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Revision 24

Added by Aaron Marcuse-Kubitza about 13 years ago

In data2xml, fixed backward (child-to-parent) pointer handling to get and set attribute values properly

View differences:

scripts/data2xml/NYBG-VegBank-VegX_mapping.csv
4 4 
"InstitutionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/firstName","/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/firstName"
5 5 
"CollectionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/lastName","/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/lastName"
6 6 
"CatalogNumber","/taxonInterpretation/museumAccessionNumber","/*s/taxonNameUsageConcept/voucher"
7 
"ScientificName","/plantName/plantName","/*s/taxonName/Simple"
7 
"ScientificName","/plantName/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion/assertion/taxonNameID->/*s/taxonName/Simple"
8 8 
"BasisOfRecord",,
9 9 
"Kingdom","/plantName[plantStatus/plantLevel=Kingdom]/plantName","/*s/taxonConcept[Rank/@code=reg]/Name"
10 10 
"Phylum","/plantName[plantStatus/plantLevel=Subkingdom]/plantName","/*s/taxonConcept[Rank/@code=phyl_div]/Name"
......
15 15 
"Species","/plantName[plantStatus/plantLevel=Species]/plantName","/*s/taxonConcept[Rank/@code=sp]/Name"
16 16 
"Subspecies","/plantName[plantStatus/plantLevel=Subspecies]/plantName","/*s/taxonConcept[Rank/@code=ssp]/Name"
17 17 
"ScientificNameAuthor","/plantConcept/reference_ID->/referenceParty/{givenName,surname}","/*s/taxonConcept/AccordingTo/Simple"
18 
"IdentifiedBy","/taxonInterpretation/PARTY_ID->/party/{givenName,middleName,surName}","/*s/taxonDetermination/partyWithRole[role=identifier]/partyID->/parties/party/individualName/{givenName,surName}"
19 
"YearIdentified","/taxonInterpretation/interpretationDate/_date/year","/*s/taxonDetermination/date/_date/year"
20 
"MonthIdentified","/taxonInterpretation/interpretationDate/_date/month","/*s/taxonDetermination/date/_date/month"
21 
"DayIdentified","/taxonInterpretation/interpretationDate/_date/day","/*s/taxonDetermination/date/_date/day"
18 
"IdentifiedBy","/taxonInterpretation/PARTY_ID->/party/{givenName,middleName,surName}","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/partyWithRole[role=identifier]/partyID->/parties/party/individualName/{givenName,surName}"
19 
"YearIdentified","/taxonInterpretation/interpretationDate/_date/year","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/year"
20 
"MonthIdentified","/taxonInterpretation/interpretationDate/_date/month","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/month"
21 
"DayIdentified","/taxonInterpretation/interpretationDate/_date/day","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/day"
22 22 
"TypeStatus",,
23 23 
"CollectorNumber",,
24 24 
"FieldNumber","/taxonInterpretation/collectionNumber","/*s/taxonNameUsageConcept/authorCode"
25 
"Collector","/taxonInterpretation/collector_ID->/party/{givenName,middleName,surName}","/*s/taxonDetermination/partyWithRole[role=collector]/partyID->/parties/party/individualName/{givenName,surName}"
25 
"Collector","/taxonInterpretation/collector_ID->/party/{givenName,middleName,surName}","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/partyWithRole[role=collector]/partyID->/parties/party/individualName/{givenName,surName}"
26 26 
"YearCollected","/taxonInterpretation/collectionDate/_date/year","/*s/plotObservation/obsStartDate/_date/year"
27 27 
"MonthCollected","/taxonInterpretation/collectionDate/_date/month","/*s/plotObservation/obsStartDate/_date/month"
28 28 
"DayCollected","/taxonInterpretation/collectionDate/_date/day","/*s/plotObservation/obsStartDate/_date/day"
......
32 32 
"Country","/namedPlace[placeSystem=area|country|territory]/placeName","/*s/plot/country"
33 33 
"StateProvince","/namedPlace[placeSystem=region|state|province]/placeName","/*s/plot/state"
34 34 
"County","/namedPlace[placeSystem=county]/placeName","/*s/plot/county"
35 
"Locality","/namedPlace/placeDescription","/*s/plot/simpleUserdefined[name=<name>]/value"
35 
"Locality","/namedPlace/placeDescription","/*s/plot/simpleUserdefined[name=locality]/value"
36 36 
"Longitude","/plot/realLongitude","/*s/plot/geospatial/DecimalLongitude"
37 37 
"Latitude","/plot/realLatitude","/*s/plot/geospatial/DecimalLatitude"
38 38 
"CoordinatePrecision","/plot/locationAccuracy","/*s/plot/geospatial/CoordinateUncertaintyInMeters"
......
41 41 
"MaximumElevation","/plot/elevation/max,plot/elevationRange/to","/*s/plot/geospatial/maximumElevationInMeters"
42 42 
"MinimumDepth","/observation/waterDepth/min","/*s/plot/geospatial/minimumDepthInMeters"
43 43 
"MaximumDepth","/observation/waterDepth/max","/*s/plot/geospatial/maximumDepthInMeters"
44 
"Sex","/userDefined[tableName=taxonInterpretation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=<name>]/value"
44 
"Sex","/userDefined[tableName=taxonInterpretation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=sex]/value"
45 45 
"PreparationType",,
46 46 
"IndividualCount",,
47 47 
"PreviousCatalogNumber",,
48 48 
"RelationshipType",,
49 49 
"RelatedCatalogItem",,
50 50 
"Notes","/taxonInterpretation/notes","/*s/taxonNameUsageConcept/note/text"
51 
"Habitat","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=<name>]/value"
52 
"PlantFungusDescription","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=<name>]/value"
53 
"Substrate","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=<name>]/value"
54 
"Vegetation","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=<name>]/value"
51 
"Habitat","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=habitat]/value"
52 
"PlantFungusDescription","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=plantFungusDescription]/value"
53 
"Substrate","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=substrate]/value"
54 
"Vegetation","/userDefined[tableName=stemLocation,userDefinedName=<name>]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=vegetation]/value"
55 55 
"UniqueNYInternalRecordNumber",,
scripts/data2xml/xpath.py
25 25
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    def __eq__(self, other): return self.__dict__ == other.__dict__
27 27 

  		




  
  28
  
    
def value(path): return path[-1].value


  		




  
  29
  
    

  		




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def set_value(path, value): path[-1].value = value


  		




  29
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class XpathParser(Parser):


  		




  ......




  116
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        if elem.is_ptr:


  		




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            target = deepcopy(path[elem_idx+1:]) # rest of path


  		




  118
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            attrs = target[types_id_level].attrs


  		




  119
  
  
    
            if len(attrs) >= 1 and attrs[0].value == None:


  		




  
  121
  
    
            if len(attrs) >= 1 and value(attrs[0]) == None:


  		




  120
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                # backward (child-to-parent) pointer with target ID attr


  		




  121
  
  
    
                attrs[0].value = xml_util.get_id(node)


  		




  
  123
  
    
                set_value(attrs[0], xml_util.get_id(node))


  		




  122
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            else: # forward (parent-to-child) pointer


  		




  123
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                id_ = xml_util.value(node)


  		




  124
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                if id_ == None:


  		












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