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1551
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aaronmk
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#!/bin/bash
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| 2 |
1541
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aaronmk
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# Imports all inputs at once
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| 4 |
1952
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aaronmk
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import_all_main ()
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{
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local self="${BASH_SOURCE[0]}"
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local selfDir="$(dirname -- "$self")"
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| 8 |
6211
|
aaronmk
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cd "$selfDir/.."
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| 9 |
1952
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aaronmk
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| 10 |
1953
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aaronmk
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if test "${BASH_LINENO[1]}" = 0; then # was run without initial "."
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| 11 |
5039
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aaronmk
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echo "Usage: . $self [vars...] (note initial \".\")"|fold -s >&2
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| 12 |
1952
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aaronmk
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return 2
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fi
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| 15 |
5917
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aaronmk
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make inputs/.TNRS/tnrs_accepted/reinstall
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make inputs/.TNRS/tnrs_other/reinstall
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| 17 |
5503
|
aaronmk
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| 18 |
5957
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aaronmk
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make inputs/.geoscrub/import "$@" &
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| 19 |
5959
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aaronmk
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sleep 5 # wait for make commands to scroll by
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| 21 |
5836
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aaronmk
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make inputs/.NCBI/import by_col=1 "$@"
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| 22 |
5943
|
aaronmk
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# Must come after NCBI for cross links to be made
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| 23 |
5957
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aaronmk
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make inputs/.TNRS/import "$@"
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| 24 |
5959
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aaronmk
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| 25 |
6208
|
aaronmk
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wait %1 # wait for asynchronous commands (geoscrub import)
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| 26 |
5503
|
aaronmk
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| 27 |
5836
|
aaronmk
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make inputs/.TNRS/tnrs/tnrs-remake wait=1 "$@" &
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| 28 |
5039
|
aaronmk
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. "$selfDir/with_all" import "$@"
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| 29 |
6210
|
aaronmk
|
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| 30 |
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after_import ()
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{
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| 32 |
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bin/make_analytical_db
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}
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| 35 |
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jobs="$(jobs -p)"
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| 36 |
6211
|
aaronmk
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(bin/waitpid $jobs; after_import) &
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| 37 |
1952
|
aaronmk
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}
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| 38 |
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import_all_main "$@"
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