2012.07 WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

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This WP6 Activity Report described the activities performed in July 2012 by Beneficiary and Task.

It is part of July Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

CNR maintained the production VREs and monitored and supported the validation activity of the new Biodiversity VRE.


None


  • maintenance, monitoring and operation of the VREs
  • collection of feedback and preparation for the new version of the Biodiversity VRE

FAO Activities

  • A FCPPS user training was conducted.
  • FAO requested, and received, a VRE for Vulnerable Marine Ecosytems fact sheet reporting. The VRE will be used in the requirements collection and definition phase of the project. A later version will be produced based on these requirements.


D6.3 is accumulating delays, due to late arrival of review reports.


  • 2 FAO staff were trainid on the use of FCPPS
  • The VME-DB VRE was created and validated (report pending)

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

Requirements to operate and own a VRE were collected for:

  • The Vulnerable Marine Ecosystem Database fact-sheet VRE
  • The Fishfinder VRE; options for a stand-alone data provider to the e-infrastructure were requested
  • The Tuna Atlas use-case; based on the ICIS VRE, but with the goal to produce all time-series using 1 format.

In addition, activities continued on the vertical integration of community applications:

  • OpenSDMX continued to be producing SDMX for FAO and IRD (Code lists)
  • Technical options were discussed with other FAo depts. in the context of code list and vocabulary management
  • The SPREAD use case was discussed from a technical perspective


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

ERCIM Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

CNR Activities

CNR activity focused on updating the existing plugins for the purpose of adapting them to Species Products Discovery.


NCBI Species Discovery Plugin

The plugin was completed. It downloads the NCBI Taxonomy database dump files, fixes errors occurring during the reading of the files and creates a PostgreSQL database.

The plugin allows the search by scientific names and common names, supporting Classification, Synonyms and NamesMapping Capability.


Obis Species Discovery Plugin

The plugin architecture has been modified in order to introduce the Plugin's Session, a session which wraps essential and reusable information for the execution of plugin task. The wrapped information includes a set of prepared statements used to improve query performances. The plugin sessions are maintained in a pool in order to reuse it in multiple plugin calls.

The text date parsing functionality has been improved in speed and supported formats using the Joda library. Here some numbers:

  • Before the changes, the dates were parsed with an avg time of 284 milliseconds per date and with 7039 unrecognized dates.
  • After the changes, the dates are parsed with an avg time of 67 milliseconds per date and with 248 unrecognized dates.

The plugin implementation now support:

  • associated Runtime Resource updates, refreshing all the plugin sessions with the new available information;
  • the plugin shutdown, in order to free all allocated resources;
  • the Classification Capability providing information about taxonomy.

The 20 seconds delay for the first element on search operation involving Scientic Name or Common Nameresult has been removed splitting the main query into two subquery. The Occurrence Point information have been expanded with full information for each point.

Finally the plugin has been synchronized with the general service architecture refactoring.


None


  • NCBI plugin completed
  • Plugins updated
  • An enhanced Obis plugin version

FIN Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

UNESCO Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

CRIA Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

IRD Activities

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


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.


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

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

The CNR activity focused on the development and the release of the following software applications:

  • Development of Social Networking facilities has started:
    • A NoSQL Database has been chosen as storage solution, specifically the Apache Cassandra distributed database is the enabling technology together with the definition of the schema (KeySpace) to support social networking.
    • An interface and its relative Cassandra implementation has been created.
    • Two portlets are currently under implementation, ShareUpdates and NewsFeed. The former for sharing user updates and the latter for showing News Feeds to portal users.
  • Software Management Widget is under development. Newly supported features are:
    • Service profile and deliverables creation for the use cases:
      • Software Registration use case: register a service profile for a software which is already stored on an infrastructure maven repository.
      • GCube Plugin use case: upload a plugin related to a gcube component and register its profile within a software gateway.
      • GCube Patch use case: upload a patch related to a software registered on the infrastructure and store it on an infrastructure maven repository.
      • AnySoftware use case: upload generic software on an infrastructure maven repository and register its profile within a software gateway.
    • Management of multiple jars within Library use case. Jars are repackaged into a single jar prior service archive creation and registration.
    • Management of maven dependencies: the user can now declare maven dependencies for each service package.
    • pom.xml creation for service archive artifact and service packages primary artifacts. The generated POMs are now shown as deliverables in the last step wizard card.
    • Helper tooltips are being replaced with a side helper window, which shows help instructions at each wizard step.


The beneficiary should report here major issues faced in the reporting period and the identified corrective actions, if any.

  • Software Management Widget, new requirements were defined:
    • Library use case must allow the upload of multiple jars within a service package. In order to upload a jar library as a primary artifact on a maven repository the provided jars must be repackaged by the web application into a single jar, therefore losing any signature on the original archives. A disclaimer regarding the latter issue must be shown to the user at the start of the wizard.
    • The user should be able to declare maven dependencies for each packages primary artifact within the use cases: GCubePlugin, GCubePatch, AnySoftware, GCubeWebService, WebApp, Library.


  • An installation of an Apache Cassandra cluster has been installed and is running on node1.p.cassandra.research-infrastructures.eu .

NKUA Activities

NKUA activites are:

  • Search portlet enhancement to support the semantic search functionality. Users can select to enable semantic search and be redirected to the xSearch portlet, which is under development by FORTH.


  • The update of the UserManagement portlet is stuck because after testing the functionality provided by the user management core library it turned out that it does not provide the desired functionality as requested at the #398 ticket.
    • Updated information is expected by the ENG


NONE

T6.4 Virtual Research Environments Development Support

NKUA Activities

  • NKUA supported the FORTH institute to setup the portal in order to enable inter-portlet interaction. Forth's XSearch portlet and gCube search portlet are interacting to support semantic search results.
  • Advises on how to build and package a portlet and its dependencies are given to avoid problems in other portlets and to be aligned with gCube's releases.


NONE


NONE

CNR Activities

CNR provided support to the validation activity performed by Yann Laurent on ICIS for the Tuna Atlas Use Case.


None


Feedback to the validation activity performed and planning of extension in agreement with the needs of the FAO community.

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