Revision 3207
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/test/VegBIEN.plots.xml.ref | ||
|---|---|---|
| 30 | 30 |
<locationnarrative>pre-Holocene; clay</locationnarrative> |
| 31 | 31 |
<centerlatitude>-3.95</centerlatitude> |
| 32 | 32 |
<centerlongitude>-73.4333</centerlongitude> |
| 33 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 34 |
<sourceaccessioncode>26102</sourceaccessioncode> |
|
| 33 | 35 |
</location> |
| 34 | 36 |
</location_id> |
| 35 | 37 |
<method_id><method><name>1 ha, stems >= 10 cm dbh</name></method></method_id> |
| ... | ... | |
| 74 | 76 |
<locationnarrative>pre-Holocene; white and brown sand</locationnarrative> |
| 75 | 77 |
<centerlatitude>-3.95</centerlatitude> |
| 76 | 78 |
<centerlongitude>-73.4333</centerlongitude> |
| 79 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 80 |
<sourceaccessioncode>26103</sourceaccessioncode> |
|
| 77 | 81 |
</location> |
| 78 | 82 |
</location_id> |
| 79 | 83 |
<method_id><method><name>1 ha, stems >= 10 cm dbh</name></method></method_id> |
| inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 10 | 10 |
<parent_id> |
| 11 | 11 |
<locationevent> |
| 12 | 12 |
<authorlocationcode>ALP-11</authorlocationcode> |
| 13 |
<location_id> |
|
| 14 |
<location> |
|
| 15 |
<sourceaccessioncode>26102</sourceaccessioncode> |
|
| 16 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 17 |
</location> |
|
| 18 |
</location_id> |
|
| 13 | 19 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
| 14 | 20 |
<sourceaccessioncode>26102</sourceaccessioncode> |
| 15 | 21 |
</locationevent> |
| 16 | 22 |
</parent_id> |
| 23 |
<location_id> |
|
| 24 |
<location> |
|
| 25 |
<sourceaccessioncode>26102; 1</sourceaccessioncode> |
|
| 26 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 27 |
</location> |
|
| 28 |
</location_id> |
|
| 17 | 29 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
| 18 | 30 |
<authorlocationcode>1</authorlocationcode> |
| 19 | 31 |
</locationevent> |
| ... | ... | |
| 112 | 124 |
<parent_id> |
| 113 | 125 |
<locationevent> |
| 114 | 126 |
<authorlocationcode>ALP-11</authorlocationcode> |
| 127 |
<location_id> |
|
| 128 |
<location> |
|
| 129 |
<sourceaccessioncode>26102</sourceaccessioncode> |
|
| 130 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 131 |
</location> |
|
| 132 |
</location_id> |
|
| 115 | 133 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
| 116 | 134 |
<sourceaccessioncode>26102</sourceaccessioncode> |
| 117 | 135 |
</locationevent> |
| 118 | 136 |
</parent_id> |
| 137 |
<location_id> |
|
| 138 |
<location> |
|
| 139 |
<sourceaccessioncode>26102; 4</sourceaccessioncode> |
|
| 140 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
|
| 141 |
</location> |
|
| 142 |
</location_id> |
|
| 119 | 143 |
<datasource_id><party><organizationname>SALVIAS-CSV</organizationname></party></datasource_id> |
| 120 | 144 |
<authorlocationcode>4</authorlocationcode> |
| 121 | 145 |
</locationevent> |
| inputs/SALVIAS-CSV/test/import.organisms.out.ref | ||
|---|---|---|
| 1 |
Inserted 43 new rows into database |
|
| 1 |
Inserted 46 new rows into database |
|
| inputs/SALVIAS-CSV/maps/VegBIEN.plots.csv | ||
|---|---|---|
| 37 | 37 |
soil_Na,"/soilobs/sodium/_units:[default=""%"",to=]/value", |
| 38 | 38 |
soil_texture,/soilobs/texture, |
| 39 | 39 |
temp_c,/temperature, |
| 40 |
plot_code,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
| 41 |
PLOT_ID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
| 40 |
plot_code,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
| 41 |
PLOT_ID,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
| 42 | 42 |
observation_type,,"Brad: SALVIAS internal metadata indicating whether the record represents an individual or aggregate observation. Rather than storing, use to decide where to store in VegX.; Aaron: VegX aggregateOrganismObservation table is missing many fields available in individualOrganismObservation, so we're mapping to individualOrganismObservation regardless of observation type" |
| 43 | 43 |
recensused,,"Brad: This is a 0/1 value, internal to SALVIAS. 1 indicates that a plot has >1 set of values, from different census events.; Aaron: Different censuses are distinguished in organisms data by different census_no values" |
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS-CSV,VegBIEN:/plantobservation,Comments |
| 2 | 2 |
census_date,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate/_date/year, |
| 3 |
plot_code,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent/authorlocationcode,"Brad: Same as plotCode, above"
|
|
| 4 |
PLOT_ID,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 5 |
subplot,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,
|
|
| 3 |
plot_code,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}","Brad: Same as plotCode, above"
|
|
| 4 |
PLOT_ID,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}","Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 5 |
subplot,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 6 | 6 |
coll_number,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string
|
| 7 | 7 |
voucher_string,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
| 8 | 8 |
habit,"/aggregateoccurrence/*_id/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
| inputs/CTFS/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 8 | 8 |
<locationevent> |
| 9 | 9 |
<obsstartdate>1981-05-03</obsstartdate> |
| 10 | 10 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
| 11 |
<location_id> |
|
| 12 |
<location> |
|
| 13 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
|
| 14 |
<sourceaccessioncode>2733</sourceaccessioncode> |
|
| 15 |
</location> |
|
| 16 |
</location_id> |
|
| 11 | 17 |
<authorlocationcode>3811</authorlocationcode> |
| 12 | 18 |
<sourceaccessioncode>2733</sourceaccessioncode> |
| 13 | 19 |
</locationevent> |
| ... | ... | |
| 64 | 70 |
<locationevent> |
| 65 | 71 |
<obsstartdate>1981-05-03</obsstartdate> |
| 66 | 72 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
| 73 |
<location_id> |
|
| 74 |
<location> |
|
| 75 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
|
| 76 |
<sourceaccessioncode>2733</sourceaccessioncode> |
|
| 77 |
</location> |
|
| 78 |
</location_id> |
|
| 67 | 79 |
<authorlocationcode>3811</authorlocationcode> |
| 68 | 80 |
<sourceaccessioncode>2733</sourceaccessioncode> |
| 69 | 81 |
</locationevent> |
| inputs/CTFS/test/import.organisms.out.ref | ||
|---|---|---|
| 1 |
Inserted 44 new rows into database |
|
| 1 |
Inserted 45 new rows into database |
|
| inputs/CTFS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 19 | 19 |
/*ID->/*s/plotObservation/simpleUserdefined[name=method]/*ID/method/name,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/method_id/_collapse:[require=name]/value/method/name, |
| 20 | 20 |
/*ID->/*s/plotObservation/obsEndDate,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsenddate, |
| 21 | 21 |
/*ID->/*s/plotObservation/obsStartDate,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate, |
| 22 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent/authorlocationcode, |
|
| 23 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 24 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 25 | 22 |
/*ID->/*s/plotObservation/simpleUserdefined[name=precipitation]/value,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/precipitation, |
| 26 | 23 |
/*ID->/*s/plotObservation/*ID->/*s/project/personnel[role=metadataProvider]/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
/*ID->/*s/plotObservation/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/projectname, |
| ... | ... | |
| 45 | 42 |
/*ID->/*s/plotObservation/temperature,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/temperature, |
| 46 | 43 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value", |
| 47 | 44 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value", |
| 48 |
/*ID->/*s/plotObservation/plotUniqueIdentifierID->/*s/plot[plotUniqueIdentifier]/plotName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode, |
|
| 49 |
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 50 |
/*ID->/*s/plotObservation/plotUniqueIdentifierID->/*s/plot[plotUniqueIdentifier]/plotUniqueIdentifier,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 45 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
/*ID->/*s/plotObservation/plotUniqueIdentifierID->/*s/plot[plotUniqueIdentifier]/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
/*ID->/*s/plotObservation/plotUniqueIdentifierID->/*s/plot[plotUniqueIdentifier]/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| 51 | 51 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
|
| 52 | 52 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
|
| 53 | 53 |
/simpleUserdefined[name=growthForm]/value,/aggregateoccurrence/*_id/taxonoccurrence/growthform, |
| inputs/SALVIAS/test/VegBIEN.plots.xml.ref | ||
|---|---|---|
| 23 | 23 |
</locationdetermination> |
| 24 | 24 |
<centerlatitude>-3.45</centerlatitude> |
| 25 | 25 |
<centerlongitude>-78.3667</centerlongitude> |
| 26 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 27 |
<sourceaccessioncode>1</sourceaccessioncode> |
|
| 26 | 28 |
</location> |
| 27 | 29 |
</location_id> |
| 28 | 30 |
<commclass> |
| ... | ... | |
| 70 | 72 |
</locationdetermination> |
| 71 | 73 |
<centerlatitude>48.0667</centerlatitude> |
| 72 | 74 |
<centerlongitude>11.5</centerlongitude> |
| 75 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 76 |
<sourceaccessioncode>2</sourceaccessioncode> |
|
| 73 | 77 |
</location> |
| 74 | 78 |
</location_id> |
| 75 | 79 |
<commclass> |
| inputs/SALVIAS/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 9 | 9 |
<parent_id> |
| 10 | 10 |
<locationevent> |
| 11 | 11 |
<authorlocationcode>c2000-1</authorlocationcode> |
| 12 |
<location_id> |
|
| 13 |
<location> |
|
| 14 |
<sourceaccessioncode>295</sourceaccessioncode> |
|
| 15 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 16 |
</location> |
|
| 17 |
</location_id> |
|
| 12 | 18 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
| 13 | 19 |
<sourceaccessioncode>295</sourceaccessioncode> |
| 14 | 20 |
</locationevent> |
| 15 | 21 |
</parent_id> |
| 22 |
<location_id> |
|
| 23 |
<location> |
|
| 24 |
<sourceaccessioncode>295; 1</sourceaccessioncode> |
|
| 25 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 26 |
</location> |
|
| 27 |
</location_id> |
|
| 16 | 28 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
| 17 | 29 |
<authorlocationcode>1</authorlocationcode> |
| 18 | 30 |
</locationevent> |
| ... | ... | |
| 100 | 112 |
<parent_id> |
| 101 | 113 |
<locationevent> |
| 102 | 114 |
<authorlocationcode>c2000-1</authorlocationcode> |
| 115 |
<location_id> |
|
| 116 |
<location> |
|
| 117 |
<sourceaccessioncode>295</sourceaccessioncode> |
|
| 118 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 119 |
</location> |
|
| 120 |
</location_id> |
|
| 103 | 121 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
| 104 | 122 |
<sourceaccessioncode>295</sourceaccessioncode> |
| 105 | 123 |
</locationevent> |
| 106 | 124 |
</parent_id> |
| 125 |
<location_id> |
|
| 126 |
<location> |
|
| 127 |
<sourceaccessioncode>295; 1</sourceaccessioncode> |
|
| 128 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
|
| 129 |
</location> |
|
| 130 |
</location_id> |
|
| 107 | 131 |
<datasource_id><party><organizationname>SALVIAS</organizationname></party></datasource_id> |
| 108 | 132 |
<authorlocationcode>1</authorlocationcode> |
| 109 | 133 |
</locationevent> |
| inputs/SALVIAS/test/import.organisms.out.ref | ||
|---|---|---|
| 1 |
Inserted 36 new rows into database |
|
| 1 |
Inserted 38 new rows into database |
|
| inputs/SALVIAS/maps/VegBIEN.plots.csv | ||
|---|---|---|
| 37 | 37 |
soil_Na,"/soilobs/sodium/_units:[default=""%"",to=]/value", |
| 38 | 38 |
soil_texture,"/soilobs/texture/_units:[default=""%"",to=]/value", |
| 39 | 39 |
Temp,/temperature, |
| 40 |
SiteCode,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
| 41 |
PlotID,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
| 40 |
SiteCode,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",Brad: plotCode is as-assigned by data provider; guranteed to be unique only within dataset (=project)
|
|
| 41 |
PlotID,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}","Brad: This is artificial internal database ID; a unique identifier within SALVIAS DB to each plot, within the table plotMetadata."
|
|
| 42 | 42 |
AccessCode,,** No input mapping for AccessCode ** |
| 43 | 43 |
ElevSource,,** No input mapping for ElevSource ** |
| 44 | 44 |
Habitat,,** No input mapping for Habitat ** |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:/plantobservation,Comments |
| 2 |
PlotCode,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent/authorlocationcode,"Brad: Same as plotCode, above"
|
|
| 3 |
PlotID,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode,"Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 4 |
Line,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode,
|
|
| 2 |
PlotCode,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}","Brad: Same as plotCode, above"
|
|
| 3 |
PlotID,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}","Brad: Not sure why this is repeated? This field and plotCode, as the same as above."
|
|
| 4 |
Line,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 5 | 5 |
coll_number,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/1",Brad: Incorrect. Map instead as for voucher_string
|
| 6 | 6 |
SourceVoucher,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc/_alt/2","Brad: OMIT. This is the verbatim text, which includes both collectors name and collection number. I would use coll_number, below."
|
| 7 | 7 |
Habit,"/aggregateoccurrence/*_id/taxonoccurrence/growthform/_map:[./{T,Arbol,palm}=tree,./{H,""Hemiepífito""}=hemiepiphyte,./{L,l,""L?"",Liana}=liana,E=epiphyte,S=shrub,Hb=herb,""vine-herbaceous""=vine,graminoid=grass,rosette=forb,*=]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait."
|
| mappings/VegX-VegBIEN.plots.csv | ||
|---|---|---|
| 19 | 19 |
/simpleUserdefined[name=method]/*ID/method/name,/method_id/_collapse:[require=name]/value/method/name, |
| 20 | 20 |
/obsEndDate,/obsenddate, |
| 21 | 21 |
/obsStartDate,/obsstartdate, |
| 22 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,/parent_id/locationevent/authorlocationcode, |
|
| 23 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 24 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 25 | 22 |
/simpleUserdefined[name=precipitation]/value,/precipitation, |
| 26 | 23 |
/*ID->/*s/project/personnel[role=metadataProvider]/organizationName,/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/projectname, |
| ... | ... | |
| 45 | 42 |
/temperature,/temperature, |
| 46 | 43 |
/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,"/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value", |
| 47 | 44 |
/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,"/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value", |
| 48 |
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode, |
|
| 49 |
/partyWithRole/*ID->/parties/party/organizationName,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 50 |
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 45 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,"/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
/partyWithRole/*ID->/parties/party/organizationName,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,":[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| mappings/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 19 | 19 |
/*ID->/*s/plotObservation/simpleUserdefined[name=method]/*ID/method/name,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/method_id/_collapse:[require=name]/value/method/name, |
| 20 | 20 |
/*ID->/*s/plotObservation/obsEndDate,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsenddate, |
| 21 | 21 |
/*ID->/*s/plotObservation/obsStartDate,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate, |
| 22 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent/authorlocationcode, |
|
| 23 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 24 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 25 | 22 |
/*ID->/*s/plotObservation/simpleUserdefined[name=precipitation]/value,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/precipitation, |
| 26 | 23 |
/*ID->/*s/plotObservation/*ID->/*s/project/personnel[role=metadataProvider]/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
/*ID->/*s/plotObservation/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/projectname, |
| ... | ... | |
| 45 | 42 |
/*ID->/*s/plotObservation/temperature,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/temperature, |
| 46 | 43 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value", |
| 47 | 44 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value", |
| 48 |
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode, |
|
| 49 |
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 50 |
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 45 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| 51 | 51 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
|
| 52 | 52 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
|
| 53 | 53 |
/simpleUserdefined[name=growthForm]/value,/aggregateoccurrence/*_id/taxonoccurrence/growthform, |
| mappings/for_review/VegX-VegBIEN.plots.csv | ||
|---|---|---|
| 19 | 19 |
/simpleUserdefined[name=method]/*ID/method/name,/method_id/_collapse/value/method/name, |
| 20 | 20 |
/obsEndDate,/obsenddate, |
| 21 | 21 |
/obsStartDate,/obsstartdate, |
| 22 |
//plot/plotName,//locationevent/authorlocationcode, |
|
| 23 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 24 |
//plot/plotUniqueIdentifier,//locationevent/sourceaccessioncode, |
|
| 25 | 22 |
/simpleUserdefined[name=precipitation]/value,/precipitation, |
| 26 | 23 |
//project/personnel[role=metadataProvider]/organizationName,/project_id/_collapse/value/project/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
//*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,/project_id/_collapse/value/project/projectname, |
| ... | ... | |
| 45 | 42 |
/temperature,/temperature, |
| 46 | 43 |
//geospatial/maximumDepthInMeters,/waterdepth/_avg/max/_units/value, |
| 47 | 44 |
//geospatial/minimumDepthInMeters,/waterdepth/_avg/min/_units/value, |
| 48 |
//plot/plotName,/authorlocationcode, |
|
| 49 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 50 |
//plot/plotUniqueIdentifier,/sourceaccessioncode, |
|
| 45 |
//plot/plotName,"/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
//party/organizationName,"/{parent_id/locationevent/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
//plot/plotUniqueIdentifier,"/{parent_id/locationevent/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
//party/organizationName,"/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
//plot/plotName,"/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
//plot/plotUniqueIdentifier,"/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| mappings/for_review/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 19 | 19 |
//plotObservation/simpleUserdefined[name=method]/*ID/method/name,//locationevent/method_id/_collapse/value/method/name, |
| 20 | 20 |
//plotObservation/obsEndDate,//locationevent/obsenddate, |
| 21 | 21 |
//plotObservation/obsStartDate,//locationevent/obsstartdate, |
| 22 |
//plot/plotName,//locationevent/authorlocationcode, |
|
| 23 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 24 |
//plot/plotUniqueIdentifier,//locationevent/sourceaccessioncode, |
|
| 25 | 22 |
//plotObservation/simpleUserdefined[name=precipitation]/value,//locationevent/precipitation, |
| 26 | 23 |
//project/personnel[role=metadataProvider]/organizationName,//locationevent/project_id/_collapse/value/project/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
//*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,//locationevent/project_id/_collapse/value/project/projectname, |
| ... | ... | |
| 45 | 42 |
//plotObservation/temperature,//locationevent/temperature, |
| 46 | 43 |
//geospatial/maximumDepthInMeters,//locationevent/waterdepth/_avg/max/_units/value, |
| 47 | 44 |
//geospatial/minimumDepthInMeters,//locationevent/waterdepth/_avg/min/_units/value, |
| 48 |
//plot/plotName,//locationevent/authorlocationcode, |
|
| 49 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 50 |
//plot/plotUniqueIdentifier,//locationevent/sourceaccessioncode, |
|
| 45 |
//plot/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
//party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
//plot/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
//party/organizationName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
//plot/plotName,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
//plot/plotUniqueIdentifier,"/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| 51 | 51 |
//taxonNameUsageConcept/voucher,"//*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate}//catalognumber_dwc",
|
| 52 | 52 |
//party/organizationName,"//*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate}//datasource_id/party/organizationname/_alt/1",
|
| 53 | 53 |
/simpleUserdefined[name=growthForm]/value,//taxonoccurrence/growthform, |
| mappings/for_review/VegX-VegBIEN.stems.csv | ||
|---|---|---|
| 19 | 19 |
//plotObservation/simpleUserdefined[name=method]/*ID/method/name,//locationevent/method_id/_collapse/value/method/name, |
| 20 | 20 |
//plotObservation/obsEndDate,//locationevent/obsenddate, |
| 21 | 21 |
//plotObservation/obsStartDate,//locationevent/obsstartdate, |
| 22 |
//plot/plotName,//locationevent/authorlocationcode, |
|
| 23 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 24 |
//plot/plotUniqueIdentifier,//locationevent/sourceaccessioncode, |
|
| 25 | 22 |
//plotObservation/simpleUserdefined[name=precipitation]/value,//locationevent/precipitation, |
| 26 | 23 |
//project/personnel[role=metadataProvider]/organizationName,//locationevent/project_id/_collapse/value/project/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
//*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,//locationevent/project_id/_collapse/value/project/projectname, |
| ... | ... | |
| 45 | 42 |
//plotObservation/temperature,//locationevent/temperature, |
| 46 | 43 |
//geospatial/maximumDepthInMeters,//locationevent/waterdepth/_avg/max/_units/value, |
| 47 | 44 |
//geospatial/minimumDepthInMeters,//locationevent/waterdepth/_avg/min/_units/value, |
| 48 |
//plot/plotName,//locationevent/authorlocationcode, |
|
| 49 |
//party/organizationName,//party/organizationname/_alt/1, |
|
| 50 |
//plot/plotUniqueIdentifier,//locationevent/sourceaccessioncode, |
|
| 45 |
//plot/plotName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
//party/organizationName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
//plot/plotUniqueIdentifier,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
//party/organizationName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
//plot/plotName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
//plot/plotUniqueIdentifier,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| 51 | 51 |
//taxonNameUsageConcept/voucher,"//*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate}//catalognumber_dwc",
|
| 52 | 52 |
//party/organizationName,"//*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate}//datasource_id/party/organizationname/_alt/1",
|
| 53 | 53 |
//individualOrganismObservation/simpleUserdefined[name=growthForm]/value,//taxonoccurrence/growthform, |
| mappings/VegX-VegBIEN.stems.csv | ||
|---|---|---|
| 19 | 19 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=method]/*ID/method/name,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/method_id/_collapse:[require=name]/value/method/name, |
| 20 | 20 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/obsEndDate,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsenddate, |
| 21 | 21 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/obsStartDate,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/obsstartdate, |
| 22 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent/authorlocationcode, |
|
| 23 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 24 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/parent_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 25 | 22 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=precipitation]/value,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/precipitation, |
| 26 | 23 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*ID->/*s/project/personnel[role=metadataProvider]/organizationName,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
| 27 | 24 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*ID->/*s/project:[personnel[role=metadataProvider]/organizationName=$/_ignore/inLabel]/title,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/project_id/_collapse:[require=projectname]/value/project:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/projectname, |
| ... | ... | |
| 45 | 42 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/temperature,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/temperature, |
| 46 | 43 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/max/_units:[default=m,to=m,to=]/value", |
| 47 | 44 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/waterdepth/_avg/min/_units:[default=m,to=m,to=]/value", |
| 48 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/authorlocationcode, |
|
| 49 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1, |
|
| 50 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode, |
|
| 45 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/plotName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent/{authorlocationcode,*_id/location/sourceaccessioncode/_alt/2},*_id/location/sourceaccessioncode/_merge/1/_alt/2}",
|
|
| 46 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1}",
|
|
| 47 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/simpleUserdefined[name=parent]/value->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent/{parent_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_alt/1},*_id/location/sourceaccessioncode/_merge/1/_alt/1}",
|
|
| 48 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation/partyWithRole/*ID->/parties/party/organizationName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{.,*_id/location}/datasource_id/party/organizationname/_alt/1",
|
|
| 49 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{authorlocationcode,*_id/location/sourceaccessioncode/_merge/2/_alt/2}",
|
|
| 50 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent:[./{.,*_id/location}/datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/{sourceaccessioncode,*_id/location/sourceaccessioncode/_merge/2/_alt/1}",
|
|
| 51 | 51 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
|
| 52 | 52 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
|
| 53 | 53 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/simpleUserdefined[name=growthForm]/value,/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/growthform, |
Also available in: Unified diff
VegBIEN: Fixing import issue related to duplicate entries in tables with children, where when a new table entry duplicates an existing entry, the 1:1 tables of that table and those tables' children are not merged, causing them to become orphaned. It is described in detail at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Import_issues#Merging-duplicates-with-children>, including the rationale for this solution. Note that this is not a bug in column-based import, it applies to row-based import as well. This commit fixes the issue for locationevent->location in plots data, by also mapping locationevent's unique keys to location.sourceaccessioncode and setting location.datasource_id.