Revision 6791
Added by Aaron Marcuse-Kubitza about 12 years ago
| inputs/.herbaria/herbaria/test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<source> |
| 10 | 10 |
<shortname>$herbariumAcronym</shortname> |
| 11 |
<sampletype>specimen</sampletype>
|
|
| 11 |
<observationtype>specimen</observationtype>
|
|
| 12 | 12 |
<sourcetype>herbarium</sourcetype> |
| 13 | 13 |
</source> |
| 14 | 14 |
</path> |
| inputs/REMIB/Specimen/test.xml.ref | ||
|---|---|---|
| 55 | 55 |
<specimenreplicate> |
| 56 | 56 |
<catalognumber_dwc>$accession_number</catalognumber_dwc> |
| 57 | 57 |
<institution_id> |
| 58 |
<sourcename> |
|
| 59 |
<matched_source_id><source><shortname>$acronym</shortname></source></matched_source_id> |
|
| 58 |
<sourcelist> |
|
| 60 | 59 |
<name>$acronym</name> |
| 61 |
</sourcename> |
|
| 60 |
<sourcename> |
|
| 61 |
<matched_source_id><source><shortname>$acronym</shortname></source></matched_source_id> |
|
| 62 |
<name>$acronym</name> |
|
| 63 |
</sourcename> |
|
| 64 |
</sourcelist> |
|
| 62 | 65 |
</institution_id> |
| 63 | 66 |
</specimenreplicate> |
| 64 | 67 |
</plantobservation> |
| ... | ... | |
| 219 | 222 |
</path> |
| 220 | 223 |
</_setDefault> |
| 221 | 224 |
</VegBIEN> |
| 222 |
Inserted 33 new rows into database |
|
| 225 |
Inserted 34 new rows into database |
|
| inputs/TRT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 28 | 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 29 | 29 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 30 | 30 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 31 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 34 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 31 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 32 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 34 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 35 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 35 | 36 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 36 | 37 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 37 | 38 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/MO/Specimen/test.xml.ref | ||
|---|---|---|
| 62 | 62 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 63 | 63 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 64 | 64 |
<institution_id> |
| 65 |
<sourcename> |
|
| 66 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 65 |
<sourcelist> |
|
| 67 | 66 |
<name>$InstitutionCode</name> |
| 68 |
</sourcename> |
|
| 67 |
<sourcename> |
|
| 68 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 69 |
<name>$InstitutionCode</name> |
|
| 70 |
</sourcename> |
|
| 71 |
</sourcelist> |
|
| 69 | 72 |
</institution_id> |
| 70 | 73 |
</specimenreplicate> |
| 71 | 74 |
</plantobservation> |
| ... | ... | |
| 282 | 285 |
</path> |
| 283 | 286 |
</_setDefault> |
| 284 | 287 |
</VegBIEN> |
| 285 |
Inserted 40 new rows into database |
|
| 288 |
Inserted 41 new rows into database |
|
| inputs/bien_web/observation/VegBIEN.csv | ||
|---|---|---|
| 22 | 22 |
observationDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 23 | 23 |
pctCover,/location/locationevent/taxonoccurrence/aggregateoccurrence/cover_fraction/_percent_to_fraction/value, |
| 24 | 24 |
collectionNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 25 |
observationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 27 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 25 |
observationID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 27 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 28 |
dataSourceName,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 28 | 29 |
observationID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 29 | 30 |
plotCode,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 30 | 31 |
plotID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| inputs/NY/Specimen/VegBIEN.csv | ||
|---|---|---|
| 23 | 23 |
Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 24 | 24 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 25 | 25 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 26 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 27 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 28 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 26 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 27 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 28 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 29 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 29 | 30 |
FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1",Usage inconsistent with DwC definition |
| 30 | 31 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 31 | 32 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/Madidi/Organism/VegBIEN.csv | ||
|---|---|---|
| 20 | 20 |
Observations,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 21 | 21 |
Tree number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 22 | 22 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 23 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 23 |
Specimen,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 24 | 24 |
Trunk,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
| 25 | 25 |
Liana presence,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue", |
| 26 | 26 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,Assuming units based on the range and precision of values |
| inputs/UNCC/Specimen/test.xml.ref | ||
|---|---|---|
| 76 | 76 |
<collectionnumber>$collectno</collectionnumber> |
| 77 | 77 |
<specimenreplicate> |
| 78 | 78 |
<institution_id> |
| 79 |
<sourcename> |
|
| 80 |
<matched_source_id><source><shortname>$herbarium</shortname></source></matched_source_id> |
|
| 79 |
<sourcelist> |
|
| 81 | 80 |
<name>$herbarium</name> |
| 82 |
</sourcename> |
|
| 81 |
<sourcename> |
|
| 82 |
<matched_source_id><source><shortname>$herbarium</shortname></source></matched_source_id> |
|
| 83 |
<name>$herbarium</name> |
|
| 84 |
</sourcename> |
|
| 85 |
</sourcelist> |
|
| 83 | 86 |
</institution_id> |
| 84 | 87 |
<sourceaccessioncode>$accession</sourceaccessioncode> |
| 85 | 88 |
</specimenreplicate> |
| ... | ... | |
| 316 | 319 |
</path> |
| 317 | 320 |
</_setDefault> |
| 318 | 321 |
</VegBIEN> |
| 319 |
Inserted 29 new rows into database |
|
| 322 |
Inserted 30 new rows into database |
|
| inputs/.herbaria/herbaria/VegBIEN.csv | ||
|---|---|---|
| 4 | 4 |
:herbarium,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype", |
| 5 | 5 |
:specimen,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left", |
| 6 | 6 |
herbariumAcronym,"/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", |
| 7 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 8 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 7 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 8 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 9 |
herbariumAcronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 9 | 10 |
City,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| 10 | 11 |
CoordinatesVerbatim,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| 11 | 12 |
Country,,"** No non-empty join mapping for OMIT ** Just importing whether a datasource is a herbarium, for now" |
| inputs/REMIB/Specimen/VegBIEN.csv | ||
|---|---|---|
| 51 | 51 |
GROUP BY acronym, accession_number |
| 52 | 52 |
HAVING count(*) > 1 |
| 53 | 53 |
-----" |
| 54 |
accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_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]
|
|
| 54 |
accession_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_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]
|
|
| 55 | 55 |
|
| 56 | 56 |
[1] Using the following query: |
| 57 | 57 |
----- |
| ... | ... | |
| 60 | 60 |
GROUP BY acronym, accession_number |
| 61 | 61 |
HAVING count(*) > 1 |
| 62 | 62 |
-----" |
| 63 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 64 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 63 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 64 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 65 |
acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 65 | 66 |
collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| 66 | 67 |
family,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/1/_taxon_family_require_std/family/_nullIf/value", |
| 67 | 68 |
genus,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/_if[@name=""if has verbatim name""]/else/matched_label_id/taxonlabel:[source_id/source/shortname=TNRS]/taxonomicname/_join_words/2/_alt/2/_join_words/1/_alt/2/_join_words/2", |
| inputs/ARIZ/Specimen/test.xml.ref | ||
|---|---|---|
| 86 | 86 |
</catalognumber_dwc> |
| 87 | 87 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 88 | 88 |
<institution_id> |
| 89 |
<sourcename> |
|
| 90 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 89 |
<sourcelist> |
|
| 91 | 90 |
<name>$InstitutionCode</name> |
| 92 |
</sourcename> |
|
| 91 |
<sourcename> |
|
| 92 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 93 |
<name>$InstitutionCode</name> |
|
| 94 |
</sourcename> |
|
| 95 |
</sourcelist> |
|
| 93 | 96 |
</institution_id> |
| 94 | 97 |
<sourceaccessioncode>$GlobalUniqueIdentifier</sourceaccessioncode> |
| 95 | 98 |
</specimenreplicate> |
| ... | ... | |
| 371 | 374 |
</path> |
| 372 | 375 |
</_setDefault> |
| 373 | 376 |
</VegBIEN> |
| 374 |
Inserted 45 new rows into database |
|
| 377 |
Inserted 46 new rows into database |
|
| inputs/MO/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
CollectorNumber,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 20 | 20 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 22 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 24 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 22 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 24 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 25 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 25 | 26 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 26 | 27 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 27 | 28 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/MT/Specimen/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
individualCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/count, |
| 13 | 13 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 14 | 14 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 15 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 17 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 15 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 17 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 18 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 18 | 19 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 19 | 20 |
id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists", |
| 20 | 21 |
establishmentMeans,"/location/locationevent/taxonoccurrence/iscultivated/_alt/2/_map:[cultivated=t,wild=f,*=]/value", |
| inputs/MT/Specimen/test.xml.ref | ||
|---|---|---|
| 23 | 23 |
</_join> |
| 24 | 24 |
</collectioncode_dwc> |
| 25 | 25 |
<institution_id> |
| 26 |
<sourcename> |
|
| 27 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 26 |
<sourcelist> |
|
| 28 | 27 |
<name>$institutionCode</name> |
| 29 |
</sourcename> |
|
| 28 |
<sourcename> |
|
| 29 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 30 |
<name>$institutionCode</name> |
|
| 31 |
</sourcename> |
|
| 32 |
</sourcelist> |
|
| 30 | 33 |
</institution_id> |
| 31 | 34 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 32 | 35 |
</specimenreplicate> |
| ... | ... | |
| 129 | 132 |
</path> |
| 130 | 133 |
</_setDefault> |
| 131 | 134 |
</VegBIEN> |
| 132 |
Inserted 26 new rows into database |
|
| 135 |
Inserted 27 new rows into database |
|
| inputs/XAL/Specimen/VegBIEN.csv | ||
|---|---|---|
| 19 | 19 |
darwin:Sex,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/definedvalue[*_id/userdefined[tablename=plantobservation,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" |
| 20 | 20 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 | 21 |
darwin:CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 22 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 24 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 22 |
darwin:CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 23 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 24 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 25 |
darwin:InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 25 | 26 |
darwin:CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 26 | 27 |
darwin:ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 27 | 28 |
darwin:Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/NCU/Specimen/VegBIEN.csv | ||
|---|---|---|
| 21 | 21 |
firstCollectorRemarks,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber,"Actually the collector's number, not remarks" |
| 22 | 22 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 23 | 23 |
CollectionGUID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 24 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
SpecimenPK,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname/_alt/1", |
|
| 27 |
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname/_alt/2", |
|
| 28 |
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name/_alt/1", |
|
| 29 |
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name/_alt/2", |
|
| 24 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 25 |
SpecimenPK,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 26 |
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_alt/1", |
|
| 27 |
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_alt/2", |
|
| 28 |
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname/_alt/1", |
|
| 29 |
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname/_alt/2", |
|
| 30 |
CatalogSeriesPrefix,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_alt/1", |
|
| 31 |
OwnerInstitution,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_alt/2", |
|
| 30 | 32 |
SpecimenPK,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 31 | 33 |
firstCollectorRemarks,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1","Actually the collector's number, not remarks" |
| 32 | 34 |
CurrentScientificNameWithAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/NCU/Specimen/test.xml.ref | ||
|---|---|---|
| 45 | 45 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 46 | 46 |
<collectioncode_dwc>$CollectionGUID</collectioncode_dwc> |
| 47 | 47 |
<institution_id> |
| 48 |
<sourcename> |
|
| 49 |
<matched_source_id> |
|
| 50 |
<source> |
|
| 51 |
<shortname> |
|
| 52 |
<_alt> |
|
| 53 |
<1>$CatalogSeriesPrefix</1> |
|
| 54 |
<2>$OwnerInstitution</2> |
|
| 55 |
</_alt> |
|
| 56 |
</shortname> |
|
| 57 |
</source> |
|
| 58 |
</matched_source_id> |
|
| 48 |
<sourcelist> |
|
| 59 | 49 |
<name> |
| 60 | 50 |
<_alt> |
| 61 | 51 |
<1>$CatalogSeriesPrefix</1> |
| 62 | 52 |
<2>$OwnerInstitution</2> |
| 63 | 53 |
</_alt> |
| 64 | 54 |
</name> |
| 65 |
</sourcename> |
|
| 55 |
<sourcename> |
|
| 56 |
<matched_source_id> |
|
| 57 |
<source> |
|
| 58 |
<shortname> |
|
| 59 |
<_alt> |
|
| 60 |
<1>$CatalogSeriesPrefix</1> |
|
| 61 |
<2>$OwnerInstitution</2> |
|
| 62 |
</_alt> |
|
| 63 |
</shortname> |
|
| 64 |
</source> |
|
| 65 |
</matched_source_id> |
|
| 66 |
<name> |
|
| 67 |
<_alt> |
|
| 68 |
<1>$CatalogSeriesPrefix</1> |
|
| 69 |
<2>$OwnerInstitution</2> |
|
| 70 |
</_alt> |
|
| 71 |
</name> |
|
| 72 |
</sourcename> |
|
| 73 |
</sourcelist> |
|
| 66 | 74 |
</institution_id> |
| 67 | 75 |
<sourceaccessioncode>$SpecimenPK</sourceaccessioncode> |
| 68 | 76 |
</specimenreplicate> |
| ... | ... | |
| 194 | 202 |
</path> |
| 195 | 203 |
</_setDefault> |
| 196 | 204 |
</VegBIEN> |
| 197 |
Inserted 40 new rows into database |
|
| 205 |
Inserted 42 new rows into database |
|
| inputs/TEAM/VL/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 18 | 18 |
Observation Date,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 19 | 19 |
Observation Date,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 20 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 20 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 21 | 21 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 22 | 22 |
Diameter at 1.3m,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"
|
| 23 | 23 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| inputs/TEAM/VT/VegBIEN.csv | ||
|---|---|---|
| 17 | 17 |
Observation Date,"/location/locationevent/_if[@name=""if subplot""]/then/_if[@name=""if has event""]/then/parent_id/locationevent/obsstartdate/_alt/2/_dateRangeStart/value", |
| 18 | 18 |
Observation Date,/location/locationevent/obsenddate/_alt/2/_dateRangeEnd/value, |
| 19 | 19 |
Observation Date,/location/locationevent/obsstartdate/_alt/2/_dateRangeStart/value, |
| 20 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 20 |
Id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 21 | 21 |
Id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 22 | 22 |
Diameter,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/diameterbreastheight_m/_cm_to_m/value,"""Tree diameter measurement. {cm}"" (Diameter definition on p. 7 at <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>)"
|
| 23 | 23 |
Tree Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/tag, |
| inputs/ACAD/Specimen/VegBIEN.csv | ||
|---|---|---|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 32 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 33 | 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 34 | 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/ACAD/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</_join> |
| 59 | 59 |
</collectioncode_dwc> |
| 60 | 60 |
<institution_id> |
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 61 |
<sourcelist> |
|
| 63 | 62 |
<name>$institutionCode</name> |
| 64 |
</sourcename> |
|
| 63 |
<sourcename> |
|
| 64 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 65 |
<name>$institutionCode</name> |
|
| 66 |
</sourcename> |
|
| 67 |
</sourcelist> |
|
| 65 | 68 |
</institution_id> |
| 66 | 69 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 70 |
</specimenreplicate> |
| ... | ... | |
| 320 | 323 |
</path> |
| 321 | 324 |
</_setDefault> |
| 322 | 325 |
</VegBIEN> |
| 323 |
Inserted 47 new rows into database |
|
| 326 |
Inserted 48 new rows into database |
|
| inputs/WIN/Specimen/VegBIEN.csv | ||
|---|---|---|
| 26 | 26 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 27 | 27 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 28 | 28 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 29 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 29 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 33 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 33 | 34 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 34 | 35 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 35 | 36 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/WIN/Specimen/test.xml.ref | ||
|---|---|---|
| 63 | 63 |
</_join> |
| 64 | 64 |
</collectioncode_dwc> |
| 65 | 65 |
<institution_id> |
| 66 |
<sourcename> |
|
| 67 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 66 |
<sourcelist> |
|
| 68 | 67 |
<name>$institutionCode</name> |
| 69 |
</sourcename> |
|
| 68 |
<sourcename> |
|
| 69 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 70 |
<name>$institutionCode</name> |
|
| 71 |
</sourcename> |
|
| 72 |
</sourcelist> |
|
| 70 | 73 |
</institution_id> |
| 71 | 74 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 72 | 75 |
</specimenreplicate> |
| ... | ... | |
| 295 | 298 |
</path> |
| 296 | 299 |
</_setDefault> |
| 297 | 300 |
</VegBIEN> |
| 298 |
Inserted 37 new rows into database |
|
| 301 |
Inserted 38 new rows into database |
|
| inputs/SALVIAS/plotObservations/VegBIEN.csv | ||
|---|---|---|
| 72 | 72 |
DetType,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 73 | 73 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| 74 | 74 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 75 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 76 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_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."
|
|
| 75 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 76 |
SourceVoucher,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_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."
|
|
| 77 | 77 |
canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 78 | 78 |
canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| 79 | 79 |
liana_infestation,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=lianaInfestation]]:[@fkey=tablerecord_id]/definedvalue", |
| inputs/U/Specimen/VegBIEN.csv | ||
|---|---|---|
| 18 | 18 |
Notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 19 | 19 |
Number,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 20 | 20 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 21 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 22 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 21 |
Barcode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 22 |
ID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 23 | 23 |
ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 24 | 24 |
Number,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 25 | 25 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join/1, |
| inputs/QFA/Specimen/VegBIEN.csv | ||
|---|---|---|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 32 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 33 | 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 34 | 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/QFA/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</_join> |
| 59 | 59 |
</collectioncode_dwc> |
| 60 | 60 |
<institution_id> |
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 61 |
<sourcelist> |
|
| 63 | 62 |
<name>$institutionCode</name> |
| 64 |
</sourcename> |
|
| 63 |
<sourcename> |
|
| 64 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 65 |
<name>$institutionCode</name> |
|
| 66 |
</sourcename> |
|
| 67 |
</sourcelist> |
|
| 65 | 68 |
</institution_id> |
| 66 | 69 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 70 |
</specimenreplicate> |
| ... | ... | |
| 334 | 337 |
</path> |
| 335 | 338 |
</_setDefault> |
| 336 | 339 |
</VegBIEN> |
| 337 |
Inserted 47 new rows into database |
|
| 340 |
Inserted 48 new rows into database |
|
| inputs/GBIF/Specimen/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
LatestDateCollected,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 13 | 13 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 14 | 14 |
CollectionCD,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 15 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 17 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 15 |
CatalogNO,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 16 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 17 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 18 |
InstitutionCD,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 18 | 19 |
ScientificNameOriginal,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
| 19 | 20 |
ScientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3", |
| 20 | 21 |
Collector,/location/locationevent/taxonoccurrence/collector_id/party/fullname, |
| inputs/GBIF/Specimen/test.xml.ref | ||
|---|---|---|
| 30 | 30 |
<catalognumber_dwc>$CatalogNO</catalognumber_dwc> |
| 31 | 31 |
<collectioncode_dwc>$CollectionCD</collectioncode_dwc> |
| 32 | 32 |
<institution_id> |
| 33 |
<sourcename> |
|
| 34 |
<matched_source_id><source><shortname>$InstitutionCD</shortname></source></matched_source_id> |
|
| 33 |
<sourcelist> |
|
| 35 | 34 |
<name>$InstitutionCD</name> |
| 36 |
</sourcename> |
|
| 35 |
<sourcename> |
|
| 36 |
<matched_source_id><source><shortname>$InstitutionCD</shortname></source></matched_source_id> |
|
| 37 |
<name>$InstitutionCD</name> |
|
| 38 |
</sourcename> |
|
| 39 |
</sourcelist> |
|
| 37 | 40 |
</institution_id> |
| 38 | 41 |
</specimenreplicate> |
| 39 | 42 |
</plantobservation> |
| ... | ... | |
| 328 | 331 |
</path> |
| 329 | 332 |
</_setDefault> |
| 330 | 333 |
</VegBIEN> |
| 331 |
Inserted 47 new rows into database |
|
| 334 |
Inserted 48 new rows into database |
|
| inputs/JBM/Specimen/VegBIEN.csv | ||
|---|---|---|
| 26 | 26 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 27 | 27 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 28 | 28 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 29 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 29 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 33 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 33 | 34 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 34 | 35 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 35 | 36 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/JBM/Specimen/test.xml.ref | ||
|---|---|---|
| 61 | 61 |
</_join> |
| 62 | 62 |
</collectioncode_dwc> |
| 63 | 63 |
<institution_id> |
| 64 |
<sourcename> |
|
| 65 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 64 |
<sourcelist> |
|
| 66 | 65 |
<name>$institutionCode</name> |
| 67 |
</sourcename> |
|
| 66 |
<sourcename> |
|
| 67 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 68 |
<name>$institutionCode</name> |
|
| 69 |
</sourcename> |
|
| 70 |
</sourcelist> |
|
| 68 | 71 |
</institution_id> |
| 69 | 72 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 70 | 73 |
</specimenreplicate> |
| ... | ... | |
| 281 | 284 |
</path> |
| 282 | 285 |
</_setDefault> |
| 283 | 286 |
</VegBIEN> |
| 284 |
Inserted 38 new rows into database |
|
| 287 |
Inserted 39 new rows into database |
|
| inputs/UBC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 32 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 33 | 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 34 | 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/UBC/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</_join> |
| 59 | 59 |
</collectioncode_dwc> |
| 60 | 60 |
<institution_id> |
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 61 |
<sourcelist> |
|
| 63 | 62 |
<name>$institutionCode</name> |
| 64 |
</sourcename> |
|
| 63 |
<sourcename> |
|
| 64 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 65 |
<name>$institutionCode</name> |
|
| 66 |
</sourcename> |
|
| 67 |
</sourcelist> |
|
| 65 | 68 |
</institution_id> |
| 66 | 69 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 70 |
</specimenreplicate> |
| ... | ... | |
| 320 | 323 |
</path> |
| 321 | 324 |
</_setDefault> |
| 322 | 325 |
</VegBIEN> |
| 323 |
Inserted 43 new rows into database |
|
| 326 |
Inserted 44 new rows into database |
|
| inputs/HIBG/Specimen/VegBIEN.csv | ||
|---|---|---|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 32 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 33 | 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 34 | 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| inputs/HIBG/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</_join> |
| 59 | 59 |
</collectioncode_dwc> |
| 60 | 60 |
<institution_id> |
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 61 |
<sourcelist> |
|
| 63 | 62 |
<name>$institutionCode</name> |
| 64 |
</sourcename> |
|
| 63 |
<sourcename> |
|
| 64 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 65 |
<name>$institutionCode</name> |
|
| 66 |
</sourcename> |
|
| 67 |
</sourcelist> |
|
| 65 | 68 |
</institution_id> |
| 66 | 69 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 70 |
</specimenreplicate> |
| ... | ... | |
| 321 | 324 |
</path> |
| 322 | 325 |
</_setDefault> |
| 323 | 326 |
</VegBIEN> |
| 324 |
Inserted 39 new rows into database |
|
| 327 |
Inserted 40 new rows into database |
|
| inputs/SpeciesLink/Specimen/VegBIEN.csv | ||
|---|---|---|
| 87 | 87 |
dwc_dwcore_CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 88 | 88 |
dwc_terms_collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 89 | 89 |
dwc_terms_collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 90 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 91 |
dwc_dwcore_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 92 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 93 |
dwc_terms_catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 94 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 95 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 96 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 97 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 98 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 99 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 90 |
conceptual_darwin_2003_1_0_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 91 |
dwc_dwcore_CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 92 |
dwc_dwcore_GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 93 |
dwc_terms_catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 94 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 95 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 96 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 97 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 98 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 99 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 100 |
conceptual_darwin_2003_1_0_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 101 |
dwc_dwcore_InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 102 |
dwc_terms_institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 100 | 103 |
dwc_dwcore_GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 101 | 104 |
dwc_terms_recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/1", |
| 102 | 105 |
conceptual_darwin_2003_1_0_FieldNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1/_alt/2","Usage inconsistent with DwC definition. This field is instead identical to recordNumber, as the following query returns zero: (takes 23 sec) |
| inputs/SpeciesLink/Specimen/test.xml.ref | ||
|---|---|---|
| 162 | 162 |
</_join> |
| 163 | 163 |
</collectioncode_dwc> |
| 164 | 164 |
<institution_id> |
| 165 |
<sourcename> |
|
| 166 |
<matched_source_id> |
|
| 167 |
<source> |
|
| 168 |
<shortname> |
|
| 169 |
<_alt> |
|
| 170 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
|
| 171 |
<1>$dwc_dwcore_InstitutionCode</1> |
|
| 172 |
<2>$dwc_terms_institutionCode</2> |
|
| 173 |
</_alt> |
|
| 174 |
</shortname> |
|
| 175 |
</source> |
|
| 176 |
</matched_source_id> |
|
| 165 |
<sourcelist> |
|
| 177 | 166 |
<name> |
| 178 | 167 |
<_alt> |
| 179 | 168 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
| ... | ... | |
| 181 | 170 |
<2>$dwc_terms_institutionCode</2> |
| 182 | 171 |
</_alt> |
| 183 | 172 |
</name> |
| 184 |
</sourcename> |
|
| 173 |
<sourcename> |
|
| 174 |
<matched_source_id> |
|
| 175 |
<source> |
|
| 176 |
<shortname> |
|
| 177 |
<_alt> |
|
| 178 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
|
| 179 |
<1>$dwc_dwcore_InstitutionCode</1> |
|
| 180 |
<2>$dwc_terms_institutionCode</2> |
|
| 181 |
</_alt> |
|
| 182 |
</shortname> |
|
| 183 |
</source> |
|
| 184 |
</matched_source_id> |
|
| 185 |
<name> |
|
| 186 |
<_alt> |
|
| 187 |
<0>$conceptual_darwin_2003_1_0_InstitutionCode</0> |
|
| 188 |
<1>$dwc_dwcore_InstitutionCode</1> |
|
| 189 |
<2>$dwc_terms_institutionCode</2> |
|
| 190 |
</_alt> |
|
| 191 |
</name> |
|
| 192 |
</sourcename> |
|
| 193 |
</sourcelist> |
|
| 185 | 194 |
</institution_id> |
| 186 | 195 |
<sourceaccessioncode>$dwc_dwcore_GlobalUniqueIdentifier</sourceaccessioncode> |
| 187 | 196 |
</specimenreplicate> |
| ... | ... | |
| 750 | 759 |
</path> |
| 751 | 760 |
</_setDefault> |
| 752 | 761 |
</VegBIEN> |
| 753 |
Inserted 47 new rows into database |
|
| 762 |
Inserted 48 new rows into database |
|
| inputs/bien_web/observation/test.xml.ref | ||
|---|---|---|
| 21 | 21 |
<collectionnumber>$collectionNumber</collectionnumber> |
| 22 | 22 |
<specimenreplicate> |
| 23 | 23 |
<institution_id> |
| 24 |
<sourcename> |
|
| 25 |
<matched_source_id><source><shortname>$dataSourceName</shortname></source></matched_source_id> |
|
| 24 |
<sourcelist> |
|
| 26 | 25 |
<name>$dataSourceName</name> |
| 27 |
</sourcename> |
|
| 26 |
<sourcename> |
|
| 27 |
<matched_source_id><source><shortname>$dataSourceName</shortname></source></matched_source_id> |
|
| 28 |
<name>$dataSourceName</name> |
|
| 29 |
</sourcename> |
|
| 30 |
</sourcelist> |
|
| 28 | 31 |
</institution_id> |
| 29 | 32 |
<sourceaccessioncode>$observationID</sourceaccessioncode> |
| 30 | 33 |
</specimenreplicate> |
| inputs/NY/Specimen/test.xml.ref | ||
|---|---|---|
| 106 | 106 |
<catalognumber_dwc>$CatalogNumber</catalognumber_dwc> |
| 107 | 107 |
<collectioncode_dwc>$CollectionCode</collectioncode_dwc> |
| 108 | 108 |
<institution_id> |
| 109 |
<sourcename> |
|
| 110 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 109 |
<sourcelist> |
|
| 111 | 110 |
<name>$InstitutionCode</name> |
| 112 |
</sourcename> |
|
| 111 |
<sourcename> |
|
| 112 |
<matched_source_id><source><shortname>$InstitutionCode</shortname></source></matched_source_id> |
|
| 113 |
<name>$InstitutionCode</name> |
|
| 114 |
</sourcename> |
|
| 115 |
</sourcelist> |
|
| 113 | 116 |
</institution_id> |
| 114 | 117 |
</specimenreplicate> |
| 115 | 118 |
</plantobservation> |
| ... | ... | |
| 413 | 416 |
</path> |
| 414 | 417 |
</_setDefault> |
| 415 | 418 |
</VegBIEN> |
| 416 |
Inserted 45 new rows into database |
|
| 419 |
Inserted 46 new rows into database |
|
| inputs/UNCC/Specimen/VegBIEN.csv | ||
|---|---|---|
| 52 | 52 |
loanto,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/6/_label[label=""loaned to""]/value", |
| 53 | 53 |
inorout,"/location/locationevent/taxonoccurrence/aggregateoccurrence/notes/_join/7/_label[label=""in or out""]/value", |
| 54 | 54 |
collectno,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/collectionnumber, |
| 55 |
accession,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1]
|
|
| 55 |
accession,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists","Globally unique, although occasionally duplicated. [1]
|
|
| 56 | 56 |
|
| 57 | 57 |
[1] Using the following query: |
| 58 | 58 |
----- |
| ... | ... | |
| 61 | 61 |
GROUP BY herbarium, accession |
| 62 | 62 |
HAVING count(*) > 1 |
| 63 | 63 |
-----" |
| 64 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 65 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 64 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 65 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 66 |
herbarium,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 66 | 67 |
accession,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode,"Globally unique, although occasionally duplicated. [1] |
| 67 | 68 |
|
| 68 | 69 |
[1] Using the following query: |
| inputs/CVS/taxonObservation_/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
collectionDate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 13 | 13 |
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 14 | 14 |
museumAccessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 15 |
museumAccessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 15 |
museumAccessionNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 16 | 16 |
stemLocation_ID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/sourceaccessioncode, |
| 17 | 17 |
OBSERVATION_ID,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 18 | 18 |
authorPlantName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
| inputs/SALVIAS-CSV/Organism/VegBIEN.csv | ||
|---|---|---|
| 71 | 71 |
det_type,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/cond/_eq:[right=indirect]/left","Brad: A SALVIAS value referring to the relationship between the voucher specimen and the observation. Affect how the identification of the specimen(latin name) is transferred to the observation. 'direct'=voucher specimen was collected from this same tree; they are one and the same individual. 'indirect'=voucher specimen was collected for a different individual, but the original data provider confirmed that this is the same species. 'default'=basically same as 'indirect'. 'uncollected'=no voucher specimen, data provider asserted that this was the name but was unable to collect. The main different is that with 'direct', 'indirect', and 'default', the scientific name can be updated automatically based on the name attached to the specimen voucher (assuming you have a link to that data, presumably from a herbarium database. Whereas, if det_type='uncollected', the name can never change because there is no specimen." |
| 72 | 72 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1",Brad: Map instead as for voucher_string |
| 73 | 73 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below." |
| 74 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 75 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_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."
|
|
| 74 |
coll_number,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1",Brad: Map instead as for voucher_string
|
|
| 75 |
voucher_string,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_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."
|
|
| 76 | 76 |
basal_diam,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/basaldiameter_m, |
| 77 | 77 |
stem_canopy_form,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 78 | 78 |
stem_canopy_position,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| inputs/ARIZ/Specimen/VegBIEN.csv | ||
|---|---|---|
| 29 | 29 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/1", |
| 30 | 30 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else/_alt/2",Don't overwrite CatalogNumberNumeric |
| 31 | 31 |
CollectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 32 |
GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 34 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 35 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 36 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 32 |
GlobalUniqueIdentifier,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 33 |
CatalogNumberNumeric,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/1", |
|
| 34 |
CatalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists/_alt/2",Don't overwrite CatalogNumberNumeric |
|
| 35 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 36 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 37 |
InstitutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 37 | 38 |
GlobalUniqueIdentifier,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 38 | 39 |
CollectorNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 39 | 40 |
ScientificNameAuthor,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2",Contains the binomial in addition to the authority |
| inputs/TRT/Specimen/test.xml.ref | ||
|---|---|---|
| 77 | 77 |
</_join> |
| 78 | 78 |
</collectioncode_dwc> |
| 79 | 79 |
<institution_id> |
| 80 |
<sourcename> |
|
| 81 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 80 |
<sourcelist> |
|
| 82 | 81 |
<name>$institutionCode</name> |
| 83 |
</sourcename> |
|
| 82 |
<sourcename> |
|
| 83 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 84 |
<name>$institutionCode</name> |
|
| 85 |
</sourcename> |
|
| 86 |
</sourcelist> |
|
| 84 | 87 |
</institution_id> |
| 85 | 88 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 86 | 89 |
</specimenreplicate> |
| ... | ... | |
| 357 | 360 |
</path> |
| 358 | 361 |
</_setDefault> |
| 359 | 362 |
</VegBIEN> |
| 360 |
Inserted 43 new rows into database |
|
| 363 |
Inserted 44 new rows into database |
|
| inputs/VegBank/taxonobservation_/VegBIEN.csv | ||
|---|---|---|
| 12 | 12 |
collectiondate,/location/locationevent/taxonoccurrence/aggregateoccurrence/collectiondate/_alt/1, |
| 13 | 13 |
notes,/location/locationevent/taxonoccurrence/aggregateoccurrence/notes, |
| 14 | 14 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 15 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists",
|
|
| 15 |
museumaccessionnumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists",
|
|
| 16 | 16 |
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists", |
| 17 | 17 |
authorplantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/1", |
| 18 | 18 |
givenname,/location/locationevent/taxonoccurrence/collector_id/party/fullname/_join_words/1, |
| inputs/TRTE/Specimen/test.xml.ref | ||
|---|---|---|
| 58 | 58 |
</_join> |
| 59 | 59 |
</collectioncode_dwc> |
| 60 | 60 |
<institution_id> |
| 61 |
<sourcename> |
|
| 62 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 61 |
<sourcelist> |
|
| 63 | 62 |
<name>$institutionCode</name> |
| 64 |
</sourcename> |
|
| 63 |
<sourcename> |
|
| 64 |
<matched_source_id><source><shortname>$institutionCode</shortname></source></matched_source_id> |
|
| 65 |
<name>$institutionCode</name> |
|
| 66 |
</sourcename> |
|
| 67 |
</sourcelist> |
|
| 65 | 68 |
</institution_id> |
| 66 | 69 |
<sourceaccessioncode>$id</sourceaccessioncode> |
| 67 | 70 |
</specimenreplicate> |
| ... | ... | |
| 319 | 322 |
</path> |
| 320 | 323 |
</_setDefault> |
| 321 | 324 |
</VegBIEN> |
| 322 |
Inserted 35 new rows into database |
|
| 325 |
Inserted 36 new rows into database |
|
| schemas/vegbien.sql | ||
|---|---|---|
| 2070 | 2070 |
|
| 2071 | 2071 |
|
| 2072 | 2072 |
-- |
| 2073 |
-- Name: sourcename; Type: TABLE; Schema: public; Owner: -; Tablespace:
|
|
| 2073 |
-- Name: sourcelist; Type: TABLE; Schema: public; Owner: -; Tablespace:
|
|
| 2074 | 2074 |
-- |
| 2075 | 2075 |
|
| 2076 |
CREATE TABLE sourcename (
|
|
| 2077 |
sourcename_id integer NOT NULL,
|
|
| 2076 |
CREATE TABLE sourcelist (
|
|
| 2077 |
sourcelist_id integer NOT NULL,
|
|
| 2078 | 2078 |
source_id integer NOT NULL, |
| 2079 |
name text NOT NULL, |
|
| 2080 |
matched_source_id integer |
|
| 2079 |
name text NOT NULL |
|
| 2081 | 2080 |
); |
| 2082 | 2081 |
|
| 2083 | 2082 |
|
| ... | ... | |
| 2343 | 2342 |
-- |
| 2344 | 2343 |
|
| 2345 | 2344 |
CREATE VIEW analytical_stem_view AS |
| 2346 |
SELECT source.shortname AS datasource, sourcename.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", coordinates.coordsaccuracy_m AS "coordinateUncertaintyInMeters", (canon_place.geovalid)::integer AS geovalid, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld", project.sourceaccessioncode AS "projectID", COALESCE(location.sourceaccessioncode, location.authorlocationcode) AS "locationName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", family_higher_plant_group.higher_plant_group AS "higherPlantGroup", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.taxonname) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[COALESCE(accepted_taxonverbatim.genus, accepted_taxonverbatim.family), COALESCE(accepted_taxonverbatim.specific_epithet, parsed_taxonverbatim.morphospecies)], ' '::text), ''::text) AS "speciesBinomialWithMorphospecies", NULLIF(array_to_string(ARRAY[accepted_taxonlabel.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened, identifiedby.fullname AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis", collector.fullname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) LEFT JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) LEFT JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) LEFT JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN threatened_taxonlabel ON ((threatened_taxonlabel.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = accepted_taxonverbatim.family))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = accepted_taxonverbatim.family) AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcename ON ((sourcename.sourcename_id = specimenreplicate.institution_id))) WHERE COALESCE(taxondetermination.iscurrent, true);
|
|
| 2345 |
SELECT source.shortname AS datasource, sourcelist.name AS "institutionCode", specimenreplicate.collectioncode_dwc AS "collectionCode", specimenreplicate.catalognumber_dwc AS "catalogNumber", specimenreplicate.sourceaccessioncode AS "occurrenceID", canon_place.country, canon_place.stateprovince AS "stateProvince", datasource_place.county, coordinates.latitude_deg AS "decimalLatitude", coordinates.longitude_deg AS "decimalLongitude", coordinates.coordsaccuracy_m AS "coordinateUncertaintyInMeters", (canon_place.geovalid)::integer AS geovalid, ("newWorldCountries"."isNewWorld")::integer AS "isNewWorld", project.sourceaccessioncode AS "projectID", COALESCE(location.sourceaccessioncode, location.authorlocationcode) AS "locationName", location.elevation_m AS "elevationInMeters", _m2_to_ha(location.area_m2) AS "plotArea_ha", method.name AS "samplingProtocol", COALESCE(locationevent.obsstartdate, parent_event.obsstartdate, aggregateoccurrence.collectiondate) AS "dateCollected", family_higher_plant_group.higher_plant_group AS "higherPlantGroup", accepted_taxonverbatim.family, accepted_taxonverbatim.genus, ((accepted_taxonverbatim.genus || ' '::text) || accepted_taxonverbatim.specific_epithet) AS "speciesBinomial", COALESCE(accepted_taxonverbatim.taxonomicname, accepted_taxonverbatim.taxonname) AS "scientificName", accepted_taxonverbatim.author AS "scientificNameAuthorship", NULLIF(array_to_string(ARRAY[COALESCE(accepted_taxonverbatim.genus, accepted_taxonverbatim.family), COALESCE(accepted_taxonverbatim.specific_epithet, parsed_taxonverbatim.morphospecies)], ' '::text), ''::text) AS "speciesBinomialWithMorphospecies", NULLIF(array_to_string(ARRAY[accepted_taxonlabel.taxonomicname, parsed_taxonverbatim.morphospecies], ' '::text), ''::text) AS "scientificNameWithMorphospecies", ((threatened_taxonlabel.taxonlabel_id IS NOT NULL))::integer AS threatened, identifiedby.fullname AS "identifiedBy", taxonoccurrence.growthform AS "growthForm", (((cultivated_family_locations.country IS NOT NULL) OR _or(taxonoccurrence.iscultivated, location.iscultivated)))::integer AS cultivated, CASE WHEN (taxonoccurrence.iscultivated IS NOT NULL) THEN taxonoccurrence.cultivatedbasis WHEN (location.iscultivated IS NOT NULL) THEN NULL::text ELSE NULL::text END AS "cultivatedBasis", collector.fullname AS "recordedBy", plantobservation.collectionnumber AS "recordNumber", _fraction_to_percent(aggregateoccurrence.cover_fraction) AS "coverPercent", _m_to_cm(stemobservation.diameterbreastheight_m) AS "diameterBreastHeight_cm", stemobservation.height_m, stemobservation.tag, stemobservation.xposition_m AS "organismX_m", stemobservation.yposition_m AS "organismY_m", taxonoccurrence.sourceaccessioncode AS "taxonOccurrenceID", taxonoccurrence.authortaxoncode AS "authorTaxonCode", plantobservation.sourceaccessioncode AS "individualID", stemobservation.authorstemcode AS "authorStemCode" FROM ((((((((((((((((((((((((((((((source JOIN location USING (source_id)) LEFT JOIN locationevent USING (location_id)) LEFT JOIN location parent_location ON ((parent_location.location_id = location.parent_id))) LEFT JOIN locationplace ON ((locationplace.location_id = COALESCE(parent_location.location_id, location.location_id)))) LEFT JOIN place datasource_place USING (place_id)) LEFT JOIN place canon_place ON ((canon_place.place_id = datasource_place.canon_place_id))) LEFT JOIN coordinates ON ((coordinates.coordinates_id = canon_place.coordinates_id))) LEFT JOIN "newWorld".iso_code_gadm ON ((iso_code_gadm."GADM country" = canon_place.country))) LEFT JOIN "newWorld"."newWorldCountries" ON (("newWorldCountries"."isoCode" = iso_code_gadm."2-digit iso code"))) LEFT JOIN taxonoccurrence USING (locationevent_id)) LEFT JOIN locationevent parent_event ON ((parent_event.locationevent_id = locationevent.parent_id))) LEFT JOIN project ON ((project.project_id = COALESCE(locationevent.project_id, parent_event.project_id)))) LEFT JOIN method ON ((method.method_id = COALESCE(locationevent.method_id, parent_event.method_id)))) LEFT JOIN party collector ON ((collector.party_id = taxonoccurrence.collector_id))) LEFT JOIN taxondetermination USING (taxonoccurrence_id)) LEFT JOIN party identifiedby ON ((identifiedby.party_id = taxondetermination.party_id))) LEFT JOIN taxonverbatim datasource_taxonverbatim USING (taxonverbatim_id)) LEFT JOIN taxonlabel datasource_taxonlabel USING (taxonlabel_id)) LEFT JOIN taxonlabel parsed_taxonlabel ON ((parsed_taxonlabel.taxonlabel_id = datasource_taxonlabel.matched_label_id))) LEFT JOIN taxonverbatim parsed_taxonverbatim ON ((parsed_taxonverbatim.taxonlabel_id = parsed_taxonlabel.taxonlabel_id))) LEFT JOIN taxonlabel accepted_taxonlabel ON ((accepted_taxonlabel.taxonlabel_id = datasource_taxonlabel.canon_label_id))) LEFT JOIN taxonverbatim accepted_taxonverbatim ON ((accepted_taxonverbatim.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN threatened_taxonlabel ON ((threatened_taxonlabel.taxonlabel_id = accepted_taxonlabel.taxonlabel_id))) LEFT JOIN aggregateoccurrence USING (taxonoccurrence_id)) LEFT JOIN family_higher_plant_group ON ((family_higher_plant_group.family = accepted_taxonverbatim.family))) LEFT JOIN cultivated_family_locations ON (((cultivated_family_locations.family = accepted_taxonverbatim.family) AND (cultivated_family_locations.country = canon_place.country)))) LEFT JOIN plantobservation USING (aggregateoccurrence_id)) LEFT JOIN stemobservation USING (plantobservation_id)) LEFT JOIN specimenreplicate USING (plantobservation_id)) LEFT JOIN sourcelist ON ((sourcelist.sourcelist_id = specimenreplicate.institution_id))) WHERE COALESCE(taxondetermination.iscurrent, true);
|
|
| 2347 | 2346 |
|
| 2348 | 2347 |
|
| 2349 | 2348 |
-- |
| ... | ... | |
| 3816 | 3815 |
|
| 3817 | 3816 |
|
| 3818 | 3817 |
-- |
| 3819 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 3818 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 3820 | 3819 |
-- |
| 3821 | 3820 |
|
| 3822 |
CREATE SEQUENCE sourcename_sourcename_id_seq
|
|
| 3821 |
CREATE SEQUENCE sourcelist_sourcelist_id_seq
|
|
| 3823 | 3822 |
START WITH 1 |
| 3824 | 3823 |
INCREMENT BY 1 |
| 3825 | 3824 |
NO MINVALUE |
| ... | ... | |
| 3828 | 3827 |
|
| 3829 | 3828 |
|
| 3830 | 3829 |
-- |
| 3831 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 3830 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 3832 | 3831 |
-- |
| 3833 | 3832 |
|
| 3834 |
ALTER SEQUENCE sourcename_sourcename_id_seq OWNED BY sourcename.sourcename_id;
|
|
| 3833 |
ALTER SEQUENCE sourcelist_sourcelist_id_seq OWNED BY sourcelist.sourcelist_id;
|
|
| 3835 | 3834 |
|
| 3836 | 3835 |
|
| 3837 | 3836 |
-- |
| 3838 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
|
|
| 3837 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
|
|
| 3839 | 3838 |
-- |
| 3840 | 3839 |
|
| 3841 | 3840 |
|
| 3842 | 3841 |
|
| 3843 | 3842 |
-- |
| 3843 |
-- Name: sourcename; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
| 3844 |
-- |
|
| 3845 |
|
|
| 3846 |
CREATE TABLE sourcename ( |
|
| 3847 |
sourcelist_id integer NOT NULL, |
|
| 3848 |
name text NOT NULL, |
|
| 3849 |
matched_source_id integer |
|
| 3850 |
); |
|
| 3851 |
|
|
| 3852 |
|
|
| 3853 |
-- |
|
| 3844 | 3854 |
-- Name: specimen; Type: TABLE; Schema: public; Owner: -; Tablespace: |
| 3845 | 3855 |
-- |
| 3846 | 3856 |
|
| ... | ... | |
| 4750 | 4760 |
|
| 4751 | 4761 |
|
| 4752 | 4762 |
-- |
| 4753 |
-- Name: sourcename_id; Type: DEFAULT; Schema: public; Owner: -
|
|
| 4763 |
-- Name: sourcelist_id; Type: DEFAULT; Schema: public; Owner: -
|
|
| 4754 | 4764 |
-- |
| 4755 | 4765 |
|
| 4756 |
ALTER TABLE ONLY sourcename ALTER COLUMN sourcename_id SET DEFAULT nextval('sourcename_sourcename_id_seq'::regclass);
|
|
| 4766 |
ALTER TABLE ONLY sourcelist ALTER COLUMN sourcelist_id SET DEFAULT nextval('sourcelist_sourcelist_id_seq'::regclass);
|
|
| 4757 | 4767 |
|
| 4758 | 4768 |
|
| 4759 | 4769 |
-- |
| ... | ... | |
| 5224 | 5234 |
|
| 5225 | 5235 |
|
| 5226 | 5236 |
-- |
| 5237 |
-- Data for Name: sourcelist; Type: TABLE DATA; Schema: public; Owner: - |
|
| 5238 |
-- |
|
| 5239 |
|
|
| 5240 |
|
|
| 5241 |
|
|
| 5242 |
-- |
|
| 5227 | 5243 |
-- Data for Name: sourcename; Type: TABLE DATA; Schema: public; Owner: - |
| 5228 | 5244 |
-- |
| 5229 | 5245 |
|
| ... | ... | |
| 5752 | 5768 |
|
| 5753 | 5769 |
|
| 5754 | 5770 |
-- |
| 5771 |
-- Name: sourcelist_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 5772 |
-- |
|
| 5773 |
|
|
| 5774 |
ALTER TABLE ONLY sourcelist |
|
| 5775 |
ADD CONSTRAINT sourcelist_pkey PRIMARY KEY (sourcelist_id); |
|
| 5776 |
|
|
| 5777 |
|
|
| 5778 |
-- |
|
| 5755 | 5779 |
-- Name: sourcename_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
| 5756 | 5780 |
-- |
| 5757 | 5781 |
|
| 5758 | 5782 |
ALTER TABLE ONLY sourcename |
| 5759 |
ADD CONSTRAINT sourcename_pkey PRIMARY KEY (sourcename_id);
|
|
| 5783 |
ADD CONSTRAINT sourcename_pkey PRIMARY KEY (sourcelist_id, name);
|
|
| 5760 | 5784 |
|
| 5761 | 5785 |
|
| 5762 | 5786 |
-- |
| ... | ... | |
| 6273 | 6297 |
|
| 6274 | 6298 |
|
| 6275 | 6299 |
-- |
| 6276 |
-- Name: sourcename_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 6300 |
-- Name: sourcelist_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 6277 | 6301 |
-- |
| 6278 | 6302 |
|
| 6279 |
CREATE UNIQUE INDEX sourcename_unique ON sourcename USING btree (source_id, (COALESCE(name, '\N'::text)));
|
|
| 6303 |
CREATE UNIQUE INDEX sourcelist_unique ON sourcelist USING btree (source_id, (COALESCE(name, '\N'::text)));
|
|
| 6280 | 6304 |
|
| 6281 | 6305 |
|
| 6282 | 6306 |
-- |
| ... | ... | |
| 7235 | 7259 |
|
| 7236 | 7260 |
|
| 7237 | 7261 |
-- |
| 7262 |
-- Name: sourcelist_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 7263 |
-- |
|
| 7264 |
|
|
| 7265 |
ALTER TABLE ONLY sourcelist |
|
| 7266 |
ADD CONSTRAINT sourcelist_source_id_fkey FOREIGN KEY (source_id) REFERENCES source(source_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 7267 |
|
|
| 7268 |
|
|
| 7269 |
-- |
|
| 7238 | 7270 |
-- Name: sourcename_matched_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
| 7239 | 7271 |
-- |
| 7240 | 7272 |
|
| ... | ... | |
| 7243 | 7275 |
|
| 7244 | 7276 |
|
| 7245 | 7277 |
-- |
| 7246 |
-- Name: sourcename_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 7278 |
-- Name: sourcename_sourcelist_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
| 7247 | 7279 |
-- |
| 7248 | 7280 |
|
| 7249 | 7281 |
ALTER TABLE ONLY sourcename |
| 7250 |
ADD CONSTRAINT sourcename_source_id_fkey FOREIGN KEY (source_id) REFERENCES source(source_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 7282 |
ADD CONSTRAINT sourcename_sourcelist_id_fkey FOREIGN KEY (sourcelist_id) REFERENCES sourcelist(sourcelist_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 7251 | 7283 |
|
| 7252 | 7284 |
|
| 7253 | 7285 |
-- |
| ... | ... | |
| 7255 | 7287 |
-- |
| 7256 | 7288 |
|
| 7257 | 7289 |
ALTER TABLE ONLY specimenreplicate |
| 7258 |
ADD CONSTRAINT specimenreplicate_institution_id_fkey FOREIGN KEY (institution_id) REFERENCES sourcename(sourcename_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 7290 |
ADD CONSTRAINT specimenreplicate_institution_id_fkey FOREIGN KEY (institution_id) REFERENCES sourcelist(sourcelist_id) ON UPDATE CASCADE ON DELETE CASCADE;
|
|
| 7259 | 7291 |
|
| 7260 | 7292 |
|
| 7261 | 7293 |
-- |
| ... | ... | |
| 7745 | 7777 |
|
| 7746 | 7778 |
|
| 7747 | 7779 |
-- |
| 7748 |
-- Name: sourcename; Type: ACL; Schema: public; Owner: -
|
|
| 7780 |
-- Name: sourcelist; Type: ACL; Schema: public; Owner: -
|
|
| 7749 | 7781 |
-- |
| 7750 | 7782 |
|
| 7751 |
REVOKE ALL ON TABLE sourcename FROM PUBLIC;
|
|
| 7752 |
REVOKE ALL ON TABLE sourcename FROM bien;
|
|
| 7753 |
GRANT ALL ON TABLE sourcename TO bien;
|
|
| 7754 |
GRANT SELECT ON TABLE sourcename TO bien_read;
|
|
| 7783 |
REVOKE ALL ON TABLE sourcelist FROM PUBLIC;
|
|
| 7784 |
REVOKE ALL ON TABLE sourcelist FROM bien;
|
|
| 7785 |
GRANT ALL ON TABLE sourcelist TO bien;
|
|
| 7786 |
GRANT SELECT ON TABLE sourcelist TO bien_read;
|
|
| 7755 | 7787 |
|
| 7756 | 7788 |
|
| 7757 | 7789 |
-- |
| ... | ... | |
| 8145 | 8177 |
|
| 8146 | 8178 |
|
| 8147 | 8179 |
-- |
| 8180 |
-- Name: sourcename; Type: ACL; Schema: public; Owner: - |
|
| 8181 |
-- |
|
| 8182 |
|
|
| 8183 |
REVOKE ALL ON TABLE sourcename FROM PUBLIC; |
|
| 8184 |
REVOKE ALL ON TABLE sourcename FROM bien; |
|
| 8185 |
GRANT ALL ON TABLE sourcename TO bien; |
|
| 8186 |
GRANT SELECT ON TABLE sourcename TO bien_read; |
|
| 8187 |
|
|
| 8188 |
|
|
| 8189 |
-- |
|
| 8148 | 8190 |
-- Name: specimen; Type: ACL; Schema: public; Owner: - |
| 8149 | 8191 |
-- |
| 8150 | 8192 |
|
| inputs/TRTE/Specimen/VegBIEN.csv | ||
|---|---|---|
| 25 | 25 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 26 | 26 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 27 | 27 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 28 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 29 |
id,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 30 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 31 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 32 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 32 | 33 |
id,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 33 | 34 |
recordNumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/1/_first/1", |
| 34 | 35 |
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/2", |
| schemas/vegbien.my.sql | ||
|---|---|---|
| 1295 | 1295 |
|
| 1296 | 1296 |
|
| 1297 | 1297 |
-- |
| 1298 |
-- Name: sourcename; Type: TABLE; Schema: public; Owner: -; Tablespace:
|
|
| 1298 |
-- Name: sourcelist; Type: TABLE; Schema: public; Owner: -; Tablespace:
|
|
| 1299 | 1299 |
-- |
| 1300 | 1300 |
|
| 1301 |
CREATE TABLE sourcename (
|
|
| 1302 |
sourcename_id int(11) NOT NULL,
|
|
| 1301 |
CREATE TABLE sourcelist (
|
|
| 1302 |
sourcelist_id int(11) NOT NULL,
|
|
| 1303 | 1303 |
source_id int(11) NOT NULL, |
| 1304 |
name varchar(255) NOT NULL, |
|
| 1305 |
matched_source_id int(11) |
|
| 1304 |
name varchar(255) NOT NULL |
|
| 1306 | 1305 |
); |
| 1307 | 1306 |
|
| 1308 | 1307 |
|
| ... | ... | |
| 2835 | 2834 |
|
| 2836 | 2835 |
|
| 2837 | 2836 |
-- |
| 2838 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 2837 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE; Schema: public; Owner: -
|
|
| 2839 | 2838 |
-- |
| 2840 | 2839 |
|
| 2841 | 2840 |
|
| 2842 | 2841 |
|
| 2843 | 2842 |
|
| 2844 | 2843 |
-- |
| 2845 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 2844 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE OWNED BY; Schema: public; Owner: -
|
|
| 2846 | 2845 |
-- |
| 2847 | 2846 |
|
| 2848 | 2847 |
|
| 2849 | 2848 |
|
| 2850 | 2849 |
|
| 2851 | 2850 |
-- |
| 2852 |
-- Name: sourcename_sourcename_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
|
|
| 2851 |
-- Name: sourcelist_sourcelist_id_seq; Type: SEQUENCE SET; Schema: public; Owner: -
|
|
| 2853 | 2852 |
-- |
| 2854 | 2853 |
|
| 2855 | 2854 |
|
| 2856 | 2855 |
|
| 2857 | 2856 |
-- |
| 2857 |
-- Name: sourcename; Type: TABLE; Schema: public; Owner: -; Tablespace: |
|
| 2858 |
-- |
|
| 2859 |
|
|
| 2860 |
CREATE TABLE sourcename ( |
|
| 2861 |
sourcelist_id int(11) NOT NULL, |
|
| 2862 |
name varchar(255) NOT NULL, |
|
| 2863 |
matched_source_id int(11) |
|
| 2864 |
); |
|
| 2865 |
|
|
| 2866 |
|
|
| 2867 |
-- |
|
| 2858 | 2868 |
-- Name: specimen; Type: TABLE; Schema: public; Owner: -; Tablespace: |
| 2859 | 2869 |
-- |
| 2860 | 2870 |
|
| ... | ... | |
| 3675 | 3685 |
|
| 3676 | 3686 |
|
| 3677 | 3687 |
-- |
| 3678 |
-- Name: sourcename_id; Type: DEFAULT; Schema: public; Owner: -
|
|
| 3688 |
-- Name: sourcelist_id; Type: DEFAULT; Schema: public; Owner: -
|
|
| 3679 | 3689 |
-- |
| 3680 | 3690 |
|
| 3681 | 3691 |
|
| ... | ... | |
| 4149 | 4159 |
|
| 4150 | 4160 |
|
| 4151 | 4161 |
-- |
| 4162 |
-- Data for Name: sourcelist; Type: TABLE DATA; Schema: public; Owner: - |
|
| 4163 |
-- |
|
| 4164 |
|
|
| 4165 |
|
|
| 4166 |
|
|
| 4167 |
-- |
|
| 4152 | 4168 |
-- Data for Name: sourcename; Type: TABLE DATA; Schema: public; Owner: - |
| 4153 | 4169 |
-- |
| 4154 | 4170 |
|
| ... | ... | |
| 4677 | 4693 |
|
| 4678 | 4694 |
|
| 4679 | 4695 |
-- |
| 4696 |
-- Name: sourcelist_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
|
| 4697 |
-- |
|
| 4698 |
|
|
| 4699 |
ALTER TABLE sourcelist |
|
| 4700 |
ADD CONSTRAINT sourcelist_pkey PRIMARY KEY (sourcelist_id); |
|
| 4701 |
|
|
| 4702 |
|
|
| 4703 |
-- |
|
| 4680 | 4704 |
-- Name: sourcename_pkey; Type: CONSTRAINT; Schema: public; Owner: -; Tablespace: |
| 4681 | 4705 |
-- |
| 4682 | 4706 |
|
| 4683 | 4707 |
ALTER TABLE sourcename |
| 4684 |
ADD CONSTRAINT sourcename_pkey PRIMARY KEY (sourcename_id);
|
|
| 4708 |
ADD CONSTRAINT sourcename_pkey PRIMARY KEY (sourcelist_id, name);
|
|
| 4685 | 4709 |
|
| 4686 | 4710 |
|
| 4687 | 4711 |
-- |
| ... | ... | |
| 5198 | 5222 |
|
| 5199 | 5223 |
|
| 5200 | 5224 |
-- |
| 5201 |
-- Name: sourcename_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 5225 |
-- Name: sourcelist_unique; Type: INDEX; Schema: public; Owner: -; Tablespace:
|
|
| 5202 | 5226 |
-- |
| 5203 | 5227 |
|
| 5204 | 5228 |
|
| ... | ... | |
| 6128 | 6152 |
|
| 6129 | 6153 |
|
| 6130 | 6154 |
-- |
| 6155 |
-- Name: sourcelist_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 6156 |
-- |
|
| 6157 |
|
|
| 6158 |
|
|
| 6159 |
|
|
| 6160 |
|
|
| 6161 |
-- |
|
| 6131 | 6162 |
-- Name: sourcename_matched_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
| 6132 | 6163 |
-- |
| 6133 | 6164 |
|
| ... | ... | |
| 6136 | 6167 |
|
| 6137 | 6168 |
|
| 6138 | 6169 |
-- |
| 6139 |
-- Name: sourcename_source_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
|
| 6170 |
-- Name: sourcename_sourcelist_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: -
|
|
| 6140 | 6171 |
-- |
| 6141 | 6172 |
|
| 6173 |
ALTER TABLE sourcename |
|
| 6174 |
ADD CONSTRAINT sourcename_sourcelist_id_fkey FOREIGN KEY (sourcelist_id) REFERENCES sourcelist(sourcelist_id) ON UPDATE CASCADE ON DELETE CASCADE; |
|
| 6142 | 6175 |
|
| 6143 | 6176 |
|
| 6144 |
|
|
| 6145 | 6177 |
-- |
| 6146 | 6178 |
-- Name: specimenreplicate_institution_id_fkey; Type: FK CONSTRAINT; Schema: public; Owner: - |
| 6147 | 6179 |
-- |
| ... | ... | |
| 6622 | 6654 |
|
| 6623 | 6655 |
|
| 6624 | 6656 |
-- |
| 6625 |
-- Name: sourcename; Type: ACL; Schema: public; Owner: -
|
|
| 6657 |
-- Name: sourcelist; Type: ACL; Schema: public; Owner: -
|
|
| 6626 | 6658 |
-- |
| 6627 | 6659 |
|
| 6628 | 6660 |
|
| ... | ... | |
| 7022 | 7054 |
|
| 7023 | 7055 |
|
| 7024 | 7056 |
-- |
| 7057 |
-- Name: sourcename; Type: ACL; Schema: public; Owner: - |
|
| 7058 |
-- |
|
| 7059 |
|
|
| 7060 |
|
|
| 7061 |
|
|
| 7062 |
|
|
| 7063 |
|
|
| 7064 |
|
|
| 7065 |
|
|
| 7066 |
-- |
|
| 7025 | 7067 |
-- Name: specimen; Type: ACL; Schema: public; Owner: - |
| 7026 | 7068 |
-- |
| 7027 | 7069 |
|
| mappings/VegCore-VegBIEN.csv | ||
|---|---|---|
| 115 | 115 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/catalognumber_dwc/_if[@name=""if indirect voucher""]/else", |
| 116 | 116 |
collectionCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/1,Brad: Not sure if mapping correct. DwC element; code for entire collection; often same as InstitutionCode; Aaron: Combining with InstitutionCode to create collection name |
| 117 | 117 |
collectionID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/collectioncode_dwc/_join/2, |
| 118 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 119 |
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/cond/_exists", |
|
| 120 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/matched_source_id/source/shortname", |
|
| 121 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcename/_if[@name=""if specimen""]/then/name", |
|
| 118 |
catalogNumber,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 119 |
occurrenceID,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/cond/_exists", |
|
| 120 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name", |
|
| 121 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/matched_source_id/source/shortname", |
|
| 122 |
institutionCode,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name", |
|
| 122 | 123 |
occurrenceID,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/sourceaccessioncode, |
| 123 | 124 |
stemCount,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemcount, |
| 124 | 125 |
authorStemCode,/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/stemobservation/authorstemcode, |
| schemas/filter_ERD.csv | ||
|---|---|---|
| 9 | 9 |
"^ALTER TABLE \b[^;]*\bFOREIGN KEY\b[^;]*\(submethod_id\) REFERENCES method\b[^;]*;",,inward |
| 10 | 10 |
"^ALTER TABLE (?!party|address|sourcecontributor|telephone)\b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES party\b[^;]*;",,inward |
| 11 | 11 |
"^ALTER TABLE (?!sourcecontributor)\b[^;]*\bFOREIGN KEY\b[^;]*\((?:source_id|commauthority_id|concept_reference_id)\) REFERENCES source\b[^;]*;",,inward |
| 12 |
"^ALTER TABLE \b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES sourcename\b[^;]*;",,inward
|
|
| 12 |
"^ALTER TABLE (?!sourcename)\b[^;]*\bFOREIGN KEY\b[^;]*\bREFERENCES sourcelist\b[^;]*;",,inward
|
|
| 13 | 13 |
"^ALTER TABLE (?:projectcontributor)\b[^;]*\bFOREIGN KEY\b[^;]*\((?:project_id)\) REFERENCES \b[^;]*;",,inward |
| 14 | 14 |
"^ALTER TABLE (?:partymember)\b[^;]*\bFOREIGN KEY\b[^;]*\((?:parentparty_id)\) REFERENCES \b[^;]*;",,inward |
| 15 | 15 |
"^ALTER TABLE (?:address)\b[^;]*\bFOREIGN KEY\b[^;]*\((?:organization_id)\) REFERENCES \b[^;]*;",,inward |
Also available in: Unified diff
schemas/vegbien.sql: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)