September 2014 - ALA-Portal

biocache-hubs customizations
by Santiago Martinez de la Riva 04 Oct '14

04 Oct '14

Hi all, I have two questions: First: I want to change some FacetNames such as State/Territory, Local Govt. Area in the _advanced.gsp, but I don't know where is located this information. Could you give some tip? and second: If I modify the biocache-hub plug-in how can i do that generic-hub uses my new biocache-hub? Thanks so muchh!!! Kind regards, Santi. --------------------------------------------------------------------------------------- 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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ProviderCode Maps: Indexing dataset with several collection code
by Santiago Martinez de la Riva 02 Oct '14

02 Oct '14

Dear all, I have some datasets which have several collection code, the question is: how can i do to create the right relationship between the dataset, the collection and the instituttion through the ProviderCodes Map, if the dataset has 2 or more collection code?? e.g: If the dataset has these collection codes: cof and co_cof. I create the provider code: cof co_cof or cof, co_cof after this I create the providerCode Map between the institution and the colecction, and I select the codes, and I don't select the checkbox "Exact". But when I process and index again the dataset, I don't get that this process indexes all the records that dataset has. Could you help please? Cheers, Santi. --------------------------------------------------------------------------------------- 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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Taxon Profile DB
by Allan Koch 30 Sep '14

30 Sep '14

Hi all, I was studing the code of Processing of biocache-store and I figured out that the biocache uses the TaxonProfile list to include Vernacular names from a scientific name ID. Is it right? If yes, how can I create or modify the TaxonProfile? I also figured out that TaxonProfile list is storaged in Cassandra ("Taxon" family collumn). Is this database filled by *TaxonProfileLoader* ( https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma… How to run this TaxonProfileLoader and with what input? or I might consider creating a Cassandra script for inserting records into the Taxon family columns? Thank you folks, 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(a)usp.br

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How can I include <g:message..> in javascript
by Santiago Martinez de la Riva 23 Sep '14

23 Sep '14

Hi all, I'm trying to modify some javascript files to do the right internationation through the message.properties file, but I don't know how can I write this code <g:message.../> into the javascript code. For example: If we have this javascript code: chartLabels: { institution_uid: 'institution',.... or title: function () { return "By " + this.chartLabel();},..... or $container.append($('<h4>Explore records by Taxonomy</h4>')); Is it possible include <g:message..> into this code, something like this: $container.append($('<h4><g:message code='public.charts.taxomony.title'/></h4>')); I've tried to do this but I obtain a javascript error. Could someone teach me how can I do this? Thanks in advance, Santi. --------------------------------------------------------------------------------------- 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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ANSIBLE SCRIPT PROBLEM - BIOCACHE-SERVICE??
by Santiago Martinez de la Riva 23 Sep '14

23 Sep '14

Dear all, I'm trying again to install the data portal through the ansible script, but all time the script stops in this part: TASK: [biocache-service | copy biocache webapss]. Does someone have the same problem?? Thanks in advance. Cheers, Santi. --------------------------------------------------------------------------------------- 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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DATASETS and MANAGE RESOURCES / COLLECTION AND INSTITUTION
by Santiago Martinez de la Riva 17 Sep '14

17 Sep '14

Hi all, I updated our collectory module with the last release, collectory 1.1.2. And I found two issues that I would like to comment you. 1) DATASETS: http://datos.gbif.es/collectory/datasets/ In this url the datasets are never loaded. You can see in the Firebug that the page has 3 erros, one of these is the next: TypeError: jQuery(...).autocomplete is not a function selectFirst: false /collec...tasets/ (línea 70, col 16) 2) ADDING RESOURCES / COLLECTION / INSTITUTION: http://datos.gbif.es/collectory/public/show/in1 In this context, we have one Institution (in1) that has 2 collections. Now I'm goin to explain the procedure that I do to create these relations: The first thing that I do is upload the resource, and after, I create the entities for that collection and that instution. In this moment, I edit the data resource and the collection for creating the relations: - The first collection "Inventario Fauna Vertebrada de la Manchuela Conquense (CUENCA), 2007 (ADIMAN-MANCHUELA-2007)" is related to the data resource "dr40" that has 2.790, the collection code is ADIMAN-MACHUELA-2007 and the internal code/id is co3. The record consumer of the data resource "dr40" are co3 and in1. (image_1) but when I create the relation between this collection and the institution, the record cosumer are (view image_2) - The second collection "Inventario de Flora y Vegetación del Municipio de Enguídanos (Cuenca), 2010 (ADIMAN-FLORA)" is related to the data resource "dr66" that has 5.291 records. The collection code is ADIMAN-FLORA and the internal code/id is co2. The record consumer of the data resource "dr66" are co2 and in1. (image_3) but when I create the relation between this collection and the institution the record cosumer are: (view image_4) I think that in both cases, image_2 and image_4, are wrong, because, how is it possible that one collection contributes with digitised records to the other? This doesn't make sense. When I have created this structure, then I do the ingest of these resource: ingest -dr dr40 ingest -dr dr66 But, what is my surprise that when I access to the page of each resource, I see that the total records of ADIMAN-MANCHUELA-2007 is the sum of the record of both collections, and ADIMAN-FLORA doesn't have records. You can see this in this links: - http://datos.gbif.es/collectory/public/show/co3 (ADIMAN-MACHUELA-2007) - http://datos.gbif.es/collectory/public/show/co2 (ADMINA-FLORA) I can also create the provider Map for both cases, but I don't exactly know, if the provider codes have to be the internal codes like: in1, co2 and co3 or the orginal codes like ADMIN, ADIMAN-FLORA and ADIMAN-MACHUELA-2007. In the image_5 and image_6, you can see the ProviderMap for this case. Two question? - Is it necessary the use of these provider maps to create the relations? - Could you explain how works this matching code? I mean, It's possible that in one collection we have two collection codes, For example: in ADIMAN-MACHUELA-2007 we have other collection code that is ADIMAN-CENSOAVUTARDA-2008. I figure up that I can define these rules with the parameters: "exact" and "Match Any Collection Code". Is right? Thanks so much for the help and sorry for this long message. PD: I'm working also with the i18n, and soon we will have translated and implemented all the variables in the project. You can see some advance in this link http://datos.gbif.es/collectory, I have had to edit some javascripts to do all the translation. --------------------------------------------------------------------------------------- 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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I don't get create the namematching with the last release of the nameindexer
by Santiago Martinez de la Riva 15 Sep '14

15 Sep '14

Hi all, We have some problems trying to generate our own namematching. Our Dwc-a has the 3 required files ( attached to mail) - The meta.xml that points to spe_lamiacea_accepted.txt. - The eml.xml - spe_lamiaceae_accepted.txt, that contains only the accepted name of that family. Also we have our own vernaculars name in the vernacular_name.txt. The question is that when I try to generate the namematching following the steps in this url https://github.com/AtlasOfLivingAustralia/ala-name-matching or using the nameindexer that it's installed in the last ansible, the names are never indexed. The process shows this text: 2014-09-12 10:07:58,559 INFO : [DwcaNameIndexer] - Generating loading index: true 2014-09-12 10:07:58,559 INFO : [DwcaNameIndexer] - Generating searching index: true 2014-09-12 10:07:58,560 INFO : [DwcaNameIndexer] - Using the DwCA name file: /data/lucene/sources/spe_lamiaceae_accepted 2014-09-12 10:07:58,560 INFO : [DwcaNameIndexer] - Using the default IRMNG name file: /data/lucene/sources/IRMNG_DWC_HOMONYMS 2014-09-12 10:07:58,560 INFO : [DwcaNameIndexer] - Using the default common name file: /data/lucene/sources/col_vernacular.txt 2014-09-12 10:07:58,642 INFO : [DwcaNameIndexer] - Starting to create the temporary loading index. 2014-09-12 10:07:59,365 INFO : [DwcaNameIndexer] - Finished creating the temporary load index with 881 concepts 2014-09-12 10:07:59,744 INFO : [ALANameIndexer] - Creating the IRMNG index from the DWCA /data/lucene/sources/IRMNG_DWC_HOMONYMS 2014-09-12 10:08:07,658 INFO : [DwcaNameIndexer] - Starting to load the common names 2014-09-12 10:08:07,699 INFO : [DwcaNameIndexer] - Finished processing 1000 common names with 0 added to index 2014-09-12 10:08:07,724 INFO : [DwcaNameIndexer] - Finished processing 2000 common names with 0 added to index ...... 2014-09-12 10:08:09,516 INFO : [DwcaNameIndexer] - Finished processing 332000 common names with 0 added to index 2014-09-12 10:08:09,518 INFO : [DwcaNameIndexer] - Finished processing 332199 common names with 0 added to index And when I try to search a scientific name through: sudo nameindexer -testSearch "scientific_name", I always obtain the same result: No match for this "scientic_name" In the beginning, we realized that your col_dwc.txt only has accepted names, then we thought that this file can only have accepted names. But also we have the this file with synonyms, and with not accepted names. But we don't get create the namematching in any case. Is it possible that are there some bug in the indexer or in the ala-name-matching-2.1-distribution? I think that our zip has the same structure that your zip (http://biocache.ala.org.au/archives/dwca-col.zip) and we have done several test with different kind of files of names. For this reason, we have thought that this possibility can exist. In other hand, I think that the Brasilian team got generate their own namematching, could someone of this team, I think that Allan did this, explain how they have generated their namematching?? Thanks a lot, 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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[Requirements list]: Latin American Nodes Meeting - Brazil
by Santiago Martinez de la Riva 10 Sep '14

10 Sep '14

Hi all, Last week Paco Pando – manager of GBIF Spain - attended the Latin American Nodes Meeting in Brazil where he could write down the most important requirements for these nodes in order to develop their own data portal based on the ALA model: Help of define an agreed list of functionalities to be put in deployable form. For instance: - DwC procedure for uploading data AND METADATA into the portal (API GBIF.ORG) - Better support for collection & institution info management. - BIE for Plinian. - CAS. - Better maps & layers management. - Geospatial module. This implies: * Code retouching. * Documentation. * A ToR for participant nodes to define commitment and contribution. Kind regards, 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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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releases for collectory, biocache-hubs and ala-name-matching
by David.Martin＠csiro.au 08 Sep '14

08 Sep '14

Hi Santiago, all, We've put out three bug releases with fixes for the links back to collection/institutions and the name matching issues. * ala-name-matching v2.1 * collectory v1.1.1 * biocache-hubs v0.57 The ansible scripts are now pointing at these versions so re-running the ala-demo.yml [1] ansible playbook will install these updates. To update your instance generic-hub, change the biocache-hubs version referenced in the grails-app/conf/BuildConfig.groovy to: runtime ":biocache-hubs:0.57" The latest builds are deployed to http://ala-demo.gbif.org. Heres an example record with institution/collection links here [2]. We also noticed a bad config setting with demo scripts that we've now fixed. The file /data/biocache/config/biocache-config.properties should have the following: caches.collections.enabled=true This was set to false and was preventing the proper display of collection, institution names in queries. Hope this helps, Dave [1] https://github.com/AtlasOfLivingAustralia/ala-install/blob/master/ansible/a… [2] http://ala-demo.gbif.org/generic-hub/occurrences/15729b22-4acb-4d9a-b52e-8c…

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Problem generating a new name index
by Santiago Martinez de la Riva 05 Sep '14

05 Sep '14

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-nam… 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@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@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@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(a)gbif.es 28014 Madrid, Spain www.gbif.es

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