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Revision 1832

Added by Aaron Marcuse-Kubitza almost 13 years ago

xml_dom.py: value(): Skip comment nodes. This fixes a bug where comments inside text elements would prevent the value from being retrieved.

View differences:

inputs/CTFS/test/VegX.organisms.xml.ref
2 2 
<VegX xmlns:tcs="http://www.tdwg.org/schemas/tcs/1.01">
3 3 
    <individualOrganismObservations id="0">
4 4 
        <individualOrganismObservation>
5 
            <individualOrganismID>0</individualOrganismID>
5 6 
            <plotObservationID>0</plotObservationID>
6 7 
            <relativePlotPosition>
7 8 
                <relativeX>-79.848494</relativeX>
......
13 14 
            </simpleUserdefined>
14 15 
        </individualOrganismObservation>
15 16 
    </individualOrganismObservations>
17 
    <individualOrganisms>
18 
        <individualOrganism id="0"><taxonNameUsageConceptID>0</taxonNameUsageConceptID></individualOrganism>
19 
        <individualOrganism id="1"><taxonNameUsageConceptID>1</taxonNameUsageConceptID></individualOrganism>
20 
    </individualOrganisms>
21 
    <taxonNameUsageConcepts>
22 
        <taxonNameUsageConcept id="0"/>
23 
        <taxonNameUsageConcept id="1"/>
24 
    </taxonNameUsageConcepts>
25 
    <taxonDeterminations>
26 
        <taxonDetermination>
27 
            <taxonNameUsageConceptID>0</taxonNameUsageConceptID>
28 
            <partyWithRole><role>computer</role></partyWithRole>
29 
            <taxonRelationshipAssertions><taxonRelationshipAssertion><assertion><taxonConceptID>0</taxonConceptID></assertion></taxonRelationshipAssertion></taxonRelationshipAssertions>
30 
        </taxonDetermination>
31 
        <taxonDetermination>
32 
            <taxonNameUsageConceptID>0</taxonNameUsageConceptID>
33 
            <partyWithRole><role>identifier</role></partyWithRole>
34 
            <taxonRelationshipAssertions>
35 
                <taxonRelationshipAssertion><assertion><taxonConceptID>1</taxonConceptID></assertion></taxonRelationshipAssertion>
36 
                <taxonRelationshipAssertion><assertion><taxonConceptID>2</taxonConceptID></assertion></taxonRelationshipAssertion>
37 
            </taxonRelationshipAssertions>
38 
        </taxonDetermination>
39 
        <taxonDetermination>
40 
            <taxonNameUsageConceptID>1</taxonNameUsageConceptID>
41 
            <partyWithRole><role>computer</role></partyWithRole>
42 
            <taxonRelationshipAssertions><taxonRelationshipAssertion><assertion><taxonConceptID>3</taxonConceptID></assertion></taxonRelationshipAssertion></taxonRelationshipAssertions>
43 
        </taxonDetermination>
44 
        <taxonDetermination>
45 
            <taxonNameUsageConceptID>1</taxonNameUsageConceptID>
46 
            <partyWithRole><role>identifier</role></partyWithRole>
47 
            <taxonRelationshipAssertions>
48 
                <taxonRelationshipAssertion><assertion><taxonConceptID>4</taxonConceptID></assertion></taxonRelationshipAssertion>
49 
                <taxonRelationshipAssertion><assertion><taxonConceptID>5</taxonConceptID></assertion></taxonRelationshipAssertion>
50 
            </taxonRelationshipAssertions>
51 
        </taxonDetermination>
52 
    </taxonDeterminations>
53 
    <taxonConcepts>
54 
        <taxonConcept id="0">
55 
            <tcs:Rank code="sp"/>
56 
            <tcs:Name>prunifolius</tcs:Name>
57 
        </taxonConcept>
58 
        <taxonConcept id="1">
59 
            <tcs:Rank code="fam"/>
60 
            <tcs:Name>Violaceae</tcs:Name>
61 
        </taxonConcept>
62 
        <taxonConcept id="2">
63 
            <tcs:Rank code="gen"/>
64 
            <tcs:Name>Hybanthus</tcs:Name>
65 
        </taxonConcept>
66 
        <taxonConcept id="3">
67 
            <tcs:Rank code="sp"/>
68 
            <tcs:Name>asterolepis</tcs:Name>
69 
        </taxonConcept>
70 
        <taxonConcept id="4">
71 
            <tcs:Rank code="fam"/>
72 
            <tcs:Name>Malvaceae</tcs:Name>
73 
        </taxonConcept>
74 
        <taxonConcept id="5">
75 
            <tcs:Rank code="gen"/>
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            <tcs:Name>Quararibea</tcs:Name>
77 
        </taxonConcept>
78 
    </taxonConcepts>
16 79 
    <plotObservations>
17 80 
        <plotObservation id="0"><obsStartDate>1981-05-03</obsStartDate></plotObservation>
18 81 
        <plotObservation id="1"><obsStartDate>1981-05-03</obsStartDate></plotObservation>
19 82 
    </plotObservations>
20 83 
    <individualOrganismObservations id="1">
21 84 
        <individualOrganismObservation>
85 
            <individualOrganismID>1</individualOrganismID>
22 86 
            <plotObservationID>1</plotObservationID>
23 87 
            <relativePlotPosition>
24 88 
                <relativeX>-79.84848</relativeX>
inputs/CTFS/test/VegBIEN.organisms.xml.ref
21 21 
                <definedvalue>1</definedvalue>
22 22 
            </definedvalue>
23 23 
        </aggregateoccurrence>
24 
        <taxondetermination>
25 
            <role>computer</role>
26 
            <iscurrent>true</iscurrent>
27 
            <plantconcept_id>
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                <plantconcept>
29 
                    <plantname_id>
30 
                        <plantname>
31 
                            <rank>species</rank>
32 
                            <plantname>prunifolius</plantname>
33 
                        </plantname>
34 
                    </plantname_id>
35 
                </plantconcept>
36 
            </plantconcept_id>
37 
        </taxondetermination>
38 
        <taxondetermination>
39 
            <role>identifier</role>
40 
            <isoriginal>true</isoriginal>
41 
            <iscurrent>true</iscurrent>
42 
            <plantconcept_id>
43 
                <plantconcept>
44 
                    <plantname_id>
45 
                        <plantname>
46 
                            <rank>genus</rank>
47 
                            <plantname>Hybanthus</plantname>
48 
                            <parent_id>
49 
                                <plantname>
50 
                                    <rank>family</rank>
51 
                                    <plantname>Violaceae</plantname>
52 
                                </plantname>
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                            </parent_id>
54 
                        </plantname>
55 
                    </plantname_id>
56 
                </plantconcept>
57 
            </plantconcept_id>
58 
        </taxondetermination>
24 59 
    </taxonoccurrence>
25 60 
    <taxonoccurrence id="1">
26 61 
        <locationevent_id><locationevent><obsstartdate>1981-05-03</obsstartdate></locationevent></locationevent_id>
......
43 78 
                <definedvalue>1</definedvalue>
44 79 
            </definedvalue>
45 80 
        </aggregateoccurrence>
81 
        <taxondetermination>
82 
            <role>computer</role>
83 
            <iscurrent>true</iscurrent>
84 
            <plantconcept_id>
85 
                <plantconcept>
86 
                    <plantname_id>
87 
                        <plantname>
88 
                            <rank>species</rank>
89 
                            <plantname>asterolepis</plantname>
90 
                        </plantname>
91 
                    </plantname_id>
92 
                </plantconcept>
93 
            </plantconcept_id>
94 
        </taxondetermination>
95 
        <taxondetermination>
96 
            <role>identifier</role>
97 
            <isoriginal>true</isoriginal>
98 
            <iscurrent>true</iscurrent>
99 
            <plantconcept_id>
100 
                <plantconcept>
101 
                    <plantname_id>
102 
                        <plantname>
103 
                            <rank>genus</rank>
104 
                            <plantname>Quararibea</plantname>
105 
                            <parent_id>
106 
                                <plantname>
107 
                                    <rank>family</rank>
108 
                                    <plantname>Malvaceae</plantname>
109 
                                </plantname>
110 
                            </parent_id>
111 
                        </plantname>
112 
                    </plantname_id>
113 
                </plantconcept>
114 
            </plantconcept_id>
115 
        </taxondetermination>
46 116 
    </taxonoccurrence>
47 117 
</VegBIEN>
inputs/CTFS/test/import.organisms.out.ref
1 
Inserted 13 new rows into database
1 
Inserted 27 new rows into database
lib/xml_dom.py
147 147 
def is_text(node): return has_one_child(node) and is_text_node(node.firstChild)
148 148 

  		




  149
  149
  
    
def value(node):


  		




  150
  
  
    
    if node.firstChild != None: return node.firstChild.nodeValue


  		




  
  150
  
    
    if is_elem(node):


  		




  
  151
  
    
        iter_ = NodeIter(node)


  		




  
  152
  
    
        util.skip(iter_, is_comment)


  		




  
  153
  
    
        try: return iter_.next().nodeValue


  		




  
  154
  
    
        except StopIteration: return None


  		




  151
  155
  
    
    else: return node.nodeValue


  		




  152
  156
  
    

  		




  153
  157
  
    
def is_whitespace(node): return is_text_node(node) and value(node).isspace()


  		












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