Task #2756
closed
Dismiss/Restore EuBrazilOpenBio infrastructure
100%
Description
The EuBrazilOpenBio portal has been just restarted, but I have noticed that all the applications are too old to work. The Storage and Workspace technologies behind the scenes have changed very much and the Web interfaces are no more compatible with them. The GeoExplorer and the Statistical Manager interfaces are the ones from 2012 (4 years have already passed! :-( ).
The other interfaces are old and non-working too.
This portal should be either upgraded along with all the services or dismissed.
Please, decide which of the two solution we should go for. Consider that a lot of resources are allocated for the machines and it seems the d4science portal is no more linked by the EubrazilOpenbio Web site.
Updated by Pasquale Pagano over 9 years ago
- Tracker changed from Support to Task
- Assignee changed from Pasquale Pagano to Massimiliano Assante
I suggest to proceed as follow since it is too costly to keep it running on a separate installation.
- to host the SpeciesLab VRE in the d4science gateway
- to dismiss the eubrazilopenbio gateway while keeping its hostname and add a redirect message that says that this VRE is now hosted by the d4science one.
- to replace the GeoExplorer, Species Discovery and Statistical Service with the ones provided by gCubeApps while properly configuring models and data sources for the VRE
- to dismiss the dedicated services allocated to this VRE
This is the easiest part. Then there are specific applications
- OccurrenceManagement was a nice to use interface dedicated to visualization and management of occurrence datasets. This portlet could be refactored to work with the versions of gCube. It should require an affordable cost.
- Ecological Niche Modelling and Cross Mappings were based on third-parties technology. I believe that we should dismiss them since no effort is provided to maintain those technologies.
Finally, I assigned the task to Massimiliano. He should prepare what is needed to run the SpeciesLab VRE in the D4science gateway. Then the people involved in this task will do the other actions according to their expertise (configure the algorithms for the VRE, adding the resources to the service scope, ... )
About the OccurrenceManagement I need to know your estimation in terms of effort.
Updated by Leonardo Candela over 9 years ago
I support Lino's plan and suggest to rename the VRE with something like "EUBrazilOpenBio Species Lab".
Updated by Gianpaolo Coro over 9 years ago
OccurrenceManagement was dismissed because it could be replaced by StatMan with only the Occurrence Management algorithms active.
Updated by Gianpaolo Coro over 9 years ago
Perhaps the easiest way is to create a VRE under gCubeApps where we put web applications for OpenBio. Currently, it is managed as a separate VO and thus requires other machines.
Updated by Pasquale Pagano over 9 years ago
Gianpaolo Coro wrote:
OccurrenceManagement was dismissed because it could be replaced by StatMan with only the Occurrence Management algorithms active.
Partially true. It added the capability to visualize the occurrence files and it was nice. However we can leave without it.
Updated by Massimiliano Assante over 9 years ago
- Status changed from New to In Progress
Updated by Massimiliano Assante over 9 years ago
Aa agreed in the meeting we had about this, we're going to deploy a new VRE named EuBrazilOpenBio under gCubeApps on services.d4science and dismiss the VO EuBrazilOpenBio and the SpeciesLab VRE contained in it.
The new EuBrazilOpenBio VRE will contain the statistical manager Occurrence Management algorithms
Updated by Massimiliano Assante over 9 years ago
- % Done changed from 0 to 90
The VRE is deployed and ready in services d4science: https://services.d4science.org/group/eubrazilopenbio
@gianpaolo.coro@isti.cnr.it please add the required statman algorithms
Updated by Gianpaolo Coro over 9 years ago
StatMan now works with several algorithms added. I see issued when drawing transect lines in GeoExplorer (@francesco.mangiacrapa@isti.cnr.it can you check, please?) and when loading the SPD main interface (@lucio.lelii@isti.cnr.it could you check, please?). I have added resources for these applications too but maybe something else is missing.
Updated by Lucio Lelii over 9 years ago
I cannot access to the new OpenBio VRE. I have just sent the request to join it.
Updated by Francesco Mangiacrapa over 9 years ago
I added the Transect runtime to EuBrazilOpenBio VRE and now the transect functionality works correctly in GeoExplorer.
Updated by Massimiliano Assante over 9 years ago
I saved the list containing SpeciesLab users (names, and emails). Perhaps we could invite these users to the new VRE @leonardo.candela@isti.cnr.it
Updated by Leonardo Candela over 9 years ago
I suggest to reconsider the set of SPD plugins, please do take into account that OpenBio was expected to deal with flora. In #3154 I identified some data providers that contain such data, namely speciesLink, Catalogue of Life, and GBIF at least. If I'm not mistaking we use to access also List of Species of the Brazilian Flora.
@massimiliano.assante@isti.cnr.it is it possible to check what was configured in SpeciesLab?
Updated by Massimiliano Assante over 9 years ago
- Assignee changed from Massimiliano Assante to Lucio Lelii
Leo, we should ask @lucio.lelii@isti.cnr.it or @valentina.marioli@isti.cnr.it
Updated by Lucio Lelii over 9 years ago
- Assignee changed from Lucio Lelii to Massimiliano Assante
What leo wrote is correct, the expected plugin for EUBrazil openBio were GBIF, speciesLink, Catalogue of Life and BrazilianFlora. But I don't kwnow which plugins you installed on the EUBrazil OpenBio portal. The plugins installed in EuBrazil OpenBio VRE is the entire set of plugin developed in SPD except BrazilianFlora.
Updated by Massimiliano Assante over 9 years ago
- Assignee changed from Massimiliano Assante to Lucio Lelii
Thanks Lucio, now that we know which SPD plugins are necessary we need the documentation to enable these plugins.
Updated by Lucio Lelii over 9 years ago
- Assignee changed from Lucio Lelii to Massimiliano Assante
You need intall the plugin jar in the node and load it in the calsspath (here you can check the component that you need : https://gcube.wiki.gcube-system.org/gcube/Biodiversity_Access).
Also you have to add the correspondant BiodiversityRepository (ServiceEndpoint) to the VRE.
Updated by Massimiliano Assante over 9 years ago
doesn't all the plugin jars come with the maven build of SPD? Or you have a specific maven profile for each deployment? I don't understand sorry.
It is probably just a matter of adding the correspondant BiodiversityRepository (ServiceEndpoint) to the VRE.
Updated by Lucio Lelii over 9 years ago
Those plugins are not part of the spd bundle. The installation is up to the infrastructure manager depending on the requirements. Looking at the monitor I can see the BiodiversityRepository resource for BrazilianFlora. In this case the problem is that the plugin is not installed on the node.
Updated by Massimiliano Assante over 9 years ago
- Assignee changed from Massimiliano Assante to Roberto Cirillo
@roberto.cirillo@isti.cnr.it please install the spd plugin(s) required on the SPD service node of gCubeApps/EuBrazilOpenBio
Updated by Roberto Cirillo over 9 years ago
- Assignee changed from Roberto Cirillo to Massimiliano Assante
The BrazilianFlora plugin has been added to gCubeApps/EuBrazilOpenBio VRE
Updated by Massimiliano Assante over 9 years ago
- Status changed from In Progress to Closed
