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Revision 85

Added by Aaron Marcuse-Kubitza about 13 years ago

Changed VegBank mappings to use XML functions (not implemented yet) to calculate averages and ranges

View differences:

scripts/lib/xpath.py
41 41
42 42 
    def _path():
43 43 
        tree = []
44 
        trailing_slash = False
45 44 
        while True:
46 45 
            # Split path
47 46 
            if parser.str_('{'):
......
58 57
59 58 
            # Attrs
60 59 
            if parser.str_('['):
61 
                elem.attrs = []
62 60 
                while True:
63 
                    path = _path()
64 
                    if parser.str_('='):
65 
                        set_value(path, parser.re(r'[\w.|]*'))
66 
                    elem.attrs.append(path)
61 
                    elem.attrs.append(_path())
67 62 
                    if not parser.str_(','): break
68 63 
                parser.str_(']', required=True)
69 64
......
80 75
81 76 
            if not parser.str_('/'): break
82 77
78 
        if parser.str_('='): set_value(tree, parser.re(r'[\w.|]*'))
79
83 80 
        # Expand * abbrs
84 81 
        for i in reversed(xrange(len(tree))):
85 82 
            elem = tree[i]
......
185 182 
        parent = node
186 183 
    return parent
187 184 

  		




  188
  
  
    
def put_obj(doc, xpath, id_, has_types, value):


  		




  
  185
  
    
def put_obj(doc, xpath, id_, has_types, value=None):


  		




  189
  186
  
    
    xpath = copy.deepcopy(xpath) # don't modify input!


  		




  190
  187
  
    
    set_id(xpath, id_, has_types)


  		




  191
  
  
    
    set_value(xpath, value)


  		




  
  188
  
    
    if value != None: set_value(xpath, value)


  		




  192
  189
  
    
    get(doc, xpath, True)


  		












  

    
      mappings/VegX-VegBank.organisms.csv
    
  





  60
  60
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude","/*_ID/observation/*_ID/plot/realLongitude"


  		




  61
  61
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/FootprintWKT","/*_ID/observation/*_ID/plot/dsgpoly"


  		




  62
  62
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters","/*_ID/observation/waterDepth/max"


  		




  63
  
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters","/*_ID/observation/*_ID/plot/{elevation/max,elevationRange/to}"


  		




  
  63
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters","/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"


  		




  64
  64
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters","/*_ID/observation/waterDepth/min"


  		




  65
  
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters","/*_ID/observation/*_ID/plot/{elevation/min,elevationRange/from}"


  		




  
  65
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters","/*_ID/observation/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"


  		




  66
  66
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation","/*_ID/observation/*_ID/plot/elevation"


  		




  67
  67
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier","/*_ID/observation/*_ID/plot/authorPlotCode"


  		




  68
  68
  
    
"/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier","/*_ID/observation/{*_ID/plot/authorPlotCode,authorObsCode}"


  		












  

    
      mappings/joins/NYBG-VegBank.organisms.csv
    
  





  29
  29
  
    
Latitude,/*_ID/observation/*_ID/plot/realLatitude


  		




  30
  30
  
    
CoordinatePrecision,/*_ID/observation/*_ID/plot/locationAccuracy


  		




  31
  31
  
    
BoundingBox,/*_ID/observation/*_ID/plot/dsgpoly


  		




  32
  
  
    
MinimumElevation,"/*_ID/observation/*_ID/plot/{elevation/min,elevationRange/from}"


  		




  33
  
  
    
MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/max,elevationRange/to}"


  		




  
  32
  
    
MinimumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"


  		




  
  33
  
    
MaximumElevation,"/*_ID/observation/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"


  		




  34
  34
  
    
MinimumDepth,/*_ID/observation/waterDepth/min


  		




  35
  35
  
    
MaximumDepth,/*_ID/observation/waterDepth/max


  		




  36
  36
  
    
Sex,"/taxonImportance/stemCount/stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/definedValue[@fkey=tableRecord_ID,userDefined[tableName=taxonInterpretation,userDefinedName=sex]]/definedValue"


  		












  

    
      mappings/joins/SALVIAS-VegBank.plots.csv
    
  





  9
  9
  
    
lat_decimal,/*_ID/plot/realLatitude


  		




  10
  10
  
    
long_decimal,/*_ID/plot/realLongitude


  		




  11
  11
  
    
elev_m,/*_ID/plot/elevation


  		




  12
  
  
    
elev_max_m,"/*_ID/plot/{elevation/max,elevationRange/to}"


  		




  13
  
  
    
elev_min_m,"/*_ID/plot/{elevation/min,elevationRange/from}"


  		




  
  12
  
    
elev_max_m,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"


  		




  
  13
  
    
elev_min_m,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"


  		




  14
  14
  
    
temp_c,"/definedValue[@fkey=tableRecord_ID,userDefined[tableName=observation,userDefinedName=temperatureC]]/definedValue"


  		




  15
  15
  
    
precip_mm,"/definedValue[@fkey=tableRecord_ID,userDefined[tableName=observation,userDefinedName=precipitationMm]]/definedValue"


  		




  16
  16
  
    
slope_aspect,/*_ID/plot/slopeAspect


  		












  

    
      mappings/VegX-VegBank.plots.csv
    
  





  28
  28
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,/*_ID/plot/realLongitude


  		




  29
  29
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/FootprintWKT,/*_ID/plot/dsgpoly


  		




  30
  30
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,/waterDepth/max


  		




  31
  
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,"/*_ID/plot/{elevation/max,elevationRange/to}"


  		




  
  31
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,"/*_ID/plot/{elevation/_avg/max,elevationRange/_range/to}"


  		




  32
  32
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,/waterDepth/min


  		




  33
  
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,"/*_ID/plot/{elevation/min,elevationRange/from}"


  		




  
  33
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,"/*_ID/plot/{elevation/_avg/min,elevationRange/_range/from}"


  		




  34
  34
  
    
/*UniqueIdentifierID->/*s/plot/geospatial/verbatimElevation,/*_ID/plot/elevation


  		




  35
  35
  
    
/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/*_ID/plot/authorPlotCode


  		




  36
  36
  
    
/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/{*_ID/plot/authorPlotCode,authorObsCode}"


  		












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