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Revision 4350

Added by Aaron Marcuse-Kubitza over 12 years ago

inputs/CTFS/: Added StemObservation/ and tables it is joined from

View differences:

inputs/CTFS/import_order.txt
1 1 
Plot
2 2 
Subplot
3 3 
PlotObservation
4 
SubplotObservation
4 
SubplotObservation
5 
StemObservation
inputs/CTFS/StemObservation/create.sql
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SELECT *
2 
FROM "StemObservation.src"
3 
LEFT JOIN "Stem.src" USING ("TreeID", "StemID")
4 
LEFT JOIN "Organism.src" USING ("TreeID")
5 
LEFT JOIN "InfraspecificEpithet.src" USING ("SpeciesID", "SubSpeciesID")
6 
LEFT JOIN "SpecificEpithet.src" USING ("SpeciesID")
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LEFT JOIN "Genus.src" USING ("GenusID")
8 
LEFT JOIN "Family.src" USING ("FamilyID")
inputs/CTFS/StemObservation/src.csv
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CTFS[Veg+],Veg+,Comments
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FamilyID,,
3 
GenusID,,
4 
SpeciesID,,
5 
SubSpeciesID,,
6 
TreeID,,
7 
StemID,,
8 
MeasureID,,
9 
CensusID,,
10 
DBH,,
11 
HOM,,
12 
PrimaryStem,,
13 
ExactDate,,
14 
StemTag,,
15 
StemDescription,,
16 
QuadratID,,
17 
PlotID,,
18 
Tag,,
19 
x,,
20 
y,,
21 
SubSpeciesCurrentTaxonFlag,,
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SubSpeciesObsoleteTaxonFlag,,
23 
SubSpeciesName,,
24 
SubSpeciesMnemonic,,
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SubSpeciesAuthority,,
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InfraSpecificLevel,,
27 
SpeciesCurrentTaxonFlag,,
28 
SpeciesObsoleteTaxonFlag,,
29 
SpeciesReferenceID,,
30 
SpeciesName,,
31 
SpeciesMnemonic,,
32 
SpeciesAuthority,,
33 
IDLevel,,
34 
FieldFamily,,
35 
Description,,
36 
Genus,,
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GenusReferenceID,,
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GenusAuthority,,
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Family,,
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ReferenceID,,
41 
row_num,,
inputs/CTFS/StemObservation/header.csv
1 
FamilyID,GenusID,SpeciesID,SubSpeciesID,TreeID,StemID,MeasureID,CensusID,DBH,HOM,PrimaryStem,ExactDate,StemTag,StemDescription,QuadratID,PlotID,Tag,x,y,SubSpeciesCurrentTaxonFlag,SubSpeciesObsoleteTaxonFlag,SubSpeciesName,SubSpeciesMnemonic,SubSpeciesAuthority,InfraSpecificLevel,SpeciesCurrentTaxonFlag,SpeciesObsoleteTaxonFlag,SpeciesReferenceID,SpeciesName,SpeciesMnemonic,SpeciesAuthority,IDLevel,FieldFamily,Description,Genus,GenusReferenceID,GenusAuthority,Family,ReferenceID,row_num
inputs/CTFS/StemObservation/map.csv
1 
CTFS[Veg+],Veg+,Comments
2 
FamilyID,,
3 
GenusID,,
4 
SpeciesID,,
5 
SubSpeciesID,,
6 
TreeID,,
7 
StemID,,
8 
MeasureID,individualID,
9 
HOM,,
10 
PrimaryStem,,
11 
ExactDate,,
12 
StemDescription,,
13 
x,organismX,
14 
y,organismY,
15 
SubSpeciesCurrentTaxonFlag,,
16 
SubSpeciesObsoleteTaxonFlag,,
17 
SubSpeciesName,,
18 
SubSpeciesMnemonic,,
19 
SubSpeciesAuthority,,
20 
InfraSpecificLevel,,
21 
SpeciesCurrentTaxonFlag,,
22 
SpeciesObsoleteTaxonFlag,,
23 
SpeciesReferenceID,,
24 
SpeciesName,,
25 
SpeciesMnemonic,,
26 
SpeciesAuthority,scientificNameAuthorship,
27 
IDLevel,,
28 
FieldFamily,,
29 
Description,,
30 
GenusReferenceID,,
31 
GenusAuthority,,
32 
ReferenceID,,
33 
row_num,,
inputs/CTFS/StemObservation/map.full.csv
1 
CTFS[Veg+],Veg+,Comments
2 
CensusID,CensusID
3 
DBH,DBH
4 
Family,Family
5 
Genus,Genus
6 
PlotID,PlotID
7 
QuadratID,QuadratID
8 
StemTag,StemTag
9 
Tag,Tag
10 
MeasureID,individualID,
11 
x,organismX,
12 
y,organismY,
13 
SpeciesAuthority,scientificNameAuthorship,
inputs/CTFS/StemObservation/VegBIEN.csv
1 
CTFS[Veg+],VegBIEN:,Comments
2 
QuadratID,"/location/_if[@name=""if subplot""]/cond/_exists/_first/1",
3 
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
4 
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode",
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PlotID,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode",
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QuadratID,"/location/locationevent/_if[@name=""if subplot""]/cond/_exists/_first/1",
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CensusID,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode",
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CensusID,"/location/locationevent/_if[@name=""if subplot""]/then/parent_id/locationevent/sourceaccessioncode",
9 
MeasureID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
10 
DBH,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
11 
StemTag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
12 
Tag,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
13 
x,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,
14 
y,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,
15 
MeasureID,/location/locationevent/taxonoccurrence/sourceaccessioncode,
16 
SpeciesAuthority,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname/_alt/1",
17 
Genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
18 
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/plantconcept/plantname_id/_simplifyPath:[next=parent_id]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
19 
QuadratID,/location/sourceaccessioncode,
inputs/CTFS/StemObservation/test.xml.ref
1 
Put template:
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<VegBIEN>
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    <location id="-1">
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        <parent_id><location><sourceaccessioncode>$PlotID</sourceaccessioncode></location></parent_id>
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        <locationevent>
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            <parent_id><locationevent><sourceaccessioncode>$CensusID</sourceaccessioncode></locationevent></parent_id>
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            <taxonoccurrence>
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                <aggregateoccurrence>
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                    <plantobservation>
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                        <sourceaccessioncode>$MeasureID</sourceaccessioncode>
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                        <stemobservation>
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                            <diameterbreastheight>$DBH</diameterbreastheight>
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                            <stemtag>
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                                <iscurrent>true</iscurrent>
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                                <tag>
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                                    <_alt>
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                                        <0>$StemTag</0>
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                                        <1>$Tag</1>
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                                    </_alt>
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                                </tag>
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                            </stemtag>
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                            <xposition>$x</xposition>
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                            <yposition>$y</yposition>
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                        </stemobservation>
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                    </plantobservation>
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                </aggregateoccurrence>
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                <sourceaccessioncode>$MeasureID</sourceaccessioncode>
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                <taxondetermination>
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                    <plantconcept_id>
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                        <plantconcept>
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                            <plantname_id>
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                                <_simplifyPath>
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                                    <next>parent_id</next>
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                                    <path>
35 
                                        <plantname>
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                                            <rank>binomial</rank>
37 
                                            <parent_id>
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                                                <plantname>
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                                                    <rank>authority</rank>
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                                                    <plantname>$SpeciesAuthority</plantname>
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                                                    <parent_id>
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                                                        <plantname>
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                                                            <rank>subspecies</rank>
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                                                            <parent_id>
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                                                                <plantname>
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                                                                    <rank>species</rank>
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                                                                    <parent_id>
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                                                                        <plantname>
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                                                                            <rank>genus</rank>
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                                                                            <plantname>$Genus</plantname>
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                                                                            <parent_id>
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                                                                                <plantname>
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                                                                                    <rank>family</rank>
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                                                                                    <plantname>$Family</plantname>
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                                                                                </plantname>
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                                                                            </parent_id>
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                                                                        </plantname>
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                                                                    </parent_id>
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                                                                </plantname>
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                                                            </parent_id>
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                                                        </plantname>
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                                                    </parent_id>
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                                                </plantname>
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                                            </parent_id>
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                                        </plantname>
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                                    </path>
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                                </_simplifyPath>
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                            </plantname_id>
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                        </plantconcept>
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                    </plantconcept_id>
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                </taxondetermination>
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            </taxonoccurrence>
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        </locationevent>
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        <sourceaccessioncode>$QuadratID</sourceaccessioncode>
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    </location>
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</VegBIEN>
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Inserted 14 new rows into database
inputs/CTFS/SpecificEpithet.src/+header.csv
1 
!"SpeciesID","SpeciesCurrentTaxonFlag","SpeciesObsoleteTaxonFlag","GenusID","SpeciesReferenceID","SpeciesName","SpeciesMnemonic","SpeciesAuthority","IDLevel","FieldFamily","Description"
inputs/CTFS/Genus.src/+header.csv
1 
!"GenusID","Genus","GenusReferenceID","GenusAuthority","FamilyID"
inputs/CTFS/InfraspecificEpithet.src/+header.csv
1 
!"SubSpeciesID","SpeciesID","SubSpeciesCurrentTaxonFlag","SubSpeciesObsoleteTaxonFlag","SubSpeciesName","SubSpeciesMnemonic","SubSpeciesAuthority","InfraSpecificLevel"

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