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Revision 7552

Added by Aaron Marcuse-Kubitza almost 12 years ago

inputs/ARIZ/: Mapped refresh

View differences:

inputs/ARIZ/import_order.txt
1 1 
Source
2 2 
Specimen
3 
omoccurrences
inputs/ARIZ/omoccurrences/header.csv
1 
occid,collid,dbpk,basisOfRecord,occurrenceID,catalogNumber,institutionID,collectionID,institutionCode,collectionCode,datasetID,otherCatalogNumbers,ownerInstitutionCode,family,scientificName,sciname,tidinterpreted,genus,specificEpithet,taxonRank,infraspecificEpithet,scientificNameAuthorship,taxonRemarks,identifiedBy,dateIdentified,identificationReferences,identificationRemarks,identificationQualifier,typeStatus,recordedBy,recordNumber,recordedById,associatedCollectors,eventDate,year,month,day,startDayOfYear,endDayOfYear,verbatimEventDate,habitat,substrate,fieldNotes,fieldnumber,occurrenceRemarks,informationWithheld,dataGeneralizations,associatedOccurrences,associatedTaxa,dynamicProperties,verbatimAttributes,attributes,reproductiveCondition,cultivationStatus,establishmentMeans,lifeStage,sex,individualCount,samplingProtocol,preparations,country,stateProvince,county,municipality,locality,localitySecurity,localitySecurityReason,decimalLatitude,decimalLongitude,geodeticDatum,coordinateUncertaintyInMeters,footprintWKT,coordinatePrecision,locationRemarks,verbatimCoordinates,verbatimCoordinateSystem,georeferencedBy,georeferenceProtocol,georeferenceSources,georeferenceVerificationStatus,georeferenceRemarks,minimumElevationInMeters,maximumElevationInMeters,verbatimElevation,previousIdentifications,disposition,genericcolumn1,genericcolumn2,modified,language,duplicateid,observeruid,processingstatus,deaccessioned,recordEnteredBy,duplicateQuantity,labelProject,dateLastModified
inputs/ARIZ/omoccurrences/map.csv
1 
ARIZ,VegCore,Filter,Comments
2 
occid,occurrenceID,/_first/1,
3 
collid,*collid,,
4 
dbpk,*dbpk,,Only populated for 2651 rows
5 
basisOfRecord,basisOfRecord,,
6 
occurrenceID,occurrenceID,/_first/2,Not populated for all rows
7 
catalogNumber,catalogNumber,,
8 
institutionID,UNUSED,,
9 
collectionID,UNUSED,,
10 
institutionCode,UNUSED,,
11 
collectionCode,UNUSED,,
12 
datasetID,UNUSED,,
13 
otherCatalogNumbers,otherCatalogNumbers,,
14 
ownerInstitutionCode,ownerInstitutionCode,,Only populated for 547 rows
15 
family,family,,
16 
scientificName,scientificName,,
17 
sciname,*sciname,,
18 
tidinterpreted,*tidinterpreted,,
19 
genus,genus,,
20 
specificEpithet,specificEpithet,,
21 
taxonRank,taxonRank,,
22 
infraspecificEpithet,infraspecificEpithet,,
23 
scientificNameAuthorship,scientificNameAuthorship,,
24 
taxonRemarks,taxonRemarks,,
25 
identifiedBy,identifiedBy,,
26 
dateIdentified,dateIdentified,,
27 
identificationReferences,identificationReferences,,
28 
identificationRemarks,identificationRemarks,,
29 
identificationQualifier,identificationQualifier,,
30 
typeStatus,typeStatus,,
31 
recordedBy,recordedBy,,
32 
recordNumber,collectorNumber,,
33 
recordedById,*recordedById,,
34 
associatedCollectors,*associatedCollectors,,
35 
eventDate,eventDate,,
36 
year,year,,
37 
month,month,,
38 
day,day,,
39 
startDayOfYear,startDayOfYear,,
40 
endDayOfYear,endDayOfYear,,
41 
verbatimEventDate,verbatimEventDate,,
42 
habitat,habitat,,
43 
substrate,*substrate,,
44 
fieldNotes,UNUSED,,
45 
fieldnumber,UNUSED,,
46 
occurrenceRemarks,occurrenceRemarks,,
47 
informationWithheld,informationWithheld,,
48 
dataGeneralizations,dataGeneralizations,,
49 
associatedOccurrences,associatedOccurrences,,
50 
associatedTaxa,associatedTaxa,,
51 
dynamicProperties,dynamicProperties,,
52 
verbatimAttributes,*verbatimAttributes,,
53 
attributes,*attributes,,
54 
reproductiveCondition,reproductiveCondition,,
55 
cultivationStatus,cultivated,,
56 
establishmentMeans,OMIT,,"Only populated for 1 row, which also has cultivationStatus"
57 
lifeStage,lifeStage,,
58 
sex,sex,,
59 
individualCount,individualCount,,
60 
samplingProtocol,samplingProtocol,,
61 
preparations,preparations,,
62 
country,country,,
63 
stateProvince,stateProvince,,
64 
county,county,,
65 
municipality,municipality,,
66 
locality,locality,,
67 
localitySecurity,*localitySecurity,,
68 
localitySecurityReason,*localitySecurityReason,,
69 
decimalLatitude,decimalLatitude,,
70 
decimalLongitude,decimalLongitude,,
71 
geodeticDatum,geodeticDatum,,
72 
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,
73 
footprintWKT,footprintWKT,,
74 
coordinatePrecision,*coordinatePrecision,,
75 
locationRemarks,locationRemarks,,
76 
verbatimCoordinates,verbatimCoordinates,,
77 
verbatimCoordinateSystem,verbatimCoordinateSystem,,
78 
georeferencedBy,georeferencedBy,,
79 
georeferenceProtocol,georeferenceProtocol,,
80 
georeferenceSources,georeferenceSources,,
81 
georeferenceVerificationStatus,georeferenceVerificationStatus,,
82 
georeferenceRemarks,georeferenceRemarks,,
83 
minimumElevationInMeters,minimumElevationInMeters,,
84 
maximumElevationInMeters,maximumElevationInMeters,,
85 
verbatimElevation,verbatimElevation,,
86 
previousIdentifications,previousIdentifications,,
87 
disposition,disposition,,
88 
genericcolumn1,*genericcolumn1,,
89 
genericcolumn2,*genericcolumn2,,
90 
modified,modified,,
91 
language,language,,
92 
duplicateid,*duplicateid,,
93 
observeruid,*observeruid,,
94 
processingstatus,*processingstatus,,
95 
deaccessioned,*deaccessioned,,
96 
recordEnteredBy,*recordEnteredBy,,
97 
duplicateQuantity,*duplicateQuantity,,
98 
labelProject,*labelProject,,
99 
dateLastModified,modified,,
inputs/ARIZ/omoccurrences/VegBIEN.csv
1 
ARIZ,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
2 
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists",
3 
occid,"/_if[@name=""if specimen""]/cond/_exists/_first/1",
4 
occurrenceID,"/_if[@name=""if specimen""]/cond/_exists/_first/2",Not populated for all rows
5 
occid,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1/_first/1",
6 
occurrenceID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/1/_first/2",Not populated for all rows
7 
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists",
8 
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists",
9 
occid,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_first/1",
10 
occurrenceID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists/_first/2",Not populated for all rows
11 
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else",
12 
verbatimElevation,"/location/elevation_m/_alt/1/_units:[to=m,to=]/value",
13 
maximumElevationInMeters,/location/elevation_m/_alt/2/_avg/max,
14 
minimumElevationInMeters,/location/elevation_m/_alt/2/_avg/min,
15 
recordNumber,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
16 
occid,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/1",
17 
occurrenceID,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/2",Not populated for all rows
18 
cultivationStatus,"/location/iscultivated/_or/1/_if[@name=""if TaxonOccurrence""]/else/_alt/2",
19 
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
20 
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
21 
samplingProtocol,/location/locationevent/*_id/method/name,
22 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/cond/_exists",
23 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsenddate/_alt/2/_dateRangeEnd/value",
24 
eventDate,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value",
25 
eventDate,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value,
26 
eventDate,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value,
27 
dateIdentified,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/determinationdate/_alt/1/_dateRangeStart/value",
28 
taxonRemarks,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/notes",
29 
identificationQualifier,"/location/locationevent/taxonoccurrence/_if[@name=""if has accepted name""]/then/taxondetermination:[determinationtype=accepted]/taxonfit",
30 
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,
31 
recordNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/authorplantcode/_first/2,
32 
sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections"
33 
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else",
34 
recordNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/else",
35 
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
36 
occid,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_first/1",
37 
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_first/2",Not populated for all rows
38 
occid,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode/_first/1,
39 
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode/_first/2,Not populated for all rows
40 
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
41 
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
42 
recordedBy,/location/locationevent/taxonoccurrence/collector_id/party/fullname,
43 
recordNumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
44 
occid,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/1",
45 
occurrenceID,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists/_first/2",Not populated for all rows
46 
cultivationStatus,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/then/_alt/2",
47 
occid,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3/_first/1,
48 
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_first/3/_first/2,Not populated for all rows
49 
identifiedBy,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/party/fullname,
50 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/_if[@name=""if has explicit parent""]/else/rank",
51 
specificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=species]/taxonepithet",
52 
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=genus]/taxonepithet",
53 
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=family]/taxonepithet",
54 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/taxonepithet,
55 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/rank,
56 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonepithet/_if[@name=""if taxonomic name is epithet""]/cond/_alt:[2=true]/1/_taxonomic_name_is_epithet/rank",
57 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
58 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
59 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2,
60 
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/3/_join_words/1,
61 
infraspecificEpithet,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/cond",
62 
taxonRank,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/1/_if[@name=""if has infraspecificEpithet""]/then",
63 
infraspecificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/5/_join_words/2,
64 
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/2,
65 
scientificNameAuthorship,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/author,
66 
family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
67 
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,
68 
specificEpithet,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/specific_epithet,
69 
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
70 
taxonRank,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/verbatimrank,
71 
dateIdentified,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
72 
taxonRemarks,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/notes,
73 
identificationQualifier,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/taxonfit,
74 
catalogNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then",
75 
recordNumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/collectionnumber/_if[@name=""if indirect voucher""]/then",
76 
locality,/location/locationnarrative/_merge/1,
77 
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
78 
coordinateUncertaintyInMeters,/location/locationplace/*_id/place/*_id/coordinates/coordsaccuracy_m/_noCV/value,
79 
footprintWKT,/location/locationplace/*_id/place/*_id/coordinates/footprintgeometry_dwc,
80 
decimalLatitude,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_nullIf:[null=0,type=float]/value",
81 
decimalLongitude,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_nullIf:[null=0,type=float]/value",
82 
verbatimCoordinates,/location/locationplace/*_id/place/*_id/coordinates/verbatimcoordinates,
83 
country,/location/locationplace/*_id/place/country,
84 
county,/location/locationplace/*_id/place/county,
85 
decimalLatitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
86 
decimalLongitude,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings"
87 
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
88 
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
89 
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
90 
stateProvince,/location/locationplace/*_id/place/stateprovince,
91 
locationRemarks,/location/notespublic,
92 
verbatimElevation,/location/verbatimelevation,
93 
associatedCollectors,,** No join mapping for *associatedCollectors **
94 
associatedOccurrences,,** No join mapping for associatedOccurrences **
95 
associatedTaxa,,** No join mapping for associatedTaxa **
96 
attributes,,** No join mapping for *attributes **
97 
basisOfRecord,,** No join mapping for basisOfRecord **
98 
collectionCode,,** No non-empty join mapping for UNUSED **
99 
collectionID,,** No non-empty join mapping for UNUSED **
100 
collid,,** No join mapping for *collid **
101 
coordinatePrecision,,** No join mapping for *coordinatePrecision **
102 
dataGeneralizations,,** No join mapping for dataGeneralizations **
103 
datasetID,,** No non-empty join mapping for UNUSED **
104 
dateLastModified,,** No join mapping for modified **
105 
day,,** No join mapping for day **
106 
dbpk,,** No join mapping for *dbpk ** Only populated for 2651 rows
107 
deaccessioned,,** No join mapping for *deaccessioned **
108 
disposition,,** No join mapping for disposition **
109 
duplicateQuantity,,** No join mapping for *duplicateQuantity **
110 
duplicateid,,** No join mapping for *duplicateid **
111 
dynamicProperties,,** No join mapping for dynamicProperties **
112 
endDayOfYear,,** No join mapping for endDayOfYear **
113 
establishmentMeans,,"** No non-empty join mapping for OMIT ** Only populated for 1 row, which also has cultivationStatus"
114 
fieldNotes,,** No non-empty join mapping for UNUSED **
115 
fieldnumber,,** No non-empty join mapping for UNUSED **
116 
genericcolumn1,,** No join mapping for *genericcolumn1 **
117 
genericcolumn2,,** No join mapping for *genericcolumn2 **
118 
geodeticDatum,,** No join mapping for geodeticDatum **
119 
georeferenceProtocol,,** No join mapping for georeferenceProtocol **
120 
georeferenceRemarks,,** No join mapping for georeferenceRemarks **
121 
georeferenceSources,,** No join mapping for georeferenceSources **
122 
georeferenceVerificationStatus,,** No join mapping for georeferenceVerificationStatus **
123 
georeferencedBy,,** No join mapping for georeferencedBy **
124 
identificationReferences,,** No join mapping for identificationReferences **
125 
identificationRemarks,,** No join mapping for identificationRemarks **
126 
informationWithheld,,** No join mapping for informationWithheld **
127 
institutionCode,,** No non-empty join mapping for UNUSED **
128 
institutionID,,** No non-empty join mapping for UNUSED **
129 
labelProject,,** No join mapping for *labelProject **
130 
language,,** No join mapping for language **
131 
lifeStage,,** No join mapping for lifeStage **
132 
localitySecurity,,** No join mapping for *localitySecurity **
133 
localitySecurityReason,,** No join mapping for *localitySecurityReason **
134 
modified,,** No join mapping for modified **
135 
month,,** No join mapping for month **
136 
municipality,,** No join mapping for municipality **
137 
observeruid,,** No join mapping for *observeruid **
138 
occurrenceRemarks,,** No join mapping for occurrenceRemarks **
139 
otherCatalogNumbers,,** No join mapping for otherCatalogNumbers **
140 
ownerInstitutionCode,,** No join mapping for ownerInstitutionCode ** Only populated for 547 rows
141 
preparations,,** No join mapping for preparations **
142 
previousIdentifications,,** No join mapping for previousIdentifications **
143 
processingstatus,,** No join mapping for *processingstatus **
144 
recordEnteredBy,,** No join mapping for *recordEnteredBy **
145 
recordedById,,** No join mapping for *recordedById **
146 
reproductiveCondition,,** No join mapping for reproductiveCondition **
147 
sciname,,** No join mapping for *sciname **
148 
startDayOfYear,,** No join mapping for startDayOfYear **
149 
substrate,,** No join mapping for *substrate **
150 
tidinterpreted,,** No join mapping for *tidinterpreted **
151 
typeStatus,,** No join mapping for typeStatus **
152 
verbatimAttributes,,** No join mapping for *verbatimAttributes **
153 
verbatimCoordinateSystem,,** No join mapping for verbatimCoordinateSystem **
154 
verbatimEventDate,,** No join mapping for verbatimEventDate **
155 
year,,** No join mapping for year **
inputs/ARIZ/omoccurrences/test.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <_setDefault id="-1">
4 
        <source_id><source><shortname>ARIZ</shortname></source></source_id>
5 
        <path>
6 
            <_simplifyPath>
7 
                <next>parent_id</next>
8 
                <path>
9 
                    <location>
10 
                        <authorlocationcode>
11 
                            <_alt>
12 
                                <1>$occid</1>
13 
                                <2>$catalogNumber</2>
14 
                            </_alt>
15 
                        </authorlocationcode>
16 
                        <elevation_m>
17 
                            <_alt>
18 
                                <1>
19 
                                    <_units>
20 
                                        <to>m</to>
21 
                                        <to></to>
22 
                                        <value>$verbatimElevation</value>
23 
                                    </_units>
24 
                                </1>
25 
                                <2>
26 
                                    <_avg>
27 
                                        <max>$maximumElevationInMeters</max>
28 
                                        <min>$minimumElevationInMeters</min>
29 
                                    </_avg>
30 
                                </2>
31 
                            </_alt>
32 
                        </elevation_m>
33 
                        <iscultivated>
34 
                            <_locationnarrative_is_cultivated>
35 
                                <locationnarrative>
36 
                                    <_join>
37 
                                        <1>$locality</1>
38 
                                        <3>$habitat</3>
39 
                                    </_join>
40 
                                </locationnarrative>
41 
                            </_locationnarrative_is_cultivated>
42 
                        </iscultivated>
43 
                        <locationevent>
44 
                            <method_id><method><name>$samplingProtocol</name></method></method_id>
45 
                            <obsenddate><_dateRangeEnd><value>$eventDate</value></_dateRangeEnd></obsenddate>
46 
                            <obsstartdate><_dateRangeStart><value>$eventDate</value></_dateRangeStart></obsstartdate>
47 
                            <taxonoccurrence>
48 
                                <aggregateoccurrence>
49 
                                    <count>$individualCount</count>
50 
                                    <plantobservation>
51 
                                        <authorplantcode>$recordNumber</authorplantcode>
52 
                                        <definedvalue fkey="tablerecord_id">
53 
                                            <userdefined_id>
54 
                                                <userdefined>
55 
                                                    <tablename>plantobservation</tablename>
56 
                                                    <userdefinedname>sex</userdefinedname>
57 
                                                </userdefined>
58 
                                            </userdefined_id>
59 
                                            <definedvalue>$sex</definedvalue>
60 
                                        </definedvalue>
61 
                                        <specimenreplicate>
62 
                                            <catalognumber_dwc>$catalogNumber</catalognumber_dwc>
63 
                                            <collectionnumber>$recordNumber</collectionnumber>
64 
                                            <sourceaccessioncode>$occid</sourceaccessioncode>
65 
                                        </specimenreplicate>
66 
                                    </plantobservation>
67 
                                </aggregateoccurrence>
68 
                                <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
69 
                                <iscultivated>$cultivationStatus</iscultivated>
70 
                                <sourceaccessioncode>$occid</sourceaccessioncode>
71 
                                <taxondetermination>
72 
                                    <party_id><party><fullname>$identifiedBy</fullname></party></party_id>
73 
                                    <taxonverbatim_id>
74 
                                        <taxonverbatim>
75 
                                            <taxonlabel_id>
76 
                                                <taxonlabel>
77 
                                                    <parent_id>
78 
                                                        <taxonlabel>
79 
                                                            <rank>$taxonRank</rank>
80 
                                                            <parent_id>
81 
                                                                <taxonlabel>
82 
                                                                    <rank>cultivar</rank>
83 
                                                                    <parent_id>
84 
                                                                        <taxonlabel>
85 
                                                                            <rank>forma</rank>
86 
                                                                            <parent_id>
87 
                                                                                <taxonlabel>
88 
                                                                                    <rank>variety</rank>
89 
                                                                                    <parent_id>
90 
                                                                                        <taxonlabel>
91 
                                                                                            <rank>subspecies</rank>
92 
                                                                                            <parent_id>
93 
                                                                                                <taxonlabel>
94 
                                                                                                    <rank>species</rank>
95 
                                                                                                    <taxonepithet>$specificEpithet</taxonepithet>
96 
                                                                                                    <parent_id>
97 
                                                                                                        <taxonlabel>
98 
                                                                                                            <rank>genus</rank>
99 
                                                                                                            <taxonepithet>$genus</taxonepithet>
100 
                                                                                                            <parent_id>
101 
                                                                                                                <taxonlabel>
102 
                                                                                                                    <rank>family</rank>
103 
                                                                                                                    <taxonepithet>$family</taxonepithet>
104 
                                                                                                                </taxonlabel>
105 
                                                                                                            </parent_id>
106 
                                                                                                        </taxonlabel>
107 
                                                                                                    </parent_id>
108 
                                                                                                </taxonlabel>
109 
                                                                                            </parent_id>
110 
                                                                                        </taxonlabel>
111 
                                                                                    </parent_id>
112 
                                                                                </taxonlabel>
113 
                                                                            </parent_id>
114 
                                                                        </taxonlabel>
115 
                                                                    </parent_id>
116 
                                                                </taxonlabel>
117 
                                                            </parent_id>
118 
                                                            <taxonepithet>$infraspecificEpithet</taxonepithet>
119 
                                                        </taxonlabel>
120 
                                                    </parent_id>
121 
                                                    <rank>$taxonRank</rank>
122 
                                                    <taxonomicname>
123 
                                                        <_merge_prefix>
124 
                                                            <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
125 
                                                            <value>
126 
                                                                <_alt>
127 
                                                                    <1>$scientificName</1>
128 
                                                                    <2>
129 
                                                                        <_join_words>
130 
                                                                            <1>
131 
                                                                                <_join_words>
132 
                                                                                    <2>$genus</2>
133 
                                                                                    <3>$specificEpithet</3>
134 
                                                                                    <5>
135 
                                                                                        <_join_words>
136 
                                                                                            <1>
137 
                                                                                                <_if name="if has infraspecificEpithet">
138 
                                                                                                    <cond>$infraspecificEpithet</cond>
139 
                                                                                                    <then>$taxonRank</then>
140 
                                                                                                </_if>
141 
                                                                                            </1>
142 
                                                                                            <2>$infraspecificEpithet</2>
143 
                                                                                        </_join_words>
144 
                                                                                    </5>
145 
                                                                                </_join_words>
146 
                                                                            </1>
147 
                                                                            <2>$scientificNameAuthorship</2>
148 
                                                                        </_join_words>
149 
                                                                    </2>
150 
                                                                </_alt>
151 
                                                            </value>
152 
                                                        </_merge_prefix>
153 
                                                    </taxonomicname>
154 
                                                </taxonlabel>
155 
                                            </taxonlabel_id>
156 
                                            <author>$scientificNameAuthorship</author>
157 
                                            <family>$family</family>
158 
                                            <genus>$genus</genus>
159 
                                            <specific_epithet>$specificEpithet</specific_epithet>
160 
                                            <taxonomicname>$scientificName</taxonomicname>
161 
                                            <verbatimrank>$taxonRank</verbatimrank>
162 
                                        </taxonverbatim>
163 
                                    </taxonverbatim_id>
164 
                                    <determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
165 
                                    <notes>$taxonRemarks</notes>
166 
                                    <taxonfit>$identificationQualifier</taxonfit>
167 
                                </taxondetermination>
168 
                            </taxonoccurrence>
169 
                        </locationevent>
170 
                        <locationnarrative>
171 
                            <_merge>
172 
                                <1>$locality</1>
173 
                                <3>
174 
                                    <_label>
175 
                                        <label>habitat</label>
176 
                                        <value>$habitat</value>
177 
                                    </_label>
178 
                                </3>
179 
                            </_merge>
180 
                        </locationnarrative>
181 
                        <locationplace>
182 
                            <place_id>
183 
                                <place>
184 
                                    <coordinates_id>
185 
                                        <coordinates>
186 
                                            <coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m>
187 
                                            <footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
188 
                                            <latitude_deg>
189 
                                                <_nullIf>
190 
                                                    <null>0</null>
191 
                                                    <type>float</type>
192 
                                                    <value>$decimalLatitude</value>
193 
                                                </_nullIf>
194 
                                            </latitude_deg>
195 
                                            <longitude_deg>
196 
                                                <_nullIf>
197 
                                                    <null>0</null>
198 
                                                    <type>float</type>
199 
                                                    <value>$decimalLongitude</value>
200 
                                                </_nullIf>
201 
                                            </longitude_deg>
202 
                                            <verbatimcoordinates>$verbatimCoordinates</verbatimcoordinates>
203 
                                        </coordinates>
204 
                                    </coordinates_id>
205 
                                    <country>$country</country>
206 
                                    <county>$county</county>
207 
                                    <matched_place_id>
208 
                                        <place>
209 
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
210 
                                            <coordinates_id>
211 
                                                <coordinates>
212 
                                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>
213 
                                                    <latitude_deg>
214 
                                                        <_nullIf>
215 
                                                            <null>0</null>
216 
                                                            <type>float</type>
217 
                                                            <value>$decimalLatitude</value>
218 
                                                        </_nullIf>
219 
                                                    </latitude_deg>
220 
                                                    <longitude_deg>
221 
                                                        <_nullIf>
222 
                                                            <null>0</null>
223 
                                                            <type>float</type>
224 
                                                            <value>$decimalLongitude</value>
225 
                                                        </_nullIf>
226 
                                                    </longitude_deg>
227 
                                                </coordinates>
228 
                                            </coordinates_id>
229 
                                            <country>$country</country>
230 
                                            <county>$county</county>
231 
                                            <stateprovince>$stateProvince</stateprovince>
232 
                                        </place>
233 
                                    </matched_place_id>
234 
                                    <stateprovince>$stateProvince</stateprovince>
235 
                                </place>
236 
                            </place_id>
237 
                        </locationplace>
238 
                        <notespublic>$locationRemarks</notespublic>
239 
                        <verbatimelevation>$verbatimElevation</verbatimelevation>
240 
                    </location>
241 
                </path>
242 
            </_simplifyPath>
243 
        </path>
244 
    </_setDefault>
245 
</VegBIEN>
246 
Inserted 40 new rows into database
inputs/ARIZ/omoccurrences/new_terms.csv
1 
occid,occurrenceID,/_first/1,
2 
cultivationStatus,cultivated,,
inputs/ARIZ/omoccurrences/unmapped_terms.csv
1 
*collid
2 
*dbpk
3 
basisOfRecord
4 
otherCatalogNumbers
5 
ownerInstitutionCode
6 
*sciname
7 
*tidinterpreted
8 
identificationReferences
9 
identificationRemarks
10 
typeStatus
11 
*recordedById
12 
*associatedCollectors
13 
year
14 
month
15 
day
16 
startDayOfYear
17 
endDayOfYear
18 
verbatimEventDate
19 
*substrate
20 
occurrenceRemarks
21 
informationWithheld
22 
dataGeneralizations
23 
associatedOccurrences
24 
associatedTaxa
25 
dynamicProperties
26 
*verbatimAttributes
27 
*attributes
28 
reproductiveCondition
29 
lifeStage
30 
preparations
31 
municipality
32 
*localitySecurity
33 
*localitySecurityReason
34 
geodeticDatum
35 
*coordinatePrecision
36 
verbatimCoordinateSystem
37 
georeferencedBy
38 
georeferenceProtocol
39 
georeferenceSources
40 
georeferenceVerificationStatus
41 
georeferenceRemarks
42 
previousIdentifications
43 
disposition
44 
*genericcolumn1
45 
*genericcolumn2
46 
modified
47 
language
48 
*duplicateid
49 
*observeruid
50 
*processingstatus
51 
*deaccessioned
52 
*recordEnteredBy
53 
*duplicateQuantity
54 
*labelProject
55 
modified

Also available in: Unified diff