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Revision 7719

Added by Aaron Marcuse-Kubitza over 11 years ago

inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL

View differences:

inputs/REMIB/Specimen/map.csv
12 12 
family,family,,
13 13 
genus,genus,,
14 14 
specificEpithet,specificEpithet,,
15 
country,country,,
16 
state,stateProvince,,
17 
county,county,,
18 
locality,locality,,
15 
country,country,"/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
16 
state,stateProvince,"/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
17 
county,county,"/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
18 
locality,locality,"/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
19 19 
long_deg,longitude_deg,"/_map:[./{""-999"",99,999,1000}=]/value",-99 is a valid longitude for Mexico
20 20 
long_min,longitude_min,"/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
21 21 
long_sec,longitude_sec,"/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
......
26 26 
coll_month,monthCollected,,
27 27 
coll_year,yearCollected,,
28 28 
collector,recordedBy,,
29 
habitat,habitat,,
29 
habitat,habitat,"/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
30 30 
preparation,preparations,,
inputs/REMIB/Specimen/VegBIEN.csv
37 37 
GROUP BY acronym, accession_number
38 38 
HAVING count(*) > 1
39 39 
-----"
40 
locality,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1,
41 
habitat,/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3,
40 
locality,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/1/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
41 
habitat,"/location/iscultivated/_or/2/_locationnarrative_is_cultivated/locationnarrative/_join/3/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
42 42 
coll_day,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/day/_nullIf:[null=0,type=float]/value",
43 43 
coll_month,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/month/_nullIf:[null=0,type=float]/value",
44 44 
coll_year,"/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/2/_date/year/_nullIf:[null=0,type=float]/value",
......
81 81 
GROUP BY acronym, accession_number
82 82 
HAVING count(*) > 1
83 83 
-----"
84 
locality,/location/locationnarrative/_merge/1,
85 
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value","Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
84 
locality,"/location/locationnarrative/_merge/1/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
85 
habitat,"/location/locationnarrative/_merge/3/_label[label=""habitat""]/value/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB); Brad: Free-text description of vegetation community where collected, frequently redundane wrt 'Vegetation'. Bob, Nick: keep as user defined or create special element?"
86 86 
lat_deg,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/deg/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
87 87 
lat_min,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/min/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
88 88 
lat_sec,"/location/locationplace/*_id/place/*_id/coordinates/latitude_deg/_dms_to_dd/sec/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
89 89 
long_deg,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/deg/_map:[./{""-999"",99,999,1000}=]/value",-99 is a valid longitude for Mexico
90 90 
long_min,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/min/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
91 91 
long_sec,"/location/locationplace/*_id/place/*_id/coordinates/longitude_deg/_dms_to_dd/sec/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
92 
country,/location/locationplace/*_id/place/country,
93 
county,/location/locationplace/*_id/place/county,
92 
country,"/location/locationplace/*_id/place/country/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
93 
county,"/location/locationplace/*_id/place/county/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
94 94 
lat_deg,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/deg/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
95 95 
lat_min,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/min/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
96 96 
lat_sec,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_dms_to_dd/sec/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
97 97 
long_deg,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/deg/_map:[./{""-999"",99,999,1000}=]/value",-99 is a valid longitude for Mexico
98 98 
long_min,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/min/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
99 99 
long_sec,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_dms_to_dd/sec/_map:[./{""-999"",""-99"",99,999,1000}=]/value",
100 
country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2,
101 
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2,
102 
state,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2,
103 
state,/location/locationplace/*_id/place/stateprovince,
100 
country,"/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
101 
county,"/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
102 
state,"/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
103 
state,"/location/locationplace/*_id/place/stateprovince/_map:[./{ND,NA}=,*=*]/value","""ND = no disponible = not available"" (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#REMIB)"
104 104 
preparation,,** No join mapping for preparations **
inputs/REMIB/Specimen/test.xml.ref
17 17 
                            <_locationnarrative_is_cultivated>
18 18 
                                <locationnarrative>
19 19 
                                    <_join>
20 
                                        <1>$locality</1>
21 
                                        <3>$habitat</3>
20 
                                        <1>
21 
                                            <_map>
22 
                                                <ND></ND>
23 
                                                <NA></NA>
24 
                                                <*>*</*>
25 
                                                <value>$locality</value>
26 
                                            </_map>
27 
                                        </1>
28 
                                        <3>
29 
                                            <_map>
30 
                                                <ND></ND>
31 
                                                <NA></NA>
32 
                                                <*>*</*>
33 
                                                <value>$habitat</value>
34 
                                            </_map>
35 
                                        </3>
22 36 
                                    </_join>
23 37 
                                </locationnarrative>
24 38 
                            </_locationnarrative_is_cultivated>
......
141 155 
                        </locationevent>
142 156 
                        <locationnarrative>
143 157 
                            <_merge>
144 
                                <1>$locality</1>
158 
                                <1>
159 
                                    <_map>
160 
                                        <ND></ND>
161 
                                        <NA></NA>
162 
                                        <*>*</*>
163 
                                        <value>$locality</value>
164 
                                    </_map>
165 
                                </1>
145 166 
                                <3>
146 167 
                                    <_label>
147 168 
                                        <label>habitat</label>
148 
                                        <value>$habitat</value>
169 
                                        <value>
170 
                                            <_map>
171 
                                                <ND></ND>
172 
                                                <NA></NA>
173 
                                                <*>*</*>
174 
                                                <value>$habitat</value>
175 
                                            </_map>
176 
                                        </value>
149 177 
                                    </_label>
150 178 
                                </3>
151 179 
                            </_merge>
......
224 252 
                                            </longitude_deg>
225 253 
                                        </coordinates>
226 254 
                                    </coordinates_id>
227 
                                    <country>$country</country>
228 
                                    <county>$county</county>
255 
                                    <country>
256 
                                        <_map>
257 
                                            <ND></ND>
258 
                                            <NA></NA>
259 
                                            <*>*</*>
260 
                                            <value>$country</value>
261 
                                        </_map>
262 
                                    </country>
263 
                                    <county>
264 
                                        <_map>
265 
                                            <ND></ND>
266 
                                            <NA></NA>
267 
                                            <*>*</*>
268 
                                            <value>$county</value>
269 
                                        </_map>
270 
                                    </county>
229 271 
                                    <matched_place_id>
230 272 
                                        <place>
231 273 
                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
......
301 343 
                                                    </longitude_deg>
302 344 
                                                </coordinates>
303 345 
                                            </coordinates_id>
304 
                                            <country>$country</country>
305 
                                            <county>$county</county>
306 
                                            <stateprovince>$state</stateprovince>
346 
                                            <country>
347 
                                                <_map>
348 
                                                    <ND></ND>
349 
                                                    <NA></NA>
350 
                                                    <*>*</*>
351 
                                                    <value>$country</value>
352 
                                                </_map>
353 
                                            </country>
354 
                                            <county>
355 
                                                <_map>
356 
                                                    <ND></ND>
357 
                                                    <NA></NA>
358 
                                                    <*>*</*>
359 
                                                    <value>$county</value>
360 
                                                </_map>
361 
                                            </county>
362 
                                            <stateprovince>
363 
                                                <_map>
364 
                                                    <ND></ND>
365 
                                                    <NA></NA>
366 
                                                    <*>*</*>
367 
                                                    <value>$state</value>
368 
                                                </_map>
369 
                                            </stateprovince>
307 370 
                                        </place>
308 371 
                                    </matched_place_id>
309 
                                    <stateprovince>$state</stateprovince>
372 
                                    <stateprovince>
373 
                                        <_map>
374 
                                            <ND></ND>
375 
                                            <NA></NA>
376 
                                            <*>*</*>
377 
                                            <value>$state</value>
378 
                                        </_map>
379 
                                    </stateprovince>
310 380 
                                </place>
311 381 
                            </place_id>
312 382 
                        </locationplace>

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