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Revision 11001

bugfix: inputs/VegBank/taxon_observation.**/: generated header.csv and related files, which were previously not generated because the error in `rm header.csv` aborted the runscript

View differences:

inputs/VegBank/taxon_observation.**/header.csv
1
row_num,locationID,eventID,aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__individual_count,diameterBreastHeight_cm,height_m,individualCount,aggregateOrganismObservationID,taxonOccurrenceID,*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,*taxonobservation_--plantconcept_reference_id,scientificName__for_nearest_taxon_concept,*taxonobservation_--plantcode,*taxonobservation_--plantdescription,*taxonobservation_--d_obscount,*taxonobservation_--d_currentaccepted,*taxonobservation_--plantconcept_accessioncode,kingdom,*taxonobservation_--Subkingdom,*taxonobservation_--Superdivision,*taxonobservation_--Division,*taxonobservation_--Subdivision,class,*taxonobservation_--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,*stemcount_--stratum_id,coverPercent,*stemcount_--basalarea,*stemcount_--biomass,*stemcount_--inferencearea,*stemcount_--stratumbase,*stemcount_--stratumheight,*stemcount_--emb_taxonimportance,*stemcount_--covercode,*stemcount_--stemdiameteraccuracy,*stemcount_--stemheightaccuracy,*stemcount_--stemtaxonarea,*stemcount_--emb_stemcount,stemID,UNUSED#stemcode,UNUSED#stemxposition,UNUSED#stemyposition,*stemlocation_--stemhealth,*stemlocation_--emb_stemlocation,*stemlocation_--stemdiameteraccuracy,*stemlocation_--stemheightaccuracy,*stemlocation_--stemtaxonarea,*stemlocation_--emb_stemcount,individualID,*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_--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
inputs/VegBank/taxon_observation.**/map.csv
1
VegBank,VegCore,Filter,Comments
2
row_num,row_num,,
3
locationID,locationID,,
4
eventID,eventID,,
5
aggregateOrganismObservationID__taxon_presence,aggregateOrganismObservationID__taxon_presence,,
6
aggregateOrganismObservationID__individual_count,aggregateOrganismObservationID__individual_count,,
7
diameterBreastHeight_cm,diameterBreastHeight_cm,,
8
height_m,height_m,,
9
individualCount,individualCount,,
10
aggregateOrganismObservationID,aggregateOrganismObservationID,,
11
taxonOccurrenceID,taxonOccurrenceID,,
12
*taxonobservation_--plantname_id,*taxonobservation_--plantname_id,,
13
*taxonobservation_--plantconcept_id,*taxonobservation_--plantconcept_id,,
14
identificationID,identificationID,,
15
*taxonobservation_--stemlocation_id,*taxonobservation_--stemlocation_id,,
16
*taxonobservation_--taxoninterpretation_plantname_id,*taxonobservation_--taxoninterpretation_plantname_id,,
17
*taxonobservation_--taxoninterpretation_party_id,*taxonobservation_--taxoninterpretation_party_id,,
18
*taxonobservation_--role_id,*taxonobservation_--role_id,,
19
identificationType,identificationType,,
20
*taxonobservation_--reference_id,*taxonobservation_--reference_id,,
21
*taxonobservation_--originalinterpretation,*taxonobservation_--originalinterpretation,,
22
*taxonobservation_--currentinterpretation,*taxonobservation_--currentinterpretation,,
23
identificationQualifier,identificationQualifier,,
24
identificationVerificationStatus,identificationVerificationStatus,,
25
UNUSED#collector_id,UNUSED#collector_id,,
26
collectorNumber,collectorNumber,,
27
*taxonobservation_--museum_id,*taxonobservation_--museum_id,,
28
accessionNumber,accessionNumber,,
29
*taxonobservation_--grouptype,*taxonobservation_--grouptype,,
30
occurrenceRemarks,occurrenceRemarks,,
31
*taxonobservation_--notespublic,*taxonobservation_--notespublic,,
32
*taxonobservation_--notesmgt,*taxonobservation_--notesmgt,,
33
*taxonobservation_--revisions,*taxonobservation_--revisions,,
34
dateIdentified,dateIdentified,,
35
dateCollected,dateCollected,,
36
*taxonobservation_--emb_taxoninterpretation,*taxonobservation_--emb_taxoninterpretation,,
37
*taxonobservation_--taxoninterpretation_accessioncode,*taxonobservation_--taxoninterpretation_accessioncode,,
38
originalScientificName,originalScientificName,,
39
*taxonobservation_--taxonobservation_reference_id,*taxonobservation_--taxonobservation_reference_id,,
40
*taxonobservation_--taxoninferencearea,*taxonobservation_--taxoninferencearea,,
41
*taxonobservation_--emb_taxonobservation,*taxonobservation_--emb_taxonobservation,,
42
*taxonobservation_--int_origplantconcept_id,*taxonobservation_--int_origplantconcept_id,,
43
EQUIV#to:authorplantname#int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,,
44
originalTaxonName,originalTaxonName,,
45
originalVernacularName,originalVernacularName,,
46
*taxonobservation_--int_origplantcode,*taxonobservation_--int_origplantcode,,
47
*taxonobservation_--int_currplantconcept_id,*taxonobservation_--int_currplantconcept_id,,
48
scientificName_verbatim,scientificName_verbatim,,
49
taxonName,taxonName,,
50
vernacularName,vernacularName,,
51
*taxonobservation_--int_currplantcode,*taxonobservation_--int_currplantcode,,
52
*taxonobservation_--taxonobservation_accessioncode,*taxonobservation_--taxonobservation_accessioncode,,
53
*taxonobservation_--plantconcept_reference_id,*taxonobservation_--plantconcept_reference_id,,
54
scientificName__for_nearest_taxon_concept,scientificName__for_nearest_taxon_concept,,
55
*taxonobservation_--plantcode,*taxonobservation_--plantcode,,
56
*taxonobservation_--plantdescription,*taxonobservation_--plantdescription,,
57
*taxonobservation_--d_obscount,*taxonobservation_--d_obscount,,
58
*taxonobservation_--d_currentaccepted,*taxonobservation_--d_currentaccepted,,
59
*taxonobservation_--plantconcept_accessioncode,*taxonobservation_--plantconcept_accessioncode,,
60
kingdom,kingdom,,
61
*taxonobservation_--Subkingdom,*taxonobservation_--Subkingdom,,
62
*taxonobservation_--Superdivision,*taxonobservation_--Superdivision,,
63
*taxonobservation_--Division,*taxonobservation_--Division,,
64
*taxonobservation_--Subdivision,*taxonobservation_--Subdivision,,
65
class,class,,
66
*taxonobservation_--Subclass,*taxonobservation_--Subclass,,
67
order,order,,
68
family,family,,
69
genus,genus,,
70
EQUIV#to:plantname#Species,EQUIV#to:plantname#Species,,
71
EQUIV#to:plantname#Subspecies,EQUIV#to:plantname#Subspecies,,
72
EQUIV#to:plantname#Variety,EQUIV#to:plantname#Variety,,
73
EQUIV#to:plantname#Forma,EQUIV#to:plantname#Forma,,
74
DUPLICATE#of:plantconcept_plantname#plantname,DUPLICATE#of:plantconcept_plantname#plantname,,
75
*taxonobservation_--plantname_reference_id,*taxonobservation_--plantname_reference_id,,
76
*taxonobservation_--dateentered,*taxonobservation_--dateentered,,
77
observationGranularity,observationGranularity,,
78
scientificName,scientificName,,
79
*stemcount_--stratum_id,*stemcount_--stratum_id,,
80
coverPercent,coverPercent,,
81
*stemcount_--basalarea,*stemcount_--basalarea,,
82
*stemcount_--biomass,*stemcount_--biomass,,
83
*stemcount_--inferencearea,*stemcount_--inferencearea,,
84
*stemcount_--stratumbase,*stemcount_--stratumbase,,
85
*stemcount_--stratumheight,*stemcount_--stratumheight,,
86
*stemcount_--emb_taxonimportance,*stemcount_--emb_taxonimportance,,
87
*stemcount_--covercode,*stemcount_--covercode,,
88
*stemcount_--stemdiameteraccuracy,*stemcount_--stemdiameteraccuracy,,
89
*stemcount_--stemheightaccuracy,*stemcount_--stemheightaccuracy,,
90
*stemcount_--stemtaxonarea,*stemcount_--stemtaxonarea,,
91
*stemcount_--emb_stemcount,*stemcount_--emb_stemcount,,
92
stemID,stemID,,
93
UNUSED#stemcode,UNUSED#stemcode,,
94
UNUSED#stemxposition,UNUSED#stemxposition,,
95
UNUSED#stemyposition,UNUSED#stemyposition,,
96
*stemlocation_--stemhealth,*stemlocation_--stemhealth,,
97
*stemlocation_--emb_stemlocation,*stemlocation_--emb_stemlocation,,
98
*stemlocation_--stemdiameteraccuracy,*stemlocation_--stemdiameteraccuracy,,
99
*stemlocation_--stemheightaccuracy,*stemlocation_--stemheightaccuracy,,
100
*stemlocation_--stemtaxonarea,*stemlocation_--stemtaxonarea,,
101
*stemlocation_--emb_stemcount,*stemlocation_--emb_stemcount,,
102
individualID,individualID,,
103
*observation_--previousobs_id,*observation_--previousobs_id,,
104
projectID,projectID,,
105
authorEventCode,authorEventCode,,
106
*observation_--dateaccuracy,*observation_--dateaccuracy,,
107
*observation_--covermethod_id,*observation_--covermethod_id,,
108
*observation_--coverdispersion,*observation_--coverdispersion,,
109
*observation_--autotaxoncover,*observation_--autotaxoncover,,
110
*observation_--stratummethod_id,*observation_--stratummethod_id,,
111
samplingProtocol,samplingProtocol,,
112
*observation_--taxonobservationarea,*observation_--taxonobservationarea,,
113
*observation_--stemsizelimit,*observation_--stemsizelimit,,
114
*observation_--stemobservationarea,*observation_--stemobservationarea,,
115
*observation_--stemsamplemethod,*observation_--stemsamplemethod,,
116
*observation_--originaldata,*observation_--originaldata,,
117
*observation_--effortlevel,*observation_--effortlevel,,
118
*observation_--plotvalidationlevel,*observation_--plotvalidationlevel,,
119
*observation_--floristicquality,*observation_--floristicquality,,
120
*observation_--bryophytequality,*observation_--bryophytequality,,
121
*observation_--lichenquality,*observation_--lichenquality,,
122
*observation_--observationnarrative,*observation_--observationnarrative,,
123
*observation_--landscapenarrative,*observation_--landscapenarrative,,
124
*observation_--homogeneity,*observation_--homogeneity,,
125
*observation_--phenologicaspect,*observation_--phenologicaspect,,
126
*observation_--representativeness,*observation_--representativeness,,
127
*observation_--standmaturity,*observation_--standmaturity,,
128
*observation_--successionalstatus,*observation_--successionalstatus,,
129
*observation_--basalarea,*observation_--basalarea,,
130
*observation_--hydrologicregime,*observation_--hydrologicregime,,
131
*observation_--soilmoistureregime,*observation_--soilmoistureregime,,
132
*observation_--soildrainage,*observation_--soildrainage,,
133
*observation_--watersalinity,*observation_--watersalinity,,
134
*observation_--waterdepth,*observation_--waterdepth,,
135
*observation_--shoredistance,*observation_--shoredistance,,
136
*observation_--soildepth,*observation_--soildepth,,
137
*observation_--organicdepth,*observation_--organicdepth,,
138
*observation_--soiltaxon_id,*observation_--soiltaxon_id,,
139
*observation_--soiltaxonsrc,*observation_--soiltaxonsrc,,
140
*observation_--percentbedrock,*observation_--percentbedrock,,
141
*observation_--percentrockgravel,*observation_--percentrockgravel,,
142
*observation_--percentwood,*observation_--percentwood,,
143
*observation_--percentlitter,*observation_--percentlitter,,
144
*observation_--percentbaresoil,*observation_--percentbaresoil,,
145
*observation_--percentwater,*observation_--percentwater,,
146
*observation_--percentother,*observation_--percentother,,
147
*observation_--nameother,*observation_--nameother,,
148
*observation_--treeht,*observation_--treeht,,
149
*observation_--shrubht,*observation_--shrubht,,
150
*observation_--fieldht,*observation_--fieldht,,
151
*observation_--nonvascularht,*observation_--nonvascularht,,
152
*observation_--submergedht,*observation_--submergedht,,
153
*observation_--treecover,*observation_--treecover,,
154
*observation_--shrubcover,*observation_--shrubcover,,
155
*observation_--fieldcover,*observation_--fieldcover,,
156
*observation_--nonvascularcover,*observation_--nonvascularcover,,
157
*observation_--floatingcover,*observation_--floatingcover,,
158
*observation_--submergedcover,*observation_--submergedcover,,
159
*observation_--dominantstratum,*observation_--dominantstratum,,
160
*observation_--growthform1type,*observation_--growthform1type,,
161
*observation_--growthform2type,*observation_--growthform2type,,
162
*observation_--growthform3type,*observation_--growthform3type,,
163
*observation_--growthform1cover,*observation_--growthform1cover,,
164
*observation_--growthform2cover,*observation_--growthform2cover,,
165
*observation_--growthform3cover,*observation_--growthform3cover,,
166
*observation_--totalcover,*observation_--totalcover,,
167
*observation_--notespublic,*observation_--notespublic,,
168
*observation_--notesmgt,*observation_--notesmgt,,
169
*observation_--revisions,*observation_--revisions,,
170
startDate,startDate,,
171
endDate,endDate,,
172
*observation_--dateentered,*observation_--dateentered,,
173
*observation_--emb_observation,*observation_--emb_observation,,
174
*observation_--interp_orig_ci_id,*observation_--interp_orig_ci_id,,
175
*observation_--interp_orig_cc_id,*observation_--interp_orig_cc_id,,
176
*observation_--interp_orig_sciname,*observation_--interp_orig_sciname,,
177
*observation_--interp_orig_code,*observation_--interp_orig_code,,
178
*observation_--interp_orig_party_id,*observation_--interp_orig_party_id,,
179
*observation_--interp_orig_partyname,*observation_--interp_orig_partyname,,
180
*observation_--interp_current_ci_id,*observation_--interp_current_ci_id,,
181
*observation_--interp_current_cc_id,*observation_--interp_current_cc_id,,
182
*observation_--interp_current_sciname,*observation_--interp_current_sciname,,
183
*observation_--interp_current_code,*observation_--interp_current_code,,
184
*observation_--interp_current_party_id,*observation_--interp_current_party_id,,
185
*observation_--interp_current_partyname,*observation_--interp_current_partyname,,
186
*observation_--interp_bestfit_ci_id,*observation_--interp_bestfit_ci_id,,
187
*observation_--interp_bestfit_cc_id,*observation_--interp_bestfit_cc_id,,
188
*observation_--interp_bestfit_sciname,*observation_--interp_bestfit_sciname,,
189
*observation_--interp_bestfit_code,*observation_--interp_bestfit_code,,
190
*observation_--interp_bestfit_party_id,*observation_--interp_bestfit_party_id,,
191
*observation_--interp_bestfit_partyname,*observation_--interp_bestfit_partyname,,
192
*observation_--toptaxon1name,*observation_--toptaxon1name,,
193
*observation_--toptaxon2name,*observation_--toptaxon2name,,
194
*observation_--toptaxon3name,*observation_--toptaxon3name,,
195
*observation_--toptaxon4name,*observation_--toptaxon4name,,
196
*observation_--toptaxon5name,*observation_--toptaxon5name,,
197
*observation_--numberoftaxa,*observation_--numberoftaxa,,
198
*observation_--accessioncode,*observation_--accessioncode,,
199
*observation_--soilobs_id,*observation_--soilobs_id,,
200
*observation_--soilhorizon,*observation_--soilhorizon,,
201
*observation_--soildepthtop,*observation_--soildepthtop,,
202
*observation_--soildepthbottom,*observation_--soildepthbottom,,
203
*observation_--soilcolor,*observation_--soilcolor,,
204
organic_percent,organic_percent,,
205
texture,texture,,
206
sand_percent,sand_percent,,
207
silt_percent,silt_percent,,
208
clay_percent,clay_percent,,
209
*observation_--soilcoarse,*observation_--soilcoarse,,
210
ph,ph,,
211
cationExchangeCapacity_cmol_kg,cationExchangeCapacity_cmol_kg,,
212
baseSaturation_percent,baseSaturation_percent,,
213
*observation_--soildescription,*observation_--soildescription,,
214
*observation_--emb_soilobs,*observation_--emb_soilobs,,
215
locationName,locationName,,
216
*plot_--reference_id,*plot_--reference_id,,
217
parentLocationID,parentLocationID,,
218
coordinateUncertaintyInMeters__from_coords,coordinateUncertaintyInMeters__from_coords,,
219
accessRights_verbatim,accessRights_verbatim,,
220
*plot_--confidentialityreason,*plot_--confidentialityreason,,
221
decimalLatitude,decimalLatitude,,
222
decimalLongitude,decimalLongitude,,
223
*plot_--authore,*plot_--authore,,
224
*plot_--authorn,*plot_--authorn,,
225
*plot_--authorzone,*plot_--authorzone,,
226
*plot_--authordatum,*plot_--authordatum,,
227
*plot_--authorlocation,*plot_--authorlocation,,
228
locality,locality,,
229
*plot_--azimuth,*plot_--azimuth,,
230
*plot_--dsgpoly,*plot_--dsgpoly,,
231
footprintWKT,footprintWKT,,
232
plotArea_m2,plotArea_m2,,
233
*plot_--standsize,*plot_--standsize,,
234
*plot_--placementmethod,*plot_--placementmethod,,
235
*plot_--permanence,*plot_--permanence,,
236
*plot_--layoutnarrative,*plot_--layoutnarrative,,
237
elevationInMeters,elevationInMeters,,
238
*plot_--elevationaccuracy,*plot_--elevationaccuracy,,
239
UNUSED#elevationrange,UNUSED#elevationrange,,
240
slopeAspect,slopeAspect,,
241
minSlopeAspect,minSlopeAspect,,
242
maxSlopeAspect,maxSlopeAspect,,
243
slopeGradient,slopeGradient,,
244
minSlopeGradient,minSlopeGradient,,
245
maxSlopeGradient,maxSlopeGradient,,
246
*plot_--topoposition,*plot_--topoposition,,
247
landform,landform,,
248
*plot_--surficialdeposits,*plot_--surficialdeposits,,
249
*plot_--rocktype,*plot_--rocktype,,
250
stateProvince,stateProvince,,
251
country,country,,
252
*plot_--submitter_surname,*plot_--submitter_surname,,
253
*plot_--submitter_givenname,*plot_--submitter_givenname,,
254
*plot_--submitter_email,*plot_--submitter_email,,
255
*plot_--notespublic,*plot_--notespublic,,
256
*plot_--notesmgt,*plot_--notesmgt,,
257
*plot_--revisions,*plot_--revisions,,
258
*plot_--dateentered,*plot_--dateentered,,
259
*plot_--emb_plot,*plot_--emb_plot,,
260
*plot_--plotrationalenarrative,*plot_--plotrationalenarrative,,
261
*plot_--accessioncode,*plot_--accessioncode,,
262
continent,continent,,
263
DUPLICATE#of:country#area|country|territory,DUPLICATE#of:country#area|country|territory,,
264
DUPLICATE#of:stateprovince#region|state|province,DUPLICATE#of:stateprovince#region|state|province,,
265
county,county,,
266
*plot_--quadrangle,*plot_--quadrangle,,
267
*plot_--Geographic Name,*plot_--Geographic Name,,
268
accessRights,accessRights,,
269
coordinateUncertaintyInMeters__from_fuzzing,coordinateUncertaintyInMeters__from_fuzzing,,
270
coordinateUncertaintyInMeters,coordinateUncertaintyInMeters,,
inputs/VegBank/taxon_observation.**/VegBIEN.csv
1
link ../../../mappings/VegCore-VegBIEN.csv
0 2

  
inputs/VegBank/taxon_observation.**/test.xml.ref
1
Put template:
2
<VegBIEN>
3
    <_setDefault id="-1">
4
        <source_id><source><shortname>VegBank.new</shortname></source></source_id>
5
        <path>
6
            <_simplifyPath>
7
                <next>parent_id</next>
8
                <path>
9
                    <location>
10
                        <authorlocationcode>$locationName</authorlocationcode>
11
                        <sourceaccessioncode>$locationID</sourceaccessioncode>
12
                        <accesslevel>$accessRights</accesslevel>
13
                        <area_m2>$plotArea_m2</area_m2>
14
                        <elevation_m>$elevationInMeters</elevation_m>
15
                        <iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
16
                        <landform>$landform</landform>
17
                        <locationevent>
18
                            <method_id><method><name>$samplingProtocol</name></method></method_id>
19
                            <project_id><project><sourceaccessioncode>$projectID</sourceaccessioncode></project></project_id>
20
                            <authoreventcode>$authorEventCode</authoreventcode>
21
                            <sourceaccessioncode>$eventID</sourceaccessioncode>
22
                            <obsenddate>$endDate</obsenddate>
23
                            <obsstartdate>$startDate</obsstartdate>
24
                            <soilsample>
25
                                <basesaturation_fraction><_percent_to_fraction><value>$baseSaturation_percent</value></_percent_to_fraction></basesaturation_fraction>
26
                                <cationexchangecapacity_cmol_kg>$cationExchangeCapacity_cmol_kg</cationexchangecapacity_cmol_kg>
27
                                <clay_fraction><_percent_to_fraction><value>$clay_percent</value></_percent_to_fraction></clay_fraction>
28
                                <organic_fraction><_percent_to_fraction><value>$organic_percent</value></_percent_to_fraction></organic_fraction>
29
                                <ph>$ph</ph>
30
                                <sand_fraction><_percent_to_fraction><value>$sand_percent</value></_percent_to_fraction></sand_fraction>
31
                                <silt_fraction><_percent_to_fraction><value>$silt_percent</value></_percent_to_fraction></silt_fraction>
32
                                <texture>$texture</texture>
33
                            </soilsample>
34
                            <taxonoccurrence>
35
                                <aggregateoccurrence>
36
                                    <collectiondate>$dateCollected</collectiondate>
37
                                    <count>$individualCount</count>
38
                                    <cover_fraction><_percent_to_fraction><value>$coverPercent</value></_percent_to_fraction></cover_fraction>
39
                                    <notes>$occurrenceRemarks</notes>
40
                                    <plantobservation>
41
                                        <authorplantcode>$collectorNumber</authorplantcode>
42
                                        <sourceaccessioncode>$individualID</sourceaccessioncode>
43
                                        <specimenreplicate>
44
                                            <catalognumber_dwc>$accessionNumber</catalognumber_dwc>
45
                                            <collectionnumber>$collectorNumber</collectionnumber>
46
                                        </specimenreplicate>
47
                                        <stemobservation>
48
                                            <diameterbreastheight_m><_cm_to_m><value>$diameterBreastHeight_cm</value></_cm_to_m></diameterbreastheight_m>
49
                                            <height_m>$height_m</height_m>
50
                                            <sourceaccessioncode>$stemID</sourceaccessioncode>
51
                                        </stemobservation>
52
                                    </plantobservation>
53
                                    <sourceaccessioncode>$aggregateOrganismObservationID</sourceaccessioncode>
54
                                </aggregateoccurrence>
55
                                <authortaxoncode>$collectorNumber</authortaxoncode>
56
                                <sourceaccessioncode>$taxonOccurrenceID</sourceaccessioncode>
57
                                <taxondetermination>
58
                                    <taxonverbatim_id>
59
                                        <taxonverbatim>
60
                                            <taxonlabel_id>
61
                                                <taxonlabel>
62
                                                    <parent_id>
63
                                                        <taxonlabel>
64
                                                            <parent_id>
65
                                                                <taxonlabel>
66
                                                                    <rank>cultivar</rank>
67
                                                                    <parent_id>
68
                                                                        <taxonlabel>
69
                                                                            <rank>forma</rank>
70
                                                                            <parent_id>
71
                                                                                <taxonlabel>
72
                                                                                    <rank>variety</rank>
73
                                                                                    <parent_id>
74
                                                                                        <taxonlabel>
75
                                                                                            <rank>subspecies</rank>
76
                                                                                            <parent_id>
77
                                                                                                <taxonlabel>
78
                                                                                                    <rank>species</rank>
79
                                                                                                    <parent_id>
80
                                                                                                        <taxonlabel>
81
                                                                                                            <rank>genus</rank>
82
                                                                                                            <taxonepithet>$genus</taxonepithet>
83
                                                                                                            <parent_id>
84
                                                                                                                <taxonlabel>
85
                                                                                                                    <rank>family</rank>
86
                                                                                                                    <taxonepithet>$family</taxonepithet>
87
                                                                                                                    <parent_id>
88
                                                                                                                        <taxonlabel>
89
                                                                                                                            <rank>order</rank>
90
                                                                                                                            <taxonepithet>$order</taxonepithet>
91
                                                                                                                            <parent_id>
92
                                                                                                                                <taxonlabel>
93
                                                                                                                                    <rank>class</rank>
94
                                                                                                                                    <taxonepithet>$class</taxonepithet>
95
                                                                                                                                    <parent_id>
96
                                                                                                                                        <taxonlabel>
97
                                                                                                                                            <rank>phylum</rank>
98
                                                                                                                                            <parent_id>
99
                                                                                                                                                <taxonlabel>
100
                                                                                                                                                    <rank>kingdom</rank>
101
                                                                                                                                                    <taxonepithet>$kingdom</taxonepithet>
102
                                                                                                                                                </taxonlabel>
103
                                                                                                                                            </parent_id>
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
                                                                                </taxonlabel>
119
                                                                            </parent_id>
120
                                                                        </taxonlabel>
121
                                                                    </parent_id>
122
                                                                </taxonlabel>
123
                                                            </parent_id>
124
                                                        </taxonlabel>
125
                                                    </parent_id>
126
                                                    <taxonomicname>
127
                                                        <_merge_prefix>
128
                                                            <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
129
                                                            <value>
130
                                                                <_alt>
131
                                                                    <1>$scientificName</1>
132
                                                                    <2>
133
                                                                        <_alt>
134
                                                                            <1>$taxonName</1>
135
                                                                            <2><_filter_genus><value>$genus</value></_filter_genus></2>
136
                                                                        </_alt>
137
                                                                    </2>
138
                                                                </_alt>
139
                                                            </value>
140
                                                        </_merge_prefix>
141
                                                    </taxonomicname>
142
                                                </taxonlabel>
143
                                            </taxonlabel_id>
144
                                            <family>$family</family>
145
                                            <genus>$genus</genus>
146
                                            <taxonname>$taxonName</taxonname>
147
                                            <taxonomicname>$scientificName</taxonomicname>
148
                                        </taxonverbatim>
149
                                    </taxonverbatim_id>
150
                                    <determinationdate><_dateRangeStart><value>$dateIdentified</value></_dateRangeStart></determinationdate>
151
                                    <determinationtype>$identificationType</determinationtype>
152
                                    <taxonfit>$identificationQualifier</taxonfit>
153
                                </taxondetermination>
154
                                <taxondetermination>
155
                                    <isoriginal>true</isoriginal>
156
                                    <taxonverbatim_id>
157
                                        <taxonverbatim>
158
                                            <taxonname>$originalTaxonName</taxonname>
159
                                            <taxonomicname>$originalScientificName</taxonomicname>
160
                                        </taxonverbatim>
161
                                    </taxonverbatim_id>
162
                                </taxondetermination>
163
                            </taxonoccurrence>
164
                        </locationevent>
165
                        <locationnarrative>$locality</locationnarrative>
166
                        <locationplace>
167
                            <place_id>
168
                                <place>
169
                                    <coordinates_id>
170
                                        <coordinates>
171
                                            <coordsaccuracy_m><_noCV><value>$coordinateUncertaintyInMeters</value></_noCV></coordsaccuracy_m>
172
                                            <footprintgeometry_dwc>$footprintWKT</footprintgeometry_dwc>
173
                                            <latitude_deg>
174
                                                <_nullIf>
175
                                                    <null>0</null>
176
                                                    <type>float</type>
177
                                                    <value>$decimalLatitude</value>
178
                                                </_nullIf>
179
                                            </latitude_deg>
180
                                            <longitude_deg>
181
                                                <_nullIf>
182
                                                    <null>0</null>
183
                                                    <type>float</type>
184
                                                    <value>$decimalLongitude</value>
185
                                                </_nullIf>
186
                                            </longitude_deg>
187
                                        </coordinates>
188
                                    </coordinates_id>
189
                                    <continent>$continent</continent>
190
                                    <country>$country</country>
191
                                    <county>$county</county>
192
                                    <matched_place_id>
193
                                        <place>
194
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
195
                                            <coordinates_id>
196
                                                <coordinates>
197
                                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>
198
                                                    <latitude_deg>
199
                                                        <_nullIf>
200
                                                            <null>0</null>
201
                                                            <type>float</type>
202
                                                            <value>$decimalLatitude</value>
203
                                                        </_nullIf>
204
                                                    </latitude_deg>
205
                                                    <longitude_deg>
206
                                                        <_nullIf>
207
                                                            <null>0</null>
208
                                                            <type>float</type>
209
                                                            <value>$decimalLongitude</value>
210
                                                        </_nullIf>
211
                                                    </longitude_deg>
212
                                                </coordinates>
213
                                            </coordinates_id>
214
                                            <country>$country</country>
215
                                            <county>$county</county>
216
                                            <stateprovince>$stateProvince</stateprovince>
217
                                        </place>
218
                                    </matched_place_id>
219
                                    <stateprovince>$stateProvince</stateprovince>
220
                                </place>
221
                            </place_id>
222
                        </locationplace>
223
                        <parent_id><location><sourceaccessioncode>$parentLocationID</sourceaccessioncode></location></parent_id>
224
                        <slopeaspect_deg>
225
                            <_alt>
226
                                <1><_compass><value>$slopeAspect</value></_compass></1>
227
                                <2>
228
                                    <_avg>
229
                                        <1>$minSlopeAspect</1>
230
                                        <2>$maxSlopeAspect</2>
231
                                    </_avg>
232
                                </2>
233
                            </_alt>
234
                        </slopeaspect_deg>
235
                        <slopegradient_fraction>
236
                            <_alt>
237
                                <1>$slopeGradient</1>
238
                                <2>
239
                                    <_avg>
240
                                        <1>$minSlopeGradient</1>
241
                                        <2>$maxSlopeGradient</2>
242
                                    </_avg>
243
                                </2>
244
                            </_alt>
245
                        </slopegradient_fraction>
246
                    </location>
247
                </path>
248
            </_simplifyPath>
249
        </path>
250
    </_setDefault>
251
</VegBIEN>
252
Inserted 21 new rows into database
inputs/VegBank/taxon_observation.**/unmapped_terms.csv
1
row_num
2
aggregateOrganismObservationID__taxon_presence
3
aggregateOrganismObservationID__individual_count
4
*taxonobservation_--plantname_id
5
*taxonobservation_--plantconcept_id
6
identificationID
7
*taxonobservation_--stemlocation_id
8
*taxonobservation_--taxoninterpretation_plantname_id
9
*taxonobservation_--taxoninterpretation_party_id
10
*taxonobservation_--role_id
11
*taxonobservation_--reference_id
12
*taxonobservation_--originalinterpretation
13
*taxonobservation_--currentinterpretation
14
identificationVerificationStatus
15
*taxonobservation_--museum_id
16
*taxonobservation_--grouptype
17
*taxonobservation_--notespublic
18
*taxonobservation_--notesmgt
19
*taxonobservation_--revisions
20
*taxonobservation_--emb_taxoninterpretation
21
*taxonobservation_--taxoninterpretation_accessioncode
22
*taxonobservation_--taxonobservation_reference_id
23
*taxonobservation_--taxoninferencearea
24
*taxonobservation_--emb_taxonobservation
25
*taxonobservation_--int_origplantconcept_id
26
originalVernacularName
27
*taxonobservation_--int_origplantcode
28
*taxonobservation_--int_currplantconcept_id
29
scientificName_verbatim
30
vernacularName
31
*taxonobservation_--int_currplantcode
32
*taxonobservation_--taxonobservation_accessioncode
33
*taxonobservation_--plantconcept_reference_id
34
scientificName__for_nearest_taxon_concept
35
*taxonobservation_--plantcode
36
*taxonobservation_--plantdescription
37
*taxonobservation_--d_obscount
38
*taxonobservation_--d_currentaccepted
39
*taxonobservation_--plantconcept_accessioncode
40
*taxonobservation_--Subkingdom
41
*taxonobservation_--Superdivision
42
*taxonobservation_--Division
43
*taxonobservation_--Subdivision
44
*taxonobservation_--Subclass
45
*taxonobservation_--plantname_reference_id
46
*taxonobservation_--dateentered
47
*stemcount_--stratum_id
48
*stemcount_--basalarea
49
*stemcount_--biomass
50
*stemcount_--inferencearea
51
*stemcount_--stratumbase
52
*stemcount_--stratumheight
53
*stemcount_--emb_taxonimportance
54
*stemcount_--covercode
55
*stemcount_--stemdiameteraccuracy
56
*stemcount_--stemheightaccuracy
57
*stemcount_--stemtaxonarea
58
*stemcount_--emb_stemcount
59
*stemlocation_--stemhealth
60
*stemlocation_--emb_stemlocation
61
*stemlocation_--stemdiameteraccuracy
62
*stemlocation_--stemheightaccuracy
63
*stemlocation_--stemtaxonarea
64
*stemlocation_--emb_stemcount
65
*observation_--previousobs_id
66
*observation_--dateaccuracy
67
*observation_--covermethod_id
68
*observation_--coverdispersion
69
*observation_--autotaxoncover
70
*observation_--stratummethod_id
71
*observation_--taxonobservationarea
72
*observation_--stemsizelimit
73
*observation_--stemobservationarea
74
*observation_--stemsamplemethod
75
*observation_--originaldata
76
*observation_--effortlevel
77
*observation_--plotvalidationlevel
78
*observation_--floristicquality
79
*observation_--bryophytequality
80
*observation_--lichenquality
81
*observation_--observationnarrative
82
*observation_--landscapenarrative
83
*observation_--homogeneity
84
*observation_--phenologicaspect
85
*observation_--representativeness
86
*observation_--standmaturity
87
*observation_--successionalstatus
88
*observation_--basalarea
89
*observation_--hydrologicregime
90
*observation_--soilmoistureregime
91
*observation_--soildrainage
92
*observation_--watersalinity
93
*observation_--waterdepth
94
*observation_--shoredistance
95
*observation_--soildepth
96
*observation_--organicdepth
97
*observation_--soiltaxon_id
98
*observation_--soiltaxonsrc
99
*observation_--percentbedrock
100
*observation_--percentrockgravel
101
*observation_--percentwood
102
*observation_--percentlitter
103
*observation_--percentbaresoil
104
*observation_--percentwater
105
*observation_--percentother
106
*observation_--nameother
107
*observation_--treeht
108
*observation_--shrubht
109
*observation_--fieldht
110
*observation_--nonvascularht
111
*observation_--submergedht
112
*observation_--treecover
113
*observation_--shrubcover
114
*observation_--fieldcover
115
*observation_--nonvascularcover
116
*observation_--floatingcover
117
*observation_--submergedcover
118
*observation_--dominantstratum
119
*observation_--growthform1type
120
*observation_--growthform2type
121
*observation_--growthform3type
122
*observation_--growthform1cover
123
*observation_--growthform2cover
124
*observation_--growthform3cover
125
*observation_--totalcover
126
*observation_--notespublic
127
*observation_--notesmgt
128
*observation_--revisions
129
*observation_--dateentered
130
*observation_--emb_observation
131
*observation_--interp_orig_ci_id
132
*observation_--interp_orig_cc_id
133
*observation_--interp_orig_sciname
134
*observation_--interp_orig_code
135
*observation_--interp_orig_party_id
136
*observation_--interp_orig_partyname
137
*observation_--interp_current_ci_id
138
*observation_--interp_current_cc_id
139
*observation_--interp_current_sciname
140
*observation_--interp_current_code
141
*observation_--interp_current_party_id
142
*observation_--interp_current_partyname
143
*observation_--interp_bestfit_ci_id
144
*observation_--interp_bestfit_cc_id
145
*observation_--interp_bestfit_sciname
146
*observation_--interp_bestfit_code
147
*observation_--interp_bestfit_party_id
148
*observation_--interp_bestfit_partyname
149
*observation_--toptaxon1name
150
*observation_--toptaxon2name
151
*observation_--toptaxon3name
152
*observation_--toptaxon4name
153
*observation_--toptaxon5name
154
*observation_--numberoftaxa
155
*observation_--accessioncode
156
*observation_--soilobs_id
157
*observation_--soilhorizon
158
*observation_--soildepthtop
159
*observation_--soildepthbottom
160
*observation_--soilcolor
161
*observation_--soilcoarse
162
*observation_--soildescription
163
*observation_--emb_soilobs
164
*plot_--reference_id
165
coordinateUncertaintyInMeters__from_coords
166
accessRights_verbatim
167
*plot_--confidentialityreason
168
*plot_--authore
169
*plot_--authorn
170
*plot_--authorzone
171
*plot_--authordatum
172
*plot_--authorlocation
173
*plot_--azimuth
174
*plot_--dsgpoly
175
*plot_--standsize
176
*plot_--placementmethod
177
*plot_--permanence
178
*plot_--layoutnarrative
179
*plot_--elevationaccuracy
180
*plot_--topoposition
181
*plot_--surficialdeposits
182
*plot_--rocktype
183
*plot_--submitter_surname
184
*plot_--submitter_givenname
185
*plot_--submitter_email
186
*plot_--notespublic
187
*plot_--notesmgt
188
*plot_--revisions
189
*plot_--dateentered
190
*plot_--emb_plot
191
*plot_--plotrationalenarrative
192
*plot_--accessioncode
193
*plot_--quadrangle
194
*plot_--Geographic Name
195
coordinateUncertaintyInMeters__from_fuzzing

Also available in: Unified diff