| 1 |
1551
|
aaronmk
|
#!/bin/bash
|
| 2 |
1541
|
aaronmk
|
# Imports all inputs at once
|
| 3 |
|
|
|
| 4 |
1952
|
aaronmk
|
import_all_main ()
|
| 5 |
|
|
{
|
| 6 |
|
|
local self="${BASH_SOURCE[0]}"
|
| 7 |
|
|
local selfDir="$(dirname -- "$self")"
|
| 8 |
6211
|
aaronmk
|
cd "$selfDir/.."
|
| 9 |
1952
|
aaronmk
|
|
| 10 |
1953
|
aaronmk
|
if test "${BASH_LINENO[1]}" = 0; then # was run without initial "."
|
| 11 |
6946
|
aaronmk
|
echo "Usage: [version=...;] . $self [vars...] (note initial \".\")"\
|
| 12 |
|
|
|fold -s >&2
|
| 13 |
1952
|
aaronmk
|
return 2
|
| 14 |
|
|
fi
|
| 15 |
7103
|
aaronmk
|
: ${version=$(make -s version)}
|
| 16 |
|
|
local dump_opts=${dump_opts---exclude-schema=public} public_import=1
|
| 17 |
|
|
export version dump_opts public_import
|
| 18 |
1952
|
aaronmk
|
|
| 19 |
6946
|
aaronmk
|
make schemas/$version/install
|
| 20 |
|
|
|
| 21 |
7121
|
aaronmk
|
local all=1; . "$selfDir/with_all" Source/import by_col=1 "$@"
|
| 22 |
6897
|
aaronmk
|
# note that this isn't affected by $import_source
|
| 23 |
6593
|
aaronmk
|
wait # wait for asynchronous commands
|
| 24 |
6896
|
aaronmk
|
unset all
|
| 25 |
6593
|
aaronmk
|
|
| 26 |
7095
|
aaronmk
|
local import_source= # Source tables have already been imported
|
| 27 |
|
|
export import_source # must come after local
|
| 28 |
6897
|
aaronmk
|
|
| 29 |
6382
|
aaronmk
|
make inputs/.herbaria/import "$@" &
|
| 30 |
|
|
sleep 5 # wait for make commands to scroll by
|
| 31 |
|
|
|
| 32 |
5957
|
aaronmk
|
make inputs/.geoscrub/import "$@" &
|
| 33 |
5959
|
aaronmk
|
sleep 5 # wait for make commands to scroll by
|
| 34 |
|
|
|
| 35 |
5836
|
aaronmk
|
make inputs/.NCBI/import by_col=1 "$@"
|
| 36 |
5959
|
aaronmk
|
|
| 37 |
6594
|
aaronmk
|
wait # wait for asynchronous commands
|
| 38 |
5503
|
aaronmk
|
|
| 39 |
7087
|
aaronmk
|
. "$selfDir/with_all" import "$@"
|
| 40 |
5836
|
aaronmk
|
make inputs/.TNRS/tnrs/tnrs-remake wait=1 "$@" &
|
| 41 |
7089
|
aaronmk
|
make inputs/.TNRS/public.unscrubbed_taxondetermination_view/scrub-remake \
|
| 42 |
|
|
wait=1 "$@" &
|
| 43 |
6210
|
aaronmk
|
|
| 44 |
|
|
after_import ()
|
| 45 |
|
|
{
|
| 46 |
|
|
bin/make_analytical_db
|
| 47 |
6958
|
aaronmk
|
|
| 48 |
6960
|
aaronmk
|
make backups/TNRS.backup-remake &
|
| 49 |
7038
|
aaronmk
|
make backups/vegbien.$version.backup/test & # uses $dump_opts
|
| 50 |
6958
|
aaronmk
|
wait # wait for asynchronous commands
|
| 51 |
6210
|
aaronmk
|
}
|
| 52 |
|
|
|
| 53 |
7121
|
aaronmk
|
local jobs="$(jobs -p)"
|
| 54 |
6211
|
aaronmk
|
(bin/waitpid $jobs; after_import) &
|
| 55 |
1952
|
aaronmk
|
}
|
| 56 |
|
|
import_all_main "$@"
|
