- ALA-Portal - lists.gbif.org

Name matching issues
by Allan Koch 27 Aug '14

27 Aug '14

Hi guys, I have two issues concerning taxon names. I will start with, probably, the easier issue. (1) We create the name matching index using a merged list from CoL and a list of Brazilian species. But these names aren't used in the autocomplete of searching page. We saw the call of AJAX and it's calling a service from BIE ( http://bie.ala.org.au/search/auto.json?callback=jQuery183029955692077055573…). The autocomplete feature can be changed to call the names from Lucene name matching index? (2) When we ingest a dataset, the process try to match the names using some techniques of fuzzy matching, is it right? But, for some names, this not occured. For example, the name "Apis melifera" is matched with "Apis (Apis) mellifera" (it an example that works well), but the name "Chrysocyon brachycrus" should match with "Chrysocyon brachyurus", and it not happen. Why the fuzzy matching is applied to some names and don't aplied to other names? 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 "*Stay hungry, stay foolish.*" Stewart Brand

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Issue in the Explore your Area section
by Santiago Martinez de la Riva 27 Aug '14

27 Aug '14

Hi all, We are testing again the ala portal, and I think that we have found a issue that I’m going to explain us below. The issue is in the "Explore your Area" section. [Case 1]. In the image1, we can see that there is one point into the area, exactly with one record. Then if we want to list this record, we can click on the option "View list of records" but the system shows us the next message: "No records found for *:*" (View image2) ". [Case 2] This is also the case, when we try to do the same with the option "View all records" (View image3). [Case 3 ]In other hand, if we try to list a specific record that we can see in the left list through the option "list of records" (View image4), in this case the system shows us this message "No records found for taxon_name:"Crepis bursifolia" ". (View image5) In general, it´s like if these operations of "Explore your Area" are not connected to the indexing of solr. But I want to do one puntualization. In the first case, it makes no sense that the system shows us that error, because we are filtering the records that we want that the system shows us, when we click on the link of the bubble of that specific point in the area. I hope this helps to trace the error. Many thanks and kind regards by SaMaxD. --------------------------------------------------------------------------------------- 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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translation tool
by Miguel Carboni 22 Aug '14

22 Aug '14

Hi all, Tim suggested us to try crowdin to translate the properties file to Spanish and I can say I'm quite satisfied with it and the chance of unifying criteria with other Spanish speaking countries. What do you think about adopting it as the tool of choice? Best, Miguel

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Re: [Ala-portal] Customising facet fields in biocache hubs
by Nick.Dosremedios＠csiro.au 08 Aug '14

08 Aug '14

Hi Daniel, I have another question. How can I define which facets are shown on the Hubs to filter occurrence data? The visible filters depends of a configuration file? This a good question and one that may help many other groups so I'd recommend posting questions like this to the GBIF ALA-portal mailing list (CCed). The facet fields that are shown in the left column of the search results can be changed via the configuration settings - either Config.groovy or the external properties file (e.g. /data/generic-hub/config/generic-hub-config.properties), depending on which you are using. The config variables starting with "facets." are responsible for this: • facets.include - comma separated list of fields to include (usually only those fields not in the default set as specified by ${biocache.baseUrl}/search/facets) • facets.exclude - comma separated list of fields to exclude. i.e. fields in the default set you don't want to appear • facets.hide - comma separated list of field that would be included the facet column but that you want to be hidden (i.e. unticked in the "customise filters" drop down). So these fields will be displayed if the user changes the default display settings and chooses to turn them on. Note you can also change the default set of facets but this is set in the biocache-service application, also via config vars (I think). You may also want to change the way facets are grouped together (see ${biocache.baseUrl}/search/grouped/facets). I'll add this info to the Wiki, as well. Cheers Nick -- Nick dos Remedios Software Developer Atlas of Living Australia<http://www.ala.org.au> National Facilities & Collections, CSIRO<http://www.csiro.au/Organisation-Structure/National-Facilities.aspx> nick.dosremedios(a)csiro.au<mailto:nick.dosremedios@csiro.au> On 8 Aug 2014, at 8:41 am, Daniel Lins <daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>> wrote: Thanks Nick!! This was the problem. I changed the javascript file and now is working fine. I have another question. How can I define which facets are shown on the Hubs to filter occurrence data? The visible filters depends of a configuration file? Thanks again!! Cheers, 2014-08-06 23:16 GMT-03:00 <Nick.Dosremedios(a)csiro.au<mailto:Nick.Dosremedios@csiro.au>>: Hi Daniel, Yes, if you think you found a bug then add it as an issue on the Gihub page. I had a look at the issue and I can see using the "Inspect element" tool in Chrome (or FireBug in FF), that when you click on the polygon is doing an AJAX lookup against the ALA prod biocache: http://biocache.ala.org.au/ws/occurrence/facets.json?q=*%3A*&wkt=POLYGON((-…<http://biocache.ala.org.au/ws/occurrence/facets.json?q=*:*&wkt=POLYGON((-58…> I think this was hard-coded by Adam, so I'll look to fixing it so it uses the config var for the bioacache URL (biocache.baseUrl ). Cheers Nick -- Nick dos Remedios Software Developer Atlas of Living Australia<http://www.ala.org.au/> National Facilities & Collections, CSIRO<http://www.csiro.au/Organisation-Structure/National-Facilities.aspx> nick.dosremedios(a)csiro.au<mailto:nick.dosremedios@csiro.au> On 7 Aug 2014, at 12:03 pm, Daniel Lins <daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>> wrote: Hi Nick, how are you? I have some questions about where we can log bugs found in ALA software. I can do this on the GitHub website? The feature that calculates the number of species and occurrences within the drawn polygon has some problems (it shows incorrect values in the balloon). Below I will describe a step-by-step test which shows the problem: 1. All test data are shown on the map (BrazilData1.png). 2. A specific point on the map has 27 occurrences (BrazilData-specificarea.png). 3. When drawing a polygon around this point, the system shown that selected area has 0 species and 0 occurrences (CalcResultWithWrongValues.png). 4. When you click "Show These records only", the system shows the 27 existing records in the selected area (FilteredDataWithCorrectValues.png). Info 1: Sometimes the system shows 0 records. Most of the time it shows incorrect values. However, when you click "Show These records only", the system displays the correct number of records. Info 2: Generally the result of calculating the amount of species is also not correct. You can access this portal on http://143.107.102.247:65002/avh-hub/occurrences/search?taxa=#tab_mapView Thanks! Cheers. -- Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com> <FilteredDataWithCorrectValues.png><CalcResultWithWrongValues.png><BrazilData-specificarea.png><BrazilData1.png> -- Daniel Lins da Silva (Mobile) 55 11 96144-4050 Research Center on Biodiversity and Computing (Biocomp) University of Sao Paulo, Brazil daniellins(a)usp.br<mailto:daniellins@usp.br> daniel.lins(a)gmail.com<mailto:daniel.lins@gmail.com>

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permission to push wiki
by Santiago Martinez de la Riva 25 Jul '14

25 Jul '14

Hi Dave, Could you give me permissions in the wiki of Github?. I'm going to add more information about i18n. My user: santiagomtzdelariva 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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Putting images in the documentation
by Burke Chih-Jen Ko [GBIF] 25 Jul '14

25 Jul '14

Hi all, Just a note here for those who need to put an image to the wiki page. From the web interface, for now we can only add an image via an URL, but in most cases we want to include the image in the wiki repo. To do this, you need to interact with the documentation.wiki.git repo[1] using git. And to be able to push changes later you'll need permission. So the first step is to express your interest by announcing your github account to the list. Then after you clone the git repo, you will see an 'img' directory inside, where we store all documentation images. Put your image inside the directory. Assuming the image name is solr-index-backup.png, adding the following line in markdown will render the image on the web page: ![Add Solr core](/AtlasOfLivingAustralia/documentation/wiki/img/solr-index-backup.png) You can then view this page as an example: https://github.com/AtlasOfLivingAustralia/documentation/wiki/System-adminis… The text in the square bracket will be used for the 'alt' attribute in the html of the image. Hope it helps, Burke [1] https://github.com/AtlasOfLivingAustralia/documentation.wiki.git

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Permission to push
by Arturo Vargas 24 Jul '14

24 Jul '14

Hi all I'm preparing some documentation that I would include in the wiki https://github.com/AtlasOfLivingAustralia/documentation github user: turoart ...besides, I want to encourage others to participate using the tools and sharing your experience Pura vida! -- <https://www.inbio.ac.cr/donaciones/> <https://www.facebook.com/inbio> <https://twitter.com/inbiocr> <http://www.youtube.com/crinbio> <http://www.linkedin.com/company/inbio>

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Red Hat installations with Ansible
by Tim Robertson [GBIF] 23 Jul '14

23 Jul '14

Hi all, During the workshop currently ongoing in Australia, some people have asked about operating system support and have had varying levels of success with using Red Hat based systems. The level of success appears to relate to the version of Ansible people use, and I believe there is a bug (or deliberate change) in Ansible 1.6.6 (not in 1.5.x) that stopped things working with an error “repository $datastax is not found”. With this commit [1] (today) the script will now run on a vanilla CentOS 6.5 installation and using Ansible version 1.6.6 and Ansible 1.5.5. Please update (git pull) and retry if you are seeing this issue. Regarding operating system selection: The ALA folks run on Ubuntu and that is the ALA supported version. Realistically other system support will have to be done by the community of adopters, which should not be difficult, but will require some basic Ansible knowledge. Thanks, Tim [1] https://github.com/AtlasOfLivingAustralia/ala-install/commit/1366d104bda867…

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Documentation project established
by Burke Chih-Jen Ko [GBIF] 22 Jul '14

22 Jul '14

Hi all, For documentation of the ALA project, we have created a repository and established initial documentation structure here: https://github.com/AtlasOfLivingAustralia/documentation If you find any errors in the docs or have any suggestions, please file them as issues. This also means the confluence wiki we used previously is now deprecated. You are very welcome to contribute to the documentation directly. Please just let us know! Thanks, Burke

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Ala-install GitHub moved
by Tim Robertson [GBIF] 22 Jul '14

22 Jul '14

Hi all, We have moved the ala-install project to the ALA github project which is: https://github.com/AtlasOfLivingAustralia/ala-install It no longer exists in the GBIF GitHub, and this is because it is primarily maintained by the ALA folks now. Thanks, Tim

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