2014.03 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 March 2014 by Beneficiary and Task.

It is part of March 2014 Monthly Activity Report.

T6.1 Virtual Research Environments Operation

CNR Activities

  • MarineSearch has been deployed in the production environment;
  • Existing Virtual Research Environments have been maintained in operation;


None


  • MarineSearch deployed in production;

FAO Activities

No specific operational activities to report.


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

T6.2 Virtual Research Environments Resources and Tools Provision

FAO Activities

Cotrix development:

  • UI ha been integrated with Unit Tests using ad-hoc patterns #2775
  • initial link model design
  • iMarine production version bugs analysis and resolution
  • fixed general issues #2777
  • Cotrix link model design (#2776)

VME development:

  • Mainly bugfixes on the persistance layer; [1]

Chimaera / SmartFish

  • SmartSearch JS components:
    • #2741 improve the oriented-object model of JS components
    • #2697 and #2690: work on search history
    • #2710 extend geofilter to searchbox widget
    • #2507 improve result model
    • #2715 Add access to GIS metadata html/url through GIS layer panel
    • #2719 start working on browser compatibility issues
    • #2725 start autocomplete improvements (now waiting from improvements server-side)


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 has worked on integrating the Featherweight Stack into the Statistical Manager portlet #2528. Furthermore, they have modified the widget version of the SM portlet to account for invokations from the Tabular Data Manager #1297.


No deviations to report.


  • The Statistical Manager interface now uses the Featherweight Stack

FIN Activities

  • BiOnym development (with CNR, FAO and E. vanden Berghe)
    • Continuous work on BiOnym interface, design and implementation (#2731 Support for Statistical Manager Integration by External Application)
    • Fixing the options available for users
    • Fixing the vocabulary of the options.
    • Writing the help info for each option.
    • Attending the weekly meetings.
    • Introduction of the paper written ([2] BiOnym paper).
  • Cleaning Data (with CRIA)
    • Analysis of the CRIA report on first dataset sent to CRIA by FIN (See CRIA activities).
    • Draft of the workplan.
  • Definition of common species (with UNESCO and CNR)
    • #2197 A Possible Definition of Common Species
    • Reviewing the status of commonness computed by the model for 70 species of the North Sea.

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

1. Implementation of a mapping service for FishBase specimen occurrence point data through mapCRIA. Service implemented in March 2012.

2. New data cleaning applications developed during 2013:

  • Blank catalogue numbers
  • Repeated catalogue numbers
  • Incomplete data fields
    • Taxonomic hierarchy: For example: when family and species data fields are not blank and genus is blank, the system shows this as missing data
    • Geographic data: For example, when country and county data fields are not blank and county is blank, the system shows this as missing data (this might be relevant if those species that occur both in rivers and sees are georeferenced.
  • Metadata that classifies data providers as predominantly marine or land vouchers. For marine specimens the data cleaning tool shows all records that fall on land as possibly having errors.

3. Preparation of a document on Data Cleaning Strategy and Applications at CRIA. Report submitted in March 2013 (Data cleaning strategy).

4. Discussion and definition of strategies to be used to produce data cleaning reports to demonstrate the usefulness of the existing tools and applications.

5. Preparation of the database to receive data from iMarine data providers.

6. Development of a data cleaning report

FishBase prepared a dataset for testing purposes (UBC dataset) and sent it to CRIA. The data cleaning tools ran without any further modification to see what applications are relevant to marine data. A report was made available on-line (First dataset from FishBase).

7. Preparation and submission of an analysis of the online report (submitted in February, 2014)

A report presenting a detailed analysis of the result obtained was produced and submitted. It was presented in five blocks: general information, taxonomic data, collection date, geographic data, and suggestions for blank fields (First dataset data cleaning analysis report).

8. Online conference

An online conference was held to discuss point-by-point of the report.

9. Future activities

An outline of future activities was prepared and discussed as an open document to guide the work to be carried out in 2014 (Data cleaning work plan draft).

IRD Activities

T6.3 Virtual Research Environments Common Interfaces and Tools

CNR Activities

On Statistical Manager

  • The Service has been enhanced by adjusting the DwCA import facility according to proxy issues on the FAO site #2706.
  • The SM SOAP methods have been extended to meet the requirements on the Featherweight Stack from the client library #2278.
  • A set of new Geoprocessing facilities has been introduced. These allow to
    • extact XY areas from a geospatial dataset,
    • extract water column values, given a XY point,
    • perform signal processing on the time trend, given a XYZ point. More importantly, the extraction is defined according to a user defined spatial resolution #1045. One of the direct outcomes of this procedure has been an occurrence enrichment procedure which attaches environmental features to a set of occurrence records. The same procedure is also applicable to vessel trajectories.
  • started the integration of a signal processing facility for non uniformly sampled time series, like the ones that will be used by the Tabular Data Manager #2703.

On supporting facilities:

  • A new WebApp was developed and released to automatically add users to VRE (without making them ask for registration) VRE Add/Remove Users from Manager: see #2653
  • A new widget was developed and released to prevent user UI interaction (through AJAX) when the session expired, see Session Checker Widget #2726
  • The ASL Notification component was enhanced to remove the word "notification" from the email notification subjects #2727.

The following web application were enhanced and released in gCube 3.1

On Share Updates component:

  • Added possibility to alert the users of a VRE when sharing an update
  • Refined the way to guess content and images when parsing HTML
  • Improved images recognition when parsing html pages having no image indication from openGraph
  • Added user agent property to http requests to avoid web servers 'complaining' HTTP 403 errors
  • Replaced all the line breaks and all the double spaces with the html version to preserve new lines in posts
  • Fixed bug when changing user avatar and minor restyle
  • Several improvements in url checkings
  • resolved problem with AdBlock plugin

On News Feed component:

  • Implemented the automatic scroll back in time for feeds (in VRE scope)
  • Fixed double notifications for post owner who commented his post
  • Fixed double notifications for post owner who liked his post
  • Fixed user referral problem when post was deleted
  • Added session checking popup
  • Fixed paste problem on replies

On Tabular Data component:

  • On "Tabular Data Table Widget"
    • Added validation and delete of duplicates
  • On "Tabular Data Column Widget"
    • Added replace and batch replace
  • Enhancements on "Tabular Data Common Events"
    • updated the types of events
  • Enhancements on "Tabular Data Portlet"
    • updated menu and behavior
  • Enhancements on "Tabular Data GWTService"
    • added operations


No deviations to report


  • Statistical Manager, Share Updates and News Feed robustness enhancements
  • Integration of Geo-spatial processing

NKUA Activities

NKUA activities for this period include:

  • UsersManagement portlet has been enhanced in order to be integrated with the HomeLibrary group manager. VRE-Managers are set as administrators to the corresponding HL group (Related ticket: #2729)
  • FullTextIndex portlet has been updated in order to use the new Index client library (Related ticket: #2735)
  • IRBootstrapper portlet has been updated in order to use the new Index and DTS client libraries (Related ticket: #2736. Moreover the ForwardIndex tasks have been removed as the Forward Index is no more used
  • SearchPortlet and ASLHttpInformationRetrieval interface are now using the SearchClient in order to fix a problem related to some jars in the webapp classpath.
  • Fixed an issue on VreInformationEditor portlet, on which portlet was failing to create a new configuration #769.


  • ForwardIndex portlet has been removed as the ForwardIndex is not used anymore


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

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