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Revision 11933

inputs/VegBank/taxon_observation.**/postprocess.sql: added the project table

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inputs/VegBank/taxon_observation.**/header.csv
1
sort_col,locationID,eventID,*stratumtype_id,*stratum_id,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID__overall_plot,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,*taxonobservation_--party_id,OMIT#authorplantname,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,OMIT#int_origplantconcept_id,OMIT#int_origplantscifull,OMIT#int_origplantscinamenoauth,OMIT#int_origplantcommon,OMIT#int_origplantcode,OMIT#int_currplantconcept_id,OMIT#int_currplantscifull,OMIT#int_currplantscinamenoauth,OMIT#int_currplantcommon,OMIT#int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,taxon_determination__is_original,taxon_determination__is_current,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,*taxonobservation--party--salutation,identifiedBy__first,identifiedBy__middle,identifiedBy__last,*taxonobservation--party--organizationname,*taxonobservation--party--currentname_id,*taxonobservation--party--contactinstructions,*taxonobservation--party--email,*taxonobservation--party--partytype,*taxonobservation--party--partypublic,*taxonobservation--party--party_d_obscount,*taxonobservation--party--accessioncode,*plantconcept_--plantconcept_reference_id,scientificName,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--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,identifiedBy,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,stratum__name,*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_--hasobservationsynonym,*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,site_name,directions_to_place,*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,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,locality,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,taxonOccurrenceID
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sort_col,projectID,locationID,eventID,*stratumtype_id,*stratum_id,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID,taxonOccurrenceID__overall_plot,*taxonobservation_--plantname_id,*taxonobservation_--plantconcept_id,*taxonobservation_--party_id,OMIT#authorplantname,*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxoninferencearea,*taxonobservation_--emb_taxonobservation,OMIT#int_origplantconcept_id,OMIT#int_origplantscifull,OMIT#int_origplantscinamenoauth,OMIT#int_origplantcommon,OMIT#int_origplantcode,OMIT#int_currplantconcept_id,OMIT#int_currplantscifull,OMIT#int_currplantscinamenoauth,OMIT#int_currplantcommon,OMIT#int_currplantcode,*taxonobservation_--taxonobservation_accessioncode,identificationID,*taxonobservation_--stemlocation_id,*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--role_id,identificationType,*taxonobservation_--reference_id,taxon_determination__is_original,taxon_determination__is_current,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,*taxonobservation--party--salutation,identifiedBy__first,identifiedBy__middle,identifiedBy__last,*taxonobservation--party--organizationname,*taxonobservation--party--currentname_id,*taxonobservation--party--contactinstructions,*taxonobservation--party--email,*taxonobservation--party--partytype,*taxonobservation--party--partypublic,*taxonobservation--party--party_d_obscount,*taxonobservation--party--accessioncode,*plantconcept_--plantconcept_reference_id,scientificName,*plantconcept_--plantcode,*plantconcept_--plantdescription,*plantconcept_--d_obscount,*plantconcept_--d_currentaccepted,*plantconcept_--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,identifiedBy,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,stratum__name,*stratumtype--stratumdescription,*observation_--previousobs_id,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_--hasobservationsynonym,*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,site_name,directions_to_place,*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,accessRights,coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters,locality,continent,DUPLICATE#of:country#area|country|territory,DUPLICATE#of:stateprovince#region|state|province,county,*plot_--quadrangle,*plot_--Geographic Name,projectName,*project--projectdescription,projectStartDate,projectEndDate,*project--d_obscount,*project--d_lastplotaddeddate,*project--accessioncode,taxonOccurrenceID
inputs/VegBank/taxon_observation.**/postprocess.sql
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NATURAL LEFT JOIN stratumtype
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NATURAL LEFT JOIN observation_
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NATURAL LEFT JOIN plot_
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NATURAL LEFT JOIN project
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$$);
16 17

  
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SELECT mk_subset_by_row_num_func(:table_str);
inputs/VegBank/taxon_observation.**/map.csv
1 1
VegBank,VegCore,Filter,Comments
2 2
sort_col,sort_col,,
3
projectID,projectID,,
3 4
locationID,locationID,,
4 5
eventID,eventID,,
5 6
*stratumtype_id,*stratumtype_id,,
......
128 129
stratum__name,stratum__name,,
129 130
*stratumtype--stratumdescription,*stratumtype--stratumdescription,,
130 131
*observation_--previousobs_id,*observation_--previousobs_id,,
131
projectID,projectID,,
132 132
authorEventCode,authorEventCode,,
133 133
*observation_--dateaccuracy,*observation_--dateaccuracy,,
134 134
*observation_--covermethod_id,*observation_--covermethod_id,,
......
297 297
county,county,,
298 298
*plot_--quadrangle,*plot_--quadrangle,,
299 299
*plot_--Geographic Name,*plot_--Geographic Name,,
300
projectName,projectName,,
301
*project--projectdescription,*project--projectdescription,,
302
projectStartDate,projectStartDate,,
303
projectEndDate,projectEndDate,,
304
*project--d_obscount,*project--d_obscount,,
305
*project--d_lastplotaddeddate,*project--d_lastplotaddeddate,,
306
*project--accessioncode,*project--accessioncode,,
300 307
taxonOccurrenceID,taxonOccurrenceID,,
inputs/VegBank/taxon_observation.**/test.xml.ref
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                        <landform>$landform</landform>
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                        <locationevent>
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                            <method_id><method><name>$samplingProtocol</name></method></method_id>
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                            <project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id>
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                            <project_id>
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                                <project>
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                                    <projectname>$projectName</projectname>
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                                    <sourceaccessioncode>$projectID</sourceaccessioncode>
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                                    <startdate>$projectStartDate</startdate>
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                                    <stopdate>$projectEndDate</stopdate>
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                                </project>
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                            </project_id>
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                            <authoreventcode>$authorEventCode</authoreventcode>
21 28
                            <sourceaccessioncode>$eventID</sourceaccessioncode>
22 29
                            <locationevent fkey="parent_id">
inputs/VegBank/taxon_observation.**/unmapped_terms.csv
205 205
coordinateUncertaintyInMeters__from_fuzzing
206 206
*plot_--quadrangle
207 207
*plot_--Geographic Name
208
*project--projectdescription
209
*project--d_obscount
210
*project--d_lastplotaddeddate
211
*project--accessioncode

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