WP9 iMarine Data Management Software Consolidated Specifications

Overview

This page contains an overview about the components and facilities provided by the gCube Data Management Software components, along with links to the software specifications and to the developers' guides. The main aim is to provide a summary of the supported software at different granularities. The facilities involve the gCube components to perform several aspects of Data Management, that is: Access, Storage, Transfer, Assessment, Harmonization and Certification.

Key Features

The WP9 facilities provide the following key features:

Data Access and Storage

Uniform model and access API over structured data

dynamically pluggable architecture of model and API transformations to and from internal and external data sources;

plugins for document, biodiversity, statistical, and semantic data sources, including sources with custom APIs and standards-based APIs;

Fine-grained access to structured data

horizontal and vertical filtering based on pattern matching;

URI-based resolution;

in-place remote updates;

Scalable access to structured data

autonomic service replication with infrastructure-wide load balancing;

Efficient and scalable storage of structured data

based on graph database technology;

Rich tooling for client and plugin development

high-level Java APIs for service access;

DSLs for pattern construction and stream manipulations;

Remote viewing mechanisms over structured data

“passive” views based on arbitrary access filters;

dynamically pluggable architecture of custom view management schemes;

Uniform modelling and access API over document data

rich descriptions of document content, metadata, annotations, parts, and alternatives

transformations from model and API of key document sources, including OAI providers;

high-level client APIs for model construction and remote access;

Uniform modelling and access API over semantic data

tree-views over RDF graph data;

transformations from model and API of key document sources, including SPARQL endpoints;

Uniform modelling and access over biodiversity data

access API tailored to biodiversity data sources;

dynamically pluggable architecture of transformations from external sources of biodiversity data;

plugins for key biodiversity data sources, including OBIS, GBIF and Catalogue of Life;

Efficient and scalable storage of files

unstructured storage back-end based on MongoDB for replication and high availability, automatic balancing for changes in load and data distribution, no single points of failure, data sharding;

no intrinsic upper bound on file size;

Standards-based and structured storage of files

POSIX-like client API;

support for hierarchical folder structures;

Data Transfer

Point to Point transfer

one writer-one reader as core functionality

Produce only what is requested

a producer-consumer model that blocks when needed and reduces the unnecessary data transfers

Intuitive stream and iterator based interface

simplified usage with reasonable default behavior for common use cases and a variety of features for increased usability and flexibility

Multiple protocols support

data transfer currently supports the following protocols: tcp and http

HTTP Broker Servlet

transfer results are exposed as an http endpoint

Reliable data transfer between Infrastructure Data Sources and Data Storages

by exploiting the uniform access interfaces provided by gCube

Structured and unstructured Data Transfer

both Tree based and File based transfer to cover all possible use-cases

Transfers to local nodes for data staging

data staging for particular use cases can be enabled on each node of the infrastructure

Advanced transfer scheduling and transfer optimization

a dedicated gCube service responsible for data transfer scheduling and transfer optimization

Transfer statistics availability

transfers are logged by the system and made available to interested consumers.

Data enrichment support

species occurrence data enrichment with environmental data dynamically acquired by data providers

data provenance recording

Standard-based data presentation

OGC standard-based Geospatial data presentation

Data Assessment, Harmonisation and Certification

Workflow-oriented tabular data manipulation

user-defined definition and execution of workflows of data manipulation steps

rich array of data manipulation facilities offered 'as-a-Service'

rich array of data mining facilities offered 'as-a-Service'

rich array of data visualisation facilities offered 'as-a-Service'

Reference-data management support

uniform model for reference-data representation including versioning and provenance

Components

Data Access and Storage

Tree-Based Access

groups components that implement access and storage facilities for structured data of arbitrary semantics, origin, and size

The subsystem focuses on uniform access to structured data for cross-domain processes, including but not limited to system processes

A subset of the components build on the generic interface and specialise it to data with domain-specific semantics, including document data and semantic data

Biodiversity Access

groups components that implement access and storage facilities for structured data with biodiversity semantics and arbitrary origin and size

The subsystem focuses on uniform access to biodiversity data for domain-specific processes and feeds into the Tree-Based Access subsystem

File-Based Access

groups components that implement access and storage facilities for unstructured data with arbitrary semantics and size

The subsystem focuses on storage and retrieval of bytestreams for arbitrary processes, including but not limited to system processes

Data Transfer

Result Set components

this family of components provide a common data transfer mechanism that aims to establish high throughput point to point on demand communication. It has been designed as a core functionality of the overall system and it can be considered as well the building block for the Data Transfer Scheduler & Agent components

Data Transfer Scheduler & Agent components

this family of components guarantees VO/VRE Administrators the possibility to transfer data among Data Sources and Data Storages. It can be exploited as well by any client or web services to implements data movement between infrastructure nodes

Data Assessment, Harmonisation and Certification

Tabular Data Service

a service supporting tabular data flow management

Time Series

a service for performing assessment and harmonization on time series

Codelist Manager

a library for performing import, harmonization and curation on code lists

Occurrence Data Reconciliation

a service for performing assessment and harmonization on occurrence points of species

Occurrence Data Enrichment Service

a service for performing enrichment of information associated to occurrence points of species

Taxon Names Reconciliation Service

a service for performing assessment and harmonization on taxa

Specifications

The specifications require preparatory information to be properly understood. In particular:

How to Develop a gCube Component

a basic guide to build a gCube Component

Buiding Components using the gCube Fetherweight Stack

a guide to develop libraries or clients for the gCube Services

Developer's Guide

the overall gCube Developer's Guide

Task oriented specifications can be found in the following:

Data Access Specifications

the specifications for the Data Access and Storage components

Data Transfer Components Specifications

the specifications for the Data Transfer components

Data Assessment ,Harmonization and Certification Specifications

the specifications for the Data Assessment, Harmonization and Certification components

Integrating Legacy Application into the WPS-Hadoop Framework

an additional guide on how to integrate external scripts in the WPS-Hadoop facilities developed in the Data Tansfer Task