Earthdata CMR access

Yes, you need to set context with session.
I could confirm that PO.DAAC OPeNDAP server requires session.
Thus, R ncdf4 package needs to do something extra like pydap example does.

-----Original Message-----
From: Ben Tupper <btupper at bigelow.org>
Sent: Thursday, April 14, 2022 7:14 AM
To: Joe Lee <hyoklee at hdfgroup.org>
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] Earthdata CMR access

Well, ncdf4 is a pretty good with OPeNDAP (which is one reason why we love it!)  Below is an example using your handy testing resource.

Hmmm. In your example using pydap, you establish a (credentialed?) session, and then open the OPeNDAP resource within that context?  I don't think I have seen that before in R, at least not for OPeNDAP.
I'll poke around and see if I can find something comparable.


### Start
library(ncdf4)

url <- "https://eosdap.hdfgroup.org:8080/opendap/data/hdf5/grid_1_2d.h5"
x <- nc_open(url)
library(ncdf4)

url <- "https://eosdap.hdfgroup.org:8080/opendap/data/hdf5/grid_1_2d.h5"
x <- nc_open(url)
temp <- ncvar_get(x, varid = "temperature",
                  start = c(2,1),
                  count = c(2,3))
temp
#      [,1] [,2] [,3]
# [1,]   10   11   12
# [2,]   10   11   12
### End


On Wed, Apr 13, 2022 at 10:25 PM Joe Lee <hyoklee at hdfgroup.org> wrote:

Wow, what a great start!



Unlike GES DISC OPeNDAP server,

I think the PODAAC OPeNDAP server that you?d like to access

doesn?t require Earthdata Login credentials.

That eliminates a lot of complications.



My suspicion is that your R ncdf4 package is not built with OPeNDAP support.

Can you check if your R ndf4 package work with our demo OPeNDAP server [1]?

If not, you may want to install ncdf4 with your own netCDF-4 library that enabled OPeNDAP support.



Once [1] works with your R ncdf4,

I think my posting [2] can help you to redirect URLs properly

for NASA credential-enabled OPeNDAP servers.



Good luck and thanks for sharing your code on GitHub!





[1]
https://eosdap.hdfgroup.org:8080/opendap/data/hdf5/grid_1_2d.h5.dmr.ht
ml

[2] https://hdfeos.org/forums/showthread.php?t=821#4



From: Ben Tupper <btupper at bigelow.org>
Sent: Wednesday, April 13, 2022 8:59 PM
To: Joe Lee <hyoklee at hdfgroup.org>
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] Earthdata CMR access



What I have can search for S3 resources, but I happen to focus on OPeNDAP instead.

As far as I can tell, the ncdf4 (and RNetCDF) packages don't provide utilities for establishing credentialed opendap connections.  That is handled by sort of a third party or some kind of wrapper.   Without credentials I can search, but without credentials I cannot open a connection to the opendap resources the search yields.

If I am understanding the error message shown at the bottom of the README (see below), the server is receiving the request but for lack of credentials is refusing access.  I'm stumped.

https://github.com/BigelowLab/cmr



On Wed, Apr 13, 2022 at 2:18 PM Joe Lee <hyoklee at hdfgroup.org> wrote:

Yes, that's the hard part that I'm referring to.

Once you pass that step, you may also want to look at another
example in MATLAB [1] to access PODAAC data on S3 using the temporary token.

I'd really appreciate your effort if you can share a working R-code
project that can both search with CMR and then access NASA data on S3.

Regards,

[1]
https://www.hdfeos.org/zoo/PODAAC/ATM_SURFACE_TEMP_HUM_WIND_PRES_day
_mean_ECCO_V4r4_nc_c.m


-----Original Message-----
From: Ben Tupper <btupper at bigelow.org>
Sent: Wednesday, April 13, 2022 1:09 PM
To: Joe Lee <hyoklee at hdfgroup.org>
Cc: r-sig-geo at r-project.org
Subject: Re: [R-sig-Geo] Earthdata CMR access

Hi,

I was planning to use the httr package or the newish httr2 package which should be able to handle the transactions.  Once a resource is tracked down via search, I plan to use the ncdf4 package to access.

I can add headers to the http requests, so presumably that can include tokens.

But I am finding even the simple stuff like using the API to
generate a token, as shown here
https://wiki.earthdata.nasa.gov/display/EL/How+to+Generate+a+User+To
ken
,  to be challenging.  Thud!

Ben

httr: https://CRAN.R-project.org/package=httr
httr2: https://CRAN.R-project.org/package=httr2
ncdf4: https://CRAN.R-project.org/package=ncdf4

On Wed, Apr 13, 2022 at 1:03 PM Joe Lee <hyoklee at hdfgroup.org> wrote:

Hi,

I'm also interested in the solution that you're seeking since I've
written a Python-equivalent CMR+OPeNDAP workflow a very long time ago [1].

It's both very tricky and difficult nowadays because NASA tries to
constrain AWS egress cost via Earthdata Login authentication.

Does R provide a cURL-like library + a temporary token-based authentication?

[1]
https://earthdata.nasa.gov/collaborate/open-data-services-and-soft
ware /api/opendap/gesdisc-airs-opendap-cmr


-----Original Message-----
From: R-sig-Geo <r-sig-geo-bounces at r-project.org> On Behalf Of Ben
Tupper
Sent: Wednesday, April 13, 2022 11:41 AM
To: r-sig-geo <r-sig-geo at r-project.org>
Subject: [R-sig-Geo] Earthdata CMR access

Hello,

I am interested in accessing physical oceanography data from
PO.DAAC (
https://earthdata.nasa.gov/eosdis/daacs/podaac) from within R
using opendap.  NASA is moving its data offerings to the cloud,
and it is adopting Common Metadata Repositories ("CMR",
https://cmr.earthdata.nasa.gov/search/site/docs/search/api.html) for searching.  CMR searching is in lieu of searching THREDDS catalogs.

I'm finding the on-ramp to using CMR tricker than I had expected given the sales pitch behind CMR (or maybe the wheels have come off my car!)  I am wondering if anyone in this community has waded into using R-based CMR to access cloud-based geospatial data, and, if so, might be willing to share some insights or provide guidance?

Regards,
Ben

--
Ben Tupper (he/him)
Bigelow Laboratory for Ocean Science East Boothbay, Maine
http://www.bigelow.org/ https://eco.bigelow.org

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--
Ben Tupper (he/him)
Bigelow Laboratory for Ocean Science East Boothbay, Maine
http://www.bigelow.org/ https://eco.bigelow.org

--
Ben Tupper (he/him)
Bigelow Laboratory for Ocean Science
East Boothbay, Maine
http://www.bigelow.org/
https://eco.bigelow.org

--

Ben Tupper Bigelow Laboratory for Ocean Sciences
https://www.bigelow.org/ Tick forecast https://eco.bigelow.org/

--
Ben Tupper (he/him)
Bigelow Laboratory for Ocean Science
East Boothbay, Maine
http://www.bigelow.org/
https://eco.bigelow.org