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5414
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aaronmk
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#!/bin/sh
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# Test-scrubs the test taxonomic names
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selfDir="$(dirname -- "$0")"
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selfDirName="$(basename -- "$selfDir")"
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cd "$selfDir/../.."
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5423
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aaronmk
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# Import names
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5812
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aaronmk
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make inputs/.TNRS/reinstall schema_only=1 # asks user for confirmation
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5668
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aaronmk
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# Must come after TNRS reinstall to recreate tnrs_input_name view
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5414
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aaronmk
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make schemas/public/reinstall # asks user for confirmation
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make inputs/"$selfDirName"/import log=
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5422
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aaronmk
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for iter in match_input_names parse_accepted_names; do
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5414
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aaronmk
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make inputs/.TNRS/tnrs/tnrs-remake log=
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yes|make schemas/public/reinstall
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5917
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aaronmk
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make inputs/.TNRS/tnrs_accepted/reinstall
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make inputs/.TNRS/tnrs_other/reinstall
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5414
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aaronmk
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make inputs/.TNRS/import log=
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make inputs/"$selfDirName"/import log=
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done
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5423
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aaronmk
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# Export results
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# Don't overwrite TNRS.backup, which contains the full TNRS cache
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make backups/TNRS.sql-remake
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mv -f backups/TNRS.sql "$selfDir/_scrub"
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5680
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aaronmk
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public=public."$selfDirName"
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5681
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aaronmk
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make schemas/"$public"/uninstall
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5680
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aaronmk
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make schemas/rename/"$public"
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make backups/"$public".sql-remake
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mv -f backups/"$public".sql "$selfDir/_scrub"
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