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cdms2.open fails on an xml file with "invalid" attributes #1942

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durack1 opened this Issue Apr 20, 2016 · 3 comments

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durack1 commented Apr 20, 2016

The following error output from ipython should explain the error enough. The .xml input file was generated using cdscan - same version as the uvcdat:

In [2]: fh = cdm.open('ORAS4_1958-2014.xml')
error near line 17: invalid attribute value positive=unknown of element axis, must be one of ('up', 'down')
---------------------------------------------------------------------------                                
AssertionError                            Traceback (most recent call last)                                
<ipython-input-2-c0e2c24bde85> in <module>()                                                               
----> 1 fh = cdm.open('ORAS4_1958-2014.xml')                                                               

/usr/local/uvcdat/2016-03-09/lib/python2.7/site-packages/cdms2/dataset.pyc in openDataset(uri, mode, template, dods, dpath, hostObj)
...

/usr/local/uvcdat/2016-03-09/lib/python2.7/site-packages/cdms2/cdmsNode.pyc in validate(self, idtable)
    359                 if type(atttype) is TupleType:
    360                     attval=self.getExternalAttr(attname)
--> 361                     assert attval in atttype, 'Invalid attribute %s=%s must be in %s'%(attname,attval,`atttype`)
    362                 elif atttype==CDML.Idref:
    363                     attval=self.getExternalAttr(attname)

AssertionError: Invalid attribute positive=unknown must be in ('up', 'down')

@durack1 durack1 changed the title from cdms2.open fails to open a file with "invalid" attributes to cdms2.open fails on an xml file with "invalid" attributes Apr 20, 2016

@durack1 durack1 added this to the 2.6 milestone Apr 24, 2016

@durack1 durack1 added cdms2 Bug labels Apr 24, 2016

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durack1 commented Apr 24, 2016

And another error:

In [1]: f = 'ocerean.ORAS4.historical.r0i0p0.mo.ocn.Omon.thetao.ver-1.latestX.xml'

In [2]: import cdms2 as cdm

In [3]: fh = cdm.open(f)
---------------------------------------------------------------------------
KeyError                                  Traceback (most recent call last)
<ipython-input-3-196c0ae1c74e> in <module>()
----> 1 fh = cdm.open(f)

/usr/local/uvcdat/2.4.1/lib/python2.7/site-packages/cdms2/dataset.pyc in openDataset(uri, mode, template, dods, dpath, hostObj)
    369             dpath = head
    370
--> 371     dataset = Dataset(uri, mode, datanode, None, dpath)
    372     return dataset
    373

/usr/local/uvcdat/2.4.1/lib/python2.7/site-packages/cdms2/dataset.pyc in __init__(self, uri, mode, datasetNode, parent, datapath)
    518         # Collect named children (having attribute 'id') into dictionaries
    519         if datasetNode is not None:
--> 520             coordsaux = self._convention_.getDsetnodeAuxAxisIds(datasetNode)
    521
    522             for node in datasetNode.getIdDict().values():

/usr/local/uvcdat/2.4.1/lib/python2.7/site-packages/cdms2/convention.pyc in getDsetnodeAuxAxisIds(self, dsetnode)
    135                     # It's not an axis node, so must be a variable, so getDomain is defined.
    136                     # Check the rank, don't include if not 1D or 2D (e.g., scalar coordinate)
--> 137                     domnode = dsetdict[item].getDomain()
    138                     if domnode.getChildCount() not in [1,2]:
    139                         continue

KeyError: 'time'

And the associated ncdump:

[durack1@crunchy 160421_data_density]$ ncdump -h /work/guilyardi/database/ORAS4/so_oras4_1m_1958_grid_T.nc
netcdf so_oras4_1m_1958_grid_T {
dimensions:
        t = UNLIMITED ; // (12 currently)
        z = 42 ;
        y = 292 ;
        x = 362 ;
variables:
        float so(t, z, y, x) ;
                so:units = "psu" ;
                so:_Fillvalue = 9.96921e+36f ;
                so:long_name = "Salinity" ;
                so:interval_write = "monthly" ;
                so:coordinates = "time depth lat lon" ;
                so:offline_operation = "time average" ;
                so:standard_name = "sea_water_salinity" ;
                so:_CoordinateAxes = "time depth lat lon" ;
                so:associate = "time depth lat lon" ;

// global attributes:
                :NCO = "4.0.7" ;
                :Conventions = "CF-1.1" ;
                :title = "ORAS4 ocean reanalysis" ;
                :institution = "ECMWF" ;
                :source = "Native Grid ORCA1 monthly average" ;
                :associated_file = "coordinates_grid_T.nc" ;
                :references = "http://www.ecmwf.int/products/forecasts/d/charts/oras4/" ;
}

@doutriaux1 doutriaux1 modified the milestones: 3.0, 2.6 May 25, 2016

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dnadeau4 commented Sep 19, 2016

@durack1 where is those XML files, I cannot find them.

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durack1 commented Sep 21, 2016

@dnadeau4 take a peek at /work/guilyardi/database/ORAS4/ORAS4_1958-2014.xml

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