Revision 3211
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 26 | 26 |
height_m,/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 27 | 27 |
stem_height_m,/overallheight,"Brad: Same as for height, but applies to individuals stems, not trees. Rare." |
| 28 | 28 |
OBSERVATION_ID,/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 29 |
tag1,"/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag/_alt/1","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
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| 30 |
stem_tag1,"/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag/_alt/2","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2"
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| 31 |
tag2,/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
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| 32 |
stem_tag2,/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag/_alt/2,Brad: see above
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| 29 |
tag1,"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/1","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
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| 30 |
stem_tag1,"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag/_alt/2","Brad: Same as tag1 & tag2, but applied to individual stems. I'm still not clear how to distinguish between methods which tag only individuals trees, and those which tag individual stems.; Quotes sort it before tag2"
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| 31 |
tag2,/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/1,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
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| 32 |
stem_tag2,/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag/_alt/2,Brad: see above
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| 33 | 33 |
x_position,/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
| 34 | 34 |
y_position,/stemobservation/yposition,Brad: See comment above for x_position |
| 35 | 35 |
basal_diam,,** No join mapping for /diameterBaseDistance[baseDistance/value=0]/diameter ** |
| inputs/CTFS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 81 | 81 |
/height,/overallheight, |
| 82 | 82 |
/simpleUserdefined[name=height]/value,/overallheight, |
| 83 | 83 |
:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,/sourceaccessioncode, |
| 84 |
/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag",Quotes sort it before tag2
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| 85 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag,
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| 84 |
/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
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| 85 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
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| 86 | 86 |
/relativePlotPosition/relativeX,/stemobservation/xposition, |
| 87 | 87 |
/relativePlotPosition/relativeY,/stemobservation/yposition, |
| 88 | 88 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/*/relatedPlot[plotRelationship=Quadrat]/relatedPlotID,,** No input mapping for /*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/*/relatedPlot[plotRelationship=Quadrat]/relatedPlotID ** |
| inputs/SALVIAS/maps/VegBIEN.stems.csv | ||
|---|---|---|
| 1 | 1 |
SALVIAS,VegBIEN:/stemobservation,Comments |
| 2 | 2 |
PlotObsID,"/*_id/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/voucher/*_id/specimenreplicate:[*_id/taxonoccurrence]}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
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| 3 | 3 |
NoInd,/*_id/plantobservation/stemcount, |
| 4 |
stem_tag1,"/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag",Quotes sort it before tag2 |
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| 5 |
stem_tag2,/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag, |
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| 6 | 4 |
basal_diam,/basaldiameter, |
| 7 | 5 |
stem_canopy_form,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 8 | 6 |
stem_canopy_position,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| ... | ... | |
| 12 | 10 |
stem_dbh,/diameterbreastheight, |
| 13 | 11 |
stem_height_m,/height, |
| 14 | 12 |
stem_height_first_branch_m,/heightfirstbranch, |
| 13 |
stem_tag1,"/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2 |
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| 14 |
stem_tag2,/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag, |
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| 15 | 15 |
origrecord_id_stems,,** No input mapping for origrecord_id_stems ** |
| 16 | 16 |
stem_id,,** No input mapping for stem_id ** |
| 17 | 17 |
tmp_del,,** No input mapping for tmp_del ** |
| inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 26 | 26 |
Ind,/authorplantcode,"Brad: Code, if any, used by the data provider to indicate an individual tree. Scope is unknown, although typically this value is unique only within plot, or sometimes only within subplot." |
| 27 | 27 |
height_m,/overallheight,Brad: Incorrect for VegBank. This is a measurement applied to a single tree. Check with Bob |
| 28 | 28 |
PlotObsID,/sourceaccessioncode,"Brad: Neither is correct; this is just an internal ID for table plotObservations. However, it has the important property of uniquely identifying an ""observation"", which is an individual tree, in the case of an individual observation, or a records of a species with an associated count of individuals or measurement of percent cover, in the case of aggregate observations. Not sure where to store this. Main point is that it is not part of the original data, but an auto_increment added later." |
| 29 |
tag1,"/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
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tag2,/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
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tag1,"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag","Brad: Another type of code, typically a number, used by the original data provider to indicate an individual tree. These are numbers on physical tags attached to the tree. Tag2 Is the same thing, only used if the first tag was lost. Obviously not a good system as it's possible a tree tag could be lost and changed more than once.; Quotes sort it before tag2"
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tag2,/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,"Brad: See commend for tag1. Your mapping for tag2 looks correct. Probably both values would go here, only nested, with one superceding the other."
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| 31 | 31 |
x_position,/stemobservation/xposition,"Brad: Correct for VegBank. I'm not so sure for VegX. Let's ask Nick about this. These are important, fundamental values of many tree plots, and should be accommodated within VegX." |
| 32 | 32 |
y_position,/stemobservation/yposition,Brad: See comment above for x_position |
| 33 | 33 |
GenAuth,,** No input mapping for GenAuth ** |
| mappings/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 81 | 81 |
/height,/overallheight, |
| 82 | 82 |
/simpleUserdefined[name=height]/value,/overallheight, |
| 83 | 83 |
:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,/sourceaccessioncode, |
| 84 |
/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag",Quotes sort it before tag2
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| 85 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag,
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/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
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| 85 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
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| 86 | 86 |
/relativePlotPosition/relativeX,/stemobservation/xposition, |
| 87 | 87 |
/relativePlotPosition/relativeY,/stemobservation/yposition, |
| mappings/for_review/VegX-VegBIEN.organisms.csv | ||
|---|---|---|
| 81 | 81 |
/height,/overallheight, |
| 82 | 82 |
/simpleUserdefined[name=height]/value,/overallheight, |
| 83 | 83 |
/simpleUserdefined[name=sourceAccessionCode]/value,/sourceaccessioncode, |
| 84 |
//individualOrganism/identificationLabel[@id=1],"/stemobservation/_collapse/value/stemtag[""""/2=true]/tag",Quotes sort it before tag2
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| 85 |
//individualOrganism/identificationLabel[@id=2],/stemobservation/_collapse/value/stemtag[iscurrent=true]:[../../../_collapse?/value/stemtag[2=true]/1=false]/tag,
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| 84 |
//individualOrganism/identificationLabel[@id=1],"//stemobservation/stemtag[""""/2=true]/tag",Quotes sort it before tag2
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| 85 |
//individualOrganism/identificationLabel[@id=2],//stemobservation/stemtag[iscurrent=true]:[../stemtag?[2=true]/1=false]/tag,
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| 86 | 86 |
//relativePlotPosition/relativeX,//stemobservation/xposition, |
| 87 | 87 |
//relativePlotPosition/relativeY,//stemobservation/yposition, |
| mappings/for_review/VegX-VegBIEN.stems.csv | ||
|---|---|---|
| 82 | 82 |
//individualOrganismObservation/simpleUserdefined[name=height]/value,//plantobservation/overallheight, |
| 83 | 83 |
//individualOrganismObservation/simpleUserdefined[name=sourceAccessionCode]/value,//plantobservation/sourceaccessioncode, |
| 84 | 84 |
//*s/aggregateOrganismObservation/*/aggregateValue/value,//plantobservation/stemcount, |
| 85 |
//individualOrganism/identificationLabel[@id=1],"//plantobservation/stemobservation/_collapse/value/stemtag[""""/2=true]/tag",Quotes sort it before tag2
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| 86 |
//individualOrganism/identificationLabel[@id=2],//plantobservation/stemobservation/_collapse/value/stemtag[iscurrent=true]:[../../../_collapse?/value/stemtag[2=true]/1=false]/tag,
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| 85 |
//individualOrganism/identificationLabel[@id=1],"//stemobservation/stemtag[""""/2=true]/tag",Quotes sort it before tag2
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| 86 |
//individualOrganism/identificationLabel[@id=2],//stemobservation/stemtag[iscurrent=true]:[../stemtag?[2=true]/1=false]/tag,
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| 87 | 87 |
//relativePlotPosition/relativeX,//stemobservation/xposition, |
| 88 | 88 |
//relativePlotPosition/relativeY,//stemobservation/yposition, |
| 89 |
//individualOrganism/identificationLabel[@id=1],"/_collapse/value/stemtag[""""/2=true]/tag",Quotes sort it before tag2 |
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| 90 |
//individualOrganism/identificationLabel[@id=2],/_collapse/value/stemtag[iscurrent=true]:[../../../_collapse?/value/stemtag[2=true]/1=false]/tag, |
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| 91 | 89 |
/diameterBaseDistance[value=0]/diameter,/basaldiameter, |
| 92 | 90 |
/simpleUserdefined[name=canopyForm]/value,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]/definedvalue", |
| 93 | 91 |
/simpleUserdefined[name=canopyPosition]/value,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]/definedvalue", |
| ... | ... | |
| 97 | 95 |
/diameterBaseDistance[baseDistance[]/value=1.37]/diameter,/diameterbreastheight, |
| 98 | 96 |
/simpleUserdefined[name=height]/value,/height, |
| 99 | 97 |
/simpleUserdefined[name=heightFirstBranch]/value,/heightfirstbranch, |
| 98 |
//individualOrganism/identificationLabel[@id=1],"/stemtag[""""/2=true]/tag",Quotes sort it before tag2 |
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| 99 |
//individualOrganism/identificationLabel[@id=2],/stemtag[iscurrent=true]:[../stemtag?[2=true]/1=false]/tag, |
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| 100 | 100 |
//relativePlotPosition/relativeX,/xposition, |
| 101 | 101 |
//relativePlotPosition/relativeY,/yposition, |
| mappings/VegX-VegBIEN.stems.csv | ||
|---|---|---|
| 82 | 82 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/simpleUserdefined[name=height]/value,/*_id/plantobservation/overallheight, |
| 83 | 83 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,/*_id/plantobservation/sourceaccessioncode, |
| 84 | 84 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/aggregateOrganismObservation[*ID]/*/aggregateValue/value,/*_id/plantobservation/stemcount, |
| 85 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/*_id/plantobservation/stemobservation/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag",Quotes sort it before tag2
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| 86 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/identificationLabel[@id=2],/*_id/plantobservation/stemobservation/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag,
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| 85 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/*_id/plantobservation/stemobservation/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2
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| 86 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/*ID->/*s/individualOrganism/identificationLabel[@id=2],/*_id/plantobservation/stemobservation/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag,
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| 87 | 87 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/relativePlotPosition/relativeX,/*_id/plantobservation/stemobservation/xposition, |
| 88 | 88 |
/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation/relativePlotPosition/relativeY,/*_id/plantobservation/stemobservation/yposition, |
| 89 |
/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/_collapse:[require=tag](/value/stemtag[""""/iscurrent/_alt/2=true])/tag",Quotes sort it before tag2 |
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| 90 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/_collapse:[require=tag](/value/stemtag[iscurrent=true]:[../../../_collapse?(/value/stemtag[iscurrent/_alt/2=true])/iscurrent/_alt/1=false])/tag, |
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| 91 | 89 |
/diameterBaseDistance[baseDistance/value=0]/diameter,/basaldiameter, |
| 92 | 90 |
/simpleUserdefined[name=canopyForm]/value,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyForm]]:[@fkey=tablerecord_id]/definedvalue", |
| 93 | 91 |
/simpleUserdefined[name=canopyPosition]/value,"/definedvalue[*_id/userdefined[tablename=stemobservation,userdefinedname=canopyPosition]]:[@fkey=tablerecord_id]/definedvalue", |
| ... | ... | |
| 97 | 95 |
/diameterBaseDistance[baseDistance[!attributeID]/value=1.37]/diameter,/diameterbreastheight, |
| 98 | 96 |
/simpleUserdefined[name=height]/value,/height, |
| 99 | 97 |
/simpleUserdefined[name=heightFirstBranch]/value,/heightfirstbranch, |
| 98 |
/*ID->/*s/individualOrganism/identificationLabel[@id=1],"/stemtag[""""/iscurrent/_alt/2=true]/tag",Quotes sort it before tag2 |
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| 99 |
/*ID->/*s/individualOrganism/identificationLabel[@id=2],/stemtag[iscurrent=true]:[../stemtag?[iscurrent/_alt/2=true]/iscurrent/_alt/1=false]/tag, |
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| 100 | 100 |
/relativePlotPosition/relativeX,/xposition, |
| 101 | 101 |
/relativePlotPosition/relativeY,/yposition, |
Also available in: Unified diff
mappings/VegX-VegBIEN.stems.csv: Removed _collapse where it's no longer needed because sql_io.put() handles that now. Note that each plantobservation will get an empty stemobservation, whether or not there are any stemtags. This can later be used to add further stemtags.