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Revision 4627

inputs/: Added [Veg+] to via map roots to indicate that the datasource and Veg+ vocabularies are combinable. This is possible now that automapped entries are no longer subtracted when this is in the map root, so there is no concern of losing comments on subtracted automapped rows. Note that this change turns on old-style automapping for these datasources, causing SALVIAS plotMetadata to acquire additional mappings.

View differences:

inputs/SALVIAS-CSV/Organism/map.csv
1
SALVIAS-CSV,Veg+,Comments
1
SALVIAS-CSV[Veg+],Veg+,Comments
2 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 3
PLOT_ID,locationID,
4 4
plot_code,plotName,
inputs/SALVIAS-CSV/Organism/map.full.csv
1
SALVIAS-CSV,Veg+,Comments
1
SALVIAS-CSV[Veg+],Veg+,Comments
2 2
basal_diam,basalDiameter,
3 3
stem_canopy_form,canopyForm,
4 4
stem_canopy_position,canopyPosition,
inputs/SALVIAS-CSV/Organism/VegBIEN.csv
1
SALVIAS-CSV,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
SALVIAS-CSV[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
subplot,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
3 3
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4 4
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",
inputs/SALVIAS-CSV/Plot/map.csv
1
SALVIAS-CSV,Veg+,Comments
1
SALVIAS-CSV[Veg+],Veg+,Comments
2 2
project,projectName,
3 3
PLOT_ID,locationID,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
4 4
plot_code,plotName,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
inputs/SALVIAS-CSV/Plot/map.full.csv
1
SALVIAS-CSV,Veg+,Comments
1
SALVIAS-CSV[Veg+],Veg+,Comments
2 2
soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
3 3
soil_base,"baseSaturation/_units:[default=""%"",to=]/value",
4 4
soil_Ca,"calcium/_units:[default=""%"",to=]/value",
inputs/SALVIAS-CSV/Plot/VegBIEN.csv
1
SALVIAS-CSV,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
SALVIAS-CSV[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
3 3
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
4 4
PLOT_ID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
inputs/CVS/Organism/map.csv
1
CVS,Veg+,Comments
1
CVS[Veg+],Veg+,Comments
2 2
authorObsCode,fieldNumber,
3 3
obsStartDate,startDate,
4 4
realLatitude,OMIT,
inputs/CVS/Organism/map.full.csv
1
CVS,Veg+,Comments
1
CVS[Veg+],Veg+,Comments
2 2
realLatitude,OMIT,
3 3
realLongitude,OMIT,
4 4
locationAccuracy-m,coordinateUncertaintyInMeters,
inputs/CVS/Organism/VegBIEN.csv
1
CVS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
CVS[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
authorObsCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/else",
3 3
locationAccuracy-m,/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,
4 4
publicLatitude,"/location/locationdetermination/latitude/_alt/1/_nullIf:[null=0,type=float]/value",
inputs/SALVIAS/plotMetadata/map.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
PlotID,locationID,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
3 3
orig_filename,,
4 4
AccessCode,,
inputs/SALVIAS/plotMetadata/map.full.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
soil_acidity,"acidity/_units:[default=""%"",to=]/value/_map:[""<0.05""=0,*=*]/value",
3 3
soil_base,"baseSaturation/_units:[default=""%"",to=]/value",
4 4
soil_Ca,"calcium/_units:[default=""%"",to=]/value",
......
14 14
LatDec,decimalLatitude,
15 15
LongDec,decimalLongitude,
16 16
date_finish,endDate,
17
habitat,habitat
17 18
Locality_Description,locality,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
18 19
PlotID,locationID,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
19 20
soil_Mg,"magnesium/_units:[default=""%"",to=]/value",
......
25 26
soil_P,"phosphorus/_units:[default=""%"",to=]/value/_map:[""<1,5""=0,*=*]/value",
26 27
plot_area_ha,plotArea,"Brad: Area in hectares. Is there any way to store units?; Aaron: VegX plot area annotation says ""Total area of the plot in square meters."" so units are fixed"
27 28
SiteCode,plotName,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
29
plotNotes,plotNotes
28 30
soil_K,"potassium/_units:[default=""%"",to=]/value",
29 31
Precip,precipitation,
30 32
project_id,projectID,
inputs/SALVIAS/plotMetadata/VegBIEN.csv
1
SALVIAS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
SALVIAS[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
SiteCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
3 3
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
4 4
PlotID,"/location/_if[@name=""if subplot""]/else/sourceaccessioncode","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
......
45 45
soil_texture,"/location/locationevent/soilobs/texture/_units:[default=""%"",to=]/value",
46 46
Temp,/location/locationevent/temperature,
47 47
Locality_Description,/location/locationnarrative/_merge/1,"Brad: No; this is free text description of locality where plot was situated, same as for DwC. Not a description of vegetation. Most likely='namedPlace.placeDescription' in VB; not sure about VX, again need to ask Nick where locality descriptions live in VX"
48
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?"
49
plotNotes,/location/notespublic,
48 50
slope_aspect,/location/slopeaspect/_alt/1/_compass/value,
49 51
slope_gradient,/location/slopegradient/_alt/1,
inputs/SALVIAS/plotMetadata/test.xml.ref
272 272
                    </soilobs>
273 273
                    <temperature>$Temp</temperature>
274 274
                </locationevent>
275
                <locationnarrative>$Locality_Description</locationnarrative>
275
                <locationnarrative>
276
                    <_merge>
277
                        <1>$Locality_Description</1>
278
                        <3>
279
                            <_label>
280
                                <label>habitat</label>
281
                                <value>$Habitat</value>
282
                            </_label>
283
                        </3>
284
                    </_merge>
285
                </locationnarrative>
286
                <notespublic>$plot_notes</notespublic>
276 287
                <slopeaspect><_compass><value>$slope_aspect</value></_compass></slopeaspect>
277 288
                <slopegradient>$slope_gradient</slopegradient>
278 289
            </location>
inputs/SALVIAS/stems/map.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
stem_id,stemID,
3 3
origrecord_id_stems,,
4 4
PlotObsID,individualID,
inputs/SALVIAS/stems/map.full.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
basal_diam,basalDiameter,
3 3
stem_canopy_form,canopyForm,
4 4
stem_canopy_position,canopyPosition,
inputs/SALVIAS/stems/VegBIEN.csv
1
SALVIAS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
SALVIAS[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
PlotObsID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/sourceaccessioncode,
3 3
NoInd,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount,
4 4
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter,
inputs/SALVIAS/plotObservations/map.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
PlotObsID,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 3
PlotID,locationID,
4 4
PlotCode,plotName,
inputs/SALVIAS/plotObservations/map.full.csv
1
SALVIAS,Veg+,Comments
1
SALVIAS[Veg+],Veg+,Comments
2 2
canopy_form,canopyForm,
3 3
canopy_position,canopyPosition,
4 4
coll_number,catalogNumber/_alt/1,Brad: Map instead as for voucher_string
inputs/SALVIAS/plotObservations/VegBIEN.csv
1
SALVIAS,VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
1
SALVIAS[Veg+],VegBIEN:/_simplifyPath:[next=parent_id]/path,Comments
2 2
Line,"/location/_if[@name=""if subplot""]/cond/_exists/_first/2",
3 3
PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1",
4 4
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists",

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