2012.12 Activity Report

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Contents

This Activity Report captures the activities performed in December 2012

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

  • Amendment of the extension of the DoW
  • Follow and submit deliverables and milestones


N/A


  • Completion of the DoW extension amendment and now under SB's review

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

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


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

WP3: Governance and Policy Development

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

Main activities:

  • FAO continued the liaison between the project and the wider community, also through WP4 feedback, and preparation for FIRMS and CWP meetings. An activity on geospatial services was initiated with DG-MARE.
  • IRD collaborated with FAO on OGC services and KB establishment.
  • FIN brought forward the opportunity to exploit the Statistical Service for Bayesian models in marine data analysis.
  • Terradue contributed an abstract and introduction to the Geospatial Cluster Work Plan

No activity reported by CNR, NKUA, ERCIM, CRIA, UNESCO


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


  • An agreement with the FishFinder group was reached for a VRE and Off-line facility.
  • Cotrix development started.
  • 6 iMarine presentations delivered.
  • Development o a common model for SmartFish

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

  • Organisation of WP4 call to dicuss about the following agenda: iMarine website review, Training (I please ask FAO to present the plans for next training activities), Dissemination event, Synergies exploitation & users involvement
  • Critical review of the iMarine website by WP4 partners. Creation of new sections: iMarine Resources, iMarine Mobile Apps, Experts Actions, Community RSS feed on the homne page
  • Dissemination and promotion of iMarine project through Christmas Greetings sent to over 470 contacts and a targeted Christmas letter sent to around 40 organisations relevant for iMarine. The letter included a brief description of iMarine offering, the link top download the application. An iMarine calendar has been shipped together with the letters.
  • Informal Meeting at ESA, to present iMarine and consider possible collaboration with ESA projects such as the Medina project.
  • Attendance to the Mediterranean Regional Database (Med-RDB) 2 days workshop, at the GFCM premises
  • Submission of 3 scientific papers:
    • Gianpaolo Coro, Pasquale Pagano, Anton Ellenbroek. Automatic Procedures to Assist in Manual Review of Marine Species Distribution Maps. Submitted to the ICANNGA'13 conference
    • Leonardo Candela, Donatella Castelli, Gianpaolo Coro, Pasquale Pagano, Fabio Sinibaldi. Species Distribution Modeling in the Cloud. Submitted to Concurrency and Computation: Practice and Experience - Special Issue on "Cloud Computing for Data-driven Science and Engineering"
    • Leonardo Candela, Donatella Castelli, Gianpaolo Coro, Federico De Faveri, Lucio Lelii, Francesco Mangiacrapa, Valentina Marioli, Pasquale Pagano. Integrating Species Occurrence Databases to Facilitate Data Analysis. Submitted to Biological Conservation - Special Issue on "Advancing online databases for global biodiversity conservation"


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


Release of the iMarine App for Android

Over 100 views on Slideshare of the slides of the "Marine Knowledge: All Projects meeting"

iMarine potential raised in the Med-RDB network - iMarine VREs demonstrated to ESA staff formerly involved in D4Science; agreement on the principle of a presentation of iMarine to a Medina workshop in spring 2013

WP5: iMarine Data e-Infrastructure Deployment and Operation

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

In the context of T5.1:

The Infrastructure has been upgraded to gCube 2.11.1. The maintenance release was deployed in order to fix some issues in the infrastructure and at portal level. CERN coordinated the upgrade by preparing as well the upgrade plan.

CERN continued also to support the NAS/ISOFTS group in order to upgrade their gCube Infrastructure, activity started at the end of the reporting period.

In the context of T5.2:

CNR Hadoop infrastructure has been doubled (13+13 nodes plus management) and a new production host for the Statistical Manager has been provided by CNR.

NKUA during this period encountered a disk failure which caused a downtime for 2 VMs. The disk was changed and the VMs was operational again in few hours. Additionally NKUA changed the way that the gcube wiki can be accessed, show that is accessible using both http and https, except of the login page that remains accessible only using secure connection

In the context of T5.3:

The Portal Accounting portlet has been refactored to maven and GXT and enhanced as described in:

https://issue.i-marine.research-infrastructures.eu/ticket/67

The component is going to be released for gCube 2.12.0


None


  • Infrastructure upgrade to gCube 2.11.1

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 (e.g. requests for subscriptions have been evaluated and either approved or rejected).

For resources and tools provision:

  • A number of plugins for SPD has been revised, namely NCBI and WoRMS;
  • The mappings performed by the various plug-ins while producing Taxonomy Item and Occurrence have been documented via a dedicated Wiki page;
  • IRD started an activity aiming at making available WPS processes;

For common interfaces and tools:

  • Home Library 4.3 - Sharing functionality has been implemented;
  • Social Portal, Social Data Sharing implementation: a number of widget has been developed;
  • GIS Publisher Service implementation started;
  • Web Application Management Portlet has been revised to comply with the new RM;
  • Species Products Discovery Portlet has been revised;
  • Software Upload Wizard has been revised;
  • Resource Management Portlet (RMP) & RMP Support Library has been reorganised;
  • ApplicationSupportLayerContent extension is enhanced to support the transformation of results coming from Tree collections;


None


  • Existing VREs have been maintained;
  • A number of widget and portlets has been revised;

WP7: Enabling-technology Integration and Distribution

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

In the reporting period E-IIS coordinated integration of gCube maintenance release 2.11.1. In total 11 integration full builds have been executed and 15 issues reported in Trac. Release integration last 8 days (from Dec 1st to Dec 8th).


NKUA has updated the gCube Distribution site for 2.11.1 release by inserting the corresponding entry in the database. Furthermore, the news for the maintenance release of gCube 2.11.1 have been published and are available here.


Nothing to report

  • gCube 2.11.1 integrated and released

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

In T8.1:

  • CNR has been working on fixing deployment related issues concerning the Deployer and Resource Manager components.
  • FAO has been involved on the development of several components included in the FeatherWeight Stack, a set of libraries that will replace the original gCore client stack. The components have been prepared for release in gCube 2.12 along with updated facilities for the testing of gCube Services (my-container) and the core gcore libraries (gcf).

In T8.2: During the month of december E-IIS has been working on integrating Single Sign-On solutions with Liferay Portal. A test infrastructure has been provided by ENG and the web browser SSO feature has been succesfully tested.

In T8.3: During december, NKUA has been working on the redesign of the Map-Reduce/Master-Worker parallel execution model abstractions. New filtering capabilities were added to the node selection mechanism of the Execution Engine and the execution nodes were modified in order to produce more detailed logs. A new round of tests has been performed in order to evaluate the performance of the Execution Engine under a demanding task.


None to report


None to report

WP9: Data Management Facilities Development

In T9.1:

  • FAO enhanced the tree-manager and its dependent components with important internal refactoring
  • CNR worked on bug fixing for the Species Discovery Service and the Storage Manager
  • CNR worked on the tree manager plugin for the SPD with enhancements aiming at software robustness

In T9.2:

  • CERN enhanced the Data Transfer facility by introducing timeouts handling
  • CERN modified the DT Libraries to meet the CL Agent library requirements
  • NKUA fixed bugs in the data exchange libraries

In T9.3:

  • CNR worked on SDMX and SDMX Time Series Datasource, to build up a SDMX repository with dynamic production of Time Series documents
  • CNR released the Occurrence Reconciliation interface which communicates with the Statistical Manager


no deviations to report.


  • Technical enhancements in the tree-manager and associated sub-components
  • Enhancements in the DT facility with timeout handling
  • The Occurrence reconciliation interface was released

WP10: Data Consumption Facilities Development

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

During the month of December, in T10.1, the integration of Fulltext Index with ElasticSearch has started. Also, a bug referred to logs of Resource Registry has been solved.

In T10.2, Data Transformation Service has been enhanced with two more useful transformation programs. Both of them contribute in visualisation facilities. Moreover, a pluggable service of the GIS publisher has been implemented, which allows the publishment of GIS data into Geoserver/Geonetwork/Thredds.

In T10.3, various enhancements have been applied on Statistical Manager, associated with data mining libraries and web portlet. The former manages complex outputs allowing the implementation of algorithms which could output tables, images and files at the same time, while for the latter, occurrence algebraic operations were added, in order to support the subtraction between two occurrence sets.

Furthermore, various visualisation methods have been explored including geospatial (lon, lat, time), non-geospatial (e.g. species population), data resulting from the processing of the above (e.g. species relocations). Also, gnuplot and graphviz libraries have been integrated with DTS, demonstrating plots and graphs respectively as an output.

In 10.4, effort was placed in dynamic discovery of the location of XSearch-Service on behalf of XSearch portlet. Also, XSearchPortlet has been refactored as a maven component.


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


  • Transformation programs have been added to DTS
  • Management of complex output by the Algorithms
  • Occurrence Points Subtraction facility
  • Occurrence Points calculations on D4Science
  • XSearchPortlet turned to maven component

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

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

During December, in T11.1, effort was spent in porting the Data Transfer Agent Library to the FeatherWeight Stack and contribution to FeatherWeight Stack documentation. Also, the development of the commons-fw-client, a specialization of the common-clients to Featherweight Stack and of a related sample client library, has been completed and the wiki documentation of the common-clients and common-gcore-clients has been updated. Moreover, several bug fixes and improvements have been done related to common-clients and commons-gcore-clients components.

In T11.2, a new version of the tree-manager-library based on the Featherweight Stack has been developed. Also, the Data Transfer Agent Library has been extended to include a transfer timeout parameter on the transfer requests. Furthermore, testing of common-security library and of the SOA3/gCube integration (gCube Security Handler) has been still in progress.

In T11.3, the port of the Search client library to FeatherWeight Stack has been completed. Also, an investigation on transforming the XSearch-Service to a gCube service has started.


Due to both an unavailability of the resources and a reorganization of the E-IIS infrastructure there was a delay of two weeks in testing of common-security library.


search-client-library implementation

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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