2012.06 WP6: Virtual Research Environments Deployment and Operation Monthly Activity By Task and Beneficiary

From IMarine Wiki

Jump to: navigation, search

Contents

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

It is part of the June Monthly Report.

T6.1 Virtual Research Environments Operation

CNR Activities

The VRE deployed in the previous period have been maintained. Moreover, a new VRE "BiodiversityResearchEnvironment" has been deployed to offer the new facility for Species Products Discovery.


No deviation to report.


  • The BiodiversityResearchEnvironment has been deployed;

FAO Activities

FAO completed a suitability test for ICIS in June. The results were forwared to CNR.


No deviation to report


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

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

No activity to report in this period. The activity in WP3 on code list manager may require that WP6 is kept informed when technology discussion start. However, the current discussion is not yet at that level.

The same applies for the SPREAD Java modules.


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 finished with the development of the NCBI plugin. The NCBI Taxonomy database dump files are used to create a database in PostgreSQL.


The NCBI Taxonomy database dump files contained some errors, so they were corrected in order to guarantee a programmatic access to the database dump. In addition, the citations file contained a field with a list of taxonomy ids separated by a single space, this made a slower search. To improve the response time of NCBI plugin, we created an extra table using the taxonomy ids as primary keys.


  • NCBI plugin implementation

FIN Activities

No activity.


Re AquaMaps VRE: There is a complete re-run pending, in particular to eliminate images with wrong points, but the cleaning of these points is still ongoing. We are reviewing the planning for that.

UNESCO Activities

A meeting with VLIZ is planned for this summer to organise a more automated way to transfer the OBIS data.


None


None

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:

  • The HomeLibrary implementation (HomeLibraryJCR) has been updated and released.
    • The model of the jackrabbit repository has been changed with the aim to improve the data retrieval performances and so also the HomeLibrary implementation has been updated to be compliant with the new repository model.
  • The Workspace Portlet GUI has been updated. A new feature called "Access from Desktop" is supported. Every item or folder in workspace is accessible via WebDAV. Click the button Access from Desktop located one the top, there you will see the direct WebDAV URL.
  • The Workspace Light Tree Widget has been updated to load faster the nodes asynchronously
  • The Species Discovery Portlet has been updated and released. The new features supported are the following:
    • advanced option of search - by Temporary (Date from - to), by Space (Bounds), by Data Source (available plug-in are: BrazilianFlora, Obis, WoRMS, GBIF, ITIS, CatalogueOfLife, SpeciesLink), by Classification (Group by Rank)
    • advanced filtering on results - by Classification (tree visualization), by Data Provider, by Data Soruce, by Rank
    • enhanced visualization criteria - a new details view of checked results is available
  • A first alpha of Tabular Data Widget has been released in preview. The Tabular Data Widget alpha version includes those new features:
    • an interface for data source definition: The Datasource is a DAO that provides an abstract interface to the data persistence. The Datasource is in charge to provide the widget with a table description and the table data. The table description is provided using the description model defined by the widget, the table data is returned using the JSON format. The Datasource mechanism lets the widget to work without a Tabular Data Library implementation.
    • a JDBC data source: The JDBC Datasource retrieve the necessary information through a JDBC connection. The table description is retrieved from the database meta-information provided by the JDBC driver. The table data is retrieved throught SQL queries.
      • In order to handle different SQL language used by different Database Management System an SQL-Dialect system has been provided. An SQL Dialect interface provides the necessary SQL statement for the JDBCDatasource operations. Each SQL Dialect is capable to declaring if it supports or not the specified DBMS product and version.
      • In order to support tables with no primary key an auto-generate column mechanism has been provided.
    • The description model has been extended in order to include a new type of column: the system column, a special column used for not-visualized information transmission like: row id, selection state, etc.
  • A Tabular Data Client web application has been produced in order to show the TabularDataWidget capabilities. The sample application is available in the svn repository.
  • A first integration of the TabularDataWidget has been reached with the Statistical Manager Portlet. The Statical Manager Portlet is now capable to show the experiment results stored in a remote DB. During the integration no particular problems have been found, only small issues promptly fixed.
  • Software Management Widget is under development. Newly supported features are:
    • Management of third party software: Third party software can be registered with Software Management Widget, which enforce case-specific rules.
    • Input Library related data: Service name, description, version and class, Package name, description and version.
    • Input Maintainers data: for each maintainer the user can define first Name, last name, email, organization.
    • Input Changelog data: for each software modification the user can give a description and (optionally) a ticket number.
    • Input License data: a license must be provided for third party components. It is automatically generated in case of gCube software.
    • Misc documents creation: Software archive related files (LICENSE, INSTALL, README, changelog.xml, MAINTAINERS) are automatically generated at the end of the wizard.
    • Service archive creation and Software Gateway registration: upload of the generated Maven artifact to a Maven repository and registration of the related service resource on the Software Gateway.
    • Wizard step descriptions and helpers: Added a general wizard description and a step helper for each wizard step.


  • Software Management Widget: a new requirement was defined:
    • The application must allow the registration on the Software Gateway of Maven artifacts which are already uploaded on infrastructure repositories.


  • A new GUI of Species Discovery Portlet has been released in gCube 2.9.0.
  • The GUI of Workspace Portlet has been updated and released in gCube 2.9.0.
  • Workspace light tree widget has been optimized and released in gCube 2.9.0.
  • First alpha of TabularDataWidget as been released and integrated in Statistical Manager Portlet.

NKUA Activities

NKUA activities are focused on the update of the SearchManager and UserManagement portlets.

  • The new functionality for the support of the semantic searh is available from the search manager portlet. The portlet offers:
    • A UI to annotate fields with the semantic keywords. Annotations are per field.
    • A UI to create new keywords under the available groups.
    • A UI to remove keywords from an existing group
  • Users Management portlet is being enhanced to provide the functionality that is described at the tickets: #398 and #400.


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

T6.4 Virtual Research Environments Development Support

NKUA 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

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

Personal tools