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Revision 10566

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/NCU/Specimen/map.csv: OwnerInstitution: remapped to specimenOwner rather than specimenHolderInstitutions. OwnerInstitution, CatalogSeriesPrefix: documented the VegCore SQL dotpath (http://wiki.vegpath.org/SQL_dotpaths) that would be used to refer to the field. this specifies the destination field at a much finer level of detail than the one-size-fits-all denormalized name.

View differences:

inputs/NCU/Specimen/map.csv
5 5 
CollectionObjectTypeID,*CollectionObjectTypeID,,
6 6 
CollectionObjectID,*CollectionObjectID,,
7 7 
database,*database,,
8 
OwnerInstitution,specimenHolderInstitutions,/_alt/2,
8 
OwnerInstitution,specimenOwner,,= specimen.owner_collection.institution.name
9 9 
CollectionGUID,collectionURL,,
10 10 
OriginalTaxonLabel,originalScientificName,,
11 11 
CurrentScientificName,taxonName,,
......
14 14 
CollectionDate,dateCollected,,
15 15 
BarCode,OMIT#BarCode,,"Omitted because this isn't specified on all rows, but SpecimenPK is"
16 16 
CatalogNumber,accessionNumber,,
17 
CatalogSeriesPrefix,specimenHolderInstitutions,/_alt/1,
17 
CatalogSeriesPrefix,specimenHolderInstitutions,,= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
18 18 
Description,occurrenceRemarks,,
19 19 
LandOwner,*LandOwner,,
20 20 
BlockLocationReason,*BlockLocationReason,,
inputs/NCU/Specimen/VegBIEN.csv
1 1 
NCU,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 3 
SpecimenPK,"/_if[@name=""if specimen""]/cond/_exists",
4 
CatalogSeriesPrefix,"/_if[@name=""if specimen""]/else/source/shortname/_first/1/_alt/1",
5 
OwnerInstitution,"/_if[@name=""if specimen""]/else/source/shortname/_first/1/_alt/2",
4 
CatalogSeriesPrefix,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
6 5 
SpecimenPK,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1",
7 6 
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
8 7 
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",
9 8 
SpecimenPK,"/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 
CatalogSeriesPrefix,"/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/_first/2/_alt/1",
11 
OwnerInstitution,"/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/_first/2/_alt/2",
9 
CatalogSeriesPrefix,"/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/_first/2",= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
12 10 
CollectionGUID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2",
13 11 
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",
14 12 
SpecimenPK,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
......
23 21 
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else","Actually the collector's number, not remarks"
24 22 
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
25 23 
SpecimenPK,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
26 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2/_alt/1",
27 
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2/_alt/2",
28 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value/_alt/1",
29 
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value/_alt/2",
24 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
25 
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
30 26 
SpecimenPK,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
31 27 
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3","Actually the collector's number, not remarks"
32 28 
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
......
70 66 
LastAnnotationDateVerbatim,,** No join mapping for *LastAnnotationDateVerbatim **
71 67 
LastAnnotationLabelTaxon,,** No join mapping for *LastAnnotationLabelTaxon **
72 68 
LastAnnotationRemarks,,** No join mapping for *LastAnnotationRemarks **
69 
OwnerInstitution,,** No join mapping for specimenOwner ** = specimen.owner_collection.institution.name
73 70 
TypeStatus,,** No join mapping for typeStatus **
74 71 
database,,** No join mapping for *database **
75 72 
lastAnnotationAgent,,** No join mapping for *lastAnnotationAgent **
inputs/NCU/Specimen/test.xml.ref
12 12 
                                <1>$SpecimenPK</1>
13 13 
                                <2>
14 14 
                                    <_join>
15 
                                        <1>
16 
                                            <_alt>
17 
                                                <1>$CatalogSeriesPrefix</1>
18 
                                                <2>$OwnerInstitution</2>
19 
                                            </_alt>
20 
                                        </1>
15 
                                        <1>$CatalogSeriesPrefix</1>
21 16 
                                        <2>$CollectionGUID</2>
22 17 
                                        <3>$CatalogNumber</3>
23 18 
                                    </_join>
......
38 33 
                                            <collectionnumber>$firstCollectorRemarks</collectionnumber>
39 34 
                                            <institution_id>
40 35 
                                                <sourcelist>
41 
                                                    <name>
42 
                                                        <_alt>
43 
                                                            <1>$CatalogSeriesPrefix</1>
44 
                                                            <2>$OwnerInstitution</2>
45 
                                                        </_alt>
46 
                                                    </name>
36 
                                                    <name>$CatalogSeriesPrefix</name>
47 37 
                                                    <sourcename>
48 38 
                                                        <name>
49 39 
                                                            <_split>
50 40 
                                                                <separator>[,;] *</separator>
51 
                                                                <value>
52 
                                                                    <_alt>
53 
                                                                        <1>$CatalogSeriesPrefix</1>
54 
                                                                        <2>$OwnerInstitution</2>
55 
                                                                    </_alt>
56 
                                                                </value>
41 
                                                                <value>$CatalogSeriesPrefix</value>
57 42 
                                                            </_split>
58 43 
                                                        </name>
59 44 
                                                    </sourcename>
inputs/NCU/Specimen/new_terms.csv
1 1 
SpecimenPK,occurrenceID,,
2 
OwnerInstitution,specimenHolderInstitutions,/_alt/2,
2 
OwnerInstitution,specimenOwner,,= specimen.owner_collection.institution.name
3 3 
CollectionGUID,collectionURL,,
4 4 
OriginalTaxonLabel,originalScientificName,,
5 5 
CurrentScientificName,taxonName,,
6 6 
CurrentScientificNameWithAuthor,scientificName,,
7 7 
CollectionDate,dateCollected,,
8 
CatalogSeriesPrefix,specimenHolderInstitutions,/_alt/1,
8 
CatalogSeriesPrefix,specimenHolderInstitutions,,= specimen.orig_collection.institution.acronym, specimen.specimenholder_institutions(0).acronym
9 9 
Description,occurrenceRemarks,,
10 10 
CityLocality,municipality,,
11 11 
Latitude1,decimalLatitude,,
inputs/NCU/Specimen/unmapped_terms.csv
3 3 
*CollectionObjectTypeID
4 4 
*CollectionObjectID
5 5 
*database
6 
specimenOwner
6 7 
typeStatus
7 8 
*LandOwner
8 9 
*BlockLocationReason

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