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Revision 11819

Added by Aaron Marcuse-Kubitza about 11 years ago

fix: inputs/CVS/observation_community/create.sql: communityName: populate from commConcept.commName instead, because commInterpretation.commname is not always populated. this requires left-joining to commConcept.

View differences:

inputs/CVS/observation_community/create.sql
1 1 
SELECT DISTINCT ON ("COMMCLASS_ID", "commInterpretation".commname) *
2 2 
FROM      "commClass"
3 3 
LEFT JOIN "commInterpretation" USING ("COMMCLASS_ID")
4 
LEFT JOIN "commConcept" USING ("COMMCONCEPT_ID")
4 5 
ORDER BY "COMMCLASS_ID", "commInterpretation".commname, "COMMINTERPRETATION_ID"
inputs/CVS/observation_community/header.csv
1 
COMMCLASS_ID,OBSERVATION_ID,classStartDate,classStopDate,inspection,tableAnalysis,multivariateAnalysis,expertSystem,classPublication_ID,classNotes,commClass--commName,commCode,commFramework,commClass--commLevel,commClass--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
1 
COMMCONCEPT_ID,COMMCLASS_ID,OBSERVATION_ID,classStartDate,classStopDate,inspection,tableAnalysis,multivariateAnalysis,expertSystem,classPublication_ID,classNotes,commClass--commName,commCode,commFramework,commClass--commLevel,commClass--accessionCode,commClass--dba_src_ID,dba_dataSource,classStopReason,COMMINTERPRETATION_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,COMMNAME_ID,reference_ID,commDescription,accessionCode,commConcept--dba_src_ID,commName,referenceText,scientific,translated,code,originalAuthorCode,common,commLevel,alliance,includeInPicklistNow,PhysGroup,FormGroup,EcolGroup,4thApproxName,NatureServeUID,classificationSystem
inputs/CVS/observation_community/map.csv
1 1 
CVS,VegCore,Filter,Comments
2 
COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,,
2 3 
COMMCLASS_ID,*observation_community--COMMCLASS_ID,,
3 4 
OBSERVATION_ID,eventID,,
4 5 
classStartDate,*observation_community--classStartDate,,
......
18 19 
dba_dataSource,*observation_community--dba_dataSource,,
19 20 
classStopReason,*observation_community--classStopReason,,
20 21 
COMMINTERPRETATION_ID,communityID,,
21 
COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,,
22 22 
commcode,*observation_community--commcode,,
23 
commname,communityName,,
23 
commname,*observation_community--commname,,
24 24 
classFit,*observation_community--classFit,,
25 25 
classConfidence,*observation_community--classConfidence,,
26 26 
commAuthority_ID,*observation_community--commAuthority_ID,,
......
38 38 
previousFit,*observation_community--previousFit,,
39 39 
orderDeterminationForEvent,*observation_community--orderDeterminationForEvent,,
40 40 
duplicateDetermination,*observation_community--duplicateDetermination,,
41 
COMMNAME_ID,*observation_community--COMMNAME_ID,,
42 
reference_ID,*observation_community--reference_ID,,
43 
commDescription,*observation_community--commDescription,,
44 
accessionCode,*observation_community--accessionCode,,
45 
commConcept--dba_src_ID,*observation_community--commConcept--dba_src_ID,,
46 
commName,communityName,,
47 
referenceText,*observation_community--referenceText,,
48 
scientific,*observation_community--scientific,,
49 
translated,*observation_community--translated,,
50 
code,*observation_community--code,,
51 
originalAuthorCode,*observation_community--originalAuthorCode,,
52 
common,*observation_community--common,,
53 
commLevel,*observation_community--commLevel,,
54 
alliance,*observation_community--alliance,,
55 
includeInPicklistNow,*observation_community--includeInPicklistNow,,
56 
PhysGroup,*observation_community--PhysGroup,,
57 
FormGroup,*observation_community--FormGroup,,
58 
EcolGroup,*observation_community--EcolGroup,,
59 
4thApproxName,*observation_community--4thApproxName,,
60 
NatureServeUID,*observation_community--NatureServeUID,,
61 
classificationSystem,*observation_community--classificationSystem,,
inputs/CVS/observation_community/new_terms.csv
1 
COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,,
1 2 
COMMCLASS_ID,*observation_community--COMMCLASS_ID,,
2 3 
OBSERVATION_ID,eventID,,
3 4 
classStartDate,*observation_community--classStartDate,,
......
17 18 
dba_dataSource,*observation_community--dba_dataSource,,
18 19 
classStopReason,*observation_community--classStopReason,,
19 20 
COMMINTERPRETATION_ID,communityID,,
20 
COMMCONCEPT_ID,*observation_community--COMMCONCEPT_ID,,
21 21 
commcode,*observation_community--commcode,,
22 
commname,communityName,,
22 
commname,*observation_community--commname,,
23 23 
classFit,*observation_community--classFit,,
24 24 
classConfidence,*observation_community--classConfidence,,
25 25 
commAuthority_ID,*observation_community--commAuthority_ID,,
......
35 35 
previousFit,*observation_community--previousFit,,
36 36 
orderDeterminationForEvent,*observation_community--orderDeterminationForEvent,,
37 37 
duplicateDetermination,*observation_community--duplicateDetermination,,
38 
COMMNAME_ID,*observation_community--COMMNAME_ID,,
39 
reference_ID,*observation_community--reference_ID,,
40 
commDescription,*observation_community--commDescription,,
41 
accessionCode,*observation_community--accessionCode,,
42 
commConcept--dba_src_ID,*observation_community--commConcept--dba_src_ID,,
43 
commName,communityName,,
44 
referenceText,*observation_community--referenceText,,
45 
scientific,*observation_community--scientific,,
46 
translated,*observation_community--translated,,
47 
code,*observation_community--code,,
48 
originalAuthorCode,*observation_community--originalAuthorCode,,
49 
common,*observation_community--common,,
50 
commLevel,*observation_community--commLevel,,
51 
alliance,*observation_community--alliance,,
52 
includeInPicklistNow,*observation_community--includeInPicklistNow,,
53 
PhysGroup,*observation_community--PhysGroup,,
54 
FormGroup,*observation_community--FormGroup,,
55 
EcolGroup,*observation_community--EcolGroup,,
56 
4thApproxName,*observation_community--4thApproxName,,
57 
NatureServeUID,*observation_community--NatureServeUID,,
58 
classificationSystem,*observation_community--classificationSystem,,
inputs/CVS/observation_community/unmapped_terms.csv
1 
*observation_community--COMMCONCEPT_ID
1 2 
*observation_community--COMMCLASS_ID
2 3 
*observation_community--classStartDate
3 4 
*observation_community--classStopDate
......
15 16 
*observation_community--commClass--dba_src_ID
16 17 
*observation_community--dba_dataSource
17 18 
*observation_community--classStopReason
18 
*observation_community--COMMCONCEPT_ID
19 19 
*observation_community--commcode
20 
*observation_community--commname
20 21 
*observation_community--classFit
21 22 
*observation_community--classConfidence
22 23 
*observation_community--commAuthority_ID
......
34 35 
*observation_community--previousFit
35 36 
*observation_community--orderDeterminationForEvent
36 37 
*observation_community--duplicateDetermination
38 
*observation_community--COMMNAME_ID
39 
*observation_community--reference_ID
40 
*observation_community--commDescription
41 
*observation_community--accessionCode
42 
*observation_community--commConcept--dba_src_ID
43 
*observation_community--referenceText
44 
*observation_community--scientific
45 
*observation_community--translated
46 
*observation_community--code
47 
*observation_community--originalAuthorCode
48 
*observation_community--common
49 
*observation_community--commLevel
50 
*observation_community--alliance
51 
*observation_community--includeInPicklistNow
52 
*observation_community--PhysGroup
53 
*observation_community--FormGroup
54 
*observation_community--EcolGroup
55 
*observation_community--4thApproxName
56 
*observation_community--NatureServeUID
57 
*observation_community--classificationSystem

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