2014.04 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 April 2014 by Beneficiary and Task.

It is part of April 2014 Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

  • The BiOnym Virtual Research Environment has been created;


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

FAO Activities

  • Testing and validation of the VME-DB facility by assisting RFMO's (Regional Fiheries Management Organizations) representatives to operate the data-entry tools and visualization tools of VME Fact-sheets.
  • Introduce new liaisons to iMarine VRE operations.


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


  • The VME-DB was readied for a large user event in May in Rome

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

  • VME security task (for a total of 4 wd) covered out of FAO Budget; no ticket yet. (Potential for re-use with NEAFC)
  • VME-DB other tasks covered by FAO reported in the FAO system.
  • SmartSearch JS components
    • #2741 improve the object-oriented model of the JS components, that allows to define default parameters & behaviors, and easily customized according to the context. An example is the function to retrieve document URI in Chimaera, that needed to be adapted to retrieve the FIRMS html factsheet URLs.
    • #2697 finish the implementation of search history
    • #2725 finish autocomplete client improvements
    • #2507 more flexibility to manage the result model (clickable title, choice to display concept information in result header/details)
    • #2772, #2773 work on browser compatibility major issues dealing with IE8+ and OpenLayers WFS dynamic layer + minor CSS issues
  • WPS / SPREAD
    • improve the SPREAD R algorithm with capacity to get intermediate or aggregated results
    • produce a small R script to address species-distribution based reallocation scenario (to be shared with Fabio Carocci)
    • discussions on WPS standard & implementation in iMarine, especially on input/output formats & relation to SM - For this, see #2635, #2604 (WPS), and #2682 (SPREAD "driver" of the discussion)


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

In the month of April, CNR has worked in several direction on Data Analysis facilities. The problem of defining the concept of common species was investigated #2197 and eventually a complete assessment on North Sea species was produced. Time Series analysis was investigated too, with an implementation of a Fourier analysis combined with a Singular Spectrum Analysis to perform periodicity detection and forecasting #2768. This technique has been applied to a use case from Indian Ocean Tuna Commission #2793 and is currently under analysis. On the Statistical Manager service side, WPS interfacing was investigated, with a preliminary analysis on the 52-North WPS service #2792.


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


  • Start of investigation on a WPS interface for the Statistical Manager
  • Common Species theoretical analysis was completed
  • Time Series Analysis was completed
  • Preliminary analysis on the IOTC use case

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

Interactions with Terradue to access a virtual machine to customize IRD processes by ourselves. Start of work related to biological observations enrichment.


Enrichment of R functions using rrdf package to generate RDF metadata related to WPS outputs.


Biological observations enrichment: a first R script enables the user to get a set of additional attributes (environmental parameters) for each geometry of a vector file (shape file or other format read by rgdal). For each paramater, this script will provide a set of values: mean value, standard deviation, min, max, spatial and temporal distance....This will be used later to annotate the quality of the enrichment Access to a virtual machine provided by Terradue is set up. Next step consists in editing processes descriptions and related java classes to enrich IRD WPS processes.

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

In the month of April CNR has worked on the development of a set of libraries to manage the database resources indexed in the i-Marine e-Infrastructure #2770. This set of libraries is meant to facilitate the access and retrieval of table elements from such databases. A set of corresponding algorithms running on the Statistical Manager has been developed too, in order to distribute database access requests.

A new Widget for Session expiration checking was implemented and released, the Session Checker Widget will be used by every portlet that needs to check if the session is still valid while the user is performing operations. If it finds the scope or the user null will popup a dialog asking the user to logout and login again. See #2726

A new portlet was development for VRE Adding and Removal of Users from the VRE Manager. This is an alternative version of Manage Users Portlet allowing a VRE-Manager to select user to add to his VRE (Channel) has to be developed in order to support the automatic adding go the user to the Home Library shared VRE Group. See #2653

On Tabular Data component:

  • On "Tabular Data WidgetX"
    • added inline filter
  • On "Tabular Data WidgetX TDX Source"
    • added support for Date type
  • On "Tabular Data Table Widget"
    • added history and discard operations
  • On "Tabular Data Column Widget"
    • updated replace operations
    • updated delete column operation
  • 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
  • Enhancements on "Tabular Data Template"
    • added the update of an existing template #2496

On Home Library component:

  • added search by date for WorkspaceItem
  • fixed bug: shared folder removal was not effective. When a folder administrator removed a shared folder, the folder was removed from the workspace of the folder admin only, but it remained in the others' workspace. Now the folder is removed from the workspace of all the users.

On Workspace component

  • Added Quick Tour Guide.
  • Fix on Workspace FileUpload Widget getting stuck after 4/5 uploads in a row #817.

On Reports Manager

  • For the VME-DB Scenario the following enhancements were performed:
    • VME-DB Close report after “Commit” #2788
    • VME-DB VRE Deletion of content of the first entry #2787

On Social Notifications

  • Removed "notification" from email notification subjects. #2727


No deviations to report.


  • Implementation of Database Resources Manager Libraries. Every ticket mentioned above is part of gCube Release 3.1

NKUA Activities

NKUA activities for this period include:

  • The development of a GWT widget for tagcloud visualization of queries. This widget will be integrated to the results portlet.
  • The release of the 'iMarine search' android application to the play store, making it publicly available.


NONE


Several portlets were released in 3.1.0 release:

  • org.gcube.portlets-admin.ft-index-management-portlet.2-3-0
  • org.gcube.portlets-admin.ir-bootstrapper-portlet.2-6-0
  • org.gcube.portlets-admin.users-management-portlet.2-1-0
  • org.gcube.portlets-admin.information-space-editor-portlet.2-7-0
  • org.gcube.portlets-user.iSearch-portlet.1-1-0

T6.4 Virtual Research Environments Development Support

NKUA Activities

Work has focused on the provisioning of the SMARTFISH case services (FARM VOVirtual Organization; ):

  • Evolution of smartfish doc processor for WIOFish html pages 2769
  • Smartfish-ds - extend "find" services with a "concept_filter" parameter 2767


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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