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Revision 4109

Added by Aaron Marcuse-Kubitza over 12 years ago

inputs: Renamed organisms table to 1.organisms so import order would be inherent in the dir name, using steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Rename-subfolders-with-import-order>

View differences:

inputs/Madidi/test/import.organisms.xml.ref
1 
Put template:
2 
<VegBIEN/>Inserted 1 new rows into database
inputs/Madidi/maps/Veg+.organisms.full.csv
1 
Madidi,Veg+,Comments
2 
Autor (revised),,
3 
Basal area,,
4 
Bole height,,
5 
Circumference,,
6 
Common name,,
7 
Crown position,,
8 
Crown shape,,
9 
Determined by,,
10 
Diameter,,
11 
Expedition,,
12 
Expedition specimen,,
13 
Family (revised),,
14 
Field family,,
15 
Field name,,
16 
Genera,,
17 
Habit,,
18 
Index collector,,
19 
Inventory code,,
20 
Inventory name,,
21 
Liana presence,,
22 
Number of inventory (expedition),,
23 
Number of inventory (general),,
24 
Number of subplot,,
25 
Observations,,
26 
Phenology,,
27 
Plot X,,
28 
Plot Y,,
29 
Plot specimen,,
30 
Project specimen,,
31 
Qualifier,,
32 
Similar specimen,,
33 
Specie+autor,,
34 
Species and morphotypes,,
35 
Specific epithet,,
36 
Specimen,,
37 
Subplot X,,
38 
Subplot Y,,
39 
Tag number,,
40 
Total height,,
41 
Tree number,,
42 
Trunk,,
43 
"Type Inventory (C, PP, TP)",,
inputs/Madidi/maps/Veg+.organisms.csv
1 
Madidi,Veg+,Comments
2 
Expedition,,
3 
Inventory name,,
4 
Number of inventory (general),,
5 
Number of inventory (expedition),,
6 
"Type Inventory (C, PP, TP)",,
7 
Inventory code,,
8 
Tag number,,
9 
Tree number,,
10 
Number of subplot,,
11 
Index collector,,
12 
Specimen,,
13 
Similar specimen,,
14 
Plot specimen,,
15 
Expedition specimen,,
16 
Project specimen,,
17 
Field family,,
18 
Field name,,
19 
Family (revised),,
20 
Specie+autor,,
21 
Genera,,
22 
Specific epithet,,
23 
Species and morphotypes,,
24 
Autor (revised),,
25 
Determined by,,
26 
Qualifier,,
27 
Common name,,
28 
Circumference,,
29 
Diameter,,
30 
Trunk,,
31 
Total height,,
32 
Bole height,,
33 
Habit,,
34 
Phenology,,
35 
Crown position,,
36 
Crown shape,,
37 
Liana presence,,
38 
Basal area,,
39 
Subplot X,,
40 
Subplot Y,,
41 
Plot X,,
42 
Plot Y,,
43 
Observations,,
inputs/Madidi/maps/src.organisms.csv
1 
Madidi,Veg+,Comments
2 
Expedition,,
3 
Inventory name,,
4 
Number of inventory (general),,
5 
Number of inventory (expedition),,
6 
"Type Inventory (C, PP, TP)",,
7 
Inventory code,,
8 
Tag number,,
9 
Tree number,,
10 
Number of subplot,,
11 
Index collector,,
12 
Specimen,,
13 
Similar specimen,,
14 
Plot specimen,,
15 
Expedition specimen,,
16 
Project specimen,,
17 
Field family,,
18 
Field name,,
19 
Family (revised),,
20 
Specie+autor,,
21 
Genera,,
22 
Specific epithet,,
23 
Species and morphotypes,,
24 
Autor (revised),,
25 
Determined by,,
26 
Qualifier,,
27 
Common name,,
28 
Circumference,,
29 
Diameter,,
30 
Trunk,,
31 
Total height,,
32 
Bole height,,
33 
Habit,,
34 
Phenology,,
35 
Crown position,,
36 
Crown shape,,
37 
Liana presence,,
38 
Basal area,,
39 
Subplot X,,
40 
Subplot Y,,
41 
Plot X,,
42 
Plot Y,,
43 
Observations,,
inputs/Madidi/maps/VegBIEN.organisms.csv
1 
Madidi,VegBIEN:,Comments
2 
Autor (revised),,** No input mapping for Autor (revised) **
3 
Basal area,,** No input mapping for Basal area **
4 
Bole height,,** No input mapping for Bole height **
5 
Circumference,,** No input mapping for Circumference **
6 
Common name,,** No input mapping for Common name **
7 
Crown position,,** No input mapping for Crown position **
8 
Crown shape,,** No input mapping for Crown shape **
9 
Determined by,,** No input mapping for Determined by **
10 
Diameter,,** No input mapping for Diameter **
11 
Expedition,,** No input mapping for Expedition **
12 
Expedition specimen,,** No input mapping for Expedition specimen **
13 
Family (revised),,** No input mapping for Family (revised) **
14 
Field family,,** No input mapping for Field family **
15 
Field name,,** No input mapping for Field name **
16 
Genera,,** No input mapping for Genera **
17 
Habit,,** No input mapping for Habit **
18 
Index collector,,** No input mapping for Index collector **
19 
Inventory code,,** No input mapping for Inventory code **
20 
Inventory name,,** No input mapping for Inventory name **
21 
Liana presence,,** No input mapping for Liana presence **
22 
Number of inventory (expedition),,** No input mapping for Number of inventory (expedition) **
23 
Number of inventory (general),,** No input mapping for Number of inventory (general) **
24 
Number of subplot,,** No input mapping for Number of subplot **
25 
Observations,,** No input mapping for Observations **
26 
Phenology,,** No input mapping for Phenology **
27 
Plot X,,** No input mapping for Plot X **
28 
Plot Y,,** No input mapping for Plot Y **
29 
Plot specimen,,** No input mapping for Plot specimen **
30 
Project specimen,,** No input mapping for Project specimen **
31 
Qualifier,,** No input mapping for Qualifier **
32 
Similar specimen,,** No input mapping for Similar specimen **
33 
Specie+autor,,** No input mapping for Specie+autor **
34 
Species and morphotypes,,** No input mapping for Species and morphotypes **
35 
Specific epithet,,** No input mapping for Specific epithet **
36 
Specimen,,** No input mapping for Specimen **
37 
Subplot X,,** No input mapping for Subplot X **
38 
Subplot Y,,** No input mapping for Subplot Y **
39 
Tag number,,** No input mapping for Tag number **
40 
Total height,,** No input mapping for Total height **
41 
Tree number,,** No input mapping for Tree number **
42 
Trunk,,** No input mapping for Trunk **
43 
"Type Inventory (C, PP, TP)",,"** No input mapping for Type Inventory (C, PP, TP) ** "
inputs/CVS/test/import.organisms.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <authorlocationcode>$authorObsCode</authorlocationcode>
5 
        <locationdetermination>
6 
            <coordsaccuracy><_noCV><value>$locationAccuracy-m</value></_noCV></coordsaccuracy>
7 
            <latitude>
8 
                <_nullIf>
9 
                    <null>0</null>
10 
                    <type>float</type>
11 
                    <value>
12 
                        <_alt>
13 
                            <1>$realLatitude</1>
14 
                            <2>$publicLatitude</2>
15 
                        </_alt>
16 
                    </value>
17 
                </_nullIf>
18 
            </latitude>
19 
            <longitude>
20 
                <_nullIf>
21 
                    <null>0</null>
22 
                    <type>float</type>
23 
                    <value>
24 
                        <_alt>
25 
                            <1>$realLongitude</1>
26 
                            <2>$publicLongitude</2>
27 
                        </_alt>
28 
                    </value>
29 
                </_nullIf>
30 
            </longitude>
31 
            <namedplace_id>
32 
                <_simplifyPath>
33 
                    <next>parent_id/namedplace</next>
34 
                    <require>placename</require>
35 
                    <path>
36 
                        <namedplace>
37 
                            <rank>county</rank>
38 
                            <placename>$county</placename>
39 
                            <parent_id>
40 
                                <namedplace>
41 
                                    <rank>stateProvince</rank>
42 
                                    <placename>$state</placename>
43 
                                </namedplace>
44 
                            </parent_id>
45 
                        </namedplace>
46 
                    </path>
47 
                </_simplifyPath>
48 
            </namedplace_id>
49 
        </locationdetermination>
50 
        <locationevent>
51 
            <authoreventcode>$authorObsCode</authoreventcode>
52 
            <obsstartdate><_date><date><_dateRangeStart><value>$obsStartDate</value></_dateRangeStart></date></_date></obsstartdate>
53 
            <taxonoccurrence>
54 
                <aggregateoccurrence><cover>$%cover</cover></aggregateoccurrence>
55 
                <authortaxoncode>$currentTaxonName sec Weakley 2006</authortaxoncode>
56 
                <taxondetermination>
57 
                    <isoriginal>true</isoriginal>
58 
                    <role>identifier</role>
59 
                    <plantconcept_id>
60 
                        <plantconcept>
61 
                            <plantname_id>
62 
                                <_simplifyPath>
63 
                                    <next>parent_id/plantname</next>
64 
                                    <require>plantname</require>
65 
                                    <path>
66 
                                        <plantname>
67 
                                            <rank>binomial</rank>
68 
                                            <plantname>$currentTaxonName sec Weakley 2006</plantname>
69 
                                        </plantname>
70 
                                    </path>
71 
                                </_simplifyPath>
72 
                            </plantname_id>
73 
                        </plantconcept>
74 
                    </plantconcept_id>
75 
                </taxondetermination>
76 
            </taxonoccurrence>
77 
        </locationevent>
78 
    </location>
79 
</VegBIEN>
80 
Inserted 16 new rows into database
inputs/CVS/maps/Veg+.organisms.full.csv
1 
CVS,Veg+,Comments
2 
locationAccuracy-m,coordinateUncertaintyInMeters,
3 
county,county,
4 
%cover,coverPercent,
5 
realLatitude,decimalLatitude/_alt/1,
6 
publicLatitude,decimalLatitude/_alt/2,
7 
realLongitude,decimalLongitude/_alt/1,
8 
publicLongitude,decimalLongitude/_alt/2,
9 
authorObsCode,fieldNumber,
10 
obsStartDate,plotEventStartDate,
11 
currentTaxonName sec Weakley 2006,scientificName,
12 
state,stateProvince,
13 
confidentialityStatus,,
inputs/CVS/maps/Veg+.organisms.csv
1 
CVS,Veg+,Comments
2 
authorObsCode,fieldNumber,
3 
obsStartDate,plotEventStartDate,
4 
realLatitude,decimalLatitude/_alt/1,
5 
realLongitude,decimalLongitude/_alt/1,
6 
locationAccuracy-m,coordinateUncertaintyInMeters,
7 
publicLatitude,decimalLatitude/_alt/2,
8 
publicLongitude,decimalLongitude/_alt/2,
9 
confidentialityStatus,,
10 
state,stateProvince,
11 
county,county,
12 
currentTaxonName sec Weakley 2006,scientificName,
13 
%cover,coverPercent,
inputs/CVS/maps/src.organisms.csv
1 
CVS,Veg+,Comments
2 
authorObsCode,,
3 
obsStartDate,,
4 
realLatitude,,
5 
realLongitude,,
6 
locationAccuracy-m,,
7 
publicLatitude,,
8 
publicLongitude,,
9 
confidentialityStatus,,
10 
state,,
11 
county,,
12 
currentTaxonName sec Weakley 2006,,
13 
%cover,,
inputs/CVS/maps/VegBIEN.organisms.csv
1 
CVS,VegBIEN:,Comments
2 
authorObsCode,/location/authorlocationcode/_alt/2,
3 
locationAccuracy-m,/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,
4 
realLatitude,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value/_alt/1",
5 
publicLatitude,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value/_alt/2",
6 
realLongitude,"/location/locationdetermination/longitude/_alt/1/_nullIf:[null=0,type=float]/value/_alt/1",
7 
publicLongitude,"/location/locationdetermination/longitude/_alt/1/_nullIf:[null=0,type=float]/value/_alt/2",
8 
county,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",
9 
state,"/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=stateProvince]/placename",
10 
authorObsCode,/location/locationevent/authoreventcode,
11 
obsStartDate,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,
12 
%cover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,
13 
currentTaxonName sec Weakley 2006,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2,
14 
currentTaxonName sec Weakley 2006,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname",
15 
confidentialityStatus,,** No input mapping for confidentialityStatus **
inputs/SALVIAS-CSV/test/import.organisms.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <authorlocationcode>
5 
            <_alt>
6 
                <1>$subplot</1>
7 
                <4>
8 
                    <_if name="if indirect voucher">
9 
                        <cond>
10 
                            <_eq>
11 
                                <right>indirect</right>
12 
                                <left>$det_type</left>
13 
                            </_eq>
14 
                        </cond>
15 
                        <else>
16 
                            <_alt>
17 
                                <1>$coll_number</1>
18 
                                <2>$voucher_string</2>
19 
                            </_alt>
20 
                        </else>
21 
                    </_if>
22 
                </4>
23 
            </_alt>
24 
        </authorlocationcode>
25 
        <locationevent>
26 
            <obsstartdate><_date><date><_dateRangeStart><value>$census_date</value></_dateRangeStart></date></_date></obsstartdate>
27 
            <taxonoccurrence>
28 
                <aggregateoccurrence>
29 
                    <count>$no_of_individuals</count>
30 
                    <cover>$cover_percent</cover>
31 
                    <definedvalue fkey="tablerecord_id">
32 
                        <userdefined_id>
33 
                            <userdefined>
34 
                                <tablename>aggregateoccurrence</tablename>
35 
                                <userdefinedname>censusNo</userdefinedname>
36 
                            </userdefined>
37 
                        </userdefined_id>
38 
                        <definedvalue>$census_no</definedvalue>
39 
                    </definedvalue>
40 
                    <linecover>$intercept_cm</linecover>
41 
                    <plantobservation>
42 
                        <collectionnumber>$individual_code</collectionnumber>
43 
                        <sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
44 
                        <specimenreplicate>
45 
                            <catalognumber_dwc>
46 
                                <_if name="if indirect voucher">
47 
                                    <cond>
48 
                                        <_eq>
49 
                                            <right>indirect</right>
50 
                                            <left>$det_type</left>
51 
                                        </_eq>
52 
                                    </cond>
53 
                                    <else>
54 
                                        <_alt>
55 
                                            <1>$coll_number</1>
56 
                                            <2>$voucher_string</2>
57 
                                        </_alt>
58 
                                    </else>
59 
                                </_if>
60 
                            </catalognumber_dwc>
61 
                        </specimenreplicate>
62 
                        <stemobservation>
63 
                            <basaldiameter>$basal_diam</basaldiameter>
64 
                            <definedvalue fkey="tablerecord_id">
65 
                                <userdefined_id>
66 
                                    <userdefined>
67 
                                        <tablename>stemobservation</tablename>
68 
                                        <userdefinedname>canopyForm</userdefinedname>
69 
                                    </userdefined>
70 
                                </userdefined_id>
71 
                                <definedvalue>$stem_canopy_form</definedvalue>
72 
                            </definedvalue>
73 
                            <definedvalue fkey="tablerecord_id">
74 
                                <userdefined_id>
75 
                                    <userdefined>
76 
                                        <tablename>stemobservation</tablename>
77 
                                        <userdefinedname>canopyPosition</userdefinedname>
78 
                                    </userdefined>
79 
                                </userdefined_id>
80 
                                <definedvalue>$stem_canopy_position</definedvalue>
81 
                            </definedvalue>
82 
                            <definedvalue fkey="tablerecord_id">
83 
                                <userdefined_id>
84 
                                    <userdefined>
85 
                                        <tablename>stemobservation</tablename>
86 
                                        <userdefinedname>lianaInfestation</userdefinedname>
87 
                                    </userdefined>
88 
                                </userdefined_id>
89 
                                <definedvalue>$stem_liana_infestation</definedvalue>
90 
                            </definedvalue>
91 
                            <definedvalue fkey="tablerecord_id">
92 
                                <userdefined_id>
93 
                                    <userdefined>
94 
                                        <tablename>stemobservation</tablename>
95 
                                        <userdefinedname>notes</userdefinedname>
96 
                                    </userdefined>
97 
                                </userdefined_id>
98 
                                <definedvalue>$notes</definedvalue>
99 
                            </definedvalue>
100 
                            <diameterbreastheight>$stem_dbh</diameterbreastheight>
101 
                            <height>
102 
                                <_alt>
103 
                                    <1>$stem_height_m</1>
104 
                                    <2>$height_m</2>
105 
                                </_alt>
106 
                            </height>
107 
                            <heightfirstbranch>
108 
                                <_alt>
109 
                                    <0>$ht_first_branch_m</0>
110 
                                    <1>$stem_height_first_branch_m</1>
111 
                                </_alt>
112 
                            </heightfirstbranch>
113 
                            <stemtag>
114 
                                <iscurrent>
115 
                                    <_alt>
116 
                                        <2>true</2>
117 
                                        <1>false</1>
118 
                                    </_alt>
119 
                                </iscurrent>
120 
                                <tag>
121 
                                    <_alt>
122 
                                        <1>$tag1</1>
123 
                                        <2>$stem_tag1</2>
124 
                                    </_alt>
125 
                                </tag>
126 
                            </stemtag>
127 
                            <stemtag>
128 
                                <iscurrent>true</iscurrent>
129 
                                <tag>
130 
                                    <_alt>
131 
                                        <1>$tag2</1>
132 
                                        <2>$stem_tag2</2>
133 
                                    </_alt>
134 
                                </tag>
135 
                            </stemtag>
136 
                            <xposition>$x_position</xposition>
137 
                            <yposition>$y_position</yposition>
138 
                        </stemobservation>
139 
                    </plantobservation>
140 
                </aggregateoccurrence>
141 
                <authortaxoncode>
142 
                    <_alt>
143 
                        <1>$individual_code</1>
144 
                        <2><_name><last>$orig_species</last></_name></2>
145 
                    </_alt>
146 
                </authortaxoncode>
147 
                <growthform>
148 
                    <_map>
149 
                        <T>tree</T>
150 
                        <Arbol>tree</Arbol>
151 
                        <palm>tree</palm>
152 
                        <H>hemiepiphyte</H>
153 
                        <Hemiepífito>hemiepiphyte</Hemiepífito>
154 
                        <L>liana</L>
155 
                        <l>liana</l>
156 
                        <L?>liana</L?>
157 
                        <Liana>liana</Liana>
158 
                        <E>epiphyte</E>
159 
                        <S>shrub</S>
160 
                        <Hb>herb</Hb>
161 
                        <vine-herbaceous>vine</vine-herbaceous>
162 
                        <graminoid>grass</graminoid>
163 
                        <rosette>forb</rosette>
164 
                        <*></*>
165 
                        <value>$habit</value>
166 
                    </_map>
167 
                </growthform>
168 
                <sourceaccessioncode>$OBSERVATION_ID</sourceaccessioncode>
169 
                <taxondetermination>
170 
                    <role>computer</role>
171 
                    <plantconcept_id>
172 
                        <plantconcept>
173 
                            <plantname_id>
174 
                                <_simplifyPath>
175 
                                    <next>parent_id/plantname</next>
176 
                                    <require>plantname</require>
177 
                                    <path>
178 
                                        <plantname>
179 
                                            <rank>binomial</rank>
180 
                                            <parent_id>
181 
                                                <plantname>
182 
                                                    <rank>authority</rank>
183 
                                                    <plantname>$specific_authority</plantname>
184 
                                                    <parent_id>
185 
                                                        <plantname>
186 
                                                            <rank>subspecies</rank>
187 
                                                            <plantname>
188 
                                                                <_name>
189 
                                                                    <first>$infra_rank_1</first>
190 
                                                                    <last>$infra_ep_1</last>
191 
                                                                </_name>
192 
                                                            </plantname>
193 
                                                            <parent_id>
194 
                                                                <plantname>
195 
                                                                    <rank>species</rank>
196 
                                                                    <plantname>$specific_epithet</plantname>
197 
                                                                    <parent_id>
198 
                                                                        <plantname>
199 
                                                                            <rank>genus</rank>
200 
                                                                            <plantname>$genus</plantname>
201 
                                                                            <parent_id>
202 
                                                                                <plantname>
203 
                                                                                    <rank>family</rank>
204 
                                                                                    <plantname>$family</plantname>
205 
                                                                                </plantname>
206 
                                                                            </parent_id>
207 
                                                                        </plantname>
208 
                                                                    </parent_id>
209 
                                                                </plantname>
210 
                                                            </parent_id>
211 
                                                        </plantname>
212 
                                                    </parent_id>
213 
                                                </plantname>
214 
                                            </parent_id>
215 
                                        </plantname>
216 
                                    </path>
217 
                                </_simplifyPath>
218 
                            </plantname_id>
219 
                        </plantconcept>
220 
                    </plantconcept_id>
221 
                </taxondetermination>
222 
                <taxondetermination>
223 
                    <isoriginal>true</isoriginal>
224 
                    <role>identifier</role>
225 
                    <plantconcept_id>
226 
                        <plantconcept>
227 
                            <plantname_id>
228 
                                <_simplifyPath>
229 
                                    <next>parent_id/plantname</next>
230 
                                    <require>plantname</require>
231 
                                    <path>
232 
                                        <plantname>
233 
                                            <rank>binomial</rank>
234 
                                            <plantname><_name><last>$orig_species</last></_name></plantname>
235 
                                            <parent_id>
236 
                                                <plantname>
237 
                                                    <rank>authority</rank>
238 
                                                    <parent_id>
239 
                                                        <plantname>
240 
                                                            <rank>subspecies</rank>
241 
                                                            <parent_id>
242 
                                                                <plantname>
243 
                                                                    <rank>species</rank>
244 
                                                                    <parent_id>
245 
                                                                        <plantname>
246 
                                                                            <rank>genus</rank>
247 
                                                                            <parent_id>
248 
                                                                                <plantname>
249 
                                                                                    <rank>family</rank>
250 
                                                                                    <plantname>$orig_family</plantname>
251 
                                                                                </plantname>
252 
                                                                            </parent_id>
253 
                                                                        </plantname>
254 
                                                                    </parent_id>
255 
                                                                </plantname>
256 
                                                            </parent_id>
257 
                                                        </plantname>
258 
                                                    </parent_id>
259 
                                                </plantname>
260 
                                            </parent_id>
261 
                                        </plantname>
262 
                                    </path>
263 
                                </_simplifyPath>
264 
                            </plantname_id>
265 
                        </plantconcept>
266 
                    </plantconcept_id>
267 
                    <taxonfit>$cf_aff</taxonfit>
268 
                </taxondetermination>
269 
                <verbatimcollectorname>
270 
                    <_name>
271 
                        <first>$coll_firstname</first>
272 
                        <last>$coll_lastname</last>
273 
                    </_name>
274 
                </verbatimcollectorname>
275 
                <voucher>
276 
                    <specimenreplicate_id>
277 
                        <specimenreplicate>
278 
                            <catalognumber_dwc>
279 
                                <_if name="if indirect voucher">
280 
                                    <cond>
281 
                                        <_eq>
282 
                                            <right>indirect</right>
283 
                                            <left>$det_type</left>
284 
                                        </_eq>
285 
                                    </cond>
286 
                                    <then>
287 
                                        <_alt>
288 
                                            <1>$coll_number</1>
289 
                                            <2>$voucher_string</2>
290 
                                        </_alt>
291 
                                    </then>
292 
                                </_if>
293 
                            </catalognumber_dwc>
294 
                        </specimenreplicate>
295 
                    </specimenreplicate_id>
296 
                </voucher>
297 
            </taxonoccurrence>
298 
        </locationevent>
299 
        <parent_id>
300 
            <location>
301 
                <authorlocationcode>$plot_code</authorlocationcode>
302 
                <sourceaccessioncode>$PLOT_ID</sourceaccessioncode>
303 
            </location>
304 
        </parent_id>
305 
    </location>
306 
</VegBIEN>
307 
Inserted 51 new rows into database
inputs/SALVIAS-CSV/maps/Veg+.organisms.full.csv
1 
SALVIAS-CSV,Veg+,Comments
2 
basal_diam,basalDiameter,
3 
stem_canopy_form,canopyForm,Brad: Should also be userDefined for VegBank.
4 
stem_canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank.
5 
coll_number,catalogNumber/_alt/1,Brad: Incorrect. Map instead as for voucher_string
6 
voucher_string,catalogNumber/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
7 
census_no,censusNumber,"Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
8 
family,computer.family,
9 
genus,computer.genus,
10 
infra_ep_1,computer.infraspecificEpithet,
11 
specific_authority,computer.scientificNameAuthorship,Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
12 
specific_epithet,computer.specificEpithet,
13 
infra_rank_1,computer.taxonRank,
14 
cover_percent,coverPercent,
15 
stem_dbh,diameterBreastHeight,
16 
orig_family,family,Brad: OMIT
17 
habit,"growthForm/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
18 
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
19 
height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
20 
ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
21 
stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
22 
cf_aff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
23 
no_of_individuals,individualCount,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
24 
OBSERVATION_ID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
25 
stem_liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank.
26 
PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
27 
plot_code,parentPlotName,"Brad: Same as plotCode, above"
28 
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
29 
-----
30 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
31 
FROM ""SALVIAS-CSV"".organisms
32 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
33 
GROUP BY ""PLOT_ID"", subplot
34 
HAVING count(DISTINCT census_date) > 1
35 
-----"
36 
subplot,plotName,
37 
tag2,previousTag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
38 
stem_tag2,previousTag/_alt/2,Brad: see above
39 
individual_code,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
40 
coll_firstname,recordedBy.givenName,Brad: See comment above
41 
coll_lastname,recordedBy.surName,"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
42 
x_position,relativePlotX,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
43 
y_position,relativePlotY,Brad: See comment above for x_position
44 
orig_species,scientificName/_name/last,Brad: OMIT
45 
notes,stemNotes,
46 
tag1,tag/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
47 
stem_tag1,tag/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
48 
intercept_cm,volumeCanopy,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
49 
det_type,voucherType,"Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
50 
collector_code,,Brad: OMIT
51 
comments,,Brad: OMIT
52 
fam_status,,Brad: OMIT. This will be determined later by using TNRS.
53 
gen_status,,Brad: OMIT. This will be determined later by using TNRS.
54 
ind_id,,Brad: OMIT
55 
species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."
inputs/SALVIAS-CSV/maps/Veg+.organisms.csv
1 
SALVIAS-CSV,Veg+,Comments
2 
OBSERVATION_ID,individualID,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
3 
PLOT_ID,parentLocationID,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
4 
plot_code,parentPlotName,"Brad: Same as plotCode, above"
5 
census_no,censusNumber,"Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
6 
census_date,plotEventStartDate,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS-CSV"".organisms
10 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PLOT_ID"", subplot
12 
HAVING count(DISTINCT census_date) > 1
13 
-----"
14 
subplot,plotName,
15 
individual_code,recordNumber,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
16 
ind_id,,Brad: OMIT
17 
tag1,tag/_alt/1,"Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once."
18 
tag2,previousTag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
19 
x_position,relativePlotX,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
20 
y_position,relativePlotY,Brad: See comment above for x_position
21 
voucher_string,catalogNumber/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
22 
coll_number,catalogNumber/_alt/1,Brad: Incorrect. Map instead as for voucher_string
23 
collector_code,,Brad: OMIT
24 
coll_lastname,recordedBy.surName,"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
25 
coll_firstname,recordedBy.givenName,Brad: See comment above
26 
det_type,voucherType,"Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
27 
fam_status,,Brad: OMIT. This will be determined later by using TNRS.
28 
gen_status,,Brad: OMIT. This will be determined later by using TNRS.
29 
species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."
30 
family,computer.family,
31 
genus,computer.genus,
32 
specific_epithet,computer.specificEpithet,
33 
specific_authority,computer.scientificNameAuthorship,Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
34 
infra_rank_1,computer.taxonRank,
35 
infra_ep_1,computer.infraspecificEpithet,
36 
cf_aff,identificationQualifier,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
37 
comments,,Brad: OMIT
38 
habit,"growthForm/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
39 
no_of_individuals,individualCount,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
40 
cover_percent,coverPercent,
41 
intercept_cm,volumeCanopy,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
42 
height_m,height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
43 
ht_first_branch_m,heightFirstBranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
44 
stem_tag1,tag/_alt/2,"Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems."
45 
stem_tag2,previousTag/_alt/2,Brad: see above
46 
stem_dbh,diameterBreastHeight,
47 
basal_diam,basalDiameter,
48 
stem_height_m,height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
49 
stem_height_first_branch_m,heightFirstBranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
50 
stem_canopy_form,canopyForm,Brad: Should also be userDefined for VegBank.
51 
stem_canopy_position,canopyPosition,Brad: Should also be userDefined for VegBank.
52 
stem_liana_infestation,lianaInfestation,Brad: Should also be userDefined for VegBank.
53 
notes,stemNotes,
54 
orig_family,family,Brad: OMIT
55 
orig_species,scientificName/_name/last,Brad: OMIT
inputs/SALVIAS-CSV/maps/src.organisms.csv
1 
SALVIAS-CSV,Veg+,Comments
2 
OBSERVATION_ID,,
3 
PLOT_ID,,
4 
plot_code,,
5 
census_no,,
6 
census_date,,
7 
subplot,,
8 
individual_code,,
9 
ind_id,,
10 
tag1,,
11 
tag2,,
12 
x_position,,
13 
y_position,,
14 
voucher_string,,
15 
coll_number,,
16 
collector_code,,
17 
coll_lastname,,
18 
coll_firstname,,
19 
det_type,,
20 
fam_status,,
21 
gen_status,,
22 
species_status,,
23 
family,,
24 
genus,,
25 
specific_epithet,,
26 
specific_authority,,
27 
infra_rank_1,,
28 
infra_ep_1,,
29 
cf_aff,,
30 
comments,,
31 
habit,,
32 
no_of_individuals,,
33 
cover_percent,,
34 
intercept_cm,,
35 
height_m,,
36 
ht_first_branch_m,,
37 
stem_tag1,,
38 
stem_tag2,,
39 
stem_dbh,,
40 
basal_diam,,
41 
stem_height_m,,
42 
stem_height_first_branch_m,,
43 
stem_canopy_form,,
44 
stem_canopy_position,,
45 
stem_liana_infestation,,
46 
notes,,
47 
orig_family,,
48 
orig_species,,
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
1 
SALVIAS-CSV,VegBIEN:,Comments
2 
subplot,/location/authorlocationcode/_alt/1,
3 
det_type,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
4 
coll_number,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
5 
voucher_string,"/location/authorlocationcode/_alt/4/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
6 
census_date,/location/locationevent/obsstartdate/_*/date/_dateRangeStart/value,"This is for the subplot, not the organism, as all organisms in a subplot have the same value for it. The following query returns no rows:
7 
-----
8 
SELECT ""PLOT_ID"", subplot, count(DISTINCT census_date) AS census_date_count
9 
FROM ""SALVIAS-CSV"".organisms
10 
WHERE subplot IS NOT NULL AND census_date IS NOT NULL
11 
GROUP BY ""PLOT_ID"", subplot
12 
HAVING count(DISTINCT census_date) > 1
13 
-----"
14 
no_of_individuals,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this."
15 
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,
16 
census_no,"/location/locationevent/taxonoccurrence/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not."
17 
intercept_cm,/location/locationevent/taxonoccurrence/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance."
18 
individual_code,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber/_alt/2,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
19 
OBSERVATION_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
20 
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
21 
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
22 
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
23 
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,
24 
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank.
25 
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank.
26 
stem_liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue",Brad: Should also be userDefined for VegBank.
27 
notes,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=notes]]:[@fkey=tablerecord_id]/definedvalue",
28 
stem_dbh,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight,
29 
stem_height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height/_alt/1,"Brad: Same as for height, but applies to individuals stems, not trees. Rare."
30 
height_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/height/_alt/2,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
31 
ht_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob
32 
stem_height_first_branch_m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/heightfirstbranch,"Brad: Should also be userDefined for VegBank. Same as for ht_first_branch_m, but applies to individuals stems, not trees. Rare."
33 
tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
34 
stem_tag1,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2"
35 
tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
36 
stem_tag2,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/2,Brad: see above
37 
x_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX."
38 
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position
39 
individual_code,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/1/_alt/2,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot."
40 
orig_species,/location/locationevent/taxonoccurrence/authortaxoncode/_alt/2/_name/last,Brad: OMIT
41 
habit,"/location/locationevent/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
42 
OBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later."
43 
specific_authority,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss.
44 
infra_rank_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first",
45 
infra_ep_1,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last",
46 
specific_epithet,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=species]/plantname",
47 
genus,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",
48 
family,"/location/locationevent/taxonoccurrence/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",
49 
orig_species,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[],do=""plantname[rank=_val]/parent_id""]/plantname[rank=binomial]/plantname/_name/last",Brad: OMIT
50 
orig_family,"/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",Brad: OMIT
51 
cf_aff,/location/locationevent/taxonoccurrence/taxondetermination[role=identifier]:[isoriginal=true]/taxonfit,"Brad: Not sure where this goes. Indicator of identification uncertainty. 'cf.'=similar to the species listed, 'aff.'=related to the species list, but not the same. You'll need to check with Bob and with Nick where these go in VegX and VegBank."
52 
coll_firstname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/first,Brad: See comment above
53 
coll_lastname,/location/locationevent/taxonoccurrence/verbatimcollectorname/_name/last,"Brad: Correct for VegBank. This is the collector of a separate specimen which vouchers this tree or species. I worry that vouchers are not properly accommodated in VegX. Again, we need to check with Nick."
54 
det_type,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider  asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen."
55 
coll_number,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/1",Brad: Incorrect. Map instead as for voucher_string
56 
voucher_string,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
57 
plot_code,/location/parent_id/location/authorlocationcode,"Brad: Same as plotCode, above"
58 
PLOT_ID,/location/parent_id/location/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
59 
collector_code,,Brad: OMIT
60 
comments,,Brad: OMIT
61 
fam_status,,Brad: OMIT. This will be determined later by using TNRS.
62 
gen_status,,Brad: OMIT. This will be determined later by using TNRS.
63 
ind_id,,Brad: OMIT
64 
species_status,,"Brad: OMIT. Except, note that if species_status=3, this indicate that name is a morphospecies and not a standard latin name. Not exactly sure how to use this in BIEN, but could be useful during the name-scrubbing process with TNRS."
inputs/CTFS/test/import.organisms.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <plantobservation id="-1">
4 
        <aggregateoccurrence_id merge="1">
5 
            <aggregateoccurrence merge="1">
6 
                <taxonoccurrence_id merge="1">
7 
                    <taxonoccurrence>
8 
                        <locationevent_id>
9 
                            <locationevent>
10 
                                <location_id>
11 
                                    <location>
12 
                                        <area>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/area</area>
13 
                                        <elevation>
14 
                                            <_alt>
15 
                                                <1>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/verbatimElevation</1>
16 
                                                <2>
17 
                                                    <_avg>
18 
                                                        <max>
19 
                                                            <_units>
20 
                                                                <default>m</default>
21 
                                                                <to>m</to>
22 
                                                                <to></to>
23 
                                                                <value><_rangeEnd><value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/maximumElevationInMeters</value></_rangeEnd></value>
24 
                                                            </_units>
25 
                                                        </max>
26 
                                                        <min>
27 
                                                            <_units>
28 
                                                                <default>m</default>
29 
                                                                <to>m</to>
30 
                                                                <to></to>
31 
                                                                <value><_rangeStart><value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/minimumElevationInMeters</value></_rangeStart></value>
32 
                                                            </_units>
33 
                                                        </min>
34 
                                                    </_avg>
35 
                                                </2>
36 
                                            </_alt>
37 
                                        </elevation>
38 
                                        <elevationrange>
39 
                                            <_range>
40 
                                                <from>
41 
                                                    <_units>
42 
                                                        <default>m</default>
43 
                                                        <to>m</to>
44 
                                                        <to></to>
45 
                                                        <value><_rangeStart><value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/minimumElevationInMeters</value></_rangeStart></value>
46 
                                                    </_units>
47 
                                                </from>
48 
                                                <to>
49 
                                                    <_units>
50 
                                                        <default>m</default>
51 
                                                        <to>m</to>
52 
                                                        <to></to>
53 
                                                        <value><_rangeEnd><value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/maximumElevationInMeters</value></_rangeEnd></value>
54 
                                                    </_units>
55 
                                                </to>
56 
                                            </_range>
57 
                                        </elevationrange>
58 
                                        <landform>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/landform</landform>
59 
                                        <locationdetermination>
60 
                                            <coordsaccuracy>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/CoordinateUncertaintyInMeters</coordsaccuracy>
61 
                                            <footprintgeometry_dwc>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/FootprintWKT</footprintgeometry_dwc>
62 
                                            <latitude>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/DecimalLatitude</latitude>
63 
                                            <longitude>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/DecimalLongitude</longitude>
64 
                                            <namedplace_id>
65 
                                                <_simplifyPath>
66 
                                                    <next>parent_id/namedplace</next>
67 
                                                    <require>placename</require>
68 
                                                    <path>
69 
                                                        <namedplace>
70 
                                                            <rank>county</rank>
71 
                                                            <placename>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/location[placeType=county]/placeName</placename>
72 
                                                            <parent_id>
73 
                                                                <namedplace>
74 
                                                                    <rank>stateProvince</rank>
75 
                                                                    <placename>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/location[placeType=state]/placeName</placename>
76 
                                                                    <parent_id>
77 
                                                                        <namedplace>
78 
                                                                            <rank>country</rank>
79 
                                                                            <placename>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/location[placeType=country]/placeName</placename>
80 
                                                                            <parent_id>
81 
                                                                                <namedplace>
82 
                                                                                    <rank>continent</rank>
83 
                                                                                    <placename>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/location[placeType=continent]/placeName</placename>
84 
                                                                                </namedplace>
85 
                                                                            </parent_id>
86 
                                                                        </namedplace>
87 
                                                                    </parent_id>
88 
                                                                </namedplace>
89 
                                                            </parent_id>
90 
                                                        </namedplace>
91 
                                                    </path>
92 
                                                </_simplifyPath>
93 
                                            </namedplace_id>
94 
                                        </locationdetermination>
95 
                                        <locationnarrative>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/locationNarrative</locationnarrative>
96 
                                        <notespublic>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/note</notespublic>
97 
                                        <slopeaspect><_compass><value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/slopeAspect</value></_compass></slopeaspect>
98 
                                        <slopegradient>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/slopeGradient</slopegradient>
99 
                                        <sourceaccessioncode>
100 
                                            <_merge>
101 
                                                <1>
102 
                                                    <_alt>
103 
                                                        <1>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotUniqueIdentifier</1>
104 
                                                        <2>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotName</2>
105 
                                                    </_alt>
106 
                                                </1>
107 
                                                <2>
108 
                                                    <_alt>
109 
                                                        <1>$/*ID-&gt;/*s/plotObservation/plotUniqueIdentifierID-&gt;/*s/plot[plotUniqueIdentifier]/plotUniqueIdentifier</1>
110 
                                                        <2>$/*ID-&gt;/*s/plotObservation/plotUniqueIdentifierID-&gt;/*s/plot[plotUniqueIdentifier]/plotName</2>
111 
                                                    </_alt>
112 
                                                </2>
113 
                                            </_merge>
114 
                                        </sourceaccessioncode>
115 
                                    </location>
116 
                                </location_id>
117 
                                <method_id><method><name>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=method]/*ID/method/name</name></method></method_id>
118 
                                <project_id>
119 
                                    <project>
120 
                                        <projectname>$/*ID-&gt;/*s/plotObservation/*ID-&gt;/*s/project/title[@id=name]</projectname>
121 
                                        <sourceaccessioncode>$/*ID-&gt;/*s/plotObservation/*ID-&gt;/*s/project/title[@id=sourceAccessionCode]</sourceaccessioncode>
122 
                                    </project>
123 
                                </project_id>
124 
                                <authorlocationcode>$/*ID-&gt;/*s/plotObservation/plotUniqueIdentifierID-&gt;/*s/plot[plotUniqueIdentifier]/plotName</authorlocationcode>
125 
                                <commclass>
126 
                                    <commdetermination>
127 
                                        <commconcept_id>
128 
                                            <commconcept>
129 
                                                <commname_id><commname><commname>$/*ID-&gt;/*s/plotObservation-&gt;/*s/communityDetermination[*ID]/*s/communityConcept/commonName</commname></commname></commname_id>
130 
                                                <commdescription>$/*ID-&gt;/*s/plotObservation-&gt;/*s/communityDetermination[*ID]/*s/communityConcept/name</commdescription>
131 
                                            </commconcept>
132 
                                        </commconcept_id>
133 
                                    </commdetermination>
134 
                                </commclass>
135 
                                <obsenddate>$/*ID-&gt;/*s/plotObservation/obsEndDate</obsenddate>
136 
                                <obsstartdate>$/*ID-&gt;/*s/plotObservation/obsStartDate</obsstartdate>
137 
                                <parent_id>
138 
                                    <locationevent>
139 
                                        <location_id>
140 
                                            <location>
141 
                                                <sourceaccessioncode>
142 
                                                    <_alt>
143 
                                                        <1>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotUniqueIdentifier</1>
144 
                                                        <2>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotName</2>
145 
                                                    </_alt>
146 
                                                </sourceaccessioncode>
147 
                                            </location>
148 
                                        </location_id>
149 
                                        <authorlocationcode>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotName</authorlocationcode>
150 
                                        <sourceaccessioncode>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=parent]/value-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/plotUniqueIdentifier</sourceaccessioncode>
151 
                                    </locationevent>
152 
                                </parent_id>
153 
                                <precipitation>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=precipitation]/value</precipitation>
154 
                                <soilobs>
155 
                                    <acidity>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=acidity]/value</acidity>
156 
                                    <basesaturation>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=base]/value</basesaturation>
157 
                                    <calcium>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=calcium]/value</calcium>
158 
                                    <carbon>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=carbon]/value</carbon>
159 
                                    <cationexchangecapacity>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=cationExchangeCapacity]/value</cationexchangecapacity>
160 
                                    <clay>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=clay]/value</clay>
161 
                                    <conductivity>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=conductivity]/value</conductivity>
162 
                                    <magnesium>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/magnesium</magnesium>
163 
                                    <nitrogen>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/nitrogen</nitrogen>
164 
                                    <organic>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=organic]/value</organic>
165 
                                    <ph>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/ph</ph>
166 
                                    <phosphorus>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/phosphorus</phosphorus>
167 
                                    <potassium>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/potassium</potassium>
168 
                                    <sand>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=sand]/value</sand>
169 
                                    <silt>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=silt]/value</silt>
170 
                                    <sodium>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=sodium]/value</sodium>
171 
                                    <texture>$/*ID-&gt;/*s/plotObservation-&gt;/*s/abioticObservation[*ID]/simpleUserdefined[name=texture]/value</texture>
172 
                                </soilobs>
173 
                                <sourceaccessioncode>$/*ID-&gt;/*s/plotObservation/plotUniqueIdentifierID-&gt;/*s/plot[plotUniqueIdentifier]/plotUniqueIdentifier</sourceaccessioncode>
174 
                                <temperature>$/*ID-&gt;/*s/plotObservation/temperature</temperature>
175 
                                <waterdepth>
176 
                                    <_avg>
177 
                                        <max>
178 
                                            <_units>
179 
                                                <default>m</default>
180 
                                                <to>m</to>
181 
                                                <to></to>
182 
                                                <value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/maximumDepthInMeters</value>
183 
                                            </_units>
184 
                                        </max>
185 
                                        <min>
186 
                                            <_units>
187 
                                                <default>m</default>
188 
                                                <to>m</to>
189 
                                                <to></to>
190 
                                                <value>$/*ID-&gt;/*s/plotObservation/*UniqueIdentifierID-&gt;/*s/plot/geospatial/minimumDepthInMeters</value>
191 
                                            </_units>
192 
                                        </min>
193 
                                    </_avg>
194 
                                </waterdepth>
195 
                            </locationevent>
196 
                        </locationevent_id>
197 
                        <growthform>$/simpleUserdefined[name=growthForm]/value</growthform>
198 
                        <sourceaccessioncode>
199 
                            <_alt>
200 
                                <3>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name</3>
201 
                                <1>$/@id</1>
202 
                                <2>$/simpleUserdefined[name=authorPlantCode]/value</2>
203 
                            </_alt>
204 
                        </sourceaccessioncode>
205 
                        <taxondetermination>
206 
                            <role>computer</role>
207 
                            <plantconcept_id>
208 
                                <plantconcept>
209 
                                    <plantname_id>
210 
                                        <_simplifyPath>
211 
                                            <next>parent_id/plantname</next>
212 
                                            <require>plantname</require>
213 
                                            <path>
214 
                                                <plantname>
215 
                                                    <rank>binomial</rank>
216 
                                                    <parent_id>
217 
                                                        <plantname>
218 
                                                            <rank>authority</rank>
219 
                                                            <parent_id>
220 
                                                                <plantname>
221 
                                                                    <rank>subspecies</rank>
222 
                                                                    <plantname>
223 
                                                                        <_name>
224 
                                                                            <first>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=TaxonomicRankBelowSubspeciesEnum])/tcs:Rank</first>
225 
                                                                            <last>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=TaxonomicRankBelowSubspeciesEnum])/tcs:Name</last>
226 
                                                                        </_name>
227 
                                                                    </plantname>
228 
                                                                    <parent_id>
229 
                                                                        <plantname>
230 
                                                                            <rank>species</rank>
231 
                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=sp])/tcs:Name</plantname>
232 
                                                                            <parent_id>
233 
                                                                                <plantname>
234 
                                                                                    <rank>genus</rank>
235 
                                                                                    <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=gen])/tcs:Name</plantname>
236 
                                                                                    <parent_id>
237 
                                                                                        <plantname>
238 
                                                                                            <rank>family</rank>
239 
                                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=fam])/tcs:Name</plantname>
240 
                                                                                        </plantname>
241 
                                                                                    </parent_id>
242 
                                                                                </plantname>
243 
                                                                            </parent_id>
244 
                                                                        </plantname>
245 
                                                                    </parent_id>
246 
                                                                </plantname>
247 
                                                            </parent_id>
248 
                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=auth])/tcs:Name</plantname>
249 
                                                        </plantname>
250 
                                                    </parent_id>
251 
                                                </plantname>
252 
                                            </path>
253 
                                        </_simplifyPath>
254 
                                    </plantname_id>
255 
                                </plantconcept>
256 
                            </plantconcept_id>
257 
                            <iscurrent>true</iscurrent>
258 
                        </taxondetermination>
259 
                        <taxondetermination>
260 
                            <role>identifier</role>
261 
                            <plantconcept_id>
262 
                                <plantconcept>
263 
                                    <plantname_id>
264 
                                        <_simplifyPath>
265 
                                            <next>parent_id/plantname</next>
266 
                                            <require>plantname</require>
267 
                                            <path>
268 
                                                <plantname>
269 
                                                    <rank>binomial</rank>
270 
                                                    <plantname>
271 
                                                        <_name>
272 
                                                            <last>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=binom])/fit</last>
273 
                                                            <first>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=binom])/tcs:Name</first>
274 
                                                        </_name>
275 
                                                    </plantname>
276 
                                                    <parent_id>
277 
                                                        <plantname>
278 
                                                            <rank>authority</rank>
279 
                                                            <parent_id>
280 
                                                                <plantname>
281 
                                                                    <rank>subspecies</rank>
282 
                                                                    <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=ssp])/tcs:Name</plantname>
283 
                                                                    <parent_id>
284 
                                                                        <plantname>
285 
                                                                            <rank>species</rank>
286 
                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank=Species])/tcs:Name</plantname>
287 
                                                                            <parent_id>
288 
                                                                                <plantname>
289 
                                                                                    <rank>genus</rank>
290 
                                                                                    <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank=Genus])/tcs:Name</plantname>
291 
                                                                                    <parent_id>
292 
                                                                                        <plantname>
293 
                                                                                            <rank>family</rank>
294 
                                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank=Family])/tcs:Name</plantname>
295 
                                                                                            <parent_id>
296 
                                                                                                <plantname>
297 
                                                                                                    <rank>order</rank>
298 
                                                                                                    <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=ord])/tcs:Name</plantname>
299 
                                                                                                    <parent_id>
300 
                                                                                                        <plantname>
301 
                                                                                                            <rank>class</rank>
302 
                                                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=cl])/tcs:Name</plantname>
303 
                                                                                                            <parent_id>
304 
                                                                                                                <plantname>
305 
                                                                                                                    <rank>subkingdom</rank>
306 
                                                                                                                    <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=phyl_div])/tcs:Name</plantname>
307 
                                                                                                                    <parent_id>
308 
                                                                                                                        <plantname>
309 
                                                                                                                            <rank>kingdom</rank>
310 
                                                                                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=reg])/tcs:Name</plantname>
311 
                                                                                                                        </plantname>
312 
                                                                                                                    </parent_id>
313 
                                                                                                                </plantname>
314 
                                                                                                            </parent_id>
315 
                                                                                                        </plantname>
316 
                                                                                                    </parent_id>
317 
                                                                                                </plantname>
318 
                                                                                            </parent_id>
319 
                                                                                        </plantname>
320 
                                                                                    </parent_id>
321 
                                                                                </plantname>
322 
                                                                            </parent_id>
323 
                                                                        </plantname>
324 
                                                                    </parent_id>
325 
                                                                </plantname>
326 
                                                            </parent_id>
327 
                                                            <plantname>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=auth])/tcs:Name</plantname>
328 
                                                        </plantname>
329 
                                                    </parent_id>
330 
                                                </plantname>
331 
                                            </path>
332 
                                        </_simplifyPath>
333 
                                    </plantname_id>
334 
                                </plantconcept>
335 
                            </plantconcept_id>
336 
                            <taxonfit>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID-&gt;/*s/taxonConcept[tcs:Rank/@code=binom])/fit</taxonfit>
337 
                            <isoriginal>true</isoriginal>
338 
                            <iscurrent>true</iscurrent>
339 
                        </taxondetermination>
340 
                        <verbatimcollectorname>
341 
                            <_name>
342 
                                <first>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID-&gt;/parties/party/individualName/givenName</first>
343 
                                <last>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=collector]/partyWithRole/*ID-&gt;/parties/party/individualName/surName</last>
344 
                            </_name>
345 
                        </verbatimcollectorname>
346 
                    </taxonoccurrence>
347 
                </taxonoccurrence_id>
348 
                <count>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value</count>
349 
                <cover>$/volumeCanopy/*ID-&gt;/*s/attribute/ordinal/coverPercent</cover>
350 
                <definedvalue fkey="tablerecord_id">
351 
                    <userdefined_id>
352 
                        <userdefined>
353 
                            <tablename>aggregateoccurrence</tablename>
354 
                            <userdefinedname>censusNo</userdefinedname>
355 
                        </userdefined>
356 
                    </userdefined_id>
357 
                    <definedvalue>$/*ID-&gt;/*s/plotObservation/simpleUserdefined[name=CensusNumber]/value</definedvalue>
358 
                </definedvalue>
359 
                <linecover>$/volumeCanopy/value</linecover>
360 
            </aggregateoccurrence>
361 
        </aggregateoccurrence_id>
362 
        <authorplantcode>$/simpleUserdefined[name=authorPlantCode]/value</authorplantcode>
363 
        <overallheight>
364 
            <_alt>
365 
                <0>$/height</0>
366 
                <1>$/simpleUserdefined[name=height]/value</1>
367 
            </_alt>
368 
        </overallheight>
369 
        <sourceaccessioncode>$/@id</sourceaccessioncode>
370 
        <stemobservation>
371 
            <stemtag>
372 
                <iscurrent>
373 
                    <_alt>
374 
                        <2>true</2>
375 
                        <1>false</1>
376 
                    </_alt>
377 
                </iscurrent>
378 
                <tag>$/*ID-&gt;/*s/individualOrganism/identificationLabel[@id=1]</tag>
379 
            </stemtag>
380 
            <stemtag>
381 
                <iscurrent>true</iscurrent>
382 
                <tag>$/*ID-&gt;/*s/individualOrganism/identificationLabel[@id=2]</tag>
383 
            </stemtag>
384 
            <xposition>$/relativePlotPosition/relativeX</xposition>
385 
            <yposition>$/relativePlotPosition/relativeY</yposition>
386 
        </stemobservation>
387 
        <_if>
388 
            <cond>
389 
                <_eq>
390 
                    <left><_ref><addr>../../../../_ignore/voucherType</addr></_ref></left>
391 
                    <right>direct</right>
392 
                </_eq>
393 
            </cond>
394 
            <else>
395 
                <aggregateoccurrence_id merge="1">
396 
                    <aggregateoccurrence merge="1">
397 
                        <taxonoccurrence_id>
398 
                            <taxonoccurrence>
399 
                                <voucher>
400 
                                    <specimenreplicate_id>
401 
                                        <specimenreplicate>
402 
                                            <catalognumber_dwc>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept/voucher</catalognumber_dwc>
403 
                                            <collectiondate>$/simpleUserdefined[name=collectionDate]/value</collectiondate>
404 
                                        </specimenreplicate>
405 
                                    </specimenreplicate_id>
406 
                                </voucher>
407 
                            </taxonoccurrence>
408 
                        </taxonoccurrence_id>
409 
                    </aggregateoccurrence>
410 
                </aggregateoccurrence_id>
411 
            </else>
412 
            <then>
413 
                <specimenreplicate>
414 
                    <catalognumber_dwc>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept/voucher</catalognumber_dwc>
415 
                    <collectiondate>$/simpleUserdefined[name=collectionDate]/value</collectiondate>
416 
                </specimenreplicate>
417 
            </then>
418 
        </_if>
419 
        <_ignore><voucherType>$/*ID-&gt;/*s/individualOrganism/*ID-&gt;/*s/taxonNameUsageConcept-&gt;/*s/taxonDetermination[*ID,partyWithRole/role=collector]/groupType</voucherType></_ignore>
420 
    </plantobservation>
421 
</VegBIEN>
422 
Inserted 34 new rows into database
inputs/SALVIAS/test/import.organisms.xml.ref
1 
Put template:
2 
<VegBIEN>
3 
    <location id="-1">
4 
        <authorlocationcode>
5 
            <_alt>
6 
                <1>$Line</1>
7 
                <4>
8 
                    <_if name="if indirect voucher">
9 
                        <cond>
10 
                            <_eq>
11 
                                <right>indirect</right>
12 
                                <left>$DetType</left>
13 
                            </_eq>
14 
                        </cond>
15 
                        <else>
16 
                            <_alt>
17 
                                <1>$coll_number</1>
18 
                                <2>$SourceVoucher</2>
19 
                            </_alt>
20 
                        </else>
21 
                    </_if>
22 
                </4>
23 
            </_alt>
24 
        </authorlocationcode>
25 
        <locationevent>
26 
            <obsenddate><_date><date><_dateRangeEnd><value>$census_date</value></_dateRangeEnd></date></_date></obsenddate>
27 
            <obsstartdate><_date><date><_dateRangeStart><value>$census_date</value></_dateRangeStart></date></_date></obsstartdate>
28 
            <taxonoccurrence>
29 
                <aggregateoccurrence>
30 
                    <count>$NoInd</count>
31 
                    <cover>$cover_percent</cover>
32 
                    <definedvalue fkey="tablerecord_id">
33 
                        <userdefined_id>
34 
                            <userdefined>
35 
                                <tablename>aggregateoccurrence</tablename>
36 
                                <userdefinedname>censusNo</userdefinedname>
37 
                            </userdefined>
38 
                        </userdefined_id>
39 
                        <definedvalue>$census_no</definedvalue>
40 
                    </definedvalue>
41 
                    <linecover>$intercept_cm</linecover>
42 
                    <notes>$Notes</notes>
43 
                    <plantobservation>
44 
                        <collectionnumber>$Ind</collectionnumber>
45 
                        <sourceaccessioncode>$PlotObsID</sourceaccessioncode>
46 
                        <specimenreplicate>
47 
                            <catalognumber_dwc>
48 
                                <_if name="if indirect voucher">
49 
                                    <cond>
50 
                                        <_eq>
51 
                                            <right>indirect</right>
52 
                                            <left>$DetType</left>
53 
                                        </_eq>
54 
                                    </cond>
55 
                                    <else>
56 
                                        <_alt>
57 
                                            <1>$coll_number</1>
58 
                                            <2>$SourceVoucher</2>
59 
                                        </_alt>
60 
                                    </else>
61 
                                </_if>
62 
                            </catalognumber_dwc>
63 
                        </specimenreplicate>
64 
                        <stemobservation>
65 
                            <definedvalue fkey="tablerecord_id">
66 
                                <userdefined_id>
67 
                                    <userdefined>
68 
                                        <tablename>stemobservation</tablename>
69 
                                        <userdefinedname>canopyForm</userdefinedname>
70 
                                    </userdefined>
71 
                                </userdefined_id>
72 
                                <definedvalue>$canopy_form</definedvalue>
73 
                            </definedvalue>
74 
                            <definedvalue fkey="tablerecord_id">
75 
                                <userdefined_id>
76 
                                    <userdefined>
77 
                                        <tablename>stemobservation</tablename>
... This diff was truncated because it exceeds the maximum size that can be displayed.

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