2017-07-19

Accessing RDA OPeNDAP endpoints with authentication

All RDA OPeNDAP supported datasets found under https://rda.ucar.edu/thredds now require user authentication for access.  Here are details on how to configure your system, such that most applications including NCL, will work properly with the authentication step (these instructions are based on what is provided by the hdfeos group):

1. RDA Registration and Setting Up Cookies

NCAR RDA OPeNDAP server access requires user registration and cookies. If you do not have RDA Login, please register first and have RDA username and password ready.

Once you have RDA Login username and password, and verify that they work by logging into https://rda.ucar.edu, you need to set up cookies to access data.  We highlight the key steps here.

To set up cookies properly, you will need the following 3 files in your home directory (e.g., /home/rdahelp on Linux or /Users/rdahelp on Mac assuming that rdahelp is your UNIX system's login name).
  1. /home/rdahelp/.netrc
  2. /home/rdahelp/.rda_cookies
  3. /home/rdahelp/.dodsrc
1.1 CREATE .NETRC FILE FOR LOGIN / PASSWORD
The first file .netrc should have RDA login and password. For example, if your username is rdahelp and password is 1234abcd, the file should have the following line.
machine rda.ucar.edu login rdahelp password 1234abcd
Please edit the above file to match your username and password. Since the file contains the password, make sure that others cannot see it by changing permission.


$chmod go-rwx /home/rdahelp/.netrc
1.2 CREATE .RDA_COOKIES FILE USING CURL OR WGET
The second file, .rda_cookies, should be created automatically by either wget or curl command.
If you like to use wget, issue the following command to create the cookie file. 
$wget --load-cookies ~/.rda_cookies --save-cookies ~/.rda_cookies --auth-no-challenge=on --keep-session-cookies https://rda.ucar.edu/thredds/dodsC/files/g/ds083.2/grib1/2000/2000.02/fnl_20000201_06_00.grib1.dds -O test.dds
If you like to use curl, issue the following command to create the cookie file. 
$curl -n -c ~/.rda_cookies -b ~/.rda_cookies -L -g --url https://rda.ucar.edu/thredds/dodsC/files/g/ds083.2/grib1/2000/2000.02/fnl_20000201_06_00.grib1.dds -o test.dods
If the above command succeeds, you will get the following output when you check the content of test.dods file.
$more test.dods
Dataset {                                                        Int32 LatLon_Projection;                                    Float32 lat[lat = 181];                                          Float32 lon[lon = 360];                                                         ... }files/g/ds083.2/grib1/2000/2000.02/fnl_20000201_06_00.grib1
If you don't see the above output, your login/password and system is not working properly with NCAR RDA OPeNDAP server. You cannot access data until this step works. If you get the same output, you can delete the temporary output test.dods file.
1.3 CREATE .DODSRC FILE FOR .NETRC AND .RDA_COOKIES FILES
The final step is to create .dodsrc file if you don't already have one and add the following lines.
HTTP.COOKIEJAR=/home/rdahelp/.rda_cookies
HTTP.NETRC=/home/rdahelp/.netrc

2. Test NCL open and read of OPeNDAP data (NCL version 6.4.0 is required)

The following example shows an example of how to test if NCL can open and read an OPeNDAP file after the above steps have been completed.
$ ncl                                                             ncl 0> f = addfile("https://rda.ucar.edu/thredds/dodsC/files/g/ds083.2/grib1/2000/2000.02/fnl_20000201_06_00.grib1","r")                     ncl 1> print(f)                                               Variable: f                                                       Type: file                                                         filename:    fnl_20000201_06_00                                   path: https://rda.ucar.edu/thredds/dodsC/files/g/ds083.2/grib1/2000/2000.02/fnl_20000201_06_00.grib1                                         file global attributes:                                              Originating_or_generating_Center : US National Weather Service, National Centres for Environmental Prediction (NCEP)          Originating_or_generating_Subcenter : 0                            GRIB_table_version : 0,2                                          ... etc                         
In the above code, the url points to the remote FNL file being served by OPeNDAP. Use print command to check if the url file is opened successfully and to see what variables are available inside the file.

2017-07-18

All RDA data transfer and processing services restored to production

All RDA data transfer and processing services have been restored to production.  Thank you for your patience during the service outage.  Please let us know if you experience any continued problems.

2017-07-10

RDA Service Outage July 14-18, 2017

All RDA data access, processing, and distribution services will be unavailable during system maintenance scheduled to take place from 5AM MDT, Friday, July 14 until 9AM MDT, Tuesday, July 18.

RDA web interface supported data discovery and request process submission capabilities are expected to remain online during this maintenance window.

Please note that if you have custom data requests where the data will expire during the outage, you can go into your user dashboard and extend the dates so that you can resume downloading when services are restored.  In your dashboard, under "Customized Data Requests", click the calendar icon next to the specific request that you want to extend.

An update will be posted when all services come back online. We apologize for the inconvenience.


2017-05-03

RDA web services down for maintenance at 1PM MDT on May 3, 2017

All RDA web services will be down for maintenance starting at 1PM MDT on May 3, 2017.  We hope to have these services back online within 2 hours of the start of the downtime.  We apologize for the inconvenience.

2017-04-26

Transferring custom file lists with Globus

The RDA has supported Globus file transfers for over two years, which enables users to transfer data files from RDA datasets to their destination endpoint using the Globus data transfer service (see http://ncarrda.blogspot.com/2015/06/transferring-rda-data-with-globus.html for details).  Transferring files using Globus is an efficient, reliable, and secure method to transfer large amounts of data from one endpoint to another.

But what if you're interested in a smaller or specific collection of files within a dataset?  In this scenario, the user would navigate to the Globus web app transfer interface and then browse through the files on the RDA shared endpoint to locate the files of interest.  This workflow, however, is not ideal from a search and discovery perspective, since users don't have the convenience of filtering the file sets via faceted browsing or viewing the supporting metadata alongside each file listed on the Globus web interface.

The standard Globus web app transfer interface.  In this workflow, users must browse through the full set of files within a RDA dataset to locate specific files to be transferred.

The good news: RDA users now have the ability to select and initiate Globus transfers of custom file sets directly from the RDA web interface without having to search for the files on the Globus transfer interface.  This method of transferring data uses the Globus Browse Endpoint helper API, and the only step required to be done by the user on the Globus web app is to select the destination endpoint that will receive the data files in the transfer.  The advantage to this approach is users are able to make use of the faceted search and discovery tools on the RDA website and avoid the bottleneck of making "blind" searches of the files on the Globus web interface.

How to make a Globus transfer of custom file sets


Starting from any RDA dataset page, go to the 'Data Access' tab, then select the 'Web file listing' link associated with any of the data products listed.  At this point, you may choose either the 'Faceted browse' or 'Complete file list' option, and then follow the instructions to locate your files of interest.

Procured file lists using the 'Complete file list' (left) and 'Faceted browse' search function (right) on the RDA website. Once a collection of files has been selected, the user initiates a Globus transfer by selecting the 'Globus' button.

To initiate a Globus transfer, select the files you wish to download, then select the 'Globus download' button.  This will redirect you to the Globus web app where you will authenticate with Globus and select the destination endpoint that will receive the data files.  After a destination endpoint has been chosen, select the 'Submit' button.  You will then be redirected back to the RDA website, at which point the data transfer will be submitted on your behalf.  A status message displaying the status of your data transfer will appear, and a notification e-mail will be sent to your RDA user e-mail address when the transfer has successfully completed.

The browse endpoint interface on the Globus web app, where users select the destination endpoint.

As a reminder, RDA users can log into the Globus web app with their RDA user e-mail login and password credentials; this is the recommended method for logging into Globus.  To do this, simply choose the 'NCAR RDA' organizational login on the Globus login page.

2017-03-23

Integrating RDA data processing capabilities into a workflow

Do you have a workflow that leverages repeated subset requests from an RDA dataset or would you like to avoid continually filling out web forms? Would you like to download data once a request is ready without checking your email?  The RDA provides the capability for users to submit subset requests and download data programmatically through the external applications API.  The API provides users with the following capabilities:

  • Get a summary of datasets that have subsetting available
  • Get a list of parameters available for subsetting by dataset
  • Submit a temporal, spatial, parameter subset request from a dataset
  • Check on data request processing status
  • Get a list of output files found in a completed data request (supports data transfer)
  • Set up a Globus endpoint share for a completed data request
  • Purge data request

A complete description of API capabilities is described here.

A couple of example applications have been developed in python that utilize the capabilities provided through the API.


  • rdams-client.py:  The rdams-client python utility can be run by registered RDA users to get parameters available for subsetting by dataset, to submit subset requests on select gridded data sets, to check on the processing status of any subset request, and to download completed request output files to a local system.   This utility may be useful to users who want integrate data subset request submission and download as part of a broader workflow. Download and execute './rdams-client.py -help' for more details (make sure to set 'rdams-client.py' as executable).  For additional information, see the CISL rdams documentation page.
  • rda-request-manager.py:  The rda-request-manager python utility can be run by registered RDA users to check RDA data request processing status, download completed request output files to a local system, and purge request files from the RDA data server.  This utility may be useful to users who submit any type of request through the web interface (subset, file format conversion, or restage data from tape for download), and would like to create a cron job to check on request processing status, and download requests as they become available, instead of waiting for email notifications and downloading data through the web interface.  Download and execute './rda-request-manager.py -help' for additional information (make sure to set 'rda-request-manager.py' as executable).

2017-03-21

All RDA data access services back online

All RDA data access services provided through the RDA web server are back online.  Subset and format conversion request processing services will remain offline through much of the afternoon, so submitted requests will hold at status "queue" until these services become available later today.

2017-03-17

All RDA data services unavailable on Tuesday, March 21

All RDA services will be taken offline to facilitate system maintenance on Tuesday, March 21.  The RDA web server (https://rda.ucar.edu) will be inaccessible during this maintenance window.  We apologize for the inconvenience.

2017-03-08

Disk Cleanup & Faster Data Transfers

Our transfer disks have been averaging 90% full. Occasionally, it has been so full that processing of new data orders has to be halted until there is more space.

In the interest of keeping your data requests flowing, we ask that you purge your data to free up disk space after you have downloaded it. Just click on the 'Purge request' button to let us know you are done.

Click on 'Purge request' after you download your data.
Please request data in chunks that you can reasonably download in the default 5 day expiration limit.

Users experience faster data transfer speeds using globus.

A few RDA users work in regions where internet speeds are especially slow. Just let us know and we can extend the 5 day expiration limit for you.  Also, consider having data shipped out to you on a hard drive.

2017-03-03

The RDA User Dashboard

One of the "perks" that you get when you register with the RDA (besides the primary one - access to data) is that everything related to your data access activities can be presented to you in a convenient dashboard. To access the dashboard, sign in to the RDA and then click the "dashboard" link at the top of the page next to your username:


In your dashboard, you will see several sections, as shown below:
I'll go through these sections in detail, one-by-one.

User Profile
Click the "Edit/Change Profile" button to open your user profile and make changes to it. You can change your email address, password, and affiliation, and you can gain access to restricted data (if you meet the requirements for access).

Bookmarked Datasets
In this section, you will see a list of all of the datasets that you have bookmarked. You can click a dataset title in the list to go directly to that dataset.

You can bookmark a dataset by clicking the hollow star next to the dataset ID (under the title) on a dataset description page:

Once bookmarked, the star will change to solid gold and the bookmark will appear in your list of bookmarked datasets. You can remove a bookmarked dataset from the dashboard, or by clicking the gold star on the dataset description page.

Customized Data Requests
Customized data requests are special requests for data that you make. These may be subsets of the data, staging of files that only reside in our tape archive, or requests to convert from the native data format to some other format. You can manage various aspects of your data requests from the dashboard:

  • Click the calendar to change the "Available Until" date. By default, data from special requests are purged (removed) from our server 5 days after they are prepared. You can extend the date by as much as two weeks, and you may request multiple extensions.
  • Click the "X" if you have finished downloading your data and you want to remove the request from your list (this will also remove the data from our server).
  • Click the envelope if you have any questions about your request. This will allow you to send a message to the dataset specialist.
You can navigate to your data request by clicking either the request number or the status (if the status is "Completed").


Globus Endpoints Shared With You
If you have requested any Globus transfers, for whole datasets and/or your customized data requests, then the shares will appear in this list. To start a data transfer, you can navigate to Globus by clicking the URL for a particular share. You can delete shares that you no longer need by clicking the "X".

Customized OPeNDAP Aggregations
Any customized OPeNDAP aggregations that you have created will appear here. You can copy and paste the URL of your aggregation into your OPeNDAP aware tools and scripts. You also can manage your aggregations:

  • Click the magnifying glass to see more detailed information about your aggregation
  • Click the "X" to delete the aggregation from your list (this will also remove the aggregation from our server)
  • Click the blue circle arrow to extend the expiration of your aggregation. Note that this option will only be available if the current date is within 7 days of the aggregation expiration. Aggregations, by default, expire 28 days after they are created, unless you request an extension. You may request multiple extensions.


Data Citation
We strongly encourage users to cite their data source(s) in published literature. Two key components of a data citation are the dataset title and the access date. You can use our data citation tool to get a citation for your data that you can use in your publication:
To begin, you need to either know the dataset that you want to cite, or the approximate date that you downloaded data from us.

If you know the dataset, click the "By Dataset" tab.

  • You will see a list of all datasets that you have downloaded from the RDA. Click the specific dataset that you want to cite. You will then see a year/month calendar for all of your accesses. For many accesses over time, the suggestion is to choose the most recent access. Click the month to get a calendar for that month. When you click a specific day, a data citation will be generated.


If you know the approximate date, click the "By Date" tab.

  • You will see a year/month calendar showing you when and how many times you downloaded data from the RDA. Click the month that you downloaded the data that you want to cite. You will then see a list of datasets that you downloaded in that month. Hopefully you will recognize that dataset that you want to cite from this list. Click the specific dataset to get a calendar for the month, and then once you click a specific day, a data citation will be generated.

Over time as we develop new services, you will see new sections appear in the dashboard. So when you need more time to download a dataset subset that you have requested, or you want to jump quickly to a dataset that you have previously used (and bookmarked), remember the RDA user dashboard.