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Re: [Ala-portal] Proposed workshop in Canberra 21-July - 25th July 2014
by David.Martin＠csiro.au 17 Jun '14

17 Jun '14

Hello all, We have had positive responses from projects in Brazil, France, Spain, Costa Rica and GBIF secretariat in Denmark. We plan to go ahead with the workshop in ALA offices, Canberra 21-25th July 2014. Below are two links to recommended accommodation in Canberra. Both of these options are within walking distance of the ALA offices. 1) Liversidge Apartments - http://accom.anu.edu.au/UAS/189.html 2) University House - http://www.anu.edu.au/unihouse/accomm/accommodation.html The ALA is happy to make accommodation bookings at these places on your behalf. We can not offer to cover the costs of the accommodation. Please send any booking requests to Heather Walsh (cc-ed). We will send out more details including an agenda & schedule in the next couple of weeks. Many thanks from the ALA team. Dave Martin ALA [1] Route from Liversidge Apartments to ALA offices https://goo.gl/maps/NIUyM [2] Route from University House to ALA offices https://goo.gl/maps/BhYvk 2014-06-11 22:38 GMT-06:00 <David.Martin(a)csiro.au<mailto:David.Martin@csiro.au>>: Dear all, Thanks for the early responses. At the moment we have expressions of interest from: GBIF: Tim and Burke Costa Rica: ? Sao Paulo: 2-3 people France: tentative 1 person? In discussion with GBIF (Tim R) we believe that this would be enough to make some good progress. Can I please ask that we have a confirmation by the 17th June of a commitment to attend? With this, we will begin arranging the workshop and logistics, and people can book flights etc. (GBIF (TR and BK) have confirmed attendance should this proceed) Cheers, Dave Martin ALA ________________________________ From: Martin, Dave (CES, Black Mountain) Sent: 06 June 2014 15:15 To: ala-portal(a)lists.gbif.org<mailto:ala-portal@lists.gbif.org> Cc: support(a)ala.org.au<mailto:support@ala.org.au>; Walsh, Heather (CES, Black Mountain); La Salle, John (CES, Black Mountain) Subject: Proposed workshop in Canberra - July 2014 Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA

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Re: [Ala-portal] Proposed workshop in Canberra 21-July - 25th July 2014
by David.Martin＠csiro.au 13 Jun '14

13 Jun '14

Dear all, Thanks for the early responses. At the moment we have expressions of interest from: GBIF: Tim and Burke Costa Rica: ? Sao Paulo: 2-3 people France: tentative 1 person? In discussion with GBIF (Tim R) we believe that this would be enough to make some good progress. Can I please ask that we have a confirmation by the 17th June of a commitment to attend? With this, we will begin arranging the workshop and logistics, and people can book flights etc. (GBIF (TR and BK) have confirmed attendance should this proceed) Cheers, Dave Martin ALA ________________________________ From: Martin, Dave (CES, Black Mountain) Sent: 06 June 2014 15:15 To: ala-portal(a)lists.gbif.org Cc: support(a)ala.org.au; Walsh, Heather (CES, Black Mountain); La Salle, John (CES, Black Mountain) Subject: Proposed workshop in Canberra - July 2014 Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA

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Update on the ALA "occurrence search" front-end system
by Nick.Dosremedios＠csiro.au 13 Jun '14

13 Jun '14

I’m writing this email to provide some background and clarification about the ALA occurrence search (front-end) web application. There are actually 2 separate versions of this web app. The old Spring MVC version which was developed over 3 years ago and a new Grails version which was developed this year. The demo site<http://ala-demo.gbif.org/> and ansible script<https://github.com/gbif/ala-install> both use the new Grails version. For those of you who have only used the ansible script, you can probably stop reading now. But for those people/groups who attended the workshop in Costa Rica last year, please read on… The new biocache-hubs Grails webapp is a direct replacement for the old hubs-wepabb Spring MVC webapp. As a number of our other front-end systems were already done in Grails, it made sense for us to migrate the hubs-webapp to Grails, as it meant there was a single layout file (and associated CSS files) required for all these apps. The webapp was written with most of the core functionality being in a Grails plugin, with a light weight client Grails app using the plugin and providing the skinning, as well as overriding any components that need customisation (i18n, views, custom URLs, etc). We aim to have the code up on Github soon (you can find it on the ALA Google code repo<https://code.google.com/p/ala-hubs/source/browse/#svn%2Ftrunk> until then - see biocache-hubs and generic-hub). Once up on Github, it will be easier for people to clone/fork our code and provide pull requests back to us, etc. We will make an announcement about the Github code repo, on this list, once we’ve moved the code over. If any of you have already created custom i18n translations for the old hubs-webapp code, could you please send me either a zip copy via email or the URL to your code repo and I’ll try and include the i18n codes into the GSP pages, etc. Cheers Nick -- Nick dos Remedios Atlas of Living Australia http://www.ala.org.au/

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Re: [Ala-portal] ALA harvest and indexing tool
by Tim Robertson [GBIF] 11 Jun '14

11 Jun '14

Hi Francisco, I am well thanks, and I hope you are too. The ALA tool can ingest DwC-A datasets from a URL (which could be an IPT or GBIF portal download for example) and they also support direct publication through file uploads. I am not sure if they have BioCASe, TAPIR and DiGIR support, but I *believe* not. It would not be particularly difficult with the GBIF crawler libraries however, for a Java developer to develop a crawler which produces DwC-A ready for ingestion into the ALA. Please can you ask these kind of questions to the user list (CC’ed) so you get the most accurate answers and so others who may have similar questions can search and discover them? Thanks, and I hope this helps, Tim On 11 Jun 2014, at 16:20, Francisco Moura <franciscomoura(a)gmail.com> wrote: > Hello Tim, how are you? > I hope you are doing well! > > Would you tell me wich tool ALA (Atlas of Living Australia) is using for harvest and indexing the occurrence datasets? > Are they using IPT to publish the occurrence datasets? > > Thank you again, > > Francisco Moura > +55 (31) 8277-8448 (Claro)

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Re: [Ala-portal] Proposed workshop in Canberra - July 2014
by Antonio Saraiva 11 Jun '14

11 Jun '14

Hi David That is good news. We really need to get more in contact with you all to move faster on our customization of ALA. We plan to have some people (2 or 3) attending the workshop. Best Antonio 2014-06-06 2:15 GMT-03:00 < <mailto:David.Martin@csiro.au> David.Martin(a)csiro.au>: Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA _______________________________________________ Ala-portal mailing list Ala-portal(a)lists.gbif.org <mailto:Ala-portal@lists.gbif.org> http://lists.gbif.org/mailman/listinfo/ala-portal

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Showing uploaded DwC-A on the map
by Burke Chih-Jen Ko [GBIF] 10 Jun '14

10 Jun '14

Hi all, I am currently writing steps to create an example data resource and to see them indexed and shown on the map. The DRAFT guide so far being: http://dev.gbif.org/wiki/pages/viewpage.action?pageId=12812301 As I finished the steps, by clicking the "view records", I couldn't find ways to see records and the map tiles. It seems no documentation about configuring this part yet, or is there anything I missed? A screenshot attached: https://dl.dropboxusercontent.com/u/66568061/mapping.png. Thanks in advance for hinting, Burke

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Sao Paulo University: Building a monitoring project around the ALA code
by Tim Robertson [GBIF] 10 Jun '14

10 Jun '14

Dear all, It is great to see so an increase in traffic on this mailing list. The group from Sao Paulo University would like to offer some background information on their work to highlight how the ALA tools are being used within a monitoring project for the reserves and national parks in Brazil. > The project will span over 300 reserves and parks, within which a variety of data will be collected in accordance with various monitoring protocols. These data are typically spreadsheet based and accommodate single species observation data, abundance data, transects, number of collection units per time etc. The data will be prepared and hosted within one or more instances of the GBIF Integrated Publishing Toolkit (IPT) in consistent formats to enable a central integration system to harvest the data and offer a discovery mechanism. This integration system will be based on a customisation of the ALA tools, and in particular the modules for the hubs, biocache, collectory, sandbox and the spatial portal, and using local dictionaries and national species lists for taxonomic organisation. > > The current focus of work is on mastering the codebase by tackling the translation into Portuguese and understanding the mechanisms to organise the data to national species lists. Once the skeleton pieces are in place, work will commence on defining the exchange formats and exploring how to accommodate and index the new data types. > > The project aims to pilot with a handful of reserves and protocols in 2014, and then target a larger scale rollout in 2015 across many reserves. > The project is being led by the Research Center on Biodiversity and Computing at Sao Paulo University, in conjunction with the Instituto Chico Mendes de Conservação da Biodiversidade (ICMbio), of the BrazilianMinistry of Environment’s and is funded by the Deutsche Gesellschaft für Internationale Zusammenarbeit (GIZ) Gmbh. > > For more information on the project please contact Antonio Saraiva (saraiva(a)usp.br), Biocomp leader, or Pedro Correa (pedro.correa(a)usp.br), project coordinador. Best wishes, Tim

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Ansible changes removes local caches - intended?
by Tim Robertson [GBIF] 10 Jun '14

10 Jun '14

Hi ALA folks With this commit: https://github.com/gbif/ala-install/commit/d5b6394f44aa82451079d84f646e200c… Things like the following were removed: -- name: determine if the application is in our local repo - local_action: stat path={{local_repo_dir}}/{{biocache_service}}.war - register: biocache_war_path - -- name: fetch application if it is not in our local repo - local_action: get_url url={{biocache_service_url}} dest={{local_repo_dir}}/{{biocache_service}}.war - when: biocache_war_path.stat.exists == false The original design was to pull the large artifacts to a local directory once (the .ala folder) so that if you were provisioning different environments (locally, uat, production etc) you weren’t troubled with huge download times for each environment. Was this an oversight perhaps? In Europe we see 10s of minutes in this stage, hence the original design to cache locally. If we get into proper maven releases and versioned artifacts deployed to nexus, we can start mirroring nexus repositories to bring back data locality too (plus it’ll use the local .m2 repo directory on the host). Any thoughts on this? Would you like me to revert those changes? Thanks, Tim

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(no subject)
by David.Martin＠csiro.au 10 Jun '14

10 Jun '14

Hello all, There have been a couple of approaches to the team at ALA asking for the possibility of a visit to help advance understanding of the system. Additionally we hear early indications of interest from the recent group who had a small workshop in Europe, but note their requests for improved documentation, processes and structure. It is short notice but we would like to propose a workshop in Canbera for developers on the week of : 21-July - 25th July 2014 During this week we would aim to: a) exchange knowledge amongst developers b) collate wiki documentation on data management, and customization of the web portal c) discuss and make progress in the processes surrounding source code management - e.g. potentially moving to Github and defining procedures for contribution, and releases Please note that at this stage and for the foreseeable future, we believe the components suitable for collaboration and adoption are: i. The biocache-hub webapp ii. The collectory webapp iii. The biocache backend processes I understand that the GBIF secretariat will commit to managing the key pieces of documentation and assist in helping structure the project. The ALA development team are committed to maintaining this codebase and using it to support applications in Australia. We don't envisage this being an off the shelf product such as the GBIF IPT, but rather a well managed open source project that people can contribute to and use as a framework to rapidly kick start their own developments. If you have interest in joining, could you please reply to this expressing interest, even if only tentative? Many thanks, Dave Martin ALA

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missing /data/biocache-load directory
by Burke Chih-Jen Ko [GBIF] 06 Jun '14

06 Jun '14

Hi all, In the installation guide there is a step[1] that creates /data/biocache-load directory manually by logging in to the virtual box. This step is created because neither the ansible playbook nor the biocache components creates that directory which is necessary for finishing the installation. I am thinking about saving this step by updating the Ansible playbook. But, is this directory supposed to be created by the biocache-hub webapp or biocache backend processes, hence it's an issue of the biocache component? If so, then I'll file an issue about this. Or I propose to update the playbook and I can do that. What do you think? Cheers, Burke [1] http://dev.gbif.org/wiki/display/ALA/02+Installation#id-02Installation-Ansi…

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