Unidata’sCommon Data Model

and theTHREDDS Data Server

John CaronUnidata/UCAR, Boulder CO

Jan 6, 2006ESIP Winter 2006

Outline

• Definitions

• Creating a Common Data (Access) Model from NetCDF, HDF5, OPeNDAP

• CDM Coordinate Systems, Data Types

• CDM implementation

• NetCDF Markup Language (NcML)

• The THREDDS Data Server

NetCDF-3

• Machine and OS independent file format for “self-describing” scientific data

• C library (Fortran, C++, Perl, IDL, MatLab, Python, Ruby), Java library

• Efficient subsetting of multidimensional arrays.

• > 20,000 downloads last year

HDF5

• Machine and OS independent file format for “self-describing” scientific data

• C library (Fortran, Java, PyTables)• Evolution from HDF4, but different.• HDF-EOS, HDF5-EOS, standard formats

for EOSDIS, ASCI, NPOESS• Parallel-IO, chunked storage, compression

filters, many data types. • Developed at NCSA, now independent

NetCDF-4

• Project funded by NASA to create new version of netCDF using the HDF5 file format.

• “Extend and merge” netCDF and HDF5– Widespread use and simplicity of netCDF– Generality and performance of HDF5

NetCDF-Java 2.2 (nj22)

• 100% Java library

• Prototype implementation of CDM

• File formats:– General: NetCDF, HDF5, OPeNDAP– Grids: GRIB1, GRIB2– Radar: NEXRAD, NIDS, DORADE– Satellite: DMSP, GINI

• Access to THREDDS catalogs

OPeNDAP

• Client-server protocol for scientific data access

• C++ client and server, Java client and server libraries.

• Current version 2.0; NASA ESE standard

• Working on new 4.0 protocol spec

THREDDS

• Originally funded by NSDL – “discovery and use of scientific data”– Middleware between data providers and users– Dataset Inventory Catalogs (XML)

• Now part of Unidata core funding– Data Serving (pull)

What’s a Data Model?

• Its about scientific data: storing, accessing

• It’s an abstraction

• Equivalent to an abstract object model in OOP

• An Abstract Data Model describes data objects and what methods you can use on them

What’s a Data Model?

• An API is the interface to the Data Model for a specific programming language

• A file format is a way to persist the objects in the Data Model.

• A data access protocol plays the role of a file format.

• The Abstract Data Model removes the details of any particular API and the persistence format.

Creating a Common Data Access Model

from NetCDF, HDF5, OPeNDAP

NetCDF-3DataModel

OPeNDAPData

Model(DAP-2)

HDF5DataModel

CommonData(Access) Model

Coordinate Systemsand Scientific Data Types

Coordinate Systems

Common Data Model Layers

Data Access

Scientific Datatypes

Grid

Point

Radial

Trajectory

Swath

Station

Coordinate Systems needed

• NetCDF, OPeNDAP, HDF data models do not have integrated coordinate systems– so georeferencing not part of API– Need conventions to specify (eg CF-1,

COARDS, etc)

• Contrast GRIB, HDF-EOS, other specialized formats

• Must be done in a general way

• Same underlying mathematics as VisAD, ASCII

Coordinate Systems

Scientific DataTypes

• Based on datasets Unidata is familiar with– APIs are evolving

• How are data points connected?• Intended to scale to large, multifile

collections• Intended to support “specialized queries”

– Space, Time

• Corresponding “standard” NetCDF file conventions

Point Observation Data

PointObsDataset Methods

// Collection of StructureData

Collection getData(

LatLonRect boundingBox,

Date start, Date end);

Trajectory Data

TrajectoryObs Methods

int getNumPoints();

StructureData getData(int point);

Station Data

StationObs Methods

// return List of Station

List getStations();

// return List of StructureData

List getData(

Station s,

Date start, Date end);

Radial Data

Radial methods

interface Radial { int getNumGates(); float getData(int gate);

float getStartingGate(); float getGateSize(); float getElevation(); float getAzimuth(); double getTime();}

Gridded Data

Grid methods

interface GridCoordSys {

CoordinateAxis getTaxis();

CoordinateAxis getXaxis();

CoordinateAxis getYaxis();

CoordinateAxis getZaxis();

Projection getProjection();

}

Array getDataCube(Range time, Range z, Range y, Range x);

Image/Swath

Standardizing NetCDF Formats

• Grid: CF-1 Convention– Need improvements for regional models

(WRF), GIS info

• Radar: “Radar Exchange Format”– With radar community (led by NCAR ATD)

• Point Observations– Unidata Observation Dataset Conventions

CDM implementations: NetCDF-4 and NetCDF-Java 2.2

34

NetCDF-4

C

Library

HDF5 Library

netCDF-4 Library

netCDF-3Interface

NetCDF-4 C Library

NetCDF-4 Status

• 4.0 Beta implements CDM access layer– complete, but waiting for HDF5 release 1.8 to

finalize file format

• 4.1: adding Coordinate Systems

• 4.?: merge OPeNDAP access (pending funding)

NetCDF-Java 2.2 (nj22)

• Prototype implementation of CDM

• File formats:– General: NetCDF, HDF5, OPeNDAP– Grids: GRIB1, GRIB2– Radar: NEXRAD, NIDS, DORADE– Satellite: DMSP, GINI

• Access to THREDDS catalogs

• Implements NcML

Coordinate Systems

Common Data Model

Data Access

Scientific Datatypes

Grid

Point

Radial

Trajectory

Swath

Station

NetcdfDataset

ApplicationScientific Datatypes

NetCDF-Java version 2.2 architecture

OPeNDAPTHREDDS

Catalog.xml

NetCDF-3

HDF5

I/O service provider

GRIB

GINI

NIDS

NetcdfFile

NetCDF-4

…Nexrad

DSMP

CoordSystem Builder

Datatype Adapter

ADDE

NetCDF-Java 2.2 Status

• Data Access layer: Beta quality– also waiting for HDF5 release to finish

NetCDF-4, commit to API

• Coordinate Systems: early Beta– Finishing docs, runtime plugability

• Data Types: Alpha, still experimenting with APIs

NetCDF Markup Language (NcML)

• XML representation of netCDF metadata (like ncdump -h)

• Create new netCDF files (like ncgen)

• Modify existing datasets– Add/delete/rename – Create logical sections of existing variables.

• Create unions and aggregations of multiple existing datasets.

<?xml version="1.0" encoding="UTF-8"?>

<netcdf xmlns="http://www.unidata.ucar.edu/schemas/netcdf/ncml-2.2" location=“/data/nids/N0R_20041119_2147">

<attribute name=“DataType" value=“Radar" /> <remove type=“attribute” name=“password" /> <variable name="Reflectivity" orgName=“R34768”> <attribute name="units" value=“dBZ" /> </variable>

</netcdf>

NcML example

NcML Aggregation

• Union

• Join Existing

• Join New

• Forecast Model Run

+ + =

+ =

NcML Aggregation Example

<netcdf xmlns=“http://www.unidata.ucar.edu/schemas/netcdf/ncml-2.2”>

<aggregation dimName="time" type="joinNew">

<variableAgg name="Temperature"/>

<variableAgg name="Pressure"/>

<scan location=“C:/data/goes/" suffix=".gini"/>

</aggregation>

</netcdf>

THREDDS Data Server

• Integrates data access with THREDDS catalogs and services

• Tomcat/Servlet, 100% Java, single war file

• Data input is netCDF Java 2.2 library

• Data output:– OPeNDAP – HTTP Server– OGC Web Coverage Server (gridded)

HTTP Tomcat Server

THREDDS Data Server

Datasets

Catalog.xml

hostname.edu

THREDDS ServerApplication

NetCDF-Javalibrary

IDD Data

•OPeNDAP

•HTTPServer

•WCS

HTTP Tomcat Server

TDS as WCS Gateway

Catalog.xml

hostname.edu

THREDDS ServerApplication

NetCDF-Javalibrary

•OPeNDAP

•HTTPServer

•WCS

OPeNDAP ServeranotherHost.org

HTTP Tomcat Server

TDS and NcML

Catalog.xml

hostname.edu

THREDDS Server Application

Netcdf-Java

•OPeNDAP

Datasets

NcML

•WCS

TDS and NcML

• Server serves the dataset “wrapped” by the NcML– Client sees OPeNDAP or WCS, not NcML

• Can “fix” metadata problems

• Can augment metadata

• Use NcML aggregation on the TDS– replaces the old “Aggregation Server”

HTTP Tomcat Server

TDS and Digital Libraries

Datasets

Catalog.xml

otherhost.gov

THREDDS ServerApplication

NetCDF-Javalibrary

•OPeNDAP

•HTTPServer

•WCS

OPeNDAP Server

hostname.edu

OAI HarvesterDL Records

TDS and Digital Libraries

• Framework to add metadata– By hand (collection level)– Automatic extraction from datasets

• Send records to existing DLs– No search

• Both collection and inventory level

Future Plans

• NetCDF-Java– Get API’s stable, docs, runtime plugability– NetCDF-4 (!)– HDF4, HDF-EOS, BUFR (need funding)

• NetCDF-4 C Library– DataTypes too immature to port– NcML?– Java on the server

TDS Future Plans

• Aggregation– Driven by IDD data (motherlode)

• Pluggable Authorization• access control by dataset• Performance• Services

– Coordinate System Verifier (eg CF-1)– Data access– Subset and get netcdf file

File Format#N

File Format#2

File Format#1

CDM

Visualization&Analysis

ConclusionN + M instead of N * M things on your TODO List!

NetCDF file

OpenDAP Server

WCS Service