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Revision 10189

inputs/.herbaria/: switched to new-style import, which renamed the columns to the VegCore names. this is done using the commands at wiki.vegpath.org/2013-06-27_conference_call#To-do-for-Aaron > "run the following for each datasource".

View differences:

inputs/.herbaria/Source/run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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inputs/.herbaria/Source/VegBIEN.csv
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herbaria,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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:primary database,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype",
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link ../../../mappings/VegCore-VegBIEN.csv
3 2

  
inputs/.herbaria/ih/run
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#!/bin/bash -e
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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inputs/.herbaria/ih/test.xml.ref
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                <next>parent_id</next>
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                <path>
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                    <source>
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                        <shortname>$acronym</shortname>
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                        <shortname>$specimenHolderInstitutions</shortname>
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                        <observationtype>specimen</observationtype>
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                        <sourcetype>herbarium</sourcetype>
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                    </source>
inputs/.herbaria/ih/VegBIEN.csv
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herbaria,VegBIEN:/_setDefault:[source_id/source/shortname/_env:[name=source]]/path/_simplifyPath:[next=parent_id]/path,Comments
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acronym,"/_if[@name=""if specimen""]/else/source/shortname/_first/1",
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:specimen,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/observationtype",
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:herbarium,"/_if[@name=""if specimen""]/else/source:[shortname/_first/2/_env:[name=source]]/sourcetype",
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:specimen,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/cond/_eq:[right=plot]/left",
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acronym,"/location/_if[@name=""if subplot""]/else/authorlocationcode/_first/3/_if[@name=""if plot""]/else/_alt/2/_if[@name=""if catalogNumber""]/then/_join/1/_if[@name=""if specimen""]/then/_first/2",
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acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/name/_first/2",
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acronym,"/location/locationevent/taxonoccurrence/aggregateoccurrence/plantobservation/specimenreplicate/institution_id/sourcelist/_if[@name=""if specimen""]/then/sourcename/name/_first/2/_split:[separator=""[,;] *""]/value",
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AddEmail,,** No join mapping for *AddEmail ** 
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AddEmuUserId,,** No join mapping for *AddEmuUserId ** 
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AddPhysCity,,** No join mapping for *AddPhysCity ** 
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AddPhysCountry,,** No join mapping for *AddPhysCountry ** 
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AddPhysPost,,** No join mapping for *AddPhysPost ** 
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AddPhysState,,** No join mapping for *AddPhysState ** 
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AddPhysStreet,,** No join mapping for *AddPhysStreet ** 
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AddPostCity,,** No join mapping for *AddPostCity ** 
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AddPostPost,,** No join mapping for *AddPostPost ** 
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AddPostState,,** No join mapping for *AddPostState ** 
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AddPostStreet,,** No join mapping for *AddPostStreet ** 
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AddWeb,,** No join mapping for *AddWeb ** 
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AdmDateModified,,** No join mapping for *AdmDateModified ** 
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AdmTimeModified,,** No join mapping for *AdmTimeModified ** 
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HisCommenced,,** No join mapping for *HisCommenced ** 
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IhhAssociatedHerbaria,,** No join mapping for *IhhAssociatedHerbaria ** 
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IhhCites,,** No join mapping for *IhhCites ** 
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IhhExchange,,** No join mapping for *IhhExchange ** 
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IhhGeography,,** No join mapping for *IhhGeography ** 
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IhhInstitutionType,,** No join mapping for *IhhInstitutionType ** 
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IhhStatus,,** No join mapping for *IhhStatus ** 
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IhhTotal,,** No join mapping for *IhhTotal ** 
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NamBranch,,** No join mapping for *NamBranch ** 
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NamDepartment,,** No join mapping for *NamDepartment ** 
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NamFax,,** No join mapping for *NamFax ** 
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NamOrganisation,,** No join mapping for *NamOrganisation ** 
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NamSection,,** No join mapping for *NamSection ** 
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NotNotes,,** No join mapping for *NotNotes ** 
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eparties_key,,** No join mapping for *eparties_key ** 
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irn,,** No join mapping for *irn ** 
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url,,** No join mapping for *url ** 
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link ../../../mappings/VegCore-VegBIEN.csv
40 2

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

  

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