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Revision 1430

VegBIEN: Moved aggregateoccurrence.growthform to taxonoccurrence

View differences:

inputs/SALVIAS/test/VegBIEN.organisms.xml.ref
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
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
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>
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        <growthform>tree</growthform>
160 160
        <taxondetermination>
161 161
            <role>computer</role>
162 162
            <iscurrent>true</iscurrent>
inputs/SALVIAS-CSV/maps/VegBIEN.organisms.csv
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
130 130
    coverindex_id int(11),
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    occurrencestatus_dwc text DEFAULT 'present' NOT NULL,
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    method_id int(11),
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    linecover double precision,
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    growthform text
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    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
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
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
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",

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