NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10

tungttnguyen · 2024-04-29T23:14:26Z

Hello Mike,

I tried one example from here but got this error message. Do you know what went wrong? Thank you very much for your help!

pst = readNWMdata(comid = 101, 
                  startDate = "2010-01-01", 
                  endDate = "2010-01-31", 
                  tz = "US/Pacific")

syntax error, unexpected WORD_WORD, expecting SCAN_ATTR or SCAN_DATASET or SCAN_ERROR

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class="single grid-container-desktop"><h1 class="text-ls-neg-2 padding-bottom-0 margin-bottom-0">USGS Geo Data Portal and THREDDS Data Server Retirement</h1><h3 class=text-normal>The GDP web interface, processing service, and THREDDS data server are being retired.</h3><div class="grid-row display-flex flex-justify border-y padding-y-1"><div><span class="display-block text-uppercase">Date Posted</span><span class=text-bold>April 10, 2024</span><span class="display-block text-uppercase margin-top-1">Last Updated</span><span class=text-bold>April 11, 2024</span></div><div><span class="display-block text-uppercase">Author</span><span class=text-bold>David Blodgett</span><br><a href=mailto:[email protected] class=text-no-underline target=blank><i class="fas fa-envelope-square text-primary-darker social-icon"></i></a><a href=https://github.com/dblodgett-usgs class=text-no-underline target=blank><i class="fab fa-github-square text-primary-darker social-icon"></i></a><a href=https://twitter.com/D_Blodgett class=text-no-underline target=blank><i class="fab fa-twitter-square text-primary-darker social-icon"></i></a><a href=https://www.usgs.gov/staff-profiles/david-l-blodgett class=text-no-underline target=blank><i class="fas fa-user text-primary-darker social-icon"></i></a></div><div><span class="display-block text-uppercase">Reading Time</span><span class=text-bold>2 minutes</span><span class="display-block text-uppercase margin-top-1">Share</span><a href="http://www.facebook.com/sharer.php?src=bm&u=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&t=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement" class="text-no-underline margin-right-1" onclick='return window.open(this.href,"PCwindow","width=550, height=350, menubar=no, toolbar=no, scrollbars=yes"),!1'><i class="fab fa-facebook text-primary-darker social-icon" aria-hidden=true></i></a><a href="https://twitter.com/intent/tweet?url=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&text=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement&tw_p=tweetbutton" class="text-no-underline margin-right-1" rel=nofollow target=_blank><i class="fab fa-twitter text-primary-darker social-icon" aria-hidden=true></i></a><a href="https://www.reddit.com/submit?url=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&title=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement" class=text-no-underline onclick='return window.open(this.href,"PCwindow","width=550, height=350, menubar=no, toolbar=no, scrollbars=yes"),!1'><i class="fab fa-reddit-alien text-primary-darker social-icon" aria-hidden=true></i></a></div></div><p><strong>UPDATED April 2024</strong></p><p>The USGS Geo Data Portal (GDP) and THREDDS Data Server have provided access to numerous datasets, including gridded data for climate and land use. Datasets can be subsetted or summarized before download using several algorithms, and these algorithms can also be applied to other datasets hosted elsewhere.</p><p>The system has been hosted via <code>cida.usgs.gov</code> since its original release in 2011. See this report for more information on GDP: Blodgett, David L., Nathaniel L. Booth, Thomas C. Kunicki, Jordan I. Walker, and Roland J. Viger. Description and testing of the Geo Data Portal: Data integration framework and Web processing services for environmental science collaboration. <a href=https://pubs.usgs.gov/of/2011/1157/>No. 2011-1157. US Geological Survey, 2011.</a></p><p><em>As of April 2024, most of the datasets the GDP supports are no longer accessible. See the THREDDS Data Server section below for more information.</em></p><p>All components of the GDP were migrated to a new hosting environment in 2022. Due to a lack of resources to maintain the software, the GDP will be retired in Summer 2024. It will be replaced by analysis ready cloud optimized direct data access via methods <a href=https://water.usgs.gov/catalog/usecases/71a9ec77-a83f-4f14-92eb-d7c3266078ce/>(such as those described here)</a> and an in development processing service based on the <a href=https://code.usgs.gov/wma/nhgf/toolsteam/gdptools>gdptools</a> python package.</p><h1 id=thredds-data-server>THREDDS Data Server</h1><p>The GDP THREDDS Data Server (<a href=https://cida.usgs.gov/thredds/>https://cida.usgs.gov/thredds/</a>) was retired due to a lack of resources to remedy a security vulnerability in April 2024. We apologize for the abrupt retirement of the system. Research and development aiming to migrate THREDDS to a cloud-based infrastructure in 2022-2023 led to the conclusion that migration away from the THREDDS data server toward cloud optimized analysis ready data access methods was necessary. This work is nearing completion and all data that were available are or will soon be available in zarr format via a freely available object store. Information regarding how to <a href=https://water.usgs.gov/catalog/usecases/8df9f64f-0f38-4849-9c6f-3d931fd2b2ba/>access the object store can be found here</a>. A Spatio Temporal Asset Catalog will be released soon to aid discovery of these datasets and OPeNDAP access (as was provided by THREDDS) to the datasets should be available again soon.</p><p>To keep up with development on STAC, see <a href=https://code.usgs.gov/wma/nhgf/stac>this repository</a>.</p><p>In the coming months, new APIs and processing capabilities will become available via api.water.usgs.gov to replace the Geo Data Portal. Stay tuned for more user friendly APIs, more cloud-ready data access options, and a generally refined ecosystem of data, services and tools. No release date is set, but please check back here for more information or reach out to <a href=mailto:[email protected]>[email protected]</a> with questions.</p><div class="grid-row border-y display-flex flex-align-center padding-y-1"><div class="display-flex flex-12"><div class=taxo-categories><h3 class=margin-y-0>Categories:</h3><ul class="usa-list usa-list--unstyled margin-right-1"><li class="display-inline-block margin-right-05"><a class="usa-tag text-no-underline" href=https://waterdata.usgs.gov/blog/categories/news/ data-taxonomy-term=news><span>News</span></a></li></ul></div><div class=taxo-keywords><h3 class=margin-y-0>Keywords:</h3><ul class="usa-list usa-list--unstyled margin-right-1"><li class="display-inline-block margin-right-05"><a class="usa-tag text-no-underline" href=https://waterdata.usgs.gov/blog/keywords/geoprocessing/ data-taxonomy-term=geoprocessing><span>Geoprocessing</span></a></li><li class="display-inline-block margin-right-05"><a class="usa-tag 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Error in open.nc(meta.obj$url) : 
  NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response

Session Information

R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] nwmTools_0.0.4       nhdplusTools_1.0.0   dataRetrieval_2.7.15 AOI_0.3.0            lubridate_1.9.3      forcats_1.0.0       
 [7] stringr_1.5.1        dplyr_1.1.4          purrr_1.0.2          readr_2.1.5          tidyr_1.3.1          tibble_3.2.1        
[13] ggplot2_3.5.1        tidyverse_2.0.0      scales_1.3.0        

loaded via a namespace (and not attached):
 [1] gtable_0.3.5        lattice_0.22-5      tzdb_0.4.0          vctrs_0.6.5         tools_4.3.3         generics_0.1.3     
 [7] curl_5.2.1          parallel_4.3.3      proxy_0.4-27        fansi_1.0.6         pkgconfig_2.0.3     Matrix_1.6-5       
[13] KernSmooth_2.23-22  data.table_1.15.4   assertthat_0.2.1    lifecycle_1.0.4     compiler_4.3.3      munsell_0.5.1      
[19] terra_1.7-71        codetools_0.2-19    fst_0.9.8           class_7.3-22        yaml_2.3.8          pillar_1.9.0       
[25] classInt_0.4-10     hydroloom_1.0.2     RNetCDF_2.9-2       tidyselect_1.2.1    rvest_1.0.4         zip_2.3.1          
[31] stringi_1.8.3       tidygeocoder_1.0.5  sf_1.0-16           arrow_15.0.1        rnaturalearth_1.0.1 fastmap_1.1.1      
[37] grid_4.3.3          colorspace_2.1-0    cli_3.6.2           magrittr_2.0.3      utf8_1.2.4          e1071_1.7-14       
[43] withr_3.0.0         bit64_4.0.5         timechange_0.3.0    httr_1.4.7          bit_4.0.5           reticulate_1.36.1  
[49] RANN_2.6.1          hms_1.1.3           png_0.1-8           fstcore_0.9.18      pbapply_1.7-2       rcartocolor_2.1.1  
[55] rlang_1.1.3         Rcpp_1.0.12         glue_1.7.0          DBI_1.2.2           xml2_1.3.6          renv_1.0.7         
[61] rstudioapi_0.16.0   jsonlite_1.8.8      R6_2.5.1            fipio_1.1.2         units_0.8-5

The text was updated successfully, but these errors were encountered:

mikejohnson51 · 2024-04-29T23:30:56Z

Hi @tungttnguyen! Thanks for reaching out. Unfortunately the USGS CIDA server was hacked and is not expected to be restored :/ That puts us in a bit of a struggle until the OSN system is back up. I can help get you access to 1.2 and 2.0 but we lost 2.1 temporarily. Are you interested?

tungttnguyen · 2024-04-30T04:43:10Z

Hi @tungttnguyen! Thanks for reaching out. Unfortunately the USGS CIDA server was hacked and is not expected to be restored :/ That puts us in a bit of a struggle until the OSN system is back up. I can help get you access to 1.2 and 2.0 but we lost 2.1 temporarily. Are you interested?

Yes please. Thanks Mike!

csimeone-usgs · 2024-04-30T20:16:10Z

@mikejohnson51, if its not too much trouble, would it be possible for me to get access to versions 1.2 and 2.0 as well? Thank for your help!

mikejohnson51 · 2024-04-30T21:08:48Z

Certainly! I will get this set this week and update you both when its done.

lindsayplatt · 2024-05-20T17:58:26Z

Hello! I am also looking for this fix. I was just trying with version = 2.0 and version = 1.2 but both failed. I am using nwmTools v0.0.4.

library(nwmTools)
nwm_output <- readNWMdata(comid = 6078267, 
                          startDate = "1993-01-01",
                          endDate = "2017-12-31",
                          version = 1.2)

syntax error, unexpected WORD_WORD, expecting SCAN_ATTR or SCAN_DATASET or SCAN_ERROR
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class="single grid-container-desktop"><h1 class="text-ls-neg-2 padding-bottom-0 margin-bottom-0">USGS Geo Data Portal and THREDDS Data Server Retirement</h1><h3 class=text-normal>The GDP web interface, processing service, and THREDDS data server are being retired.</h3><div class="grid-row display-flex flex-justify border-y padding-y-1"><div><span class="display-block text-uppercase">Date Posted</span><span class=text-bold>April 10, 2024</span><span class="display-block text-uppercase margin-top-1">Last Updated</span><span class=text-bold>April 23, 2024</span></div><div><span class="display-block text-uppercase">Author</span><span class=text-bold>David Blodgett</span><br><a href=mailto:[email protected] class=text-no-underline target=blank><i class="fas fa-envelope-square text-primary-darker social-icon"></i></a><a href=https://github.com/dblodgett-usgs class=text-no-underline target=blank><i class="fab fa-github-square text-primary-darker social-icon"></i></a><a href=https://twitter.com/D_Blodgett class=text-no-underline target=blank><i class="fab fa-twitter-square text-primary-darker social-icon"></i></a><a href=https://www.usgs.gov/staff-profiles/david-l-blodgett class=text-no-underline target=blank><i class="fas fa-user text-primary-darker social-icon"></i></a></div><div><span class="display-block text-uppercase">Reading Time</span><span class=text-bold>2 minutes</span><span class="display-block text-uppercase margin-top-1">Share</span><a href="http://www.facebook.com/sharer.php?src=bm&u=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&t=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement" class="text-no-underline margin-right-1" onclick='return window.open(this.href,"PCwindow","width=550, height=350, menubar=no, toolbar=no, scrollbars=yes"),!1'><i class="fab fa-facebook text-primary-darker social-icon" aria-hidden=true></i></a><a href="https://twitter.com/intent/tweet?url=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&text=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement&tw_p=tweetbutton" class="text-no-underline margin-right-1" rel=nofollow target=_blank><i class="fab fa-twitter text-primary-darker social-icon" aria-hidden=true></i></a><a href="https://www.reddit.com/submit?url=https%3a%2f%2fwaterdata.usgs.gov%2fblog%2fgdp-moving%2f&title=USGS%20Geo%20Data%20Portal%20and%20THREDDS%20Data%20Server%20Retirement" class=text-no-underline onclick='return window.open(this.href,"PCwindow","width=550, height=350, menubar=no, toolbar=no, scrollbars=yes"),!1'><i class="fab fa-reddit-alien text-primary-darker social-icon" aria-hidden=true></i></a></div></div><p><strong>UPDATED April 2024</strong></p><p>The USGS Geo Data Portal (GDP) and THREDDS Data Server have provided access to numerous datasets, including gridded data for climate and land use. Datasets can be subsetted or summarized before download using several algorithms, and these algorithms can also be applied to other datasets hosted elsewhere.</p><p>The system has been hosted via <code>cida.usgs.gov</code> since its original release in 2011. See this report for more information on GDP: Blodgett, David L., Nathaniel L. Booth, Thomas C. Kunicki, Jordan I. Walker, and Roland J. Viger. Description and testing of the Geo Data Portal: Data integration framework and Web processing services for environmental science collaboration. <a href=https://pubs.usgs.gov/of/2011/1157/>No. 2011-1157. US Geological Survey, 2011.</a></p><p><em>As of April 2024, most of the datasets the GDP supports are no longer accessible. See the THREDDS Data Server section below for more information.</em></p><p>All components of the GDP were migrated to a new hosting environment in 2022. Due to a lack of resources to maintain the software, the GDP will be retired in Summer 2024. It will be replaced by analysis ready cloud optimized direct data access via methods <a href=https://water.usgs.gov/catalog/usecases/71a9ec77-a83f-4f14-92eb-d7c3266078ce/>(such as those described here)</a> and an in development processing service based on the <a href=https://code.usgs.gov/wma/nhgf/toolsteam/gdptools>gdptools</a> python package.</p><h1 id=thredds-data-server>THREDDS Data Server</h1><p>The GDP THREDDS Data Server (<a href=https://cida.usgs.gov/thredds/>https://cida.usgs.gov/thredds/</a>) was retired due to a lack of resources to remedy a security vulnerability in April 2024. We apologize for the abrupt retirement of the system. Research and development aiming to migrate THREDDS to a cloud-based infrastructure in 2022-2023 led to the conclusion that migration away from the THREDDS data server toward cloud optimized analysis ready data access methods was necessary. This work is nearing completion and all data that were available are or will soon be available in zarr format via a freely available object store. Information regarding how to <a href=https://water.usgs.gov/catalog/usecases/8df9f64f-0f38-4849-9c6f-3d931fd2b2ba/>access the object store can be found here</a>. A Spatio Temporal Asset Catalog will be released soon to aid discovery of these datasets and OPeNDAP access (as was provided by THREDDS) to the datasets should be available again soon.</p><p>To keep up with development on STAC, see <a href=https://code.usgs.gov/wma/nhgf/stac>this repository</a>.</p><p>In the coming months, new APIs and processing capabilities will become available via api.water.usgs.gov to replace the Geo Data Portal. Stay tuned for more user friendly APIs, more cloud-ready data access options, and a generally refined ecosystem of data, services and tools. No release date is set, but please check back here for more information or reach out to <a href=mailto:[email protected]>[email protected]</a> with questions.</p><div class="grid-row border-y display-flex flex-align-center padding-y-1"><div class="display-flex flex-12"><div class=taxo-categories><h3 class=margin-y-0>Categories:</h3><ul class="usa-list usa-list--unstyled margin-right-1"><li class="display-inline-block margin-right-05"><a class="usa-tag text-no-underline" href=https://waterdata.usgs.gov/blog/categories/news/ data-taxonomy-term=news><span>News</span></a></li></ul></div><div class=taxo-keywords><h3 class=margin-y-0>Keywords:</h3><ul class="usa-list usa-list--unstyled margin-right-1"><li class="display-inline-block margin-right-05"><a class="usa-tag text-no-underline" href=https://waterdata.usgs.gov/blog/keywords/geoprocessing/ data-taxonomy-term=geoprocessing><span>Geoprocessing</span></a></li><li class="display-inline-block margin-right-05"><a class="usa-tag 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Error in open.nc(meta.obj$url) : 
  NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response

RizaJamshidi · 2024-05-29T20:37:31Z

Hello! I just wanted to follow up and see if there is access to any version of NWM reanalysis data. I tried, but I got the same error.

mmalish · 2024-08-13T15:09:58Z

Hi Mike,
Is there a way that I could also get access to 1.2 and 2.0? Thanks for your help!

lindsayplatt · 2024-08-13T15:38:52Z

Just following up on my adventure with accessing NWM data as I needed a solution fairly quickly. I ended up not using nwmTools (though I hope I can switch back to it in the future) and accessed the raw Zarr files from Amazon S3. It was most certainly slower than what I imagine nwmTools could do for me but if you need a solution, this could work for you. Here is my tiny code example.

agropunk · 2024-12-06T23:17:19Z

Hi, I'm getting this same error and would love to get access to 1.2 or 2.0. Thanks!

lindsayplatt mentioned this issue May 20, 2024

Add streamflow lindsayplatt/episodic-river-salinization-model#5

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NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10

NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10

tungttnguyen commented Apr 29, 2024

mikejohnson51 commented Apr 29, 2024

tungttnguyen commented Apr 30, 2024

csimeone-usgs commented Apr 30, 2024

mikejohnson51 commented Apr 30, 2024

lindsayplatt commented May 20, 2024

RizaJamshidi commented May 29, 2024

mmalish commented Aug 13, 2024

lindsayplatt commented Aug 13, 2024

agropunk commented Dec 6, 2024

NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10

NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10

Comments

tungttnguyen commented Apr 29, 2024

mikejohnson51 commented Apr 29, 2024

tungttnguyen commented Apr 30, 2024

csimeone-usgs commented Apr 30, 2024

mikejohnson51 commented Apr 30, 2024

lindsayplatt commented May 20, 2024

RizaJamshidi commented May 29, 2024

mmalish commented Aug 13, 2024

lindsayplatt commented Aug 13, 2024

agropunk commented Dec 6, 2024