2014.07 WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

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=== IRD Activities ===
=== IRD Activities ===
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''The beneficiary should report here a summary of the activities performed in the reporting period ''
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''Activities have been focused on observations enrichment with environmental parameters from netCDF files and enrichment of RDF annotations from bibliographic references''
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<xh4> Deviations and Corrective Actions </xh4>
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<xh4> Observations enrichment with environmental parameters </xh4>
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''The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.''
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* Input parameter to specify the Spatial Reference System has been added (default being EPSG:4326) to support SRS reprojection. Other additional input parameters (based on OGC / WFS  options labels): "featureID" to restrict the process to a specific Feature of the Dataset, "count"..
 +
* a subset of the netCDF is created (by overlapping the convexhull of the observations) to restrict the processing only to the relevant part of the netCDF.
 +
* a comparison between onboard SST observations and estimated SST from this process has been performed to validate the method.
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* tests and validation on WPS server.
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<xh4> Achievements </xh4>
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<xh4> Enrichment of RDF annotations for Zotero bibliographic references </xh4>
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''The beneficiary should report here a bullet list highlighting the main achievements of the reporting period''
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*Improvement of annotation methods based on Lucene: Dublin Core metadata elements ("title", "description" and subjects") are browsed to generate and index and a score for the main keywords. A comparison of these keywords is made with those of an ontology to create new annotations of "foaf:agents", "species"...A script has been set up to turn CSV files storing a list of contacts into "foaf:agents" objects. Now, we can link people to their bibliographic references by using URIs for people and topics managed in ontologies.
 +
*starting a new code to turn existing metadata describing databases into RDF metadata annotated with URIs of ontologies.
 +
* publication of these new RDF triples on Ecoscope SPARQL endpoint.
== T6.3 Virtual Research Environments Common Interfaces and Tools ==
== T6.3 Virtual Research Environments Common Interfaces and Tools ==

Revision as of 16:02, 5 September 2014

Contents

This WP6 Activity Report described the activities performed in July 2014 by Beneficiary and Task.

It is part of July '14 Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

A complete re-harvesting of the gCubeApps collections has been performed. In particular a set of 47 OAI-PMH collections has been identified to populate the gCubeApps Information Space.


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

T6.2 Virtual Research Environments Resources and Tools Provision

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

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

During the month of July CNR activities concentrated on supporting the EACoP with tools to analyze real use cases. In particular, Time Series Analysis was enhanced to meet the requirements of analyses for IOTC and ICES #3010. Activity on Common species definition went forward, with Unesco analysing the possible usages of the clustering analysis that was implemented. An assessment with respect to the work done by Tom Webb (Univ. of Sheffield) about commonness ranking has been finalized and a paper was planned to resume such comparison #2197. Finally, the Statistical Manager portlet was deployed and tested with proper functional tests #2984. Activity continued also on the Database Manager application, with enhancements about the portlet #2960.


no deviations to report.


  • The Statistical Manager portlet reached a further stable milestone

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.


CRIA studied and tested BiOnym and recommended that only authority files be used to compare names as we believe that all systems and frameworks should use and be based on valid names. The idea is also to contribute to correct names that are in official lists and legislations. If ASFIS has all kind of names - valid and synonyms with or without spelling errors, names that are so outdated that are not included in TAFs, or even names that should be included in TAFs - we believe that these names should be qualified as such (valid, synonym, not found). Or else all systems will just continue perpetuating errors. We believe that the idea of a name service should also work on trying to improve the quality of names. In order check names and compare results with BiOnym we proposed the following activities:

  • write a program in PERL, in our environment to test names
  • use our “phonetic” algorithm to match names
  • use the Catalogue of Life as the authority file
  • use the files that were sent us as input for testing purposes so that the results can be compared with the tests with BiOnym
  • produce outputs that we believe are of interest to our data providers and users (we imagine this is the same public for IMarine)
  • document the process and send a report and codes.

If the program is approved CRIA can help test its implementation to be carried out by FIN.

IRD Activities

Activities have been focused on observations enrichment with environmental parameters from netCDF files and enrichment of RDF annotations from bibliographic references


  • Input parameter to specify the Spatial Reference System has been added (default being EPSG:4326) to support SRS reprojection. Other additional input parameters (based on OGC / WFS options labels): "featureID" to restrict the process to a specific Feature of the Dataset, "count"..
  • a subset of the netCDF is created (by overlapping the convexhull of the observations) to restrict the processing only to the relevant part of the netCDF.
  • a comparison between onboard SST observations and estimated SST from this process has been performed to validate the method.
  • tests and validation on WPS server.


  • Improvement of annotation methods based on Lucene: Dublin Core metadata elements ("title", "description" and subjects") are browsed to generate and index and a score for the main keywords. A comparison of these keywords is made with those of an ontology to create new annotations of "foaf:agents", "species"...A script has been set up to turn CSV files storing a list of contacts into "foaf:agents" objects. Now, we can link people to their bibliographic references by using URIs for people and topics managed in ontologies.
  • starting a new code to turn existing metadata describing databases into RDF metadata annotated with URIs of ontologies.
  • publication of these new RDF triples on Ecoscope SPARQL endpoint.

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

On Tabular Data component:

  • Split and Merge operations were updated to integrate the elimination of the source columns and others bug fixing
  • Group By operation was updated to fix group for multi-column
  • On "Tabular Data Column"
    • updated batch replace operation
  • On "Tabular Data Table Widget"
    • updated operation edit row
    • updated operation add row
  • Create "Union Wizard" component
    • union operation is added
  • 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


On Workspace component:

  • Enhancement: Realized a new facility to add other administrators to a shared folder through "workspace sharing widget"
  • Fixed: Broken Breadcrumb for long path #813
  • Fixed: Icon association to file type/extension problem #894

On GeoExplorer component:

  • Enhancement: the configurations to show exporting metadata types (Simple, ISOCore and Inspire), Default Layers and Base Layers are read from Generic Resoruce #2969

On Reports Manager component:

  • For the VME-DB use case the Filter by RFMO (Regional Fishery Management Organisation) View was implemented and released. This allows users belonging to an RFMO to only work on their VMEs. see #2438
  • For the VME-DB use case the Rich text editor capability was added and released, see #2786

On Contact Information component:

  • The Contact Information Portlet development has started, it visualises the user's entered contact information such as LinkedIn profile, twitter account, Facebook, personal websites etc. see #3004


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

ASL servlets are updated to fix some authentication issues


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


Release of several components in 3.3 gCube release:

  • users-management-portlet.2-3-0
  • ir-bootstrapper-portlet.2-8-0

T6.4 Virtual Research Environments Development Support

NKUA Activities

NKUA has performed functional tests on all its portlets released or affected from the 3.3 release.


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

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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