Revision 7791
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/CTFS/import_order.txt | ||
|---|---|---|
| 5 | 5 |
SubplotObservation |
| 6 | 6 |
TaxonOccurrence |
| 7 | 7 |
StemObservation |
| 8 |
AggregateObservation |
|
| inputs/CTFS/AggregateObservation/map.csv | ||
|---|---|---|
| 1 |
CTFS,VegCore,Filter,Comments |
|
| 2 |
DWstagingID,occurrenceID,, |
|
| 3 |
Country,country,, |
|
| 4 |
Province,stateProvince,, |
|
| 5 |
Plot,locationName,, |
|
| 6 |
CensusName,authorEventCode,, |
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| 7 |
Latitude ,decimalLatitude,, |
|
| 8 |
Longitude ,decimalLongitude,, |
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| 9 |
Elevation ,elevationInMeters,,Assuming units based on the range and precision of values |
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| 10 |
Genus ,genus,, |
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| 11 |
speciesname,specificEpithet,, |
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| 12 |
subspecies,subspecies,, |
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| 13 |
StartDate,startDate,, |
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| 14 |
EndDate,endDate,, |
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| 15 |
MeanDate,*MeanDate,, |
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| 16 |
Abund,individualCount,, |
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| 17 |
VegCategory,growthForm,, |
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| 18 |
maxDBHcm,diameterBreastHeight_cm,/_avg/1, |
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| 19 |
minDBHcm,diameterBreastHeight_cm,/_avg/2, |
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| 20 |
PlotSize,plotArea_ha,,Assuming units based on the range and precision of values compared to the PlotShape values |
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| 21 |
PlotShape,footprintWKT,, |
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| inputs/CTFS/AggregateObservation/VegBIEN.csv | ||
|---|---|---|
| 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
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| 2 |
DWstagingID,"/_if[@name=""if specimen""]/cond/_exists", |
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| 3 |
Plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 4 |
CensusName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
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| 5 |
DWstagingID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1", |
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| 6 |
DWstagingID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
|
| 7 |
Plot,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
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| 8 |
PlotSize,/location/area_m2/_ha_to_m2/value,Assuming units based on the range and precision of values compared to the PlotShape values |
|
| 9 |
Elevation ,/location/elevation_m/_alt/1,Assuming units based on the range and precision of values |
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| 10 |
DWstagingID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
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| 11 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
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| 12 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
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| 13 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
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| 14 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 15 |
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", |
|
| 16 |
CensusName,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
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| 17 |
EndDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
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| 18 |
StartDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
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| 19 |
EndDate,/location/locationevent/obsenddate/_alt/1, |
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| 20 |
StartDate,/location/locationevent/obsstartdate/_alt/1, |
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| 21 |
Abund,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
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| 22 |
DWstagingID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
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| 23 |
DWstagingID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
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| 24 |
maxDBHcm,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value/_avg/1, |
|
| 25 |
minDBHcm,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value/_avg/2, |
|
| 26 |
CensusName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 27 |
Plot,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
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| 28 |
VegCategory,/location/locationevent/taxonoccurrence/growthform, |
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| 29 |
DWstagingID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
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| 30 |
DWstagingID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3, |
|
| 31 |
subspecies,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=subspecies]/taxonepithet", |
|
| 32 |
speciesname,"/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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| 33 |
Genus ,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet", |
|
| 34 |
Genus ,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2, |
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| 35 |
speciesname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1, |
|
| 36 |
subspecies,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/4, |
|
| 37 |
Genus ,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
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| 38 |
speciesname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet, |
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| 39 |
PlotShape,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
|
| 40 |
Latitude ,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
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| 41 |
Longitude ,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
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| 42 |
Country,/location/locationplace/*_id/place/country, |
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| 43 |
Latitude ,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 44 |
Longitude ,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
|
| 45 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 46 |
Province,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 47 |
Province,/location/locationplace/*_id/place/stateprovince, |
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| 48 |
MeanDate,,** No join mapping for *MeanDate ** |
|
| inputs/CTFS/AggregateObservation/test.xml.ref | ||
|---|---|---|
| 1 |
Put template: |
|
| 2 |
<VegBIEN> |
|
| 3 |
<_setDefault id="-1"> |
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| 4 |
<source_id><source><shortname>CTFS</shortname></source></source_id> |
|
| 5 |
<path> |
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| 6 |
<_simplifyPath> |
|
| 7 |
<next>parent_id</next> |
|
| 8 |
<path> |
|
| 9 |
<location> |
|
| 10 |
<authorlocationcode>$Plot</authorlocationcode> |
|
| 11 |
<area_m2><_ha_to_m2><value>$PlotSize</value></_ha_to_m2></area_m2> |
|
| 12 |
<elevation_m>$Elevation </elevation_m> |
|
| 13 |
<locationevent> |
|
| 14 |
<authoreventcode>$CensusName</authoreventcode> |
|
| 15 |
<obsenddate>$EndDate</obsenddate> |
|
| 16 |
<obsstartdate>$StartDate</obsstartdate> |
|
| 17 |
<taxonoccurrence> |
|
| 18 |
<aggregateoccurrence> |
|
| 19 |
<count>$Abund</count> |
|
| 20 |
<plantobservation> |
|
| 21 |
<specimenreplicate><sourceaccessioncode>$DWstagingID</sourceaccessioncode></specimenreplicate> |
|
| 22 |
<stemobservation> |
|
| 23 |
<diameterbreastheight_m> |
|
| 24 |
<_cm_to_m> |
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| 25 |
<value> |
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| 26 |
<_avg> |
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| 27 |
<1>$maxDBHcm</1> |
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| 28 |
<2>$minDBHcm</2> |
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| 29 |
</_avg> |
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| 30 |
</value> |
|
| 31 |
</_cm_to_m> |
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| 32 |
</diameterbreastheight_m> |
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| 33 |
</stemobservation> |
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| 34 |
</plantobservation> |
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| 35 |
</aggregateoccurrence> |
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| 36 |
<growthform>$VegCategory</growthform> |
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| 37 |
<sourceaccessioncode>$DWstagingID</sourceaccessioncode> |
|
| 38 |
<taxondetermination> |
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| 39 |
<taxonverbatim_id> |
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| 40 |
<taxonverbatim> |
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| 41 |
<taxonlabel_id> |
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| 42 |
<taxonlabel> |
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| 43 |
<parent_id> |
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| 44 |
<taxonlabel> |
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| 45 |
<parent_id> |
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| 46 |
<taxonlabel> |
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| 47 |
<rank>cultivar</rank> |
|
| 48 |
<parent_id> |
|
| 49 |
<taxonlabel> |
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| 50 |
<rank>forma</rank> |
|
| 51 |
<parent_id> |
|
| 52 |
<taxonlabel> |
|
| 53 |
<rank>variety</rank> |
|
| 54 |
<parent_id> |
|
| 55 |
<taxonlabel> |
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| 56 |
<rank>subspecies</rank> |
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| 57 |
<taxonepithet>$subspecies</taxonepithet> |
|
| 58 |
<parent_id> |
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| 59 |
<taxonlabel> |
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| 60 |
<rank>species</rank> |
|
| 61 |
<taxonepithet>$speciesname</taxonepithet> |
|
| 62 |
<parent_id> |
|
| 63 |
<taxonlabel> |
|
| 64 |
<rank>genus</rank> |
|
| 65 |
<taxonepithet>$Genus </taxonepithet> |
|
| 66 |
</taxonlabel> |
|
| 67 |
</parent_id> |
|
| 68 |
</taxonlabel> |
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| 69 |
</parent_id> |
|
| 70 |
</taxonlabel> |
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| 71 |
</parent_id> |
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| 72 |
</taxonlabel> |
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| 73 |
</parent_id> |
|
| 74 |
</taxonlabel> |
|
| 75 |
</parent_id> |
|
| 76 |
</taxonlabel> |
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| 77 |
</parent_id> |
|
| 78 |
</taxonlabel> |
|
| 79 |
</parent_id> |
|
| 80 |
<taxonomicname> |
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| 81 |
<_join_words> |
|
| 82 |
<2>$Genus </2> |
|
| 83 |
<3>$speciesname</3> |
|
| 84 |
<4>$subspecies</4> |
|
| 85 |
</_join_words> |
|
| 86 |
</taxonomicname> |
|
| 87 |
</taxonlabel> |
|
| 88 |
</taxonlabel_id> |
|
| 89 |
<genus>$Genus </genus> |
|
| 90 |
<specific_epithet>$speciesname</specific_epithet> |
|
| 91 |
</taxonverbatim> |
|
| 92 |
</taxonverbatim_id> |
|
| 93 |
</taxondetermination> |
|
| 94 |
</taxonoccurrence> |
|
| 95 |
</locationevent> |
|
| 96 |
<locationplace> |
|
| 97 |
<place_id> |
|
| 98 |
<place> |
|
| 99 |
<coordinates_id> |
|
| 100 |
<coordinates> |
|
| 101 |
<footprintgeometry_dwc>$PlotShape</footprintgeometry_dwc> |
|
| 102 |
<latitude_deg> |
|
| 103 |
<_nullIf> |
|
| 104 |
<null>0</null> |
|
| 105 |
<type>float</type> |
|
| 106 |
<value>$Latitude </value> |
|
| 107 |
</_nullIf> |
|
| 108 |
</latitude_deg> |
|
| 109 |
<longitude_deg> |
|
| 110 |
<_nullIf> |
|
| 111 |
<null>0</null> |
|
| 112 |
<type>float</type> |
|
| 113 |
<value>$Longitude </value> |
|
| 114 |
</_nullIf> |
|
| 115 |
</longitude_deg> |
|
| 116 |
</coordinates> |
|
| 117 |
</coordinates_id> |
|
| 118 |
<country>$Country</country> |
|
| 119 |
<matched_place_id> |
|
| 120 |
<place> |
|
| 121 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 122 |
<coordinates_id> |
|
| 123 |
<coordinates> |
|
| 124 |
<source_id><source><shortname>geoscrub</shortname></source></source_id> |
|
| 125 |
<latitude_deg> |
|
| 126 |
<_nullIf> |
|
| 127 |
<null>0</null> |
|
| 128 |
<type>float</type> |
|
| 129 |
<value>$Latitude </value> |
|
| 130 |
</_nullIf> |
|
| 131 |
</latitude_deg> |
|
| 132 |
<longitude_deg> |
|
| 133 |
<_nullIf> |
|
| 134 |
<null>0</null> |
|
| 135 |
<type>float</type> |
|
| 136 |
<value>$Longitude </value> |
|
| 137 |
</_nullIf> |
|
| 138 |
</longitude_deg> |
|
| 139 |
</coordinates> |
|
| 140 |
</coordinates_id> |
|
| 141 |
<country>$Country</country> |
|
| 142 |
<stateprovince>$Province</stateprovince> |
|
| 143 |
</place> |
|
| 144 |
</matched_place_id> |
|
| 145 |
<stateprovince>$Province</stateprovince> |
|
| 146 |
</place> |
|
| 147 |
</place_id> |
|
| 148 |
</locationplace> |
|
| 149 |
</location> |
|
| 150 |
</path> |
|
| 151 |
</_simplifyPath> |
|
| 152 |
</path> |
|
| 153 |
</_setDefault> |
|
| 154 |
</VegBIEN> |
|
| 155 |
Inserted 29 new rows into database |
|
| inputs/CTFS/AggregateObservation/new_terms.csv | ||
|---|---|---|
| 1 |
DWstagingID,occurrenceID,, |
|
| 2 |
Province,stateProvince,, |
|
| 3 |
Plot,locationName,, |
|
| 4 |
CensusName,authorEventCode,, |
|
| 5 |
Abund,individualCount,, |
|
| 6 |
VegCategory,growthForm,, |
|
| 7 |
maxDBHcm,diameterBreastHeight_cm,/_avg/1, |
|
| 8 |
minDBHcm,diameterBreastHeight_cm,/_avg/2, |
|
| 9 |
PlotSize,plotArea_ha,,Assuming units based on the range and precision of values compared to the PlotShape values |
|
| 10 |
PlotShape,footprintWKT,, |
|
| inputs/CTFS/AggregateObservation/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*MeanDate |
|
Also available in: Unified diff
Added inputs/CTFS/AggregateObservation/ from BIEN2 data