2013.04 Activity Report

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Contents

This Activity Report captures the activities performed in April 2013

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

  • SB teleconference call participation and minutes taking
  • Bi-monthly effort report consolidation for March and April 2013 (missing: Trust IT, UNESCO, CRIA, IRD)
  • Payment proceed for E-IIS and Terradue
  • Edward's subcontract completion
  • Monitor and submit of the due deliverables and milestone achievement statements


None


  • Edward's subcontract completion
  • Periodic report template to be sent out in June and deadline of contribution: 15 July 2013

WP2: Project Management

  • Organization and chairing of monthly Steering Board conference call (26.04);
  • Organization and chairing of the monthly PEB (22.04);
  • Participation in the Programme Committee of the Biodiversity Informatics Conference as iMarine representative;
  • Liaising with the Research Data Alliance (RDA);
  • Preparation of the Programme of the iMarine Workshop to be held on 14-15 May 2013 in Brussels;
  • Meeting with the coordinator of EMODNET Physics (12.04);
  • Day-by-day monitoring of technological and scientific activities.


N/A


  • Monthly Steering Board and Project Executive Board conference calls;
  • iMarine accepted as case to be studied within the RDA Legal Interoperability WG;
  • Programme of the iMarine Workshop to be held on 14-15 May 2013 in Brussels;
  • Liaising with new projects and initiatives.

WP3: Governance and Policy Development

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

In T3.1 only FAO reported activity:

  • Finalize and distribute iMarine Board meeting report;
  • Finalize and distribute iMarine Advisory Council report;
  • Finalize and analyze iMarine Sustainability survey;
  • Liaise with FAO departments on code list management opportunities;

http://wiki.i-marine.eu/index.php/Ecosystem_Approach_Community_of_Practice:_SpeciesNameFinder

  • Liaise with Sub-contractors on expected project activities.

In T3.2 only FAO reported activity:

In T3.3 activity was reported by FAO, and Terradue

  • Cotrix development continued; Continue on UI, import / export. Continue on architecture and data model.
  • SPREAD development restarted; the algorithm has been refactored, tested and validated (operational).
  • Geospatial processing: FAO Areas: a set of WPS processings has been developed to process the master data, and discriminate the target usages (FIGIS internal vs. Public dissemination). Based on user feedback, metadata quality has improved.
  • FLOD: service to enrich GEONETWORK metalayer with ASFIS, FIGIS ID and WORMS ID.
  • FLOD: new species set of ASFIS requires import of WoRMS species equivalent and their mappings

Terradue:

  • Hadoop clarification during T-COM and Board wrt SPREAD.
  • SPREAD will be integrated as a standalone Java application under WPS-hadoop in WP9 (activity to be planned)


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


  • the march iMarine Board and Advisory Council Meetings reports were circulated in draft.
  • The EA-CoP VRE for the Board wiki pages have been produced, and are ready for Board members usage.

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

AppliFish:

FAO publishes a news on AppliFish on FAO's Intranet. http://bscw.research-infrastructures.eu/bscw/bscw.cgi/d279980/AppliFish%20on%20FAO%27s%20intranet%20_%20April%202013.png


iMarine events:

  • International Conference on Adaptive and Natural Computing Algorithms, ICANNGA’13 - Poster presentation by Giampaolo Coro, CNR-ISTI


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

Press Clippings on AppliFish http://www.campaniaonline.it/arriva-applifish-la-prima-app-smartphone-dedicata-allecosistema-marino-550-specie-a-portata-di-clic/

WP5: iMarine Data e-Infrastructure Deployment and Operation

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

for T5.1:

Some changes have been applied to the production infrastructure by CERN, in particular the definition of a pre-production environment. The Ecosystem VOVirtual Organization; has been moved as pre-production environment with the dismissal of the DRIVER and HEPGateway VREs. A new Software Gateway has been also deployed in order to point to gcube-staging repository. The deployment of 2.14 components in pre-production was also started ( and completed in May)

The preparation of the infrastructure upgrade to gCube 2.14 was completed and the Milestone MS26 achieved.

for T5.2:

NKUA scheduled the creation of a Virtual Machine for migration of portal.d4science.org, which will be performed later in June.

for T5.3:

Messaging components have been upgraded to use the messaging endpoint library. The components upgraded have been released in gCube 2.1.4 Monitoring probes component has been dismissed and removed from the GHN.


FIN is still not contributing to the WP.

CNR had to fix a HW/SW Misconfiguration on two xen host, all VM were restarted and reconfigured, also upgraded to fix CVE-2013-0871 kernel bug.


Milestone MS26 achieved

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 request for a new VRE supporting Taxon Name Disambiguation has been raised;
  • the Aquamaps layers has been revised to comply with the policy on metadata;

For resources and tools provision:

  • Adding new data sources to the SDI: myOceans and World Ocean Atlas;
  • Developing plugin for exposing FAO data sources (figisapps.fao.org and data.fao.org) via the TM;
  • Reinforced the OAI-PMH (e.g. DOI resolver added) and the SPD TM plugins (e.g. SPQL 2.0 compliancy);
  • Revised the SPD plug-ins (e.g. to align with the SPD Service 2.0);

For common interfaces and tools:

  • Social facilities has been reinforced:
    • News Feed has been enhanced, e.g. smart refresh, VRE scope;
    • Share update has been reinforced, e.g. mention people;
    • About VRE has been revised, e.g. to exploit news feed;
  • Activation record widget revised to support new TM plugins;
  • Workspace facilities reinforced, e.g. to support a proper sharing notification mechanism;
  • GeoExplorer/GISViewer revised to improve the access to GeoNetwork metadata;
  • SPD enhanced for bug fixing and SPQL 2.0;
  • AquaMaps enhanced for bug fixing and maps visualisation;
  • Revised the email messages informing users on request approval / rejection;
  • Revised the results portlet to deal with TM content;
  • Revised the IRBootstrapper to deal with TM content;


No activity has been reported by ERCIM, FIN, UNESCO, CRIA and IRD.


  • Existing VREs has been maintained;
  • AquaMaps layers metadata have been reinforced;
  • Release of a new version of the OAI-PMH TM Plugin;
  • Release of a new version of the SPD Tree Manager Plugin;
  • Release of a new version of all the SPD Plugins;
  • Release of a new version of Social facilities;
  • Release of a new version of Activation Record Widget;
  • Release of a new version of SPD, Workspace, GeoExplorer and GISViewer, AquaMaps;
  • Release of UserProfilePortlet 1.5.0, ResultsPortlet 2.0.0, CollectionsNavigator and Search portlets, UsersManagement portlet 1.8.0, IRBootstrapper portlet 2.2.0;
  • Release of Android gcube Search application 1.2.0;
  • Release of InteractiveLayers 1.0.0;

WP7: Enabling-technology Integration and Distribution

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

In the reporting period integration of releases gCube 2.14.0 started. As usual, E-IIS coordinated the integration activities scheduling nightly builds of the entire project plus partial builds of subsystems.

During the period, the ETICS instance at E-IIS facilities was made available on 16th April to gCube developers:

  • 10 worker nodes (to be increased according to needs) was made available to execute remote builds;
  • whole gcube datamodel was imported from the ETICS instance hosted at CERN;
  • E-IIS monitored status of the instance providing support to users;

In task T7.2, CNR updated some pages of wiki guides:

  • Security services: SOA3 connector, Authentication, User management
  • Administrator guides on configuration of security services
  • GCube clients integration with security


  • Nothing to report


  • gCube moved to ETICS instance installed at E-IIS facilities

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

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

  • Solved integration issues with deployer service and prepared components for release in gCube 2.14
  • Added documentation on common-encryption library
  • Development on software-gateway: added constraint on profile service version (must be less than 1.0.0). Not released in gCube 2.14.

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

  • Started a collaboration between E-IIS and CNR on the reorganization of the wiki pages related to security solutions.
  • Authentication and Authorization
    • Most of the activities concerning the development of SOA3 Authorization have been completed. Authentication module is already complete and under test.
    • Activities on deployment of first secure VOVirtual Organization; have started: client integration, test of SOA3 Authentication and Authorization module.
    • Development of service-to-service authentication mechanism, policy management portlet and policy definition guide has progressed and will be completed in May.
  • Resource accounting
    • Resource model definition activity has been completed (wiki)
    • Started development of client libraries for publisher/consumers of accounting records.
    • Started development of resource accounting portlet that will show customized views and graphs for the collected accounting records.

T8.3 - Workflow Management Facilities:

  • Completed development of the component that creates SOAP messages by parsing WSDL documents.
  • Extended JDL language (gJDL) is now able to describe DAGs of web services.
  • Implementation of Map/Reduce supporting PE2ng operators has been completed. A new workflow adaptor will be created in order to support this new operator.
  • Evaluation of PE2ng on UMD infrastructure is ongoing.
  • Resource registry has been refactored in order to use gCube storage facilities (storage manager). A reset operation has been implemented on the resource registry in order to avoid restarts of the container.


None to report.


T8.1

Released deployer-service components (v. 2.4.1-1). Solved integration issues.

T8.2

Accounting: completed activity on the definition of the accounting model.

T8.3

  • gJDL is now able to describe DAG (Directed Acyclic Graph) jobs of web services, then executed through PE2ng.
  • Implementation of Map/Reduce supporting PE2ng operators has been completed.
  • Released components in gCube 2.14 with minor changes.

WP9: Data Management Facilities Development

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

  • In T9.1:

CNR worked on SDMX libraries. In particular they collaborated with FAO on the development of Cotrix by explaining the usage of sdmx-registry-client libraries and some basic concepts of the SDMX standards. On the technical side, CNR modified the sdmx-registry-client libraries in order to hide the usage of Spring IOC container from clients. The SDMX libraries were updated accordingly. Enhancements were made also on the libraries dependencies.

The SPQL 2.0 language was released for the Species Discovery Service. The Storage Manager was updated to version 2.0.0, which involves the implementation of new features for managing remote files.

  • In T9.2:

On the Data Transfer components CERN upgraded the code to the new version of the Storage Manager libraries. They also added enhancements on the Storage Manager portlet with smarter facilities to manage files and remote folders. Terradue concluded the WPS-Hadoop implementation by including the kernel density IRD algorithm. They exposed the algorithms through the T2 infrastructure.

  • In T9.3:

CNR continued the development of the cube-manager component and API module. They faced issues concerning the integration with Mondrian analysis and SDMX data/metadata. CNR managed, at design level, the management of geospatial data attached to the Time Series. Several DB related approaches were tested and implemented within the library in order to achieve sufficient performances for common operations (data query, table cloning, transformations).


no deviations to report


  • Release of the SPQL 2.0 language
  • Enhancement of the Storage Manager
  • Enhancement of the Storage Manager Portlet
  • Release of a WPS-Hadoop instance endowed with a kernel density estimation algorithm

WP10: Data Consumption Facilities Development

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

In T10.1, the implementation of Forward Index using Couchbase has finished and only testing and integration with the portlet is remaining. Also, the implementation of data fusion operator has progressed. Regarding the documentation of FullText Index, the Admin page and Developer's guide have been authored. Moreover, Storage Handling has been refactored to use Storage Manager.

In T10.2, gCube Data Transformation Service is now able to produce forward index rowsets out of Tree Manager Collections. Also, both personalization services, UserProfileAccess and ProfileAdministration, have been refactored to use the storage system.

In T10.3, on Data Mining side, the Trendylyzer facility was approached, which aims at finding biodiversity indicators from the Obis data. Regarding Statistical Manager, the Service was enhanced in its design, in order to account the management of external data sources. Also library changes focused on the comparison between OGC maps and consequently on the retrieval of information from OGC maps. Furthermore, facilities to perform Digital Signal Processing were integrated.

On the visualization side, the geographical layers "hidden" into the NetCDF files downloadable from the MyOcean and the World Ocean Atlas repositories were explored and indexed. The layers were eventually published in production environment under the standard ISO 19139 format.

In advance, QuantitativePropertiesVisualisation is reaplced by a visualisation library, called InteractiveLayers. It is intended to extend the GeoExplorer visualisation capabilities, providing time filtering for the available layers on the GeoExplorer. wikipage is updated with detailed info. Lastly, main use-cases of the OWS Context OGC standard in iMarine have been developed.

In T10.4, XSearch components have been updated for the release of gCube 2.14.0. Also, alternative designs for XSearch components were still under investigation. Moreover, a paper has been written describing a successful application of the XSearch technology on the domain of patent search. Lastly, potential workflows in FAO-FIPS for code lists and reference data have been reviewed as long with the potential of adding semantic services to Cotrix, e.g. to feed FLOD.


  • Development of the QuantitativePropertiesVisualisation is discontinued. Its functionality is planned to be provided by the InteractiveLayers component.


  • Preparation of released components in gCube 2.14.0
  • Integration of Digital Signal Processing facilities in the statistical libraries
  • Publication of environmental layers from MyOceans and World Ocean Atlas under standard ISO 19139 format.
  • A wikipage has been created to support further development of the visualization libraries.
  • Produced internal discussion documents:
    • CLM Architectural patterns - second round - "Exploring Role and Roadmap to a FIPS Repository Service"
    • Cotrix-Semantic Repository data workflow - (C.Baldassarre, F.Simeoni)
  • A successful application of the XSearch technology on the domain of patent search is described in the following paper which acknowledges the support of iMarine:
    • P. Fafalios, M. Salampasis and Y. Tzitzikas, Exploratory Patent Search with Faceted Search and Configurable Entity Mining. In procs of the 1st International Workshop on Integrating IR technologies for Professional Search in conjunction with the 35th European Conference on Information Retrieval (ECIR’13), Moscow, Russia.

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

During April, in T11.2, effort was spent on delevoloping Client Libraries for GHN Manager and Resource Manager. Also, support was provided for the integration of the GHNManager Client with the common-security-library. Moreover, in the context of the deployment of the secure VOVirtual Organization; a new Shutdown client for the GHNClient Manager has been implemented. Furthermore, FeatherWeight Stack was integrated in the GHN Distribution.

In T11.3, effort was spent on finishing the refactoring of ASLContent in order to fully support Tree-Manager model and making changes to comply ASL components with ASLContent model. Also, Client Libraries for FullTextIndex and the GeoIndex has been developed and released. Finally, a teleconference about the remaining effort took place.


None


The following components have been released in gCube 2.14.0:

  • application-support-layer-content.5-0-0
  • application-support-layer-core.3-3-0
  • application-support-layer-http-content-access.1-0-2
  • application-support-layer-http-information-retrieval.1-2-0
  • application-support-layer-oai_ore.1-0-1
  • application-support-layer-oai_pmh.1-6-0
  • application-support-layer-search.4-0-0
  • application-support-layer-userprofile.3-1-0
  • fulltextindexnode-client-library.1-0-0
  • geoindexmanagement-client-library.1-0-0
  • geoindexupdater-client-library.1-0-0
  • geoindexlookup-client-library.1-0-0

Also, following component has been released on HEAD:

  • secure-ghnmanager-client.HEAD

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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