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Revision 10931

inputs/VegBank/taxonobservation_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

View differences:

inputs/VegBank/taxonobservation_/map.csv
12 12
int_origplantcommon,originalVernacularName,,
13 13
int_origplantcode,*int_origplantcode,,
14 14
int_currplantconcept_id,*int_currplantconcept_id,,
15
int_currplantscifull,scientificName,/_alt/1,
15
int_currplantscifull,scientificName_verbatim,,
16 16
int_currplantscinamenoauth,taxonName,,
17 17
int_currplantcommon,vernacularName,,
18 18
int_currplantcode,*int_currplantcode,,
......
43 43
taxoninterpretation_accessioncode,*taxoninterpretation_accessioncode,,
44 44
plantname_id,*plantname_id,,
45 45
plantconcept_reference_id,*plantconcept_reference_id,,
46
plantconcept_plantname,scientificName,/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
46
plantconcept_plantname,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
47 47
plantcode,*plantcode,,
48 48
plantdescription,*plantdescription,,
49 49
d_obscount,*d_obscount,,
......
67 67
plantname_reference_id,*plantname_reference_id,,
68 68
dateentered,*dateentered,,
69 69
:plot,observationGranularity,,
70
scientificName,scientificName,,
inputs/VegBank/taxonobservation_/VegBIEN.csv
21 21
observation_id,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/cond/_exists",
22 22
collectionnumber,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/2/_first/3",
23 23
int_origplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/1",
24
int_currplantscifull,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/1",
25
plantconcept_plantname,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2/_alt/2","when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
24
scientificName,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/2",
26 25
int_currplantscinamenoauth,"/location/locationevent/taxonoccurrence/authortaxoncode/_if[@name=""if in plot""]/then/_first/3/_first/3",
27 26
collectionnumber,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
28 27
taxonobservation_id,"/location/locationevent/taxonoccurrence/iscultivated/_alt/1/_if[@name=""if TaxonOccurrence""]/cond/_exists",
......
33 32
Class,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=class]/taxonepithet",
34 33
Kingdom,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/parent_id/taxonlabel/parent_id/_forEach:[in:[cultivar,forma,variety,subspecies,species,genus,family,order,class,phylum,],do=""taxonlabel[rank=_val]/parent_id""]/taxonlabel[rank=kingdom]/taxonepithet",
35 34
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/prefix/_taxon_family_require_std/family,
36
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/1,
37
plantconcept_plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
35
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/1,
38 36
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/1,
39 37
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/*_id/taxonlabel/taxonomicname/_merge_prefix/value/_alt/2/_join_words/1/_alt/2/_join_words/2/_filter_genus/value,includes genus author
40 38
Family,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/family,
41 39
Genus,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/genus,includes genus author
42 40
int_currplantscinamenoauth,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonname,
43
int_currplantscifull,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/1,
44
plantconcept_plantname,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
41
scientificName,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/*_id/taxonverbatim/taxonomicname,
45 42
taxonobservation_id,"/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/_if[@name=""if has taxondetermination""]/cond/_exists",
46 43
interpretationdate,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationdate/_alt/1/_dateRangeStart/value,
47 44
interpretationtype,/location/locationevent/taxonoccurrence/taxondetermination[!isoriginal]/determinationtype,
......
70 67
int_currplantcode,,** No join mapping for *int_currplantcode ** 
71 68
int_currplantcommon,,** No join mapping for vernacularName ** 
72 69
int_currplantconcept_id,,** No join mapping for *int_currplantconcept_id ** 
70
int_currplantscifull,,** No join mapping for scientificName_verbatim ** 
73 71
int_origplantcode,,** No join mapping for *int_origplantcode ** 
74 72
int_origplantcommon,,** No join mapping for originalVernacularName ** 
75 73
int_origplantconcept_id,,** No join mapping for *int_origplantconcept_id ** 
......
81 79
plantcode,,** No join mapping for *plantcode ** 
82 80
plantconcept_accessioncode,,** No join mapping for *plantconcept_accessioncode ** 
83 81
plantconcept_id,,** No join mapping for *plantconcept_id ** 
82
plantconcept_plantname,,"** No join mapping for scientificName__for_nearest_taxon_concept ** when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
84 83
plantconcept_reference_id,,** No join mapping for *plantconcept_reference_id ** 
85 84
plantdescription,,** No join mapping for *plantdescription ** 
86 85
plantname,,** No non-empty join mapping for DUPLICATE#of:plantconcept_plantname#plantname ** exact duplicate
inputs/VegBank/taxonobservation_/test.xml.ref
97 97
                                                            <prefix><_taxon_family_require_std><family>$Family</family></_taxon_family_require_std></prefix>
98 98
                                                            <value>
99 99
                                                                <_alt>
100
                                                                    <1>
101
                                                                        <_alt>
102
                                                                            <1>$int_currplantscifull</1>
103
                                                                            <2>$plantconcept_plantname</2>
104
                                                                        </_alt>
105
                                                                    </1>
100
                                                                    <1>$scientificName</1>
106 101
                                                                    <2>
107 102
                                                                        <_alt>
108 103
                                                                            <1>$int_currplantscinamenoauth</1>
......
118 113
                                            <family>$Family</family>
119 114
                                            <genus>$Genus</genus>
120 115
                                            <taxonname>$int_currplantscinamenoauth</taxonname>
121
                                            <taxonomicname>
122
                                                <_alt>
123
                                                    <1>$int_currplantscifull</1>
124
                                                    <2>$plantconcept_plantname</2>
125
                                                </_alt>
126
                                            </taxonomicname>
116
                                            <taxonomicname>$scientificName</taxonomicname>
127 117
                                        </taxonverbatim>
128 118
                                    </taxonverbatim_id>
129 119
                                    <determinationdate><_dateRangeStart><value>$interpretationdate</value></_dateRangeStart></determinationdate>
inputs/VegBank/taxonobservation_/new_terms.csv
2 2
int_origplantscifull,EQUIV#to:authorplantname#int_origplantscifull,, = originalScientificName_scrubbed
3 3
int_origplantscinamenoauth,originalTaxonName,,
4 4
int_origplantcommon,originalVernacularName,,
5
int_currplantscifull,scientificName,/_alt/1,
5
int_currplantscifull,scientificName_verbatim,,
6 6
int_currplantscinamenoauth,taxonName,,
7 7
int_currplantcommon,vernacularName,,
8 8
interpretationdate,dateIdentified,,
9 9
collectiondate,dateCollected,,
10
plantconcept_plantname,scientificName,/_alt/2,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
10
plantconcept_plantname,scientificName__for_nearest_taxon_concept,,"when int_currplantscifull also provided, this often leaves out lower ranks. however, int_currplantscifull is not always provided when this is."
11 11
plantname,DUPLICATE#of:plantconcept_plantname#plantname,,exact duplicate
inputs/VegBank/taxonobservation_/unmapped_terms.csv
6 6
originalVernacularName
7 7
*int_origplantcode
8 8
*int_currplantconcept_id
9
scientificName_verbatim
9 10
vernacularName
10 11
*int_currplantcode
11 12
*taxonobservation_accessioncode
......
27 28
*taxoninterpretation_accessioncode
28 29
*plantname_id
29 30
*plantconcept_reference_id
31
scientificName__for_nearest_taxon_concept
30 32
*plantcode
31 33
*plantdescription
32 34
*d_obscount

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