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Greetings Spicer, I think there is an issue with your new project variable. In previous files, it's a float, https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/FRF_20191206_1179_FRF_NAVD88_LARC_GPS_UTC_v20191209_grid_latlon.nc.ascii?project%5B0:1:0%5D Dataset { Float64 project[time = 1]; } frf/geomorphology/DEMs/surveyDEM/FRF_20191206_1179_FRF_NAVD88_LARC_GPS_UTC_v20191209_grid_latlon.nc; --------------------------------------------- project[1] -999.0 but in the new latest file, it's a string: https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/FRF_20200110_1180_FRF_NAVD88_LARC_GPS_UTC_v20200113_grid_latlon.nc.ascii?project Dataset { String project; } frf/geomorphology/DEMs/surveyDEM/FRF_20200110_1180_FRF_NAVD88_LARC_GPS_UTC_v20200113_grid_latlon.nc; --------------------------------------------- project, "F" That might cause new kinds of issues for a full variable read. Cheers! Sean On Fri, Jan 31, 2020 at 3:33 PM Spicer Bak <spicer.bak.frf@xxxxxxxxx> wrote: > Hey Sean, > Glad we were able to help find that bug, but I don't think the "project" > variable (or lack of) is the root of our problem as i chose your option 3 > (my mistake, this was supposed to be the same after the last one) and i > have similar response. Good news, when i add the #noprefetch option, it > seems to fix it. hopefully this helps provide answers. Demonstrated by > below code. > > # Failure with python (matlab as well) > import netCDF4 as nc > for url in urls: > print(nc.Dataset(url)['time']) > variables= nc.Dataset(url).variables.keys() > for var in variables: > try: > nc.Dataset(url)[var][0] > print('Success! {} from {}'.format(var, url)) > except IndexError: > print("won't load variable {} from {}".format(var, url)) > url += "#noprefetch" > nc.Dataset(url)[var][0] > print('Success! {} from {}'.format(var, url)) > except IndexError as e: > print("FAIL: load variable {} from {}".format(var, url)) > > print(' {}'.format(e)) > > > > On Fri, Jan 31, 2020 at 4:25 PM Sean Arms <sarms@xxxxxxxx> wrote: > >> I thought it was working for me, but for the wrong reasons. Sorry about >> that. But, now I have it. >> >> The error message from the server is...well...garbage. That's something >> we need to look into. The underlying problem here is that the new data file >> does not include the variable project. Because variable "project" exists in >> the other files (or more specifically, the first file of the aggregation), >> and specifically because it has time as it's outer dimension, currently it >> must exist in all files of the aggregation. So, we can make an ascii >> request for that variable specifically, and request everything up to the >> last value, and it works [0:1:424]: >> >> >> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/surveyDEM.ncml.ascii?project%5B0:1:424%5D >> >> >> However, once we ask for the last value, it bombs [0:1:424] : >> >> >> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/surveyDEM.ncml.ascii?project%5B0:1:425%5D >> >> It's only like this for the full read code path, though. If I slice it >> from [1:1:424] (skip the first value), it works >> >> >> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/surveyDEM.ncml.ascii?project%5B1:1:425%5D >> >> ...and the missing value gets filled with a zero, because why not (well, >> ok, I can think of a few reasons). So, from the TDS side, and more >> specifically netCDF-Java, this is a bug (well, bugs, because returning zero >> isn't quite the thing to do here either). >> >> From what I can understand, netCDF-C tries to preload some data from >> remote servers (if the variable is considered "small enough"), and because >> the variable "project" is "small enough", the library tries to grab it all >> and the request bombs out. You can tell the C library to not do that by >> adding "#noprefetch" at the end of the url when opening the dataset, but >> that just delays things (unless you or the underlying library you are using >> never tries to fully read the variable "project"). So, in your sample >> python code, pass Netcdf4Python's Dataset the following URL and give it a >> spin: >> >> >> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/surveyDEM.ncml#noprefetch >> >> Cool...so what to do until I can get this fixed. Three things off the top >> of my head: >> >> 1. Add "#noprefetch" to your URL (and anyone else using the dataset). >> Barf. >> 2. Use NcML in the aggregation to remove the variable "project" all >> together, as it seems to be -999.0 when it does exist anyways. >> 3. Add the variable "project" to the latest file (NcML or by rewriting >> it). >> >> Sorry this took so long to debug. There will be a fix, it will just take >> some time (maybe early next week since I believe I know exactly what needs >> done and where). >> >> Cheers, >> >> Sean >> >> >> On Fri, Jan 31, 2020 at 12:27 PM Spicer Bak <spicer.bak.frf@xxxxxxxxx> >> wrote: >> >>> Hey Sean, >>> Thanks for getting back to me. I was still getting the same symptoms >>> earlier today. Did it work on second inquiry for you? >>> >>> I did make a change to that last file so the dim's match up with >>> previous. After I did that, checked again to make sure that wasn't causing >>> the problem. Seems i still am getting the same IndexError i was getting, >>> so this (as you mentioned) is not the root of the problem. >>> >>> On Fri, Jan 31, 2020 at 11:03 AM Sean Arms <sarms@xxxxxxxx> wrote: >>> >>>> Greetings Spicer, >>>> >>>> It looks like you have solved the issue? I was having problems the >>>> other day as well. I downloaded the files locally to see if I could >>>> reproduce the issue, and I am unable to do so now. However, I do see >>>> something that might cause an issue down the road. The dimension order on >>>> some of the variables in the latest file does not match what is in other >>>> files. For example, if we compare the latest file: >>>> >>>> >>>> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/FRF_20200110_1180_FRF_NAVD88_LARC_GPS_UTC_v20200113_grid_latlon.nc.dds >>>> >>>> with next latest file: >>>> >>>> >>>> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/FRF_20191206_1179_FRF_NAVD88_LARC_GPS_UTC_v20191209_grid_latlon.nc.dds >>>> >>>> The dimensionality of latitude, longitude, northing, and easting switch >>>> from (xFRF, yFRF) (20191206) to (yFRF, xFRF) (20200113).Might not be a big >>>> issue overall since the use of an NcML file on the server (as opposed to >>>> NcML directly in the catalog) uses the first file of the aggregation as >>>> template. >>>> >>>> Cheers, >>>> >>>> Sean >>>> >>>> >>>> On Wed, Jan 29, 2020 at 3:03 PM Spicer Bak <spicer.bak.frf@xxxxxxxxx> >>>> wrote: >>>> >>>>> hello TDS community, >>>>> I have a problem I'm quite pickled on. We had a dataset that was >>>>> working fine until (i think) we pushed the latest file. Our server is >>>>> continually updated with new files and all of the other datasets seem to >>>>> work fine. >>>>> >>>>> I'm able to get the data from the individual file URLS, but not the >>>>> time concatenated ncml file. I can display the file or variables, but not >>>>> obtain any of the data through OPeNDAP, but i'm able to see the data >>>>> returned via the "get ASCII" button on the OPeNDAP page. The below python >>>>> script demonstrates the problem: >>>>> >>>>> # success with ncml: >>>>> >>>>> https://chldata.erdc.dren.mil/thredds/dodsC/frf/geomorphology/DEMs/surveyDEM/surveyDEM.ncml.ascii?latitude%5B0:1:0%5D%5B0:1:0%5D,time%5B0:1:425%5D,elevation%5B0:1:0%5D%5B0:1:0%5D%5B0:1:0%5D >>>>> >>>>> # Failure with python (matlab as well) >>>>> import netCDF4 as nc >>>>> for url in urls: >>>>> print(nc.Dataset(url)['time']) >>>>> variables= nc.Dataset(url).variables.keys() >>>>> for var in variables: >>>>> try: >>>>> nc.Dataset(url)[var][0] >>>>> print('Success! {} from {}'.format(var, url)) >>>>> except IndexError as e: >>>>> print("won't load variable {} from {}".format(var, url)) >>>>> >>>>> print(' {}'.format(e)) >>>>> >>>>> Any help would be much appreciated! >>>>> >>>>> -- >>>>> +++++++++++++++++++++++++++ >>>>> Spicer Bak, PhD >>>>> USACE CHL Field Research Facility >>>>> 252-305-9975 >>>>> _______________________________________________ >>>>> NOTE: All exchanges posted to Unidata maintained email lists are >>>>> recorded in the Unidata inquiry tracking system and made publicly >>>>> available through the web. Users who post to any of the lists we >>>>> maintain are reminded to remove any personal information that they >>>>> do not want to be made public. >>>>> >>>>> >>>>> thredds mailing list >>>>> thredds@xxxxxxxxxxxxxxxx >>>>> For list information or to unsubscribe, visit: >>>>> https://www.unidata.ucar.edu/mailing_lists/ >>>>> >>>> >>> >>> -- >>> +++++++++++++++++++++++++++ >>> Spicer Bak, PhD >>> USACE CHL Field Research Facility >>> 252-305-9975 >>> >> > > -- > +++++++++++++++++++++++++++ > Spicer Bak, PhD > USACE CHL Field Research Facility > 252-305-9975 >
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