2014.05 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 May 2014 by Beneficiary and Task.

It is part of May 2014 Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

The previously deployed Virtual Research Environments have been maintained in operation;


None


The previously deployed Virtual Research Environments have been maintained in operation;

FAO Activities

  • Continued deep user validation of VMEDB, and content development


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

FAO Activity on Cotrix:

  • VR plugin for VRE Workpaces (to get WS data to Cotrix), and
  • plugin integration in Cotrix.
  • support for "Lineage Mapping" generation and publication.
  • direct tickets: 2649,2830,2832,2620
  • related tickets: 2809, 2810, 2831
  • installed security certificates (2716)
  • more than 60 improvements and fixes between I/O and management facilities, across all layers (functionality, usability, stability)
  • attribute descriptions and the separate codelists metadata presentation, in progress (#2867, #2868)

VME DB Activities

  • 1d activity related to WP6 reported


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

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

CNR has worked on several enhancements on the Statistical Manager. In particular,

  • scoping management has been enhanced #2858,
  • error from an algorithm has been propagated to the Portlet #2859,
  • multiple D4Science job are now much more controlled #2860,
  • tables importing now reports possible parsing errors [1]
  • the new SPD model has been re-aligned with the SM importing facilities #2821.

The development on the Databases resources manager library has continued #2770 and came to an end in terms of back-end processing. The work is now focusing on providing a web interface.

CNR also worked on building a WPS interface to the SM #2792. The activity is still in progress.

For what regards data analysis, WFS integration has been enhanced by reporting the complete range of features from a GIS layer #2812.

Finally, Time Series Spectral Analysis has arrived to a milestone version #1045.


no deviations to report.


  • The Statistical Manager has been reinforced
  • WFS integration has been enhanced
  • Time Series Analysis implementation has been completed

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

Since may, IRD work on WPS has focused on "biological observations enrichment". The iMarine wiki page explains the general approach [2]. Regarding linked data, we started to investigate the opportunity to reuse xlink for bibliographic references annotations.


The use case of biological observations enrichment with environmental parameters started at the end of March. In addition to previous work, we introduced some default methods to collect the set of pixels (cells of series of grids managed in netCDF-CF files). Alternative methods will be discussed internaly with the researchers and set up in the R code step by step.


WPS, so far, we have a default method for:

  • temporal buffer,
  • spatial buffer,
  • calculation of environmental parameters characteristics (mean value).


'WPS, so far, we have a default method for:

  • setting up the FORTH Xlink application (sources in SVN:[3] ),
  • first try running SPARQL queries is working (issues to run Virtuso queries).

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

On Reports Manager

  • The Reports Manager has been enhanced by adding the DwCA import facility according to proxy issues on the FAO site #2828.
  • Added accounting information through Home Library. #2340.

On Workspace

  • Workspace Notification on ItemUpdated fails #843
  • Workspace: update of images fails in the backend #845
  • Integrated the Workspace Trash #2497
  • Added item number in grid #2824
  • A readable name added to display the GCubeGroup #2839
  • The sharing panel was "extracted" as widget from workspace #2683

On Home Library component:

  • added a "Fulltext Search by All Properties in Node", for instance: find nodes with type 'WorkspaceItem' where any property contains 'xxxxx' string. #550
  • added search by properties ("find all that have such properties") #2811
  • fixed bug in trash folder: HL used the original parentId to restore an item, even if the parent was in the trash folder. A control has been added to HL to avoid this situation. If the parent is in the trash folder, the item will be restored to the workspace root. #2497
  • added a readable name to GCubeGroup. Example: Workspace will display "devVRE" instead of "gcube-devsec-devVRE". #2835
  • fixed bug overwriting a file. #2836
  • hidden default groups of Jackrabbit: GroupAdmin and UserAdmin have been hidden in the list of groups. #2791
  • investigated HL performance issues across network domains #2831

On gCube Portal

  • The gCube Portal bundle distribution was mavenized with success, see #2838.

Several bugs were fixed on various components:

  • Light Tree Visualization Error #2822
  • Mail Messages from iMarine message system #2689
  • FishFinder / View structure #966
  • Portal bundle missing jars #2537
  • FishFinder / Section Metadata #967
  • Message-Send (WsMail) Widget Session Expiration problem
  • Workspace file upload Widget (hangs when file size greater than 2GB)

On Tabular Data component:

  • Create "Tabular Data Extract Codelist" component
    • extracts codelist from tabular resource
  • On "Tabular Data Table Widget"
    • added operation edit row
    • added operation add row
  • On "Tabular Data Column"
    • added operation add column
    • updated batch replace operation
  • Create "Tabular Data Operation" component
    • started work on split operation #2834
    • started work merge operation #2834
  • Enhancements on "Tabular Data Common Events"
    • updated the types of events
  • Enhancements on "Tabular Data Portlet"
    • updated menu and behavior
  • Enhancements on "Tabular Data GWTService"
    • added operations


No deviations to report.


NKUA Activities

NKUA activities for this period include:

  • Completed the development of the tagcloud visualization widget (Related ticket: #2804)
  • Results portlet has been enhanced:
    • A button for tagcloud visualization of the current query's terms has been added (Related ticket: #2816)
    • The navigation toolbar has been added to the end of each result page to ease the navigation (Related ticket: #2755)
  • UsersManagement portlet has been enhanced in order to apply the filtering always on the initial data (Related ticket: #2813)
  • ElasticSearch portlet has been updated and now uses the latest Elastic Search UI. This fixes an issue with the overview tab (Related ticket: #2840)
  • IRBootstrapper portlet enhancements:
    • The portlet is updated in order to use the new OpenSearch client (Related ticket: #2805)
    • A clear button has been added in the 'Submitted Jobs Info' tab for clearing the persisted logs (Related ticket: #2837)


  • In order to fix a jar clash issue in the production portal the Fulltext Index portlet has been updated to include the latest 'commons.io' jar into its classloader so as not to use the old jar part of the common classpath


T6.4 Virtual Research Environments Development Support

NKUA Activities

  • During this period NKUA has deployed and tested the new "gCore-free" portal bundle and has identified several minor issues that are addressed from CNR.
  • NKUA supported the further development of the SMARTFISH case. Support for french language has been added #2833 and a REST service has been integrated for harvesting data #2856. Furthermore a new API for integrating extractors to xLink has been implemented #2800.




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

T6.5 Serving New Scenarios

CNR Activities

CNR has also worked on the BiOnym interface, giving support, machines, testing and algorithm enhancements #2016.

Effort has been spent also in analysing datasets coming from the Indian Ocean Tuna Commission (IOTC) #2793. This activity is strategic for the sustainability plan and produced an experiment page for dissemination purposes.

Other activity is focusing on analysing Vessels transmitted information datasets from NEAFC, applying techniques by ICES to detect fishery exploitation #2861. Furthermore a call conference was held in May between FAO and CNR to perform the initial Analysis for the NEAFC case.


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


FAO 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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