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Revision 4828

mappings/VegCore-VegBIEN.csv: Remapped tag to new stemobservation.tag

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/tag,
17
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
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><tag>$TreeNumber</tag></stemtag>
36
                                    <tag>$TreeNumber</tag>
37 37
                                    <xposition_m>$X_1haPlot</xposition_m>
38 38
                                    <yposition_m>$Y_1haPlot</yposition_m>
39 39
                                </stemobservation>
......
55 55
        </path>
56 56
    </_simplifyPath>
57 57
</VegBIEN>
58
Inserted 17 new rows into database
58
Inserted 16 new rows into database
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/tag,
17
TreeNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
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><tag>$TreeNumber</tag></stemtag>
36
                                    <tag>$TreeNumber</tag>
37 37
                                    <xposition_m>$X_1haPlot</xposition_m>
38 38
                                    <yposition_m>$Y_1haPlot</yposition_m>
39 39
                                </stemobservation>
......
55 55
        </path>
56 56
    </_simplifyPath>
57 57
</VegBIEN>
58
Inserted 17 new rows into database
58
Inserted 16 new rows into database
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/tag,
21
Tag number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
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><tag>$Tag number</tag></stemtag>
35
                                    <tag>$Tag number</tag>
36 36
                                    <xposition_m>$Subplot X</xposition_m>
37 37
                                    <yposition_m>$Subplot Y</yposition_m>
38 38
                                </stemobservation>
......
106 106
        </path>
107 107
    </_simplifyPath>
108 108
</VegBIEN>
109
Inserted 30 new rows into database
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Inserted 28 new rows into database
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/tag/_alt/1/_alt/1,The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above
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."
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."
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."
50
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag/_alt/1/_alt/1,The second tag supercedes the first. The stem tag supercedes the tree tag. Brad: see above
51
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
52
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
53
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
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
100 100
                                            <1>$stem_height_first_branch_m</1>
101 101
                                        </_alt>
102 102
                                    </heightfirstbranch_m>
103
                                    <stemtag>
104
                                        <tag>
105
                                            <_alt>
106
                                                <1>
107
                                                    <_alt>
108
                                                        <1>$stem_tag2</1>
109
                                                        <2>$stem_tag1</2>
110
                                                    </_alt>
111
                                                </1>
112
                                                <2>
113
                                                    <_alt>
114
                                                        <1>$tag2</1>
115
                                                        <2>$tag1</2>
116
                                                    </_alt>
117
                                                </2>
118
                                            </_alt>
119
                                        </tag>
120
                                    </stemtag>
103
                                    <tag>
104
                                        <_alt>
105
                                            <1>
106
                                                <_alt>
107
                                                    <1>$stem_tag2</1>
108
                                                    <2>$stem_tag1</2>
109
                                                </_alt>
110
                                            </1>
111
                                            <2>
112
                                                <_alt>
113
                                                    <1>$tag2</1>
114
                                                    <2>$tag1</2>
115
                                                </_alt>
116
                                            </2>
117
                                        </_alt>
118
                                    </tag>
121 119
                                    <xposition_m>$x_position</xposition_m>
122 120
                                    <yposition_m>$y_position</yposition_m>
123 121
                                </stemobservation>
......
206 204
        </path>
207 205
    </_simplifyPath>
208 206
</VegBIEN>
209
Inserted 41 new rows into database
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Inserted 39 new rows into database
inputs/CTFS/StemObservation/VegBIEN.csv
12 12
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
13 13
StemID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode,
14 14
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
15
StemTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,
16
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,
15
StemTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
16
Tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
17 17
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
18 18
y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
19 19
MeasureID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2,
inputs/CTFS/StemObservation/test.xml.ref
20 20
                                <stemobservation>
21 21
                                    <authorstemcode>$StemID</authorstemcode>
22 22
                                    <diameterbreastheight_m>$DBH</diameterbreastheight_m>
23
                                    <stemtag>
24
                                        <tag>
25
                                            <_alt>
26
                                                <0>$StemTag</0>
27
                                                <1>$Tag</1>
28
                                            </_alt>
29
                                        </tag>
30
                                    </stemtag>
23
                                    <tag>
24
                                        <_alt>
25
                                            <0>$StemTag</0>
26
                                            <1>$Tag</1>
27
                                        </_alt>
28
                                    </tag>
31 29
                                    <xposition_m>$x</xposition_m>
32 30
                                    <yposition_m>$y</yposition_m>
33 31
                                </stemobservation>
......
51 49
        </path>
52 50
    </_simplifyPath>
53 51
</VegBIEN>
54
Inserted 14 new rows into database
52
Inserted 13 new rows into database
inputs/FIA/Organism/VegBIEN.csv
11 11
BasalDiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m,
12 12
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m,
13 13
Height,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,
14
TreeTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag/tag,
14
TreeTag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
15 15
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/genus,
16 16
SpecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonpath/species,
17 17
County,/location/locationplace/*_id/placepath/county,
inputs/FIA/Organism/test.xml.ref
54 54
                                    <basaldiameter_m>$BasalDiameter</basaldiameter_m>
55 55
                                    <diameterbreastheight_m>$DBH</diameterbreastheight_m>
56 56
                                    <height_m>$Height</height_m>
57
                                    <stemtag><tag>$TreeTag</tag></stemtag>
57
                                    <tag>$TreeTag</tag>
58 58
                                </stemobservation>
59 59
                            </plantobservation>
60 60
                        </aggregateoccurrence>
......
80 80
        </path>
81 81
    </_simplifyPath>
82 82
</VegBIEN>
83
Inserted 13 new rows into database
83
Inserted 12 new rows into database
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/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."
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."
14
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
15
stem_tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
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
61 61
                                    <height_m>$stem_height_m</height_m>
62 62
                                    <heightfirstbranch_m>$stem_height_first_branch_m</heightfirstbranch_m>
63 63
                                    <sourceaccessioncode>$stem_id</sourceaccessioncode>
64
                                    <stemtag>
65
                                        <tag>
66
                                            <_alt>
67
                                                <1>$stem_tag2</1>
68
                                                <2>$stem_tag1</2>
69
                                            </_alt>
70
                                        </tag>
71
                                    </stemtag>
64
                                    <tag>
65
                                        <_alt>
66
                                            <1>$stem_tag2</1>
67
                                            <2>$stem_tag1</2>
68
                                        </_alt>
69
                                    </tag>
72 70
                                </stemobservation>
73 71
                            </plantobservation>
74 72
                        </aggregateoccurrence>
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/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."
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."
47
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
48
tag1,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/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."
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
81 81
                                    <diameterbreastheight_m>$temp_dbh</diameterbreastheight_m>
82 82
                                    <height_m>$height_m</height_m>
83 83
                                    <heightfirstbranch_m>$ht_first_branch_m</heightfirstbranch_m>
84
                                    <stemtag>
85
                                        <tag>
86
                                            <_alt>
87
                                                <1>$tag2</1>
88
                                                <2>$tag1</2>
89
                                            </_alt>
90
                                        </tag>
91
                                    </stemtag>
84
                                    <tag>
85
                                        <_alt>
86
                                            <1>$tag2</1>
87
                                            <2>$tag1</2>
88
                                        </_alt>
89
                                    </tag>
92 90
                                    <xposition_m>$x_position</xposition_m>
93 91
                                    <yposition_m>$y_position</yposition_m>
94 92
                                </stemobservation>
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/tag,
103
tag,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag,
104 104
organismX,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition_m,
105 105
organismY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition_m,
106 106
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,//stemtag/tag,
103
tag,//stemobservation/tag,
104 104
organismX,//stemobservation/xposition_m,
105 105
organismY,//stemobservation/yposition_m,
106 106
recordNumber,//taxonoccurrence/authortaxoncode,

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