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Revision 7518

Added by Aaron Marcuse-Kubitza about 12 years ago

inputs/ARIZ/Specimen/map.csv: Fixed bug where the column names for InstitutionCode and CollectionCode were reversed in the source data

View differences:

inputs/ARIZ/Specimen/map.csv
2 2 
GlobalUniqueIdentifier,occurrenceID,,
3 3 
DateLastModified,modified,,
4 4 
BasisOfRecord,basisOfRecord,,
5 
InstitutionCode,institutionCode,,
6 
CollectionCode,collectionCode,,
5 
InstitutionCode,collectionCode,,Column names are reversed
6 
CollectionCode,institutionCode,,Column names are reversed
7 7 
CatalogNumber,catalogNumber,/_alt/2,Don't overwrite CatalogNumberNumeric
8 8 
CatalogNumberNumeric,catalogNumber,/_alt/1,
9 9 
Collector,recordedBy,,
inputs/ARIZ/Specimen/VegBIEN.csv
2 2 
GlobalUniqueIdentifier,"/_if[@name=""if specimen""]/cond/_exists",
3 3 
CatalogNumberNumeric,"/_if[@name=""if specimen""]/cond/_exists/_alt/1",
4 4 
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric
5 
InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
5 
CollectionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",Column names are reversed
6 6 
GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1",
7 7 
CatalogNumberNumeric,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1",
8 8 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric
9 9 
GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
10 10 
CatalogNumberNumeric,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/1",
11 11 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric
12 
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then",
13 
CollectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
12 
CollectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then",Column names are reversed
13 
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",Column names are reversed
14 14 
CatalogNumberNumeric,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/1",
15 15 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric
16 16 
MaximumElevationInMeters,/location/elevation_m/_alt/2/_avg/max,"Contains some verbatim values, including ranges and units"
......
33 33 
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
34 34 
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",
35 35 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric
36 
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
36 
InstitutionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Column names are reversed; Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name
37 37 
CollectorNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else",
38 38 
GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
39 39 
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1",
40 40 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric
41 
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name",
42 
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_split:[separator=""[,;] *""]/value",
41 
CollectionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name",Column names are reversed
42 
CollectionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_split:[separator=""[,;] *""]/value",Column names are reversed
43 43 
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
44 44 
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
45 45 
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",Contains the binomial in addition to the authority
inputs/ARIZ/Specimen/test.xml.ref
12 12 
                                <1>$GlobalUniqueIdentifier</1>
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                                <2>
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                                    <_join>
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                                        <1>$InstitutionCode</1>
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                                        <2>$CollectionCode</2>
15 
                                        <1>$CollectionCode</1>
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                                        <2>$InstitutionCode</2>
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                                        <3>
18 18 
                                            <_alt>
19 19 
                                                <1>$CatalogNumberNumeric</1>
......
84 84 
                                                    <2>$CatalogNumber</2>
85 85 
                                                </_alt>
86 86 
                                            </catalognumber_dwc>
87 
                                            <collectioncode_dwc>$CollectionCode</collectioncode_dwc>
87 
                                            <collectioncode_dwc>$InstitutionCode</collectioncode_dwc>
88 88 
                                            <collectionnumber>$CollectorNumber</collectionnumber>
89 89 
                                            <institution_id>
90 90 
                                                <sourcelist>
91 
                                                    <name>$InstitutionCode</name>
91 
                                                    <name>$CollectionCode</name>
92 92 
                                                    <sourcename>
93 93 
                                                        <name>
94 94 
                                                            <_split>
95 95 
                                                                <separator>[,;] *</separator>
96 
                                                                <value>$InstitutionCode</value>
96 
                                                                <value>$CollectionCode</value>
97 97 
                                                            </_split>
98 98 
                                                        </name>
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                                                    </sourcename>

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