2013.09 Activity Report

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Contents

This Activity Report captures the activities performed in September 2013

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

  • Review 2 participation
  • General Assembly Meeting organisation in Brussels.
  • Periodic Report 2 submission


N/A


WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Project review preparation & meeting attendance (final rehearsal 11.09 - review 12.09);
  • Organization of a working meeting between iMarine and project officers from DG-Mare, DG-RTD and DG-ENV;
  • Attendance of the RDA Conference (Washington, 16-18.09) as iMarine representative;
  • Organization and chairing of the SB meeting call (09.09);
  • Review and prioritization of the liaisons activities;
  • New liaisons established;
  • Organization and chairing of the PEB meeting call (26.09);
  • Preparation of the Governing Board Meeting (13.09);
  • iMarine shared workspace operation and maintenance.


No major issues.


  • Project second review;
  • Meeting between iMarine and project officers from DG-Mare, DG-RTD and DG-ENV;
  • PEB and SB meetings;
  • Activity prioritization's;
  • New liaisons.

WP3: Governance and Policy Development

WP Leader: FAO - Participants: ERCIM, CNR, NKUA, FORTH, TERRADUE, FIN, UNESCO, CRIA, IRD

T3.1

  • Participate to meetings; review, RDA
  • Prepar for meetings: EMODNET, and Board
  • Prepare NEAFC Subcontract, liaise with e.g. Fridtjhof Nansen, DCF, FishFrame

T3.2

  • iMarine Policy Document on Data Access and Sharing further edited; guidelines and best practices.

T3.3

FORTH

  • Continued collecting feedback and new domain requirements to continue the design/implementation/testing of a new release (Version 3.0.0) of the MarineTLO: #2046
  • Continued preparing the documentation of the MarineTLO #1764
  • Extended the design and the implementation of the MarineTLO #2046
  • Extended the Mapping and Transformation rules from imarine data source to MarineTLO and testing the forthcoming outcomes #2046
  • Documentation of the process of constructing MarineTLO-based Warehouse #1848

IRD

Semantics

  • Present ConnectCube at the review in Brussels
  • Release of TLO 3.0.
  • Collaboration with NKUA on SmartFish

Geospatial cluster:

  • improving the genericity of processes by introducing new input parameters enabling the mapping for different structure (semantic of columns labels). This should validating by running processes with FAO datasets
  • grouping IRD indicators in a R package.


The major issues faced in the reporting period and the identified corrective actions should be reported here


  • Succesful presentations at the review
  • iMarine Policy Document on Data Access and Sharing new version.

WP4: Communication, Dissemination and Training

WP Leader: TRUST-IT - Participants: CNR, NKUA, FAO

  • Finalisation of the May 2013 Workshop Report and circulation to the meeting participants.
  • Website: new website implementation & content revision
  • Events:
  • Biodiversity Informatics in Europe, 3-6 September 2013, Rome Italy:
    • 2 presentations
      • Donatella Castelli, Virtual Research Environments as a Data Infrastructure facility
      • Johannes Keizer, Marc Taconet, Integrating agricultural science with biodiversity science
    • 1 demo session
      • D10 iMarine facilities for empowering biodiversity science, Coro, G., Ellenbroek, A. & Pagano, P.
        • The demo has covered: Exploiting the iMarine Biodiversity Research Environment to demonstrate the facilities the infrastructure offers to collect occurrence points and then analyze/project those points and access species taxon names from several data sources / Exploiting the iMarine Scalable Data Mining environment for demonstrating the facilities that the infrastructure offers to perform analysis, mining and modeling of biogeographic data / Exploiting the Ecological Modelling Research Environment to demonstrate the facilities that the infrastructure offers to discover, access, compare, and export geo - referenced products.
    • 1 poster session http://uripreview.i-marine.eu/167a37cb-3e85-4ab7-b3b5-7cb0fb740749.pdf
  • F2F Meeting with EMODNET, 13 September 2013, Brussels, Belgium
  • 2 presenation and 1 poster session at the IMDIS conference, Lucca 2013
    • Presentations:
      • Donatella Castelli, Pasquale Pagano,Leonardo Candela and Gianpaolo Coro. The iMarine Data Bonanza: Improving Data Discovery and Management through an Hybrid Data Infrastructure
      • Ward Appeltans, Peter Pissierssens,Gianpaolo Coro, Angela Italiano, Pasquale Pagano, Anton Ellenbroek and Tom Webb. Trendylyzer: a Long-Term Trend Analysis on Biogeographic Data
    • Poster session:
      • Gianpaolo Coro, Antonio Gioia, Pasquale Pagano and Leonardo Candela. A Service for Statistical Analysis of Marine Data in a Distributed e-Infrastructure


The major issues faced in the reporting period and the identified corrective actions should be reported here


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

WP5: iMarine Data e-Infrastructure Deployment and Operation

WP Leader: CERN - Participants: CNR, NKUA, FAO, FIN

In the context of T5.1

Participation to the 2nd iMarine review rehearsals and meeting in Rome and Bruxelles.

The QA infrastructure (in particular the portal ) was upgraded to gCube 2.16.1 (2204), and plans for the infrastructure upgrade were prepared and shared to the project wiki (http://wiki.i-marine.eu/index.php/Resources_Upgrade#gCube_2.16.1).

A Distribution for the SmartGears framework has been prepared (2170)

In the context of T5.2

CNR installed a new server for R computation and RStudio while NKUA upgraded WMS and LB server to UMD-3 (needed for SHA-2 WMS alarm and ticket).

In the context of T5.3

Nothing to report


none


  • Infrastructure upgrade to gCube 2.16.1

WP6: Virtual Research Environments Deployment and Operation

WP Leader: CNR - Participants: ERCIM, NKUA, FAO, FIN, UNESCO, CRIA, IRD

For Virtual Research Environments Operation:

  • the previously deployed Virtual Research Environments have been maintained in operation;

For resources and tools provision:

  • Species Name Reconciliation development continued,
  • COTRIX development continued, e.g. code-list management completed;
  • IRD tuna indicators development continued, e.g.

For common interfaces and tools:

  • existing portlets have been revised to rely on FWS;
  • existing portlets have been revised to rely on the latest version of GWT (2.5.1);
  • the HL has been reinforced, e.g. by removing the portal dependency;


Few contribution circulated. In some cases, activity reported is not accompanied by tickets.


  • Existing VREs have been maintained;
  • A lot of portlets have been revised to rely on FWS and GWT latest version (2.5.1);

WP7: Enabling-technology Integration and Distribution

WP Leader: E-IIS - Participants: CNR, NKUA

  • Attendance to the 2nd iMarine review rehearsal and meeting in Bruxelles.
  • gCube 2.16.1 released on 24th September. In total, for this release, 11 integration builds were ran and 2 integration issues have been identified and managed through Trac system.
  • Operation of the ETICS service.
  • NKUA has updated the gCube Distribution site for 2.16.1 release by inserting the corresponding entry in the database. Furthermore, the news for the maintenance release of gCube 2.16.1 have been published and are available on the iMarine website.


  • none


  • release of gCube 2.16.0

WP8: iMarine Data e-Infrastructure Enabling Technology Development

WP Leader: CNR - Participants: NKUA, E-IIS, FAO

T8.1 - Enabling-technology Development :

  • Developed FWS compliant client library for softwareGateway service. To be released in gCube 2.17.
  • Continued development of FWS compliant registry-publisher library. Will be released in gCube 2.17.
  • Developed CLI application that allows to invoke softwaregateway service. To be released in gCube 2.17.
  • Continued development and bugfixing activity on smartgears related components in order to prepare the first release in gCube 2.17. Work focused on:
    • smartgears distribution scripts
    • web app that listens for container shutdowns and propagate the events to common-smartgears
    • replacement of components that works against the zero dependency approach
    • refinement of test framework
    • FWS extensions for smartgears
    • Improved cleanup procedures
    • Improved mixed content handling in generic resources (common-gcore-resources)

T8.2 - Data e-Infrastructure Policy-oriented Security Facilities:

  • continued the activities on security integration at portal side and the integration of the SAML Identity Federation with Registration and Login Portlets. The integration is yet to be completed.
  • completed the support on DN Based security

T8.3 - Workflow Management Facilities:

  • Resource Registry extension to support a per VOVirtual Organization; configuration for updaters has started.
  • Queuing mechanism of the Execution Engine has been documented on the Developer's Guide.


None to report.


None to report.

WP9: Data Management Facilities Development

WP Leader: CNR - Participants: NKUA, CERN, TERRADUE, FAO

In T9.1: CNR updated documentation to manage the storage manager library.

In T9.2: CERN ported the Scheduler and Storage management portlet to gwt 2.5.1. They also refactored the components in order to remove dependencies from gCore. They continued in the development on the StorageManagement portlet.

In T9.3: CNR updated the sdmx registry client libraries to the latest version released by MetadataTechnology and changed the dependent gCube components consequently. CNR completed the design phase of the Tabula Data Manager. The final result is the creation of two software modules: the operation-api, that describes the interface of tabular data embeddable data workers and the service-client-api, that describes the client library interface. A mock of the API that presents basic functionalities has also been developed in order to let developers start with the implementation of client applications (the UI). A further module, named "shared libs" contains classes to be used both on server and client side.

On the SDMX Codelist import/export side, a software module that handles tabular data sdmx operations has been created. SDMX codelist import/export features have been added and tested on available sdmx codelists.



  • Refactoring of the Scheduler and Storage manager portler to avoid the dependency from gCube
  • Update to the latest version of the sdmx registry client libraries

WP10: Data Consumption Facilities Development

WP Leader: NKUA - Participants: CNR, FORTH, TERRADUE, FAO

During the month of September, in T10.1, OpenSearch was enhanced in the way of adding unicode characters support. gCQL parser was extended for that reason. Also, an lesser incident that caused browsing failure was examined and solved. Moreover, effort was put into consolidation of the work done with Oozie and SST/WCS. Activity also involved visualisation of the results.

In T10.2, Bio-Oracle layers have been integrated and the Map Comparison procedure has been updated in order to provide support for ESRI ASCII raster files.

In T10.3, there has been an investigation on parameters that are involved in the formula for common species estimation. Also, a procedure on how to extract absence points from obis based on statistical considerations has been addressed. At last, the activity on SSB vs Recruits estimation resulted with an implemented model that produced promising results.

In T10.4, further work has been placed on X-Link implementation and testing.


none


  • Import of the Bio-Oracle layers
  • Account for the ESRI ASCII raster files in the Maps Comparison procedure
  • SSB vs Recruits produced promising results
  • The parameters for the common species formula were calculated
  • Visualisation of the SST enrichement time-series prototype

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

WP Leader: NKUA - Participants: CNR, CERN, E-IIS, FORTH, TERRADUE, FAO

During September, in T11.2 effort was spent on testing and supporting the GHN Manager client integration with common-security libraries. Also the work on the OWC4J continued and is focused on WFS.

In T11.3 effort was spent on simplifying the gCube Data Transformation Service client library APIs. Also, the development client libraries for OpenSearch has started. Furthermore, Resource Registry integration with FeatherWeight Stack testing has been continued and the development of client libraries the personalization service has been completed. Furthermore, ASL Http interface has been extended in order to retrieve the content within the links of the tree collections. Finally, some bug fixes on ASL were done regarding the Session and Search query construction.


None


None

Progress and Achievements by WP and Beneficiary

WP1: Administrative and Financial Management Monthly Activity By Task and Beneficiary

WP2: Project Management Monthly Activity By Task and Beneficiary

WP3: Governance and Policy Development Monthly Activity By Task and Beneficiary

WP4: Communication, Dissemination and Training Monthly Activity By Task and Beneficiary

WP5: iMarine Data e-Infrastructure Deployment and Operation Monthly Activity By Task and Beneficiary

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

WP7: Enabling-technology Integration and Distribution Monthly Activity By Task and Beneficiary

WP8: iMarine Data e-Infrastructure Enabling Technology Development Monthly Activity By Task and Beneficiary

WP9: Data Management Facilities Development Monthly Activity By Task and Beneficiary

WP10: Data Consumption Facilities Development Monthly Activity By Task and Beneficiary

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development Monthly Activity By Task and Beneficiary

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