.apache.lucene.index.StandardDirectoryReader.open(StandardDirectoryReader.java:52)
        at org.apache.lucene.index.DirectoryReader.open(DirectoryReader.java:65)
        at au.org.ala.names.search.ALANameSearcher.<init>(ALANameSearcher.java:122)
        at au.org.ala.names.search.DwcaNameIndexer.main(DwcaNameIndexer.java:465)


Because the nameindexer didn't generate the necessary files:

Help meee!! xD

Cheers,
SaMa


---------------------------------------------------------------------------------------
Santiago Martínez de la Riva
GBIF.ES, Unidad de Coordinación         Tel. +34 91 4203017 x 273
Real Jardín Botánico - CSIC                     Fax +34 91 429 2405
Plaza de Murillo, 2                                     sama at gbif.es
28014 Madrid, Spain                                 www.gbif.es
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