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Revision 4825

mappings/VegCore-VegBIEN.csv: Removed no longer used previousTag and the complex mapping logic that attempts to place both tags in VegBIEN in the correct order but does not work for column-based import. tag: Removed iscurrent=true because there is now only one tag field.

View differences:

inputs/TEAM/VL/VegBIEN.csv
14 14
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,
15 15
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
16 16
dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
17
TreeNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
17
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
18 18
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
19 19
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
20 20
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
inputs/TEAM/VL/test.xml.ref
33 33
                                <specimenreplicate><sourceaccessioncode>$ID</sourceaccessioncode></specimenreplicate>
34 34
                                <stemobservation>
35 35
                                    <diameterbreastheight_m>$dbh</diameterbreastheight_m>
36
                                    <stemtag>
37
                                        <iscurrent>true</iscurrent>
38
                                        <tag>$TreeNumber</tag>
39
                                    </stemtag>
36
                                    <stemtag><tag>$TreeNumber</tag></stemtag>
40 37
                                    <xposition_m>$X_1haPlot</xposition_m>
41 38
                                    <yposition_m>$Y_1haPlot</yposition_m>
42 39
                                </stemobservation>
inputs/TEAM/VT/VegBIEN.csv
14 14
ObservationDate,/location/locationevent/obsstartdate/_*/date/_alt/2/_dateRangeStart/value,
15 15
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,
16 16
dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
17
TreeNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
17
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
18 18
X_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
19 19
Y_1haPlot,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
20 20
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/family,
inputs/TEAM/VT/test.xml.ref
33 33
                                <specimenreplicate><sourceaccessioncode>$ID</sourceaccessioncode></specimenreplicate>
34 34
                                <stemobservation>
35 35
                                    <diameterbreastheight_m>$dbh</diameterbreastheight_m>
36
                                    <stemtag>
37
                                        <iscurrent>true</iscurrent>
38
                                        <tag>$TreeNumber</tag>
39
                                    </stemtag>
36
                                    <stemtag><tag>$TreeNumber</tag></stemtag>
40 37
                                    <xposition_m>$X_1haPlot</xposition_m>
41 38
                                    <yposition_m>$Y_1haPlot</yposition_m>
42 39
                                </stemobservation>
inputs/Madidi/Organism/VegBIEN.csv
18 18
Liana presence,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",
19 19
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
20 20
Total height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
21
Tag number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
21
Tag number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
22 22
Subplot X,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
23 23
Subplot Y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
24 24
Tree number,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,
inputs/Madidi/Organism/test.xml.ref
32 32
                                    </definedvalue>
33 33
                                    <diameterbreastheight_m>$Diameter</diameterbreastheight_m>
34 34
                                    <height_m>$Total height</height_m>
35
                                    <stemtag>
36
                                        <iscurrent>true</iscurrent>
37
                                        <tag>$Tag number</tag>
38
                                    </stemtag>
35
                                    <stemtag><tag>$Tag number</tag></stemtag>
39 36
                                    <xposition_m>$Subplot X</xposition_m>
40 37
                                    <yposition_m>$Subplot Y</yposition_m>
41 38
                                </stemobservation>
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
47 47
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m/_alt/2,
48 48
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,
49 49
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
50
stem_tag2,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1/_alt/1",The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above; Quotes sort it before tag2
51
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2"
52
tag2,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2/_alt/1","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
53
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2/_alt/2","The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
50
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/1/_alt/1,The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above; Quotes sort it before tag2
51
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/1/_alt/2,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2"
52
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/2/_alt/1,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
53
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/2/_alt/2,"The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
54 54
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots"
55 55
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position
56 56
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
inputs/SALVIAS-CSV/Organism/test.xml.ref
101 101
                                        </_alt>
102 102
                                    </heightfirstbranch_m>
103 103
                                    <stemtag>
104
                                        <iscurrent>true</iscurrent>
105 104
                                        <tag>
106 105
                                            <_alt>
107 106
                                                <1>
inputs/CTFS/StemObservation/VegBIEN.csv
12 12
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
13 13
StemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
14 14
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
15
StemTag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
16
Tag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
15
StemTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
16
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
17 17
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
18 18
y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
19 19
MeasureID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
inputs/CTFS/StemObservation/test.xml.ref
21 21
                                    <authorstemcode>$StemID</authorstemcode>
22 22
                                    <diameterbreastheight_m>$DBH</diameterbreastheight_m>
23 23
                                    <stemtag>
24
                                        <iscurrent>true</iscurrent>
25 24
                                        <tag>
26 25
                                            <_alt>
27 26
                                                <0>$StemTag</0>
inputs/FIA/Organism/VegBIEN.csv
11 11
BasalDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m,
12 12
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
13 13
Height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
14
TreeTag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
14
TreeTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
15 15
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
16 16
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
17 17
County,/location/locationplace/*_id/placepath/county,
inputs/FIA/Organism/test.xml.ref
54 54
                                    <basaldiameter_m>$BasalDiameter</basaldiameter_m>
55 55
                                    <diameterbreastheight_m>$DBH</diameterbreastheight_m>
56 56
                                    <height_m>$Height</height_m>
57
                                    <stemtag>
58
                                        <iscurrent>true</iscurrent>
59
                                        <tag>$TreeTag</tag>
60
                                    </stemtag>
57
                                    <stemtag><tag>$TreeTag</tag></stemtag>
61 58
                                </stemobservation>
62 59
                            </plantobservation>
63 60
                        </aggregateoccurrence>
inputs/SALVIAS/stems/VegBIEN.csv
11 11
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
12 12
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,"Brad: Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
13 13
stem_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode,
14
stem_tag2,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
15
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
14
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/1,"The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
15
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/2,"The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
16 16
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
17 17
origrecord_id_stems,,** No join mapping for origrecord_id_stems ** 
18 18
plotobs_id_index,,** No join mapping for plotobs_id_index ** 
inputs/SALVIAS/stems/test.xml.ref
62 62
                                    <heightfirstbranch_m>$stem_height_first_branch_m</heightfirstbranch_m>
63 63
                                    <sourceaccessioncode>$stem_id</sourceaccessioncode>
64 64
                                    <stemtag>
65
                                        <iscurrent>true</iscurrent>
66 65
                                        <tag>
67 66
                                            <_alt>
68 67
                                                <1>$stem_tag2</1>
inputs/SALVIAS/plotObservations/VegBIEN.csv
44 44
temp_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
45 45
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
46 46
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,
47
tag2,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
48
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2","The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
47
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/1,"The second tag supercedes the first. Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other.; Quotes sort it before tag2"
48
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag/_alt/2,"The second tag supercedes the first. Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
49 49
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,"Brad: These are important, fundamental values of many tree plots"
50 50
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,Brad: See comment above for x_position
51 51
Ind,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
inputs/SALVIAS/plotObservations/test.xml.ref
82 82
                                    <height_m>$height_m</height_m>
83 83
                                    <heightfirstbranch_m>$ht_first_branch_m</heightfirstbranch_m>
84 84
                                    <stemtag>
85
                                        <iscurrent>true</iscurrent>
86 85
                                        <tag>
87 86
                                            <_alt>
88 87
                                                <1>$tag2</1>
mappings/Veg+.terms.csv
363 363
subplotID,"http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.subplot, http://rs.tdwg.org/dwc/terms/#locationID","5, 56",
364 364
subplotX,"http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.subplot, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/relatedPlot/relativeSpatialCoordinate/relativeX","5, ",
365 365
subplotY,"http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.subplot, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/relatedPlot/relativeSpatialCoordinate/relativeY","5, ",
366
previousTag,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.tag1,8,Number replaced with named prefix for clarity
367 366
tag,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.tag2,9,Number removed for clarity
368 367
plotArea_ha,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+metadata.plot_area_ha,,
369 368
precipitation,http://salvias.net/Documents/salvias_data_dictionary.html#Plot+metadata.precip_mm,13,Expanded for clarity
mappings/VegCore-VegBIEN.csv
100 100
height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
101 101
heightFirstBranch,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch_m,
102 102
stemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode,
103
tag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
104
previousTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
103
tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,Quotes sort it before tag2
105 104
organismX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
106 105
organismY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
107 106
recordNumber,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1,
mappings/for_review/VegCore-VegBIEN.csv
100 100
height,//stemobservation/height_m,
101 101
heightFirstBranch,//stemobservation/heightfirstbranch_m,
102 102
stemID,//stemobservation/sourceaccessioncode,
103
tag,"//stemobservation/stemtag[""""/iscurrent=true]/tag",Quotes sort it before tag2
104
previousTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag:[../stemtag?[iscurrent=true]/iscurrent=false]/tag,
103
tag,//stemtag/tag,Quotes sort it before tag2
105 104
organismX,//stemobservation/xposition_m,
106 105
organismY,//stemobservation/yposition_m,
107 106
recordNumber,//taxonoccurrence/authortaxoncode,

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