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Revision 3203

Added by Aaron Marcuse-Kubitza over 12 years ago

VegBIEN: Fixing import issue related to duplicate entries in tables with children, where when a new table entry duplicates an existing entry, the 1:1 tables of that table and those tables' children are not merged, causing them to become orphaned. It is described in detail at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Import_issues#Merging-duplicates-with-children&gt;, including the rationale for this solution. Note that this is not a bug in column-based import, it applies to row-based import as well. This commit fixes the issue for specimenreplicate->...->location, by also mapping specimenreplicate's unique keys to location.sourceaccessioncode and setting location.datasource_id.

View differences:

inputs/QMOR/maps/VegBIEN.specimens.csv
1 
QMOR[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
QMOR[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
coordinateUncertaintyInMeters,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
footprintWKT,/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91
4 4 
county,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
......
14 14 
decimalLongitude,"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86
15 15 
verbatimLongitude,"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,82
16 16 
eventDate,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/2",,44
17 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
17 
collectionID,/collectionnumber/_alt/2,,9
18 18 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
19 19 
dateIdentified,/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/2,,120
20 20 
identifiedBy,"/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
......
29 29 
phylum,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
30 30 
kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
31 31 
recordedBy,/verbatimcollectorname,,23
32 
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
33 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
34 
institutionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,8
35 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
36 
id,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
32 
institutionID,"/{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/1",,8
33 
catalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
34 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
35 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
36 
id,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
37 37 
acceptedNameUsage,,** No non-empty join mapping for acceptedNameUsage **
38 38 
basisOfRecord,,** No non-empty join mapping for basisOfRecord **
39 39 
behavior,,** No non-empty join mapping for behavior **
mappings/for_review/DwC2-VegBIEN.specimens.csv
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/","VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
coordinateUncertaintyInMeters,//locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
coordinatePrecision,//locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
4 4 
footprintWKT,//locationdetermination/footprintgeometry_dwc,,91
......
18 18 
maximumDepthInMeters,//locationevent/waterdepth/_avg/max/_units/value,,75
19 19 
minimumDepthInMeters,//locationevent/waterdepth/_avg/min/_units/value,,74
20 20 
eventDate,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value",,44
21 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
21 
recordNumber,/collectionnumber/_alt/1,,22
22 
collectionID,/collectionnumber/_alt/2,,9
23 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
22 24 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
23 25 
fieldNotes,/description/_merge/1,,
24 26 
taxonRemarks,/description/_merge/2,,158
......
35 37 
phylum,"/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
36 38 
kingdom,"/taxondetermination[role=identifier]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
37 39 
recordedBy,/verbatimcollectorname,,23
40 
institutionID,"/{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/1",,8
41 
catalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
42 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
38 43 
establishmentMeans,"/{growthform/_map,iscultivated/_map,isnative/_map}/value",,30
39 
catalogNumber,/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
40 
recordNumber,/collectionnumber/_alt/1,,22
41 
collectionID,/collectionnumber/_alt/2,,9
42 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43 
institutionID,//party/organizationname/_alt/1,,8
44 
institutionCode,//party/organizationname,,
45 
occurrenceID,/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
44 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
45 
occurrenceID,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
46 46 
acceptedNameUsage,,,135
47 47 
acceptedNameUsageID,,,128
48 48 
associatedMedia,,,36
mappings/DwC.cs-VegBIEN.specimens.csv
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/",VegBIEN:/specimenreplicate,Comments,Order
1 
"DwC::[@xmlns:dcterms=""http://purl.org/dc/terms/""]/list:[institutionID=$/_ignore/inLabel]/","VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
coordinateUncertaintyInMeters,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
coordinatePrecision,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
4 4 
boundingBox,/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91
......
32 32 
yearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
33 33 
eventDate,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/2",,44
34 34 
collectedDate,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/3",,44
35 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
35 
collectorNumber,/collectionnumber/_alt/1/_alt/1,,22
36 
recordNumber,/collectionnumber/_alt/1/_alt/2,,22
37 
collectionID,/collectionnumber/_alt/2,,9
38 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
36 39 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
37 40 
fieldNotes,/description/_merge/1,,
38 41 
notes,/description/_merge/1,,
......
60 63 
kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
61 64 
collector,/verbatimcollectorname,,23
62 65 
recordedBy,/verbatimcollectorname,,23
66 
institutionID,"/{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/1",,8
67 
catalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
68 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
63 69 
establishmentMeans,"/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
64 
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
65 
collectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
66 
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/2,,22
67 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
68 
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
69 
institutionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1,,8
70 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
71 
globalUniqueIdentifier,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
72 
id,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
73 
occurrenceID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
70 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
71 
globalUniqueIdentifier,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
72 
id,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
73 
occurrenceID,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
74 74 
acceptedNameUsage,,,135
75 75 
acceptedNameUsageID,,,128
76 76 
accessRights,,** No non-empty join mapping for dcterms:accessRights ** Versions without namespace
inputs/MT/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
14 16 
                            </namedplace_id>
15 17 
                        </locationdetermination>
16 18 
                        <locationnarrative>Canada</locationnarrative>
19 
                        <sourceaccessioncode>1</sourceaccessioncode>
17 20 
                    </location>
18 21 
                </location_id>
19 22 
            </locationevent>
20 23 
        </locationevent_id>
21 
        <collectioncode_dwc>MT</collectioncode_dwc>
24 
        <collectionnumber>urn:lsid:biocol.org:col:14437</collectionnumber>
22 25 
        <taxondetermination>
23 26 
            <isoriginal>true</isoriginal>
24 27 
            <iscurrent>true</iscurrent>
......
40 43 
                </plantconcept>
41 44 
            </plantconcept_id>
42 45 
        </taxondetermination>
43 
        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
44 
        <collectionnumber>urn:lsid:biocol.org:col:14437</collectionnumber>
46 
        <collectioncode_dwc>MT</collectioncode_dwc>
45 47 
        <institution_id><party><organizationname>Universit&#233; de Montr&#233;al Biodiversity Centre</organizationname></party></institution_id>
46 48 
        <sourceaccessioncode>1</sourceaccessioncode>
47 49 
    </specimenreplicate>
48 50 
    <specimenreplicate id="1">
51 
        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
49 52 
        <locationevent_id>
50 53 
            <locationevent>
51 54 
                <location_id>
52 55 
                    <location>
56 
                        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
53 57 
                        <locationdetermination>
54 58 
                            <namedplace_id>
55 59 
                                <namedplace>
......
59 63 
                            </namedplace_id>
60 64 
                        </locationdetermination>
61 65 
                        <locationnarrative>Canada</locationnarrative>
66 
                        <sourceaccessioncode>2</sourceaccessioncode>
62 67 
                    </location>
63 68 
                </location_id>
64 69 
            </locationevent>
65 70 
        </locationevent_id>
66 
        <collectioncode_dwc>MT</collectioncode_dwc>
71 
        <collectionnumber>urn:lsid:biocol.org:col:14437</collectionnumber>
67 72 
        <taxondetermination>
68 73 
            <isoriginal>true</isoriginal>
69 74 
            <iscurrent>true</iscurrent>
......
85 90 
                </plantconcept>
86 91 
            </plantconcept_id>
87 92 
        </taxondetermination>
88 
        <datasource_id><party><organizationname>MT</organizationname></party></datasource_id>
89 
        <collectionnumber>urn:lsid:biocol.org:col:14437</collectionnumber>
93 
        <collectioncode_dwc>MT</collectioncode_dwc>
90 94 
        <institution_id><party><organizationname>Universit&#233; de Montr&#233;al Biodiversity Centre</organizationname></party></institution_id>
91 95 
        <sourceaccessioncode>2</sourceaccessioncode>
92 96 
    </specimenreplicate>
inputs/MT/maps/VegBIEN.specimens.csv
1 
MT[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
MT[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
continent,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,country,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=continent]/placename",Brad: OMIT,59
3 3 
locality,/*_id/locationevent/*_id/location/locationnarrative/_merge/1,,68
4 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
4 
collectionID,/collectionnumber/_alt/2,,9
5 5 
genus,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=genus]/plantname",,147
6 6 
family,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=family]/plantname",,146
7 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
7 8 
establishmentMeans,"/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value",,30
8 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
9 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
10 
id,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
9 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
10 
id,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
11 11 
basisOfRecord,,** No non-empty join mapping for basisOfRecord **
12 12 
countryCode,,** No non-empty join mapping for countryCode **
13 13 
datasetName,,** No non-empty join mapping for datasetName **
inputs/XAL/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
38 40 
                        <elevationrange/>
39 41 
                        <centerlatitude>22.267</centerlatitude>
40 42 
                        <centerlongitude>-104.633</centerlongitude>
43 
                        <sourceaccessioncode>IE; XAL; K400001</sourceaccessioncode>
41 44 
                    </location>
42 45 
                </location_id>
43 46 
                <waterdepth>1000.0</waterdepth>
......
45 48 
                <obsenddate/>
46 49 
            </locationevent>
47 50 
        </locationevent_id>
48 
        <collectioncode_dwc>XAL</collectioncode_dwc>
51 
        <collectionnumber>7086</collectionnumber>
49 52 
        <definedvalue fkey="tablerecord_id">
50 53 
            <userdefined_id>
51 54 
                <userdefined>
......
120 123 
            </plantconcept_id>
121 124 
        </taxondetermination>
122 125 
        <verbatimcollectorname>J.A. Machuca N.</verbatimcollectorname>
123 
        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
124 126 
        <catalognumber_dwc>K400001</catalognumber_dwc>
125 
        <collectionnumber>7086</collectionnumber>
127 
        <collectioncode_dwc>XAL</collectioncode_dwc>
126 128 
        <institution_id><party><organizationname>IE</organizationname></party></institution_id>
127 129 
    </specimenreplicate>
128 130 
    <specimenreplicate id="1">
131 
        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
129 132 
        <locationevent_id>
130 133 
            <locationevent>
131 134 
                <location_id>
132 135 
                    <location>
136 
                        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
133 137 
                        <locationdetermination>
134 138 
                            <namedplace_id>
135 139 
                                <namedplace>
......
163 167 
                        <elevationrange/>
164 168 
                        <centerlatitude>17.644</centerlatitude>
165 169 
                        <centerlongitude>-96.529</centerlongitude>
170 
                        <sourceaccessioncode>IE; XAL; K400002</sourceaccessioncode>
166 171 
                    </location>
167 172 
                </location_id>
168 173 
                <waterdepth>2430.0</waterdepth>
......
170 175 
                <obsenddate/>
171 176 
            </locationevent>
172 177 
        </locationevent_id>
173 
        <collectioncode_dwc>XAL</collectioncode_dwc>
178 
        <collectionnumber>1216</collectionnumber>
174 179 
        <definedvalue fkey="tablerecord_id">
175 180 
            <userdefined_id>
176 181 
                <userdefined>
......
245 250 
            </plantconcept_id>
246 251 
        </taxondetermination>
247 252 
        <verbatimcollectorname>C. Gallardo H. y  et al.</verbatimcollectorname>
248 
        <datasource_id><party><organizationname>XAL</organizationname></party></datasource_id>
249 253 
        <catalognumber_dwc>K400002</catalognumber_dwc>
250 
        <collectionnumber>1216</collectionnumber>
254 
        <collectioncode_dwc>XAL</collectioncode_dwc>
251 255 
        <institution_id><party><organizationname>IE</organizationname></party></institution_id>
252 256 
    </specimenreplicate>
253 257 
</VegBIEN>
inputs/XAL/maps/VegBIEN.specimens.csv
1 
"XAL[DwC,darwin:]:/content/record/",VegBIEN:/specimenreplicate,Comments,Order
1 
"XAL[DwC,darwin:]:/content/record/","VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
CoordinatePrecision,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
3 3 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
4 4 
StateProvince,"/*_id/locationevent/*_id/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",,65
......
14 14 
DayCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
15 15 
MonthCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
16 16 
YearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
17 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
17 
CollectorNumber,/collectionnumber/_alt/1/_alt/1,,22
18 
FieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
18 19 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
19 20 
Notes,/description/_merge/1,,
20 21 
DayIdentified,"/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,120
......
32 33 
Phylum,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
33 34 
Kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
34 35 
Collector,/verbatimcollectorname,,23
35 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
36 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
37 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
38 
InstitutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
36 
CatalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
37 
CollectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
38 
InstitutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
39 39 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
40 40 
DateLastModified,,** No non-empty join mapping for DateLastModified **
41 41 
IndividualCount,,** No non-empty join mapping for IndividualCount **
inputs/NY/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
38 40 
                        <elevationrange>0.0</elevationrange>
39 41 
                        <centerlatitude>-11.80</centerlatitude>
40 42 
                        <centerlongitude>-71.40</centerlongitude>
43 
                        <sourceaccessioncode>816590</sourceaccessioncode>
41 44 
                    </location>
42 45 
                </location_id>
43 46 
                <obsstartdate>1984-08-20</obsstartdate>
44 47 
                <obsenddate/>
45 48 
            </locationevent>
46 49 
        </locationevent_id>
47 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
50 
        <collectionnumber>9877</collectionnumber>
48 51 
        <description>plant fungus: with rough brown bark, almost no buttressing, 1 m diam; fallen fruit and leaves</description>
49 52 
        <taxondetermination>
50 53 
            <isoriginal>true</isoriginal>
......
98 101 
            </plantconcept_id>
99 102 
        </taxondetermination>
100 103 
        <verbatimcollectorname>R. B. Foster</verbatimcollectorname>
101 
        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
102 104 
        <catalognumber_dwc>00682023</catalognumber_dwc>
103 
        <collectionnumber>9877</collectionnumber>
105 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
104 106 
        <institution_id><party><organizationname>NY</organizationname></party></institution_id>
105 107 
        <sourceaccessioncode>816590</sourceaccessioncode>
106 108 
    </specimenreplicate>
107 109 
    <specimenreplicate id="1">
110 
        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
108 111 
        <locationevent_id>
109 112 
            <locationevent>
110 113 
                <location_id>
111 114 
                    <location>
115 
                        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
112 116 
                        <locationdetermination>
113 117 
                            <namedplace_id>
114 118 
                                <namedplace>
......
136 140 
                        <elevationrange>0.0</elevationrange>
137 141 
                        <centerlatitude>17.40</centerlatitude>
138 142 
                        <centerlongitude>-88.50</centerlongitude>
143 
                        <sourceaccessioncode>220541</sourceaccessioncode>
139 144 
                    </location>
140 145 
                </location_id>
141 146 
                <obsstartdate>1994-01-17</obsstartdate>
142 147 
                <obsenddate/>
143 148 
            </locationevent>
144 149 
        </locationevent_id>
145 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
150 
        <collectionnumber>545</collectionnumber>
146 151 
        <taxondetermination>
147 152 
            <isoriginal>true</isoriginal>
148 153 
            <iscurrent>true</iscurrent>
......
177 182 
            </plantconcept_id>
178 183 
        </taxondetermination>
179 184 
        <verbatimcollectorname>J. B. Walker</verbatimcollectorname>
180 
        <datasource_id><party><organizationname>NY</organizationname></party></datasource_id>
181 185 
        <catalognumber_dwc>200996</catalognumber_dwc>
182 
        <collectionnumber>545</collectionnumber>
186 
        <collectioncode_dwc>Herbarium</collectioncode_dwc>
183 187 
        <institution_id><party><organizationname>NY</organizationname></party></institution_id>
184 188 
        <sourceaccessioncode>220541</sourceaccessioncode>
185 189 
    </specimenreplicate>
inputs/NY/maps/VegBIEN.specimens.csv
1 
NY[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
NY[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
CoordinatePrecision,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
3 3 
BoundingBox,/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91
4 4 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
......
18 18 
DayCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
19 19 
MonthCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
20 20 
YearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
21 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
21 
CollectorNumber,/collectionnumber/_alt/1/_alt/1,,22
22 
FieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
22 23 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
23 24 
Notes,/description/_merge/1/_merge/1,,
24 25 
PlantFungusDescription,"/description/_merge/1/_merge/2/_label[label=""plant fungus""]/value",,
......
37 38 
Phylum,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
38 39 
Kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
39 40 
Collector,/verbatimcollectorname,,23
40 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
42 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43 
InstitutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
44 
UniqueNYInternalRecordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
41 
CatalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
42 
CollectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
43 
InstitutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
44 
UniqueNYInternalRecordNumber,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
45 45 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
46 46 
DateLastModified,,** No non-empty join mapping for DateLastModified **
47 47 
IndividualCount,,** No non-empty join mapping for IndividualCount **
inputs/UNCC/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
19 21 
                                </namedplace>
20 22 
                            </namedplace_id>
21 23 
                        </locationdetermination>
24 
                        <sourceaccessioncode>34293</sourceaccessioncode>
22 25 
                    </location>
23 26 
                </location_id>
24 27 
                <obsstartdate>1972-06-25</obsstartdate>
25 28 
                <obsenddate/>
26 29 
            </locationevent>
27 30 
        </locationevent_id>
28 
        <collectioncode_dwc>UNCCD</collectioncode_dwc>
29 31 
        <taxondetermination>
30 32 
            <isoriginal>true</isoriginal>
31 33 
            <iscurrent>true</iscurrent>
......
42 44 
            </plantconcept_id>
43 45 
        </taxondetermination>
44 46 
        <verbatimcollectorname>DAGGY, T.</verbatimcollectorname>
45 
        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
47 
        <collectioncode_dwc>UNCCD</collectioncode_dwc>
46 48 
        <sourceaccessioncode>34293</sourceaccessioncode>
47 49 
    </specimenreplicate>
48 50 
    <specimenreplicate id="1">
51 
        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
49 52 
        <locationevent_id>
50 53 
            <locationevent>
51 54 
                <location_id>
52 55 
                    <location>
56 
                        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
53 57 
                        <locationdetermination>
54 58 
                            <namedplace_id>
55 59 
                                <namedplace>
......
64 68 
                                </namedplace>
65 69 
                            </namedplace_id>
66 70 
                        </locationdetermination>
71 
                        <sourceaccessioncode>34294</sourceaccessioncode>
67 72 
                    </location>
68 73 
                </location_id>
69 74 
                <obsstartdate>1972-06-25</obsstartdate>
70 75 
                <obsenddate/>
71 76 
            </locationevent>
72 77 
        </locationevent_id>
73 
        <collectioncode_dwc>UNCCD</collectioncode_dwc>
74 78 
        <taxondetermination>
75 79 
            <isoriginal>true</isoriginal>
76 80 
            <iscurrent>true</iscurrent>
......
87 91 
            </plantconcept_id>
88 92 
        </taxondetermination>
89 93 
        <verbatimcollectorname>DAGGY, T.</verbatimcollectorname>
90 
        <datasource_id><party><organizationname>UNCC</organizationname></party></datasource_id>
94 
        <collectioncode_dwc>UNCCD</collectioncode_dwc>
91 95 
        <sourceaccessioncode>34294</sourceaccessioncode>
92 96 
    </specimenreplicate>
93 97 
</VegBIEN>
inputs/UNCC/maps/VegBIEN.specimens.csv
1 
UNCC[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
UNCC[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
county,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
3 3 
state,"/*_id/locationevent/*_id/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",,65
4 4 
country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
......
7 7 
collday,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
8 8 
collmonth,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
9 9 
collyear,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
10 
herbarium,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
10 
collectno,/collectionnumber/_alt/1/_alt/1,,22
11 11 
comment1,/description/_merge/1/_merge/1,,
12 12 
comment2,/description/_merge/1/_merge/2,,
13 13 
comment3,/description/_merge/1/_merge/3,,
......
25 25 
collector1,/verbatimcollectorname/_merge/2,,23
26 26 
collector2,/verbatimcollectorname/_merge/3,,23
27 27 
collector3,/verbatimcollectorname/_merge/4,,23
28 
herbarium,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
28 29 
cultivated,"/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value/_map:[Y=cultivated,N=wild,*=]/value",Ignore other values,30
29 
collectno,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
30 
accession,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
30 
accession,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
31 31 
filler,,"Where used, same as family"
32 32 
flower,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
33 33 
fruit,,"** No non-empty join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?"
inputs/ACAD/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
36 38 
                        <locationnarrative>West Gore; habitat: dry field</locationnarrative>
37 39 
                        <centerlatitude>45.094243</centerlatitude>
38 40 
                        <centerlongitude>-63.778249</centerlongitude>
41 
                        <sourceaccessioncode>8</sourceaccessioncode>
39 42 
                    </location>
40 43 
                </location_id>
41 44 
                <obsstartdate>1932-09-19</obsstartdate>
42 45 
                <obsenddate/>
43 46 
            </locationevent>
44 47 
        </locationevent_id>
45 
        <collectioncode_dwc>ACAD</collectioncode_dwc>
48 
        <collectionnumber>urn:lsid:biocol.org:col:13294</collectionnumber>
46 49 
        <taxondetermination>
47 50 
            <isoriginal>true</isoriginal>
48 51 
            <iscurrent>true</iscurrent>
......
113 116 
            </plantconcept_id>
114 117 
        </taxondetermination>
115 118 
        <verbatimcollectorname>Wallace, FM</verbatimcollectorname>
116 
        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
117 119 
        <catalognumber_dwc>11186</catalognumber_dwc>
118 
        <collectionnumber>urn:lsid:biocol.org:col:13294</collectionnumber>
120 
        <collectioncode_dwc>ACAD</collectioncode_dwc>
119 121 
        <institution_id><party><organizationname>Acadia University</organizationname></party></institution_id>
120 122 
        <sourceaccessioncode>8</sourceaccessioncode>
121 123 
    </specimenreplicate>
122 124 
    <specimenreplicate id="1">
125 
        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
123 126 
        <locationevent_id>
124 127 
            <locationevent>
125 128 
                <location_id>
126 129 
                    <location>
130 
                        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
127 131 
                        <locationdetermination>
128 132 
                            <namedplace_id>
129 133 
                                <namedplace>
......
155 159 
                        <locationnarrative>Middleboro; habitat: pasture</locationnarrative>
156 160 
                        <centerlatitude>45.737092</centerlatitude>
157 161 
                        <centerlongitude>-63.57842</centerlongitude>
162 
                        <sourceaccessioncode>17</sourceaccessioncode>
158 163 
                    </location>
159 164 
                </location_id>
160 165 
                <obsstartdate>1938-07-09</obsstartdate>
161 166 
                <obsenddate/>
162 167 
            </locationevent>
163 168 
        </locationevent_id>
164 
        <collectioncode_dwc>ACAD</collectioncode_dwc>
169 
        <collectionnumber>urn:lsid:biocol.org:col:13294</collectionnumber>
165 170 
        <taxondetermination>
166 171 
            <isoriginal>true</isoriginal>
167 172 
            <iscurrent>true</iscurrent>
......
226 231 
            </plantconcept_id>
227 232 
        </taxondetermination>
228 233 
        <verbatimcollectorname>Manning, K</verbatimcollectorname>
229 
        <datasource_id><party><organizationname>ACAD</organizationname></party></datasource_id>
230 234 
        <catalognumber_dwc>12602</catalognumber_dwc>
231 
        <collectionnumber>urn:lsid:biocol.org:col:13294</collectionnumber>
235 
        <collectioncode_dwc>ACAD</collectioncode_dwc>
232 236 
        <institution_id><party><organizationname>Acadia University</organizationname></party></institution_id>
233 237 
        <sourceaccessioncode>17</sourceaccessioncode>
234 238 
    </specimenreplicate>
inputs/ACAD/maps/VegBIEN.specimens.csv
1 
ACAD[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
ACAD[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
county,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
3 3 
stateProvince,"/*_id/locationevent/*_id/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",,65
4 4 
country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
......
8 8 
decimalLatitude,"/*_id/locationevent/*_id/location/{locationdetermination/latitude,centerlatitude}/_alt/1/_nullIf:[null=0,type=float]/value",,85
9 9 
decimalLongitude,"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86
10 10 
eventDate,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/2",,44
11 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
11 
recordNumber,/collectionnumber/_alt/1/_alt/2,,22
12 
collectionID,/collectionnumber/_alt/2,,9
12 13 
dateIdentified,/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/2,,120
13 14 
identifiedBy,"/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
14 15 
scientificName,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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","Brad: Bob, Nick, please is this mapping OK?",134
......
22 23 
phylum,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
23 24 
kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
24 25 
recordedBy,/verbatimcollectorname,,23
25 
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
26 
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/2,,22
27 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
28 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
29 
id,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
26 
catalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
27 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
28 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
29 
id,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
30 30 
basisOfRecord,,** No non-empty join mapping for basisOfRecord **
31 31 
bibliographicCitation,,** No non-empty join mapping for bibliographicCitation **
32 32 
dynamicProperties,,** No non-empty join mapping for dynamicProperties **
inputs/REMIB/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
30 32 
                        <locationnarrative>ND; habitat: ND</locationnarrative>
31 33 
                        <centerlatitude>99</centerlatitude>
32 34 
                        <centerlongitude>-999</centerlongitude>
35 
                        <sourceaccessioncode>1764</sourceaccessioncode>
33 36 
                    </location>
34 37 
                </location_id>
35 38 
                <obsstartdate>1979-12-09</obsstartdate>
36 39 
                <obsenddate/>
37 40 
            </locationevent>
38 41 
        </locationevent_id>
39 
        <collectioncode_dwc>XAL</collectioncode_dwc>
40 42 
        <taxondetermination>
41 43 
            <isoriginal>true</isoriginal>
42 44 
            <iscurrent>true</iscurrent>
......
65 67 
            </plantconcept_id>
66 68 
        </taxondetermination>
67 69 
        <verbatimcollectorname>B. Guerrero C.</verbatimcollectorname>
68 
        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
70 
        <collectioncode_dwc>XAL</collectioncode_dwc>
69 71 
        <sourceaccessioncode>1764</sourceaccessioncode>
70 72 
    </specimenreplicate>
71 73 
    <specimenreplicate id="1">
74 
        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
72 75 
        <locationevent_id>
73 76 
            <locationevent>
74 77 
                <location_id>
75 78 
                    <location>
79 
                        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
76 80 
                        <locationdetermination>
77 81 
                            <namedplace_id>
78 82 
                                <namedplace>
......
98 102 
                        <locationnarrative>ND; habitat: ND</locationnarrative>
99 103 
                        <centerlatitude>99</centerlatitude>
100 104 
                        <centerlongitude>-999</centerlongitude>
105 
                        <sourceaccessioncode>1479</sourceaccessioncode>
101 106 
                    </location>
102 107 
                </location_id>
103 108 
                <obsstartdate>1982-02-11</obsstartdate>
104 109 
                <obsenddate/>
105 110 
            </locationevent>
106 111 
        </locationevent_id>
107 
        <collectioncode_dwc>XAL</collectioncode_dwc>
108 112 
        <taxondetermination>
109 113 
            <isoriginal>true</isoriginal>
110 114 
            <iscurrent>true</iscurrent>
......
133 137 
            </plantconcept_id>
134 138 
        </taxondetermination>
135 139 
        <verbatimcollectorname>J.I. Calzada</verbatimcollectorname>
136 
        <datasource_id><party><organizationname>REMIB</organizationname></party></datasource_id>
140 
        <collectioncode_dwc>XAL</collectioncode_dwc>
137 141 
        <sourceaccessioncode>1479</sourceaccessioncode>
138 142 
    </specimenreplicate>
139 143 
</VegBIEN>
inputs/REMIB/maps/VegBIEN.specimens.csv
1 
REMIB[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
REMIB[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
county,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
3 3 
state,"/*_id/locationevent/*_id/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",,65
4 4 
country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
......
9 9 
coll_day,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
10 10 
coll_month,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
11 11 
coll_year,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
12 
acronym,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
13 12 
specificEpithet,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_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",,149
14 13 
genus,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_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",,147
15 14 
family,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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",,146
16 15 
collector,/verbatimcollectorname,,23
17 
accession_number,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
16 
acronym,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
17 
accession_number,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
18 18 
lat_min,,** No input mapping for lat_min **
19 19 
lat_sec,,** No input mapping for lat_sec **
20 20 
long_min,,** No input mapping for long_min **
inputs/U/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
18 20 
                        <locationnarrative>Cayenne, Ile de Cayenne</locationnarrative>
19 21 
                        <centerlatitude>4.933333333</centerlatitude>
20 22 
                        <centerlongitude>-52.33333333</centerlongitude>
23 
                        <sourceaccessioncode>2225</sourceaccessioncode>
21 24 
                    </location>
22 25 
                </location_id>
23 26 
                <obsstartdate>1969-09-21</obsstartdate>
24 27 
                <obsenddate/>
25 28 
            </locationevent>
26 29 
        </locationevent_id>
30 
        <collectionnumber>7</collectionnumber>
27 31 
        <taxondetermination>
28 32 
            <role>identifier</role>
29 33 
            <determinationdate>1979-01-01</determinationdate>
......
54 58 
            </plantconcept_id>
55 59 
        </taxondetermination>
56 60 
        <verbatimcollectorname>Burgot, S.J.</verbatimcollectorname>
57 
        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
58 61 
        <catalognumber_dwc>U  0125259</catalognumber_dwc>
59 
        <collectionnumber>7</collectionnumber>
60 62 
        <sourceaccessioncode>2225</sourceaccessioncode>
61 63 
    </specimenreplicate>
62 64 
    <specimenreplicate id="1">
65 
        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
63 66 
        <locationevent_id>
64 67 
            <locationevent>
65 68 
                <location_id>
66 69 
                    <location>
70 
                        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
67 71 
                        <locationdetermination>
68 72 
                            <namedplace_id>
69 73 
                                <namedplace>
......
77 81 
                        <locationnarrative>Cayenne, Ile de Cayenne</locationnarrative>
78 82 
                        <centerlatitude>4.933333333</centerlatitude>
79 83 
                        <centerlongitude>-52.33333333</centerlongitude>
84 
                        <sourceaccessioncode>44268708</sourceaccessioncode>
80 85 
                    </location>
81 86 
                </location_id>
82 87 
                <obsstartdate>1970-09-21</obsstartdate>
83 88 
                <obsenddate/>
84 89 
            </locationevent>
85 90 
        </locationevent_id>
91 
        <collectionnumber>5</collectionnumber>
86 92 
        <taxondetermination>
87 93 
            <isoriginal>true</isoriginal>
88 94 
            <iscurrent>true</iscurrent>
......
105 111 
            </plantconcept_id>
106 112 
        </taxondetermination>
107 113 
        <verbatimcollectorname>Burgot, S.J.</verbatimcollectorname>
108 
        <datasource_id><party><organizationname>U</organizationname></party></datasource_id>
109 114 
        <catalognumber_dwc>U  0233032</catalognumber_dwc>
110 
        <collectionnumber>5</collectionnumber>
111 115 
        <sourceaccessioncode>44268708</sourceaccessioncode>
112 116 
    </specimenreplicate>
113 117 
</VegBIEN>
inputs/U/maps/VegBIEN.specimens.csv
1 
U[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
U[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
Country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
3 3 
Gazetteer,"/*_id/locationevent/*_id/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/1","Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
4 4 
Newgazett,"/*_id/locationevent/*_id/location/locationnarrative/_merge/2/_merge/1/_label[label=""gazetteer""]/value/_merge/2","Only used in 1 row; Brad: Correct for VB; Nick, is there no specific element for locality description in VegX? Definitely need one.",69
......
9 9 
Colldd,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
10 10 
Collmm,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
11 11 
Collyy,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
12 
Number,/collectionnumber/_alt/1/_alt/2,,22
12 13 
Notes,/description/_merge/1,,
13 14 
Detyy,"/taxondetermination[role=identifier]/determinationdate/_*/date/_dateRangeStart/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,120
14 15 
Detby,"/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
......
16 17 
Family,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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",,146
17 18 
Collector,/verbatimcollectorname/_merge/1,,23
18 19 
Addcoll,/verbatimcollectorname/_merge/2,,23
19 
Barcode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
20 
Number,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/2,,22
21 
ID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
20 
Barcode,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
21 
ID,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
22 22 
Alt,,What is this?
23 23 
Alt2,,What is this?
24 24 
Coorsyst,,** No input mapping for Coorsyst **
inputs/ARIZ/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
20 22 
                            </namedplace_id>
21 23 
                        </locationdetermination>
22 24 
                        <locationnarrative>Iguala, Hwy. 95, 4/10 mi. So. of La Cabana Motel. Dry valley.</locationnarrative>
25 
                        <sourceaccessioncode>Herbarium:ARIZ:dbsn104</sourceaccessioncode>
23 26 
                    </location>
24 27 
                </location_id>
25 28 
                <obsstartdate>1971-01-23</obsstartdate>
26 29 
                <obsenddate/>
27 30 
            </locationevent>
28 31 
        </locationevent_id>
29 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
32 
        <collectionnumber>36</collectionnumber>
30 33 
        <description>Much branched shrub with long white thorns and pale yellow catkins.</description>
31 34 
        <taxondetermination>
32 35 
            <role>identifier</role>
......
75 78 
            </plantconcept_id>
76 79 
        </taxondetermination>
77 80 
        <verbatimcollectorname>J. Freeland</verbatimcollectorname>
78 
        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
79 81 
        <catalognumber_dwc>104</catalognumber_dwc>
80 
        <collectionnumber>36</collectionnumber>
82 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
81 83 
        <institution_id><party><organizationname>Herbarium</organizationname></party></institution_id>
82 84 
        <sourceaccessioncode>Herbarium:ARIZ:dbsn104</sourceaccessioncode>
83 85 
    </specimenreplicate>
84 86 
    <specimenreplicate id="1">
87 
        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
85 88 
        <locationevent_id>
86 89 
            <locationevent>
87 90 
                <location_id>
88 91 
                    <location>
92 
                        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
89 93 
                        <locationdetermination>
90 94 
                            <namedplace_id>
91 95 
                                <namedplace>
......
95 99 
                            </namedplace_id>
96 100 
                        </locationdetermination>
97 101 
                        <locationnarrative>Grown in University of Arizona (tucson, AZ) greenhouses from seeds provided by the USDA, Plant Introduction accession 220085. .</locationnarrative>
102 
                        <sourceaccessioncode>Herbarium:ARIZ:dbsn198483</sourceaccessioncode>
98 103 
                    </location>
99 104 
                </location_id>
100 105 
                <obsstartdate>1993-02-01</obsstartdate>
101 106 
                <obsenddate/>
102 107 
            </locationevent>
103 108 
        </locationevent_id>
104 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
109 
        <collectionnumber>172</collectionnumber>
105 110 
        <taxondetermination>
106 111 
            <role>identifier</role>
107 112 
            <determinationdate>1993-02-01</determinationdate>
......
149 154 
            </plantconcept_id>
150 155 
        </taxondetermination>
151 156 
        <verbatimcollectorname>M. F. Wojciechowski &amp; M. J. Sanderson</verbatimcollectorname>
152 
        <datasource_id><party><organizationname>ARIZ</organizationname></party></datasource_id>
153 157 
        <catalognumber_dwc>198483</catalognumber_dwc>
154 
        <collectionnumber>172</collectionnumber>
158 
        <collectioncode_dwc>ARIZ</collectioncode_dwc>
155 159 
        <institution_id><party><organizationname>Herbarium</organizationname></party></institution_id>
156 160 
        <sourceaccessioncode>Herbarium:ARIZ:dbsn198483</sourceaccessioncode>
157 161 
    </specimenreplicate>
inputs/ARIZ/maps/VegBIEN.specimens.csv
1 
ARIZ[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
ARIZ[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
CoordinateUncertaintyInMeters,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
BoundingBox,/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91
4 4 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
......
18 18 
DayCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
19 19 
MonthCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
20 20 
YearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
21 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
21 
CollectorNumber,/collectionnumber/_alt/1/_alt/1,,22
22 
FieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
22 23 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
23 24 
FieldNotes,/description/_merge/1,,
24 25 
Remarks,/description/_merge/2,,158
......
37 38 
Phylum,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subkingdom]/plantname",,143
38 39 
Kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
39 40 
Collector,/verbatimcollectorname,,23
40 
CatalogNumberNumeric,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
41 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
42 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43 
InstitutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
44 
GlobalUniqueIdentifier,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
41 
CatalogNumberNumeric,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
42 
CollectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
43 
InstitutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
44 
GlobalUniqueIdentifier,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
45 45 
AgeClass,,** No non-empty join mapping for lifeStage **
46 46 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
47 47 
CatalogNumber,,Map to nothing so it doesn't overwrite CatalogNumberNumeric
inputs/GBIF/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
13 15 
                                </namedplace>
14 16 
                            </namedplace_id>
15 17 
                        </locationdetermination>
18 
                        <sourceaccessioncode>GOET-Typen; Type herbarium, Gottingen (GOET); 3390</sourceaccessioncode>
16 19 
                    </location>
17 20 
                </location_id>
18 21 
            </locationevent>
19 22 
        </locationevent_id>
20 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
21 23 
        <taxondetermination>
22 24 
            <isoriginal>true</isoriginal>
23 25 
            <iscurrent>true</iscurrent>
......
58 60 
            </plantconcept_id>
59 61 
        </taxondetermination>
60 62 
        <verbatimcollectorname>PRINGLE</verbatimcollectorname>
61 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
62 63 
        <catalognumber_dwc>3390</catalognumber_dwc>
64 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
63 65 
        <institution_id><party><organizationname>GOET-Typen</organizationname></party></institution_id>
64 66 
    </specimenreplicate>
65 67 
    <specimenreplicate id="1">
68 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
66 69 
        <locationevent_id>
67 70 
            <locationevent>
68 71 
                <location_id>
69 72 
                    <location>
73 
                        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
70 74 
                        <locationdetermination>
71 75 
                            <namedplace_id>
72 76 
                                <namedplace>
......
75 79 
                                </namedplace>
76 80 
                            </namedplace_id>
77 81 
                        </locationdetermination>
82 
                        <sourceaccessioncode>GOET-Typen; Type herbarium, Gottingen (GOET); 3395</sourceaccessioncode>
78 83 
                    </location>
79 84 
                </location_id>
80 85 
            </locationevent>
81 86 
        </locationevent_id>
82 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
83 87 
        <taxondetermination>
84 88 
            <isoriginal>true</isoriginal>
85 89 
            <iscurrent>true</iscurrent>
......
120 124 
            </plantconcept_id>
121 125 
        </taxondetermination>
122 126 
        <verbatimcollectorname>ANDERSSON</verbatimcollectorname>
123 
        <datasource_id><party><organizationname>GBIF</organizationname></party></datasource_id>
124 127 
        <catalognumber_dwc>3395</catalognumber_dwc>
128 
        <collectioncode_dwc>Type herbarium, Gottingen (GOET)</collectioncode_dwc>
125 129 
        <institution_id><party><organizationname>GOET-Typen</organizationname></party></institution_id>
126 130 
    </specimenreplicate>
127 131 
</VegBIEN>
inputs/GBIF/maps/VegBIEN.specimens.csv
1 
GBIF[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
GBIF[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
3 3 
StateProvince,"/*_id/locationevent/*_id/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",,65
4 4 
Country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
......
10 10 
DecimalLongitude,"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,86
11 11 
VerbatimLongitude,"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value",,82
12 12 
LatestDateCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/2",,44
13 
CollectionCD,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
14 13 
IdentifiedBy,"/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
15 14 
ScientificName,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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","Brad: Bob, Nick, please is this mapping OK?",134
16 15 
AuthorOfScientificName,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_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: Mapping probably incorrect. This DwC element refers to scientific name author; does not correspond to the VegBank and VegX elements you have listed (Bob, Nick�where does name author belong in VegBank and VegX?); Aaron: The mapped VegX element is the author linked to the taxon name, so it seems like this is the scientific name author",153
......
19 18 
Genus,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_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",,147
20 19 
Family,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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",,146
21 20 
Collector,/verbatimcollectorname,,23
22 
CatalogNO,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
23 
InstitutionCD,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
21 
CatalogNO,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
22 
CollectionCD,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
23 
InstitutionCD,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
24 24 
GBIFFamilyOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/first ** DwC doesn't fully support taxonomic redeterminations
25 25 
GBIFGenusOriginal,,** No non-empty join mapping for originalNameUsage/_alt/2/_name/middle ** DwC doesn't fully support taxonomic redeterminations
26 26 
LastDateModified,,** No non-empty join mapping for DateLastModified **
inputs/NCU-NCSC/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
25 27 
                                </namedplace>
26 28 
                            </namedplace_id>
27 29 
                        </locationdetermination>
30 
                        <sourceaccessioncode>0</sourceaccessioncode>
28 31 
                    </location>
29 32 
                </location_id>
30 33 
                <obsstartdate>1994-06-25</obsstartdate>
31 34 
                <obsenddate/>
32 35 
            </locationevent>
33 36 
        </locationevent_id>
34 
        <collectioncode_dwc>NCU</collectioncode_dwc>
35 37 
        <taxondetermination>
36 38 
            <isoriginal>true</isoriginal>
37 39 
            <iscurrent>true</iscurrent>
......
47 49 
                </plantconcept>
48 50 
            </plantconcept_id>
49 51 
        </taxondetermination>
52 
        <catalognumber_dwc>NCU00090254</catalognumber_dwc>
53 
        <collectioncode_dwc>NCU</collectioncode_dwc>
50 54 
        <growthform/>
51 55 
        <iscultivated>f</iscultivated>
52 56 
        <isnative/>
53 
        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
54 
        <catalognumber_dwc>NCU00090254</catalognumber_dwc>
55 57 
        <sourceaccessioncode>0</sourceaccessioncode>
56 58 
    </specimenreplicate>
57 59 
    <specimenreplicate id="1">
60 
        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
58 61 
        <locationevent_id>
59 62 
            <locationevent>
60 63 
                <location_id>
61 64 
                    <location>
65 
                        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
62 66 
                        <locationdetermination>
63 67 
                            <coordsaccuracy>1000</coordsaccuracy>
64 68 
                            <namedplace_id>
......
84 88 
                        </locationdetermination>
85 89 
                        <centerlatitude>35.1611111</centerlatitude>
86 90 
                        <centerlongitude>-79.3486111</centerlongitude>
91 
                        <sourceaccessioncode>1</sourceaccessioncode>
87 92 
                    </location>
88 93 
                </location_id>
89 94 
                <obsstartdate>1965-05-08</obsstartdate>
90 95 
                <obsenddate/>
91 96 
            </locationevent>
92 97 
        </locationevent_id>
93 
        <collectioncode_dwc>WEWO</collectioncode_dwc>
94 98 
        <taxondetermination>
95 99 
            <isoriginal>true</isoriginal>
96 100 
            <iscurrent>true</iscurrent>
......
106 110 
                </plantconcept>
107 111 
            </plantconcept_id>
108 112 
        </taxondetermination>
113 
        <collectioncode_dwc>WEWO</collectioncode_dwc>
109 114 
        <growthform/>
110 115 
        <iscultivated>f</iscultivated>
111 116 
        <isnative/>
112 
        <datasource_id><party><organizationname>NCU-NCSC</organizationname></party></datasource_id>
113 117 
        <sourceaccessioncode>1</sourceaccessioncode>
114 118 
    </specimenreplicate>
115 119 
</VegBIEN>
inputs/NCU-NCSC/maps/VegBIEN.specimens.csv
1 
NCU-NCSC[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
NCU-NCSC[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
Accuracy,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
4 4 
State,"/*_id/locationevent/*_id/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",,65
......
6 6 
Lat (-=S),"/*_id/locationevent/*_id/location/{locationdetermination/latitude,centerlatitude}/_alt/1/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",,81
7 7 
Long (-=W),"/*_id/locationevent/*_id/location/{locationdetermination/longitude,centerlongitude}/_alt/1/_nullIf:[null=0,type=float]/value/_replace:[""\?$""=]/value",,82
8 8 
Collect Date,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/3",,44
9 
SeriesName,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
10 9 
Full Taxon Name,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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","Brad: Bob, Nick, please is this mapping OK?",134
10 
Barcode,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
11 
SeriesName,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
11 12 
Cultivated?,"/{growthform/_map:[./{tree,shrub,liana,vine,herb,hemiepiphyte,epiphyte,grass,forb,moss,lichen,fungus,""floating aquatic"",""submerged aquatic""}=*,*=],iscultivated/_map:[cultivated=t,wild=f,*=],isnative/_map:[native=t,exotic=f,*=]}/value/_map:[Yes=cultivated,No=wild]/value",,30
12 
Barcode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
13 
Accession Number,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
13 
Accession Number,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
14 14 
Alt E/W,,** No input mapping for Alt E/W **
15 15 
Alt N/S,,** No input mapping for Alt N/S **
16 16 
Elevation,,** No non-empty join mapping for VerbatimElevation **
inputs/SpeciesLink/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
38 40 
                        <elevationrange>0.0</elevationrange>
39 41 
                        <centerlatitude>-6.73845</centerlatitude>
40 42 
                        <centerlongitude>-35.1385666667</centerlongitude>
43 
                        <sourceaccessioncode>96848826</sourceaccessioncode>
41 44 
                    </location>
42 45 
                </location_id>
43 46 
                <obsstartdate>2009-09-09</obsstartdate>
44 47 
                <obsenddate/>
45 48 
            </locationevent>
46 49 
        </locationevent_id>
47 
        <collectioncode_dwc>JPB</collectioncode_dwc>
50 
        <collectionnumber>27</collectionnumber>
48 51 
        <description>&#193;rvore; ca. de 4,5m Alt.; bot&#227;o floral com colora&#231;ao verde.</description>
49 52 
        <taxondetermination>
50 53 
            <role>identifier</role>
......
100 103 
            </plantconcept_id>
101 104 
        </taxondetermination>
102 105 
        <verbatimcollectorname>Silva, F.O.</verbatimcollectorname>
103 
        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
104 106 
        <catalognumber_dwc>43226</catalognumber_dwc>
105 
        <collectionnumber>27</collectionnumber>
107 
        <collectioncode_dwc>JPB</collectioncode_dwc>
106 108 
        <institution_id><party><organizationname>UFPB</organizationname></party></institution_id>
107 109 
        <sourceaccessioncode>96848826</sourceaccessioncode>
108 110 
    </specimenreplicate>
109 111 
    <specimenreplicate id="1">
112 
        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
110 113 
        <locationevent_id>
111 114 
            <locationevent>
112 115 
                <location_id>
113 116 
                    <location>
117 
                        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
114 118 
                        <locationdetermination>
115 119 
                            <namedplace_id>
116 120 
                                <namedplace>
......
142 146 
                        <locationnarrative>Mata de Igap&#243;. Margens inundadas.</locationnarrative>
143 147 
                        <centerlatitude>-2.8333333333</centerlatitude>
144 148 
                        <centerlongitude>-67.8333333333</centerlongitude>
149 
                        <sourceaccessioncode>96848863</sourceaccessioncode>
145 150 
                    </location>
146 151 
                </location_id>
147 152 
                <obsstartdate>1986-11-18</obsstartdate>
148 153 
                <obsenddate/>
149 154 
            </locationevent>
150 155 
        </locationevent_id>
151 
        <collectioncode_dwc>JPB</collectioncode_dwc>
156 
        <collectionnumber>2745</collectionnumber>
152 157 
        <description>&#193;rvore pequena com 5m de altura; frutos jovens esverdeados. Boca do rio Tonantins, abaixo de Vila Velha. Frequente.</description>
153 158 
        <taxondetermination>
154 159 
            <role>identifier</role>
......
204 209 
            </plantconcept_id>
205 210 
        </taxondetermination>
206 211 
        <verbatimcollectorname>Lima, H.C.</verbatimcollectorname>
207 
        <datasource_id><party><organizationname>SpeciesLink</organizationname></party></datasource_id>
208 212 
        <catalognumber_dwc>14046</catalognumber_dwc>
209 
        <collectionnumber>2745</collectionnumber>
213 
        <collectioncode_dwc>JPB</collectioncode_dwc>
210 214 
        <institution_id><party><organizationname>UFPB</organizationname></party></institution_id>
211 215 
        <sourceaccessioncode>96848863</sourceaccessioncode>
212 216 
    </specimenreplicate>
inputs/SpeciesLink/maps/VegBIEN.specimens.csv
1 
"SpeciesLink[DwC,dwc_dwcore_,dwc_curatorial_,dwc_geospatial_,http__purl_org_,dwc_terms_,conceptual_darwin_2003_1_0_]",VegBIEN:/specimenreplicate,Comments,Order
1 
"SpeciesLink[DwC,dwc_dwcore_,dwc_curatorial_,dwc_geospatial_,http__purl_org_,dwc_terms_,conceptual_darwin_2003_1_0_]","VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
coordinateUncertaintyInMeters,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/1,,88
3 3 
CoordinatePrecision,/*_id/locationevent/*_id/location/locationdetermination/coordsaccuracy/_noCV/value/_alt/2,,89
4 4 
BoundingBox,/*_id/locationevent/*_id/location/locationdetermination/footprintgeometry_dwc,,91
......
38 38 
DayCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
39 39 
MonthCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
40 40 
YearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
41 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
42 
collectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
41 
CollectorNumber,/collectionnumber/_alt/1/_alt/1,,22
42 
recordNumber,/collectionnumber/_alt/1/_alt/2,,22
43 
collectionID,/collectionnumber/_alt/2,,9
44 
FieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
45 
fieldNumber,/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
43 46 
Sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
44 47 
sex,"/definedvalue[*_id/userdefined[tablename=specimenreplicate,userdefinedname=sex]]:[@fkey=tablerecord_id]/definedvalue","Brad: OMIT. Apparently not used by this institution and of uncertain applicability to plants. With other collections, *sometimes* used for phenological information (if specimen in flower, in fruit, sterile, etc.). If so, this is important information we should keep. Bob, Nick, anywhere for phenological information in VB and VX?; Aaron: Keeping it because it's useful for some collections",26
45 48 
Notes,/description/_merge/1,,
......
75 78 
kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
76 79 
Collector,/verbatimcollectorname,,23
77 80 
recordedBy,/verbatimcollectorname,,23
78 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
79 
catalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
80 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
81 
recordNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/2,,22
82 
collectionID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/2,,9
83 
FieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
84 
fieldNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/3,"Brad: Correct for VB, not sure about VX; Nick, is there an element in VX fo Collection Number?",53
85 
InstitutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
86 
institutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
87 
GlobalUniqueIdentifier,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
81 
CatalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
82 
catalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
83 
CollectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
84 
collectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
85 
InstitutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
86 
institutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
87 
GlobalUniqueIdentifier,"/{sourceaccessioncode,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/1}","Brad: OMIT; Aaron: We need this field because it is the only ID column with an entry in every row; Brad: OK, use this as primary key",19
88 88 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
89 89 
DateLastModified,,** No non-empty join mapping for DateLastModified **
90 90 
DayOfYear,,** No non-empty join mapping for JulianDay **
inputs/MO/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
25 27 
                                </namedplace>
26 28 
                            </namedplace_id>
27 29 
                        </locationdetermination>
30 
                        <sourceaccessioncode>MO; Tropicos; 1</sourceaccessioncode>
28 31 
                    </location>
29 32 
                </location_id>
30 33 
            </locationevent>
31 34 
        </locationevent_id>
32 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
35 
        <collectionnumber>10572</collectionnumber>
33 36 
        <taxondetermination>
34 37 
            <isoriginal>true</isoriginal>
35 38 
            <iscurrent>true</iscurrent>
......
76 79 
            </plantconcept_id>
77 80 
        </taxondetermination>
78 81 
        <verbatimcollectorname>Wiggins</verbatimcollectorname>
79 
        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
80 82 
        <catalognumber_dwc>1</catalognumber_dwc>
81 
        <collectionnumber>10572</collectionnumber>
83 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
82 84 
        <institution_id><party><organizationname>MO</organizationname></party></institution_id>
83 85 
    </specimenreplicate>
84 86 
    <specimenreplicate id="1">
87 
        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
85 88 
        <locationevent_id>
86 89 
            <locationevent>
87 90 
                <location_id>
88 91 
                    <location>
92 
                        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
89 93 
                        <locationdetermination>
90 94 
                            <namedplace_id>
91 95 
                                <namedplace>
......
109 113 
                        <locationnarrative>Foot of Mt. Mulanje along the Nakholu stream just aboe Lauderdale Forest.</locationnarrative>
110 114 
                        <elevation>800.0</elevation>
111 115 
                        <elevationrange/>
116 
                        <sourceaccessioncode>MO; Tropicos; 2</sourceaccessioncode>
112 117 
                    </location>
113 118 
                </location_id>
114 119 
                <obsstartdate>1985-10-29</obsstartdate>
115 120 
                <obsenddate/>
116 121 
            </locationevent>
117 122 
        </locationevent_id>
118 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
123 
        <collectionnumber>6723</collectionnumber>
119 124 
        <taxondetermination>
120 125 
            <isoriginal>true</isoriginal>
121 126 
            <iscurrent>true</iscurrent>
......
168 173 
            </plantconcept_id>
169 174 
        </taxondetermination>
170 175 
        <verbatimcollectorname>J.D. &amp; E.G. Chapman</verbatimcollectorname>
171 
        <datasource_id><party><organizationname>MO</organizationname></party></datasource_id>
172 176 
        <catalognumber_dwc>2</catalognumber_dwc>
173 
        <collectionnumber>6723</collectionnumber>
177 
        <collectioncode_dwc>Tropicos</collectioncode_dwc>
174 178 
        <institution_id><party><organizationname>MO</organizationname></party></institution_id>
175 179 
    </specimenreplicate>
176 180 
</VegBIEN>
inputs/MO/maps/VegBIEN.specimens.csv
1 
MO[DwC],VegBIEN:/specimenreplicate,Comments,Order
1 
MO[DwC],"VegBIEN:/specimenreplicate:[./{.,*_id/locationevent/*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]",Comments,Order
2 2 
County,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=county]/placename",,66
3 3 
StateProvince,"/*_id/locationevent/*_id/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",,65
4 4 
Country,"/*_id/locationevent/*_id/location/locationdetermination/namedplace_id/_simplifyPath:[next=""parent_id/namedplace"",require=placename]/path/_forEach:[in:[county,stateProvince,],do=""namedplace[rank=_val]/parent_id""]/namedplace[rank=country]/placename",Brad: Required; reject record if this field NULL,63
......
11 11 
DayCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/day/_nullIf:[null=0,type=float]/value",,44
12 12 
MonthCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/month/_nullIf:[null=0,type=float]/value",,44
13 13 
YearCollected,"/*_id/locationevent/{obsstartdate/_*/date/_dateRangeStart,obsenddate/_*/date/_dateRangeEnd}/value/_alt/1/_date/year/_nullIf:[null=0,type=float]/value",,44
14 
CollectionCode,/collectioncode_dwc,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
14 
CollectorNumber,/collectionnumber/_alt/1/_alt/1,,22
15 15 
convertednotes,/description/_merge/1,,
16 16 
IdentifiedBy,"/taxondetermination[role=identifier]:[iscurrent=true]/*_id/party/{givenname/_namePart/first,middlename/_namePart/middle,surname/_namePart/last}",Brad: Bob: does this look correct for VegBank?,119
17 17 
ScientificName,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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","Brad: Bob, Nick, please is this mapping OK?",134
......
22 22 
family,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=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",,146
23 23 
Kingdom,"/taxondetermination[role=identifier]:[isoriginal=true,iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,subspecies,species,genus,family,order,class,subkingdom,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=kingdom]/plantname",,142
24 24 
Collector,/verbatimcollectorname,,23
25 
CatalogNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc,"Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
26 
CollectorNumber,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectionnumber/_alt/1/_alt/1,,22
27 
InstitutionCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/institution_id/party/organizationname,,
25 
CatalogNumber,"/{catalognumber_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/3}","Brad: Not sure if mapping correct. Nick, is there an element for institutional accession codes in VegX?; Aaron: This can't be used as the accession code (primary key) because some rows don't have a value for it",20
26 
CollectionCode,"/{collectioncode_dwc,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/2}",Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name,12
27 
InstitutionCode,"/{institution_id/party/organizationname,*_id/locationevent/*_id/location/sourceaccessioncode/_alt/2/_merge/1}",,
28 28 
BasisOfRecord,,** No non-empty join mapping for BasisOfRecord **
29 29 
DateLastModified,,** No non-empty join mapping for DateLastModified **
30 30 
IndividualCount,,** No non-empty join mapping for IndividualCount **
inputs/QMOR/test/VegBIEN.specimens.xml.ref
1 1 
<?xml version="1.0" ?>
2 2 
<VegBIEN>
3 3 
    <specimenreplicate id="0">
4 
        <datasource_id><party><organizationname>QMOR</organizationname></party></datasource_id>
4 5 
        <locationevent_id>
5 6 
            <locationevent>
6 7 
                <location_id>
7 8 
                    <location>
9 
                        <datasource_id><party><organizationname>QMOR</organizationname></party></datasource_id>
8 10 
                        <locationdetermination>
9 11 
                            <namedplace_id>
10 12 
                                <namedplace>
......
26 28 
                            </namedplace_id>
27 29 
                        </locationdetermination>
28 30 
                        <locationnarrative>Rigaud</locationnarrative>
31 
                        <sourceaccessioncode>1</sourceaccessioncode>
29 32 
                    </location>
30 33 
                </location_id>
31 34 
                <obsstartdate>1938-06-02</obsstartdate>
32 35 
                <obsenddate/>
33 36 
            </locationevent>
34 37 
        </locationevent_id>
35 
        <collectioncode_dwc>QMOR</collectioncode_dwc>
38 
        <collectionnumber>urn:lsid:biocol.org:col:34164</collectionnumber>
36 39 
        <definedvalue fkey="tablerecord_id">
37 40 
            <userdefined_id>
38 41 
                <userdefined>
......
107 110 
            </plantconcept_id>
108 111 
        </taxondetermination>
... This diff was truncated because it exceeds the maximum size that can be displayed.

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