Revision 11107
Added by Aaron Marcuse-Kubitza about 11 years ago
| test.xml.ref | ||
|---|---|---|
| 8 | 8 |
<path> |
| 9 | 9 |
<location> |
| 10 | 10 |
<locationevent> |
| 11 |
<taxonoccurrence> |
|
| 12 |
<taxondetermination> |
|
| 13 |
<taxonverbatim_id> |
|
| 14 |
<taxonverbatim> |
|
| 15 |
<taxonlabel_id> |
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| 16 |
<taxonlabel> |
|
| 17 |
<parent_id> |
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| 18 |
<taxonlabel> |
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| 19 |
<rank>$taxonRank</rank> |
|
| 20 |
<parent_id> |
|
| 21 |
<taxonlabel> |
|
| 22 |
<rank>cultivar</rank> |
|
| 23 |
<parent_id> |
|
| 24 |
<taxonlabel> |
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| 25 |
<rank>forma</rank> |
|
| 26 |
<parent_id> |
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| 27 |
<taxonlabel> |
|
| 28 |
<rank>variety</rank> |
|
| 29 |
<parent_id> |
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| 30 |
<taxonlabel> |
|
| 31 |
<rank>subspecies</rank> |
|
| 32 |
<parent_id> |
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| 33 |
<taxonlabel> |
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| 34 |
<rank>species</rank> |
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| 35 |
<taxonepithet>$specificEpithet</taxonepithet> |
|
| 36 |
<parent_id> |
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| 37 |
<taxonlabel> |
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| 38 |
<rank>genus</rank> |
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| 39 |
<taxonepithet>$genus</taxonepithet> |
|
| 40 |
<parent_id> |
|
| 41 |
<taxonlabel> |
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| 42 |
<rank>family</rank> |
|
| 43 |
<taxonepithet>$family</taxonepithet> |
|
| 44 |
<parent_id> |
|
| 45 |
<taxonlabel> |
|
| 46 |
<rank>order</rank> |
|
| 47 |
<taxonepithet>$order</taxonepithet> |
|
| 48 |
<parent_id> |
|
| 49 |
<taxonlabel> |
|
| 50 |
<rank>class</rank> |
|
| 51 |
<taxonepithet>$class</taxonepithet> |
|
| 52 |
<parent_id> |
|
| 53 |
<taxonlabel> |
|
| 54 |
<rank>phylum</rank> |
|
| 55 |
<taxonepithet>$phylum</taxonepithet> |
|
| 56 |
<parent_id> |
|
| 57 |
<taxonlabel> |
|
| 58 |
<rank>kingdom</rank> |
|
| 59 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 60 |
</taxonlabel> |
|
| 61 |
</parent_id> |
|
| 62 |
</taxonlabel> |
|
| 63 |
</parent_id> |
|
| 64 |
</taxonlabel> |
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| 65 |
</parent_id> |
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| 66 |
</taxonlabel> |
|
| 67 |
</parent_id> |
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| 68 |
</taxonlabel> |
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| 69 |
</parent_id> |
|
| 70 |
</taxonlabel> |
|
| 71 |
</parent_id> |
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| 72 |
</taxonlabel> |
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| 73 |
</parent_id> |
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| 74 |
</taxonlabel> |
|
| 75 |
</parent_id> |
|
| 76 |
</taxonlabel> |
|
| 77 |
</parent_id> |
|
| 78 |
</taxonlabel> |
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| 79 |
</parent_id> |
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| 80 |
</taxonlabel> |
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| 81 |
</parent_id> |
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| 82 |
</taxonlabel> |
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| 83 |
</parent_id> |
|
| 84 |
<rank>$taxonRank</rank> |
|
| 85 |
<sourceaccessioncode>$taxonID</sourceaccessioncode> |
|
| 86 |
<taxonepithet> |
|
| 87 |
<_if name="if taxonomic name is epithet"> |
|
| 88 |
<cond> |
|
| 89 |
<_alt> |
|
| 90 |
<2>true</2> |
|
| 91 |
<1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1> |
|
| 92 |
</_alt> |
|
| 93 |
</cond> |
|
| 94 |
<then>$taxonNameOrEpithet</then> |
|
| 95 |
</_if> |
|
| 96 |
</taxonepithet> |
|
| 97 |
<taxonomicname> |
|
| 98 |
<_merge_prefix> |
|
| 99 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 100 |
<value> |
|
| 101 |
<_alt> |
|
| 102 |
<2> |
|
| 103 |
<_join_words> |
|
| 104 |
<1> |
|
| 105 |
<_join_words> |
|
| 106 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 107 |
<3>$specificEpithet</3> |
|
| 108 |
</_join_words> |
|
| 109 |
</1> |
|
| 110 |
<2>$scientificNameAuthorship</2> |
|
| 111 |
</_join_words> |
|
| 112 |
</2> |
|
| 113 |
<3>$taxonNameOrEpithet</3> |
|
| 114 |
</_alt> |
|
| 115 |
</value> |
|
| 116 |
</_merge_prefix> |
|
| 117 |
</taxonomicname> |
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| 118 |
</taxonlabel> |
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| 119 |
</taxonlabel_id> |
|
| 120 |
<author>$scientificNameAuthorship</author> |
|
| 121 |
<family>$family</family> |
|
| 122 |
<genus>$genus</genus> |
|
| 123 |
<specific_epithet>$specificEpithet</specific_epithet> |
|
| 124 |
<verbatimrank>$taxonRank</verbatimrank> |
|
| 125 |
</taxonverbatim> |
|
| 126 |
</taxonverbatim_id> |
|
| 127 |
</taxondetermination> |
|
| 128 |
</taxonoccurrence> |
|
| 11 |
<locationevent fkey="parent_id"> |
|
| 12 |
<taxonoccurrence> |
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| 13 |
<taxondetermination> |
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| 14 |
<taxonverbatim_id> |
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| 15 |
<taxonverbatim> |
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| 16 |
<taxonlabel_id> |
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| 17 |
<taxonlabel> |
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| 18 |
<parent_id> |
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| 19 |
<taxonlabel> |
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| 20 |
<rank>$taxonRank</rank> |
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| 21 |
<parent_id> |
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| 22 |
<taxonlabel> |
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| 23 |
<rank>cultivar</rank> |
|
| 24 |
<parent_id> |
|
| 25 |
<taxonlabel> |
|
| 26 |
<rank>forma</rank> |
|
| 27 |
<parent_id> |
|
| 28 |
<taxonlabel> |
|
| 29 |
<rank>variety</rank> |
|
| 30 |
<parent_id> |
|
| 31 |
<taxonlabel> |
|
| 32 |
<rank>subspecies</rank> |
|
| 33 |
<parent_id> |
|
| 34 |
<taxonlabel> |
|
| 35 |
<rank>species</rank> |
|
| 36 |
<taxonepithet>$specificEpithet</taxonepithet> |
|
| 37 |
<parent_id> |
|
| 38 |
<taxonlabel> |
|
| 39 |
<rank>genus</rank> |
|
| 40 |
<taxonepithet>$genus</taxonepithet> |
|
| 41 |
<parent_id> |
|
| 42 |
<taxonlabel> |
|
| 43 |
<rank>family</rank> |
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| 44 |
<taxonepithet>$family</taxonepithet> |
|
| 45 |
<parent_id> |
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| 46 |
<taxonlabel> |
|
| 47 |
<rank>order</rank> |
|
| 48 |
<taxonepithet>$order</taxonepithet> |
|
| 49 |
<parent_id> |
|
| 50 |
<taxonlabel> |
|
| 51 |
<rank>class</rank> |
|
| 52 |
<taxonepithet>$class</taxonepithet> |
|
| 53 |
<parent_id> |
|
| 54 |
<taxonlabel> |
|
| 55 |
<rank>phylum</rank> |
|
| 56 |
<taxonepithet>$phylum</taxonepithet> |
|
| 57 |
<parent_id> |
|
| 58 |
<taxonlabel> |
|
| 59 |
<rank>kingdom</rank> |
|
| 60 |
<taxonepithet>$kingdom</taxonepithet> |
|
| 61 |
</taxonlabel> |
|
| 62 |
</parent_id> |
|
| 63 |
</taxonlabel> |
|
| 64 |
</parent_id> |
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| 65 |
</taxonlabel> |
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| 66 |
</parent_id> |
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| 67 |
</taxonlabel> |
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| 68 |
</parent_id> |
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| 69 |
</taxonlabel> |
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| 70 |
</parent_id> |
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| 71 |
</taxonlabel> |
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| 72 |
</parent_id> |
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| 73 |
</taxonlabel> |
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| 74 |
</parent_id> |
|
| 75 |
</taxonlabel> |
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| 76 |
</parent_id> |
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| 77 |
</taxonlabel> |
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| 78 |
</parent_id> |
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| 79 |
</taxonlabel> |
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| 80 |
</parent_id> |
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| 81 |
</taxonlabel> |
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| 82 |
</parent_id> |
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| 83 |
</taxonlabel> |
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| 84 |
</parent_id> |
|
| 85 |
<rank>$taxonRank</rank> |
|
| 86 |
<sourceaccessioncode>$taxonID</sourceaccessioncode> |
|
| 87 |
<taxonepithet> |
|
| 88 |
<_if name="if taxonomic name is epithet"> |
|
| 89 |
<cond> |
|
| 90 |
<_alt> |
|
| 91 |
<2>true</2> |
|
| 92 |
<1><_taxonomic_name_is_epithet><rank>$taxonRank</rank></_taxonomic_name_is_epithet></1> |
|
| 93 |
</_alt> |
|
| 94 |
</cond> |
|
| 95 |
<then>$taxonNameOrEpithet</then> |
|
| 96 |
</_if> |
|
| 97 |
</taxonepithet> |
|
| 98 |
<taxonomicname> |
|
| 99 |
<_merge_prefix> |
|
| 100 |
<prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix> |
|
| 101 |
<value> |
|
| 102 |
<_alt> |
|
| 103 |
<2> |
|
| 104 |
<_join_words> |
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| 105 |
<1> |
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| 106 |
<_join_words> |
|
| 107 |
<2><_filter_genus><value>$genus</value></_filter_genus></2> |
|
| 108 |
<3>$specificEpithet</3> |
|
| 109 |
</_join_words> |
|
| 110 |
</1> |
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| 111 |
<2>$scientificNameAuthorship</2> |
|
| 112 |
</_join_words> |
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| 113 |
</2> |
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| 114 |
<3>$taxonNameOrEpithet</3> |
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| 115 |
</_alt> |
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| 116 |
</value> |
|
| 117 |
</_merge_prefix> |
|
| 118 |
</taxonomicname> |
|
| 119 |
</taxonlabel> |
|
| 120 |
</taxonlabel_id> |
|
| 121 |
<author>$scientificNameAuthorship</author> |
|
| 122 |
<family>$family</family> |
|
| 123 |
<genus>$genus</genus> |
|
| 124 |
<specific_epithet>$specificEpithet</specific_epithet> |
|
| 125 |
<verbatimrank>$taxonRank</verbatimrank> |
|
| 126 |
</taxonverbatim> |
|
| 127 |
</taxonverbatim_id> |
|
| 128 |
</taxondetermination> |
|
| 129 |
</taxonoccurrence> |
|
| 130 |
</locationevent> |
|
| 129 | 131 |
</locationevent> |
| 130 | 132 |
</location> |
| 131 | 133 |
</path> |
Also available in: Unified diff
bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.