Revision 7815
Added by Aaron Marcuse-Kubitza almost 12 years ago
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 26 | 26 |
GROUP BY herbarium, accession |
| 27 | 27 |
HAVING count(*) > 1 |
| 28 | 28 |
-----" |
| 29 |
herbarium,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/1/_map:[UNCCD=UNCC,*=*]/value","""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode). UNCCD likely = UNCC database." |
|
| 30 | 29 |
accession,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/3/_if[@name=""if indirect voucher""]/else","Globally unique, although occasionally duplicated. [1] Bob says this is actually the catalogNumber. |
| 31 | 30 |
|
| 32 | 31 |
[1] Using the following query: |
| ... | ... | |
| 70 | 69 |
GROUP BY herbarium, accession |
| 71 | 70 |
HAVING count(*) > 1 |
| 72 | 71 |
-----" |
| 73 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/1/_map:[UNCCD=UNCC,*=*]/value","""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode). UNCCD likely = UNCC database." |
|
| 74 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/1/_map:[UNCCD=UNCC,*=*]/value","""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode). UNCCD likely = UNCC database." |
|
| 75 | 72 |
collectno,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 76 | 73 |
SciName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3", |
| 77 | 74 |
collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/1, |
| ... | ... | |
| 127 | 124 |
filler,,"** No join mapping for *filler ** Where used, same as family" |
| 128 | 125 |
flower,,** No join mapping for *flower ** |
| 129 | 126 |
fruit,,** No join mapping for *fruit ** |
| 127 |
herbarium,,"** No join mapping for specimenIndexer/_map:[UNCCD=UNCC,*=*]/value ** ""The name or acronym in use by the institution that donated the collection"" (https://projects.nceas.ucsb.edu/nceas/attachments/download/593/UNCC-validation-Peet.xlsx#institutionCode). UNCCD likely = UNCC database." |
|
| 130 | 128 |
leaves,,** No join mapping for *leaves ** |
| 131 | 129 |
root,,** No join mapping for *root ** |
| 132 | 130 |
sheetno,,** No join mapping for associatedMedia ** ? |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 7 | 7 |
<next>parent_id</next> |
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 |
<authorlocationcode> |
|
| 11 |
<_join> |
|
| 12 |
<1> |
|
| 13 |
<_map> |
|
| 14 |
<UNCCD>UNCC</UNCCD> |
|
| 15 |
<*>*</*> |
|
| 16 |
<value>$herbarium</value> |
|
| 17 |
</_map> |
|
| 18 |
</1> |
|
| 19 |
<3>$accession</3> |
|
| 20 |
</_join> |
|
| 21 |
</authorlocationcode> |
|
| 10 |
<authorlocationcode>$accession</authorlocationcode> |
|
| 22 | 11 |
<iscultivated> |
| 23 | 12 |
<_locationnarrative_is_cultivated> |
| 24 | 13 |
<locationnarrative> |
| ... | ... | |
| 88 | 77 |
<specimenreplicate> |
| 89 | 78 |
<catalognumber_dwc>$accession</catalognumber_dwc> |
| 90 | 79 |
<collectionnumber>$collectno</collectionnumber> |
| 91 |
<institution_id> |
|
| 92 |
<sourcelist> |
|
| 93 |
<name> |
|
| 94 |
<_map> |
|
| 95 |
<UNCCD>UNCC</UNCCD> |
|
| 96 |
<*>*</*> |
|
| 97 |
<value>$herbarium</value> |
|
| 98 |
</_map> |
|
| 99 |
</name> |
|
| 100 |
<sourcename> |
|
| 101 |
<name> |
|
| 102 |
<_map> |
|
| 103 |
<UNCCD>UNCC</UNCCD> |
|
| 104 |
<*>*</*> |
|
| 105 |
<value>$herbarium</value> |
|
| 106 |
</_map> |
|
| 107 |
</name> |
|
| 108 |
</sourcename> |
|
| 109 |
</sourcelist> |
|
| 110 |
</institution_id> |
|
| 111 | 80 |
</specimenreplicate> |
| 112 | 81 |
</plantobservation> |
| 113 | 82 |
</aggregateoccurrence> |
| ... | ... | |
| 273 | 242 |
</path> |
| 274 | 243 |
</_setDefault> |
| 275 | 244 |
</VegBIEN> |
| 276 |
Inserted 26 new rows into database |
|
| 245 |
Inserted 24 new rows into database |
|
| inputs/UNCC/Specimen/unmapped_terms.csv | ||
|---|---|---|
| 1 |
specimenIndexer |
|
| 1 | 2 |
*leaves |
| 2 | 3 |
*flower |
| 3 | 4 |
*fruit |
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
accessionNumber,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 18 | 18 |
dataProviderRecordID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 19 | 19 |
occurrenceID,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/cond/_exists", |
| 20 |
specimenIndexer,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/1", |
|
| 21 | 20 |
specimenHolders,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2", |
| 22 | 21 |
collection,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/1", |
| 23 | 22 |
collectionURL,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/2/_join/2", |
| ... | ... | |
| 180 | 179 |
accessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 181 | 180 |
dataProviderRecordID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 182 | 181 |
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 183 |
specimenIndexer,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/1", |
|
| 184 | 182 |
specimenHolders,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2", |
| 185 |
specimenIndexer,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/1", |
|
| 186 | 183 |
specimenHolders,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value", |
| 187 | 184 |
dataProviderRecordID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 188 | 185 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| mappings/for_review/VegCore-VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
accessionNumber,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists", |
| 18 | 18 |
dataProviderRecordID,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists", |
| 19 | 19 |
occurrenceID,"/location/authorlocationcode/_if[@name=""if specimen""]/cond/_exists", |
| 20 |
specimenIndexer,"/location/authorlocationcode/_if[@name=""if specimen""]/then", |
|
| 21 | 20 |
specimenHolders,"/location/authorlocationcode/_if[@name=""if specimen""]/then", |
| 22 | 21 |
collection,"/location/authorlocationcode/_if[@name=""if catalogNumber""]/then", |
| 23 | 22 |
collectionURL,"/location/authorlocationcode/_if[@name=""if catalogNumber""]/then", |
| ... | ... | |
| 180 | 179 |
accessionNumber,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 181 | 180 |
dataProviderRecordID,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 182 | 181 |
occurrenceID,"//institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
| 183 |
specimenIndexer,"//institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 184 | 182 |
specimenHolders,"//institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
| 185 |
specimenIndexer,"//institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 186 | 183 |
specimenHolders,"//institution_id/sourcelist/sourcename/name/_split:[separator=""[,;] *""]/value", |
| 187 | 184 |
dataProviderRecordID,//specimenreplicate/sourceaccessioncode, |
| 188 | 185 |
occurrenceID,//specimenreplicate/sourceaccessioncode, |
Also available in: Unified diff
mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder