2012.03 Activity Report

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Contents

This Activity Report captures the activities performed in March 2012.

This report is organized in two parts:

Progress and Achievements at WP level

WP1: Administrative and Financial Management

WP Leader: ERCIM - Participants: CNR

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

WP2: Project Management

WP Leader: CNR - Participants: NKUA, FAO

Scientific and technical activities were supervised and monitored. Several interactions were held with FAO to organize the iMarine Advisory Council and iMarine Board contribution to the Sustainability Plan. The monthly PEB (4 March) and SB (6 March) teleconferences were organised and minutes were prepared and distributed. A f2f TCom was organized and held on 14-16 March in Rome. The scientific and technical directors of the project and the chair of the iMarine board participated in several events establishing liaisons with other projects e.g. ICRI2012 (21-23 March, 2012, Copenhagen), D4Life final workshop (28-29 March, 2012, Reading (UK); ABNJ meeting (20 March, Rome), EGI Community Forum 2012 (26-30 March, Munich). Interactions with representatives of the ScienceSoft initiative occurred to refine the objectives of this initiative.


No major issues.


  • Monitoring of the Scientific and technical activities;
  • Monthly PEB (4 March) and SB (6 March);
  • f2f TCom (14-16 March)
  • Liaisons with other EU Projects (e.g. EuroMarine, JPI Oceans, BioVel)

WP3: Governance and Policy Development

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

FAO organized the iMarine Board meeting and advisory council.

All WP participants contributed extensively when so requested, as reported in BSCW and in the forthcoming meeting reports.

Other activities in the WP included; Continuous organization of SDMX Codelist management facilities, interaction with LOD2, AgInfra and FAO CIO department representatives, and with FAO policy offiers for the definition of data access and sharing policies.

FAO is also in the process of recruiting staff to promote of the use of espacially the ICIS components.


Deliverables 3.1 and 6.2 Could not be produced before the iMarine Board meeting, and now have high priority.


During the reporting period:

  • The imarine Board meeting was held in Rome;
  • The imarine Board advisory council met in Rome
  • Representatives of iMarine discussed areas of collaboration with the FAO ABNJ initiative
  • Representatives of the iMarine Board that act as Cluster focal points presented initial imarine Board work plans;

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


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

CERN coordinated, planned and performed the infrastructure upgrade to gCube 2.8.0 which included the installation of the new iMarine Gateway (https://portal.i-marine.d4science.org ). Together with the upgrade of the infrastructure, the INSPIRE VOVirtual Organization; has been decommissioned and some of the resources moved to the Ecosystem VOVirtual Organization; , including the HEPGateway VRE. Some issue related to iMarine portal crash and SMS protocol resolution inside tomcat6 has been investigated and a Production conf call has been organized. The status and the plan for WP5 has been presented during iMarine TCOM meeting.

One additional node (rstudio.p.d4science.research-infrastructure.eu) equipped with Tomcat 6.0.35 and the Tomcat Virtual Platform has been joined to the e-Infrastructure

Regarding T5.3, CERN has worked on the extension of the Messaging consumer and Portal accounting portlet to integrate new accounting data, in particular Template/report, WebApp Management and Documents Workflow.

In addition the solution for Resource Usage Tracking developed by ENG in VENUS-C has been evaluated and a presentation has been given during the iMarine TCom to present the integration steps within gCube.


  • The Server in Kiel site reported a controller failure; server can not be restarted. External support from Transtec-Support ongoing. Since the server is running the AquaMaps Service for the AquaMaps VRE we have decided to add to the VRE the service running under gCubeApps VOVirtual Organization; .
  • A quite important issue regarding the iMarine portal crash is under investigation.


  • new iMarine Gateway Deployed in production.
  • Infrastructure upgrade to gCube 2.8.0 performed in collaboration with NKUA, CNR, FAO and FIN site Managers.
  • INSPIRE VOVirtual Organization; Decommissioned
  • The integration of the Usage Tracker system developed for VENUS-C has been planned during the TCOM

WP6: Virtual Research Environments Deployment and Operation

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

The activities performed in this reporting period focused on (a) the maintenance of the existing VREs, (b) resources and tools provision, (c) the enhancement of the portal technology;

For what concerns "VREs operation", the 13 defined and deployed in the previous period have been maintained. There are no pending requests for additional VREs stemming from the EA-CoP through the WP3.

For what concerns "resources and tools provision", the Species Service discovery facility has been enhanced by adding new functions for occurrence points management, production of occurrence points maps, interaction with the workspace and enhancement of the products visualisation. Besides this, FIN worked on the production of two new data sets (implementing HCAF - Half-Degree Cell Authority File) for the AquaMaps application that include new 2100 environmental parameter fields.

For what concerns "common interfaces and tools", ...


  • D6.2 Applications and Tools Development Plan (Lead beneficiary FAO, due date M3 a.k.a. January 2012) has not been produced;
    • CNR will liaise with FAO to finalise the deliverable;


  • An enhanced version of the Species Service discovery facility has been developed;
  • Two new versions of the HCAF with 2100 environmental parameters data has been produced;

WP7: Enabling-technology Integration and Distribution

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

In task T7.1, E-IIS coordinated the integration of gCube 2.8.0 release. 23 integration builds have been ran and several defects have been discovered and reported in software being released. E-IIS also carried out deployment testing of software under release.

CNR designed and started the implementation of a component called Software Gateway Client that will be used by ETICS to upload build artifacts into the Software Gateway

E-IIS prepared, and CNR contributed, the "Bringing Maven in gCube" session at the 1st TCOM event.


None


  • gCube 2.8.0 released

WP8: iMarine Data e-Infrastructure Enabling Technology Development

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

In the reporting period, many WP8 activities focused on cross-task and cross-WP knowledge sharing and harmonization. Following the releases of MS33 and MS34 and the opportunity given by the 1st TCOM, WP8 had several occasions for talking over the proposed solutions and gather feedback:

  • all the tasks presented the current status of their activities at the meeting;
  • T8.1 and T8.2 had a very fruitful working session. The discussion (joined also by WP5) led to some milestone agreements on T8.2 future directions according to the zero-dependency approach followed in T8.1;
  • T8.3 discussed with WP9 about PE2ng evolution and statistical analysis service
  • following the TCOM, T8.1 and T8.4 had a conference call to map the points/feedback discussed at the TCOM onto the Resource Model and its implementation. Another call will follow in April to complete the analysis and shape solutions.
  • T8.1 and WG 11.1 established a close collaboration to solve the so-called gCore client issue: how to avoid that a client of gCube service brings the whole gCore runtime stack as dependency.

Regarding the implementation activities:

  • the implementation on the new Software Gateway is almost completed. Stubs and service have been deployed in the development infrastructure (T8.1);
  • the implementation of the common-resources-publisher is ongoing but has been slowed but a non trivial issue: since it interacts with the Information System, based on on the current runtime stack, we need to understand how to avoid dependencies between this and the new stack (T8.1);

About the analysis activities:

  • T8.3 had greatly advanced the design of the PE2ng workflow capabilities in a long term basis, including: parallel execution model abstractions, dynamic plans, output status reporting and failure recovery, provenance tracking, improved Matchmaking and Deployment, enhancement of error handling capabilities, persistence workflow, and User Interface and control;
  • T8.2 completed the design of the architecture of SOA3, a complete security framework providing authentication, authorization, accounting, user management services and identity federation.

Finally:

  • T8.1 and T8.4 prepared a workplan of their future activities for the implementation of the new resource management functions described in MS33 and createe a set of TRAC tickets according to such a schedule;
  • T8.2 has finalized and released Milestone MS34.


  • A close collaboration with the CL working group of WP11 has been established to solve the so-called gCore client issue: how to avoid that clients of gCube service bring a whole gCore runtime stack as dependency.


  • workplan (also reported in TRAC tickets) for the implementation of the new resource management functions described in MS33
  • Software Gateway moved towards end of its implementation phase
  • common-resources-publisher's final interface defined and implementation started
  • Milestone MS34
  • Feedback from other technical WPs and new requirements collected on resources' classification for the Facet-based Resource Model

WP9: Data Management Facilities Development

In T9.1:

  • FAO implemented a new version of the Stream API for properly interacting with gRS2.
  • CNR finished with the integration of OBIS and GBIF plugin, with the retrieval of occurrence points and specimens. The WORMS integration was also started.

In T9.2:

  • CERN finalized the design of the gCube Data Transfer facility. They decided to work on a "pure" gcube solution for Data Transfer instead of extending and integrating the EMI FTS.
  • NKUA worked on incorporating gRS2 into the new gCube Data Transfer Service. In particular effort was made in supporting HTTP as gRS2 transfer method.
  • Terradue: Targeting the data management demonstration at the FAO TCom, we developed a complete prototype of an Hadoop Map/Reduce working cluster called by a 52 North WPS interface. Now with the approval of the community, we are re-designing the entire wps-hadoop connector to have a 100% usable API for those who want implement their own processes. The next step will be a complete documentation on the whole developing chain in wps-hadoop. Target end of April.

In T9.3:

  • CNR reported enhancements on the integration of R into the d4Science infrastructure and the correction of some bugs on the Time Series service\interface.


nothing to report.


  • new version of the Stream API
  • complete version of the OBIS and GBIF plugins
  • start of the interface to WORMS
  • finalization of the gCube Data Transfer facility
  • finalization of gRS2 transfer method supporting HTTP
  • enhanced interaction with R

WP10: Data Consumption Facilities Development

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

In the context of Data Manipulation, the implementation of the revised Data Transformation Service which enables distributed execution via PE2ng is complete. The new implementation is going to be extensively tested in terms of integrity and performance and any additional needed features will be integrated. In addition, fault tolerance will be investigated and functionality in this area will be integrated into the implementation.

Work regarding Data Mining in this period was focused on Bio-Climate Analysis. Experiments were performed using a benchmark set from Fish Base data source, two tables indicating the values of environmental parameters and a modeling system able to produce spatial probability distributions, in order to evaluate the impact of climate changes on marine species distribution. The analysis was performed by enriching the functionalities yet present on the AquaMaps gCube application by means of new technological facilities that were added to the Statistical Manager. Furthermore, the development of the Spatial REallocation of Aquatic Data (SPREAD) functionality is continuing. The addressing of delays experienced by consuming Aquamaps data from a remote infrastructure due to different technologies used in FAO and the D4S infrastructure is under investigation.

In the direction of providing Semantic Data Analysis facilities, the development of the X-Search service prototype is complete. Among the features the latter provides are: snippet-based result clustering, snippet or content-based entity mining, gradual faceted search, query restriction based on selected entities or clusters and semantic information retrieval for identified entities. Two versions have been implemented, the first one being a general version and the second operating over Fisheries Global Information System (FIGIS) search component and Fisheries Linked Open Data (FLOD) SPARQL endpoint. In the specific area of entity mining, ways to enrich keyword search where the identified entities are linked to entities in FLOD endpoint are being investigated. In this direction the lead partner, FORTH, has collaborated with FAO in order to identify 4 relevant categories with 8,592 FLOD-networked entities in total.

Finally, in the area of Data Retrieval, work is being performed in the direction of improving the Resource Registry component in terms of flexibility, supporting new policies for retrieval and update and also in terms of architecture, by adopting a plug in oriented architecture. In addition, steps are being taken towards the successful interfacing of the gCube Search System with X-Search by investigating and solving problems that are being encountered.


None


None

WP11: Data e-Infrastructures Integration and Interoperability Facilities Development

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

A concrete time plan for the WP activities for the next period has been established to deal with the deviations from the interaction needs with other WPs. The timeline for T11.2 and T11.3 was aligned to that of T11.1 that needs to take feedback from other WPs too. The schedule of activities was presented and discussed with all partners to conclude to decisions:

  • M6: Delivery date for Framework Specification
  • Involvement of all WP partners in framework evaluation during M6.
  • Launching of T11.2 and T11.3 during M6 through individual investigation for APIs specification within each WG.
  • Two more functional categories (Computation Consumption and Infrastructure Management) involving areas of APIs in need of alignment to the WP standardizations have been identified and included in the WP targeting objectives.

Specific working groups have been assigned for the APIs specification for each functional category, in the context of the top-down approach towards interoperability, that will guide the work in tasks T11.2 and T11.3.

The work on the model for Java client API that mediates access system services has been continued and the current draft of the model has been enriched with:

  • a model of proxy operations that take or return collection of values;
  • a model of asynchronous operations based on polling, callback, or streaming;
  • a model of scope management

The model is about to be circulated to involve all WP partners for evaluation before its establishment and adoption. The estimated commencement of activities for all the functional categories that will provide input for the top-down approach of the framework definition process is M6. However, in the context of Data Management APIs specification that falls under the T11.2 objectives, the streams library has already been re-designed in line with the recommendations and requirements identified in T11.1. The new library is under source control and has been integrated in the Tree-Based Subsystem of the Data Access and Storage Facilities.


None to report


- the new streams library

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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