2013.03 Activity Report

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Contents

This Activity Report captures the activities performed in March 2013.

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

  • iMarine Advisory Council participation
  • Reimbursement process for members of iMarine Board and Advisory Council Board
  • Non-disclosure Agreement signed and sending DoW, GA to VUB (Edward's subcontract)
  • Exchange with PO in setting review date for Period 2
  • Monitor and submit of the due deliverables and milestone achievement statements: Delaying: MS3 (Second annual meeting of the Governing Board) and MS23 (Delivery of Virtual Event and Project Event)


N/A


  • iMarine Advisory Council participation
  • Non-disclosure Agreement signed and sending DoW, GA to VUB (Edward's subcontract)

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

  • Organization and chairing of monthly Steering Board (15.03) and PEB (11.03) conference calls;
  • Planning of the iMarine Board and Council meetings;
  • Organization of the March TCom (20-23 March, 27-28 March);
  • Coordination with some partners to put in place appropriate risk management and recovery actions;
  • Participation of the Project Scientific and Technical Directors in the DG-CNECT e-Infrastructure Concertation Meeting (Brussels) as project representatives;
  • Participation of the Project Technical Directors in the Event "Towards a Roadmap for Research Infrastructures on Biodiversity and Ecosystem research in Europe" (Brussels) as project representative;
  • Further steps in the scientific organization of the iMarine event in Brussels in May;
  • Liaising with other EU projects for including iMarine among the contributors to the "European Biodiversity Informatics" conference on 3-6 September at FAO;
  • Telco with representatives of CoL to discuss about the preparation of an MoU between iMarine and this initiative;
  • Liaising with NEAFC and VLIZ on sub-contracts;
  • Day-by-day monitoring of technological activities.


N/A


  • Monthly SB and PEB conference calls;
  • March TCom;
  • Recovery actions put in place;
  • Participation in EU organized events;
  • iMarine May event Draft Agenda and initial list of invitees;
  • Networking for the organization of future events.

WP3: Governance and Policy Development

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

T3.1:

  • iMarine Board Meeting organized in Rome (2d);
  • iMarine Advisory Council organized in Rome (1d);
  • iMarine technical progress reported to Board; environmental enrichment, statistical service, biodiversity tools, LOD engineering, etc.
  • iMarine Board VRE presented;
  • Several cluster pages were edited to meet iMarine Board expectations.

T3.2

  • iMarine Data Access and Sharing policy presented to Board;
  • AppliFish data and policies reviewed with iMarine Board and FAO representatives.

T3.3

  • TLO new version, OWL mappings, OWLIM repository produced. Filled with data from e.g. Ecoscope, WoRMS, and FLOD.
  • Cotrix development in Bangkok resulted in additional screens. In Rome discussions on objectives and support scenarios to other departments such as the Economics dept.
  • SPREAD discussed at TCom, action for implementation identified as WPS Hadoop service with Terradue;
  • Review Terradue Hadoop streaming and Hadoop Map Reduce;
  • Geospatial infrastructures of FAO and iMarine brought closer;
  • LOD engineering proposal prepared and presented;
  • IRD and FORTH produced a set of competence queries for the TLO covering fact-sheets;
  • IRD produces OGC WPS metadata from RR codes with 52 North WPS server.


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


  • iMarine Board Reports and Board Work-plan;
  • Environmental enrichment of species occurrences data aligned with Board expectations;
  • Wiki pages for Board activities reviewed;
  • Survey on exploitation models towards sustainability broadcasted to Board members;
  • See T3.3 for a list of achievements.

WP4: Communication, Dissemination and Training

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

The WP leader should report here a summary of the activities performed in the reporting period

Dissemination graphics material:

  • iMarine Gateway Icons revision

iMarine participation to events:

  • Event Title: XXII Session of the IOC Committee on International Oceanographic Data and Information Exchange

Venue: Centro Social, Cívico y Cultural Rivera, Ensenada, Baja California, México Dates: 11- 15 March, 2013 Brief Description of Event: iMarine Representative: Ward Appeltans, OBIS Target Audience: Communities attending the event: Dissemination material: iMarine flier disseminated at the event Impact (post event) : http://www.slideshare.net/OBIS-IOC

  • Event Title: e-Concertation meeting"

Venue: Brussels, Belgium Dates: 6-7 March, 2013 Brief Description of Event: The 10th e-Infrastructure Concertation Meeting is organised by the Commission Services with the support of the e-ScienceTalk project. The main aim of the meeting is to bring projects together in order to discuss issues related to the completion of the 7th Framework Programme and the start of an e-infrastructures activity during Horizon 2020 (2014-2020). Reason of iMarine Participation: iMarine has won the second prize of the Concertation Meeting Project Success Story Competition in the Better Society category. iMarine Representative: Donatella Castelli & Pasquale Pagano, CNR ISTI Target Audience: European Commission + FP7 Projects Communities attending the event: European Commission + FP7 Projects Dissemination material: iMarine Success Story - iMarine flier Impact (post event) : Presentation & promotion of AppliFish and of the iMarine Project http://www.i-marine.eu/Content/Multimedia.aspx?id=49ec3b08-39da-4a6b-876d-b3bbd3d1f2d1

  • "Understanding the iMarine opportunity" presentation for the Advisory Council - 27 March 2013

News: iMarine wins the second prize of the Concertation Meeting Project Success Story Competition http://www.i-marine.eu/Content/Multimedia.aspx?id=49ec3b08-39da-4a6b-876d-b3bbd3d1f2d1

Presentation Cool tools and high level experts for fisheries management and knowledge on SlideShare http://www.slideshare.net/iMarine283644/cool-tools-and-high-level-experts-for-fisheries-management-and-knowledge



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

Tot Downloads: 11 March 2013 509 IOS - 178 Android : 687

40 downloads after the eConcertation meeting.

Cool tools and high level experts for fisheries management and knowledge presentation on slideshare reached 219 downloads

FAO’s news on AppliFish (59 stories detected, 6 languages): News release “AppliFish, marine knowledge at the touch of a button” issued 12 March in Arabic, English, French, Russian, Spanish, Italian

Selection of stories

  • Crean aplicación para cuidar peces en extinción - El Tiempo – 13/03-13 23:03
  • Océans : la FAO lance une application mobile d'information sur plus de 550 espèces marines pour faciliter une consommation durable - Radio des Nations Unies (FR) – 12/03-13 20:46
  • Want To Know About The Sushi You're Buying? Applifish, The UN’s New Mobile App, Can Tell You - International Business Times UK – 12/03-13 20:30
  • FAO destaca nueva aplicación sobre medio marino CINU – 12/03-13 19:22
  • Applifish, con un clic sai che pesce mangi Lettera 43 – 12/03-13 18:14
  • Fao, applifish con un click sai che pesce mangi - ANSA.it – 12/03-13 17:01
  • Centro de Noticias de la ONU - FAO destaca nueva aplicación sobre medio marino - Un News Center – 12/03-13 16:45
  • Una nueva aplicación ofrece información sobre más de 550 especies marinas - El Mercurio Digital – 12/03-13 16:23
  • Una nueva aplicación ofrece información sobre más de 550 especies marinas - Globedia – 12/03-13 16:13
  • Applifish: come conoscere più di 550 specie marine con un clic - Greenreport - Quotidiano Ambientale – 12/03-13 16:07
  • UN-supported mobile application provides consumers with information on fish they buy - Un News Center – 12/03-13 15:04
  • Une application fournit des informations gratuites aux internautes sur plus de 550 espèces marines (FAO) - 2012 | Algérie – 12/03-13 13:00
  • Nasce ‘Applifish’ una app per informarsi sull’ambiente marino - Prima Online – 12/03-13 12:24
  • Nasce 'Applifish' una app per informarsi sull'ambiente marino - La Stampa.it – 12/03-13 12:24
  • AppliFish, marine knowledge at the touch of a button - EIN Presswire – 12/03-13 12:06

WP5: iMarine Data e-Infrastructure Deployment and Operation

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

Activities concerting T5.1:

A new version of gCube has been deployed in the production infrastructure ( gCube 2.13). CERN was responsible for part of the integration testing, pre-production validation and coordination of the upgrade.

A new BOM for maven based portlets had been developed 1313 and the documentation for BOMs has been completed (https://gcube.wiki.gcube-system.org/gcube/index.php/GCube_Maven_BOMs)

The GHN has been extended in order to contain by default a logger configuration for JUL 1132

Activities concerting T5.2:

CNR installed 2 new databases nodes for FishBase and SeaLIfeBase data and made available 10 new VMs for production ( node1.d4science.org-node10.d4science.org), 7 VMs have been also configured to setup the secure testing infra ( ghns, portal , soa3 and shibolett)

The two iMarine grid sites have been upgraded to UMD 2 by CNR and NKUA site managers. CERN was coordinating the upgrade activities.

Activities concerting T5.3:

CERN developed a new library in order to transparently retrieve Message Broker endpoints 1374 The library is going to be released in gCube 2.14.

A first version of the Aquamaps Images webapp Nagios Probe has been developed and installed in our production Nagios server 1289


None


  • Infrastructure upgrade to gCube 2.13
  • UMD sites upgrade to UMD2

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;
  • A new VRE named FishFinderVRE (#1493) has been defined and deployed;

For resources and tools provision:

  • the integration between FAO and iMarine SDIs continued (namely GeoNetwork);
  • the porting of FishBase and SeaLifeBase databases, from MySQL to Postgres was completed;

For common interfaces and tools:

  • Social Facilities has been improved by integrating Document Workflow Suite notifications;
  • Reports Management has been enhanced;
  • Workspace facilities has been enhanced to support shared folders;
  • Results portlet has been revised to deal with content coming from ASL;
  • Bug fixing (e.g. Home Library);


  • the deployment of the VRE conceived to offer search (and semantic one) facilities (#1190) has been postponed to wait for the forthcoming gCube release;


  • the FishFinderVRE has been deployed;

WP7: Enabling-technology Integration and Distribution

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

E-IIS coordinated the integration process of gCube release 2.13.0, eventually released on March the 20th. In total 20 integration builds of the entire project plus several partial builds have been executed. E-IIS scheduled execution of deployment tests of all services in the release and opened tickets for detected issues.

E-IIS worked at the set-up of a new ETICS instance at E-IIS facilities. An initial partial import of gCube data has been done and several tests have been carried out of the new instance's functionalities and BTRT's builds. The import scripts have been slightly improved to handle better potential issues during the final import.

E-IIS carried out tests for adoption of jdk 1.7 in future gCube releases. In particular, in this phase, integration of gCube components with jdk 1.7 has been tested carrying out some builds of the entire projects and analysing the results.

NKUA kept the gCube distribution site up to date with latest gCube 2.13.0 release.

Concerning documentation, NKUA finalised the documentation validation procedure (#1430).


Nothing to report


  • gCube 2.13.0 delivered

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

T8.1 - Data e-Infrastructure Enabling-technology Development:

  • Bugfixing activity on the registry-publisher. The issues were related to the update of resources published on multiple scopes.
  • Documentation on the registry-publisher has been updated on the gcube wiki.

T 8.2 - Policy-oriented Security Facilities:

  • Integration tests for SOA3 Authentication module has been completed.
  • Documentation has been completed for the components that are developed up to now. Documentation has not yet been linked on the wiki sections.
  • Started to work on
    • Authorization SOA3: work on this task is divided into two macro areas. The components are expected to be delivered in the first half of may.
      • Policy definition portlet
      • Core SOA3 connector and policy management components
    • Resource accounting:
      • started work on the definition of data model resource types for accounting purposes. Up to now four data types were identified: data access (tree manager), execution, storage, service (gcube soap service).
      • Discussion has started on how to model those types and on how to implement the notification system.
      • Development of components has started and the solution is expected to be provided in the first half of july.

Modifications will be required to the authentication module: delegation paradigm used for user-to-service auth is not well suited for the service-to-service case. We cannot accept to have certificates and credentials for every service. The solution envisioned makes use of a trusted network of ghns. Credentials and roles are associated to a ghn and services authenticate as services of a ghn using its credentials. Solution will be delivered in the next months.

T 8.3 - Workflow Management Facilities:

  • Progress has been made on the workflow orchestration layer:
    • JDL language has been extended in order to enable description of DAG jobs different than Normal. New implementation, comprising a parser, has been named gJDL.
    • Development of a WSDL parser for gCube services, that extracts the service class, the namespace and the input and output types of a WS operation, to create request and response SOAP envelope templates.
  • Completed performance evaluation of PE2ng (#document - open with Microsoft Word). Results indicate that the amount of the execution time decreases proportionally with the number of nodes. Further performance tests will be done on the UMD infrastructure and results will be compared with the one in the report.
  • PE2ng operators development is ongoing and near to completion. The system has been integrated with the new version of storage-manager, therefore removing legacy gcube stack.
  • Documentation on Workflow Management is up to date.


None.


T 8.2 - Policy-oriented Security Facilities:

  • SOA3 Authentication Module and Connector

WP9: Data Management Facilities Development

In T9.1:

CNR worked on the definition of a new SPQL language to query the Species Product Discovery Service. SPD was equipped with a new plugin for accessing World Register of Deep Sea Species, using the WoRDSS web service. The OAI Tree Manager Plugin was modified in order to retrieve a tree collection and related documentation was produces. CNR worked on the Storage Manager too, in particular to make the library rely upon the FWS and to enhance File uploading. Documentation was produced too, on the Infrastructure wiki pages.

In T9.2:

CERN worked on Data Transfer to introduce the Http URI resolver for the SMP protocol. Furthermore, they integrated Data Transfer with the Messaging Common Library in order to use it when submitting or retrieving the result of transfers. Finally they worked on the implementation of a new portlet for the Storage Manager.

Terradue worked on the enhancement of the WPS-hadoop system. Furthermore, they integrated the IRD kernel density contour lines legacy application. Finally, Terradue relased an SPD client to be published as a facility through the WPS-H.

In T9.3:

CNR worked on the design of the Tabular Data System (ex TimeSeries). In particular they tried to address all the requirements that had been previously collected. Eventually they produced a list of components to be delivered. CNR started developing the cube-manager library and produced prototype implementations for both the interface (cube-manager-api) and the implementation (cube-manager). The interface should provide means for extending the Tabular Data features.


no deviations to report.


  • The SPQL language was defined
  • The OAI Tree Manager Plugin was enhanced
  • The Storage Manager was enhanced
  • SPD was equipped with the new WoRDSS plugin
  • Http URI resolver for SMP protocol was implemented
  • WPS-hadoop with enhancements was implemented
  • The new Tabular Data System was completely designed

WP10: Data Consumption Facilities Development

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

During the month of March, in the context of T10.1, effort was placed on the integration of Forward Index with the Couchbase. Also, the documentation of FullText Index has started.

The WOA 2009 cleansing service is now available as an OpenSearch catalogue.

In T10.2, the featherweight version of gDTS client libraries was released along with bug fixed libraries.

In T10.3, the Taxa Match Algorithm by FIN was integrated with SM, and published in development environment. To such aim the databases of FishBase and SeaLifeBase were translated to Postgres and made available to the infrastructure. Also, algorithm for estimation of length-weight relationships was run in parallel, reducing significantly the execution time.

Furthermore, an interactive time window filter was made available for all existing time series maps, integrated as OpenLayer's layer.

Moreover, the implementation of OWS Context Library is under exploration.

In T10.4, a problem was faced that caused semantic data enrichment failure. A fix will be included in the upcoming release. Also, work has been done in designing of an approach for the requirement about enriching RDF files with the URIs of named entities. At last, the alternative architecture designs of XSearch components are still under investigation.


nothing to report


  • The following components have been released in gCube 2.13.0
    • Search related
    • gCube Data transformation Service related
  • WOA2009 data cleansing web service
  • FIN Taxa Match is now integrated with the SM
  • R script for calculating weight-length relationships were run in parallel
  • Enrichment of the timeseries maps with an interactive time window filter

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

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

During March, in T11.2, effort was spent on studying the possible development of a common client library to support http based services interaction. Also, a guide related to the integration of common-fws-client with Jersey, for REST services, has been published. Moreover, the integration test of the common-security with Feather Weight Stack and the GHNs has been completed and the documentation has been released. ENG started a support activity for the partners involved in the integration of clients with common-security library.

In T11.3, effort was spent on refactoring the ASLContent , in order to be compatible and handle the Tree-Manager model. Also, the Client Library for gCube Data Transformation Service has been released. Furthermore, there have been some bug fixing in some ASL components. Finally, the activity of integrating the Portal with the Feather Weight Stack has been planned by opening the related tickets.


None


The following components have been released in gCube 2.13.0:

  • common-security library
  • application-support-layer-core.3-2-2
  • application-support-layer-search.3-2-0
  • application-support-layer-content.4-2-0
  • application-support-layer-http-information-retrieval.1-1-0
  • application-support-layer-http-infrastructure-login.1-0-3
  • http-access-management.1-0-2
  • gcube-search-library.1-1-0
  • data-transformation-client-library.2-0-0

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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