June 2014 - ALA-Portal - lists.gbif.org

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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ala-geo-spatial
by Paulo André 02 Jun '14

02 Jun '14

Hi We've deployed ala-geo-spatial project. We've found 2 issues: - No WebApplicationContext found: no ContextLoaderListener registered? - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.FacetCacheImpl] failed java.lang.IllegalArgumentException: [null/search/grouped/facets] is not a valid HTTP URL Have you ever seen this issues? BR Paulo 18:29:16.705 [main] ERROR org.zkoss.zk.ui.util.Configuration - Failed to invoke class org.zkoss.spring.init.SecurityWebAppInit java.lang.IllegalStateException: No WebApplicationContext found: no ContextLoaderListener registered? at org.springframework.web.context.support.WebApplicationContextUtils.getRequiredWebApplicationContext(WebApplicationContextUtils.java:84) at org.zkoss.spring.init.SecurityWebAppInit.init(SecurityWebAppInit.java:47) at org.zkoss.zk.ui.util.Configuration.invokeWebAppInits(Configuration.java:733) at org.zkoss.zk.ui.impl.AbstractWebApp.init(AbstractWebApp.java:204) at org.zkoss.zk.ui.http.SimpleWebApp.init(SimpleWebApp.java:58) at org.zkoss.zk.ui.http.WebManager.<init>(WebManager.java:228) at org.zkoss.zk.ui.http.HttpSessionListener23.contextInitialized(HttpSessionListener23.java:140) at org.apache.catalina.core.StandardContext.listenerStart(StandardContext.java:4206) at org.apache.catalina.core.StandardContext.start(StandardContext.java:4705) at org.apache.catalina.core.ContainerBase.addChildInternal(ContainerBase.java:799) at org.apache.catalina.core.ContainerBase.addChild(ContainerBase.java:779) at org.apache.catalina.core.StandardHost.addChild(StandardHost.java:601) at org.apache.catalina.startup.HostConfig.deployDescriptor(HostConfig.java:675) at org.apache.catalina.startup.HostConfig.deployDescriptors(HostConfig.java:601) at org.apache.catalina.startup.HostConfig.deployApps(HostConfig.java:502) at org.apache.catalina.startup.HostConfig.start(HostConfig.java:1317) at org.apache.catalina.startup.HostConfig.lifecycleEvent(HostConfig.java:324) at org.apache.catalina.util.LifecycleSupport.fireLifecycleEvent(LifecycleSupport.java:142) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1065) at org.apache.catalina.core.StandardHost.start(StandardHost.java:840) at org.apache.catalina.core.ContainerBase.start(ContainerBase.java:1057) at org.apache.catalina.core.StandardEngine.start(StandardEngine.java:463) at org.apache.catalina.core.StandardService.start(StandardService.java:525) at org.apache.catalina.core.StandardServer.start(StandardServer.java:754) at org.apache.catalina.startup.Catalina.start(Catalina.java:595) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) 2014-05-22 18:29:21,980 ERROR [pool-2-thread-1] (MethodInvokingRunnable.java:68) - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.FacetCacheImpl] failed java.lang.IllegalArgumentException: [null/search/grouped/facets] is not a valid HTTP URL at org.springframework.web.util.UriUtils.encodeHttpUrl(UriUtils.java:245) at org.springframework.web.client.RestTemplate$HttpUrlTemplate.encodeUri(RestTemplate.java:651) at org.springframework.web.util.UriTemplate.expand(UriTemplate.java:140) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:400) at org.springframework.web.client.RestTemplate.getForObject(RestTemplate.java:199) at au.org.ala.spatial.data.FacetCacheImpl.reloadCache(FacetCacheImpl.java:59) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) at org.springframework.scheduling.support.MethodInvokingRunnable.run(MethodInvokingRunnable.java:65) at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:51) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744) 2014-05-22 18:29:21,991 ERROR [pool-2-thread-1] (MethodInvokingRunnable.java:68) - Invocation of method 'reloadCache' on target class [class au.org.ala.spatial.data.SpeciesListUtil] failed java.lang.NullPointerException at java.lang.StringBuilder.<init>(StringBuilder.java:109) at au.org.ala.spatial.data.SpeciesListUtil.getLists(SpeciesListUtil.java:70) at au.org.ala.spatial.data.SpeciesListUtil.getNumberOfPublicSpeciesLists(SpeciesListUtil.java:61) at au.org.ala.spatial.data.SpeciesListUtil.reloadCache(SpeciesListUtil.java:40) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:606) at org.springframework.util.MethodInvoker.invoke(MethodInvoker.java:273) at org.springframework.scheduling.support.MethodInvokingRunnable.run(MethodInvokingRunnable.java:65) at org.springframework.scheduling.support.DelegatingErrorHandlingRunnable.run(DelegatingErrorHandlingRunnable.java:51) at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471) at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:304) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:178) at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:293) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at java.lang.Thread.run(Thread.java:744)

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