Tim Pugh-SPEDDEXES 2014

How OPeNDAP has transformed the way we do science plus snapshots of
recent developments and BoM‟s operational systems built on this technology
Tim Pugh
SPEDDEXES workshop
17-21 March 2014

Evolution
• Traditionally…
– Scientific research is conducted in a quiet room in isolation
utilising unique data, scripts, and code
– Scientific collaboration is conducted at conferences with file
sharing by FTP or HTTP bulk download
• Today
– Scientific research is being driven to shared research services
and supported infrastructure
• To relieve the scientist of laborious developments
• To manage more complex machinery
• To improve scientific integrity and collaboration
• To work within managed and supported infrastructure
– Science is moving from file sharing to data sharing collaboration

CAWCR Research Data
Server
• Location: http://opendap.bom.gov.au:8080/thredds
• Unidata THREDDS Data Server v4.2.8
• http://www.unidata.ucar.edu/projects/THREDDS/tech/TDS.html
• The THREDDS Data Server (TDS) is a JavaSevlet, and is contained in a single
war file, which allows very easy installation into Tomcat web server.

OPeNDAP Now Is:
• An acronym
– “Open-source Project for a Network Data Access
Protocol”
– Often a synonym for “DAP”
• A not-for-profit corp. developing/supporting
– “DAPx” - a web-services protocol for data access
• Deployed by hundreds of data providers internationally
• Employed in many analysis packages (MATLAB, e.g.)
• Designated a “Community Standard” by NASA
– Server & client implementations* of DAP
*Note: there are other implementations

BROAD VISION
1. A world in which a single data access protocol is used for the
exchange of data between network-based applications regardless
of discipline.
2. A layer above TCP/IP providing for syntactic and semantic
consistency not available in existing protocols such as FTP.

Fundamental Objective
of OPENDAP
• The fundamental objective of OPeNDAP and OPeNDAP Inc. is to
facilitate internet access to scientific data
• This is done by:
• Providing a protocol (DAP) to access data over the internet,
• Hiding the format (and organization) in which the data are stored from
the user, and
• Providing subsetting (and other) capabilities for the data at the server
• OPeNDAP is based on a multi-tier architecture
• OPeNDAP software is open source

OPeNDAP Data-Type
Philosophy
the OPeNDAP data model has few data types
simplified programming/lowered risk of errors
they are intentionally discipline-neutral
better trans-domain utility & programmer uptake
they nonetheless fill discipline-specific needs
netCDF-like (good in contexts where, e.g., data might
represent functions with 4- or 5-D domains)
sequences & selections match dbms sensibilities

TDS Server
• TDS is THREDDS Data Server
– THREDDS is Thematic Real-time Environmental Distributed Data Services
– Middleware to bridge the gap between data providers and data users
– THREDDS Data Server (TDS), a web server that provides catalog, metadata,
and data access services for scientific datasets.
– The TDS is open source, 100% Java, and runs inside the open source Tomcat
Servlet container.
• Unidata‟s Common Data Model
– merges the OPeNDAP, netCDF, and HDF5 data models to create a common API
for scientific data
– implemented by the NetCDF Java library
– read netCDF, OPeNDAP, HDF5, HDF4, GRIB 1 & 2, BUFR, NEXRAD 2 & 3,
GEMPAK, MCIDAS, GINI, among others
– A pluggable framework allows other developers to add readers for their own
specialized formats.
– provides standard APIs for geo-referencing coordinate systems, and specialized
queries for scientific feature types like Grid, Point, and Radial datasets

Some of the Technology
in the TDS
1. THREDDS Dataset Inventory Catalogs provide virtual directories of available data and
associated metadata.
2. The Netcdf-Java/CDM library reads NetCDF, OpenDAP, and HDF5 datasets, as well as other
binary formats such as GRIB and NEXRAD, essentially an (extended) netCDF view of the data.
3. TDS can use the NetCDF Markup Language (NcML) to modify and create virtual aggregations of
datasets.
4. An integrated server provides OPeNDAP access with subsetting data access method.
5. An integrated server provides bulk file access through the HTTP protocol.
6. An integrated server provides data access through the OpenGIS Consortium (OGC) Web
Coverage Service (WCS) protocol, for any "gridded" dataset whose coordinate system
information is complete.
7. An integrated server provides data access through the OpenGIS Consortium (OGC) Web Map
Service (WMS) protocol, for any "gridded" dataset whose coordinate system information is
complete.
8. The integrated ncISO server provides automated metadata analysis and ISO metadata
generation.

THREDDS Catalog
• The goal is…
– to simplify the discovery and use of scientific data and to allow scientific
publications and educational materials to reference scientific data.
– initial focus was to allow data users to find datasets that are pertinent to their
specific education and research needs, access the data, and use them without
necessarily downloading the entire file to their local system.
– Catalogs are the heart of the data access services, and is the THREDDS
concept. Catalogs consist of XML documents that describe on-line datasets.
– Catalogs can contain arbitrary metadata, however we also defined a standard set
of metadata to bridge to discovery centers
• CF (Climate & Forecast) and Unidata Data Discovery metadata

Spectrum of
Use Cases
Application Data
Representation
OGC data model
domain specific
geospatial, 1-D, 2-D
DAP2 data model
domain neutral
n-D, time series
**DAP4 data model
domain neutral
new data types and data
structures
streaming, compressed,
chunked
Common Data Model (CDM)
domain specific
Future data model
domain neutral??
Application Types
Programmatic / Langauge
API
FORTRAN, C/C++, JAVA,
Python, NetCDF, Java NetCDF
Programmatic / Tools
NetCDF, NCO, PyDAP
Custom Tools: OPeNDAP
crawler, ocean_prep
Interactive Data Viewer
IDV, Panolopy, IDL, MATLAB,
iPython (matplotlib), NCL, web
browser (metadata)
Interactive Analysis
MATLAB, IDL, iPython, NCL
Custom Application: Inudation
Modeller
Web Application
Live Access Server
IMOS Data Portal (WMS)
Custom Java Servlet
Programming
DAP2 Legacy Code
existing tools
DAP2 New Code
New tools
**DAP4 programming
legacy code support
**DAP4 programming
new data model and protocols
streaming support
**DAP4 programming
Asynchronous access modes,
server-side processing
Data Access
Protocol
Metadata Request
das, dds, ddx
ASCII/Binary Data Request
Simple data representation
DAP Binary Object Request NcML Data Request
aggregation, virtual data sets
**DAP4
server-side operations, async
access mode, new data model,
posting
Syntax
Return data set info
file.nc.dds - readable
file.nc.ddx - XML
file.nc.asc - ASCII data return
Select variables
file.nc.dods?var1,var2,var3
subset arrays
file.dods?var1(0:1:10)
Return file translations
file.nc.netcdf - NetCDF file
Server-side operations
file.nc?GEOLOC()
Async access mode
??
Clients
Programmatic Access
Tsunami inudation modeller,
NetCDF,
NCO, PyDAP, PyNetCDF,
MATLAB, IDL, …
Interactive Access
Web browser - Catalog
MATLAB, IDL, Python,
Panolopy,…
Data Library & Catalog
Service
metadata harvesting
directory listings
remote THREDDS services
Web Service
Java servlet, Java applet
Geospatial Information Service
OPeNDAP data service
Analysis Service
Live Access Server
Service Capabilities
DAP2 response
metadata, dods, ASCII / Binary
**DAP4 Response
async access mode, server-
side, streaming,
NcML
Aggregation service
Virtual Data Set Service
Remote Data Access
Metadata Conversion and
RDF
metadata definitions,
translations (-> ISO) sematics,
ontalogy
CF->ISO, CF->WMS, CF->WCS
Layered Services
Catalogue service
WMS, WCS services
Authentication
Conformance checks
CF metadata check
ISO metadata check
**DAP4 features listed is my estimation and not the official specification

Use Case limitations
• Time to access data is dependent on the following
factors:
• Hardware and network performance
• Selection of variables and dimensions
• Number of data requests to be issued
− Latency inherent in the data request
• Number of concurrent accesses to the server

DAP-enabled client
tools/applications
OPeNDAP Clients (partial list) http://opendap.org/whatClients
1. Web browser returning ASCII data
2. Pydap - is a pure Python library implementation of the DAP2
3. NetCDF - is a set of software libraries and self-describing, machine-
independent data formats with interfaces to Python, FORTRAN, C/C++,
and Java languages
4. NCO – comprises a dozen standalone, command-line programs that take
netCDF files as input
5. MATLAB – a high-level technical computing language and interactive
environment for algorithm development, data visualization, data analysis,
and numerical computation
6. Panoply – Panoply is a cross-platform application which plots geo-gridded
arrays from netCDF, HDF and GRIB datasets.

Developments by
Bureau and CSIRO
• Development of web portals for data access services and
information systems in climate and environment
– Seasonal Climate Outlook Rebuild (Roald de Wit)
– Natural Resource Management (NRM) Climate Change Portal (Tim
Erwin)
– eReef‟s Marine Quality Dashboard and data services (Jonathon Hodge)
– National Environmental Information Infrastructure (NEII) (Andrew Woolf)
– CAWCR research data services (Duan Beckett)
• Establish Climate Data Publishing services at NCI
– NCI, CSIRO, Bureau of Meteorology, CoE CSS
– Earth System Grid (ESG)
– Climate and Weather Science Laboratory (CWSLab)

Project overview
• More interactivity and functionality needed
• Demand for POAMA multi-week forecast products
• Long term view of seamless transition
between forecasts
• Building upon experiences /
technologies from other BoM
projects
(e.g.MetEye and PASAP/PACCSAP)

SCO-R architecture
MapCache
BOM.Map / BOM.App
Custom WMS Service
(Python)

Climate Futures
Climate Futures approach to the provision of regional climate projection information
CMAR/CLIMATE ADAPTATION FLAGSHIP
Tim Erwin
Acknowledgements: Penny Whetton, Kevin Hennessy, John Clarke, David Kent
28 October 2013

Climate Data
• Processed from climate model data (CMIP3 and CMIP5)
• NetCDF file format
• 10 variables (temperature, rainfall, humidity...)
• 20 year seasonal averages (2030, 2035, ..., 2090)
• Base period (1950 – 2005) stored as monthly time span
• Catalogued in THREDDS server
– Allows DAP access
• Django
• THREDDS catalogues are parsed and stored
– model, variable, dap url, layer name, time span

ZOO-Project
(WPS Server)
• Consists of: Kernel, API, Service
• Works with Apache through a cgi file and a conf file
• Support several common programming languages C/C++,
Fortran, Python, PHP, Perl, Java, JavaScript
• Used to create area average of gridded data using non-
rectangular mask
• Predefined mask
• Polygon (GML,KML,GEOM)
• Not limited to geographic operations

OPeNDAP Technology
Developments
• DAP4 protocol and data model implementation (OPULS)
– OPULS (an OPeNDAP-Unidata collaboration)
– DAP4 (to supersede DAP2)
– Experimental extensions (Async access, UGRID subsets)
• DAP2 & DAP4 JSON response type
– Improve javascript client utilisation of DAP services
• ncWMS integration and WMS extensions
– contour map types
– THREDDS and Hyrax integration of ncWMS
• Programmatic Data Access for secure services
– RDSI DaSh project to support programmatic data access
– Integration within reX Identity and Authorisation Management

DAP4 Experiments
• DAP4 provides more complete support for functions
including metadata responses (DAP2 does not provide
this; a gap in the DAP2 specification)
– Experiments with Unstructured Grid (irregular mesh) subsetting
– Binning: returns a distribution (as a raster of boolean values on a
user-specified grid) of data values satisfying some criteria
– Masking: accepts a raster of zero/nonzero values as a query
argument, perhaps as a geospatial selection criterion
• OPeNDAP are running several experimental mini-
projects within its context:
– Asynchronous access, data streaming, cloud computing and an
expanded, function-based, server-side processing system

thank you – have a great experience
Tim F. Pugh
HPC and CWSLab Project Lead
Melbourne, Victoria, Australia
Email: t.pugh@bom.gov.au
Office: +61 3 9669 4345

Workshop
Use-Cases
Application Data
Representation
DAP2 data model
domain neutral
n-D, time series
Application Types
Programmatic / Langauge
API
FORTRAN, C/C++, JAVA,
Python, NetCDF, Java Netcdf,
PyDAP
Programmatic / Tools
NetCDF, NCO, PyDAP
Custom Tools: OPeNDAP
crawler
Interactive Data Viewer
Panolopy, MATLAB, NCL, web
browser
Programming
DAP2 Legacy Code
existing tools:
DAP2 New Code
New tools
Data Access
Protocol
Metadata Request
das, dds, ddx
ASCII/Binary Data Request
Simple data representation
DAP Binary Object Request NcML Data Request
aggregation
Syntax
Return metadata info
file.nc.das - readable
file.nc.dds - readable
file.nc.ddx - XML metadata
file.nc.help - help info
Select vars and return data
file.nc.asc?var1,var2,var3
file.nc.dods?var1,var2,var3
subset arrays, return data
file.asc?var1(0:1:10)
file.dods?var1(0:1:10)
Return file translations
file.nc.netcdf - NetCDF file
Server-side operations
file.nc?GEOLOC()
Clients
Programmatic Access
NetCDF, NCO, PyDAP,
PyNetCDF
Interactive Access
Web browser - Catalog
Python, MATLAB, Panolopy
Service Capabilities
DAP2 response
THREDDS data service
Hyrax data service
NcML
Aggregation service
Layered Services
Catalog service
WMS

Pydap client
• >>> from pydap.client import open_url
• >>> dataset = open_url('http://test.opendap.org/dap/data/nc/coads_climatology.nc')
• >>> var = dataset['SST']
• >>> var.shape
• (12, 90, 180)
• >>> var.type
• <class 'pydap.model.Float32'>
• >>> print var[0,10:14,10:14] # this will download data from the server
• <class 'pydap.model.GridType'>
• with data
• [[ -1.26285708e+00 -9.99999979e+33 -9.99999979e+33 -9.99999979e+33]
• [ -7.69166648e-01 -7.79999971e-01 -6.75454497e-01 -5.95714271e-01]
• [ 1.28333330e-01 -5.00000156e-02 -6.36363626e-02 -1.41666666e-01]
• [ 6.38000011e-01 8.95384610e-01 7.21666634e-01 8.10000002e-01]]
• and axes
• 366.0
• [-69. -67. -65. -63.]
• [ 41. 43. 45. 47.]

NetCDF client
• >>> import netCDF4
• >>> url = 'http://test.opendap.org/dap/data/nc/coads_climatology.nc‟
• >>> dataset = netCDF4.Dataset(url)
• >>> var = dataset.variables['SST']
• >>> var.shape
• (12, 90, 180)
• >>> print var[0,10:14,10:14] # this will download data from the server
• <class 'pydap.model.GridType'>
• with data
• [[-1.26285707951 -- -- --]
• [-0.769166648388 -0.77999997139 -0.675454497337 -0.595714271069]
• [0.128333330154 -0.0500000156462 -0.0636363625526 -0.141666665673]
• [0.638000011444 0.895384609699 0.721666634083 0.810000002384]]
• >>> print var
• <type 'netCDF4.Variable'>
• float32 SST('TIME', 'COADSY', 'COADSX')
• …

MATLAB and SNCtools
• % ex_snctools_opendap.m
• % Read from a remote OPeNDAP server with the same file
• %
• ncRef =
'http://opendap.bom.gov.au:8080/thredds/dodsC/gamssa_4deg/2011/201111
06-ABOM-L4LRfnd-GLOB-v01-fv01.nc'
• nc_dump( ncRef );
• pause
• temp = nc_varget( ncRef, 'analysed_sst');
• lon = nc_varget( ncRef, 'lon');
• lat = nc_varget( ncRef, 'lat');
• imagesc(lat, lon, temp); axis xy

MATLAB and NJTbx
demo
• % ex_njtbx.m
• % Read from a remote OPeNDAP server with the same file
• %
• ncRef =
'http://opendap.bom.gov.au:8080/thredds/dodsC/gamssa_4deg/2011/201111
06-ABOM-L4LRfnd-GLOB-v01-fv01.nc'
• nj_info( ncRef )
• pause
• [temp, grid] = nj_grid_varget(ncRef,'analysed_sst');
• imagesc(grid.lon, grid.lat, temp); axis xy; colorbar

Tomcat/[Apache]
dodsC
fileServer
wms
ncss
THREDDS services
syntax
{contextPath} = “thredds” (servlet default name)
{service} = “fileServer” | “dodsC” | “wms” | “wcs”
• Bulk File Transfer
fileServer = HTTP Server (any file)
• Remote access, subsetting CDM files
dodsC = OPeNDAP (any CDM file)
wms = Web Map Server (grids)
wcs = Web Coverage Server (grids)
ncss = NetCDF Subset Service (grids)
admin = Administration/debug interface
Note, each server can change the service name in
the xml catalogue.
http://{server:port}/{contextPath}/{service}/...
wcs
Catalogs
thredds

Hyrax service syntax
Tomcat/[Apache]
opendap
hyrax
docs
{contextPath} = “opendap” (servlet default name)
{service} = “hyrax” | “admin” | “docs”
hyrax = catalog interface
admin = administration interface (v1.8+)
docs = documentation (v1.8+)
Note, each server can change the service name
within the server configuration file.
http://{server:port}/{contextPath}/{service}/…
http://test.opendap.org/opendap/hyrax/...e.g.
admin

Hyrax Data Service
• DAP2 and DAP3.x as the protocol develops
• Other dataset responses*
• ASCII & NetCDF renderings of data (not limited to
data natively stored in netCDF)
• RDF
• ISO 19115 and the conformance rubric (Hyrax 1.8)
• Other server responses**
• THREDDS catalogs
Tomcat/[Apache]
Hyrax
DAP2
RDF*
Catalogs**
DAP3.x
Note: Hyrax and TDS are not mutually excusive;
Sites can install both with little extra effort.

Data Discovery and
Access
• Data discovery services
• NASA‟s Global Change Master Directory
− http://gcmd.nasa.gov
• IMOS eMII portal
− http://imosmest.aodn.org.au/geonetwork/srv/en/main.home
− Help --> http://emii1.its.utas.edu.au/drupal/?q=node/25
• TERN AusCover portal
− http://data.auscover.org.au/
• My Ocean portal
− http://www.myocean.eu/web/24-catalogue.php
• TPAC Digital Library
− http://dl.tpac.org.au
• Data access services
• Unidata‟s THREDDS Data Service
− http://www.unidata.ucar.edu/projects/THREDDS/
• OPeNDAP‟s Hyrax Data Service
− http://opendap.org/download/hyrax.html
• NOAA‟s ERDDAP Data Service
− http://coastwatch.pfeg.noaa.gov/erddap

Some of the Technology
in Hyrax
1. THREDDS Dataset Inventory Catalogs provide virtual directories of available data and
associated metadata.
2. Supports many formats and data stores: netCDF3, netCDF4, HDF4, HDF5, FreeForm, SQL data
bases
3. Uses a plug-in based architecture and includes tools to write custom handlers
4. NetCDF Markup Language (NcML) to modify and create virtual aggregations of datasets.
5. OPeNDAP access with subsetting data access method.
6. bulk file access through the HTTP protocol.
7. ncISO server provides automated metadata analysis and ISO metadata generation.
8. RDF output - Metadata as triples; used with web-based reasoning systems
9. Code that has passed a formal security audit
10. A true multi-system architecture that can fit in a variety of enterprise settings
11. An administrator‟s interface

DAP Responses
• DAP2 defines three response types:
• DAS: A text document that contains data set attributes
• DDS: A text document that contains data set variable types and names
• DODS: A quasi-multipart MIME document that contains the DDS and
associated binary values for a data request
• DAP3.x defines two additional response types:
• DDX: An XML document that combines both variable type and name
information along with attributes
• DataDDX: A multipart MIME document that combines a DDX with the
associated binary values for a data request
TDS and Hyrax both support DAP2; Hyrax includes support for DAP3, TDS
has support for the DDX

Some Definitions
DAP = Data Access Protocol
 Model used to describe the data;
 Request syntax and semantics; and
 Response syntax and semantics.
 The data structure returned to the user
OPeNDAP
 The software that forms the service;
 Numerous implementations (Hyrax (reference), THREDDS,…);
 Core/libraries for client applications and services.
THREDDS / Hyrax
 A service framework (portal) that contains the OPeNDAP
service;

Decipher the URL
• http://opendap.bom.gov.au:8080/thredds/dodsC/gamssa_4deg/2011/201111
06-ABOM-L4LRfnd-GLOB-v01-fv01.nc.ascii?lon[0:1:1439]
• Given the OPeNDAP data request above, decipher the URL.
− Request Protocol? http
− Host name:port? //opendap.bom.gov.au:8080/
− ContextPath? thredds/
− Service? dodsC/
− Unique path to data set? gamssa_4deg/2009/
− Data reference? 20111106-ABOM-L4LRfnd-GLOB-v01-fv01.nc
− Return type? ascii
− Return variables? ?lon
− Return variable indice range? [0:1:1439] --> [start:skip:end]

NcML
NetCDF Meta Language
NcML can provide two basic features:
• Augmenting/Modifying data sets with new
• Attributes
• Values
• Combining two or more data sets (i.e., files) in an aggregation
Three kinds of aggregation are supported:
• Tile files
• Join files along an existing axis
• Join files along a new axis
While very powerful, these aggregations are not applicable to every
data set made up of multiple files

DAP4 Summary
• DAP (DAP2 and DAP4) is based on datasets built of
variables that share the characteristics of programming
languages
• Constraints are used to subset data on the server
• DAP4 is a REST API
• DAP4 specifies „modern‟ web services
– While DAP2 was a data model only, DAP4 includes specification
of the web services
• DAP4 provides more complete support for functions

Tim Pugh-SPEDDEXES 2014

More Related Content

What's hot (20)

Viewers also liked (7)

Similar to Tim Pugh-SPEDDEXES 2014 (20)

More from aceas13tern (20)

Recently uploaded (20)

Tim Pugh-SPEDDEXES 2014