Revision 6409
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/SALVIAS-CSV/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/REMIB/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>REMIB</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/FIA/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>primary database</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>FIA</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
NY,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
UniqueNYInternalRecordNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
UniqueNYInternalRecordNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 87 | 90 |
County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 88 | 91 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 89 | 92 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 90 |
CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 91 |
UniqueNYInternalRecordNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 92 |
InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 93 | 93 |
BasisOfRecord,,** No join mapping for basisOfRecord ** |
| 94 | 94 |
CollectorNumber,,** No non-empty join mapping for UNUSED ** |
| 95 | 95 |
DateLastModified,,** No join mapping for dcterms:modified ** |
| inputs/Madidi/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:primary database,/source/sourcetype, |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
UNCC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
accession,"/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1] |
|
| 3 |
|
|
| 4 |
[1] Using the following query: |
|
| 5 |
----- |
|
| 6 |
SELECT herbarium, accession, count(*) |
|
| 7 |
FROM ""UNCC"".""Specimen"" |
|
| 8 |
GROUP BY herbarium, accession |
|
| 9 |
HAVING count(*) > 1 |
|
| 10 |
-----" |
|
| 11 |
herbarium,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 12 |
accession,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1","Globally unique, although occasionally duplicated. [1] |
| 3 | 13 |
|
| 4 | 14 |
[1] Using the following query: |
| ... | ... | |
| 135 | 145 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 136 | 146 |
state,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 137 | 147 |
state,/location/locationplace/*_id/place/stateprovince, |
| 138 |
accession,"/source/shortname/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1] |
|
| 139 |
|
|
| 140 |
[1] Using the following query: |
|
| 141 |
----- |
|
| 142 |
SELECT herbarium, accession, count(*) |
|
| 143 |
FROM ""UNCC"".""Specimen"" |
|
| 144 |
GROUP BY herbarium, accession |
|
| 145 |
HAVING count(*) > 1 |
|
| 146 |
-----" |
|
| 147 |
herbarium,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 148 | 148 |
filler,,"** No join mapping for *filler ** Where used, same as family" |
| 149 | 149 |
flower,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?" |
| 150 | 150 |
fruit,,"** No join mapping for reproductiveCondition/_map:[A=*,I=*,M=*]/value ** Main values are A, I, and M. What do they mean?" |
| inputs/CVS/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>primary database</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>CVS</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS-CSV,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
coll_number,"/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 3 |
voucher_string,"/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 2 | 4 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 5 |
plot_code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 6 |
PLOT_ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| ... | ... | |
| 145 | 147 |
PLOT_ID,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1", |
| 146 | 148 |
plot_code,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 147 | 149 |
subplot,/location/sourceaccessioncode/_join/2, |
| 148 |
coll_number,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 149 |
voucher_string,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 150 | 150 |
collector_code,,** No join mapping for *collector_code ** Brad: OMIT |
| 151 | 151 |
comments,,** No join mapping for *comments ** Brad: OMIT |
| 152 | 152 |
fam_status,,** No join mapping for *fam_status ** Brad: OMIT. This will be determined later by using TNRS. |
| inputs/REMIB/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
REMIB,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/FIA/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
FIA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:primary database,/source/sourcetype, |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TRT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 92 | 95 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 93 | 96 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 94 | 97 |
verbatimElevation,/location/verbatimelevation, |
| 95 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 96 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 97 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 98 | 98 |
associatedMedia,,** No join mapping for associatedMedia ** |
| 99 | 99 |
associatedReferences,,** No join mapping for associatedReferences ** |
| 100 | 100 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
MT,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 4 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 6 |
institutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| ... | ... | |
| 28 | 30 |
genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus, |
| 29 | 31 |
locality,/location/locationnarrative/_merge/1, |
| 30 | 32 |
continent,/location/locationplace/*_id/place/continent, |
| 31 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 33 | 33 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| 34 | 34 |
countryCode,,** No join mapping for countryCode ** |
| 35 | 35 |
datasetName,,** No join mapping for datasetName ** |
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
XAL:/content/record/,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
darwin:CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
darwin:InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 4 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 5 |
darwin:CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 6 |
darwin:InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| ... | ... | |
| 74 | 76 |
darwin:County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 75 | 77 |
darwin:StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 76 | 78 |
darwin:StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 77 |
darwin:CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 78 |
darwin:InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 79 | 79 |
darwin:BasisOfRecord,,** No join mapping for basisOfRecord ** |
| 80 | 80 |
darwin:CoordinatePrecision,,** No non-empty join mapping for UNUSED ** |
| 81 | 81 |
darwin:DateLastModified,,** No join mapping for dcterms:modified ** |
| inputs/TEAM/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:primary database,/source/sourcetype, |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/TEAM/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>primary database</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>TEAM</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 3 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 4 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 5 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| ... | ... | |
| 48 | 49 |
Subplot Number,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists", |
| 49 | 50 |
1ha Plot Number,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 50 | 51 |
Subplot Number,/location/sourceaccessioncode/_join/2, |
| 51 |
Id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 52 | 52 |
Comments,,** No join mapping for *Comments ** |
| 53 | 53 |
Condition Codes,,** No join mapping for *Condition Codes ** |
| 54 | 54 |
Data Level,,** No join mapping for *Data Level ** |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TEAM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 3 |
Subplot Number,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 4 |
1ha Plot Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 5 |
Id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| ... | ... | |
| 48 | 49 |
Subplot Number,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/cond/_exists", |
| 49 | 50 |
1ha Plot Number,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 50 | 51 |
Subplot Number,/location/sourceaccessioncode/_join/2, |
| 51 |
Id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 52 | 52 |
Comments,,** No join mapping for *Comments ** |
| 53 | 53 |
Condition Codes,,** No join mapping for *Condition Codes ** |
| 54 | 54 |
Data Level,,** No join mapping for *Data Level ** |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
ACAD,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 86 | 89 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 87 | 90 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 88 | 91 |
verbatimElevation,/location/verbatimelevation, |
| 89 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 90 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 91 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 92 | 92 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| 93 | 93 |
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** |
| 94 | 94 |
dynamicProperties,,** No join mapping for dynamicProperties ** |
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
WIN,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 81 | 84 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 82 | 85 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 83 | 86 |
verbatimElevation,/location/verbatimelevation, |
| 84 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 85 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 86 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 87 | 87 |
associatedMedia,,** No join mapping for associatedMedia ** |
| 88 | 88 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| 89 | 89 |
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** |
| inputs/CTFS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
CTFS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:primary database,/source/sourcetype, |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/CTFS/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>primary database</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>CTFS</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/SALVIAS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/SALVIAS/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>SALVIAS</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
coll_number,"/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 3 |
SourceVoucher,"/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 2 | 4 |
Line,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 5 |
PlotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 6 |
PlotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| ... | ... | |
| 143 | 145 |
PlotID,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1", |
| 144 | 146 |
PlotCode,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 145 | 147 |
Line,/location/sourceaccessioncode/_join/2, |
| 146 |
coll_number,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string |
|
| 147 |
SourceVoucher,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
|
| 148 | 148 |
GenAuth,,** No join mapping for *GenAuth ** |
| 149 | 149 |
IsMorpho,,** No join mapping for *IsMorpho ** |
| 150 | 150 |
OrigAuth,,** No join mapping for *OrigAuth ** |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
U,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Barcode,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
ID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 4 |
ID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 5 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 6 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 46 | 48 |
Lat,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/latitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
| 47 | 49 |
Long,"/location/locationplace/*_id/place/matched_place_id/place:[.,source_id/source/shortname=geoscrub]/*_id/coordinates:[source_id/source/shortname=geoscrub]/_first/2/longitude_deg/_nullIf:[null=0,type=float]/value",""".,"" sorts it with other coordinates mappings" |
| 48 | 50 |
Country,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/country/_first/2, |
| 49 |
Barcode,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 50 |
ID,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 51 | 51 |
Alt,,** No join mapping for *Alt ** What is this? |
| 52 | 52 |
Alt2,,** No join mapping for *Alt2 ** What is this? |
| 53 | 53 |
Coorsyst,,** No join mapping for *Coorsyst ** |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
QFA,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 85 | 88 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 86 | 89 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 87 | 90 |
verbatimElevation,/location/verbatimelevation, |
| 88 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 89 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 90 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 91 | 91 |
acceptedNameUsage,,** No join mapping for acceptedNameUsage ** |
| 92 | 92 |
associatedReferences,,** No join mapping for associatedReferences ** |
| 93 | 93 |
associatedSequences,,** No join mapping for associatedSequences ** |
| inputs/GBIF/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/GBIF/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>GBIF</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
GBIF,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
CatalogNO,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
InstitutionCD,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 4 |
CatalogNO,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 5 |
CatalogNO,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 6 |
InstitutionCD,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| ... | ... | |
| 68 | 70 |
County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 69 | 71 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 70 | 72 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 71 |
CatalogNO,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 72 |
InstitutionCD,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 73 | 73 |
0,,** No join mapping for *0 ** |
| 74 | 74 |
1,,** No join mapping for *1 ** |
| 75 | 75 |
25,,** No join mapping for *25 ** |
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
JBM,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 68 | 71 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 69 | 72 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 70 | 73 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 71 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 72 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 73 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 74 | 74 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| 75 | 75 |
countryCode,,** No join mapping for countryCode ** |
| 76 | 76 |
datasetID,,** No join mapping for datasetID ** |
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
HIBG,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 86 | 89 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 87 | 90 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 88 | 91 |
verbatimElevation,/location/verbatimelevation, |
| 89 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 90 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 91 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 92 | 92 |
associatedMedia,,** No join mapping for associatedMedia ** |
| 93 | 93 |
basisOfRecord,,** No join mapping for basisOfRecord ** |
| 94 | 94 |
bibliographicCitation,,** No join mapping for dcterms:bibliographicCitation ** |
| inputs/SpeciesLink/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SpeciesLink,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/SpeciesLink/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>SpeciesLink</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
SpeciesLink,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
conceptual_darwin_2003_1_0_CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
dwc_dwcore_CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
dwc_dwcore_GlobalUniqueIdentifier,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 5 |
dwc_terms_catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 6 |
conceptual_darwin_2003_1_0_InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 7 |
dwc_dwcore_InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 8 |
dwc_terms_institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 9 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 10 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 11 |
dwc_dwcore_CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| ... | ... | |
| 286 | 293 |
conceptual_darwin_2003_1_0_StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 287 | 294 |
dwc_dwcore_StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 288 | 295 |
dwc_terms_stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 289 |
conceptual_darwin_2003_1_0_CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 290 |
dwc_dwcore_CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 291 |
dwc_dwcore_GlobalUniqueIdentifier,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 292 |
dwc_terms_catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 293 |
conceptual_darwin_2003_1_0_InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 294 |
dwc_dwcore_InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 295 |
dwc_terms_institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 296 | 296 |
conceptual_darwin_2003_1_0_BasisOfRecord,,** No join mapping for basisOfRecord ** |
| 297 | 297 |
conceptual_darwin_2003_1_0_CoordinatePrecision,,** No join mapping for coordinatePrecision ** |
| 298 | 298 |
conceptual_darwin_2003_1_0_DateLastModified,,** No join mapping for dcterms:modified ** |
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
UBC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 85 | 88 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 86 | 89 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 87 | 90 |
verbatimElevation,/location/verbatimelevation, |
| 88 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 89 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 90 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 91 | 91 |
associatedMedia,,** No join mapping for associatedMedia ** |
| 92 | 92 |
associatedReferences,,** No join mapping for associatedReferences ** |
| 93 | 93 |
associatedSequences,,** No join mapping for associatedSequences ** |
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
bien_web,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
observationID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
dataSourceName,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 4 |
plotCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 3 | 5 |
plotID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| 4 | 6 |
observationID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| ... | ... | |
| 66 | 68 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 67 | 69 |
plotID,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1", |
| 68 | 70 |
plotCode,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 69 |
observationID,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 70 |
dataSourceName,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 71 | 71 |
abund,,** No join mapping for *abund ** |
| 72 | 72 |
abund1,,** No join mapping for *abund1 ** |
| 73 | 73 |
abund10,,** No join mapping for *abund10 ** |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
Madidi,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Specimen,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 3 |
Number of subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 4 |
Inventory name,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| 4 | 5 |
Inventory code,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/2/_if[@name=""if locationID""]/cond/_exists", |
| ... | ... | |
| 78 | 79 |
Inventory code,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/1", |
| 79 | 80 |
Inventory name,"/location/sourceaccessioncode/_join/1/_if[@name=""if subplot and unique only within parent""]/then/_first/2", |
| 80 | 81 |
Number of subplot,/location/sourceaccessioncode/_join/2, |
| 81 |
Specimen,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 82 | 82 |
Basal area,,"** No join mapping for *Basal area ** Would be basalDiameter, but need formula to translate" |
| 83 | 83 |
Bole height,,** No join mapping for *Bole height ** trunk height |
| 84 | 84 |
Circumference,,** No join mapping for *Circumference ** |
| inputs/Madidi/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>primary database</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>Madidi</shortname> |
|
| 11 |
<sourcetype>primary database</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/CVS/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
CVS,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:primary database,/source/sourcetype, |
|
| 2 |
:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| inputs/.herbaria/herbaria/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
herbaria,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
herbariumAcronym,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 3 |
:herbarium,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 2 | 4 |
herbariumAcronym,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| 3 | 5 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
| 4 | 6 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
| 5 |
herbariumAcronym,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 6 |
:herbarium,/source/sourcetype, |
|
| 7 | 7 |
City,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| 8 | 8 |
CoordinatesVerbatim,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| 9 | 9 |
Country,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| inputs/SALVIAS-CSV/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>SALVIAS-CSV</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
REMIB,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
accession_number,"/_if[@name=""if specimen""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
|
|
| 3 |
|
|
| 4 |
[1] Using the following query: |
|
| 5 |
----- |
|
| 6 |
SELECT acronym, accession_number, count(*) |
|
| 7 |
FROM ""REMIB"".""Specimen"" |
|
| 8 |
GROUP BY acronym, accession_number |
|
| 9 |
HAVING count(*) > 1 |
|
| 10 |
-----" |
|
| 11 |
acronym,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 12 |
accession_number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
|
| 3 | 13 |
|
| 4 | 14 |
[1] Using the following query: |
| ... | ... | |
| 86 | 96 |
county,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 87 | 97 |
state,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 88 | 98 |
state,/location/locationplace/*_id/place/stateprovince, |
| 89 |
accession_number,"/source/shortname/_if[@name=""if specimen""]/cond/_exists","Not globally unique, only (usually) unique within the institution providing the data (""acronym""). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution. [1]
|
|
| 90 |
|
|
| 91 |
[1] Using the following query: |
|
| 92 |
----- |
|
| 93 |
SELECT acronym, accession_number, count(*) |
|
| 94 |
FROM ""REMIB"".""Specimen"" |
|
| 95 |
GROUP BY acronym, accession_number |
|
| 96 |
HAVING count(*) > 1 |
|
| 97 |
-----" |
|
| 98 |
acronym,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 99 | 99 |
lat_min,,** No join mapping for *lat_min ** |
| 100 | 100 |
lat_sec,,** No join mapping for *lat_sec ** |
| 101 | 101 |
long_min,,** No join mapping for *long_min ** |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
ARIZ,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
GlobalUniqueIdentifier,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
CatalogNumberNumeric,"/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 4 |
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 5 |
InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 6 |
GlobalUniqueIdentifier,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 7 |
CatalogNumberNumeric,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/1", |
| 4 | 8 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
| ... | ... | |
| 95 | 99 |
County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 96 | 100 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 97 | 101 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 98 |
GlobalUniqueIdentifier,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 99 |
CatalogNumberNumeric,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 100 |
CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 101 |
InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 102 | 102 |
AgeClass,,** No join mapping for lifeStage ** |
| 103 | 103 |
BasisOfRecord,,** No join mapping for basisOfRecord ** |
| 104 | 104 |
DateLastModified,,** No join mapping for dcterms:modified ** |
| inputs/NCU-NCSC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
NCU-NCSC,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
Accession Number,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
Barcode,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 4 |
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 5 |
Barcode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 6 |
Accession Number,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 36 | 38 |
State,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 37 | 39 |
State,/location/locationplace/*_id/place/stateprovince, |
| 38 | 40 |
Elevation,/location/verbatimelevation, |
| 39 |
Accession Number,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 40 |
Barcode,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 41 | 41 |
Alt E/W,,** No join mapping for *Alt E/W ** |
| 42 | 42 |
Alt N/S,,** No join mapping for *Alt N/S ** |
| 43 | 43 |
FIPS,,** No join mapping for *FIPS ** FIPS county code |
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
museumaccessionnumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 2 | 3 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 4 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 5 |
museumaccessionnumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else", |
| ... | ... | |
| 51 | 52 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/1, |
| 52 | 53 |
authorplantname,/location/locationevent/taxonoccurrence/taxondetermination[isoriginal=true]/*_id/taxonverbatim/taxonname, |
| 53 | 54 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/voucher/*_id/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/then", |
| 54 |
museumaccessionnumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 55 | 55 |
Division,,** No join mapping for *Division ** |
| 56 | 56 |
Subclass,,** No join mapping for *Subclass ** |
| 57 | 57 |
Subdivision,,** No join mapping for *Subdivision ** |
| inputs/VegBank/Source/test.xml.ref | ||
|---|---|---|
| 5 | 5 |
<path> |
| 6 | 6 |
<_simplifyPath> |
| 7 | 7 |
<next>parent_id</next> |
| 8 |
<path><source><sourcetype>aggregator</sourcetype></source></path> |
|
| 8 |
<path> |
|
| 9 |
<source> |
|
| 10 |
<shortname>VegBank</shortname> |
|
| 11 |
<sourcetype>aggregator</sourcetype> |
|
| 12 |
</source> |
|
| 13 |
</path> |
|
| 9 | 14 |
</_simplifyPath> |
| 10 | 15 |
</path> |
| 11 | 16 |
</_setDefault> |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegCore,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
occurrenceID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname", |
|
| 5 |
referenceType,"/_if[@name=""if specimen""]/else/source/sourcetype", |
|
| 2 | 6 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 7 |
subplotID,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 4 | 8 |
plotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode", |
| ... | ... | |
| 386 | 390 |
subplotY,//location/sublocationyposition_m, |
| 387 | 391 |
verbatimElevation,//location/verbatimelevation, |
| 388 | 392 |
verbatimElevation_m,//location/verbatimelevation, |
| 389 |
catalogNumber,"//source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 390 |
occurrenceID,"//source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 391 |
institutionCode,"//source/shortname/_if[@name=""if specimen""]/else", |
|
| 392 |
referenceType,//source/sourcetype, |
|
| 393 | 393 |
OMIT,, |
| 394 | 394 |
PRIVATE,, |
| 395 | 395 |
UNUSED,, |
| inputs/VegBank/Source/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegBank,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
:aggregator,/source/sourcetype, |
|
| 2 |
:aggregator,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
VegCore,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
occurrenceID,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 5 |
referenceType,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
|
| 2 | 6 |
subplot,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 3 | 7 |
subplotID,"/location/_if[@name=""if subplot""]/cond/_exists", |
| 4 | 8 |
plotName,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/1", |
| ... | ... | |
| 386 | 390 |
subplotY,/location/sublocationyposition_m, |
| 387 | 391 |
verbatimElevation,/location/verbatimelevation, |
| 388 | 392 |
verbatimElevation_m,/location/verbatimelevation, |
| 389 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 390 |
occurrenceID,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 391 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 392 |
referenceType,/source/sourcetype, |
|
| 393 | 393 |
OMIT,, |
| 394 | 394 |
PRIVATE,, |
| 395 | 395 |
UNUSED,, |
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
MO,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
CatalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
InstitutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 4 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 3 | 5 |
CatalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 4 | 6 |
InstitutionCode,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then", |
| ... | ... | |
| 63 | 65 |
County,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/county/_first/2, |
| 64 | 66 |
StateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 65 | 67 |
StateProvince,/location/locationplace/*_id/place/stateprovince, |
| 66 |
CatalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 67 |
InstitutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 68 | 68 |
BasisOfRecord,,** No join mapping for basisOfRecord ** |
| 69 | 69 |
DateLastModified,,** No join mapping for dcterms:modified ** |
| 70 | 70 |
TypeStatus,,** No join mapping for typeStatus ** |
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 1 | 1 |
TRTE,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments |
| 2 |
catalogNumber,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 3 |
id,"/_if[@name=""if specimen""]/cond/_exists", |
|
| 4 |
institutionCode,"/_if[@name=""if specimen""]/else/source/shortname/_first/1", |
|
| 2 | 5 |
id,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/1", |
| 3 | 6 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/cond/_exists", |
| 4 | 7 |
catalogNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| ... | ... | |
| 84 | 87 |
stateProvince,/location/locationplace/*_id/place/matched_place_id/place:[source_id/source/shortname=geoscrub]/stateprovince/_first/2, |
| 85 | 88 |
stateProvince,/location/locationplace/*_id/place/stateprovince, |
| 86 | 89 |
verbatimElevation,/location/verbatimelevation, |
| 87 |
catalogNumber,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 88 |
id,"/source/shortname/_if[@name=""if specimen""]/cond/_exists", |
|
| 89 |
institutionCode,"/source/shortname/_if[@name=""if specimen""]/else", |
|
| 90 | 90 |
associatedMedia,,** No join mapping for associatedMedia ** |
| 91 | 91 |
associatedReferences,,** No join mapping for associatedReferences ** |
| 92 | 92 |
associatedTaxa,,** No join mapping for associatedTaxa ** |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source