Revision 1430
Added by Aaron Marcuse-Kubitza almost 13 years ago
inputs/SALVIAS/test/VegBIEN.organisms.xml.ref | ||
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40 | 40 |
</userdefined_id> |
41 | 41 |
<definedvalue>1</definedvalue> |
42 | 42 |
</definedvalue> |
43 |
<growthform>tree</growthform> |
|
44 | 43 |
</aggregateoccurrence> |
44 |
<growthform>tree</growthform> |
|
45 | 45 |
<taxondetermination> |
46 | 46 |
<role>computer</role> |
47 | 47 |
<iscurrent>true</iscurrent> |
... | ... | |
136 | 136 |
</userdefined_id> |
137 | 137 |
<definedvalue>1</definedvalue> |
138 | 138 |
</definedvalue> |
139 |
<growthform>tree</growthform> |
|
140 | 139 |
</aggregateoccurrence> |
140 |
<growthform>tree</growthform> |
|
141 | 141 |
<taxondetermination> |
142 | 142 |
<role>computer</role> |
143 | 143 |
<iscurrent>true</iscurrent> |
inputs/SALVIAS/maps/VegBIEN.organisms.csv | ||
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21 | 21 |
NoInd,/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
22 | 22 |
cover_percent,/aggregateoccurrence/cover, |
23 | 23 |
census_no,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
24 |
Habit,"/aggregateoccurrence/growthform/_map:[_closed=1,./{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." |
|
25 | 24 |
intercept_cm,/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
25 |
Habit,"/growthform/_map:[_closed=1,./{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." |
|
26 | 26 |
census_date,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate/_*/date, |
27 | 27 |
infra_rank_1,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
28 | 28 |
auth,"/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
inputs/SALVIAS-CSV/test/VegBIEN.organisms.xml.ref | ||
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52 | 52 |
</userdefined_id> |
53 | 53 |
<definedvalue>1</definedvalue> |
54 | 54 |
</definedvalue> |
55 |
<growthform>tree</growthform> |
|
56 | 55 |
</aggregateoccurrence> |
56 |
<growthform>tree</growthform> |
|
57 | 57 |
<taxondetermination> |
58 | 58 |
<role>computer</role> |
59 | 59 |
<iscurrent>true</iscurrent> |
... | ... | |
155 | 155 |
</userdefined_id> |
156 | 156 |
<definedvalue>1</definedvalue> |
157 | 157 |
</definedvalue> |
158 |
<growthform>tree</growthform> |
|
159 | 158 |
</aggregateoccurrence> |
159 |
<growthform>tree</growthform> |
|
160 | 160 |
<taxondetermination> |
161 | 161 |
<role>computer</role> |
162 | 162 |
<iscurrent>true</iscurrent> |
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv | ||
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27 | 27 |
no_of_individuals,/aggregateoccurrence/count,"Brad: Incorrect for VegX. This is a count of number of indiiduals for an *aggregate* observation. For VegBank, I'm not sure. Not exactly the same as stemCount. An individual tree could have 3 stems but would still only count as 1. We need to check with Bob on this." |
28 | 28 |
cover_percent,/aggregateoccurrence/cover, |
29 | 29 |
census_no,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue","Brad: Assigned by SALVIAS. 1 for first plot, then 2, 3, etc. I can't recall if we even have repeat censuses in SALVIAS. Probably not." |
30 |
habit,"/aggregateoccurrence/growthform/_map:[T=tree,H=hemiepiphyte,L=liana,E=epiphyte,S=shrub,Hb=herb]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
31 | 30 |
intercept_cm,/aggregateoccurrence/linecover,"Brad: Incorrect for VegBank This is an aggregate observation. Used in line-intercept methodology only, describes the point along centerline at which an individual intercepts the center line of the plot. Used to determin relative abundance." |
31 |
habit,"/growthform/_map:[T=tree,H=hemiepiphyte,L=liana,E=epiphyte,S=shrub,Hb=herb]/value","Brad: Incorrect for VegBank, correct for VegX. This is growth form (tree, shrub, herb, etc.). It is an observation of a trait." |
|
32 | 32 |
infra_rank_1,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
33 | 33 |
specific_authority,"/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname",Brad: Incorrect. This is the author of the scientificName. The should be a place for this in the taxonomic name elements of VegB and VegX. Let's discuss. |
34 | 34 |
infra_ep_1,"/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/last", |
schemas/vegbien.my.sql | ||
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130 | 130 |
coverindex_id int(11), |
131 | 131 |
occurrencestatus_dwc text DEFAULT 'present' NOT NULL, |
132 | 132 |
method_id int(11), |
133 |
linecover double precision, |
|
134 |
growthform text |
|
133 |
linecover double precision |
|
135 | 134 |
); |
136 | 135 |
|
137 | 136 |
|
... | ... | |
2284 | 2283 |
taxonoccurrence_id int(11) NOT NULL, |
2285 | 2284 |
locationevent_id int(11), |
2286 | 2285 |
accessioncode text, |
2287 |
verbatimcollectorname text |
|
2286 |
verbatimcollectorname text, |
|
2287 |
growthform text |
|
2288 | 2288 |
); |
2289 | 2289 |
|
2290 | 2290 |
|
schemas/vegbien.sql | ||
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216 | 216 |
occurrencestatus_dwc occurrencestatus_dwc DEFAULT 'present'::occurrencestatus_dwc NOT NULL, |
217 | 217 |
method_id integer, |
218 | 218 |
linecover double precision, |
219 |
growthform taxonclass, |
|
220 | 219 |
CONSTRAINT aggregateoccurrence_plantobservation_count_1 CHECK (((plantobservation_id IS NULL) OR (NOT (count IS DISTINCT FROM 1)))) |
221 | 220 |
); |
222 | 221 |
|
... | ... | |
2671 | 2670 |
taxonoccurrence_id integer NOT NULL, |
2672 | 2671 |
locationevent_id integer, |
2673 | 2672 |
accessioncode text, |
2674 |
verbatimcollectorname text |
|
2673 |
verbatimcollectorname text, |
|
2674 |
growthform taxonclass |
|
2675 | 2675 |
); |
2676 | 2676 |
|
2677 | 2677 |
|
mappings/VegX-VegBIEN.organisms.csv | ||
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86 | 86 |
/simpleUserdefined[name=count]/value,/aggregateoccurrence/count, |
87 | 87 |
/simpleUserdefined[name=coverPercent]/value,/aggregateoccurrence/cover, |
88 | 88 |
/simpleUserdefined[name=censusNo]/value,"/aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]:[@fkey=tablerecord_id]/definedvalue", |
89 |
/simpleUserdefined[name=growthForm]/value,/aggregateoccurrence/growthform, |
|
90 | 89 |
/simpleUserdefined[name=interceptCm]/value,/aggregateoccurrence/linecover, |
90 |
/simpleUserdefined[name=growthForm]/value,/growthform, |
|
91 | 91 |
/simpleUserdefined[name=collectionDate]/value,/specimenreplicate:[datasource_id/party/organizationname/_alt/2=$/_ignore/inLabel]/collectiondate, |
92 | 92 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=TaxonomicRankBelowSubspeciesEnum])/Rank","/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,authority,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
93 | 93 |
"/*ID->/*s/individualOrganism/*sID->/*s/taxonNameUsageConcept->/*s/taxonDetermination[*ID,partyWithRole/role=computer]/*s/taxonRelationshipAssertion(/assertion/*ID->/*s/taxonConcept[Rank/@code=auth])/Name","/taxondetermination[role=computer]:[iscurrent=true]/*_id/plantconcept/plantname_id/_simplifyPath:[next=""parent_id/plantname"",require=plantname]/path/_forEach:[in:[binomial,],do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname", |
mappings/for_review/VegX-VegBIEN.organisms.csv | ||
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86 | 86 |
/simpleUserdefined[name=count]/value,//aggregateoccurrence/count, |
87 | 87 |
/simpleUserdefined[name=coverPercent]/value,//aggregateoccurrence/cover, |
88 | 88 |
/simpleUserdefined[name=censusNo]/value,"//aggregateoccurrence/definedvalue[*_id/userdefined[tablename=aggregateoccurrence,userdefinedname=censusNo]]/definedvalue", |
89 |
/simpleUserdefined[name=growthForm]/value,//aggregateoccurrence/growthform, |
|
90 | 89 |
/simpleUserdefined[name=interceptCm]/value,//aggregateoccurrence/linecover, |
90 |
/simpleUserdefined[name=growthForm]/value,/growthform, |
|
91 | 91 |
/simpleUserdefined[name=collectionDate]/value,//specimenreplicate/collectiondate, |
92 | 92 |
//*s/taxonConcept[@code=TaxonomicRankBelowSubspeciesEnum]/Rank,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=subspecies]/plantname/_name/first", |
93 | 93 |
//*s/taxonConcept[@code=auth]/Name,"/taxondetermination[role=computer]/*_id/plantconcept/plantname_id/_simplifyPath/path/_forEach:[do=""plantname[rank=_val]/parent_id""]/plantname[rank=authority]/plantname", |
Also available in: Unified diff
VegBIEN: Moved aggregateoccurrence.growthform to taxonoccurrence