Revision 11814
Added by Aaron Marcuse-Kubitza about 11 years ago
| inputs/CVS/import_order.txt | ||
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| 9 | 9 |
taxon_observation.** |
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^taxon_observation.**.sample |
| 11 | 11 |
observationContributor_ |
| 12 |
observation_community |
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| inputs/CVS/observation_community/create.sql | ||
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SELECT DISTINCT ON ("COMMCLASS_ID", "commInterpretation".commname) *
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FROM "commClass" |
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LEFT JOIN "commInterpretation" USING ("COMMCLASS_ID")
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ORDER BY "COMMCLASS_ID", "commInterpretation".commname, "COMMINTERPRETATION_ID" |
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| inputs/CVS/observation_community/header.csv | ||
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COMMCLASS_ID,OBSERVATION_ID,classStartDate,classStopDate,inspection,tableAnalysis,multivariateAnalysis,expertSystem,classPublication_ID,classNotes,commName,commCode,commFramework,commLevel,accessionCode,commClass--dba_src_ID,dba_dataSource,classStopReason,COMMINTERPRETATION_ID,COMMCONCEPT_ID,commcode,commname,classFit,classConfidence,commAuthority_ID,notes,type,nomenclaturalType,dba_src_ID,framework_id,primaryDetermination,primaryDeterminationStatus,primaryComments,primaryStartDate,primarySTOPDate,dba_interpretationStatus,previousFit,orderDeterminationForEvent,duplicateDetermination |
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| inputs/CVS/observation_community/run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| inputs/CVS/observation_community/map.csv | ||
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CVS,VegCore,Filter,Comments |
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COMMCLASS_ID,*observation_community--COMMCLASS_ID,, |
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OBSERVATION_ID,eventID,, |
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classStartDate,*observation_community--classStartDate,, |
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classStopDate,*observation_community--classStopDate,, |
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inspection,*observation_community--inspection,, |
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tableAnalysis,*observation_community--tableAnalysis,, |
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multivariateAnalysis,*observation_community--multivariateAnalysis,, |
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expertSystem,*observation_community--expertSystem,, |
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classPublication_ID,*observation_community--classPublication_ID,, |
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classNotes,*observation_community--classNotes,, |
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commName,*observation_community--commName,, |
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commCode,*observation_community--commCode,, |
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commFramework,*observation_community--commFramework,, |
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commLevel,*observation_community--commLevel,, |
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accessionCode,*observation_community--accessionCode,, |
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commClass--dba_src_ID,*observation_community--commClass--dba_src_ID,, |
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dba_dataSource,*observation_community--dba_dataSource,, |
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classStopReason,*observation_community--classStopReason,, |
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COMMINTERPRETATION_ID,communityID,, |
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COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,, |
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commcode,*observation_community--commcode,, |
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commname,communityName,, |
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classFit,*observation_community--classFit,, |
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classConfidence,*observation_community--classConfidence,, |
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commAuthority_ID,*observation_community--commAuthority_ID,, |
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notes,*observation_community--notes,, |
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type,*observation_community--type,, |
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nomenclaturalType,*observation_community--nomenclaturalType,, |
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dba_src_ID,*observation_community--dba_src_ID,, |
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framework_id,*observation_community--framework_id,, |
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primaryDetermination,*observation_community--primaryDetermination,, |
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primaryDeterminationStatus,*observation_community--primaryDeterminationStatus,, |
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primaryComments,*observation_community--primaryComments,, |
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primaryStartDate,*observation_community--primaryStartDate,, |
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primarySTOPDate,*observation_community--primarySTOPDate,, |
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dba_interpretationStatus,*observation_community--dba_interpretationStatus,, |
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previousFit,*observation_community--previousFit,, |
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orderDeterminationForEvent,*observation_community--orderDeterminationForEvent,, |
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duplicateDetermination,*observation_community--duplicateDetermination,, |
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| inputs/CVS/observation_community/VegBIEN.csv | ||
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link ../../../mappings/VegCore-VegBIEN.csv |
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| 0 | 2 | |
| inputs/CVS/observation_community/test.xml.ref | ||
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<!--put template--> |
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<VegBIEN> |
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<_setDefault id="-1"> |
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<source_id><source><shortname>CVS.new</shortname></source></source_id> |
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<path> |
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<_simplifyPath> |
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<next>parent_id</next> |
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<path> |
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<location> |
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<locationevent> |
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<sourceaccessioncode>$eventID</sourceaccessioncode> |
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<commclass> |
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<commdetermination> |
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<commconcept_id> |
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<commconcept> |
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<commname_id><commname><commname>$communityID</commname></commname></commname_id> |
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<commdescription>$communityName</commdescription> |
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</commconcept> |
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</commconcept_id> |
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</commdetermination> |
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</commclass> |
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<locationevent fkey="parent_id"><sourceaccessioncode>$eventID</sourceaccessioncode></locationevent> |
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</locationevent> |
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</location> |
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</path> |
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</_simplifyPath> |
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</path> |
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</_setDefault> |
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</VegBIEN> |
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Inserted 9 new rows into database |
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| inputs/CVS/observation_community/new_terms.csv | ||
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COMMCLASS_ID,*observation_community--COMMCLASS_ID,, |
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OBSERVATION_ID,eventID,, |
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classStartDate,*observation_community--classStartDate,, |
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classStopDate,*observation_community--classStopDate,, |
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inspection,*observation_community--inspection,, |
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tableAnalysis,*observation_community--tableAnalysis,, |
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multivariateAnalysis,*observation_community--multivariateAnalysis,, |
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expertSystem,*observation_community--expertSystem,, |
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classPublication_ID,*observation_community--classPublication_ID,, |
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classNotes,*observation_community--classNotes,, |
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commName,*observation_community--commName,, |
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commCode,*observation_community--commCode,, |
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commFramework,*observation_community--commFramework,, |
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commLevel,*observation_community--commLevel,, |
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accessionCode,*observation_community--accessionCode,, |
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commClass--dba_src_ID,*observation_community--commClass--dba_src_ID,, |
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dba_dataSource,*observation_community--dba_dataSource,, |
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classStopReason,*observation_community--classStopReason,, |
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COMMINTERPRETATION_ID,communityID,, |
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COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,, |
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commcode,*observation_community--commcode,, |
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commname,communityName,, |
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classFit,*observation_community--classFit,, |
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classConfidence,*observation_community--classConfidence,, |
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commAuthority_ID,*observation_community--commAuthority_ID,, |
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nomenclaturalType,*observation_community--nomenclaturalType,, |
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dba_src_ID,*observation_community--dba_src_ID,, |
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framework_id,*observation_community--framework_id,, |
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primaryDetermination,*observation_community--primaryDetermination,, |
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primaryDeterminationStatus,*observation_community--primaryDeterminationStatus,, |
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primaryComments,*observation_community--primaryComments,, |
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primaryStartDate,*observation_community--primaryStartDate,, |
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primarySTOPDate,*observation_community--primarySTOPDate,, |
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dba_interpretationStatus,*observation_community--dba_interpretationStatus,, |
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previousFit,*observation_community--previousFit,, |
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orderDeterminationForEvent,*observation_community--orderDeterminationForEvent,, |
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duplicateDetermination,*observation_community--duplicateDetermination,, |
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| inputs/CVS/observation_community/unmapped_terms.csv | ||
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| 1 |
*observation_community--COMMCLASS_ID |
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*observation_community--classStartDate |
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*observation_community--classStopDate |
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*observation_community--inspection |
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*observation_community--tableAnalysis |
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*observation_community--multivariateAnalysis |
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*observation_community--expertSystem |
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*observation_community--classPublication_ID |
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*observation_community--classNotes |
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*observation_community--commName |
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*observation_community--commCode |
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*observation_community--commFramework |
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*observation_community--commLevel |
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*observation_community--accessionCode |
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*observation_community--commClass--dba_src_ID |
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*observation_community--dba_dataSource |
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*observation_community--classStopReason |
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*observation_community--COMMCONCEPT_ID |
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*observation_community--commcode |
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*observation_community--classFit |
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*observation_community--classConfidence |
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*observation_community--commAuthority_ID |
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*observation_community--notes |
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*observation_community--type |
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*observation_community--nomenclaturalType |
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*observation_community--dba_src_ID |
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*observation_community--framework_id |
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*observation_community--primaryDetermination |
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*observation_community--primaryDeterminationStatus |
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*observation_community--primaryComments |
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*observation_community--primaryStartDate |
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*observation_community--primarySTOPDate |
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*observation_community--dba_interpretationStatus |
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*observation_community--previousFit |
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*observation_community--orderDeterminationForEvent |
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*observation_community--duplicateDetermination |
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Also available in: Unified diff
added inputs/CVS/observation_community/, as for VegBank