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Revision 5031

Added by Aaron Marcuse-Kubitza about 12 years ago

input.Makefile: Staging tables installation: `%/install: %/create.sql`: Don't add a row number column to the created table because it is now added automatically to the temp table by column-based import (row-based import now also does not require a pkey for DB inputs)

View differences:

inputs/VegBank/plot_/VegBIEN.csv
56 56 
reference_id,,** No join mapping for *reference_id **
57 57 
revisions,,** No join mapping for *revisions **
58 58 
rocktype,,** No join mapping for *rocktype **
59 
row_num,,** No join mapping for *row_num **
60 59 
standsize,,** No join mapping for *standsize **
61 60 
submitter_email,,** No join mapping for *submitter_email **
62 61 
submitter_givenname,,** No join mapping for *submitter_givenname **
inputs/REMIB/Specimen/header.csv
1 
acronym,accession_number,family,genus,specificEpithet,country,state,county,locality,long_deg,long_min,long_sec,lat_deg,lat_min,lat_sec,coll_day,coll_month,coll_year,collector,habitat,preparation,row_num
1 
acronym,accession_number,family,genus,specificEpithet,country,state,county,locality,long_deg,long_min,long_sec,lat_deg,lat_min,lat_sec,coll_day,coll_month,coll_year,collector,habitat,preparation
inputs/CTFS/StemObservation/header.csv
1 
FamilyID,GenusID,SpeciesID,SubSpeciesID,TreeID,StemID,MeasureID,CensusID,DBH,HOM,PrimaryStem,ExactDate,StemTag,StemDescription,QuadratID,PlotID,Tag,x,y,SubSpeciesCurrentTaxonFlag,SubSpeciesObsoleteTaxonFlag,SubSpeciesName,SubSpeciesMnemonic,SubSpeciesAuthority,InfraSpecificLevel,SpeciesCurrentTaxonFlag,SpeciesObsoleteTaxonFlag,SpeciesReferenceID,SpeciesName,SpeciesMnemonic,SpeciesAuthority,IDLevel,FieldFamily,Description,Genus,GenusReferenceID,GenusAuthority,Family,ReferenceID,row_num
1 
FamilyID,GenusID,SpeciesID,SubSpeciesID,TreeID,StemID,MeasureID,CensusID,DBH,HOM,PrimaryStem,ExactDate,StemTag,StemDescription,QuadratID,PlotID,Tag,x,y,SubSpeciesCurrentTaxonFlag,SubSpeciesObsoleteTaxonFlag,SubSpeciesName,SubSpeciesMnemonic,SubSpeciesAuthority,InfraSpecificLevel,SpeciesCurrentTaxonFlag,SpeciesObsoleteTaxonFlag,SpeciesReferenceID,SpeciesName,SpeciesMnemonic,SpeciesAuthority,IDLevel,FieldFamily,Description,Genus,GenusReferenceID,GenusAuthority,Family,ReferenceID
inputs/CTFS/StemObservation/map.csv
38 38 
GenusAuthority,*GenusAuthority,,
39 39 
Family,family,,
40 40 
ReferenceID,*ReferenceID,,
41 
row_num,*row_num,,
inputs/CTFS/StemObservation/VegBIEN.csv
54 54 
SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic **
55 55 
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag **
56 56 
TreeID,,** No join mapping for *TreeID **
57 
row_num,,** No join mapping for *row_num **
inputs/CTFS/StemObservation/unmapped_terms.csv
22 22 
*GenusReferenceID
23 23 
*GenusAuthority
24 24 
*ReferenceID
25 
*row_num
inputs/CTFS/TaxonOccurrence/header.csv
1 
FamilyID,GenusID,SpeciesID,SubSpeciesID,SpeciesInvID,CensusID,PlotID,SubSpeciesCurrentTaxonFlag,SubSpeciesObsoleteTaxonFlag,SubSpeciesName,SubSpeciesMnemonic,SubSpeciesAuthority,InfraSpecificLevel,SpeciesCurrentTaxonFlag,SpeciesObsoleteTaxonFlag,SpeciesReferenceID,SpeciesName,SpeciesMnemonic,SpeciesAuthority,IDLevel,FieldFamily,Description,Genus,GenusReferenceID,GenusAuthority,Family,ReferenceID,row_num
1 
FamilyID,GenusID,SpeciesID,SubSpeciesID,SpeciesInvID,CensusID,PlotID,SubSpeciesCurrentTaxonFlag,SubSpeciesObsoleteTaxonFlag,SubSpeciesName,SubSpeciesMnemonic,SubSpeciesAuthority,InfraSpecificLevel,SpeciesCurrentTaxonFlag,SpeciesObsoleteTaxonFlag,SpeciesReferenceID,SpeciesName,SpeciesMnemonic,SpeciesAuthority,IDLevel,FieldFamily,Description,Genus,GenusReferenceID,GenusAuthority,Family,ReferenceID
inputs/CTFS/TaxonOccurrence/map.csv
26 26 
GenusAuthority,*GenusAuthority,,
27 27 
Family,family,,
28 28 
ReferenceID,*ReferenceID,,
29 
row_num,*row_num,,
inputs/CTFS/TaxonOccurrence/VegBIEN.csv
36 36 
SubSpeciesID,,** No join mapping for *SubSpeciesID **
37 37 
SubSpeciesMnemonic,,** No join mapping for *SubSpeciesMnemonic **
38 38 
SubSpeciesObsoleteTaxonFlag,,** No join mapping for *SubSpeciesObsoleteTaxonFlag **
39 
row_num,,** No join mapping for *row_num **
inputs/CTFS/TaxonOccurrence/unmapped_terms.csv
17 17 
*GenusReferenceID
18 18 
*GenusAuthority
19 19 
*ReferenceID
20 
*row_num
inputs/CTFS/Plot/header.csv
1 
CountryID,PlotID,PlotName,LocationName,Latitude,Longitude,Elevation,ReferenceX,ReferenceY,SizeOfSite,ShapeOfSite,DescriptionOfSite,CountryName,row_num
1 
CountryID,PlotID,PlotName,LocationName,Latitude,Longitude,Elevation,ReferenceX,ReferenceY,SizeOfSite,ShapeOfSite,DescriptionOfSite,CountryName
inputs/CTFS/Plot/map.csv
20 20 
ShapeOfSite,footprintWKT,,
21 21 
DescriptionOfSite,locality,,
22 22 
CountryName,country,,
23 
row_num,*row_num,,
inputs/CTFS/Plot/VegBIEN.csv
27 27 
CountryID,,** No join mapping for *CountryID **
28 28 
ReferenceX,,** No join mapping for *ReferenceX ** Rarely used
29 29 
ReferenceY,,** No join mapping for *ReferenceY ** Rarely used
30 
row_num,,** No join mapping for *row_num **
inputs/CTFS/Plot/unmapped_terms.csv
1 1 
*CountryID
2 2 
*ReferenceX
3 3 
*ReferenceY
4 
*row_num
inputs/input.Makefile
222 222 
%/install %/header.csv: %/create.sql _always
223 223 
	($(inDatasrc); echo 'CREATE TABLE "$*" AS'; cat $<; echo ';')|"time" \
224 224 
$(psqlAsBien) --echo-all --set=table='"$*"' $(logInstall*)
225 
	-$(addRowNum)
226 225 
	$(exportHeader)
227 
# ignore errors if create.sql already added a primary key
228 
addRowNum = echo 'ALTER TABLE "$(datasrc)"."$*"\
229 
ADD COLUMN row_num serial NOT NULL PRIMARY KEY;'|$(psqlAsBien) $(logInstall*Add)
230 226 

  		




  231
  227
  
    
%/install: _always


  		




  232
  228
  
    
	$(if $(isRef),$(exportHeader),$(if $(nonXml),$(import_install_)))


  		












  

    
      inputs/VegBank/taxonobservation_/header.csv
    
  





  1
  
  
    
plantconcept_id,taxonobservation_id,observation_id,authorplantname,taxonobservation_reference_id,taxoninferencearea,emb_taxonobservation,int_origplantconcept_id,int_origplantscifull,int_origplantscinamenoauth,int_origplantcommon,int_origplantcode,int_currplantconcept_id,int_currplantscifull,int_currplantscinamenoauth,int_currplantcommon,int_currplantcode,taxonobservation_accessioncode,taxoninterpretation_id,stemlocation_id,taxoninterpretation_plantname_id,party_id,role_id,interpretationtype,reference_id,originalinterpretation,currentinterpretation,taxonfit,taxonconfidence,collector_id,collectionnumber,museum_id,museumaccessionnumber,grouptype,notes,notespublic,notesmgt,revisions,interpretationdate,collectiondate,emb_taxoninterpretation,taxoninterpretation_accessioncode,plantname_id,plantconcept_reference_id,plantname,plantcode,plantdescription,d_obscount,d_currentaccepted,plantconcept_accessioncode,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma,row_num


  		




  
  1
  
    
plantconcept_id,taxonobservation_id,observation_id,authorplantname,taxonobservation_reference_id,taxoninferencearea,emb_taxonobservation,int_origplantconcept_id,int_origplantscifull,int_origplantscinamenoauth,int_origplantcommon,int_origplantcode,int_currplantconcept_id,int_currplantscifull,int_currplantscinamenoauth,int_currplantcommon,int_currplantcode,taxonobservation_accessioncode,taxoninterpretation_id,stemlocation_id,taxoninterpretation_plantname_id,party_id,role_id,interpretationtype,reference_id,originalinterpretation,currentinterpretation,taxonfit,taxonconfidence,collector_id,collectionnumber,museum_id,museumaccessionnumber,grouptype,notes,notespublic,notesmgt,revisions,interpretationdate,collectiondate,emb_taxoninterpretation,taxoninterpretation_accessioncode,plantname_id,plantconcept_reference_id,plantname,plantcode,plantdescription,d_obscount,d_currentaccepted,plantconcept_accessioncode,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma


  		












  

    
      inputs/VegBank/taxonobservation_/map.csv
    
  





  63
  63
  
    
Subspecies,subspecies,,


  		




  64
  64
  
    
Variety,variety,,


  		




  65
  65
  
    
Forma,forma,,


  		




  66
  
  
    
row_num,*row_num,,


  		












  

    
      inputs/VegBank/taxonobservation_/VegBIEN.csv
    
  





  67
  67
  
    
reference_id,,** No join mapping for *reference_id ** 


  		




  68
  68
  
    
revisions,,** No join mapping for *revisions ** 


  		




  69
  69
  
    
role_id,,** No join mapping for *role_id ** 


  		




  70
  
  
    
row_num,,** No join mapping for *row_num ** 


  		




  71
  70
  
    
stemlocation_id,,** No join mapping for *stemlocation_id ** 


  		




  72
  71
  
    
taxonconfidence,,** No join mapping for *taxonconfidence ** 


  		




  73
  72
  
    
taxoninferencearea,,** No join mapping for *taxoninferencearea ** 


  		












  

    
      inputs/VegBank/taxonobservation_/unmapped_terms.csv
    
  





  45
  45
  
    
*Division


  		




  46
  46
  
    
*Subdivision


  		




  47
  47
  
    
*Subclass


  		




  48
  
  
    
*row_num


  		












  

    
      inputs/VegBank/plantconcept_/header.csv
    
  





  1
  
  
    
plantconcept_id,plantname_id,plantconcept_reference_id,plantname,plantcode,plantdescription,d_obscount,d_currentaccepted,plantconcept_accessioncode,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma,row_num


  		




  
  1
  
    
plantconcept_id,plantname_id,plantconcept_reference_id,plantname,plantcode,plantdescription,d_obscount,d_currentaccepted,plantconcept_accessioncode,Kingdom,Subkingdom,Superdivision,Division,Subdivision,Class,Subclass,Order,Family,Genus,Species,Subspecies,Variety,Forma


  		












  

    
      inputs/VegBank/observation_/header.csv
    
  





  1
  
  
    
observation_id,previousobs_id,plot_id,project_id,authorobscode,dateaccuracy,covermethod_id,coverdispersion,autotaxoncover,stratummethod_id,methodnarrative,taxonobservationarea,stemsizelimit,stemobservationarea,stemsamplemethod,originaldata,effortlevel,plotvalidationlevel,floristicquality,bryophytequality,lichenquality,observationnarrative,landscapenarrative,homogeneity,phenologicaspect,representativeness,standmaturity,successionalstatus,basalarea,hydrologicregime,soilmoistureregime,soildrainage,watersalinity,waterdepth,shoredistance,soildepth,organicdepth,soiltaxon_id,soiltaxonsrc,percentbedrock,percentrockgravel,percentwood,percentlitter,percentbaresoil,percentwater,percentother,nameother,treeht,shrubht,fieldht,nonvascularht,submergedht,treecover,shrubcover,fieldcover,nonvascularcover,floatingcover,submergedcover,dominantstratum,growthform1type,growthform2type,growthform3type,growthform1cover,growthform2cover,growthform3cover,totalcover,notespublic,notesmgt,revisions,obsstartdate,obsenddate,dateentered,emb_observation,interp_orig_ci_id,interp_orig_cc_id,interp_orig_sciname,interp_orig_code,interp_orig_party_id,interp_orig_partyname,interp_current_ci_id,interp_current_cc_id,interp_current_sciname,interp_current_code,interp_current_party_id,interp_current_partyname,interp_bestfit_ci_id,interp_bestfit_cc_id,interp_bestfit_sciname,interp_bestfit_code,interp_bestfit_party_id,interp_bestfit_partyname,toptaxon1name,toptaxon2name,toptaxon3name,toptaxon4name,toptaxon5name,numberoftaxa,accessioncode,soilobs_id,soilhorizon,soildepthtop,soildepthbottom,soilcolor,soilorganic,soiltexture,soilsand,soilsilt,soilclay,soilcoarse,soilph,exchangecapacity,basesaturation,soildescription,emb_soilobs,row_num


  		




  
  1
  
    
observation_id,previousobs_id,plot_id,project_id,authorobscode,dateaccuracy,covermethod_id,coverdispersion,autotaxoncover,stratummethod_id,methodnarrative,taxonobservationarea,stemsizelimit,stemobservationarea,stemsamplemethod,originaldata,effortlevel,plotvalidationlevel,floristicquality,bryophytequality,lichenquality,observationnarrative,landscapenarrative,homogeneity,phenologicaspect,representativeness,standmaturity,successionalstatus,basalarea,hydrologicregime,soilmoistureregime,soildrainage,watersalinity,waterdepth,shoredistance,soildepth,organicdepth,soiltaxon_id,soiltaxonsrc,percentbedrock,percentrockgravel,percentwood,percentlitter,percentbaresoil,percentwater,percentother,nameother,treeht,shrubht,fieldht,nonvascularht,submergedht,treecover,shrubcover,fieldcover,nonvascularcover,floatingcover,submergedcover,dominantstratum,growthform1type,growthform2type,growthform3type,growthform1cover,growthform2cover,growthform3cover,totalcover,notespublic,notesmgt,revisions,obsstartdate,obsenddate,dateentered,emb_observation,interp_orig_ci_id,interp_orig_cc_id,interp_orig_sciname,interp_orig_code,interp_orig_party_id,interp_orig_partyname,interp_current_ci_id,interp_current_cc_id,interp_current_sciname,interp_current_code,interp_current_party_id,interp_current_partyname,interp_bestfit_ci_id,interp_bestfit_cc_id,interp_bestfit_sciname,interp_bestfit_code,interp_bestfit_party_id,interp_bestfit_partyname,toptaxon1name,toptaxon2name,toptaxon3name,toptaxon4name,toptaxon5name,numberoftaxa,accessioncode,soilobs_id,soilhorizon,soildepthtop,soildepthbottom,soilcolor,soilorganic,soiltexture,soilsand,soilsilt,soilclay,soilcoarse,soilph,exchangecapacity,basesaturation,soildescription,emb_soilobs


  		












  

    
      inputs/VegBank/observation_/map.csv
    
  





  113
  113
  
    
basesaturation,baseSaturation_percent,,"""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>)"


  		




  114
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soildescription,*soildescription,,


  		




  115
  115
  
    
emb_soilobs,*emb_soilobs,,


  		




  116
  
  
    
row_num,*row_num,,


  		












  

    
      inputs/VegBank/observation_/VegBIEN.csv
    
  





  88
  88
  
    
previousobs_id,,** No join mapping for *previousobs_id ** 


  		




  89
  89
  
    
representativeness,,** No join mapping for *representativeness ** 


  		




  90
  90
  
    
revisions,,** No join mapping for *revisions ** 


  		




  91
  
  
    
row_num,,** No join mapping for *row_num ** 


  		




  92
  91
  
    
shoredistance,,** No join mapping for *shoredistance ** 


  		




  93
  92
  
    
shrubcover,,** No join mapping for *shrubcover ** 


  		




  94
  93
  
    
shrubht,,** No join mapping for *shrubht ** 


  		












  

    
      inputs/VegBank/observation_/unmapped_terms.csv
    
  





  97
  97
  
    
*soilcoarse


  		




  98
  98
  
    
*soildescription


  		




  99
  99
  
    
*emb_soilobs


  		




  100
  
  
    
*row_num


  		












  

    
      inputs/VegBank/plot_/header.csv
    
  





  1
  
  
    
plot_id,authorplotcode,reference_id,parent_id,reallatitude,reallongitude,locationaccuracy,confidentialitystatus,confidentialityreason,latitude,longitude,authore,authorn,authorzone,authordatum,authorlocation,locationnarrative,azimuth,dsgpoly,shape,area,standsize,placementmethod,permanence,layoutnarrative,elevation,elevationaccuracy,elevationrange,slopeaspect,minslopeaspect,maxslopeaspect,slopegradient,minslopegradient,maxslopegradient,topoposition,landform,surficialdeposits,rocktype,stateprovince,country,submitter_surname,submitter_givenname,submitter_email,notespublic,notesmgt,revisions,dateentered,emb_plot,plotrationalenarrative,accessioncode,continent,area|country|territory,region|state|province,county,quadrangle,Geographic Name,row_num


  		




  
  1
  
    
plot_id,authorplotcode,reference_id,parent_id,reallatitude,reallongitude,locationaccuracy,confidentialitystatus,confidentialityreason,latitude,longitude,authore,authorn,authorzone,authordatum,authorlocation,locationnarrative,azimuth,dsgpoly,shape,area,standsize,placementmethod,permanence,layoutnarrative,elevation,elevationaccuracy,elevationrange,slopeaspect,minslopeaspect,maxslopeaspect,slopegradient,minslopegradient,maxslopegradient,topoposition,landform,surficialdeposits,rocktype,stateprovince,country,submitter_surname,submitter_givenname,submitter_email,notespublic,notesmgt,revisions,dateentered,emb_plot,plotrationalenarrative,accessioncode,continent,area|country|territory,region|state|province,county,quadrangle,Geographic Name


  		












  

    
      inputs/VegBank/plot_/map.csv
    
  





  55
  55
  
    
county,county,,


  		




  56
  56
  
    
quadrangle,*quadrangle,,


  		




  57
  57
  
    
Geographic Name,*Geographic Name,,


  		




  58
  
  
    
row_num,*row_num,,


  		












  

    
      inputs/VegBank/plot_/unmapped_terms.csv
    
  





  28
  28
  
    
*accessioncode


  		




  29
  29
  
    
*quadrangle


  		




  30
  30
  
    
*Geographic Name


  		




  31
  
  
    
*row_num


  		












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