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Revision 11009

bugfix: inputs/VegBank/stemlocation_/map.csv: remapped stemcount-related fields to OMIT, so that these don't collide with fields of the same name in stemcount_ when they are left-joined together in taxon_observation.** . having the same name causes these to be incorrectly interpreted as shared fkey columns in the NATURAL JOIN (and without the NATURAL JOIN, they would instead be collision errors).

View differences:

inputs/VegBank/stemlocation_/map.csv
7 7
stemhealth,*stemlocation_--stemhealth,,this *is* populated
8 8
emb_stemlocation,*stemlocation_--emb_stemlocation,,
9 9
taxonimportance_id,aggregateOrganismObservationID__taxon_presence,,
10
stemdiameter,diameterBreastHeight_cm,,"""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>)"
11
stemdiameteraccuracy,*stemlocation_--stemdiameteraccuracy,,
12
stemheight,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>)"
13
stemheightaccuracy,*stemlocation_--stemheightaccuracy,,
14
stemcount,individualCount,,
15
stemtaxonarea,*stemlocation_--stemtaxonarea,,
16
emb_stemcount,*stemlocation_--emb_stemcount,,
10
stemdiameter,OMIT#stemdiameter,,
11
stemdiameteraccuracy,OMIT#stemdiameteraccuracy,,
12
stemheight,OMIT#stemheight,,
13
stemheightaccuracy,OMIT#stemheightaccuracy,,
14
stemcount,OMIT#stemcount,,
15
stemtaxonarea,OMIT#stemtaxonarea,,
16
emb_stemcount,OMIT#emb_stemcount,,
inputs/VegBank/stemlocation_/test.xml.ref
10 10
                        <locationevent>
11 11
                            <taxonoccurrence>
12 12
                                <aggregateoccurrence>
13
                                    <count>$individualCount</count>
14 13
                                    <plantobservation>
15 14
                                        <sourceaccessioncode>$individualID</sourceaccessioncode>
16
                                        <stemobservation>
17
                                            <diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
18
                                            <height_m>$height_m</height_m>
19
                                            <sourceaccessioncode>$stemID</sourceaccessioncode>
20
                                        </stemobservation>
15
                                        <stemobservation><sourceaccessioncode>$stemID</sourceaccessioncode></stemobservation>
21 16
                                    </plantobservation>
22 17
                                    <sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode>
23 18
                                </aggregateoccurrence>
inputs/VegBank/stemlocation_/new_terms.csv
3 3
stemhealth,*stemlocation_--stemhealth,,this *is* populated
4 4
emb_stemlocation,*stemlocation_--emb_stemlocation,,
5 5
taxonimportance_id,aggregateOrganismObservationID__taxon_presence,,
6
stemdiameter,diameterBreastHeight_cm,,"""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>)"
7
stemdiameteraccuracy,*stemlocation_--stemdiameteraccuracy,,
8
stemheightaccuracy,*stemlocation_--stemheightaccuracy,,
9
stemtaxonarea,*stemlocation_--stemtaxonarea,,
10
emb_stemcount,*stemlocation_--emb_stemcount,,
6
stemdiameter,OMIT#stemdiameter,,
7
stemdiameteraccuracy,OMIT#stemdiameteraccuracy,,
8
stemheightaccuracy,OMIT#stemheightaccuracy,,
9
stemtaxonarea,OMIT#stemtaxonarea,,
10
emb_stemcount,OMIT#emb_stemcount,,
inputs/VegBank/stemlocation_/unmapped_terms.csv
2 2
*stemlocation_--stemhealth
3 3
*stemlocation_--emb_stemlocation
4 4
aggregateOrganismObservationID__taxon_presence
5
*stemlocation_--stemdiameteraccuracy
6
*stemlocation_--stemheightaccuracy
7
*stemlocation_--stemtaxonarea
8
*stemlocation_--emb_stemcount
inputs/VegBank/taxon_observation.**/header.csv
1
sort_col,locationID,eventID,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,diameterBreastHeight_cm,height_m,individualCount,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,*taxonobservation_--Subkingdom,*taxonobservation_--Superdivision,*taxonobservation_--Division,*taxonobservation_--Subdivision,class,*taxonobservation_--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,*stemcount_--stemdiameteraccuracy,*stemcount_--stemheightaccuracy,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,*stemlocation_--stemdiameteraccuracy,*stemlocation_--stemheightaccuracy,*stemlocation_--stemtaxonarea,*stemlocation_--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,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,*taxonobservation_--Subkingdom,*taxonobservation_--Superdivision,*taxonobservation_--Division,*taxonobservation_--Subdivision,class,*taxonobservation_--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
inputs/VegBank/taxon_observation.**/map.csv
4 4
eventID,eventID,,
5 5
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,,
6 6
aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID__individual_count,,
7
diameterBreastHeight_cm,diameterBreastHeight_cm,,
8
height_m,height_m,,
9
individualCount,individualCount,,
10 7
aggregateOrganismObservationID,aggregateOrganismObservationID,,
11 8
taxonOccurrenceID,taxonOccurrenceID,,
12 9
*taxonobservation_--plantname_id,*taxonobservation_--plantname_id,,
......
85 82
*stemcount_--stratumheight,*stemcount_--stratumheight,,
86 83
*stemcount_--emb_taxonimportance,*stemcount_--emb_taxonimportance,,
87 84
*stemcount_--covercode,*stemcount_--covercode,,
85
diameterBreastHeight_cm,diameterBreastHeight_cm,,
88 86
*stemcount_--stemdiameteraccuracy,*stemcount_--stemdiameteraccuracy,,
87
height_m,height_m,,
89 88
*stemcount_--stemheightaccuracy,*stemcount_--stemheightaccuracy,,
89
individualCount,individualCount,,
90 90
*stemcount_--stemtaxonarea,*stemcount_--stemtaxonarea,,
91 91
*stemcount_--emb_stemcount,*stemcount_--emb_stemcount,,
92 92
stemID,stemID,,
......
95 95
UNUSED#stemyposition,UNUSED#stemyposition,,
96 96
*stemlocation_--stemhealth,*stemlocation_--stemhealth,,
97 97
*stemlocation_--emb_stemlocation,*stemlocation_--emb_stemlocation,,
98
*stemlocation_--stemdiameteraccuracy,*stemlocation_--stemdiameteraccuracy,,
99
*stemlocation_--stemheightaccuracy,*stemlocation_--stemheightaccuracy,,
100
*stemlocation_--stemtaxonarea,*stemlocation_--stemtaxonarea,,
101
*stemlocation_--emb_stemcount,*stemlocation_--emb_stemcount,,
98
OMIT#stemdiameter,OMIT#stemdiameter,,
99
OMIT#stemdiameteraccuracy,OMIT#stemdiameteraccuracy,,
100
OMIT#stemheight,OMIT#stemheight,,
101
OMIT#stemheightaccuracy,OMIT#stemheightaccuracy,,
102
OMIT#stemcount,OMIT#stemcount,,
103
OMIT#stemtaxonarea,OMIT#stemtaxonarea,,
104
OMIT#emb_stemcount,OMIT#emb_stemcount,,
102 105
individualID,individualID,,
103 106
*observation_--previousobs_id,*observation_--previousobs_id,,
104 107
projectID,projectID,,
inputs/VegBank/taxon_observation.**/unmapped_terms.csv
58 58
*stemcount_--emb_stemcount
59 59
*stemlocation_--stemhealth
60 60
*stemlocation_--emb_stemlocation
61
*stemlocation_--stemdiameteraccuracy
62
*stemlocation_--stemheightaccuracy
63
*stemlocation_--stemtaxonarea
64
*stemlocation_--emb_stemcount
65 61
*observation_--previousobs_id
66 62
*observation_--dateaccuracy
67 63
*observation_--covermethod_id

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