Revision 11438
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/VegBank/taxonobservation_/postprocess.sql | ||
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| 2 | 2 |
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| 3 | 3 |
SELECT create_if_not_exists($$CREATE INDEX $$||:table_str||%'__parent'||$$ ON $$||:table_str||$$ ("eventID")$$); -- runtime: 2 s ("2416.676 ms") @starscream
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| 4 | 4 |
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SELECT mk_derived_col((:table_str, 'scientificName'), |
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$$_alt("scientificName_verbatim", "scientificName__for_nearest_taxon_concept")$$)
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; -- runtime: 15 s ("Time: 12334.893 ms") @starscream
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| 11 | 5 |
SELECT create_if_not_exists($$ALTER TABLE $$||:table_str||$$ ADD PRIMARY KEY ("identificationID")$$); -- runtime: 1 s ("Time: 1342.115 ms") @starscream
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| inputs/VegBank/taxonobservation_/map.csv | ||
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| 31 | 31 |
taxonobservation_reference_id,*taxonobservation_--taxonobservation_reference_id,, |
| 32 | 32 |
taxoninferencearea,*taxonobservation_--taxoninferencearea,, |
| 33 | 33 |
emb_taxonobservation,*taxonobservation_--emb_taxonobservation,, |
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int_origplantconcept_id,*taxonobservation_--int_origplantconcept_id,,
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int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,, = originalScientificName_scrubbed
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int_origplantscinamenoauth,originalTaxonName,,
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int_origplantcommon,originalVernacularName,,
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int_origplantcode,*taxonobservation_--int_origplantcode,,
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int_currplantconcept_id,*taxonobservation_--int_currplantconcept_id,,
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int_currplantscifull,scientificName_verbatim,,
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int_currplantscinamenoauth,taxonName,,
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int_currplantcommon,vernacularName,,
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int_currplantcode,*taxonobservation_--int_currplantcode,,
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int_origplantconcept_id,OMIT#int_origplantconcept_id,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_origplantscifull,OMIT#int_origplantscifull,,"omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = EQUIV#to:authorplantname#int_origplantscifull, originalScientificName_scrubbed"
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int_origplantscinamenoauth,OMIT#int_origplantscinamenoauth,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = originalTaxonName
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int_origplantcommon,OMIT#int_origplantcommon,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = originalVernacularName
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int_origplantcode,OMIT#int_origplantcode,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_currplantconcept_id,OMIT#int_currplantconcept_id,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_currplantscifull,OMIT#int_currplantscifull,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = scientificName_verbatim
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int_currplantscinamenoauth,OMIT#int_currplantscinamenoauth,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = taxonName
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int_currplantcommon,OMIT#int_currplantcommon,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = vernacularName
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int_currplantcode,OMIT#int_currplantcode,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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| 44 | 44 |
taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,, |
| 45 | 45 |
*plantconcept_--plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,, |
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scientificName__for_nearest_taxon_concept,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."
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scientificName__for_nearest_taxon_concept,scientificName,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is." |
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| 47 | 47 |
*plantconcept_--plantcode,*plantconcept_--plantcode,, |
| 48 | 48 |
*plantconcept_--plantdescription,*plantconcept_--plantdescription,, |
| 49 | 49 |
*plantconcept_--d_obscount,*plantconcept_--d_obscount,, |
| inputs/VegBank/taxonobservation_/test.xml.ref | ||
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| 99 | 99 |
<value> |
| 100 | 100 |
<_alt> |
| 101 | 101 |
<1>$scientificName</1> |
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<2> |
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<_alt> |
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<1>$taxonName</1> |
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<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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</_alt> |
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</2> |
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<2><_filter_genus><value>$genus</value></_filter_genus></2> |
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| 108 | 103 |
</_alt> |
| 109 | 104 |
</value> |
| 110 | 105 |
</_merge_prefix> |
| ... | ... | |
| 113 | 108 |
</taxonlabel_id> |
| 114 | 109 |
<family>$family</family> |
| 115 | 110 |
<genus>$genus</genus> |
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<taxonname>$taxonName</taxonname> |
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| 117 | 111 |
<taxonomicname>$scientificName</taxonomicname> |
| 118 | 112 |
</taxonverbatim> |
| 119 | 113 |
</taxonverbatim_id> |
| ... | ... | |
| 123 | 117 |
</taxondetermination> |
| 124 | 118 |
<taxondetermination> |
| 125 | 119 |
<isoriginal>true</isoriginal> |
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<taxonverbatim_id> |
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<taxonverbatim> |
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<taxonname>$originalTaxonName</taxonname> |
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<taxonomicname>$originalScientificName</taxonomicname> |
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</taxonverbatim> |
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</taxonverbatim_id> |
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<taxonverbatim_id><taxonverbatim><taxonomicname>$originalScientificName</taxonomicname></taxonverbatim></taxonverbatim_id> |
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| 132 | 121 |
</taxondetermination> |
| 133 | 122 |
</taxonoccurrence> |
| 134 | 123 |
</locationevent> |
| inputs/VegBank/taxonobservation_/new_terms.csv | ||
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| 20 | 20 |
observation_id,eventID,, |
| 21 | 21 |
taxoninferencearea,*taxonobservation_--taxoninferencearea,, |
| 22 | 22 |
emb_taxonobservation,*taxonobservation_--emb_taxonobservation,, |
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int_origplantconcept_id,*taxonobservation_--int_origplantconcept_id,,
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int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,, = originalScientificName_scrubbed
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int_origplantscinamenoauth,originalTaxonName,,
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int_origplantcommon,originalVernacularName,,
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int_origplantcode,*taxonobservation_--int_origplantcode,,
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int_currplantconcept_id,*taxonobservation_--int_currplantconcept_id,,
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int_currplantscifull,scientificName_verbatim,,
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int_currplantscinamenoauth,taxonName,,
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int_currplantcommon,vernacularName,,
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int_currplantcode,*taxonobservation_--int_currplantcode,,
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int_origplantconcept_id,OMIT#int_origplantconcept_id,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_origplantscifull,OMIT#int_origplantscifull,,"omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = EQUIV#to:authorplantname#int_origplantscifull, originalScientificName_scrubbed"
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int_origplantscinamenoauth,OMIT#int_origplantscinamenoauth,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = originalTaxonName
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int_origplantcommon,OMIT#int_origplantcommon,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = originalVernacularName
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int_origplantcode,OMIT#int_origplantcode,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_currplantconcept_id,OMIT#int_currplantconcept_id,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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int_currplantscifull,OMIT#int_currplantscifull,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = scientificName_verbatim
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int_currplantscinamenoauth,OMIT#int_currplantscinamenoauth,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = taxonName
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int_currplantcommon,OMIT#int_currplantcommon,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). = vernacularName
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| 32 |
int_currplantcode,OMIT#int_currplantcode,,omitted because not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead).
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| 33 | 33 |
taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,, |
| 34 |
scientificName__for_nearest_taxon_concept,scientificName,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is." |
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| 34 | 35 |
plantname,DUPLICATE#of:plantconcept_plantname#plantname,,exact duplicate |
| 35 | 36 |
plantname_reference_id,*taxonobservation_--plantname_reference_id,, |
| 36 | 37 |
dateentered,*taxonobservation_--dateentered,, |
| inputs/VegBank/taxonobservation_/unmapped_terms.csv | ||
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| 20 | 20 |
*taxonobservation_--taxonobservation_reference_id |
| 21 | 21 |
*taxonobservation_--taxoninferencearea |
| 22 | 22 |
*taxonobservation_--emb_taxonobservation |
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*taxonobservation_--int_origplantconcept_id |
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originalVernacularName |
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*taxonobservation_--int_origplantcode |
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*taxonobservation_--int_currplantconcept_id |
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scientificName_verbatim |
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vernacularName |
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*taxonobservation_--int_currplantcode |
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| 30 | 23 |
*taxonobservation_--taxonobservation_accessioncode |
| 31 | 24 |
*plantconcept_--plantconcept_reference_id |
| 32 |
scientificName__for_nearest_taxon_concept |
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| 33 | 25 |
*plantconcept_--plantcode |
| 34 | 26 |
*plantconcept_--plantdescription |
| 35 | 27 |
*plantconcept_--d_obscount |
| inputs/VegBank/taxon_observation.**/header.csv | ||
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| 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,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,*plantconcept_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*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,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,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,*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,taxonOccurrenceID |
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| 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,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,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,*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,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,*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,taxonOccurrenceID |
|
| inputs/VegBank/taxon_observation.**/map.csv | ||
|---|---|---|
| 38 | 38 |
*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxonobservation_reference_id,, |
| 39 | 39 |
*taxonobservation_--taxoninferencearea,*taxonobservation_--taxoninferencearea,, |
| 40 | 40 |
*taxonobservation_--emb_taxonobservation,*taxonobservation_--emb_taxonobservation,, |
| 41 |
*taxonobservation_--int_origplantconcept_id,*taxonobservation_--int_origplantconcept_id,,
|
|
| 42 |
EQUIV#to:authorplantname#int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,,
|
|
| 43 |
originalTaxonName,originalTaxonName,,
|
|
| 44 |
originalVernacularName,originalVernacularName,,
|
|
| 45 |
*taxonobservation_--int_origplantcode,*taxonobservation_--int_origplantcode,,
|
|
| 46 |
*taxonobservation_--int_currplantconcept_id,*taxonobservation_--int_currplantconcept_id,,
|
|
| 47 |
scientificName_verbatim,scientificName_verbatim,,
|
|
| 48 |
taxonName,taxonName,,
|
|
| 49 |
vernacularName,vernacularName,,
|
|
| 50 |
*taxonobservation_--int_currplantcode,*taxonobservation_--int_currplantcode,,
|
|
| 41 |
OMIT#int_origplantconcept_id,OMIT#int_origplantconcept_id,,
|
|
| 42 |
OMIT#int_origplantscifull,OMIT#int_origplantscifull,,
|
|
| 43 |
OMIT#int_origplantscinamenoauth,OMIT#int_origplantscinamenoauth,,
|
|
| 44 |
OMIT#int_origplantcommon,OMIT#int_origplantcommon,,
|
|
| 45 |
OMIT#int_origplantcode,OMIT#int_origplantcode,,
|
|
| 46 |
OMIT#int_currplantconcept_id,OMIT#int_currplantconcept_id,,
|
|
| 47 |
OMIT#int_currplantscifull,OMIT#int_currplantscifull,,
|
|
| 48 |
OMIT#int_currplantscinamenoauth,OMIT#int_currplantscinamenoauth,,
|
|
| 49 |
OMIT#int_currplantcommon,OMIT#int_currplantcommon,,
|
|
| 50 |
OMIT#int_currplantcode,OMIT#int_currplantcode,,
|
|
| 51 | 51 |
*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,, |
| 52 | 52 |
*plantconcept_--plantconcept_reference_id,*plantconcept_--plantconcept_reference_id,, |
| 53 |
scientificName__for_nearest_taxon_concept,scientificName__for_nearest_taxon_concept,,
|
|
| 53 |
scientificName,scientificName,,
|
|
| 54 | 54 |
*plantconcept_--plantcode,*plantconcept_--plantcode,, |
| 55 | 55 |
*plantconcept_--plantdescription,*plantconcept_--plantdescription,, |
| 56 | 56 |
*plantconcept_--d_obscount,*plantconcept_--d_obscount,, |
| ... | ... | |
| 74 | 74 |
*taxonobservation_--plantname_reference_id,*taxonobservation_--plantname_reference_id,, |
| 75 | 75 |
*taxonobservation_--dateentered,*taxonobservation_--dateentered,, |
| 76 | 76 |
observationGranularity,observationGranularity,, |
| 77 |
scientificName,scientificName,, |
|
| 78 | 77 |
coverPercent,coverPercent,, |
| 79 | 78 |
*stemcount_--basalarea,*stemcount_--basalarea,, |
| 80 | 79 |
*stemcount_--biomass,*stemcount_--biomass,, |
| inputs/VegBank/taxon_observation.**/test.xml.ref | ||
|---|---|---|
| 120 | 120 |
<value> |
| 121 | 121 |
<_alt> |
| 122 | 122 |
<1>$scientificName</1> |
| 123 |
<2> |
|
| 124 |
<_alt> |
|
| 125 |
<1>$taxonName</1> |
|
| 126 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 127 |
</_alt> |
|
| 128 |
</2> |
|
| 123 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 129 | 124 |
</_alt> |
| 130 | 125 |
</value> |
| 131 | 126 |
</_merge_prefix> |
| ... | ... | |
| 134 | 129 |
</taxonlabel_id> |
| 135 | 130 |
<family>$family</family> |
| 136 | 131 |
<genus>$genus</genus> |
| 137 |
<taxonname>$taxonName</taxonname> |
|
| 138 | 132 |
<taxonomicname>$scientificName</taxonomicname> |
| 139 | 133 |
</taxonverbatim> |
| 140 | 134 |
</taxonverbatim_id> |
| ... | ... | |
| 144 | 138 |
</taxondetermination> |
| 145 | 139 |
<taxondetermination> |
| 146 | 140 |
<isoriginal>true</isoriginal> |
| 147 |
<taxonverbatim_id> |
|
| 148 |
<taxonverbatim> |
|
| 149 |
<taxonname>$originalTaxonName</taxonname> |
|
| 150 |
<taxonomicname>$originalScientificName</taxonomicname> |
|
| 151 |
</taxonverbatim> |
|
| 152 |
</taxonverbatim_id> |
|
| 141 |
<taxonverbatim_id><taxonverbatim><taxonomicname>$originalScientificName</taxonomicname></taxonverbatim></taxonverbatim_id> |
|
| 153 | 142 |
</taxondetermination> |
| 154 | 143 |
</taxonoccurrence> |
| 155 | 144 |
</locationevent> |
| inputs/VegBank/taxon_observation.**/unmapped_terms.csv | ||
|---|---|---|
| 25 | 25 |
*taxonobservation_--taxonobservation_reference_id |
| 26 | 26 |
*taxonobservation_--taxoninferencearea |
| 27 | 27 |
*taxonobservation_--emb_taxonobservation |
| 28 |
*taxonobservation_--int_origplantconcept_id |
|
| 29 |
originalVernacularName |
|
| 30 |
*taxonobservation_--int_origplantcode |
|
| 31 |
*taxonobservation_--int_currplantconcept_id |
|
| 32 |
scientificName_verbatim |
|
| 33 |
vernacularName |
|
| 34 |
*taxonobservation_--int_currplantcode |
|
| 35 | 28 |
*taxonobservation_--taxonobservation_accessioncode |
| 36 | 29 |
*plantconcept_--plantconcept_reference_id |
| 37 |
scientificName__for_nearest_taxon_concept |
|
| 38 | 30 |
*plantconcept_--plantcode |
| 39 | 31 |
*plantconcept_--plantdescription |
| 40 | 32 |
*plantconcept_--d_obscount |
Also available in: Unified diff
fix: inputs/VegBank/taxonobservation_/map.csv: remapped int_* to OMIT because these are not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). see wiki.vegpath.org/Spot-checking#2013-10-10 > Mike Lee's conference call feedback.