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Revision 11023

inputs/VegBank/taxon_observation.**/postprocess.sql: added stratum, stratumtype to the left-join

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inputs/VegBank/taxon_observation.**/header.csv
1
sort_col,locationID,eventID,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_party_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,*taxonobservation_--originalinterpretation,*taxonobservation_--currentinterpretation,identificationQualifier,identificationVerificationStatus,UNUSED#collector_id,collectorNumber,*taxonobservation_--museum_id,accessionNumber,*taxonobservation_--grouptype,occurrenceRemarks,*taxonobservation_--notespublic,*taxonobservation_--notesmgt,*taxonobservation_--revisions,dateIdentified,dateCollected,*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--taxoninterpretation_accessioncode,originalScientificName,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,*taxonobservation_--int_origplantconcept_id,EQUIV#to:authorplantname#int_origplantscifull,originalTaxonName,originalVernacularName,*taxonobservation_--int_origplantcode,*taxonobservation_--int_currplantconcept_id,scientificName_verbatim,taxonName,vernacularName,*taxonobservation_--int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*taxonobservation_--plantcode,*taxonobservation_--plantdescription,*taxonobservation_--d_obscount,*taxonobservation_--d_currentaccepted,*taxonobservation_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,EQUIV#to:plantname#Species,EQUIV#to:plantname#Subspecies,EQUIV#to:plantname#Variety,EQUIV#to:plantname#Forma,DUPLICATE#of:plantconcept_plantname#plantname,*taxonobservation_--plantname_reference_id,*taxonobservation_--dateentered,observationGranularity,scientificName,*stemcount_--stratum_id,coverPercent,*stemcount_--basalarea,*stemcount_--biomass,*stemcount_--inferencearea,*stemcount_--stratumbase,*stemcount_--stratumheight,*stemcount_--emb_taxonimportance,*stemcount_--covercode,diameterBreastHeight_cm,*stemcount_--stemdiameteraccuracy,height_m,*stemcount_--stemheightaccuracy,individualCount,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,OMIT#stemdiameter,OMIT#stemdiameteraccuracy,OMIT#stemheight,OMIT#stemheightaccuracy,OMIT#stemcount,OMIT#stemtaxonarea,OMIT#emb_stemcount,individualID,*observation_--previousobs_id,projectID,authorEventCode,*observation_--dateaccuracy,*observation_--covermethod_id,*observation_--coverdispersion,*observation_--autotaxoncover,*observation_--stratummethod_id,samplingProtocol,*observation_--taxonobservationarea,*observation_--stemsizelimit,*observation_--stemobservationarea,*observation_--stemsamplemethod,*observation_--originaldata,*observation_--effortlevel,*observation_--plotvalidationlevel,*observation_--floristicquality,*observation_--bryophytequality,*observation_--lichenquality,*observation_--observationnarrative,*observation_--landscapenarrative,*observation_--homogeneity,*observation_--phenologicaspect,*observation_--representativeness,*observation_--standmaturity,*observation_--successionalstatus,*observation_--basalarea,*observation_--hydrologicregime,*observation_--soilmoistureregime,*observation_--soildrainage,*observation_--watersalinity,*observation_--waterdepth,*observation_--shoredistance,*observation_--soildepth,*observation_--organicdepth,*observation_--soiltaxon_id,*observation_--soiltaxonsrc,*observation_--percentbedrock,*observation_--percentrockgravel,*observation_--percentwood,*observation_--percentlitter,*observation_--percentbaresoil,*observation_--percentwater,*observation_--percentother,*observation_--nameother,*observation_--treeht,*observation_--shrubht,*observation_--fieldht,*observation_--nonvascularht,*observation_--submergedht,*observation_--treecover,*observation_--shrubcover,*observation_--fieldcover,*observation_--nonvascularcover,*observation_--floatingcover,*observation_--submergedcover,*observation_--dominantstratum,*observation_--growthform1type,*observation_--growthform2type,*observation_--growthform3type,*observation_--growthform1cover,*observation_--growthform2cover,*observation_--growthform3cover,*observation_--totalcover,*observation_--notespublic,*observation_--notesmgt,*observation_--revisions,startDate,endDate,*observation_--dateentered,*observation_--emb_observation,*observation_--interp_orig_ci_id,*observation_--interp_orig_cc_id,*observation_--interp_orig_sciname,*observation_--interp_orig_code,*observation_--interp_orig_party_id,*observation_--interp_orig_partyname,*observation_--interp_current_ci_id,*observation_--interp_current_cc_id,*observation_--interp_current_sciname,*observation_--interp_current_code,*observation_--interp_current_party_id,*observation_--interp_current_partyname,*observation_--interp_bestfit_ci_id,*observation_--interp_bestfit_cc_id,*observation_--interp_bestfit_sciname,*observation_--interp_bestfit_code,*observation_--interp_bestfit_party_id,*observation_--interp_bestfit_partyname,*observation_--toptaxon1name,*observation_--toptaxon2name,*observation_--toptaxon3name,*observation_--toptaxon4name,*observation_--toptaxon5name,*observation_--numberoftaxa,*observation_--accessioncode,*observation_--soilobs_id,*observation_--soilhorizon,*observation_--soildepthtop,*observation_--soildepthbottom,*observation_--soilcolor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilcoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soildescription,*observation_--emb_soilobs,locationName,*plot_--reference_id,parentLocationID,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityreason,decimalLatitude,decimalLongitude,*plot_--authore,*plot_--authorn,*plot_--authorzone,*plot_--authordatum,*plot_--authorlocation,locality,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standsize,*plot_--placementmethod,*plot_--permanence,*plot_--layoutnarrative,elevationInMeters,*plot_--elevationaccuracy,UNUSED#elevationrange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoposition,landform,*plot_--surficialdeposits,*plot_--rocktype,stateProvince,country,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--notespublic,*plot_--notesmgt,*plot_--revisions,*plot_--dateentered,*plot_--emb_plot,*plot_--plotrationalenarrative,*plot_--accessioncode,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters
1
sort_col,locationID,eventID,*stratumtype_id,*stratum_id,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_party_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,*taxonobservation_--originalinterpretation,*taxonobservation_--currentinterpretation,identificationQualifier,identificationVerificationStatus,UNUSED#collector_id,collectorNumber,*taxonobservation_--museum_id,accessionNumber,*taxonobservation_--grouptype,occurrenceRemarks,*taxonobservation_--notespublic,*taxonobservation_--notesmgt,*taxonobservation_--revisions,dateIdentified,dateCollected,*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--taxoninterpretation_accessioncode,originalScientificName,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,*taxonobservation_--int_origplantconcept_id,EQUIV#to:authorplantname#int_origplantscifull,originalTaxonName,originalVernacularName,*taxonobservation_--int_origplantcode,*taxonobservation_--int_currplantconcept_id,scientificName_verbatim,taxonName,vernacularName,*taxonobservation_--int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*taxonobservation_--plantcode,*taxonobservation_--plantdescription,*taxonobservation_--d_obscount,*taxonobservation_--d_currentaccepted,*taxonobservation_--plantconcept_accessioncode,kingdom,*Subkingdom,*Superdivision,*Division,*Subdivision,class,*Subclass,order,family,genus,EQUIV#to:plantname#Species,EQUIV#to:plantname#Subspecies,EQUIV#to:plantname#Variety,EQUIV#to:plantname#Forma,DUPLICATE#of:plantconcept_plantname#plantname,*taxonobservation_--plantname_reference_id,*taxonobservation_--dateentered,observationGranularity,scientificName,coverPercent,*stemcount_--basalarea,*stemcount_--biomass,*stemcount_--inferencearea,*stemcount_--stratumbase,*stemcount_--stratumheight,*stemcount_--emb_taxonimportance,*stemcount_--covercode,diameterBreastHeight_cm,*stemcount_--stemdiameteraccuracy,height_m,*stemcount_--stemheightaccuracy,individualCount,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,OMIT#stemdiameter,OMIT#stemdiameteraccuracy,OMIT#stemheight,OMIT#stemheightaccuracy,OMIT#stemcount,OMIT#stemtaxonarea,OMIT#emb_stemcount,individualID,*stratum--observation_id,*stratum--stratummethod_id,*stratum--stratumname,*stratum--stratumheight,*stratum--stratumbase,*stratum--stratumcover,*stratum--stratumdescription,*stratumtype--stratummethod_id,*stratumtype--stratumindex,*stratumname,*stratumtype--stratumdescription,*observation_--previousobs_id,projectID,authorEventCode,*observation_--dateaccuracy,*observation_--covermethod_id,*observation_--coverdispersion,*observation_--autotaxoncover,*observation_--stratummethod_id,samplingProtocol,*observation_--taxonobservationarea,*observation_--stemsizelimit,*observation_--stemobservationarea,*observation_--stemsamplemethod,*observation_--originaldata,*observation_--effortlevel,*observation_--plotvalidationlevel,*observation_--floristicquality,*observation_--bryophytequality,*observation_--lichenquality,*observation_--observationnarrative,*observation_--landscapenarrative,*observation_--homogeneity,*observation_--phenologicaspect,*observation_--representativeness,*observation_--standmaturity,*observation_--successionalstatus,*observation_--basalarea,*observation_--hydrologicregime,*observation_--soilmoistureregime,*observation_--soildrainage,*observation_--watersalinity,*observation_--waterdepth,*observation_--shoredistance,*observation_--soildepth,*observation_--organicdepth,*observation_--soiltaxon_id,*observation_--soiltaxonsrc,*observation_--percentbedrock,*observation_--percentrockgravel,*observation_--percentwood,*observation_--percentlitter,*observation_--percentbaresoil,*observation_--percentwater,*observation_--percentother,*observation_--nameother,*observation_--treeht,*observation_--shrubht,*observation_--fieldht,*observation_--nonvascularht,*observation_--submergedht,*observation_--treecover,*observation_--shrubcover,*observation_--fieldcover,*observation_--nonvascularcover,*observation_--floatingcover,*observation_--submergedcover,*observation_--dominantstratum,*observation_--growthform1type,*observation_--growthform2type,*observation_--growthform3type,*observation_--growthform1cover,*observation_--growthform2cover,*observation_--growthform3cover,*observation_--totalcover,*observation_--notespublic,*observation_--notesmgt,*observation_--revisions,startDate,endDate,*observation_--dateentered,*observation_--emb_observation,*observation_--interp_orig_ci_id,*observation_--interp_orig_cc_id,*observation_--interp_orig_sciname,*observation_--interp_orig_code,*observation_--interp_orig_party_id,*observation_--interp_orig_partyname,*observation_--interp_current_ci_id,*observation_--interp_current_cc_id,*observation_--interp_current_sciname,*observation_--interp_current_code,*observation_--interp_current_party_id,*observation_--interp_current_partyname,*observation_--interp_bestfit_ci_id,*observation_--interp_bestfit_cc_id,*observation_--interp_bestfit_sciname,*observation_--interp_bestfit_code,*observation_--interp_bestfit_party_id,*observation_--interp_bestfit_partyname,*observation_--toptaxon1name,*observation_--toptaxon2name,*observation_--toptaxon3name,*observation_--toptaxon4name,*observation_--toptaxon5name,*observation_--numberoftaxa,*observation_--accessioncode,*observation_--soilobs_id,*observation_--soilhorizon,*observation_--soildepthtop,*observation_--soildepthbottom,*observation_--soilcolor,organic_percent,texture,sand_percent,silt_percent,clay_percent,*observation_--soilcoarse,ph,cationExchangeCapacity_cmol_kg,baseSaturation_percent,*observation_--soildescription,*observation_--emb_soilobs,locationName,*plot_--reference_id,parentLocationID,coordinateUncertaintyInMeters__from_coords,accessRights_verbatim,*plot_--confidentialityreason,decimalLatitude,decimalLongitude,*plot_--authore,*plot_--authorn,*plot_--authorzone,*plot_--authordatum,*plot_--authorlocation,locality,*plot_--azimuth,*plot_--dsgpoly,footprintWKT,plotArea_m2,*plot_--standsize,*plot_--placementmethod,*plot_--permanence,*plot_--layoutnarrative,elevationInMeters,*plot_--elevationaccuracy,UNUSED#elevationrange,slopeAspect,minSlopeAspect,maxSlopeAspect,slopeGradient,minSlopeGradient,maxSlopeGradient,*plot_--topoposition,landform,*plot_--surficialdeposits,*plot_--rocktype,stateProvince,country,*plot_--submitter_surname,*plot_--submitter_givenname,*plot_--submitter_email,*plot_--notespublic,*plot_--notesmgt,*plot_--revisions,*plot_--dateentered,*plot_--emb_plot,*plot_--plotrationalenarrative,*plot_--accessioncode,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters
inputs/VegBank/taxon_observation.**/postprocess.sql
7 7
FROM              taxonobservation_
8 8
NATURAL LEFT JOIN stemcount_
9 9
NATURAL LEFT JOIN stemlocation_
10
NATURAL LEFT JOIN stratum
11
NATURAL LEFT JOIN stratumtype
10 12
NATURAL LEFT JOIN observation_
11 13
NATURAL LEFT JOIN plot_
12 14
$$);
inputs/VegBank/taxon_observation.**/map.csv
2 2
sort_col,sort_col,,
3 3
locationID,locationID,,
4 4
eventID,eventID,,
5
*stratumtype_id,*stratumtype_id,,
6
*stratum_id,*stratum_id,,
5 7
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,,
6 8
aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID__individual_count,,
7 9
aggregateOrganismObservationID,aggregateOrganismObservationID,,
......
73 75
*taxonobservation_--dateentered,*taxonobservation_--dateentered,,
74 76
observationGranularity,observationGranularity,,
75 77
scientificName,scientificName,,
76
*stemcount_--stratum_id,*stemcount_--stratum_id,,
77 78
coverPercent,coverPercent,,
78 79
*stemcount_--basalarea,*stemcount_--basalarea,,
79 80
*stemcount_--biomass,*stemcount_--biomass,,
......
103 104
OMIT#stemtaxonarea,OMIT#stemtaxonarea,,
104 105
OMIT#emb_stemcount,OMIT#emb_stemcount,,
105 106
individualID,individualID,,
107
*stratum--observation_id,*stratum--observation_id,,
108
*stratum--stratummethod_id,*stratum--stratummethod_id,,
109
*stratum--stratumname,*stratum--stratumname,,
110
*stratum--stratumheight,*stratum--stratumheight,,
111
*stratum--stratumbase,*stratum--stratumbase,,
112
*stratum--stratumcover,*stratum--stratumcover,,
113
*stratum--stratumdescription,*stratum--stratumdescription,,
114
*stratumtype--stratummethod_id,*stratumtype--stratummethod_id,,
115
*stratumtype--stratumindex,*stratumtype--stratumindex,,
116
*stratumname,*stratumname,,
117
*stratumtype--stratumdescription,*stratumtype--stratumdescription,,
106 118
*observation_--previousobs_id,*observation_--previousobs_id,,
107 119
projectID,projectID,,
108 120
authorEventCode,authorEventCode,,
inputs/VegBank/taxon_observation.**/unmapped_terms.csv
1 1
sort_col
2
*stratumtype_id
3
*stratum_id
2 4
aggregateOrganismObservationID__taxon_presence
3 5
aggregateOrganismObservationID__individual_count
4 6
*taxonobservation_--plantname_id
......
44 46
*Subclass
45 47
*taxonobservation_--plantname_reference_id
46 48
*taxonobservation_--dateentered
47
*stemcount_--stratum_id
48 49
*stemcount_--basalarea
49 50
*stemcount_--biomass
50 51
*stemcount_--inferencearea
......
58 59
*stemcount_--emb_stemcount
59 60
*stemlocation_--stemhealth
60 61
*stemlocation_--emb_stemlocation
62
*stratum--observation_id
63
*stratum--stratummethod_id
64
*stratum--stratumname
65
*stratum--stratumheight
66
*stratum--stratumbase
67
*stratum--stratumcover
68
*stratum--stratumdescription
69
*stratumtype--stratummethod_id
70
*stratumtype--stratumindex
71
*stratumname
72
*stratumtype--stratumdescription
61 73
*observation_--previousobs_id
62 74
*observation_--dateaccuracy
63 75
*observation_--covermethod_id

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