cdscan KeyError: 'height' #421
Description
Describe the bug
I can read in a netcdf file without issue, but when I try to read in data from a cdscan-generated xml that points to that same file, I get KeyError: 'height'.
To Reproduce
Steps to reproduce the behavior (on feedback2.llnl.gov):
-
I am able to open this netcdf file without any problem:
f=cdms2.open('/p/css03/esgf_publish/CMIP6/CMIP/KIOST/KIOST-ESM/abrupt-4xCO2/r1i1p1f1/Amon/tas/gr1/v20191106/tas_Amon_KIOST-ESM_abrupt-4xCO2_r1i1p1f1_gr1_185001-200012.nc') -
Generate an xml pointing to this file via cdscan:
In [69]: import os
In [70]: os.system('cdscan -x temp.xml /p/css03/esgf_publish/CMIP6/CMIP/KIOST/KIOST-ESM/abrupt-4xCO2/r1i1p1f1/Amon/tas/gr1/v20191106/tas_Amon_KIOST-ESM_abrupt-4xCO2_r1i1p1f1_gr1_185001-200012.nc')
Finding common directory ...
Common directory: /p/css03/esgf_publish/CMIP6/CMIP/KIOST/KIOST-ESM/abrupt-4xCO2/r1i1p1f1/Amon/tas/gr1/v20191106/
Scanning files ...
/p/css03/esgf_publish/CMIP6/CMIP/KIOST/KIOST-ESM/abrupt-4xCO2/r1i1p1f1/Amon/tas/gr1/v20191106/tas_Amon_KIOST-ESM_abrupt-4xCO2_r1i1p1f1_gr1_185001-200012.nc
Setting reference time units to days since 1850-01-01
temp.xml written
Out[70]: 0
- Now, try to open this xml file:
In [71]: f=cdms2.open('temp.xml')
KeyError Traceback (most recent call last)
in
----> 1 f=cdms2.open('temp.xml')
~/workdir2/miniconda3/envs/cdat82/lib/python3.7/site-packages/cdms2/dataset.py in openDataset(uri, mode, template, dods, dpath, hostObj)
570 dpath = head
571
--> 572 dataset = Dataset(uri, mode, datanode, None, dpath)
573 return dataset
574
~/workdir2/miniconda3/envs/cdat82/lib/python3.7/site-packages/cdms2/dataset.py in init(self, uri, mode, datasetNode, parent, datapath)
762 # Collect named children (having attribute 'id') into dictionaries
763 if datasetNode is not None:
--> 764 coordsaux = self.convention.getDsetnodeAuxAxisIds(datasetNode)
765
766 for node in list(datasetNode.getIdDict().values()):
~/workdir2/miniconda3/envs/cdat82/lib/python3.7/site-packages/cdms2/convention.py in getDsetnodeAuxAxisIds(self, dsetnode)
147 # Check the rank, don't include if not 1D or 2D (e.g.,
148 # scalar coordinate)
--> 149 domnode = dsetdict[item].getDomain()
150 if domnode.getChildCount() not in [1, 2]:
151 continue
KeyError: 'height'
Expected behavior
I expected no problem opening this xml file, just as I experienced no problem opening the netcdf that it points to.
Environment Information
`conda info`
(cdat82) -bash-4.1$ conda info
active environment : cdat82
active env location : /work/zelinka1/workdir2/miniconda3/envs/cdat82
shell level : 2
user config file : /work/zelinka1/.condarc
populated config files : /work/zelinka1/.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 3.7.4.final.0
virtual packages : __glibc=2.12
base environment : /work/zelinka1/workdir2/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/cdat/label/v82/linux-64
https://conda.anaconda.org/cdat/label/v82/noarch
https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /work/zelinka1/workdir2/miniconda3/pkgs
/work/zelinka1/.conda/pkgs
envs directories : /work/zelinka1/workdir2/miniconda3/envs
/work/zelinka1/.conda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.7.4 Linux/2.6.32-754.28.1.el6.x86_64 rhel/6.10 glibc/2.12
UID:GID : 25073:1026
netrc file : None
offline mode : False
`conda config --show-sources`
(cdat82) -bash-4.1$ conda config --show-sources
==> /work/zelinka1/.condarc <==
ssl_verify: False
channel_priority: strict
channels:
- cdat/label/v82
- conda-forge
- defaults
`conda list --show-channel-urls`
(cdat82) -bash-4.1$ conda list --show-channel-urls
# packages in environment at /work/zelinka1/workdir2/miniconda3/envs/cdat82:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 0_gnu conda-forge
alabaster 0.7.12 py_0 conda-forge
astroid 2.3.3 py37_1 conda-forge
attrdict 2.0.1 py_0 conda-forge
attrs 19.3.0 py_0 conda-forge
autopep8 1.5 py_0 conda-forge
babel 2.8.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
basemap 1.2.1 py37hd759880_1 conda-forge
beautifulsoup4 4.8.2 py37_0 conda-forge
bleach 3.1.0 py_0 conda-forge
bokeh 1.4.0 py37_0 conda-forge
bzip2 1.0.8 h516909a_2 conda-forge
ca-certificates 2020.6.20 hecda079_0 conda-forge
cartopy 0.17.0 py37hd759880_1006 conda-forge
cdat 8.2 3 cdat/label/v82
cdat_info 8.2 py_7 conda-forge
cdms2 3.1.4 pypi_0 pypi
cdp 1.6.0 py_0 conda-forge
cdtime 3.1.2 py37h7eb8c7e_6 conda-forge
cdutil 8.2 py_2 cdat/label/v82
certifi 2020.6.20 py37hc8dfbb8_0 conda-forge
cffi 1.13.2 py37h8022711_0 conda-forge
cftime 1.2.1 py37h03ebfcd_0 conda-forge
chardet 3.0.4 py37_1003 conda-forge
cibots 0.3 py37_1001 conda-forge
click 7.0 py_0 conda-forge
climlab 0.7.6 py37hc7d476f_1 conda-forge
cloudpickle 1.3.0 py_0 conda-forge
cryptography 2.8 py37h72c5cf5_1 conda-forge
curl 7.68.0 hf8cf82a_0 conda-forge
cycler 0.10.0 py_2 conda-forge
cytoolz 0.10.1 py37h516909a_0 conda-forge
dask 2.10.1 py_0 conda-forge
dask-core 2.10.1 py_0 conda-forge
dbus 1.13.6 he372182_0 conda-forge
decorator 4.4.1 py_0 conda-forge
defusedxml 0.6.0 py_0 conda-forge
distarray 2.12.2 py_1 conda-forge
distributed 2.10.0 py_0 conda-forge
docopt 0.6.2 py_1 conda-forge
docutils 0.16 py37_0 conda-forge
dv3d 8.2 py_0 cdat/label/v82
entrypoints 0.3 py37_1000 conda-forge
eofs 1.4.0 py_0 conda-forge
esmf 7.1.0 hcda5390_1008 conda-forge
esmpy 7.1.0 py37h5ca1d4c_3 conda-forge
expat 2.2.9 he1b5a44_2 conda-forge
ffmpeg 4.2 h167e202_0 conda-forge
flake8 3.7.9 py37_0 conda-forge
fontconfig 2.13.1 h86ecdb6_1001 conda-forge
freetype 2.10.0 he983fc9_1 conda-forge
fsspec 0.6.2 py_0 conda-forge
future 0.18.2 py37_0 conda-forge
g2clib 1.6.0 hf3f1b0b_9 conda-forge
genutil 8.2 py37hc1659b7_3 conda-forge
geos 3.7.2 he1b5a44_2 conda-forge
gettext 0.19.8.1 hc5be6a0_1002 conda-forge
ghostscript 9.22 hf484d3e_1001 conda-forge
glib 2.58.3 py37h6f030ca_1002 conda-forge
gmp 6.2.0 he1b5a44_1 conda-forge
gnutls 3.6.5 hd3a4fd2_1002 conda-forge
gst-plugins-base 1.14.5 h0935bb2_2 conda-forge
gstreamer 1.14.5 h36ae1b5_2 conda-forge
hdf4 4.2.13 hf30be14_1003 conda-forge
hdf5 1.10.5 nompi_h3c11f04_1104 conda-forge
heapdict 1.0.1 py_0 conda-forge
icu 64.2 he1b5a44_1 conda-forge
idna 2.8 py37_1000 conda-forge
imagesize 1.2.0 py_0 conda-forge
importlib_metadata 1.5.0 py37_0 conda-forge
ipykernel 5.1.4 py37h5ca1d4c_0 conda-forge
ipython 7.12.0 py37h5ca1d4c_0 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
ipywidgets 7.5.1 py_0 conda-forge
isort 4.3.21 py37_0 conda-forge
jasper 1.900.1 h07fcdf6_1006 conda-forge
jedi 0.16.0 py37_0 conda-forge
jeepney 0.4.2 py_0 conda-forge
jinja2 2.11.1 py_0 conda-forge
jpeg 9c h14c3975_1001 conda-forge
jsonschema 3.2.0 py37_0 conda-forge
jupyter 1.0.0 py_2 conda-forge
jupyter_client 5.3.4 py37_1 conda-forge
jupyter_console 6.0.0 py_0 conda-forge
jupyter_core 4.6.2 py37_0 conda-forge
keyring 21.1.0 py37_0 conda-forge
kiwisolver 1.1.0 py37hc9558a2_0 conda-forge
krb5 1.16.4 h2fd8d38_0 conda-forge
lame 3.100 h14c3975_1001 conda-forge
lazy-object-proxy 1.4.3 py37h516909a_1 conda-forge
ld_impl_linux-64 2.33.1 h53a641e_8 conda-forge
libblas 3.8.0 11_openblas conda-forge
libcblas 3.8.0 11_openblas conda-forge
libcdms 3.1.2 h7dcd879_5 conda-forge
libcf 1.0.3 py37hb508d2e_1 conda-forge
libclang 9.0.1 default_hde54327_0 conda-forge
libcurl 7.68.0 hda55be3_0 conda-forge
libdrs 3.1.2 h6e990d7_7 conda-forge
libdrs_f 3.1.2 h322d3c2_6 conda-forge
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 he1b5a44_1006 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-ng 9.2.0 h24d8f2e_2 conda-forge
libgfortran-ng 7.3.0 hdf63c60_5 conda-forge
libgomp 9.2.0 h24d8f2e_2 conda-forge
libiconv 1.15 h516909a_1005 conda-forge
liblapack 3.8.0 11_openblas conda-forge
libllvm9 9.0.1 hc9558a2_0 conda-forge
libnetcdf 4.6.2 h303dfb8_1003 conda-forge
libopenblas 0.3.6 h6e990d7_6 conda-forge
libpng 1.6.37 hed695b0_0 conda-forge
libsodium 1.0.17 h516909a_0 conda-forge
libssh2 1.8.2 h22169c7_2 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
libtiff 4.1.0 hc3755c2_3 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxkbcommon 0.10.0 he1b5a44_0 conda-forge
libxml2 2.9.10 hee79883_0 conda-forge
libxslt 1.1.33 h31b3aaa_0 conda-forge
locket 0.2.0 py_2 conda-forge
lxml 4.5.0 py37he3881c9_1 conda-forge
lz4-c 1.8.3 he1b5a44_1001 conda-forge
markupsafe 1.1.1 py37h516909a_0 conda-forge
matplotlib 3.1.3 py37_0 conda-forge
matplotlib-base 3.1.3 py37h250f245_0 conda-forge
mccabe 0.6.1 py_1 conda-forge
mechanicalsoup 0.12.0 py_0 conda-forge
mistune 0.8.4 py37h516909a_1000 conda-forge
mpi 1.0 mpich conda-forge
mpich 3.3.2 hc856adb_0 conda-forge
msgpack-python 0.6.2 py37hc9558a2_0 conda-forge
nb_conda 2.2.1 py37_2 conda-forge
nb_conda_kernels 2.2.2 py37_0 conda-forge
nbconvert 5.6.1 py37_0 conda-forge
nbformat 5.0.4 py_0 conda-forge
ncurses 6.1 hf484d3e_1002 conda-forge
netcdf-fortran 4.4.5 h0789656_1004 conda-forge
netcdf4 1.5.1.2 py37h73a1b54_1 conda-forge
nettle 3.4.1 h1bed415_1002 conda-forge
notebook 6.0.3 py37_0 conda-forge
nspr 4.25 he1b5a44_0 conda-forge
nss 3.47 he751ad9_0 conda-forge
numpy 1.17.5 py37h95a1406_0 conda-forge
numpydoc 0.9.2 py_0 conda-forge
olefile 0.46 py_0 conda-forge
openblas 0.3.6 h6e990d7_6 conda-forge
openh264 1.8.0 hdbcaa40_1000 conda-forge
openssl 1.1.1g h516909a_0 conda-forge
output_viewer 1.3.1 py_1 conda-forge
owslib 0.19.1 py_0 conda-forge
packaging 20.1 py_0 conda-forge
pandas 1.0.1 py37hb3f55d8_0 conda-forge
pandoc 2.9.1.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.6.1 py_0 conda-forge
partd 1.1.0 py_0 conda-forge
pcre 8.44 he1b5a44_0 conda-forge
pexpect 4.8.0 py37_0 conda-forge
pickleshare 0.7.5 py37_1000 conda-forge
pillow 7.0.0 py37hefe7db6_0 conda-forge
pip 20.0.2 py_2 conda-forge
proj4 5.2.0 he1b5a44_1006 conda-forge
prometheus_client 0.7.1 py_0 conda-forge
prompt_toolkit 2.0.10 py_0 conda-forge
psutil 5.6.7 py37h516909a_0 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
ptyprocess 0.6.0 py_1001 conda-forge
pycodestyle 2.5.0 py_0 conda-forge
pycparser 2.19 py37_1 conda-forge
pydap 3.2.2 py37_1000 conda-forge
pyepsg 0.4.0 py_0 conda-forge
pyflakes 2.1.1 py_0 conda-forge
pygments 2.5.2 py_0 conda-forge
pykdtree 1.3.1 py37hc1659b7_1002 conda-forge
pylint 2.4.4 py37_0 conda-forge
pyopenssl 19.1.0 py37_0 conda-forge
pyparsing 2.4.6 py_0 conda-forge
pyproj 1.9.6 py37h516909a_1002 conda-forge
pyqt 5.12.3 py37hcca6a23_1 conda-forge
pyqt5-sip 4.19.18 pypi_0 pypi
pyqtwebengine 5.12.1 pypi_0 pypi
pyrsistent 0.15.7 py37h516909a_0 conda-forge
pyshp 2.1.0 py_0 conda-forge
pysocks 1.7.1 py37_0 conda-forge
pyspharm 1.0.9 py37h7eb8c7e_1004 conda-forge
python 3.7.6 h357f687_2 conda-forge
python-dateutil 2.8.1 py_0 conda-forge
python_abi 3.7 1_cp37m conda-forge
pytz 2019.3 py_0 conda-forge
pyyaml 5.3 py37h516909a_0 conda-forge
pyzmq 18.1.1 py37h1768529_0 conda-forge
qt 5.12.5 hd8c4c69_1 conda-forge
qtawesome 0.7.0 py_0 conda-forge
qtconsole 4.6.0 py_0 conda-forge
qtpy 1.9.0 py_0 conda-forge
readline 8.0 hf8c457e_0 conda-forge
regrid2 3.1.4 pypi_0 pypi
requests 2.22.0 py37_1 conda-forge
requests-cache 0.5.2 pypi_0 pypi
rope 0.16.0 py_0 conda-forge
scipy 1.4.1 py37h921218d_0 conda-forge
secretstorage 3.1.2 py37_0 conda-forge
send2trash 1.5.0 py_0 conda-forge
setuptools 45.2.0 py37_0 conda-forge
shapely 1.6.4 py37hec07ddf_1006 conda-forge
six 1.14.0 py37_0 conda-forge
snowballstemmer 2.0.0 py_0 conda-forge
sortedcontainers 2.1.0 py_0 conda-forge
soupsieve 1.9.4 py37hc8dfbb8_1 conda-forge
sphinx 2.4.1 py_0 conda-forge
sphinxcontrib-applehelp 1.0.1 py_0 conda-forge
sphinxcontrib-devhelp 1.0.1 py_0 conda-forge
sphinxcontrib-htmlhelp 1.0.2 py_0 conda-forge
sphinxcontrib-jsmath 1.0.1 py_0 conda-forge
sphinxcontrib-qthelp 1.0.2 py_0 conda-forge
sphinxcontrib-serializinghtml 1.1.3 py_0 conda-forge
spyder 3.3.6 py37_1 conda-forge
spyder-kernels 0.5.2 py37_0 conda-forge
sqlite 3.30.1 hcee41ef_0 conda-forge
tblib 1.6.0 py_0 conda-forge
terminado 0.8.3 py37_0 conda-forge
testpath 0.4.4 py_0 conda-forge
tk 8.6.10 hed695b0_0 conda-forge
toolz 0.10.0 py_0 conda-forge
tornado 6.0.3 py37h516909a_4 conda-forge
traitlets 4.3.3 py37_0 conda-forge
typed-ast 1.4.1 py37h516909a_0 conda-forge
udunits2 2.2.27.6 h4e0c4b3_1001 conda-forge
urllib3 1.25.7 py37_0 conda-forge
vcs 8.2 py_2 cdat/label/v82
vcsaddons 8.2 py37h516909a_1 cdat/label/v82
vtk-cdat 8.2.0.8.2 py37h3df8362_0 cdat/label/v82
wcwidth 0.1.8 py_0 conda-forge
webencodings 0.5.1 py_1 conda-forge
webob 1.8.6 py_0 conda-forge
wheel 0.34.2 py_1 conda-forge
widgetsnbextension 3.5.1 py37_0 conda-forge
windspharm 1.7.0 py37_1001 conda-forge
wk 8.2 py_0 cdat/label/v82
wrapt 1.11.2 py37h516909a_0 conda-forge
wurlitzer 2.0.0 py37_0 conda-forge
x264 1!152.20180806 h14c3975_0 conda-forge
xarray 0.15.0 py_0 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.3 h516909a_0 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
yaml 0.2.2 h516909a_1 conda-forge
zeromq 4.3.2 he1b5a44_2 conda-forge
zict 1.0.0 py_0 conda-forge
zipp 2.2.0 py_0 conda-forge
zlib 1.2.11 h516909a_1006 conda-forge
zstd 1.4.4 h3b9ef0a_1 conda-forge