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Revision 3931

mappings/VegCSV-VegBIEN.specimens.csv: catalogNumber: Default to mapping via plantobservation rather than via voucher when no voucherType is specified, in order to be consistent with the specimens data mapping for catalogNumber

View differences:

inputs/SALVIAS-CSV/test/import.organisms.xml.ref
25 25
                    <name>specimenreplicate_via</name>
26 26
                    <cond>
27 27
                        <_eq>
28
                            <right>direct</right>
28
                            <right>indirect</right>
29 29
                            <left>$det_type</left>
30 30
                        </_eq>
31 31
                    </cond>
32 32
                    <else>
33
                        <voucher>
34
                            <specimenreplicate_id>
33
                        <aggregateoccurrence merge="1">
34
                            <plantobservation merge="1">
35 35
                                <specimenreplicate>
36 36
                                    <catalognumber_dwc>
37 37
                                        <_alt>
......
40 40
                                        </_alt>
41 41
                                    </catalognumber_dwc>
42 42
                                </specimenreplicate>
43
                            </specimenreplicate_id>
44
                        </voucher>
43
                            </plantobservation>
44
                        </aggregateoccurrence>
45 45
                    </else>
46 46
                    <then>
47
                        <aggregateoccurrence merge="1">
48
                            <plantobservation merge="1">
47
                        <voucher>
48
                            <specimenreplicate_id>
49 49
                                <specimenreplicate>
50 50
                                    <catalognumber_dwc>
51 51
                                        <_alt>
......
54 54
                                        </_alt>
55 55
                                    </catalognumber_dwc>
56 56
                                </specimenreplicate>
57
                            </plantobservation>
58
                        </aggregateoccurrence>
57
                            </specimenreplicate_id>
58
                        </voucher>
59 59
                    </then>
60 60
                </_if>
61 61
                <aggregateoccurrence>
......
316 316
        </sourceaccessioncode>
317 317
    </location>
318 318
</VegBIEN>
319
Inserted 56 new rows into database
319
Inserted 54 new rows into database
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
5 5
plot_code,/location/locationevent/parent_id/locationevent/*_id/location/sourceaccessioncode/_alt/2,"Brad: Same as plotCode, above","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/plotName","3, 1"
6 6
plot_code,/location/locationevent/parent_id/locationevent/authorlocationcode,"Brad: Same as plotCode, above","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/plotName","3, 1"
7 7
PLOT_ID,/location/locationevent/parent_id/locationevent/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above.","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://rs.tdwg.org/dwc/terms/#occurrenceID","3, 0"
8
det_type,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/cond/_eq:[right=direct]/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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
9
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
10
voucher_string,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
11
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
12
voucher_string,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
8
det_type,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
9
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
10
voucher_string,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
11
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
12
voucher_string,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
13 13
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.",http://rs.tdwg.org/dwc/terms/#individualCount,25
14 14
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/attributes/attribute/ordinal/coverPercent,0
15 15
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.; Expanded for clarity",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.census_no,3
inputs/SALVIAS/test/import.organisms.xml.ref
24 24
                    <name>specimenreplicate_via</name>
25 25
                    <cond>
26 26
                        <_eq>
27
                            <right>direct</right>
27
                            <right>indirect</right>
28 28
                            <left>$DetType</left>
29 29
                        </_eq>
30 30
                    </cond>
31 31
                    <else>
32
                        <voucher>
33
                            <specimenreplicate_id>
32
                        <aggregateoccurrence merge="1">
33
                            <plantobservation merge="1">
34 34
                                <specimenreplicate>
35 35
                                    <catalognumber_dwc>
36 36
                                        <_alt>
......
39 39
                                        </_alt>
40 40
                                    </catalognumber_dwc>
41 41
                                </specimenreplicate>
42
                            </specimenreplicate_id>
43
                        </voucher>
42
                            </plantobservation>
43
                        </aggregateoccurrence>
44 44
                    </else>
45 45
                    <then>
46
                        <aggregateoccurrence merge="1">
47
                            <plantobservation merge="1">
46
                        <voucher>
47
                            <specimenreplicate_id>
48 48
                                <specimenreplicate>
49 49
                                    <catalognumber_dwc>
50 50
                                        <_alt>
......
53 53
                                        </_alt>
54 54
                                    </catalognumber_dwc>
55 55
                                </specimenreplicate>
56
                            </plantobservation>
57
                        </aggregateoccurrence>
56
                            </specimenreplicate_id>
57
                        </voucher>
58 58
                    </then>
59 59
                </_if>
60 60
                <aggregateoccurrence>
inputs/SALVIAS/maps/VegBIEN.organisms.csv
4 4
PlotCode,/location/locationevent/parent_id/locationevent/*_id/location/sourceaccessioncode/_alt/2,"Brad: Same as plotCode, above","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/plotName","3, 1"
5 5
PlotCode,/location/locationevent/parent_id/locationevent/authorlocationcode,"Brad: Same as plotCode, above","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot/plotName","3, 1"
6 6
PlotID,/location/locationevent/parent_id/locationevent/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above.","http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=plot&entity=dba_tabledescription&where=where_tablename#PARENT_ID, http://rs.tdwg.org/dwc/terms/#occurrenceID","3, 0"
7
DetType,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/cond/_eq:[right=direct]/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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
8
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
9
SourceVoucher,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
10
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
11
SourceVoucher,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
7
DetType,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/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.; values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
8
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
9
SourceVoucher,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
10
coll_number,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/1,Brad: Incorrect. Map instead as for voucher_string,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
11
SourceVoucher,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/voucher/*_id/specimenreplicate/catalognumber_dwc/_alt/2,"Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below.",http://rs.tdwg.org/dwc/terms/#catalogNumber,20
12 12
census_date,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_dateRangeStart/value/_*/date,,http://rs.tdwg.org/dwc/terms/#eventDate,44
13 13
NoInd,/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.",http://rs.tdwg.org/dwc/terms/#individualCount,25
14 14
cover_percent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/attributes/attribute/ordinal/coverPercent,0
mappings/VegCSV-VegBIEN.specimens.csv
45 45
sodium,/location/locationevent/soilobs/sodium,Expanded for clarity,http://nimoy.nceas.ucsb.edu/phpmyadmin/index.php?db=salvias_plots&table=plotMetadata&target=tbl_structure.php#soil_Na,41
46 46
texture,/location/locationevent/soilobs/texture,,http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilObs&entity=dba_tabledescription&where=where_tablename#soilTexture,7
47 47
plotID,/location/locationevent/sourceaccessioncode,,"http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot, http://rs.tdwg.org/dwc/terms/#occurrenceID",", 0"
48
voucherType,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/cond/_eq:[right=direct]/left,"values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
49
catalogNumber,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/voucher/*_id/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
50
catalogNumber,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
48
voucherType,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/cond/_eq:[right=indirect]/left,"values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
49
catalogNumber,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/else/aggregateoccurrence:[@merge=1]/plantobservation:[@merge=1]/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
50
catalogNumber,/location/locationevent/taxonoccurrence/_if:[name=specimenreplicate_via]/then/voucher/*_id/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
51 51
eventDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_*/date/_dateRangeStart/value,,http://rs.tdwg.org/dwc/terms/#eventDate,44
52 52
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count,,http://rs.tdwg.org/dwc/terms/#individualCount,25
53 53
coverPercent,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/attributes/attribute/ordinal/coverPercent,0
mappings/for_review/VegCSV-VegBIEN.specimens.csv
46 46
texture,//soilobs/texture,,http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=soilObs&entity=dba_tabledescription&where=where_tablename#soilTexture,7
47 47
plotID,//locationevent/sourceaccessioncode,,"http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/plots/plot, http://rs.tdwg.org/dwc/terms/#occurrenceID",", 0"
48 48
voucherType,//locationevent/taxonoccurrence,"values: direct, indirect",http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data.det_type,17
49
catalogNumber,//locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
49 50
catalogNumber,//locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
50
catalogNumber,//locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc,,http://rs.tdwg.org/dwc/terms/#catalogNumber,20
51 51
eventDate,//aggregateoccurrence/collectiondate/_*/date,,http://rs.tdwg.org/dwc/terms/#eventDate,44
52 52
individualCount,//aggregateoccurrence/count,,http://rs.tdwg.org/dwc/terms/#individualCount,25
53 53
coverPercent,//aggregateoccurrence/cover,,http://wiki.tdwg.org/twiki/pub/Vegetation/WebHome/VegX_Schema_1.5.3_proposed.zip#/veg.xsd#/attributes/attribute/ordinal/coverPercent,0

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