Revision 10943
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/VegBank/plot_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
authorplotcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
|
| 3 |
plot_id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 4 |
plot_id,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
authorplotcode,"/location/_if[@name=""if subplot""]/then/parent_id/location/authorlocationcode", |
|
| 6 |
plot_id,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 7 |
accessRights,/location/accesslevel, |
|
| 8 |
area,/location/area_m2,"""Total area of the plot in m2"" (area definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 9 |
elevation,/location/elevation_m/_alt/1,"has only 5 decimal places of precision, with only 9s and random #s after that. ""The elevation of the plot origin in meters above sea level"" (elevation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename>)" |
|
| 10 |
locationnarrative,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1, |
|
| 11 |
landform,/location/landform, |
|
| 12 |
authorplotcode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/authorlocationcode/_if[@name=""if subplot""]/then", |
|
| 13 |
plot_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 14 |
authorplotcode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 15 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 16 |
locationnarrative,/location/locationnarrative/_merge/1, |
|
| 17 |
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value, |
|
| 18 |
shape,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc, |
|
| 19 |
latitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 20 |
longitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value", |
|
| 21 |
continent,/location/locationplace/*_id/place/continent, |
|
| 22 |
country,/location/locationplace/*_id/place/country, |
|
| 23 |
county,/location/locationplace/*_id/place/county, |
|
| 24 |
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" |
|
| 25 |
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" |
|
| 26 |
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
|
| 27 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
|
| 28 |
stateprovince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
|
| 29 |
stateprovince,/location/locationplace/*_id/place/stateprovince, |
|
| 30 |
parent_id,/location/parent_id/location/sourceaccessioncode, |
|
| 31 |
slopeaspect,/location/slopeaspect_deg/_alt/1/_compass/value, |
|
| 32 |
minslopeaspect,/location/slopeaspect_deg/_alt/2/_avg/1, |
|
| 33 |
maxslopeaspect,/location/slopeaspect_deg/_alt/2/_avg/2, |
|
| 34 |
slopegradient,/location/slopegradient_fraction/_alt/1, |
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| 35 |
minslopegradient,/location/slopegradient_fraction/_alt/2/_avg/1, |
|
| 36 |
maxslopegradient,/location/slopegradient_fraction/_alt/2/_avg/2, |
|
| 37 |
plot_id,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 38 |
plot_id,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 39 |
Geographic Name,,** No join mapping for *Geographic Name ** |
|
| 40 |
accessioncode,,** No join mapping for *accessioncode ** |
|
| 41 |
area|country|territory,,** No non-empty join mapping for DUPLICATE#of:country#area|country|territory ** |
|
| 42 |
authordatum,,** No join mapping for *authordatum ** |
|
| 43 |
authore,,** No join mapping for *authore ** |
|
| 44 |
authorlocation,,** No join mapping for *authorlocation ** |
|
| 45 |
authorn,,** No join mapping for *authorn ** |
|
| 46 |
authorzone,,** No join mapping for *authorzone ** |
|
| 47 |
azimuth,,** No join mapping for *azimuth ** |
|
| 48 |
confidentialityreason,,** No join mapping for *confidentialityreason ** |
|
| 49 |
confidentialitystatus,,** No join mapping for accessRights_verbatim ** |
|
| 50 |
dateentered,,** No join mapping for *dateentered ** |
|
| 51 |
dsgpoly,,** No join mapping for *dsgpoly ** |
|
| 52 |
elevationaccuracy,,** No join mapping for *elevationaccuracy ** |
|
| 53 |
elevationrange,,** No non-empty join mapping for UNUSED#elevationrange ** |
|
| 54 |
emb_plot,,** No join mapping for *emb_plot ** |
|
| 55 |
layoutnarrative,,** No join mapping for *layoutnarrative ** |
|
| 56 |
locationaccuracy,,** No join mapping for coordinateUncertaintyInMeters__from_coords ** |
|
| 57 |
notesmgt,,** No join mapping for *notesmgt ** |
|
| 58 |
notespublic,,** No join mapping for *notespublic ** |
|
| 59 |
permanence,,** No join mapping for *permanence ** |
|
| 60 |
placementmethod,,** No join mapping for *placementmethod ** |
|
| 61 |
plotrationalenarrative,,** No join mapping for *plotrationalenarrative ** |
|
| 62 |
quadrangle,,** No join mapping for *quadrangle ** |
|
| 63 |
reference_id,,** No join mapping for *reference_id ** |
|
| 64 |
region|state|province,,** No non-empty join mapping for DUPLICATE#of:stateprovince#region|state|province ** |
|
| 65 |
revisions,,** No join mapping for *revisions ** |
|
| 66 |
rocktype,,** No join mapping for *rocktype ** |
|
| 67 |
standsize,,** No join mapping for *standsize ** |
|
| 68 |
submitter_email,,** No join mapping for *submitter_email ** |
|
| 69 |
submitter_givenname,,** No join mapping for *submitter_givenname ** |
|
| 70 |
submitter_surname,,** No join mapping for *submitter_surname ** |
|
| 71 |
surficialdeposits,,** No join mapping for *surficialdeposits ** |
|
| 72 |
topoposition,,** No join mapping for *topoposition ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 73 | 2 | |
| inputs/VegBank/stemcount_/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
|
| 4 | 4 |
SELECT mk_derived_col((:table_str, 'aggregateOrganismObservationID'), |
| 5 |
$$_join("taxonimportance_id"::text, "stemcount_id"::text)$$)
|
|
| 5 |
$$_join("aggregateOrganismObservationID__taxon_presence"::text, "aggregateOrganismObservationID__individual_count"::text)$$)
|
|
| 6 | 6 |
; -- runtime: 15 s ("Time: 15805.876 ms") @starscream
|
| inputs/VegBank/stemcount_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/stemcount_/map.csv | ||
|---|---|---|
| 26 | 26 |
stemcount,individualCount,, |
| 27 | 27 |
stemtaxonarea,*stemtaxonarea,, |
| 28 | 28 |
emb_stemcount,*emb_stemcount,, |
| 29 |
aggregateOrganismObservationID,aggregateOrganismObservationID,, |
|
| inputs/VegBank/stemcount_/test.xml.ref | ||
|---|---|---|
| 10 | 10 |
<locationevent> |
| 11 | 11 |
<taxonoccurrence> |
| 12 | 12 |
<aggregateoccurrence> |
| 13 |
<count>$stemcount</count>
|
|
| 14 |
<cover_fraction><_percent_to_fraction><value>$cover</value></_percent_to_fraction></cover_fraction> |
|
| 13 |
<count>$individualCount</count>
|
|
| 14 |
<cover_fraction><_percent_to_fraction><value>$coverPercent</value></_percent_to_fraction></cover_fraction>
|
|
| 15 | 15 |
<plantobservation> |
| 16 | 16 |
<stemobservation> |
| 17 |
<diameterbreastheight_m><_cm_to_m><value>$stemdiameter</value></_cm_to_m></diameterbreastheight_m>
|
|
| 18 |
<height_m>$stemheight</height_m>
|
|
| 17 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
|
|
| 18 |
<height_m>$height_m</height_m>
|
|
| 19 | 19 |
</stemobservation> |
| 20 | 20 |
</plantobservation> |
| 21 | 21 |
<sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode> |
| 22 | 22 |
</aggregateoccurrence> |
| 23 |
<sourceaccessioncode>$taxonobservation_id</sourceaccessioncode>
|
|
| 23 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
|
|
| 24 | 24 |
</taxonoccurrence> |
| 25 | 25 |
</locationevent> |
| 26 | 26 |
</location> |
| inputs/VegBank/stemcount_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
taxonobservation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
| 3 |
|
|
| 4 |
[1] The following query returns rows: |
|
| 5 |
----- |
|
| 6 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
| 7 |
FROM ""VegBank"".taxonimportance |
|
| 8 |
GROUP BY taxonobservation_id |
|
| 9 |
HAVING count(distinct taxonimportance_id) > 1 |
|
| 10 |
-----" |
|
| 11 |
stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
|
| 12 |
cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
|
| 13 |
stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
| 14 |
stemheight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
| 15 |
aggregateOrganismObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
|
| 16 |
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
| 17 |
|
|
| 18 |
[1] The following query returns rows: |
|
| 19 |
----- |
|
| 20 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
| 21 |
FROM ""VegBank"".taxonimportance |
|
| 22 |
GROUP BY taxonobservation_id |
|
| 23 |
HAVING count(distinct taxonimportance_id) > 1 |
|
| 24 |
-----" |
|
| 25 |
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1,"Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
| 26 |
|
|
| 27 |
[1] The following query returns rows: |
|
| 28 |
----- |
|
| 29 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
| 30 |
FROM ""VegBank"".taxonimportance |
|
| 31 |
GROUP BY taxonobservation_id |
|
| 32 |
HAVING count(distinct taxonimportance_id) > 1 |
|
| 33 |
-----" |
|
| 34 |
aggregateOrganismObservationID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
|
| 35 |
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists","Note that taxonimportance is not 1:1 with taxonobservation [1]. |
|
| 36 |
|
|
| 37 |
[1] The following query returns rows: |
|
| 38 |
----- |
|
| 39 |
SELECT taxonobservation_id, count(distinct taxonimportance_id) |
|
| 40 |
FROM ""VegBank"".taxonimportance |
|
| 41 |
GROUP BY taxonobservation_id |
|
| 42 |
HAVING count(distinct taxonimportance_id) > 1 |
|
| 43 |
-----" |
|
| 44 |
basalarea,,** No join mapping for *basalarea ** |
|
| 45 |
biomass,,** No join mapping for *biomass ** |
|
| 46 |
covercode,,** No join mapping for *covercode ** |
|
| 47 |
emb_stemcount,,** No join mapping for *emb_stemcount ** |
|
| 48 |
emb_taxonimportance,,** No join mapping for *emb_taxonimportance ** |
|
| 49 |
inferencearea,,** No join mapping for *inferencearea ** |
|
| 50 |
stemcount_id,,** No join mapping for aggregateOrganismObservationID__individual_count ** |
|
| 51 |
stemdiameteraccuracy,,** No join mapping for *stemdiameteraccuracy ** |
|
| 52 |
stemheightaccuracy,,** No join mapping for *stemheightaccuracy ** |
|
| 53 |
stemtaxonarea,,** No join mapping for *stemtaxonarea ** |
|
| 54 |
stratum_id,,** No join mapping for *stratum_id ** |
|
| 55 |
stratumbase,,** No join mapping for *stratumbase ** |
|
| 56 |
stratumheight,,** No join mapping for *stratumheight ** |
|
| 57 |
taxonimportance_id,,** No join mapping for aggregateOrganismObservationID__taxon_presence ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 58 | 2 | |
| inputs/VegBank/observation_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("observation_id")$$); -- runtime: ~0 ("Time: 1.838 ms") @starscream
|
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("eventID")$$); -- runtime: ~0 ("Time: 1.838 ms") @starscream
|
|
| inputs/VegBank/observation_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/observation_/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<sourceaccessioncode>$plot_id</sourceaccessioncode>
|
|
| 10 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 11 | 11 |
<locationevent> |
| 12 |
<method_id><method><name>$methodnarrative</name></method></method_id>
|
|
| 13 |
<project_id><project><sourceaccessioncode>$project_id</sourceaccessioncode></project></project_id>
|
|
| 14 |
<authoreventcode>$authorobscode</authoreventcode>
|
|
| 15 |
<sourceaccessioncode>$observation_id</sourceaccessioncode>
|
|
| 16 |
<obsenddate>$obsenddate</obsenddate>
|
|
| 17 |
<obsstartdate>$obsstartdate</obsstartdate>
|
|
| 12 |
<method_id><method><name>$samplingProtocol</name></method></method_id>
|
|
| 13 |
<project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id>
|
|
| 14 |
<authoreventcode>$authorEventCode</authoreventcode>
|
|
| 15 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 16 |
<obsenddate>$endDate</obsenddate>
|
|
| 17 |
<obsstartdate>$startDate</obsstartdate>
|
|
| 18 | 18 |
<soilsample> |
| 19 |
<basesaturation_fraction><_percent_to_fraction><value>$basesaturation</value></_percent_to_fraction></basesaturation_fraction>
|
|
| 20 |
<cationexchangecapacity_cmol_kg>$exchangecapacity</cationexchangecapacity_cmol_kg>
|
|
| 21 |
<clay_fraction><_percent_to_fraction><value>$soilclay</value></_percent_to_fraction></clay_fraction>
|
|
| 22 |
<organic_fraction><_percent_to_fraction><value>$soilorganic</value></_percent_to_fraction></organic_fraction>
|
|
| 23 |
<ph>$soilph</ph>
|
|
| 24 |
<sand_fraction><_percent_to_fraction><value>$soilsand</value></_percent_to_fraction></sand_fraction>
|
|
| 25 |
<silt_fraction><_percent_to_fraction><value>$soilsilt</value></_percent_to_fraction></silt_fraction>
|
|
| 26 |
<texture>$soiltexture</texture>
|
|
| 19 |
<basesaturation_fraction><_percent_to_fraction><value>$baseSaturation_percent</value></_percent_to_fraction></basesaturation_fraction>
|
|
| 20 |
<cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg>
|
|
| 21 |
<clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction>
|
|
| 22 |
<organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction>
|
|
| 23 |
<ph>$ph</ph> |
|
| 24 |
<sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction>
|
|
| 25 |
<silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction>
|
|
| 26 |
<texture>$texture</texture> |
|
| 27 | 27 |
</soilsample> |
| 28 | 28 |
</locationevent> |
| 29 | 29 |
</location> |
| inputs/VegBank/observation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
plot_id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 3 |
authorobscode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else", |
|
| 4 |
plot_id,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 5 |
plot_id,"/location/_if[@name=""if subplot""]/then/parent_id/location/sourceaccessioncode", |
|
| 6 |
methodnarrative,/location/locationevent/*_id/method/name, |
|
| 7 |
project_id,/location/locationevent/*_id/project/sourceaccessioncode, |
|
| 8 |
authorobscode,"/location/locationevent/_if[@name=""if subplot""]/else/authoreventcode", |
|
| 9 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 10 |
authorobscode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 11 |
obsenddate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 13 |
obsstartdate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 14 |
plot_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/*_id/location/sourceaccessioncode/_if[@name=""if subplot""]/then", |
|
| 15 |
authorobscode,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/authoreventcode", |
|
| 16 |
obsenddate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/1", |
|
| 17 |
obsstartdate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/1", |
|
| 18 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 19 |
obsenddate,/location/locationevent/obsenddate/_alt/1, |
|
| 20 |
obsstartdate,/location/locationevent/obsstartdate/_alt/1, |
|
| 21 |
basesaturation,/location/locationevent/soilsample/basesaturation_fraction/_percent_to_fraction/value,"""Percent base saturation"" (baseSaturation definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 22 |
exchangecapacity,/location/locationevent/soilsample/cationexchangecapacity_cmol_kg, |
|
| 23 |
soilclay,/location/locationevent/soilsample/clay_fraction/_percent_to_fraction/value,"""Percent clay in the soil horizon"" (soilClay definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 24 |
soilorganic,/location/locationevent/soilsample/organic_fraction/_percent_to_fraction/value,"""Percent organic content of the soil"" (soilOrganic definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 25 |
soilph,/location/locationevent/soilsample/ph, |
|
| 26 |
soilsand,/location/locationevent/soilsample/sand_fraction/_percent_to_fraction/value,"""Percent sand in the soil horizon"" (soilSand definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 27 |
soilsilt,/location/locationevent/soilsample/silt_fraction/_percent_to_fraction/value,"""Percent silt in the soil horizon"" (soilSilt definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 28 |
soiltexture,/location/locationevent/soilsample/texture, |
|
| 29 |
authorobscode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 30 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 31 |
plot_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 32 |
plot_id,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
|
| 33 |
plot_id,"/location/sourceaccessioncode/_first/2/_if[@name=""if locationID""]/then/_if[@name=""if subplot""]/then/_join/1", |
|
| 34 |
accessioncode,,** No join mapping for *accessioncode ** |
|
| 35 |
autotaxoncover,,** No join mapping for *autotaxoncover ** |
|
| 36 |
basalarea,,** No join mapping for *basalarea ** |
|
| 37 |
bryophytequality,,** No join mapping for *bryophytequality ** |
|
| 38 |
coverdispersion,,** No join mapping for *coverdispersion ** |
|
| 39 |
covermethod_id,,** No join mapping for *covermethod_id ** |
|
| 40 |
dateaccuracy,,** No join mapping for *dateaccuracy ** |
|
| 41 |
dateentered,,** No join mapping for *dateentered ** |
|
| 42 |
dominantstratum,,** No join mapping for *dominantstratum ** |
|
| 43 |
effortlevel,,** No join mapping for *effortlevel ** |
|
| 44 |
emb_observation,,** No join mapping for *emb_observation ** |
|
| 45 |
emb_soilobs,,** No join mapping for *emb_soilobs ** |
|
| 46 |
fieldcover,,** No join mapping for *fieldcover ** |
|
| 47 |
fieldht,,** No join mapping for *fieldht ** |
|
| 48 |
floatingcover,,** No join mapping for *floatingcover ** |
|
| 49 |
floristicquality,,** No join mapping for *floristicquality ** |
|
| 50 |
growthform1cover,,** No join mapping for *growthform1cover ** |
|
| 51 |
growthform1type,,** No join mapping for *growthform1type ** |
|
| 52 |
growthform2cover,,** No join mapping for *growthform2cover ** |
|
| 53 |
growthform2type,,** No join mapping for *growthform2type ** |
|
| 54 |
growthform3cover,,** No join mapping for *growthform3cover ** |
|
| 55 |
growthform3type,,** No join mapping for *growthform3type ** |
|
| 56 |
homogeneity,,** No join mapping for *homogeneity ** |
|
| 57 |
hydrologicregime,,** No join mapping for *hydrologicregime ** |
|
| 58 |
interp_bestfit_cc_id,,** No join mapping for *interp_bestfit_cc_id ** |
|
| 59 |
interp_bestfit_ci_id,,** No join mapping for *interp_bestfit_ci_id ** |
|
| 60 |
interp_bestfit_code,,** No join mapping for *interp_bestfit_code ** |
|
| 61 |
interp_bestfit_party_id,,** No join mapping for *interp_bestfit_party_id ** |
|
| 62 |
interp_bestfit_partyname,,** No join mapping for *interp_bestfit_partyname ** |
|
| 63 |
interp_bestfit_sciname,,** No join mapping for *interp_bestfit_sciname ** |
|
| 64 |
interp_current_cc_id,,** No join mapping for *interp_current_cc_id ** |
|
| 65 |
interp_current_ci_id,,** No join mapping for *interp_current_ci_id ** |
|
| 66 |
interp_current_code,,** No join mapping for *interp_current_code ** |
|
| 67 |
interp_current_party_id,,** No join mapping for *interp_current_party_id ** |
|
| 68 |
interp_current_partyname,,** No join mapping for *interp_current_partyname ** |
|
| 69 |
interp_current_sciname,,** No join mapping for *interp_current_sciname ** |
|
| 70 |
interp_orig_cc_id,,** No join mapping for *interp_orig_cc_id ** |
|
| 71 |
interp_orig_ci_id,,** No join mapping for *interp_orig_ci_id ** |
|
| 72 |
interp_orig_code,,** No join mapping for *interp_orig_code ** |
|
| 73 |
interp_orig_party_id,,** No join mapping for *interp_orig_party_id ** |
|
| 74 |
interp_orig_partyname,,** No join mapping for *interp_orig_partyname ** |
|
| 75 |
interp_orig_sciname,,** No join mapping for *interp_orig_sciname ** |
|
| 76 |
landscapenarrative,,** No join mapping for *landscapenarrative ** |
|
| 77 |
lichenquality,,** No join mapping for *lichenquality ** |
|
| 78 |
nameother,,** No join mapping for *nameother ** |
|
| 79 |
nonvascularcover,,** No join mapping for *nonvascularcover ** |
|
| 80 |
nonvascularht,,** No join mapping for *nonvascularht ** |
|
| 81 |
notesmgt,,** No join mapping for *notesmgt ** |
|
| 82 |
notespublic,,** No join mapping for *notespublic ** |
|
| 83 |
numberoftaxa,,** No join mapping for *numberoftaxa ** |
|
| 84 |
observationnarrative,,** No join mapping for *observationnarrative ** |
|
| 85 |
organicdepth,,** No join mapping for *organicdepth ** |
|
| 86 |
originaldata,,** No join mapping for *originaldata ** |
|
| 87 |
percentbaresoil,,** No join mapping for *percentbaresoil ** |
|
| 88 |
percentbedrock,,** No join mapping for *percentbedrock ** |
|
| 89 |
percentlitter,,** No join mapping for *percentlitter ** |
|
| 90 |
percentother,,** No join mapping for *percentother ** |
|
| 91 |
percentrockgravel,,** No join mapping for *percentrockgravel ** |
|
| 92 |
percentwater,,** No join mapping for *percentwater ** |
|
| 93 |
percentwood,,** No join mapping for *percentwood ** |
|
| 94 |
phenologicaspect,,** No join mapping for *phenologicaspect ** |
|
| 95 |
plotvalidationlevel,,** No join mapping for *plotvalidationlevel ** |
|
| 96 |
previousobs_id,,** No join mapping for *previousobs_id ** |
|
| 97 |
representativeness,,** No join mapping for *representativeness ** |
|
| 98 |
revisions,,** No join mapping for *revisions ** |
|
| 99 |
shoredistance,,** No join mapping for *shoredistance ** |
|
| 100 |
shrubcover,,** No join mapping for *shrubcover ** |
|
| 101 |
shrubht,,** No join mapping for *shrubht ** |
|
| 102 |
soilcoarse,,"** No join mapping for *soilcoarse ** ""percent coarse fragments in the soil"" (soilCoarse definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilobs&entity=dba_tabledescription&where=where_tablename>)" |
|
| 103 |
soilcolor,,** No join mapping for *soilcolor ** |
|
| 104 |
soildepth,,** No join mapping for *soildepth ** |
|
| 105 |
soildepthbottom,,** No join mapping for *soildepthbottom ** |
|
| 106 |
soildepthtop,,** No join mapping for *soildepthtop ** |
|
| 107 |
soildescription,,** No join mapping for *soildescription ** |
|
| 108 |
soildrainage,,** No join mapping for *soildrainage ** |
|
| 109 |
soilhorizon,,** No join mapping for *soilhorizon ** |
|
| 110 |
soilmoistureregime,,** No join mapping for *soilmoistureregime ** |
|
| 111 |
soilobs_id,,** No join mapping for *soilobs_id ** |
|
| 112 |
soiltaxon_id,,** No join mapping for *soiltaxon_id ** |
|
| 113 |
soiltaxonsrc,,** No join mapping for *soiltaxonsrc ** |
|
| 114 |
standmaturity,,** No join mapping for *standmaturity ** |
|
| 115 |
stemobservationarea,,** No join mapping for *stemobservationarea ** |
|
| 116 |
stemsamplemethod,,** No join mapping for *stemsamplemethod ** |
|
| 117 |
stemsizelimit,,** No join mapping for *stemsizelimit ** |
|
| 118 |
stratummethod_id,,** No join mapping for *stratummethod_id ** |
|
| 119 |
submergedcover,,** No join mapping for *submergedcover ** |
|
| 120 |
submergedht,,** No join mapping for *submergedht ** |
|
| 121 |
successionalstatus,,** No join mapping for *successionalstatus ** |
|
| 122 |
taxonobservationarea,,** No join mapping for *taxonobservationarea ** |
|
| 123 |
toptaxon1name,,** No join mapping for *toptaxon1name ** |
|
| 124 |
toptaxon2name,,** No join mapping for *toptaxon2name ** |
|
| 125 |
toptaxon3name,,** No join mapping for *toptaxon3name ** |
|
| 126 |
toptaxon4name,,** No join mapping for *toptaxon4name ** |
|
| 127 |
toptaxon5name,,** No join mapping for *toptaxon5name ** |
|
| 128 |
totalcover,,** No join mapping for *totalcover ** |
|
| 129 |
treecover,,** No join mapping for *treecover ** |
|
| 130 |
treeht,,** No join mapping for *treeht ** |
|
| 131 |
waterdepth,,** No join mapping for *waterdepth ** |
|
| 132 |
watersalinity,,** No join mapping for *watersalinity ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 133 | 2 | |
| inputs/VegBank/stemlocation_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("stemlocation_id")$$); -- runtime: 0.1 s ("Time: 74.164 ms") @starscream
|
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("stemID")$$); -- runtime: 0.1 s ("Time: 74.164 ms") @starscream
|
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 |
SELECT mk_derived_col((:table_str, 'individualID'), $$stemlocation_id$$) ; -- runtime: ~0 ("Time: 1.562 ms") @starscream
|
|
| 6 |
SELECT mk_derived_col((:table_str, 'individualID'), $$"stemID"$$) ; -- runtime: ~0 ("Time: 1.562 ms") @starscream
|
|
| 7 | 7 |
|
| 8 | 8 |
SELECT mk_derived_col((:table_str, 'aggregateOrganismObservationID'), |
| 9 |
$$_join("taxonimportance_id"::text, "stemcount_id"::text)$$)
|
|
| 9 |
$$_join("aggregateOrganismObservationID__taxon_presence"::text, "aggregateOrganismObservationID__individual_count"::text)$$)
|
|
| 10 | 10 |
; -- runtime: 0.5 s ("Time: 441.059 ms") @starscream
|
| inputs/VegBank/stemlocation_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/stemlocation_/map.csv | ||
|---|---|---|
| 14 | 14 |
stemcount,individualCount,, |
| 15 | 15 |
stemtaxonarea,*stemtaxonarea,, |
| 16 | 16 |
emb_stemcount,*emb_stemcount,, |
| 17 |
aggregateOrganismObservationID,aggregateOrganismObservationID,, |
|
| 18 |
individualID,individualID,, |
|
| inputs/VegBank/stemlocation_/test.xml.ref | ||
|---|---|---|
| 10 | 10 |
<locationevent> |
| 11 | 11 |
<taxonoccurrence> |
| 12 | 12 |
<aggregateoccurrence> |
| 13 |
<count>$stemcount</count>
|
|
| 13 |
<count>$individualCount</count>
|
|
| 14 | 14 |
<plantobservation> |
| 15 | 15 |
<sourceaccessioncode>$individualID</sourceaccessioncode> |
| 16 | 16 |
<stemobservation> |
| 17 |
<diameterbreastheight_m><_cm_to_m><value>$stemdiameter</value></_cm_to_m></diameterbreastheight_m>
|
|
| 18 |
<height_m>$stemheight</height_m>
|
|
| 19 |
<sourceaccessioncode>$stemlocation_id</sourceaccessioncode>
|
|
| 17 |
<diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
|
|
| 18 |
<height_m>$height_m</height_m>
|
|
| 19 |
<sourceaccessioncode>$stemID</sourceaccessioncode>
|
|
| 20 | 20 |
</stemobservation> |
| 21 | 21 |
</plantobservation> |
| 22 | 22 |
<sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode> |
| inputs/VegBank/stemlocation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
individualID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 3 |
stemcount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
|
| 4 |
individualID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode/_first/2, |
|
| 5 |
stemdiameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""The diameter of the stem in centimeters"" (stemDiameter definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
| 6 |
stemheight,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height_m,"""The measured height of the stem in meters"" (stemHeight definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>)" |
|
| 7 |
stemlocation_id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
|
| 8 |
aggregateOrganismObservationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/sourceaccessioncode, |
|
| 9 |
individualID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
|
| 10 |
stemlocation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_if[@name=""if individual""]/cond/_exists", |
|
| 11 |
individualID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 12 |
aggregateOrganismObservationID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/cond/_exists", |
|
| 13 |
individualID,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/2/_if[@name=""if organism in AggregateOccurrence""]/else/_first/2", |
|
| 14 |
emb_stemcount,,** No join mapping for *emb_stemcount ** |
|
| 15 |
emb_stemlocation,,** No join mapping for *emb_stemlocation ** |
|
| 16 |
stemcode,,** No non-empty join mapping for UNUSED#stemcode ** |
|
| 17 |
stemcount_id,,** No join mapping for aggregateOrganismObservationID__individual_count ** |
|
| 18 |
stemdiameteraccuracy,,** No join mapping for *stemdiameteraccuracy ** |
|
| 19 |
stemhealth,,** No join mapping for *stemhealth ** this *is* populated |
|
| 20 |
stemheightaccuracy,,** No join mapping for *stemheightaccuracy ** |
|
| 21 |
stemtaxonarea,,** No join mapping for *stemtaxonarea ** |
|
| 22 |
stemxposition,,"** No non-empty join mapping for UNUSED#stemxposition ** ""The X-coordinate of the stem position in m"" (stemXPosition definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemlocation&entity=dba_tabledescription&where=where_tablename>)" |
|
| 23 |
stemyposition,,"** No non-empty join mapping for UNUSED#stemyposition ** ""The Y-coordinate of the stem position, as above"" (stemYPosition definition at <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemlocation&entity=dba_tabledescription&where=where_tablename>)" |
|
| 24 |
taxonimportance_id,,** No join mapping for aggregateOrganismObservationID__taxon_presence ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 25 | 2 | |
| inputs/VegBank/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
|
|
| 0 | 3 | |
| inputs/VegBank/taxonobservation_/postprocess.sql | ||
|---|---|---|
| 2 | 2 |
|
| 3 | 3 |
|
| 4 | 4 |
SELECT mk_derived_col((:table_str, 'scientificName'), |
| 5 |
$$_alt("int_currplantscifull", "plantconcept_plantname")$$)
|
|
| 5 |
$$_alt("scientificName_verbatim", "scientificName__for_nearest_taxon_concept")$$)
|
|
| 6 | 6 |
; -- runtime: 15 s ("Time: 12334.893 ms") @starscream
|
| inputs/VegBank/taxonobservation_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/taxonobservation_/map.csv | ||
|---|---|---|
| 42 | 42 |
collectiondate,dateCollected,, |
| 43 | 43 |
emb_taxoninterpretation,*emb_taxoninterpretation,, |
| 44 | 44 |
taxoninterpretation_accessioncode,*taxoninterpretation_accessioncode,, |
| 45 |
plantname_id,*plantname_id,, |
|
| 46 | 45 |
plantconcept_reference_id,*plantconcept_reference_id,, |
| 47 | 46 |
plantconcept_plantname,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is." |
| 48 | 47 |
plantcode,*plantcode,, |
| ... | ... | |
| 68 | 67 |
plantname_reference_id,*plantname_reference_id,, |
| 69 | 68 |
dateentered,*dateentered,, |
| 70 | 69 |
:plot,observationGranularity,, |
| 71 |
scientificName,scientificName,, |
|
| inputs/VegBank/taxonobservation_/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode> |
|
| 11 |
<_if name="if plot"> |
|
| 12 |
<cond> |
|
| 13 |
<_eq> |
|
| 14 |
<right>plot</right> |
|
| 15 |
<left>$observationGranularity</left> |
|
| 16 |
</_eq> |
|
| 17 |
</cond> |
|
| 18 |
<else>$accessionNumber</else> |
|
| 19 |
</_if> |
|
| 20 |
</authorlocationcode> |
|
| 10 | 21 |
<locationevent> |
| 11 |
<sourceaccessioncode>$observation_id</sourceaccessioncode>
|
|
| 22 |
<sourceaccessioncode>$eventID</sourceaccessioncode>
|
|
| 12 | 23 |
<taxonoccurrence> |
| 13 | 24 |
<aggregateoccurrence> |
| 14 |
<collectiondate>$collectiondate</collectiondate>
|
|
| 15 |
<notes>$notes</notes>
|
|
| 25 |
<collectiondate>$dateCollected</collectiondate>
|
|
| 26 |
<notes>$occurrenceRemarks</notes>
|
|
| 16 | 27 |
<plantobservation> |
| 17 |
<authorplantcode>$collectionnumber</authorplantcode>
|
|
| 28 |
<authorplantcode>$collectorNumber</authorplantcode>
|
|
| 18 | 29 |
<specimenreplicate> |
| 19 |
<catalognumber_dwc>$museumaccessionnumber</catalognumber_dwc>
|
|
| 20 |
<collectionnumber>$collectionnumber</collectionnumber>
|
|
| 30 |
<catalognumber_dwc>$accessionNumber</catalognumber_dwc>
|
|
| 31 |
<collectionnumber>$collectorNumber</collectionnumber>
|
|
| 21 | 32 |
</specimenreplicate> |
| 22 | 33 |
</plantobservation> |
| 23 | 34 |
</aggregateoccurrence> |
| 24 |
<authortaxoncode>$collectionnumber</authortaxoncode>
|
|
| 25 |
<sourceaccessioncode>$taxonobservation_id</sourceaccessioncode>
|
|
| 35 |
<authortaxoncode>$collectorNumber</authortaxoncode>
|
|
| 36 |
<sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
|
|
| 26 | 37 |
<taxondetermination> |
| 27 | 38 |
<taxonverbatim_id> |
| 28 | 39 |
<taxonverbatim> |
| ... | ... | |
| 48 | 59 |
<parent_id> |
| 49 | 60 |
<taxonlabel> |
| 50 | 61 |
<rank>genus</rank> |
| 51 |
<taxonepithet>$Genus</taxonepithet>
|
|
| 62 |
<taxonepithet>$genus</taxonepithet>
|
|
| 52 | 63 |
<parent_id> |
| 53 | 64 |
<taxonlabel> |
| 54 | 65 |
<rank>family</rank> |
| 55 |
<taxonepithet>$Family</taxonepithet>
|
|
| 66 |
<taxonepithet>$family</taxonepithet>
|
|
| 56 | 67 |
<parent_id> |
| 57 | 68 |
<taxonlabel> |
| 58 | 69 |
<rank>order</rank> |
| 59 |
<taxonepithet>$Order</taxonepithet>
|
|
| 70 |
<taxonepithet>$order</taxonepithet>
|
|
| 60 | 71 |
<parent_id> |
| 61 | 72 |
<taxonlabel> |
| 62 | 73 |
<rank>class</rank> |
| 63 |
<taxonepithet>$Class</taxonepithet>
|
|
| 74 |
<taxonepithet>$class</taxonepithet>
|
|
| 64 | 75 |
<parent_id> |
| 65 | 76 |
<taxonlabel> |
| 66 | 77 |
<rank>phylum</rank> |
| 67 | 78 |
<parent_id> |
| 68 | 79 |
<taxonlabel> |
| 69 | 80 |
<rank>kingdom</rank> |
| 70 |
<taxonepithet>$Kingdom</taxonepithet>
|
|
| 81 |
<taxonepithet>$kingdom</taxonepithet>
|
|
| 71 | 82 |
</taxonlabel> |
| 72 | 83 |
</parent_id> |
| 73 | 84 |
</taxonlabel> |
| ... | ... | |
| 94 | 105 |
</parent_id> |
| 95 | 106 |
<taxonomicname> |
| 96 | 107 |
<_merge_prefix> |
| 97 |
<prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
|
|
| 108 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
|
|
| 98 | 109 |
<value> |
| 99 | 110 |
<_alt> |
| 100 | 111 |
<1>$scientificName</1> |
| 101 | 112 |
<2> |
| 102 | 113 |
<_alt> |
| 103 |
<1>$int_currplantscinamenoauth</1>
|
|
| 104 |
<2><_filter_genus><value>$Genus</value></_filter_genus></2>
|
|
| 114 |
<1>$taxonName</1>
|
|
| 115 |
<2><_filter_genus><value>$genus</value></_filter_genus></2>
|
|
| 105 | 116 |
</_alt> |
| 106 | 117 |
</2> |
| 107 | 118 |
</_alt> |
| ... | ... | |
| 110 | 121 |
</taxonomicname> |
| 111 | 122 |
</taxonlabel> |
| 112 | 123 |
</taxonlabel_id> |
| 113 |
<family>$Family</family>
|
|
| 114 |
<genus>$Genus</genus>
|
|
| 115 |
<taxonname>$int_currplantscinamenoauth</taxonname>
|
|
| 124 |
<family>$family</family>
|
|
| 125 |
<genus>$genus</genus>
|
|
| 126 |
<taxonname>$taxonName</taxonname>
|
|
| 116 | 127 |
<taxonomicname>$scientificName</taxonomicname> |
| 117 | 128 |
</taxonverbatim> |
| 118 | 129 |
</taxonverbatim_id> |
| 119 |
<determinationdate><_dateRangeStart><value>$interpretationdate</value></_dateRangeStart></determinationdate>
|
|
| 120 |
<determinationtype>$interpretationtype</determinationtype>
|
|
| 121 |
<taxonfit>$taxonfit</taxonfit>
|
|
| 130 |
<determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
|
|
| 131 |
<determinationtype>$identificationType</determinationtype>
|
|
| 132 |
<taxonfit>$identificationQualifier</taxonfit>
|
|
| 122 | 133 |
</taxondetermination> |
| 123 | 134 |
<taxondetermination> |
| 124 | 135 |
<isoriginal>true</isoriginal> |
| 125 | 136 |
<taxonverbatim_id> |
| 126 | 137 |
<taxonverbatim> |
| 127 |
<taxonname>$int_origplantscinamenoauth</taxonname>
|
|
| 128 |
<taxonomicname>$authorplantname</taxonomicname>
|
|
| 138 |
<taxonname>$originalTaxonName</taxonname>
|
|
| 139 |
<taxonomicname>$originalScientificName</taxonomicname>
|
|
| 129 | 140 |
</taxonverbatim> |
| 130 | 141 |
</taxonverbatim_id> |
| 131 | 142 |
</taxondetermination> |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
|
| 2 |
museumaccessionnumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
:plot,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype", |
|
| 4 |
:plot,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left", |
|
| 5 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
|
| 6 |
museumaccessionnumber,"/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 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
|
| 8 |
collectionnumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 9 |
taxonobservation_id,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 10 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/else/sourceaccessioncode", |
|
| 11 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists", |
|
| 12 |
observation_id,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/sourceaccessioncode", |
|
| 13 |
interpretationdate,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value", |
|
| 14 |
taxonfit,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit", |
|
| 15 |
collectiondate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
|
| 16 |
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/1, |
|
| 17 |
collectionnumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2, |
|
| 18 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
|
| 19 |
collectionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else", |
|
| 20 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 21 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
|
| 22 |
collectionnumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
|
| 23 |
int_origplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1", |
|
| 24 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2", |
|
| 25 |
int_currplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
|
| 26 |
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 27 |
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
|
| 28 |
taxonobservation_id,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/1, |
|
| 29 |
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",includes genus author |
|
| 30 |
Family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet", |
|
| 31 |
Order,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=order]/taxonepithet", |
|
| 32 |
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet", |
|
| 33 |
Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet", |
|
| 34 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family, |
|
| 35 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1, |
|
| 36 |
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1, |
|
| 37 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,includes genus author |
|
| 38 |
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family, |
|
| 39 |
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,includes genus author |
|
| 40 |
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname, |
|
| 41 |
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname, |
|
| 42 |
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists", |
|
| 43 |
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value, |
|
| 44 |
interpretationtype,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationtype, |
|
| 45 |
taxonfit,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit, |
|
| 46 |
int_origplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
|
| 47 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonomicname, |
|
| 48 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
|
| 49 |
collectionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then", |
|
| 50 |
Division,,** No join mapping for *Division ** |
|
| 51 |
Forma,,** No non-empty join mapping for EQUIV#to:plantname#Forma ** *full* taxonomic name at that rank |
|
| 52 |
Species,,** No non-empty join mapping for EQUIV#to:plantname#Species ** *full* taxonomic name at that rank |
|
| 53 |
Subclass,,** No join mapping for *Subclass ** |
|
| 54 |
Subdivision,,** No join mapping for *Subdivision ** |
|
| 55 |
Subkingdom,,** No join mapping for *Subkingdom ** |
|
| 56 |
Subspecies,,** No non-empty join mapping for EQUIV#to:plantname#Subspecies ** *full* taxonomic name at that rank |
|
| 57 |
Superdivision,,** No join mapping for *Superdivision ** |
|
| 58 |
Variety,,** No non-empty join mapping for EQUIV#to:plantname#Variety ** *full* taxonomic name at that rank |
|
| 59 |
collector_id,,** No non-empty join mapping for UNUSED#collector_id ** |
|
| 60 |
currentinterpretation,,** No join mapping for *currentinterpretation ** |
|
| 61 |
d_currentaccepted,,** No join mapping for *d_currentaccepted ** |
|
| 62 |
d_obscount,,** No join mapping for *d_obscount ** |
|
| 63 |
dateentered,,** No join mapping for *dateentered ** |
|
| 64 |
emb_taxoninterpretation,,** No join mapping for *emb_taxoninterpretation ** |
|
| 65 |
emb_taxonobservation,,** No join mapping for *emb_taxonobservation ** |
|
| 66 |
grouptype,,** No join mapping for *grouptype ** |
|
| 67 |
int_currplantcode,,** No join mapping for *int_currplantcode ** |
|
| 68 |
int_currplantcommon,,** No join mapping for vernacularName ** |
|
| 69 |
int_currplantconcept_id,,** No join mapping for *int_currplantconcept_id ** |
|
| 70 |
int_currplantscifull,,** No join mapping for scientificName_verbatim ** |
|
| 71 |
int_origplantcode,,** No join mapping for *int_origplantcode ** |
|
| 72 |
int_origplantcommon,,** No join mapping for originalVernacularName ** |
|
| 73 |
int_origplantconcept_id,,** No join mapping for *int_origplantconcept_id ** |
|
| 74 |
int_origplantscifull,,** No non-empty join mapping for EQUIV#to:authorplantname#int_origplantscifull ** = originalScientificName_scrubbed |
|
| 75 |
museum_id,,** No join mapping for *museum_id ** |
|
| 76 |
notesmgt,,** No join mapping for *notesmgt ** |
|
| 77 |
notespublic,,** No join mapping for *notespublic ** |
|
| 78 |
originalinterpretation,,** No join mapping for *originalinterpretation ** |
|
| 79 |
plantcode,,** No join mapping for *plantcode ** |
|
| 80 |
plantconcept_accessioncode,,** No join mapping for *plantconcept_accessioncode ** |
|
| 81 |
plantconcept_id,,** No join mapping for *plantconcept_id ** |
|
| 82 |
plantconcept_plantname,,"** No join mapping for scientificName__for_nearest_taxon_concept ** when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is." |
|
| 83 |
plantconcept_reference_id,,** No join mapping for *plantconcept_reference_id ** |
|
| 84 |
plantdescription,,** No join mapping for *plantdescription ** |
|
| 85 |
plantname,,** No non-empty join mapping for DUPLICATE#of:plantconcept_plantname#plantname ** exact duplicate |
|
| 86 |
plantname_id,,** No join mapping for *plantname_id ** |
|
| 87 |
plantname_reference_id,,** No join mapping for *plantname_reference_id ** |
|
| 88 |
reference_id,,** No join mapping for *reference_id ** |
|
| 89 |
revisions,,** No join mapping for *revisions ** |
|
| 90 |
role_id,,** No join mapping for *role_id ** |
|
| 91 |
stemlocation_id,,** No join mapping for *stemlocation_id ** |
|
| 92 |
taxonconfidence,,** No join mapping for identificationVerificationStatus ** |
|
| 93 |
taxoninferencearea,,** No join mapping for *taxoninferencearea ** |
|
| 94 |
taxoninterpretation_accessioncode,,** No join mapping for *taxoninterpretation_accessioncode ** |
|
| 95 |
taxoninterpretation_id,,** No join mapping for *taxoninterpretation_id ** |
|
| 96 |
taxoninterpretation_party_id,,** No join mapping for *taxoninterpretation_party_id ** |
|
| 97 |
taxoninterpretation_plantname_id,,** No join mapping for *taxoninterpretation_plantname_id ** |
|
| 98 |
taxonobservation_accessioncode,,** No join mapping for *taxonobservation_accessioncode ** |
|
| 99 |
taxonobservation_reference_id,,** No join mapping for *taxonobservation_reference_id ** |
|
| 1 |
link ../../../mappings/VegCore-VegBIEN.csv |
|
| 100 | 2 | |
| inputs/VegBank/taxonobservation_/unmapped_terms.csv | ||
|---|---|---|
| 1 |
*plantname_id |
|
| 1 | 2 |
*plantconcept_id |
| 2 | 3 |
*taxonobservation_reference_id |
| 3 | 4 |
*taxoninferencearea |
| ... | ... | |
| 26 | 27 |
*revisions |
| 27 | 28 |
*emb_taxoninterpretation |
| 28 | 29 |
*taxoninterpretation_accessioncode |
| 29 |
*plantname_id |
|
| 30 | 30 |
*plantconcept_reference_id |
| 31 | 31 |
scientificName__for_nearest_taxon_concept |
| 32 | 32 |
*plantcode |
| inputs/VegBank/plot_/postprocess.sql | ||
|---|---|---|
| 1 | 1 |
SELECT util.search_path_append('util');
|
| 2 | 2 |
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("plot_id")$$); -- runtime: 0.2 s ("Time: 238.474 ms") @starscream
|
|
| 3 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("locationID")$$); -- runtime: 0.2 s ("Time: 238.474 ms") @starscream
|
|
| 4 | 4 |
|
| 5 | 5 |
|
| 6 | 6 |
-- map_*() derived cols |
| ... | ... | |
| 26 | 26 |
LANGUAGE sql IMMUTABLE |
| 27 | 27 |
COST 100; |
| 28 | 28 |
|
| 29 |
SELECT mk_derived_col((:table_str, 'accessRights'), $$map_access_rights("confidentialitystatus")$$); -- runtime: 1 s ("Time: 1270.464 ms") @starscream
|
|
| 29 |
SELECT mk_derived_col((:table_str, 'accessRights'), $$map_access_rights("accessRights_verbatim")$$); -- runtime: 1 s ("Time: 1270.464 ms") @starscream
|
|
| 30 | 30 |
|
| 31 | 31 |
CREATE OR REPLACE FUNCTION map_fuzzing(value integer) |
| 32 | 32 |
RETURNS double precision AS |
| ... | ... | |
| 48 | 48 |
LANGUAGE sql IMMUTABLE |
| 49 | 49 |
COST 100; |
| 50 | 50 |
|
| 51 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters__from_fuzzing'), $$map_fuzzing("confidentialitystatus")$$); -- runtime: 1 s ("Time: 1134.143 ms") @starscream
|
|
| 51 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters__from_fuzzing'), $$map_fuzzing("accessRights_verbatim")$$); -- runtime: 1 s ("Time: 1134.143 ms") @starscream
|
|
| 52 | 52 |
|
| 53 | 53 |
|
| 54 | 54 |
SELECT mk_derived_col((:table_str, 'coordinateUncertaintyInMeters'), |
| 55 |
$$GREATEST("coordinateUncertaintyInMeters__from_fuzzing", "locationaccuracy")$$)
|
|
| 55 |
$$GREATEST("coordinateUncertaintyInMeters__from_fuzzing", "coordinateUncertaintyInMeters__from_coords")$$)
|
|
| 56 | 56 |
; -- runtime: 1 s ("Time: 712.548 ms") @starscream
|
| inputs/VegBank/plot_/run | ||
|---|---|---|
| 1 |
#!/bin/bash -e |
|
| 2 |
. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
|
|
| 0 | 3 | |
| inputs/VegBank/plot_/map.csv | ||
|---|---|---|
| 53 | 53 |
county,county,, |
| 54 | 54 |
quadrangle,*quadrangle,, |
| 55 | 55 |
Geographic Name,*Geographic Name,, |
| 56 |
accessRights,accessRights,, |
|
| 57 |
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,, |
|
| inputs/VegBank/plot_/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode>$authorplotcode</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$plot_id</sourceaccessioncode>
|
|
| 10 |
<authorlocationcode>$locationName</authorlocationcode>
|
|
| 11 |
<sourceaccessioncode>$locationID</sourceaccessioncode>
|
|
| 12 | 12 |
<accesslevel>$accessRights</accesslevel> |
| 13 |
<area_m2>$area</area_m2>
|
|
| 14 |
<elevation_m>$elevation</elevation_m> |
|
| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locationnarrative</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 13 |
<area_m2>$plotArea_m2</area_m2>
|
|
| 14 |
<elevation_m>$elevationInMeters</elevation_m>
|
|
| 15 |
<iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
|
|
| 16 | 16 |
<landform>$landform</landform> |
| 17 |
<locationnarrative>$locationnarrative</locationnarrative>
|
|
| 17 |
<locationnarrative>$locality</locationnarrative>
|
|
| 18 | 18 |
<locationplace> |
| 19 | 19 |
<place_id> |
| 20 | 20 |
<place> |
| 21 | 21 |
<coordinates_id> |
| 22 | 22 |
<coordinates> |
| 23 | 23 |
<coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m> |
| 24 |
<footprintgeometry_dwc>$shape</footprintgeometry_dwc>
|
|
| 24 |
<footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
|
|
| 25 | 25 |
<latitude_deg> |
| 26 | 26 |
<_nullIf> |
| 27 | 27 |
<null>0</null> |
| 28 | 28 |
<type>float</type> |
| 29 |
<value>$latitude</value>
|
|
| 29 |
<value>$decimalLatitude</value>
|
|
| 30 | 30 |
</_nullIf> |
| 31 | 31 |
</latitude_deg> |
| 32 | 32 |
<longitude_deg> |
| 33 | 33 |
<_nullIf> |
| 34 | 34 |
<null>0</null> |
| 35 | 35 |
<type>float</type> |
| 36 |
<value>$longitude</value>
|
|
| 36 |
<value>$decimalLongitude</value>
|
|
| 37 | 37 |
</_nullIf> |
| 38 | 38 |
</longitude_deg> |
| 39 | 39 |
</coordinates> |
| ... | ... | |
| 51 | 51 |
<_nullIf> |
| 52 | 52 |
<null>0</null> |
| 53 | 53 |
<type>float</type> |
| 54 |
<value>$latitude</value>
|
|
| 54 |
<value>$decimalLatitude</value>
|
|
| 55 | 55 |
</_nullIf> |
| 56 | 56 |
</latitude_deg> |
| 57 | 57 |
<longitude_deg> |
| 58 | 58 |
<_nullIf> |
| 59 | 59 |
<null>0</null> |
| 60 | 60 |
<type>float</type> |
| 61 |
<value>$longitude</value>
|
|
| 61 |
<value>$decimalLongitude</value>
|
|
| 62 | 62 |
</_nullIf> |
| 63 | 63 |
</longitude_deg> |
| 64 | 64 |
</coordinates> |
| 65 | 65 |
</coordinates_id> |
| 66 | 66 |
<country>$country</country> |
| 67 | 67 |
<county>$county</county> |
| 68 |
<stateprovince>$stateprovince</stateprovince>
|
|
| 68 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 69 | 69 |
</place> |
| 70 | 70 |
</matched_place_id> |
| 71 |
<stateprovince>$stateprovince</stateprovince>
|
|
| 71 |
<stateprovince>$stateProvince</stateprovince>
|
|
| 72 | 72 |
</place> |
| 73 | 73 |
</place_id> |
| 74 | 74 |
</locationplace> |
| 75 |
<parent_id><location><sourceaccessioncode>$parent_id</sourceaccessioncode></location></parent_id>
|
|
| 75 |
<parent_id><location><sourceaccessioncode>$parentLocationID</sourceaccessioncode></location></parent_id>
|
|
| 76 | 76 |
<slopeaspect_deg> |
| 77 | 77 |
<_alt> |
| 78 |
<1><_compass><value>$slopeaspect</value></_compass></1>
|
|
| 78 |
<1><_compass><value>$slopeAspect</value></_compass></1>
|
|
| 79 | 79 |
<2> |
| 80 | 80 |
<_avg> |
| 81 |
<1>$minslopeaspect</1>
|
|
| 82 |
<2>$maxslopeaspect</2>
|
|
| 81 |
<1>$minSlopeAspect</1>
|
|
| 82 |
<2>$maxSlopeAspect</2>
|
|
| 83 | 83 |
</_avg> |
| 84 | 84 |
</2> |
| 85 | 85 |
</_alt> |
| 86 | 86 |
</slopeaspect_deg> |
| 87 | 87 |
<slopegradient_fraction> |
| 88 | 88 |
<_alt> |
| 89 |
<1>$slopegradient</1>
|
|
| 89 |
<1>$slopeGradient</1>
|
|
| 90 | 90 |
<2> |
| 91 | 91 |
<_avg> |
| 92 |
<1>$minslopegradient</1>
|
|
| 93 |
<2>$maxslopegradient</2>
|
|
| 92 |
<1>$minSlopeGradient</1>
|
|
| 93 |
<2>$maxSlopeGradient</2>
|
|
| 94 | 94 |
</_avg> |
| 95 | 95 |
</2> |
| 96 | 96 |
</_alt> |
Also available in: Unified diff
inputs/VegBank/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource