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Revision 26

Added by Aaron Marcuse-Kubitza about 13 years ago

In data2xml, fixed pointer handling to deal with pointer targets that are themselves pointers

View differences:

scripts/data2xml/NYBG-VegBank-VegX_mapping.csv
1 1 
"NYBG","VegBank","VegX"
2 2 
"key",,
3 3 
"DateLastModified",,
4 
"InstitutionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/firstName","/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/firstName"
5 
"CollectionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/lastName","/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/lastName"
6 
"CatalogNumber","/taxonInterpretation/museumAccessionNumber","/*s/taxonNameUsageConcept/voucher"
7 
"ScientificName","/plantName/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonNameID->/*s/taxonName/Simple"
4 
"InstitutionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/firstName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/firstName"
5 
"CollectionCode","/taxonInterpretation/museum_ID->/party/OrganizationName/_name/lastName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept/partyWithRole/partyID->/parties/party/organizationName/_name/lastName"
6 
"CatalogNumber","/taxonInterpretation/museumAccessionNumber","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept/voucher"
7 
"ScientificName","/plantName/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonNameID->/*s/taxonName/Simple"
8 8 
"BasisOfRecord",,
9 
"Kingdom","/plantName[plantStatus/plantLevel=Kingdom]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=reg]/Name"
10 
"Phylum","/plantName[plantStatus/plantLevel=Subkingdom]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=phyl_div]/Name"
11 
"Class","/plantName[plantStatus/plantLevel=Class]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=cl]/Name"
12 
"Order","/plantName[plantStatus/plantLevel=Order]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=ord]/Name"
13 
"Family","/plantName[plantStatus/plantLevel=Family]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=fam]/Name"
14 
"Genus","/plantName[plantStatus/plantLevel=Genus]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=gen]/Name"
15 
"Species","/plantName[plantStatus/plantLevel=Species]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=sp]/Name"
16 
"Subspecies","/plantName[plantStatus/plantLevel=Subspecies]/plantName","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=ssp]/Name"
17 
"ScientificNameAuthor","/plantConcept/reference_ID->/referenceParty/{givenName,surname}","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept/AccordingTo/Simple"
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"
9 
"Kingdom","/plantName[plantStatus/plantLevel=Kingdom]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=reg]/Name"
10 
"Phylum","/plantName[plantStatus/plantLevel=Subkingdom]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=phyl_div]/Name"
11 
"Class","/plantName[plantStatus/plantLevel=Class]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=cl]/Name"
12 
"Order","/plantName[plantStatus/plantLevel=Order]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=ord]/Name"
13 
"Family","/plantName[plantStatus/plantLevel=Family]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=fam]/Name"
14 
"Genus","/plantName[plantStatus/plantLevel=Genus]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=gen]/Name"
15 
"Species","/plantName[plantStatus/plantLevel=Species]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=sp]/Name"
16 
"Subspecies","/plantName[plantStatus/plantLevel=Subspecies]/plantName","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept[Rank/@code=ssp]/Name"
17 
"ScientificNameAuthor","/plantConcept/reference_ID->/referenceParty/{givenName,surname}","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/*s/taxonRelationshipAssertion!/assertion/taxonConceptID->/*s/taxonConcept/AccordingTo/Simple"
18 
"IdentifiedBy","/taxonInterpretation/PARTY_ID->/party/{givenName,middleName,surName}","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/partyWithRole[role=identifier]/partyID->/parties/party/individualName/{givenName,surName}"
19 
"YearIdentified","/taxonInterpretation/interpretationDate/_date/year","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/year"
20 
"MonthIdentified","/taxonInterpretation/interpretationDate/_date/month","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/month"
21 
"DayIdentified","/taxonInterpretation/interpretationDate/_date/day","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/date/_date/day"
22 22 
"TypeStatus",,
23 23 
"CollectorNumber",,
24 
"FieldNumber","/taxonInterpretation/collectionNumber","/*s/taxonNameUsageConcept/authorCode"
25 
"Collector","/taxonInterpretation/collector_ID->/party/{givenName,middleName,surName}","/*s/taxonNameUsageConcept->/*s/taxonDetermination[taxonNameUsageConceptID]/partyWithRole[role=collector]/partyID->/parties/party/individualName/{givenName,surName}"
24 
"FieldNumber","/taxonInterpretation/collectionNumber","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept/authorCode"
25 
"Collector","/taxonInterpretation/collector_ID->/party/{givenName,middleName,surName}","/*s/individualOrganism/taxonNameUsageConceptsID->/*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"
......
47 47 
"PreviousCatalogNumber",,
48 48 
"RelationshipType",,
49 49 
"RelatedCatalogItem",,
50 
"Notes","/taxonInterpretation/notes","/*s/taxonNameUsageConcept/note/text"
50 
"Notes","/taxonInterpretation/notes","/*s/individualOrganism/taxonNameUsageConceptsID->/*s/taxonNameUsageConcept/note/text"
51 51 
"Habitat","/userDefined[tableName=stemLocation,userDefinedName=habitat]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=habitat]/value"
52 52 
"PlantFungusDescription","/userDefined[tableName=stemLocation,userDefinedName=plantFungusDescription]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=plantFungusDescription]/value"
53 53 
"Substrate","/userDefined[tableName=stemLocation,userDefinedName=substrate]/definedValue ","/*s/individualOrganismObservation/simpleUserdefined[name=substrate]/value"
scripts/data2xml/xpath.py
82 82
83 83 
    def _value(self): return self._match_re(r'[\w.|]+', required=True)
84 84 

  		




  85
  
  
    
types_id_level = 1


  		




  
  85
  
    
instance_level = 1


  		




  86
  86
  
    

  		




  
  87
  
    
def obj(path):


  		




  
  88
  
    
    obj_path = deepcopy(path[:instance_level+1])


  		




  
  89
  
    
    obj_path[-1].is_ptr = False # prevent pointer w/o target


  		




  
  90
  
    
    return obj_path


  		




  
  91
  
    

  		




  87
  92
  
    
def set_id(path, id_, has_types=True):


  		




  88
  
  
    
    if has_types: id_level = types_id_level


  		




  
  93
  
    
    if has_types: id_level = instance_level


  		




  89
  94
  
    
    else: id_level = 0


  		




  90
  95
  
    
    path[id_level].attrs.append([XpathElem('id', id_, is_attr=True)])


  		




  91
  96
  
    

  		




  ......




  125
  130
  
    
        # Follow pointer


  		




  126
  131
  
    
        if elem.is_ptr:


  		




  127
  132
  
    
            path = deepcopy(path[elem_idx+1:]) # rest of path


  		




  128
  
  
    
            attrs = path[types_id_level].attrs


  		




  
  133
  
    
            attrs = path[instance_level].attrs


  		




  129
  134
  
    
            if len(attrs) >= 1 and value(attrs[0]) == None:


  		




  130
  135
  
    
                # backward (child-to-parent) pointer with target ID attr


  		




  131
  136
  
    
                set_value(attrs[0], xml_util.get_id(node))


  		




  132
  137
  
    
            else: # forward (parent-to-child) pointer


  		




  133
  138
  
    
                id_ = xml_util.value(node)


  		




  134
  
  
    
                obj_path = path[:types_id_level+1] # target object


  		




  
  139
  
    
                obj_path = obj(path) # target object


  		




  135
  140
  
    
                if id_ == None or get(doc, obj_path, False, True) == None:


  		




  136
  141
  
    
                    # no target or target attrs don't match


  		




  137
  142
  
    
                    if not create: return None


  		




  138
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  139
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                    # Use last target object's ID + 1


  		




  140
  
  
    
                    last_path = deepcopy(obj_path)


  		




  141
  
  
    
                    last_path[-1].attrs = [] # just get by tag name


  		




  142
  
  
    
                    last = get(doc, last_path, False, True)


  		




  
  145
  
    
                    obj_path[-1].attrs = [] # just get by tag name


  		




  
  146
  
    
                    last = get(doc, obj_path, False, True)


  		




  143
  147
  
    
                    if last != None: id_ = str(int(xml_util.get_id(last)) + 1)


  		




  144
  148
  
    
                    else: id_ = '0'


  		




  145
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