NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response

mikejohnson51 / nwmTools

Set of tools to work with National Water Model output

Creative Commons Zero v1.0 Universal

17 stars 5 forks source link

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:dblodgett@usgs.gov 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:dblodgett@usgs.gov>dblodgett@usgs.gov</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 text-no-underline" href=https://waterdata.usgs.gov/blog/keywords/geo-data-portal/ data-taxonomy-term=geo-data-portal><span>Geo Data Portal</span></a></li><li class="display-inline-block margin-right-05"><a class="usa-tag text-no-underline" href=https://waterdata.usgs.gov/blog/keywords/thredds/ data-taxonomy-term=thredds><span>THREDDS</span></a></li></ul></div><div class=taxo-tags><h3 class=margin-y-0>Tags:</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/tags/cloud-transition/ data-taxonomy-term=cloud-transition><span>cloud-transition</span></a></li></ul></div></div></div><div class="grid-row flex-justify-end flex-align-center"><h3 class=margin-right-1>Share:</h3><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" 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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

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

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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:dblodgett@usgs.gov 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. 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NetCDF: Malformed or inaccessible DAP2 DDS or DAP4 DMR response #10