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Revision 11277

Added by Aaron Marcuse-Kubitza about 11 years ago

inputs/CVS/taxonObservation_/map.csv: collector_ID: remapped it to UNUSED and removed the join to party via it, like in VegBank

View differences:

inputs/CVS/taxonObservation_/create.sql
1 1 
SELECT *
2 2 
FROM "taxonObservation"
3 3 
LEFT JOIN "taxonInterpretation" USING ("TAXONOBSERVATION_ID")
4 
LEFT JOIN party collector ON collector."PARTY_ID" = "taxonInterpretation"."collector_ID"
5 4 
LEFT JOIN "plantConcept_" USING ("PLANTCONCEPT_ID")
6 5 
;
inputs/CVS/taxonObservation_/header.csv
1 
PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PARTY_ID,salutation,givenName,middleName,surName,suffix,entry_userInitials,organizationName,currentName_ID,contactInstructions,email,accessionCode,partyType,dba_src_ID,dba_unsure,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,genus,subgenus,section,composite species,species,subspecies,composite variety,variety
1 
PLANTCONCEPT_ID,TAXONOBSERVATION_ID,OBSERVATION_ID,authorPlantName,taxonObservation_reference_ID,currentTaxonInterpPlantConcept_ID,taxonInferenceArea,taxonObservation_accessionCode,taxonObservation_dba_src_ID,cust_cvs_corner1Presence,cust_cvs_corner2Presence,cust_cvs_corner3Presence,cust_cvs_corner4Presence,cust_cvs_corner5Presence,entry_herbLineID,entry_treeLineID,taxonObservation_entry_sppID,entry_unknownSp,entry_sortOrder,cust_cvs_collectionFlag,taxonObservationNotes,temp_taxonUpToDate,TAXONINTERPRETATION_ID,stemLocation_ID,interpretationDate,taxonInterpretation_PLANTNAME_ID,taxonInterpretation_PARTY_ID,ROLE_ID,interpretationType,reference_ID,originalInterpretation,currentInterpretation,taxonFit,taxonConfidence,collector_ID,collectionNumber,collectionDate,museum_ID,museumAccessionNumber,groupType,notes,notesPublic,notesMgt,revisions,taxonInterpretation_dba_src_ID,taxonInterpretation_accessionCode,PLANTNAME_ID,plantConcept_reference_ID,plantname,plantNameWithAuthority,plantCode,plantDescription,plantConcept_accessionCode,plantConcept_dba_src_ID,plantConcept_entry_sppID,USDAPlantsCode,VascularPlant,denorm_kingdom,denorm_division,denorm_category,denorm_family,denorm_genus,denorm_species,denorm_triAbbr,denorm_triName,denorm_quadAbbr,denorm_quadName,denorm_hybridX,taxonLevel,taxonRank,lowestParentName,lowestParentConcept_ID,lowestChildRank,commonName,growthForm_short,woody,exotic,usda_code,usda_growthForm,Kingdom,Subkingdom,Division,Class,Subclass,Order,composite family,family,tribe,composite genus,genus,subgenus,section,composite species,species,subspecies,composite variety,variety
inputs/CVS/taxonObservation_/map.csv
33 33 
currentInterpretation,*currentInterpretation,,
34 34 
taxonFit,identificationQualifier,,
35 35 
taxonConfidence,identificationVerificationStatus,,
36 
collector_ID,*collector_ID,,
36 
collector_ID,UNUSED#collector_ID,,
37 37 
collectionNumber,collectorNumber,,
38 38 
collectionDate,dateCollected,,
39 39 
museum_ID,*museum_ID,,
......
45 45 
revisions,*revisions,,
46 46 
taxonInterpretation_dba_src_ID,*taxonInterpretation_dba_src_ID,,
47 47 
taxonInterpretation_accessionCode,*taxonInterpretation_accessionCode,,
48 
PARTY_ID,*PARTY_ID,,
49 
salutation,*salutation,,
50 
givenName,recordedBy_givenName,,
51 
middleName,*middleName,,
52 
surName,recordedBy_surName,,
53 
suffix,*suffix,,
54 
entry_userInitials,*entry_userInitials,,
55 
organizationName,*organizationName,,
56 
currentName_ID,*currentName_ID,,
57 
contactInstructions,*contactInstructions,,
58 
email,*email,,
59 48 
accessionCode,*accessionCode,,
60 49 
partyType,*partyType,,
61 50 
dba_src_ID,*dba_src_ID,,
inputs/CVS/taxonObservation_/VegBIEN.csv
26 26 
authorPlantName,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
27 27 
plantNameWithAuthority,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
28 28 
plantname,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
29 
givenName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/collector_id/party/fullname/_join_words/1,
30 
surName,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/collector_id/party/fullname/_join_words/2,
31 29 
TAXONOBSERVATION_ID,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
32 30 
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
33 31 
TAXONOBSERVATION_ID,/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/sourceaccessioncode/_first/1,
......
67 65 
collectionNumber,"/location/locationevent/locationevent:[@fkey=parent_id]/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
68 66 
Division,,** No join mapping for *division/_alt/2 **
69 67 
Kingdom,,** No non-empty join mapping for DUPLICATE#of:denorm_kingdom#Kingdom **
70 
PARTY_ID,,** No join mapping for *PARTY_ID **
71 68 
PLANTCONCEPT_ID,,** No join mapping for *PLANTCONCEPT_ID **
72 69 
PLANTNAME_ID,,** No join mapping for *PLANTNAME_ID **
73 70 
ROLE_ID,,** No join mapping for *ROLE_ID **
......
77 74 
USDAPlantsCode,,** No join mapping for *USDAPlantsCode **
78 75 
VascularPlant,,** No join mapping for *VascularPlant **
79 76 
accessionCode,,** No join mapping for *accessionCode **
80 
collector_ID,,** No join mapping for *collector_ID **
77 
collector_ID,,** No non-empty join mapping for UNUSED#collector_ID **
81 78 
commonName,,** No join mapping for vernacularName **
82 79 
composite family,,** No join mapping for *composite family **
83 80 
composite genus,,** No join mapping for *composite genus **
84 81 
composite species,,** No join mapping for *composite species **
85 82 
composite variety,,** No non-empty join mapping for EQUIV#to:species#composite variety ** full taxonomic name at that rank
86 
contactInstructions,,** No join mapping for *contactInstructions **
87 83 
currentInterpretation,,** No join mapping for *currentInterpretation **
88 
currentName_ID,,** No join mapping for *currentName_ID **
89 84 
currentTaxonInterpPlantConcept_ID,,** No join mapping for *currentTaxonInterpPlantConcept_ID **
90 85 
cust_cvs_collectionFlag,,** No join mapping for *cust_cvs_collectionFlag **
91 86 
cust_cvs_corner1Presence,,** No join mapping for *cust_cvs_corner1Presence **
......
101 96 
denorm_quadAbbr,,** No join mapping for infraspecificRank2 ** sometimes misparsed as the last + sign in the plantNameWithAuthority
102 97 
denorm_quadName,,** No join mapping for infraspecificEpithet2 ** sometimes misparsed as the part after the last + sign in the plantNameWithAuthority
103 98 
denorm_triAbbr,,** No join mapping for infraspecificRank **
104 
email,,** No join mapping for *email **
105 99 
entry_herbLineID,,** No join mapping for *entry_herbLineID **
106 100 
entry_sortOrder,,** No join mapping for *entry_sortOrder **
107 101 
entry_treeLineID,,** No join mapping for *entry_treeLineID **
108 102 
entry_unknownSp,,** No join mapping for *entry_unknownSp **
109 
entry_userInitials,,** No join mapping for *entry_userInitials **
110 103 
exotic,,** No join mapping for *exotic **
111 104 
family,,** No non-empty join mapping for DUPLICATE#of:denorm_family#family **
112 105 
groupType,,** No join mapping for *groupType **
......
114 107 
lowestChildRank,,** No join mapping for *lowestChildRank **
115 108 
lowestParentConcept_ID,,** No join mapping for *lowestParentConcept_ID **
116 109 
lowestParentName,,** No join mapping for *lowestParentName **
117 
middleName,,** No join mapping for *middleName **
118 110 
museum_ID,,** No join mapping for *museum_ID **
119 111 
notesMgt,,** No join mapping for *notesMgt **
120 112 
notesPublic,,** No join mapping for *notesPublic **
121 
organizationName,,** No join mapping for *organizationName **
122 113 
originalInterpretation,,** No join mapping for *originalInterpretation **
123 114 
partyType,,** No join mapping for *partyType **
124 115 
plantCode,,** No join mapping for *plantCode **
......
129 120 
plantDescription,,** No join mapping for *plantDescription **
130 121 
reference_ID,,** No join mapping for *reference_ID **
131 122 
revisions,,** No join mapping for *revisions **
132 
salutation,,** No join mapping for *salutation **
133 123 
section,,** No join mapping for *section **
134 124 
species,,** No join mapping for speciesBinomial ** full taxonomic name at that rank
135 125 
subgenus,,** No join mapping for subgenus **
136 126 
subspecies,,** No non-empty join mapping for EQUIV#to:species#subspecies ** full taxonomic name at that rank
137 
suffix,,** No join mapping for *suffix **
138 127 
taxonConfidence,,** No join mapping for identificationVerificationStatus **
139 128 
taxonInferenceArea,,** No join mapping for *taxonInferenceArea **
140 129 
taxonInterpretation_PARTY_ID,,** No join mapping for *taxonInterpretation_PARTY_ID **
inputs/CVS/taxonObservation_/test.xml.ref
25 25 
                                        </plantobservation>
26 26 
                                    </aggregateoccurrence>
27 27 
                                    <authortaxoncode>$collectionNumber</authortaxoncode>
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                                    <collector_id>
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                                        <party>
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                                            <fullname>
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                                                <_join_words>
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                                                    <1>$givenName</1>
33 
                                                    <2>$surName</2>
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                                                </_join_words>
35 
                                            </fullname>
36 
                                        </party>
37 
                                    </collector_id>
38 28 
                                    <sourceaccessioncode>$TAXONOBSERVATION_ID</sourceaccessioncode>
39 29 
                                    <taxondetermination>
40 30 
                                        <taxonverbatim_id>
inputs/CVS/taxonObservation_/new_terms.csv
2 2 
stemLocation_ID,stemID,,
3 3 
interpretationDate,dateIdentified,,
4 4 
collectionDate,dateCollected,,
5 
givenName,recordedBy_givenName,,
6 
surName,recordedBy_surName,,
7 5 
plantname,taxonName,,
8 6 
plantNameWithAuthority,scientificName,,
9 7 
denorm_kingdom,kingdom,,
inputs/CVS/taxonObservation_/unmapped_terms.csv
25 25 
*originalInterpretation
26 26 
*currentInterpretation
27 27 
identificationVerificationStatus
28 
*collector_ID
29 28 
*museum_ID
30 29 
*groupType
31 30 
*notesPublic
......
33 32 
*revisions
34 33 
*taxonInterpretation_dba_src_ID
35 34 
*taxonInterpretation_accessionCode
36 
*PARTY_ID
37 
*salutation
38 
*middleName
39 
*suffix
40 
*entry_userInitials
41 
*organizationName
42 
*currentName_ID
43 
*contactInstructions
44 
*email
45 35 
*accessionCode
46 36 
*partyType
47 37 
*dba_src_ID

Also available in: Unified diff