Revision 3230
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/CTFS/test/VegX.organisms.xml.ref | ||
|---|---|---|
| 12 | 12 |
<name>censusNo</name> |
| 13 | 13 |
<value>1</value> |
| 14 | 14 |
</simpleUserdefined> |
| 15 |
<simpleUserdefined> |
|
| 16 |
<name>sourceAccessionCode</name> |
|
| 17 |
<value>657208</value> |
|
| 18 |
</simpleUserdefined> |
|
| 15 | 19 |
</individualOrganismObservation> |
| 16 | 20 |
<individualOrganismObservation id="1"> |
| 17 | 21 |
<individualOrganismID>1</individualOrganismID> |
| ... | ... | |
| 24 | 28 |
<name>censusNo</name> |
| 25 | 29 |
<value>1</value> |
| 26 | 30 |
</simpleUserdefined> |
| 31 |
<simpleUserdefined> |
|
| 32 |
<name>sourceAccessionCode</name> |
|
| 33 |
<value>657215</value> |
|
| 34 |
</simpleUserdefined> |
|
| 27 | 35 |
</individualOrganismObservation> |
| 28 | 36 |
</individualOrganismObservations> |
| 29 | 37 |
<individualOrganisms> |
| ... | ... | |
| 31 | 39 |
<individualOrganism id="1"><taxonNameUsageConceptID>1</taxonNameUsageConceptID></individualOrganism> |
| 32 | 40 |
</individualOrganisms> |
| 33 | 41 |
<taxonNameUsageConcepts> |
| 34 |
<taxonNameUsageConcept id="0"/>
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|
| 35 |
<taxonNameUsageConcept id="1"/>
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|
| 42 |
<taxonNameUsageConcept id="0"><partyWithRole><partyID>1</partyID></partyWithRole></taxonNameUsageConcept>
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|
| 43 |
<taxonNameUsageConcept id="1"><partyWithRole><partyID>3</partyID></partyWithRole></taxonNameUsageConcept>
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|
| 36 | 44 |
</taxonNameUsageConcepts> |
| 37 | 45 |
<taxonDeterminations> |
| 38 | 46 |
<taxonDetermination> |
| ... | ... | |
| 86 | 94 |
</plotObservation> |
| 87 | 95 |
<plotObservation id="1"> |
| 88 | 96 |
<obsStartDate>1981-05-03</obsStartDate> |
| 89 |
<partyWithRole><partyID>1</partyID></partyWithRole>
|
|
| 97 |
<partyWithRole><partyID>2</partyID></partyWithRole>
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|
| 90 | 98 |
<plotUniqueIdentifierID>1</plotUniqueIdentifierID> |
| 91 | 99 |
</plotObservation> |
| 92 | 100 |
</plotObservations> |
| 93 | 101 |
<parties> |
| 94 | 102 |
<party id="0"><organizationName>CTFS</organizationName></party> |
| 95 | 103 |
<party id="1"><organizationName>CTFS</organizationName></party> |
| 104 |
<party id="2"><organizationName>CTFS</organizationName></party> |
|
| 105 |
<party id="3"><organizationName>CTFS</organizationName></party> |
|
| 96 | 106 |
</parties> |
| 97 | 107 |
<plots> |
| 98 | 108 |
<plot id="0"> |
| inputs/CTFS/test/VegBIEN.organisms.xml.ref | ||
|---|---|---|
| 1 | 1 |
<?xml version="1.0" ?> |
| 2 | 2 |
<VegBIEN> |
| 3 | 3 |
<plantobservation id="0"> |
| 4 |
<sourceaccessioncode>657208</sourceaccessioncode> |
|
| 4 | 5 |
<aggregateoccurrence> |
| 5 | 6 |
<taxonoccurrence_id> |
| 6 | 7 |
<taxonoccurrence> |
| 8 |
<voucher> |
|
| 9 |
<specimenreplicate_id> |
|
| 10 |
<specimenreplicate> |
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| 11 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
|
| 12 |
<sourceaccessioncode>657208</sourceaccessioncode> |
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| 13 |
</specimenreplicate> |
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| 14 |
</specimenreplicate_id> |
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| 15 |
</voucher> |
|
| 7 | 16 |
<locationevent_id> |
| 8 | 17 |
<locationevent> |
| 9 | 18 |
<obsstartdate>1981-05-03</obsstartdate> |
| ... | ... | |
| 63 | 72 |
</stemobservation> |
| 64 | 73 |
</plantobservation> |
| 65 | 74 |
<plantobservation id="1"> |
| 75 |
<sourceaccessioncode>657215</sourceaccessioncode> |
|
| 66 | 76 |
<aggregateoccurrence> |
| 67 | 77 |
<taxonoccurrence_id> |
| 68 | 78 |
<taxonoccurrence> |
| 79 |
<voucher> |
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| 80 |
<specimenreplicate_id> |
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| 81 |
<specimenreplicate> |
|
| 82 |
<datasource_id><party><organizationname>CTFS</organizationname></party></datasource_id> |
|
| 83 |
<sourceaccessioncode>657215</sourceaccessioncode> |
|
| 84 |
</specimenreplicate> |
|
| 85 |
</specimenreplicate_id> |
|
| 86 |
</voucher> |
|
| 69 | 87 |
<locationevent_id> |
| 70 | 88 |
<locationevent> |
| 71 | 89 |
<obsstartdate>1981-05-03</obsstartdate> |
| inputs/CTFS/maps/VegX.organisms.csv | ||
|---|---|---|
| 3 | 3 |
/*ID->/*s/plotObservation/plotUniqueIdentifierID->/*s/plot[plotUniqueIdentifier]/plotUniqueIdentifier,/*ID->/*s/plotObservation:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier, |
| 4 | 4 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/*/relatedPlot[plotRelationship=Quadrat]/relatedPlotID,, |
| 5 | 5 |
/*ID->/*s/plotObservation/simpleUserdefined[name=CensusNumber]/value,/simpleUserdefined[name=censusNo]/value, |
| 6 |
/@id,:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value, |
|
| 6 | 7 |
"/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank=Species])/tcs:Name","/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=sp])/tcs:Name", |
| 7 | 8 |
"/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank=Genus])/tcs:Name","/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=gen])/tcs:Name", |
| 8 | 9 |
"/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank=Family])/tcs:Name","/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,!partyWithRole]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[tcs:Rank/@code=fam])/tcs:Name", |
| inputs/CTFS/maps/VegX.organisms.full.csv | ||
|---|---|---|
| 84 | 84 |
/simpleUserdefined[name=height]/value,/simpleUserdefined[name=height]/value |
| 85 | 85 |
/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent,/volumeCanopy/*ID->/*s/attribute/ordinal/coverPercent |
| 86 | 86 |
/volumeCanopy/value,/volumeCanopy/value |
| 87 |
:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value
|
|
| 87 |
/@id,:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,
|
|
| 88 | 88 |
/*ID->/*s/plotObservation/*UniqueIdentifierID->/*s/plot/*/relatedPlot[plotRelationship=Quadrat]/relatedPlotID,, |
| inputs/CTFS/maps/VegBIEN.organisms.csv | ||
|---|---|---|
| 1 | 1 |
CTFS[VegX]:/*s/individualOrganismObservation,VegBIEN:/plantobservation,Comments |
| 2 |
:[*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/simpleUserdefined[name=sourceAccessionCode]/value,"/""""/{sourceaccessioncode,_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode}",Quotes sort it with other _ifs
|
|
| 2 |
/@id,"/""""/{sourceaccessioncode,_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/sourceaccessioncode}",Quotes sort it with other _ifs
|
|
| 3 | 3 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept:[partyWithRole/*ID->/parties/party/organizationName=$/_ignore/inLabel]/voucher,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/catalognumber_dwc",
|
| 4 | 4 |
/simpleUserdefined[name=collectionDate]/value,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate",
|
| 5 | 5 |
/*ID->/*s/individualOrganism/*ID->/*s/taxonNameUsageConcept/partyWithRole/*ID->/parties/party/organizationName,"/_if:[cond/_eq:[left/_ref[addr=""../../../../_ignore/voucherType""],right=direct]]/{then/specimenreplicate,else/aggregateoccurrence/*_id/taxonoccurrence/voucher/*_id/specimenreplicate}/:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/datasource_id/party/organizationname/_alt/1",
|
Also available in: Unified diff
inputs/CTFS/maps/VegX.organisms.csv: Mapped VegX sourceAccessionCode = VegBIEN plantobservation,specimenreplicate.sourceaccessioncode so that specimenreplicate would have a required key