[Ala-portal] Names Generator Issues
Natasha.Quimby at csiro.au
Natasha.Quimby at csiro.au
Fri Apr 4 00:09:39 CEST 2014
Hi Allan,
The names in the AnimaisMonitiradosProcessados.csv do not follow the format expected by the DwcA. According to the meta.xml:
<core encoding="utf-8" fieldsTerminatedBy="\t" linesTerminatedBy="\n" fieldsEnclosedBy='"'
ignoreHeaderLines="1" rowType="http://rs.tdwg.org/dwc/terms/Taxon">
Thus all fields should be quoted and separated by a tab character.
I think that this may be causing the issue for you. Can you change the format of your names to follow the same format as the col entries? Let me know if this solves your issue.
Regards
Natasha
From: Allan Koch <allan.kv at gmail.com<mailto:allan.kv at gmail.com>>
Date: Friday, 4 April 2014 1:37 AM
To: Natasha Carter <natasha.quimby at csiro.au<mailto:natasha.quimby at csiro.au>>
Cc: "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
Hi Natasha,
I´m sending the files that I appended to col_dwc.txt and col_vernacular.txt.
I used this Linux command to append those files:
cat AnimaisMonitoradosProcessados.csv >> col_dwc.txt
cat vernacularNameAnimaisMonitoradosProcessados.csv >> col_vernacular.txt
Thank you for help.
Allan Koch Veiga
Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
2014-04-02 18:43 GMT-03:00 <Natasha.Quimby at csiro.au<mailto:Natasha.Quimby at csiro.au>>:
Hi Allan,
The line of code that you are getting the NPE in is:
return blacklist.contains(scientificName.trim())
This implies to me that the scientific name that is being supplied is null.
You mentioned earlier that you had 109 species that you needed to add to the CoL DwcA. Could you please send the lines that you added to the DwcA?
Thanks.
Regards
Natasha
From: Allan Koch <allan.kv at gmail.com<mailto:allan.kv at gmail.com>>
Date: Thursday, 3 April 2014 4:53 AM
To: Natasha Carter <natasha.quimby at csiro.au<mailto:natasha.quimby at csiro.au>>
Cc: "Martin, Dave (CES, Black Mountain)" <David.Martin at csiro.au<mailto:David.Martin at csiro.au>>, "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
Hi Natasha,
I ran DwcaNameIndexer with default CoL list, with any modification, and it works correctly.
But, it not works when I ran with a modified file. I merged into the CoL taxon concepts list and vernacular names our taxon concepts and vernacular names.
For now, I not include the IRMNG_DWC_HOMONYMS.
Sou, I ran this command:
java -cp .:names.jar au.org.ala.checklist.lucene.DwcaNameIndexer --all --dwca /[ABSOLUT_PATH]/dwca-col-merge-animais/col_dwc.txt --target /[ABSOLUT_PATH]/index/mergeColAnimaisCommon/ --common /[ABSOLUT_PATH]/col_vernacular_merge_animais.txt
This is the output:
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Apr 02, 2014 1:54:17 PM au.org.ala.checklist.lucene.DwcaNameIndexer createLoadingIndex
INFO: Starting to create the temporary loading index.
Apr 02, 2014 1:59:55 PM au.org.ala.checklist.lucene.DwcaNameIndexer createLoadingIndex
INFO: Finished creating the temporary load index with 2474452 concepts
Apr 02, 2014 2:05:00 PM au.org.ala.checklist.lucene.CBCreateLuceneIndex createALAIndexDocument
WARNING: urn:lsid:catalogueoflife.org:taxon:e0bc6ece-2dc5-11e0-98c6-2ce70255a436:col20120124 X humeralis has issues creating a soundex: String index out of range: -1
Apr 02, 2014 2:05:00 PM au.org.ala.checklist.lucene.CBCreateLuceneIndex createALAIndexDocument
WARNING: urn:lsid:catalogueoflife.org:taxon:e0aac25d-2dc5-11e0-98c6-2ce70255a436:col20120124 X cinerea has issues creating a soundex: String index out of range: -1
Apr 02, 2014 2:05:00 PM au.org.ala.checklist.lucene.CBCreateLuceneIndex createALAIndexDocument
WARNING: urn:lsid:catalogueoflife.org:taxon:e0c2f680-2dc5-11e0-98c6-2ce70255a436:col20120124 X lineatus has issues creating a soundex: String index out of range: -1
Apr 02, 2014 2:05:00 PM au.org.ala.checklist.lucene.CBCreateLuceneIndex createALAIndexDocument
WARNING: urn:lsid:catalogueoflife.org:taxon:e1590b50-2dc5-11e0-98c6-2ce70255a436:col20120124 X has issues creating a soundex: String index out of range: -1
Apr 02, 2014 2:21:18 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d74fcd5e-29c1-102b-9a4a-00304854f820:col20120124 Animalia 1 2455490
Apr 02, 2014 2:26:37 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d755b8fe-29c1-102b-9a4a-00304854f820:col20120124 Plantae 2455491 3065868
Apr 02, 2014 2:26:50 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d755c2e0-29c1-102b-9a4a-00304854f820:col20120124 Bacteria 3065869 3089350
Apr 02, 2014 2:27:10 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d76c1e8c-29c1-102b-9a4a-00304854f820:col20120124 Protozoa 3089351 3127338
Apr 02, 2014 2:27:20 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d7656902-29c1-102b-9a4a-00304854f820:col20120124 Chromista 3127339 3145930
Apr 02, 2014 2:27:22 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d76df252-29c1-102b-9a4a-00304854f820:col20120124 Viruses 3145931 3150922
Apr 02, 2014 2:28:21 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d770c428-29c1-102b-9a4a-00304854f820:col20120124 Fungi 3150923 3262754
Apr 02, 2014 2:28:22 PM au.org.ala.checklist.lucene.DwcaNameIndexer generateIndex
INFO: Finished loading urn:lsid:catalogueoflife.org:taxon:d77cda9c-29c1-102b-9a4a-00304854f820:col20120124 Archaea 3262755 3263584
java.lang.NullPointerException
at au.org.ala.checklist.lucene.CBCreateLuceneIndex.isBlacklisted(CBCreateLuceneIndex.java:769)
at au.org.ala.checklist.lucene.CBCreateLuceneIndex.createALAIndexDocument(CBCreateLuceneIndex.java:779)
at au.org.ala.checklist.lucene.CBCreateLuceneIndex.createALAIndexDocument(CBCreateLuceneIndex.java:747)
at au.org.ala.checklist.lucene.DwcaNameIndexer.addIndex(DwcaNameIndexer.java:321)
at au.org.ala.checklist.lucene.DwcaNameIndexer.generateIndex(DwcaNameIndexer.java:252)
at au.org.ala.checklist.lucene.DwcaNameIndexer.create(DwcaNameIndexer.java:85)
at au.org.ala.checklist.lucene.DwcaNameIndexer.main(DwcaNameIndexer.java:386)
Any idea about what coud be the problem?
If you want I can send you col_dwc.txt and col_vernacular_merge_animais.txt files that I used.
Thank you,
Allan Koch Veiga
Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
2014-03-20 18:44 GMT-03:00 <Natasha.Quimby at csiro.au<mailto:Natasha.Quimby at csiro.au>>:
Hi Allan,
We have finished writing a DWCA Names index generator. It requires a single DwCA that contains all the scientific names that you wish to add (including synonyms).
There is an example Catalogue of Life DwcA that can be downloaded here: http://biocache.ala.org.au/archives/dwca-col.zip You will need to modify the col_dwc.txt file to include any additional species.
The name matching index can also support common name. Here are the Catalogue of Life common names that can be loaded in conjunction to the Darwin Core Archive: http://biocache.ala.org.au/archives/col_vernacular.txt.zip
The name matching supports homonym detection. Homonym detection is supported through the using of IRMNG. You can download the IRMNG DwCA for homonyms from the following URL: www.cmar.csiro.au/datacentre/downloads/IRMNG_DWC_HOMONYMS.zip<http://www.cmar.csiro.au/datacentre/downloads/IRMNG_DWC_HOMONYMS.zip>
Here is the code for the DwcaNameIndexer : http://code.google.com/p/ala-portal/source/browse/trunk/ala-name-matching/src/main/java/au/org/ala/checklist/lucene/DwcaNameIndexer.java
An assembly jar file for this can be downloaded from our maven repository : http://maven.ala.org.au/repository/au/org/ala/ala-name-matching/1.3-SNAPSHOT/ala-name-matching-1.3-SNAPSHOT-assembly.jar
To generate the name using the assembly jar:
1) Rename the jar :
mv ala-name-matching-1.3-SNAPSHOT-assembly.jar names.jar
2) Extract the lib directory:
jar –xf names.jar lib
3) Generate the names index – here is the command that I used.
java –cp .:names.jar au.org.ala.checklist.lucene.DwcaNameIndexer --all --dwca /data/bie-staging/names-lists/dwca-col --target /data/lucene/testdwc-namematching --irmng /data/bie-staging/irmng/IRMNG_DWC_HOMONYMS --common /data/bie-staging/ala-names/col_vernacular.txt
Please be aware that the names indexing could take over an hour to complete.
Let me know if you have any questions.
Regards
Natasha
From: Allan Koch <allan.kv at gmail.com<mailto:allan.kv at gmail.com>>
Date: Wednesday, 19 March 2014 12:44 AM
To: Natasha Carter <natasha.quimby at csiro.au<mailto:natasha.quimby at csiro.au>>
Cc: "Martin, Dave (CES, Black Mountain)" <David.Martin at csiro.au<mailto:David.Martin at csiro.au>>, "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
Hi Natasha,
That´s great. Thank you very much.
We are waiting for the DwC-A with CoL list for we merging our names.
We are excited with this news.
Thank you again,
Allan Koch Veiga
Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
2014-03-18 3:03 GMT-03:00 <Natasha.Quimby at csiro.au<mailto:Natasha.Quimby at csiro.au>>:
Hi Allan,
We would provide a DwCA with the Catalogue of Life species in it. Yes, you will need to add your species to this file in the same format. If you want your species to be merged into the Catalogue of life hierarchy you will need to provide appropriate parentIds.
We would provide a tool within the ala-name-matching (available as a jar file in our maven repository) to generate a list based on a DwCA. You would need to run the tool pointing at your modified DwCA.
We will let you know when this is available.
Hope that this all makes sense.
Regards
Natasha
From: Allan Koch <allan.kv at gmail.com<mailto:allan.kv at gmail.com>>
Date: Tuesday, 18 March 2014 7:34 AM
To: Natasha Carter <natasha.quimby at csiro.au<mailto:natasha.quimby at csiro.au>>
Cc: "Martin, Dave (CES, Black Mountain)" <David.Martin at csiro.au<mailto:David.Martin at csiro.au>>, "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
Hi Natasha,
It would be great. We have 109 species that we need to include in the current name matching index.
It would be great if you send me a DwC-A with CoL names. I will need just to add these 109 species in that archive in the same format, right?
How will work this proposed solution?
Will you provide a souce code, a compiled program (JAR) or we will send to you the DwC-A and you will generate the Lucene index?
Thank you very much for helping.
Best regards,
Allan Koch Veiga
Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
2014-03-17 3:12 GMT-03:00 <Natasha.Quimby at csiro.au<mailto:Natasha.Quimby at csiro.au>>:
Hi Allan,
The ala-name-generator is useful if you want to use the Australian National Species list as the main source for your namematching index. We would not suggest using this to supplement the name matching index with additional species.
In order to support custom species lists we are planning an enhancement to generate the namematching index from a DarwinCore Archive. We would envision that all the species would be provided as a single DWCA with the attached meta.xml. We think that this could be achieved in the 1-2 week window that you mentioned. We could provide a DWCA which contains Catalogue of Life as a basis for you to start with. You can then add additional names to the DWCA as you please. Do you think that this would suit you needs?
Regards
Natasha
From: Allan Koch <allan.kv at gmail.com<mailto:allan.kv at gmail.com>>
Date: Saturday, 15 March 2014 4:19 AM
To: "Martin, Dave (CES, Black Mountain)" <David.Martin at csiro.au<mailto:David.Martin at csiro.au>>
Cc: "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
I thank you for the quick answer David and Tim .
We have studied the process to create the namematching index based on the National List of Australia and I see that reproducing the same process to create a new National List is quite complex.
But, for now, we just have the demand to include some names that aren´t included in current namematching index.
If we understood, we need at first, run the Names Generator with the input of a set of CSVs from APNI, APC e AFD. Based on the output of the Names Generator we run the Name Mathcing for creating the LUCENE index, right?
If it´s right, it would be great If we could execute this same standard process, but with de input CSVs modified, with our set of names included in these CSVs (in the same format).
In the future (after this 3 months) we can study the possibility to generate our complete National List .
But for now, we need to include a set of names in the namematching index.
It could be possible to be realized in a short time, in one or two weeks?
Best regards,
Allan Koch Veiga
Núcleo de Pesquisa em Biodiversidade e Computação - BioComp
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 8401-2277
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
2014-03-12 23:15 GMT-03:00 <David.Martin at csiro.au<mailto:David.Martin at csiro.au>>:
Thanks Allan, Paulo, Tim.
We appreciate your efforts in setting this software upm locally, and thanks for emailing the list.
1) Versioning
While we are on the track of making this software re-usable by other projects/organisations, it is still very early days. Versioning and packaging are things that we need to tackle properly in the 3 month evaulation period [2] and we are working with GBIF on the best approach here (see Tim's email regarding Ansible). To date, the ALA environment itself is the only place these components are used in production and we manage these closely ourselves. We havent had a need to tightly version components, but as other projects become reliant we need to do this properly. At this point it time, I'd recommend ignoring developments on branches within SVN.
2) ala-name-generator
We didn't anticipate that other projects would be using the ala-name-generator code at this stage (or at all), and instead would rely on the Catalogue of Life names lucene index we've produced [1]. The ala-name-generator code as it currently is isnt suitable for use outside the Australian context. It is dealing with some of the quirks of Australian species lists and merging some elements from different sources. We should have marked wikis to that effect.
That said, we appreciate the need for other projects to use their own taxonomic checklists. This was something I'd hope we tackle in the 3 month evaluation period [2]. There's a few of potential approaches here we are exploring and we'll email this list soon with some progress on this front. I suggest in the meantime, projects make use of the existing index [1].
Thanks again,
Dave Martin
ALA
[1] http://biocache.ala.org.au/archives/col_namematching.tgz
[2] See GBIF's email sent 21st Feb 2014 - "Biodiversity data portals: Using the ALA tooling"
From: "Tim Robertson [GBIF]" <trobertson at gbif.org<mailto:trobertson at gbif.org>>
Date: Thursday, 13 March 2014 2:16 am
To: Paulo André <pfilipak at gmail.com<mailto:pfilipak at gmail.com>>
Cc: "Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>" <Ala-portal at lists.gbif.org<mailto:Ala-portal at lists.gbif.org>>
Subject: Re: [Ala-portal] Names Generator Issues
Hi Paulo
Those are all good comments - I'll make sure the ALA dev team are following those issues.
As this goes forward, it is clear that code releases are going to be needed, so we get immutable binaries in nexus and tagged SVN branches. I'll try and raise this with Dave Martin.
I'll try and follow the resolutions for the issues you log, build an artifact and verify the same results.
I'm not so much into scala, but IIRC I saw that issue with another artifact. The solution was to run this before running the command line:
jar -xf ala-names-generator-1.0-SNAPSHOT-assembly.jar lib
I found this in the way they run the biocache command line tools in:
https://ala-portal.googlecode.com/svn/trunk/biocache-install/ubuntu/install.sh
It may not be the solution, but worth trying.
I hope this helps,
Tim
On Mar 12, 2014, at 3:57 PM, Paulo André wrote:
Tim
I had have several issues on https://code.google.com/p/ala-portal/source/browse/#svn%2Ftrunk%2Fala-names-generator<https://code.google.com/p/ala-portal/source/browse/#svn/trunk/ala-names-generator>
I wrote on Jira: http://dev.gbif.org/issues/browse/ALA
[]'s
Paulo Andre Filipak
2014-03-12 11:51 GMT-03:00 Tim Robertson [GBIF] <trobertson at gbif.org<mailto:trobertson at gbif.org>>:
Hi Allan,
I am sure the ALA folks will comment when they wake up. But...
It doesn't appear to be published as an artifact in the ALA maven repository:
http://maven.ala.org.au/repository/au/org/ala/
You could build from source from: https://code.google.com/p/ala-portal/source/browse/#svn%2Ftrunk%2Fala-names-generator<https://code.google.com/p/ala-portal/source/browse/#svn/trunk/ala-names-generator>
I presume using something along the lines of "mvn clean assembly:assembly"
I hope this helps provide some options,
Tim
On Mar 12, 2014, at 3:32 PM, Allan Koch wrote:
Does anyone knows where I can download this jar: ala-names-generator-1.0-SNAPSHOT-assembly.jar?
I´m trying to generate a new Taxon Name List based on NSL for the Biocache processing.
This instructions has been followed:
http://code.google.com/p/ala-portal/wiki/UpgradeALANames
According the instructions, I need to run this command:
java -Xmx1G -Xms1G -cp .:ala-names-generator-1.0-SNAPSHOT-assembly.jar au.org.ala.names.NamesGenerator --all
But, I can´t find this JAR.
We are trying to build the Scala Project, but we are having some troubles.
Would help me, for while, if I could run a ready JAR.
Best regards,
Allan Koch Veiga
Research Center on Biodiversity and Computing - BioComp
University of São Paulo
Laboratório de Automação Agrícola - LAA
Depto. de Engenharia de Computação e Sistemas Digitais - PCS
Engenharia Elétrica - Escola Politécnica da USP
Celular: +55 11 98401-2277<tel:%2B55%2011%2098401-2277>
Email: allan.kv at usp.br<mailto:allan.kv at usp.br>
"Stay hungry, stay foolish." Stewart Brand
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GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
Tel: +45 3532 1487<tel:%2B45%203532%201487> Mob: +45 2826 1487<tel:%2B45%202826%201487> Fax: +45 2875 1480<tel:%2B45%202875%201480>
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