2013.06 WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

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This WP6 Activity Report described the activities performed in June 2013 by Beneficiary and Task.

It is part of June Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

The previously created VREs have been maintained;


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


  • Existing VREs have been maintained;

FAO Activities

Some 4 hrs was spent on operating the FishfinderVRE. All other VRE operations related to validations, and are reported in WP3.


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

Preparation of a general purpose matching component #1913:

  • Redesign and implementation of the matching component aimed at exposing a domain-independent interface to clients (tagline: "general purpose matching component for the identification of relationships between concepts and entities"). Completion required 10 to 15 days. CNR will be informed to review the results.
  • Design and implement a standalone library that will include the core functionalities of the matching component and a distributed-computation model that will not necessarily require a supporting distributed infrastructure. Completion required 5 to 7 days.

Preparation of Code list management and matching

  • Cotrix development of UI, Virtual repository and code lifecyle management


None


The components were delivered and analyzed. A work-plan is in the making.

ERCIM Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

CNR Activities

  • Importing the layers referring to marine regions from www.marineregions.org in the iMarine SDI (#1742)
  • OAI Tree Manager Plugin has been fixed
    • The HTTP URI Resolver could not solve the OAI-PMH id; it has been fixed implementing custom escaping/unescaping. (#655)
    • The Tree Manager from OAI Tree Manager Plugin got too many open connections. That issue was fixed reducing the amount of open connections to the OAI repositories. (#643)
    • There were some issues on the pom. They were fixed using the BOM instead of single dependecies. (#1833)
  • FIGIS Tree Manager Plugin has been fixed
    • FIGIS got an exception when installing the plugin and restarting the container, this because of the Runtime Resosource that was called when the scope was not yet set. (#1845)
    • There were some issues on the pom as in OAI Tree Manager Plugin. They were fixed using the BOM instead of single dependecies. (#1833)
  • data.fao.org Tree Manager Plugin
    • We started working on the integration of data.fao.org for Tree Manager, using the APIs described at api.data.fao.org. data.fao.org provides access to several datasets organized in topics (catalogue). Our idea was to implement a plugin of the TM and then register new collections for each topic related to iMarine, but currently the only way to get data is through the website. The possibility to get data through the APIs will be available by the end of September. We have been working on this plugin and nowadays it can get all the metadata about datasets and databases, but, of course, the data is missing. We have decided to postpone the completion of the test until the APIs will be available. (#1593)


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


  • Fixed and released of a new version of the OAI-PMH TM Plugin;
  • Fixed and released of a new version of the FIGIS TM Plugin;
  • Started to work on a new plugin for the integration of data.fao.org in TM.

FIN Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

UNESCO Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

CRIA Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

IRD Activities

To enrich the Tuna Atlas use case, IRD is using: 1) Semantic cluster activities: TLO based repository and related SPARQL endpoint 2) Geospatial cluster activities: iMarine WPS server and related processes to display indicators for tuna species. IRD has started to build a website designed to publish some data from these clusters on the web. It is based on the StrutsĀ² MVC framework. The model consists of a set of action classes designed to relate SPARQL queries from JSPs to one or several SPARQL endpoints, to handle the returned result and to expose it to the JSP in a convenient form.


  • Semantic cluster activities: Ecoscope application has been used as a basis for the Tuna Atlas application. However, this application doesn't work on top of a single knowledge base but uses now iMarine Sparql endpoint. Instead of Jena methods to query Ecoscope KB, this application uses now TLO based SPARQL queries. RDF classes and properties to relate outputs of WPS processes to species / agents have been tested and modified. Conf call with Forth to use TLO and update it...
  • Geospatial cluster activities: Run, describe (RDF) and store a new set of processes outputs to enable the tuna atlas use case demo with geospatial cluster results.


  • Semantic cluster activities: The views consist of JSPs, using StrutsĀ² tags, whose content is built from TLO based SPARQL query and related results. The views can be loaded at once, or progressively using AJAX. AJAX is interesting in this context as it enables to fill some sections of the fact sheets before the endpoint(s) responds to all the queries.

The SPARQL queries are stored in the JSPs so that the website remains flexible : It's possible to alter or add content from the repository without having to recompile the source project. Similarly, when the endpoint's datastructure change, it's possible to update the website simply by updating the JSP pages. A default endpoint is configured at the website level, so that it's not necessary to provided it for each query. However it's possible to surcharge it by providing a endpoint's url at the query level.

At the moment the website focus on species and their attached processes, but it's planed to extend it to the other types of resources available in the repository.

  • Geospatial cluster activities: creation of a new WFS layer for a process dealing with fish size frequencies and related processes:
    • Atlas_i9_RelativeSizeFrequenciesBySchoolType : build a graph of relative distribution of size frequencies according to school type for a given species
    • Atlas_i10_RelativeSizeFrequenciesByDecade : build a graph of relative distribution of size frequencies by decade for a given species

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

The CNR activity focused on the development and the release of the following software applications:

On GisViewer, Geo-explorer, Gcube-Geo-explorer, Geo-explorer-portlet components:

  • Enhancements in GeoExplorer was implemented to standardize the access to GeoNetwork and ISO 10139 Metadata visualization

On Workspace Tree, Workspace Portlet components:

  • These components were enhanced to meet the requests coming from the User Community:
    • Provide support for share link, Related ticket: #1504
    • Sharing data, Related ticket: #230
    • Edit description on sharing, Related ticket: #1822
  • Bugs fixed, Related Tickets: #628, #633, #630

On Runtime Resource Creator Portlet component:

  • The Runtime Resource editor now preserves the encrypted attributes value when loading an existing resource.

On Templates Portlet component:

  • The box for repetitive elements now allows to add more than a prefixed of elements.


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

NKUA Activities

NKUA activities for this period include:

  • IRBootstrapper portlet removed all the types, datatypes and tasks that were interacting with the dismissed content management system and the previous index services (Related ticket: #1899)
  • A new visualizer has been created in Results portlet to handle objects coming from collections with type: "FIGIS". Both for metadata and for content. (Related ticket: #1912)
  • Minor changes have been applied to the results visualization (Related ticket: #1894)
  • Several bug fixings have been applied to the Results portlet icluding:
    • Browse field query results' presentation
    • The submission of a simple search query when a result of a browse field operation is clicked
    • Save query option to basket


NONE

NONE

T6.4 Virtual Research Environments Development Support

NKUA Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

CNR Activities

The beneficiary should report here a summary of the activities performed in the reporting period


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


The beneficiary should report here a bullet list highlighting the main achievements of the reporting period

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