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Revision 6485

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/NY/Specimen/map.csv: Omit UniqueNYInternalRecordNumber to avoid confusion since this is an internal-only ID. This makes InstitutionCode+CollectionCode+CatalogNumber the globally unique identifier instead.

View differences:

inputs/NY/Specimen/map.csv
52 52 
PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",
53 53 
Substrate,locality,"/_join/2/_label[label=""substrate""]/value",
54 54 
Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",
55 
UniqueNYInternalRecordNumber,occurrenceID,,
55 
UniqueNYInternalRecordNumber,OMIT,,"Globally unique when provided, but omitted to avoid confusion since this is an internal-only ID"
inputs/NY/Specimen/VegBIEN.csv
1 1 
NY,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 2 
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists",
3 
UniqueNYInternalRecordNumber,"/_if[@name=""if specimen""]/cond/_exists",
4 3 
InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
5 
UniqueNYInternalRecordNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1",
6 4 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
7 5 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
8 
UniqueNYInternalRecordNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
9 6 
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then",
10 7 
CollectionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1",
11 8 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",
12 9 
MaximumElevation,/location/elevation_m/_alt/2/_avg/max,
13 10 
MinimumElevation,/location/elevation_m/_alt/2/_avg/min/_nullIf:[null=.]/value,
14 11 
FieldNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition
15 
UniqueNYInternalRecordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
16 12 
Locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/1,
17 13 
Substrate,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/2/_label[label=""substrate""]/value",
18 14 
Vegetation,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_join/3/_label[label=""vegetation""]/value",
......
28 24 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
29 25 
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
30 26 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
31 
UniqueNYInternalRecordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
32 27 
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname",
33 28 
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name",
34 
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
35 29 
FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",Usage inconsistent with DwC definition
36 30 
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
37 31 
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
38 32 
FieldNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",Usage inconsistent with DwC definition
39 
UniqueNYInternalRecordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
40 
UniqueNYInternalRecordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3,
41 33 
IdentifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
42 34 
ScientificName,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/null/_first/1",
43 35 
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value",
......
104 96 
RelationshipType,,** No join mapping for relationshipOfResource **
105 97 
TimeOfDay,,** No join mapping for eventTime **
106 98 
TypeStatus,,** No join mapping for typeStatus **
99 
UniqueNYInternalRecordNumber,,"** No non-empty join mapping for OMIT ** Globally unique when provided, but omitted to avoid confusion since this is an internal-only ID"
107 100 
key,,** No non-empty join mapping for OMIT ** UniqueNYInternalRecordNumber is a better pkey
inputs/NY/Specimen/test.xml.ref
8 8 
                <path>
9 9 
                    <location>
10 10 
                        <authorlocationcode>
11 
                            <_alt>
12 
                                <1>$UniqueNYInternalRecordNumber</1>
13 
                                <2>
14 
                                    <_join>
15 
                                        <1>$InstitutionCode</1>
16 
                                        <2>$CollectionCode</2>
17 
                                        <3>$CatalogNumber</3>
18 
                                    </_join>
19 
                                </2>
20 
                            </_alt>
11 
                            <_join>
12 
                                <1>$InstitutionCode</1>
13 
                                <2>$CollectionCode</2>
14 
                                <3>$CatalogNumber</3>
15 
                            </_join>
21 16 
                        </authorlocationcode>
22 17 
                        <elevation_m>
23 18 
                            <_avg>
......
116 111 
                                                    <name>$InstitutionCode</name>
117 112 
                                                </sourcename>
118 113 
                                            </institution_id>
119 
                                            <sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode>
120 114 
                                        </specimenreplicate>
121 115 
                                    </plantobservation>
122 116 
                                </aggregateoccurrence>
123 117 
                                <collector_id><party><fullname>$Collector</fullname></party></collector_id>
124 
                                <sourceaccessioncode>$UniqueNYInternalRecordNumber</sourceaccessioncode>
125 118 
                                <taxondetermination>
126 119 
                                    <party_id><party><fullname>$IdentifiedBy</fullname></party></party_id>
127 120 
                                    <taxonverbatim_id>
inputs/NY/Specimen/new_terms.csv
2 2 
PlantFungusDescription,fieldNotes,"/_join/2/_label[label=""plant fungus""]/value",
3 3 
Substrate,locality,"/_join/2/_label[label=""substrate""]/value",
4 4 
Vegetation,locality,"/_join/3/_label[label=""vegetation""]/value",
5 
UniqueNYInternalRecordNumber,occurrenceID,,
5 
UniqueNYInternalRecordNumber,OMIT,,"Globally unique when provided, but omitted to avoid confusion since this is an internal-only ID"

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