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Revision 6558

inputs/NVS/: Renamed Organism to AggregateOccurrence because this actually contains aggregated samplings

View differences:

inputs/NVS/Organism/new_terms.csv
1
Project Abbreviation,projectName,,
2
Plot,locationName,,
3
Taxon Growth Form,growthForm,,
4
Taxon Obs Note,taxonRemarks,,
inputs/NVS/Organism/unmapped_terms.csv
1
*Method Name
2
*Species Code
3
*Verbatim Code
4
*Taxon Bio Status
5
*Taxon Palatibility
6
*Tier
7
*Tier Description
8
*Tier ID
9
*Category
10
*Category Description
11
*Parent Plot Obs ID
12
*Sample Method ID
inputs/NVS/Organism/map.csv
1
NVS,VegCore,Filter,Comments
2
Project Abbreviation,projectName,,
3
Plot,locationName,,
4
Sub Plot,subplot,,
5
Method Name,*Method Name,,
6
Species Code,*Species Code,,
7
Species Name,specificEpithet,,
8
Verbatim Code,*Verbatim Code,,
9
Taxon Bio Status,*Taxon Bio Status,,
10
Taxon Palatibility,*Taxon Palatibility,,
11
Taxon Growth Form,growthForm,,
12
Tier,*Tier,,
13
Tier Description,*Tier Description,,
14
Tier ID,*Tier ID,,
15
Category,*Category,,
16
Category Description,*Category Description,,
17
Taxon Obs Note,taxonRemarks,,
18
Parent Plot Obs ID,*Parent Plot Obs ID,,
19
Sample Method ID,*Sample Method ID,,
inputs/NVS/Organism/test.xml.ref
1
Put template:
2
<VegBIEN>
3
    <_setDefault id="-1">
4
        <source_id><source><shortname>NVS</shortname></source></source_id>
5
        <path>
6
            <_simplifyPath>
7
                <next>parent_id</next>
8
                <path>
9
                    <location>
10
                        <parent_id><location><authorlocationcode>$Plot</authorlocationcode></location></parent_id>
11
                        <authorlocationcode>$Sub Plot</authorlocationcode>
12
                        <locationevent>
13
                            <project_id><project><projectname>$Project Abbreviation</projectname></project></project_id>
14
                            <taxonoccurrence>
15
                                <growthform>$Taxon Growth Form</growthform>
16
                                <taxondetermination>
17
                                    <taxonverbatim_id>
18
                                        <taxonverbatim>
19
                                            <taxonlabel_id>
20
                                                <taxonlabel>
21
                                                    <matched_label_id>
22
                                                        <taxonlabel>
23
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
24
                                                            <taxonomicname>$Species Name</taxonomicname>
25
                                                        </taxonlabel>
26
                                                    </matched_label_id>
27
                                                    <parent_id>
28
                                                        <taxonlabel>
29
                                                            <parent_id>
30
                                                                <taxonlabel>
31
                                                                    <rank>cultivar</rank>
32
                                                                    <parent_id>
33
                                                                        <taxonlabel>
34
                                                                            <rank>forma</rank>
35
                                                                            <parent_id>
36
                                                                                <taxonlabel>
37
                                                                                    <rank>variety</rank>
38
                                                                                    <parent_id>
39
                                                                                        <taxonlabel>
40
                                                                                            <rank>subspecies</rank>
41
                                                                                            <parent_id>
42
                                                                                                <taxonlabel>
43
                                                                                                    <rank>species</rank>
44
                                                                                                    <taxonepithet>$Species Name</taxonepithet>
45
                                                                                                </taxonlabel>
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                                                                                            </parent_id>
47
                                                                                        </taxonlabel>
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                                                                                    </parent_id>
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                                                                                </taxonlabel>
50
                                                                            </parent_id>
51
                                                                        </taxonlabel>
52
                                                                    </parent_id>
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                                                                </taxonlabel>
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                                                            </parent_id>
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                                                        </taxonlabel>
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                                                    </parent_id>
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                                                    <taxonomicname>$Species Name</taxonomicname>
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                                                </taxonlabel>
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                                            </taxonlabel_id>
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                                            <specific_epithet>$Species Name</specific_epithet>
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                                        </taxonverbatim>
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                                    </taxonverbatim_id>
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                                    <notes>$Taxon Obs Note</notes>
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                                </taxondetermination>
65
                            </taxonoccurrence>
66
                        </locationevent>
67
                        <sourceaccessioncode>
68
                            <_join>
69
                                <1>$Plot</1>
70
                                <2>$Sub Plot</2>
71
                            </_join>
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                        </sourceaccessioncode>
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                    </location>
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                </path>
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            </_simplifyPath>
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        </path>
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    </_setDefault>
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</VegBIEN>
79
Inserted 17 new rows into database
inputs/NVS/Organism/VegBIEN.csv
1
NVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
Sub Plot,"/location/_if[@name=""if subplot""]/cond/_exists",
3
Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4
Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
5
Sub Plot,/location/authorlocationcode,
6
Project Abbreviation,/location/locationevent/*_id/project/projectname,
7
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
8
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",
9
Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
10
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",
11
Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
12
Taxon Growth Form,/location/locationevent/taxonoccurrence/growthform,
13
Species Name,"/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/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
14
Species Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
15
Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
16
Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
17
Taxon Obs Note,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes,
18
Sub Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists",
19
Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2",
20
Sub Plot,/location/sourceaccessioncode/_join/2,
21
Category,,** No join mapping for *Category ** 
22
Category Description,,** No join mapping for *Category Description ** 
23
Method Name,,** No join mapping for *Method Name ** 
24
Parent Plot Obs ID,,** No join mapping for *Parent Plot Obs ID ** 
25
Sample Method ID,,** No join mapping for *Sample Method ID ** 
26
Species Code,,** No join mapping for *Species Code ** 
27
Taxon Bio Status,,** No join mapping for *Taxon Bio Status ** 
28
Taxon Palatibility,,** No join mapping for *Taxon Palatibility ** 
29
Tier,,** No join mapping for *Tier ** 
30
Tier Description,,** No join mapping for *Tier Description ** 
31
Tier ID,,** No join mapping for *Tier ID ** 
32
Verbatim Code,,** No join mapping for *Verbatim Code ** 
inputs/NVS/AggregateOccurrence/map.csv
1
NVS,VegCore,Filter,Comments
2
Project Abbreviation,projectName,,
3
Plot,locationName,,
4
Sub Plot,subplot,,
5
Method Name,*Method Name,,
6
Species Code,*Species Code,,
7
Species Name,specificEpithet,,
8
Verbatim Code,*Verbatim Code,,
9
Taxon Bio Status,*Taxon Bio Status,,
10
Taxon Palatibility,*Taxon Palatibility,,
11
Taxon Growth Form,growthForm,,
12
Tier,*Tier,,
13
Tier Description,*Tier Description,,
14
Tier ID,*Tier ID,,
15
Category,*Category,,
16
Category Description,*Category Description,,
17
Taxon Obs Note,taxonRemarks,,
18
Parent Plot Obs ID,*Parent Plot Obs ID,,
19
Sample Method ID,*Sample Method ID,,
inputs/NVS/AggregateOccurrence/VegBIEN.csv
1
NVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2
Sub Plot,"/location/_if[@name=""if subplot""]/cond/_exists",
3
Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4
Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode",
5
Sub Plot,/location/authorlocationcode,
6
Project Abbreviation,/location/locationevent/*_id/project/projectname,
7
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists",
8
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/cond/_first/2",
9
Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then",
10
Sub Plot,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/cond/_first/2",
11
Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
12
Taxon Growth Form,/location/locationevent/taxonoccurrence/growthform,
13
Species Name,"/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/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1",
14
Species Name,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
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Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
16
Species Name,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
17
Taxon Obs Note,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes,
18
Sub Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists",
19
Plot,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2",
20
Sub Plot,/location/sourceaccessioncode/_join/2,
21
Category,,** No join mapping for *Category ** 
22
Category Description,,** No join mapping for *Category Description ** 
23
Method Name,,** No join mapping for *Method Name ** 
24
Parent Plot Obs ID,,** No join mapping for *Parent Plot Obs ID ** 
25
Sample Method ID,,** No join mapping for *Sample Method ID ** 
26
Species Code,,** No join mapping for *Species Code ** 
27
Taxon Bio Status,,** No join mapping for *Taxon Bio Status ** 
28
Taxon Palatibility,,** No join mapping for *Taxon Palatibility ** 
29
Tier,,** No join mapping for *Tier ** 
30
Tier Description,,** No join mapping for *Tier Description ** 
31
Tier ID,,** No join mapping for *Tier ID ** 
32
Verbatim Code,,** No join mapping for *Verbatim Code ** 
inputs/NVS/AggregateOccurrence/test.xml.ref
1
Put template:
2
<VegBIEN>
3
    <_setDefault id="-1">
4
        <source_id><source><shortname>NVS</shortname></source></source_id>
5
        <path>
6
            <_simplifyPath>
7
                <next>parent_id</next>
8
                <path>
9
                    <location>
10
                        <parent_id><location><authorlocationcode>$Plot</authorlocationcode></location></parent_id>
11
                        <authorlocationcode>$Sub Plot</authorlocationcode>
12
                        <locationevent>
13
                            <project_id><project><projectname>$Project Abbreviation</projectname></project></project_id>
14
                            <taxonoccurrence>
15
                                <growthform>$Taxon Growth Form</growthform>
16
                                <taxondetermination>
17
                                    <taxonverbatim_id>
18
                                        <taxonverbatim>
19
                                            <taxonlabel_id>
20
                                                <taxonlabel>
21
                                                    <matched_label_id>
22
                                                        <taxonlabel>
23
                                                            <source_id><source><shortname>TNRS</shortname></source></source_id>
24
                                                            <taxonomicname>$Species Name</taxonomicname>
25
                                                        </taxonlabel>
26
                                                    </matched_label_id>
27
                                                    <parent_id>
28
                                                        <taxonlabel>
29
                                                            <parent_id>
30
                                                                <taxonlabel>
31
                                                                    <rank>cultivar</rank>
32
                                                                    <parent_id>
33
                                                                        <taxonlabel>
34
                                                                            <rank>forma</rank>
35
                                                                            <parent_id>
36
                                                                                <taxonlabel>
37
                                                                                    <rank>variety</rank>
38
                                                                                    <parent_id>
39
                                                                                        <taxonlabel>
40
                                                                                            <rank>subspecies</rank>
41
                                                                                            <parent_id>
42
                                                                                                <taxonlabel>
43
                                                                                                    <rank>species</rank>
44
                                                                                                    <taxonepithet>$Species Name</taxonepithet>
45
                                                                                                </taxonlabel>
46
                                                                                            </parent_id>
47
                                                                                        </taxonlabel>
48
                                                                                    </parent_id>
49
                                                                                </taxonlabel>
50
                                                                            </parent_id>
51
                                                                        </taxonlabel>
52
                                                                    </parent_id>
53
                                                                </taxonlabel>
54
                                                            </parent_id>
55
                                                        </taxonlabel>
56
                                                    </parent_id>
57
                                                    <taxonomicname>$Species Name</taxonomicname>
58
                                                </taxonlabel>
59
                                            </taxonlabel_id>
60
                                            <specific_epithet>$Species Name</specific_epithet>
61
                                        </taxonverbatim>
62
                                    </taxonverbatim_id>
63
                                    <notes>$Taxon Obs Note</notes>
64
                                </taxondetermination>
65
                            </taxonoccurrence>
66
                        </locationevent>
67
                        <sourceaccessioncode>
68
                            <_join>
69
                                <1>$Plot</1>
70
                                <2>$Sub Plot</2>
71
                            </_join>
72
                        </sourceaccessioncode>
73
                    </location>
74
                </path>
75
            </_simplifyPath>
76
        </path>
77
    </_setDefault>
78
</VegBIEN>
79
Inserted 17 new rows into database
inputs/NVS/AggregateOccurrence/new_terms.csv
1
Project Abbreviation,projectName,,
2
Plot,locationName,,
3
Taxon Growth Form,growthForm,,
4
Taxon Obs Note,taxonRemarks,,
inputs/NVS/AggregateOccurrence/unmapped_terms.csv
1
*Method Name
2
*Species Code
3
*Verbatim Code
4
*Taxon Bio Status
5
*Taxon Palatibility
6
*Tier
7
*Tier Description
8
*Tier ID
9
*Category
10
*Category Description
11
*Parent Plot Obs ID
12
*Sample Method ID

Also available in: Unified diff