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Revision 14786

added inputs/Cyrille_traits/

View differences:

trunk/inputs/Cyrille_traits/Source/header.csv
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row_num
trunk/inputs/Cyrille_traits/Source/data.csv
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2

  
trunk/inputs/Cyrille_traits/Source/run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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trunk/inputs/Cyrille_traits/Source/map.csv
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Cyrille_traits,VegCore,Filter,Comments
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row_num,*row_num,,
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:primary database,sourceType,,
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:specimen,observationGranularity,,
trunk/inputs/Cyrille_traits/Source/test.xml.ref
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<!--put template-->
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<VegBIEN>
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    <_setDefault id="-1">
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        <source_id><source><shortname>Cyrille_traits.new</shortname></source></source_id>
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        <path>
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            <_simplifyPath>
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                <next>parent_id</next>
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                <path>
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                    <source>
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                        <shortname>Cyrille_traits.new</shortname>
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                        <observationtype>specimen</observationtype>
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                        <sourcetype>primary database</sourcetype>
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                    </source>
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                </path>
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            </_simplifyPath>
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        </path>
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    </_setDefault>
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</VegBIEN>
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Inserted 1 new rows into database
trunk/inputs/Cyrille_traits/Source/VegBIEN.csv
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link ../../../mappings/VegCore-VegBIEN.csv
0 2

  
trunk/inputs/Cyrille_traits/Source/unmapped_terms.csv
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*row_num
trunk/inputs/Cyrille_traits/import_order.txt
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Source
2
trait_observation
trunk/inputs/Cyrille_traits/run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/datasrc_dir.run
0 3

  
trunk/inputs/Cyrille_traits/table.run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run
0 3

  
trunk/inputs/Cyrille_traits/Makefile
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include ../input.Makefile
trunk/inputs/Cyrille_traits/trait_observation/header.csv
1
row_num,Family,Genus,Species,Intraspecific rank,var./subsp.,Taxon,Authority,Trait name,Trait value,Unit,Method,Region,Country,State/province,Lower political,Locality description,latitude,Longitude,Elevation,Source,URL  source,Source citation,Source Id,Visiting date,Reference number,Access,Project PI,Project PI contact,Observation,Authorship,Authorship contact
trunk/inputs/Cyrille_traits/trait_observation/run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
0 3

  
trunk/inputs/Cyrille_traits/trait_observation/header.txt
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Family,Genus,Species,Intraspecific rank,var./subsp.,Taxon,Authority,Trait name,Trait value,Unit,Method,Region,Country,State/province,Lower political,Locality description,latitude,Longitude,Elevation,Source,URL  source,Source citation,Source Id,Visiting date,Reference number,Access,Project PI,Project PI contact,Observation,Authorship,Authorship contact
trunk/inputs/Cyrille_traits/trait_observation/map.csv
1
Cyrille_traits,VegCore,Filter,Comments
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row_num,dataProviderRecordID,,
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Family,family,,
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Genus,genus,,
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Species,specificEpithet,,
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Intraspecific rank,infraspecificRank,,
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var./subsp.,infraspecificEpithet,,
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Taxon,taxonName,,
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Authority,scientificNameAuthorship,,
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Trait name,measurementName,,
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Trait value,measurementValue,,
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Unit,measurementUnit,,
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Method,samplingProtocol,,
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Region,continent,,
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Country,country,,
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State/province,stateProvince,,
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Lower political,county,,
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Locality description,locality,,
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latitude,latitude_DMS,,
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Longitude,longitude_DMS,,
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Elevation,verbatimElevation_m,,
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Source,projectName,,"should also be firstPublisher and dataset, but those aren’t mapped yet"
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URL  source,*URL  source,,"should be datasetURL, but that isn’t mapped yet for occurrence records"
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Source citation,bibliographicCitation,,bibliographicCitation of the dataset
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Source Id,collectorNumber,,
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Visiting date,dateCollected,,
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Reference number,projectID,,
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Access,accessRights,,
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Project PI,recordedBy,,
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Project PI contact,*Project PI contact,,
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Observation,occurrenceRemarks,,sometimes contains basisOfRecord
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Authorship,*Authorship,,
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Authorship contact,*Authorship contact,,
trunk/inputs/Cyrille_traits/trait_observation/test.xml.ref
1
<!--put template-->
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<VegBIEN>
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    <_setDefault id="-1">
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        <source_id><source><shortname>Cyrille_traits.new</shortname></source></source_id>
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        <path>
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            <_simplifyPath>
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                <next>parent_id</next>
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                <path>
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                    <location>
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                        <authorlocationcode>$dataProviderRecordID</authorlocationcode>
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                        <accesslevel>$accessRights</accesslevel>
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                        <elevation_m>
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                            <_avg>
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                                <1><_rangeStart><value>$verbatimElevation_m</value></_rangeStart></1>
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                                <2><_rangeEnd><value>$verbatimElevation_m</value></_rangeEnd></2>
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                            </_avg>
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                        </elevation_m>
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                        <elevationrange_m>
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                            <_range>
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                                <from><_rangeStart><value>$verbatimElevation_m</value></_rangeStart></from>
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                                <to><_rangeEnd><value>$verbatimElevation_m</value></_rangeEnd></to>
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                            </_range>
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                        </elevationrange_m>
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                        <iscultivated><_locationnarrative_is_cultivated><locationnarrative>$locality</locationnarrative></_locationnarrative_is_cultivated></iscultivated>
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                        <locationevent>
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                            <method_id><method><name>$samplingProtocol</name></method></method_id>
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                            <project_id>
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                                <project>
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                                    <projectname>$projectName</projectname>
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                                    <sourceaccessioncode>$projectID</sourceaccessioncode>
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                                </project>
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                            </project_id>
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                            <locationevent fkey="parent_id">
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                                <taxonoccurrence>
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                                    <aggregateoccurrence>
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                                        <collectiondate>$dateCollected</collectiondate>
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                                        <notes>$occurrenceRemarks</notes>
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                                        <plantobservation>
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                                            <authorplantcode>$collectorNumber</authorplantcode>
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                                            <specimenreplicate>
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                                                <collectionnumber>$collectorNumber</collectionnumber>
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                                                <sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
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                                            </specimenreplicate>
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                                        </plantobservation>
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                                    </aggregateoccurrence>
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                                    <collector_id><party><fullname>$recordedBy</fullname></party></collector_id>
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                                    <sourceaccessioncode>$dataProviderRecordID</sourceaccessioncode>
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                                    <taxondetermination>
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                                        <taxonverbatim_id>
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                                            <taxonverbatim>
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                                                <taxonlabel_id>
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                                                    <taxonlabel>
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                                                        <parent_id>
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                                                            <taxonlabel>
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                                                                <parent_id>
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                                                                    <taxonlabel>
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                                                                        <rank>cultivar</rank>
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                                                                        <parent_id>
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                                                                            <taxonlabel>
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                                                                                <rank>forma</rank>
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                                                                                <parent_id>
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                                                                                    <taxonlabel>
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                                                                                        <rank>variety</rank>
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                                                                                        <parent_id>
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                                                                                            <taxonlabel>
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                                                                                                <rank>subspecies</rank>
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                                                                                                <parent_id>
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                                                                                                    <taxonlabel>
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                                                                                                        <rank>species</rank>
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                                                                                                        <taxonepithet>$specificEpithet</taxonepithet>
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                                                                                                        <parent_id>
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                                                                                                            <taxonlabel>
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                                                                                                                <rank>genus</rank>
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                                                                                                                <taxonepithet>$genus</taxonepithet>
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                                                                                                                <parent_id>
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                                                                                                                    <taxonlabel>
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                                                                                                                        <rank>family</rank>
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                                                                                                                        <taxonepithet>$family</taxonepithet>
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                                                                                                                    </taxonlabel>
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                                                                                                                </parent_id>
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                                                                                                            </taxonlabel>
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                                                                                                        </parent_id>
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                                                                                                    </taxonlabel>
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                                                                                                </parent_id>
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                                                                                            </taxonlabel>
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                                                                                        </parent_id>
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                                                                                    </taxonlabel>
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                                                                                </parent_id>
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                                                                            </taxonlabel>
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                                                                        </parent_id>
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                                                                    </taxonlabel>
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                                                                </parent_id>
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                                                                <taxonepithet>$infraspecificEpithet</taxonepithet>
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                                                            </taxonlabel>
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                                                        </parent_id>
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                                                        <taxonomicname>
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                                                            <_merge_prefix>
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                                                                <prefix><_taxon_family_require_std><family>$family</family></_taxon_family_require_std></prefix>
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                                                                <value>
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                                                                    <_join_words>
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                                                                        <1>
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                                                                            <_alt>
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                                                                                <1>$taxonName</1>
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                                                                                <2>
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                                                                                    <_join_words>
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                                                                                        <2><_filter_genus><value>$genus</value></_filter_genus></2>
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                                                                                        <3>$specificEpithet</3>
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                                                                                        <5>$infraspecificEpithet</5>
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                                                                                    </_join_words>
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                                                                                </2>
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                                                                            </_alt>
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                                                                        </1>
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                                                                        <2>$scientificNameAuthorship</2>
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                                                                    </_join_words>
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                                                                </value>
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                                                            </_merge_prefix>
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                                                        </taxonomicname>
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                                                    </taxonlabel>
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                                                </taxonlabel_id>
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                                                <author>$scientificNameAuthorship</author>
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                                                <family>$family</family>
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                                                <genus>$genus</genus>
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                                                <specific_epithet>$specificEpithet</specific_epithet>
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                                                <taxonname>$taxonName</taxonname>
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                                            </taxonverbatim>
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                                        </taxonverbatim_id>
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                                    </taxondetermination>
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                                    <trait>
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                                        <name>$measurementName</name>
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                                        <units>$measurementUnit</units>
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                                        <value>$measurementValue</value>
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                                    </trait>
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                                </taxonoccurrence>
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                            </locationevent>
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                        </locationevent>
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                        <locationnarrative>$locality</locationnarrative>
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                        <locationplace>
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                            <place_id>
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                                <place>
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                                    <coordinates_id>
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                                        <coordinates>
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                                            <latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg>
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                                            <longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg>
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                                            <verbatimlatitude>$latitude_DMS</verbatimlatitude>
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                                            <verbatimlongitude>$longitude_DMS</verbatimlongitude>
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                                        </coordinates>
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                                    </coordinates_id>
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                                    <continent>$continent</continent>
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                                    <country>$country</country>
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                                    <county>$county</county>
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                                    <matched_place_id>
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                                        <place>
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                                            <source_id><source><shortname>geoscrub</shortname></source></source_id>
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                                            <coordinates_id>
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                                                <coordinates>
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                                                    <source_id><source><shortname>geoscrub</shortname></source></source_id>
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                                                    <latitude_deg><_dms_to_dd><value>$latitude_DMS</value></_dms_to_dd></latitude_deg>
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                                                    <longitude_deg><_dms_to_dd><value>$longitude_DMS</value></_dms_to_dd></longitude_deg>
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                                                </coordinates>
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                                            </coordinates_id>
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                                            <country>$country</country>
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                                            <county>$county</county>
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                                            <stateprovince>$stateProvince</stateprovince>
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                                        </place>
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                                    </matched_place_id>
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                                    <stateprovince>$stateProvince</stateprovince>
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                                </place>
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                            </place_id>
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                        </locationplace>
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                        <verbatimelevation>$verbatimElevation_m</verbatimelevation>
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                    </location>
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                </path>
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            </_simplifyPath>
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        </path>
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    </_setDefault>
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</VegBIEN>
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Inserted 33 new rows into database
trunk/inputs/Cyrille_traits/trait_observation/VegBIEN.csv
1
link ../../../mappings/VegCore-VegBIEN.csv
0 2

  
trunk/inputs/Cyrille_traits/trait_observation/new_terms.csv
1
row_num,dataProviderRecordID,,
2
Intraspecific rank,infraspecificRank,,
3
var./subsp.,infraspecificEpithet,,
4
Taxon,taxonName,,
5
Authority,scientificNameAuthorship,,
6
Region,continent,,
7
Lower political,county,,
8
Locality description,locality,,
9
Source citation,bibliographicCitation,,bibliographicCitation of the dataset
10
Source Id,collectorNumber,,
11
Visiting date,dateCollected,,
12
Reference number,projectID,,
13
Access,accessRights,,
14
Project PI,recordedBy,,
15
Observation,occurrenceRemarks,,sometimes contains basisOfRecord
trunk/inputs/Cyrille_traits/trait_observation/unmapped_terms.csv
1
infraspecificRank
2
*URL  source
3
bibliographicCitation
4
*Project PI contact
5
*Authorship
6
*Authorship contact

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