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Revision 10206

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/CTFS/*/map.csv: added *.src.row_num from joined tables so that the map.csv input columns would match the staging table. this is needed for the staging table column renaming, which is positional rather than name-based to work with any existing column name.

View differences:

inputs/CTFS/StemObservation/map.csv
5 5 
SubSpeciesID,*SubSpeciesID,,
6 6 
TreeID,*TreeID,,
7 7 
StemID,authorStemCode,,
8 
StemObservation.src.row_num,*StemObservation.src.row_num,,
8 9 
MeasureID,individualID,,
9 10 
CensusID,eventID,,
10 11 
DBH,diameterBreastHeight_cm,,Assuming units based on the range and precision of values. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>.
11 12 
HOM,*HOM,,
12 13 
PrimaryStem,*PrimaryStem,,
13 14 
ExactDate,*ExactDate,,
15 
Stem.src.row_num,*Stem.src.row_num,,
14 16 
StemTag,tag,,
15 17 
StemDescription,*StemDescription,,
18 
Organism.src.row_num,*Organism.src.row_num,,
16 19 
QuadratID,subplot,,Not globally unique; unique only within Site
17 20 
PlotID,locationID,,
18 21 
Tag,tag,,
19 22 
x,organismX_m,,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."
20 23 
y,organismY_m,,"Assuming units based on the size of values relative to plot area, which has units of ha. Not documented in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>."
24 
InfraspecificEpithet.src.row_num,*InfraspecificEpithet.src.row_num,,
21 25 
SubSpeciesCurrentTaxonFlag,*SubSpeciesCurrentTaxonFlag,,
22 26 
SubSpeciesObsoleteTaxonFlag,*SubSpeciesObsoleteTaxonFlag,,
23 27 
SubSpeciesName,subspecies,,
24 28 
SubSpeciesMnemonic,*SubSpeciesMnemonic,,
25 29 
SubSpeciesAuthority,*SubSpeciesAuthority,,
26 30 
InfraSpecificLevel,*InfraSpecificLevel,,
31 
SpecificEpithet.src.row_num,*SpecificEpithet.src.row_num,,
27 32 
SpeciesCurrentTaxonFlag,*SpeciesCurrentTaxonFlag,,
28 33 
SpeciesObsoleteTaxonFlag,*SpeciesObsoleteTaxonFlag,,
29 34 
SpeciesReferenceID,*SpeciesReferenceID,,
......
33 38 
IDLevel,*IDLevel,,
34 39 
FieldFamily,*FieldFamily,,
35 40 
Description,*Description,,
41 
Genus.src.row_num,*Genus.src.row_num,,
36 42 
Genus,genus,,
37 43 
GenusReferenceID,*GenusReferenceID,,
38 44 
GenusAuthority,*GenusAuthority,,
45 
Family.src.row_num,*Family.src.row_num,,
39 46 
Family,family,,
40 47 
ReferenceID,*ReferenceID,,
inputs/CTFS/StemObservation/VegBIEN.csv
45 45 
QuadratID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/2",Not globally unique; unique only within Site
46 46 
Description,,** No join mapping for *Description **
47 47 
ExactDate,,** No join mapping for *ExactDate **
48 
Family.src.row_num,,** No join mapping for *Family.src.row_num **
48 49 
FamilyID,,** No join mapping for *FamilyID **
49 50 
FieldFamily,,** No join mapping for *FieldFamily **
51 
Genus.src.row_num,,** No join mapping for *Genus.src.row_num **
50 52 
GenusAuthority,,** No join mapping for *GenusAuthority **
51 53 
GenusID,,** No join mapping for *GenusID **
52 54 
GenusReferenceID,,** No join mapping for *GenusReferenceID **
53 55 
HOM,,** No join mapping for *HOM **
54 56 
IDLevel,,** No join mapping for *IDLevel **
55 57 
InfraSpecificLevel,,** No join mapping for *InfraSpecificLevel **
58 
InfraspecificEpithet.src.row_num,,** No join mapping for *InfraspecificEpithet.src.row_num **
59 
Organism.src.row_num,,** No join mapping for *Organism.src.row_num **
56 60 
PrimaryStem,,** No join mapping for *PrimaryStem **
57 61 
ReferenceID,,** No join mapping for *ReferenceID **
58 62 
SpeciesCurrentTaxonFlag,,** No join mapping for *SpeciesCurrentTaxonFlag **
......
60 64 
SpeciesMnemonic,,** No join mapping for *SpeciesMnemonic **
61 65 
SpeciesObsoleteTaxonFlag,,** No join mapping for *SpeciesObsoleteTaxonFlag **
62 66 
SpeciesReferenceID,,** No join mapping for *SpeciesReferenceID **
67 
SpecificEpithet.src.row_num,,** No join mapping for *SpecificEpithet.src.row_num **
68 
Stem.src.row_num,,** No join mapping for *Stem.src.row_num **
63 69 
StemDescription,,** No join mapping for *StemDescription **
70 
StemObservation.src.row_num,,** No join mapping for *StemObservation.src.row_num **
64 71 
SubSpeciesAuthority,,** No join mapping for *SubSpeciesAuthority **
65 72 
SubSpeciesCurrentTaxonFlag,,** No join mapping for *SubSpeciesCurrentTaxonFlag **
66 73 
SubSpeciesID,,** No join mapping for *SubSpeciesID **
inputs/CTFS/StemObservation/unmapped_terms.csv
3 3 
*SpeciesID
4 4 
*SubSpeciesID
5 5 
*TreeID
6 
*StemObservation.src.row_num
6 7 
*HOM
7 8 
*PrimaryStem
8 9 
*ExactDate
10 
*Stem.src.row_num
9 11 
*StemDescription
12 
*Organism.src.row_num
13 
*InfraspecificEpithet.src.row_num
10 14 
*SubSpeciesCurrentTaxonFlag
11 15 
*SubSpeciesObsoleteTaxonFlag
12 16 
*SubSpeciesMnemonic
13 17 
*SubSpeciesAuthority
14 18 
*InfraSpecificLevel
19 
*SpecificEpithet.src.row_num
15 20 
*SpeciesCurrentTaxonFlag
16 21 
*SpeciesObsoleteTaxonFlag
17 22 
*SpeciesReferenceID
......
19 24 
*IDLevel
20 25 
*FieldFamily
21 26 
*Description
27 
*Genus.src.row_num
22 28 
*GenusReferenceID
23 29 
*GenusAuthority
30 
*Family.src.row_num
24 31 
*ReferenceID
inputs/CTFS/TaxonOccurrence/map.csv
3 3 
GenusID,*GenusID,,
4 4 
SpeciesID,*SpeciesID,,
5 5 
SubSpeciesID,*SubSpeciesID,,
6 
TaxonOccurrence.src.row_num,*TaxonOccurrence.src.row_num,,
6 7 
SpeciesInvID,taxonOccurrenceID,,
7 8 
CensusID,eventID,,
8 9 
PlotID,locationID,,
10 
InfraspecificEpithet.src.row_num,*InfraspecificEpithet.src.row_num,,
9 11 
SubSpeciesCurrentTaxonFlag,*SubSpeciesCurrentTaxonFlag,,
10 12 
SubSpeciesObsoleteTaxonFlag,*SubSpeciesObsoleteTaxonFlag,,
11 13 
SubSpeciesName,subspecies,,
12 14 
SubSpeciesMnemonic,*SubSpeciesMnemonic,,
13 15 
SubSpeciesAuthority,*SubSpeciesAuthority,,
14 16 
InfraSpecificLevel,UNUSED,,
17 
SpecificEpithet.src.row_num,*SpecificEpithet.src.row_num,,
15 18 
SpeciesCurrentTaxonFlag,*SpeciesCurrentTaxonFlag,,
16 19 
SpeciesObsoleteTaxonFlag,*SpeciesObsoleteTaxonFlag,,
17 20 
SpeciesReferenceID,*SpeciesReferenceID,,
......
21 24 
IDLevel,*IDLevel,,
22 25 
FieldFamily,*FieldFamily,,
23 26 
Description,*Description,,
27 
Genus.src.row_num,*Genus.src.row_num,,
24 28 
Genus,genus,,
25 29 
GenusReferenceID,*GenusReferenceID,,
26 30 
GenusAuthority,*GenusAuthority,,
31 
Family.src.row_num,*Family.src.row_num,,
27 32 
Family,family,,
28 33 
ReferenceID,*ReferenceID,,
inputs/CTFS/TaxonOccurrence/VegBIEN.csv
28 28 
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists",
29 29 
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1",
30 30 
Description,,** No join mapping for *Description **
31 
Family.src.row_num,,** No join mapping for *Family.src.row_num **
31 32 
FamilyID,,** No join mapping for *FamilyID **
32 33 
FieldFamily,,** No join mapping for *FieldFamily **
34 
Genus.src.row_num,,** No join mapping for *Genus.src.row_num **
33 35 
GenusAuthority,,** No join mapping for *GenusAuthority **
34 36 
GenusID,,** No join mapping for *GenusID **
35 37 
GenusReferenceID,,** No join mapping for *GenusReferenceID **
36 38 
IDLevel,,** No join mapping for *IDLevel **
37 39 
InfraSpecificLevel,,** No non-empty join mapping for UNUSED **
40 
InfraspecificEpithet.src.row_num,,** No join mapping for *InfraspecificEpithet.src.row_num **
38 41 
ReferenceID,,** No join mapping for *ReferenceID **
39 42 
SpeciesCurrentTaxonFlag,,** No join mapping for *SpeciesCurrentTaxonFlag **
40 43 
SpeciesID,,** No join mapping for *SpeciesID **
41 44 
SpeciesMnemonic,,** No join mapping for *SpeciesMnemonic **
42 45 
SpeciesObsoleteTaxonFlag,,** No join mapping for *SpeciesObsoleteTaxonFlag **
43 46 
SpeciesReferenceID,,** No join mapping for *SpeciesReferenceID **
47 
SpecificEpithet.src.row_num,,** No join mapping for *SpecificEpithet.src.row_num **
44 48 
SubSpeciesAuthority,,** No join mapping for *SubSpeciesAuthority **
45 49 
SubSpeciesCurrentTaxonFlag,,** No join mapping for *SubSpeciesCurrentTaxonFlag **
46 50 
SubSpeciesID,,** No join mapping for *SubSpeciesID **
47 51 
SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic **
48 52 
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag **
53 
TaxonOccurrence.src.row_num,,** No join mapping for *TaxonOccurrence.src.row_num **
inputs/CTFS/TaxonOccurrence/unmapped_terms.csv
2 2 
*GenusID
3 3 
*SpeciesID
4 4 
*SubSpeciesID
5 
*TaxonOccurrence.src.row_num
6 
*InfraspecificEpithet.src.row_num
5 7 
*SubSpeciesCurrentTaxonFlag
6 8 
*SubSpeciesObsoleteTaxonFlag
7 9 
*SubSpeciesMnemonic
8 10 
*SubSpeciesAuthority
11 
*SpecificEpithet.src.row_num
9 12 
*SpeciesCurrentTaxonFlag
10 13 
*SpeciesObsoleteTaxonFlag
11 14 
*SpeciesReferenceID
......
13 16 
*IDLevel
14 17 
*FieldFamily
15 18 
*Description
19 
*Genus.src.row_num
16 20 
*GenusReferenceID
17 21 
*GenusAuthority
22 
*Family.src.row_num
18 23 
*ReferenceID
inputs/CTFS/Plot/map.csv
1 1 
CTFS,VegCore,Filter,Comments
2 2 
CountryID,*CountryID,,
3 
Plot.src.row_num,*Plot.src.row_num,,
3 4 
PlotID,locationID,,
4 5 
PlotName,locationName,,
5 6 
LocationName,locality,,
......
19 20 
SizeOfSite,plotArea_ha,,"""Size in hectares"" (SizeOfSite comments in <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/CTFS/_src/ctfs-comments_worksheet.xls>)"
20 21 
ShapeOfSite,footprintWKT,,
21 22 
DescriptionOfSite,locality,,
23 
Country.src.row_num,*Country.src.row_num,,
22 24 
CountryName,country,,
inputs/CTFS/Plot/VegBIEN.csv
31 31 
CountryName,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
32 32 
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists",
33 33 
PlotID,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1",
34 
Country.src.row_num,,** No join mapping for *Country.src.row_num **
34 35 
CountryID,,** No join mapping for *CountryID **
36 
Plot.src.row_num,,** No join mapping for *Plot.src.row_num **
35 37 
ReferenceX,,** No join mapping for *ReferenceX ** Rarely used
36 38 
ReferenceY,,** No join mapping for *ReferenceY ** Rarely used
inputs/CTFS/Plot/unmapped_terms.csv
1 1 
*CountryID
2 
*Plot.src.row_num
2 3 
*ReferenceX
3 4 
*ReferenceY
5 
*Country.src.row_num

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