2014.06 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 2014 by Beneficiary and Task.

It is part of June '14 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

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

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

Cotrix: 2 PM (Main activity)

  • design and implementation of metadata page and codelist schemas;
  • customisation of Lineage Mappings with Lineage Attributes, shift to property-based search
  • usability improvements including: better import wizards, filter bars on all tables, codelist grouping options, regular table rows, (all) form uplifting, better attribute rendering, upload optimisations, attribute descriptions, better paging options, more confirm dialogs, authorship tracking, better layout management, system vs. domain attributes separation, tooltips;
  • bug fixing
  • release of Cotrix 0.2.0 in gCube 3.3.0 (Etics, SVN, Git procedures)

Specific tickets


VME-DB (not fully accounted for as iMarine, as usual most goes to FAO budget).

Tickets:

A couple of hours of activity for the NEAFC2ICES :


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 June CNR worked on several enhancements of the Statistical Manager at both service and interface sides. A widget version of the portlet was finalized #1297, file importing now allows to take resources from the workspace #2920, requests for algorithms running on D4Science have been better managed #2860 #2858 and errors from the algorithms are now reported to the interface #2859.

Furthermore, CNR built a WPS interface for the Statistical Manager, which was certified (for the BiOnym algorithm) by the Taverna Development Team #2792.

Activities on database management were completed at backend side #2770. The development of a portlet for such system has started #2960.

New data operations and validations for the Tabular Data Manager service have been developed (Column merging / splitting #2834, Union #2583, Ambiguos Value Validation) and others operations have been enhanced (Extract codelist, Change to Dimension). CNR worked with FAO for the definition of a Mapping file format for Cotrix / TabularData integration.

CNR aided FAO in the import of the SPREAD R-scripts on the infrastructure #2900.

Activities regarded possible stakeholders requirements coming from IOTC, ICES and NEAFC. Procedures from the Statistical Manager were used for stakeholders' datasets #2861#2793 #2938. Eventually, the activity resulted in the creation of two wiki pages and in a sequence of conference calls with these possible stakeholders.

Supporting BiOnym developments #2016. An official technical report has been produced, which describes many details of this activity #techrep. The BiOnym portlet developed by FIN is now linked on the production portal of i-Marine.


No deviations to report.


  • Enhancements on the Statistical Manager Portlet and Service
  • WPS interface for BiOnym
  • Development of the Database Management facilities achieved a major release

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

Two kind of activities have been performed: improvement of R script for biological observations enrichment and annotation of Zotero bibliographic references in RDF with Ecoscope/TLO URIs


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


Main achievements for Biological observations enrichment are

  • a new parameter has been added ('InsertTime' to enable the users to specify a given date or period when geometries don't have this kind of attribute. For example, it enables to calculate the mean temperature for EEZ or Longhhurst provinces (which are not related to / delivered with temporal attributes),
  • enabling new data formats as input parameters (WFS, shape...)
  • when environmental data are not covering all features, the process doesn't stop anymore and returns instead a "-99999' value for non covered / overlapped features.
  • enabling new data formats for outputs
  • the process can be now executed on the WPS server (example of execute process with longurst provinces provided by WFS and SST data provided by OPeNDAP)
  • For now WPS result is provided as CSV / text file

Main achievements for Zotero RDF bibliographic references

  • name of authors are turned in URIs by using foaf:person instances of Ecoscope
  • first version of a script enabling the text mining of title and description (Dublin Core elements) and transformation of relevant terms in URIs (related to Ecoscope and TLO URIs: species...)
  • a first Lucene index of Zotero RDF bibliographic has been made (will be reused lated to add new concepts)

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

On Tabular Data component:

  • Completed activity on "Task Widget" #2819
  • Completed Split and Merge operations #2834
  • Realized Group By" operation #2892
  • On "Tabular Data Share"
    • added share for groups
  • On "Tabular Data Table Widget"
    • added denormalize operation
    • added normalize operation
    • updated history and discard
    • updated validations and added context menu
  • Create "Tabular Data Codelist Mapping Import"
    • import codelist mapping
  • On "Tabular Data Extract Codelist"
    • updated wizard
  • On "Tabular Data Column Widget"
    • added mapping to ChangeColumnTypePanel
    • updated replace row
    • updated batch replace
  • Enhancements on "Tabular Data Information"
    • updated the information shown
  • Enhancements on "Tabular Data Common Events"
    • updated the types of events
  • Enhancements on "Tabular Data Toolbox"
    • updated list of panels
  • Enhancements on "Tabular Data Widgetx"
    • added single column display
    • updated errors diplay
    • updated context menu
    • updated header column menu of grid
  • Enhancements on "Tabular Data Open"
    • updated tabular resource informations
  • Enhancements on "Tabular Data Portlet"
    • updated menu and behavior
  • Enhancements on "Tabular Data GWTService"
    • added operations
    • added security exception handling

On Workspace Sharing Widget component:

  • Integrated sharing with groups #2897

On Workspace component:

  • Fixed: not enough space to display the full group name #2797

On Home Library component:

  • Added progress number to filename when a file/folder is copied and a file/folder with the same name already exists in such folder. #2937
  • Fixed bug in Message Facility: the messages were not shown to the user.
  • Caught Error unzipping an archive: the error was not properly propagated to the user. The ZIP archive was not valid and the user was not informed. The solution was the propagation of the error and the visualization in human readable format. #823
  • Fixed bug: Download a folder does not appear correctly in the history of the folder. The bug has been fixed using the folder name shown to the user instead of the node in Jackrabbit (an identifier). #2636
  • Fixed bug: Error removing SmartFolder from the Workspace. #761


No deviations to report.


  • Analysis for IOTC was produced
  • Analysis for NEAFC\ICES data was produced
  • A technical report was produced for BiOnym

NKUA Activities

NKUA activities for this period include:

  • IRBootstrapper portlet has been enhanced to support the creation of the SRU collection resources. Moreover it now offers a task for indexing Relational DBs. The DB info is available as a Generic Resource on IS (Related ticket: #2953)
  • UsersManagement portlet has been enhanced to make the shown grid able to show a lot of different columns. (Related ticket: #2954)
  • tagcloud-visualisation-widget has been enhanced to display a loading icon until the data are visualized and showing several notifications in case of failure. (Related ticket: #2952)


NONE


Several portlets have been released in the 3.2 release:

  • org.gcube.portlets-user.search-portlet.3-4-0
  • org.gcube.portlets-user.results-portlet.5-5-0
  • org.gcube.portlets-widgets.tagcloud-visualisation-widget.1-0-0
  • org.gcube.portlets-admin.search-manager-portlet.1-6-0
  • org.gcube.portlets-admin.ir-bootstrapper-portlet.2-7-0
  • org.gcube.portlets-admin.elastic-search-portlet.1-1-0
  • org.gcube.portlets-admin.ft-index-management-portlet.2-3-1
  • org.gcube.portlets-admin.users-management-portlet.2-2-0

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

Liaison with Institute of Geosciences and Earth Resources (IGG), CNR, for the creation of a Virtual Research Environment;


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

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

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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