bes
Updated for version 3.20.6
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This version of the BES requires libdap-3.20.4
See the release page for a complete list of bugs fixed in this release.
Hyrax 1.16 has prototype support for subset-in-place of HDF5 and NetCDF4 data files that are stored on AWS S3. See the preliminary documentation in https://github.com/OPENDAP/bes/blob/master/modules/dmrpp_module/data/README.md.
The new support includes software that can configure data in S3 and on disk so that it can be served (and subset) in-place from S3 without reformatting the original data files. Support for other web object stores besides S3 has also been demonstrated.
We have added support for Datasets served by Hyrax now provide information Google and other search engines need to make these data findable. All dataset landing pages and catalog navigation (contents.html) pages now contain embedded json-ld which crawlers such as Google Dataset Search, NSF's GeoCODES, and other data sensitive web crawlers use for indexing datasets. In order to facilitate this, certain steps can be taken by the server administrator to bring the Hyrax service to Google (and other) crawlers attention. LINK TO JSON-LD README.MD. Our work on JSON-LD support was funded by NSF Grant #1740704.
We have added experimental support for STARE (Spatio Temporal Adaptive-Resolution Encoding) as part of our work on NASA ACCESS grant 17-ACCESS17-0039.
The BES uses a number of configuration files, and until now, a site has to customize these for their server. Each server installation would overwrite those files. No more. Now you can put all your configuration values in
/etc/bes/site.conf
And be configent that they will never be overwritten by a new install. The site.conf
file is always read last, so parameters set there override values set elsewhere.
A new cache has been added to the BES for Metadata Responses (aka, the MDS or Metadata Store). This cache is unlike the other BES caches in that it is intended to be operated as either a 'cache' or a 'store.' In the latter case, items added will never be removed - it is an open-ended place where metadata response objects will be kept indefinitely. The MDS contents (as a cache or a store) will survive Hyrax restarts.
The MDS was initially built to speed responses when data are stored on high- latency devices like Amazon's S3 storage system. We have special features in Hyrax to handle data kept on those kinds of data stores and the MDS can provide clients with fast access to the metadata for those data very quickly. After our initial tests of the MDS, we decided to make it a general feature of the server, available to data served from data stored on spinning disk in addition to S3.
Note: The MDS is not used for requests that using server-side function processing.
The MDS configuration can be found in the dap.conf configuration file. Here are the default settings:
DAP.GlobalMetadataStore.path = @datadir@/mds DAP.GlobalMetadataStore.prefix = mds
DAP.GlobalMetadataStore.size = 200
DAP.GlobalMetadataStore.ledger = @datadir@/mds_ledger.txt
For datasets that contain geo-spatial data, we now provide the option to get those data (and related metadata) encoded using the covjson format. (See https://covjson.org/). Thanks to Corey Hemphill, Riley Rimer, and Lewis McGibbney for this contribution.
It has long been possible to define 'catalogs' for data that reside on other kinds of data stores (e.g., relational data base systems). The datasets defined by these catalogs appear(ed) in the directory listings as if they are directories of data files, just like datasets that actually are files on a spinning disk.
We have generalized this system so that it is much easier to use. As an example of new Catalog sub-system's ease of use, we have implemented a new module that reads information about datasets from NASA's Common Metadata Repository (CMR) and uses that to display a Virtual Directory for NASA data, where the hierarchical relationships between data files is derived entirely from data read a CMR-support web API.
This software is currently available in source form only - contact us if you would like to extend the BES Catalog system for your own data collections. To build Hyrax with this feature enabled, build either in developer mode (./configure ... –enable-developer) or using the spepcial configuration option –enable-cmr.
CF option:
BESInterface/XMLInterface improved
Testing/Logging Improvements
New Server function: range() This function returns the min and max values of a variable and, for a vector, a boolean indicating that it is monotonic.
GeoTiff file can now be aggregated.
See NEWS for more information.
New features:
This release fixes a number of bugs:
Added support for cached metadata objects.
Server functions can now return multiple values using specially-named Structure variables.
The code now builds using gcc-6.
See NEWS for other details.
See the INSTALL file for build instructions, including special instructions for building from a (git) cloned repo. This code can build one of two distinct ways and that requires a tiny bit setup.
For more information on Hyrax and the BES, please visit our documentation wiki at docs.opendap.org. This will include the latest install and build instructions, the latest configuration information, tutorials, how to develop new modules for the BES, and more.
This version has significant performance improvements for aggregations, particularly those that use the JoinNew directive.
Contents
The code on the master branch now supports both DAP2 and DAP4 responses, and the data format handlers do as well. Because of that, it must be linked with libdap 3.14, not libdap older versions of libdap (libdap 3.14 contains support for both DAP2 and DAP4, while the older 'libdap' supports only DAP2). If you need to get the DAP2-only version of the software, use the branch named 'dap2'. Please commit only fixes there.
Each of the handlers, which can be built as submodules within this code, also has DAP2 and DAP4 support on their master branch and a 'dap2' branch for the DAP2-only code.
Here there's a bes-config script which will be installing in $prefix/bin that can be used to determine where the libraries and their header files have been installed. This directory also contains some documentation files.
dispatch: This is where the bulk of the BES source code resides. server: The BES server and standalone executables; build using dispatch cmdln: A command line client which can communicate with the bes server.
dap: A module that implements the (OPeN)DAP access.
modules: All the modules that are part of a standard Hyrax distribution. The configure script looks for their dependencies and only tries to build the ones that can be built. Note that the HDF4 and 5 modules are pulled in from separate git repositories.
xmlcommand: The BES/dispatch software is a framework. The basic commands recognized by it are defined and implemented by software in this directory.
standalone: The 'standalone version of the server; used for testing.
apache: An Apache module, currently not part of the default build
ppt: The PPT implementation. The BES uses PPT for its communication
templates: A collection of source files which can be used as templates when you write your own handlers/modules, et cetera.
conf: Where the automake and autoconf configuration files live
docs: Where some bes documentation resides
The latest and most comprehensive Hyrax documentation is here.
The BES API Documentation is here
Once the BES software has been installed, you will need to make a few changes to the BES configuration file, which is the bes.conf located in prefix/etc/bes/bes.conf
. Module and handler configuration files will be installed in the prefix/etc/bes/modules
directory.
Only a few parameters need to be modified to get the BES up and running for the first time. These parameters are located at the top of the configuration file are are:
BES.ServerAdministrator
BES.User=user_name
BES.Group=group_name
BES.LogName=./bes.log
With this configuration you will be able to start the BES. No handlers or modules have been installed yet, so you won't be able to serve data, but the BES should run.
For the BES to run with Hyrax, additional changes will need to be made to the dap.conf and dap-server.conf files, which are located in the modules directory prefix/etc/bes/modules
. The dap module should be installed by default with the BES. If the dap.conf file is not found, be sure that you have libdap installed. The dap-server module, known as the General purpose handlers, adds responses for the DAP ascii response, the DAP info response, and the DAP html form response. You will need to get the dap-server module. You should see a dap-server.conf file in the modules directory.
The changes required for Hyrax are:
BES.Catalog.catalog.RootDirectory = path_to_root_data_directory
BES.Catalog.catalog.Include=;
BES.Catalog.catalog.Exclude=^..*;
The only possible configuration parameter that you may need to change is the one that maps a file to a data handler. This parameter is called BES.catalog.TypeMatch, and is found in each of the data handler configuration files, such as nc.conf. The default values should work.
The value of this parameter is a semicolon separated list that matches the name you used in the BES.modules parameter with different datasets. The BES uses regular expressions to identify different types of datasets. In the example given in the file, any dataset name that ends in '.nc' will be accessed using the netcdf hander (because the name 'nc' is used here with the regular expression '.*.nc'; note that the BES uses regular expressions like Unix grep, not file globbing patterns like a command shell). Since the name 'nc' was associated with the netcdf module in the modules section, the netcdf module will be used to access any dataset whose name that ends in '.nc'.
The regular expressions shown in the examples are simple. However, the entire dataset name is used, so it's easy to associate different modules with datasets based on much more than just the 'file name extension' even though that is the most common case.
To test your regular expression for the TypeMatch parameter, or the Include and Exclude parameters, use the supplied besregtest program. Simply run besregtest to discover its usage.
By default, The BES for Hyrax comes with a suite of handlers that read a number of data formats. However, you can install custom handlers that are not distributed by default. I'll use the SQL handler as an example.
Get the SQL handler source code from http://github.com/opendap/, making sure that the version supports Hyrax. Expand the tar.gz file and follow the instructions with the following caveat: If you have installed the BES using a prefix other than /usr/local (the default), make sure that the correct bes-config is being run. If you are having problems compiling or linking the handler, try using not only –prefix=... but also –with-bes=... when you configure the handler.
Once built, install the handler using 'make install'. This will install the BES module and a configuration file to use for that module. Each module will have its own configuration file. In this case it is nc.conf and installed in the prefix/etc/bes/modules
directory. The next time the BES is run, this configuration file will be read and the netcdf module loaded. No modifications are necessary.
To test the server, open a new terminal window and start the bes by using the bes control script besctl, which is installed in prefix/bin
. using the -c switch to name the configuration file. If the server standalone starts correctly it should print something like the following to stdout:
Go back to your first window and run the bescmdln program. Use the -h (host) and -p (port) switches to tell it how to connect to the BES.
Try some simple commands:
Note that all commands must end with a semicolon except 'exit'.
Now try to get a DAP response using a handler you registered (the BES supports a fairly complex syntax which I won't explain fully here):
If you got something similar (you would have used a different dataset name from "data'nc'fnoc1.nc" and thus would get a different DAS response) the BES is configured correctly and is running.
To stop the BES use the bes control script with the stop option:
Note: Constraints and the bes command line client
Constraints are added to the 'define' command using the modifier 'with' like so:
If there is a list of containers instead of just one, then there can be a list of <container>.constraint="" clauses.
The OPeNDAP BES code is copyrighted using the GNU Lesser GPL. See the file COPYING or contact the Free Software Foundation, Inc., at 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. Older versions of the BES were copyrighted by the University Corporation for Atmospheric Research; see the file COPYRIGHT_UCAR. The BES uses PicoSHA2 - a library that provides an implementation of the SHA256 hashing algorithm; its copyright follows Copyright (C) 2017 okdshin Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.