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Revision 4064

Added by Aaron Marcuse-Kubitza over 12 years ago

mappings/VegCSV-VegBIEN.specimens.csv: Mapped voucherType to indirect voucher _if statements' conditions

View differences:

inputs/SALVIAS-CSV/test/import.organisms.xml.ref
6 6 
                <1>$subplot</1>
7 7 
                <3>
8 8 
                    <_if name="if indirect voucher">
9 
                        <cond>
10 
                            <_eq>
11 
                                <right>indirect</right>
12 
                                <left>$det_type</left>
13 
                            </_eq>
14 
                        </cond>
9 15 
                        <else>
10 16 
                            <_alt>
11 17 
                                <1>$coll_number</1>
......
158 164 
                        <1>$OBSERVATION_ID</1>
159 165 
                        <2>
160 166 
                            <_if name="if indirect voucher">
167 
                                <cond>
168 
                                    <_eq>
169 
                                        <right>indirect</right>
170 
                                        <left>$det_type</left>
171 
                                    </_eq>
172 
                                </cond>
161 173 
                                <else>
162 174 
                                    <_alt>
163 175 
                                        <1>$coll_number</1>
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
1 1 
SALVIAS-CSV,VegBIEN:,Comments
2 2 
subplot,/location/authorlocationcode/_alt/1,
3 
det_type,"/location/authorlocationcode/_alt/3/_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."
3 4 
coll_number,"/location/authorlocationcode/_alt/3/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
4 5 
voucher_string,"/location/authorlocationcode/_alt/3/_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."
5 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:
......
37 38 
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position
38 39 
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."
39 40 
OBSERVATION_ID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/1,"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."
41 
det_type,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_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."
40 42 
coll_number,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
41 43 
voucher_string,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_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."
42 44 
individual_code,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/3,"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."
inputs/SALVIAS/test/import.organisms.xml.ref
6 6 
                <1>$Line</1>
7 7 
                <3>
8 8 
                    <_if name="if indirect voucher">
9 
                        <cond>
10 
                            <_eq>
11 
                                <right>indirect</right>
12 
                                <left>$DetType</left>
13 
                            </_eq>
14 
                        </cond>
9 15 
                        <else>
10 16 
                            <_alt>
11 17 
                                <1>$coll_number</1>
......
130 136 
                        <1>$PlotObsID</1>
131 137 
                        <2>
132 138 
                            <_if name="if indirect voucher">
139 
                                <cond>
140 
                                    <_eq>
141 
                                        <right>indirect</right>
142 
                                        <left>$DetType</left>
143 
                                    </_eq>
144 
                                </cond>
133 145 
                                <else>
134 146 
                                    <_alt>
135 147 
                                        <1>$coll_number</1>
inputs/SALVIAS/maps/VegBIEN.organisms.csv
1 1 
SALVIAS,VegBIEN:,Comments
2 2 
Line,/location/authorlocationcode/_alt/1,
3 
DetType,"/location/authorlocationcode/_alt/3/_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."
3 4 
coll_number,"/location/authorlocationcode/_alt/3/_merge/3/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
4 5 
SourceVoucher,"/location/authorlocationcode/_alt/3/_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."
5 6 
census_date,/location/locationevent/obsenddate/_*/date/_dateRangeEnd/value/_alt/1,"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:
......
40 41 
y_position,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,Brad: See comment above for x_position
41 42 
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 43 
PlotObsID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/1,"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."
44 
DetType,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_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."
43 45 
coll_number,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Incorrect. Map instead as for voucher_string
44 46 
SourceVoucher,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_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."
45 47 
Ind,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/3,"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."
mappings/VegCSV-VegBIEN.specimens.csv
2 2 
plotArea,/location/area,
3 3 
plotName,/location/authorlocationcode/_alt/1,
4 4 
fieldNumber,/location/authorlocationcode/_alt/2,
5 
voucherType,"/location/authorlocationcode/_alt/3/_merge/3/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left",
5 6 
catalogNumber,"/location/authorlocationcode/_alt/3/_merge/3/_if[@name=""if indirect voucher""]/else",
6 7 
verbatimElevation,"/location/elevation/_alt/1/_replace:[""\bca\.?""=]/value",
7 8 
maximumElevationInMeters,"/location/elevation/_alt/2/_avg/max/_units:[default=m,to=m,to=]/value/_replace:[""\bca\.?""=]/value",
......
71 72 
relativePlotY,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/yposition,
72 73 
growthForm,/location/locationevent/taxonoccurrence/growthform,
73 74 
occurrenceID,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/1,
75 
voucherType,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left",
74 76 
catalogNumber,"/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/2/_if[@name=""if indirect voucher""]/else",
75 77 
recordNumber,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/3,
76 78 
scientificName,/location/locationevent/taxonoccurrence/sourceaccessioncode/_alt/4,
mappings/for_review/VegCSV-VegBIEN.specimens.csv
2 2 
plotArea,//location/area,
3 3 
plotName,//location/authorlocationcode,
4 4 
fieldNumber,//location/authorlocationcode,
5 
voucherType,"//location/authorlocationcode/_if[@name=""if indirect voucher""]/cond",
5 6 
catalogNumber,"//location/authorlocationcode/_if[@name=""if indirect voucher""]/else",
6 7 
verbatimElevation,//location/elevation,
7 8 
maximumElevationInMeters,//location/elevation,
......
71 72 
relativePlotY,//stemobservation/yposition,
72 73 
growthForm,//taxonoccurrence/growthform,
73 74 
occurrenceID,//taxonoccurrence/sourceaccessioncode,
75 
voucherType,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if indirect voucher""]/cond",
74 76 
catalogNumber,"//taxonoccurrence/sourceaccessioncode/_if[@name=""if indirect voucher""]/else",
75 77 
recordNumber,//taxonoccurrence/sourceaccessioncode,
76 78 
scientificName,//taxonoccurrence/sourceaccessioncode,

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