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 [[alternative HTML version deleted]]
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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