| 1 |
8291
|
aaronmk
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#!/bin/bash -e
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| 2 |
8287
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aaronmk
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. "$(dirname "${BASH_SOURCE[0]}")"/../table.run
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| 3 |
8303
|
aaronmk
|
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| 4 |
8705
|
aaronmk
|
if self_not_included; then
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| 5 |
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| 6 |
9461
|
aaronmk
|
herbaria_filter.ih.csv_/make()
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| 7 |
9434
|
aaronmk
|
{
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| 8 |
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echo_func; set_make_vars; check_target_exists
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| 10 |
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use_local
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| 11 |
9554
|
aaronmk
|
limit= query='SELECT DISTINCT acronym FROM herbaria.ih ORDER BY acronym' \
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| 12 |
9434
|
aaronmk
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to_target pg_export
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}
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| 14 |
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| 15 |
9637
|
aaronmk
|
plant_fraction/make()
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| 16 |
9483
|
aaronmk
|
{
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| 17 |
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echo_func; set_make_vars; mk_table_esc
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| 19 |
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use_local_remote
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| 20 |
9627
|
aaronmk
|
if remaking; then table=plant_fraction table_esc= mk_drop|mysql_ANSI; fi
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| 21 |
9626
|
aaronmk
|
(benign_error=1 mysql <<'EOF'
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| 22 |
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CREATE TABLE `plant_fraction` (
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| 23 |
9592
|
aaronmk
|
`institution_code` varchar(255) NOT NULL PRIMARY KEY,
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| 24 |
9629
|
aaronmk
|
`plant_fraction` float NOT NULL,
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KEY `plant_fraction` (`plant_fraction`)
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| 26 |
9628
|
aaronmk
|
) ENGINE=MyISAM DEFAULT CHARSET=utf8
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| 27 |
9592
|
aaronmk
|
EOF
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| 28 |
9626
|
aaronmk
|
) || table=plant_fraction skip_table || return 0
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| 29 |
9483
|
aaronmk
|
mysql_ANSI <<EOF
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| 30 |
9592
|
aaronmk
|
INSERT INTO "plant_fraction"
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| 31 |
9483
|
aaronmk
|
SELECT
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| 32 |
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institution_code
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| 33 |
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, COUNT(family LIKE '%aceae%' OR family IN ('Compositae','Gramineae','Palmae','Guttiferae','Cruciferae','Labiatae','Umbelliferae','Leguminosae'))/COUNT(*)
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| 34 |
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AS plant_fraction
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| 35 |
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FROM ${limit:+(SELECT * FROM }$table_esc ${limit:+$(prefix= limit)) s}
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| 36 |
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GROUP BY institution_code
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| 37 |
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ORDER BY institution_code
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| 38 |
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EOF
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| 39 |
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}
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| 40 |
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| 41 |
9637
|
aaronmk
|
plant_fraction/seal()
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| 42 |
9633
|
aaronmk
|
{
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| 43 |
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echo_func; set_make_vars
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| 44 |
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| 45 |
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use_local_remote
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| 46 |
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table=plant_fraction table_esc= mysql_seal_table
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| 47 |
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}
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| 48 |
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| 49 |
9639
|
aaronmk
|
plant_fraction_for_herbaria_filter/make()
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| 50 |
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{
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| 51 |
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echo_func; set_make_vars; mk_table_esc
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| 52 |
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| 53 |
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use_local_remote
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| 54 |
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if remaking; then
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| 55 |
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table=plant_fraction_for_herbaria_filter table_esc= mk_drop|mysql_ANSI
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| 56 |
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fi
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| 57 |
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(benign_error=1 mysql <<'EOF'
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| 58 |
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CREATE VIEW `plant_fraction_for_herbaria_filter` AS
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| 59 |
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SELECT * FROM `plant_fraction`
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| 60 |
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WHERE plant_fraction >= 0.8
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| 61 |
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EOF
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| 62 |
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) || table=plant_fraction_for_herbaria_filter skip_table || return 0
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| 63 |
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}
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| 64 |
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| 65 |
9638
|
aaronmk
|
herbaria_filter/make()
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| 66 |
9433
|
aaronmk
|
{
|
| 67 |
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echo_func; set_make_vars
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| 68 |
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| 69 |
9659
|
aaronmk
|
use_local_remote
|
| 70 |
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local table="$target_stem"
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| 71 |
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if remaking; then mk_drop|mysql_ANSI; remake=; fi
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| 72 |
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| 73 |
9661
|
aaronmk
|
herbaria_filter.ih.csv_/make
|
| 74 |
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plant_fraction_for_herbaria_filter/make
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| 75 |
9434
|
aaronmk
|
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| 76 |
9643
|
aaronmk
|
(benign_error=1 mysql <<'EOF'
|
| 77 |
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CREATE TABLE `herbaria_filter` (
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| 78 |
9663
|
aaronmk
|
`institution_code` varchar(255) NOT NULL PRIMARY KEY
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| 79 |
9664
|
aaronmk
|
) ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='contains all of IH.vegpath.org?&Index+Herbariorum'
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| 80 |
9433
|
aaronmk
|
EOF
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| 81 |
9643
|
aaronmk
|
) || skip_table || return 0
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| 82 |
9661
|
aaronmk
|
mysql_ANSI <<EOF
|
| 83 |
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INSERT INTO "herbaria_filter"
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| 84 |
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SELECT institution_code FROM plant_fraction_for_herbaria_filter
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| 85 |
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EOF
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| 86 |
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append=1 mysql_import <"$top_dir"/herbaria_filter.ih.csv_
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| 87 |
9433
|
aaronmk
|
}
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| 88 |
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| 89 |
9665
|
aaronmk
|
herbaria_filter/seal()
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| 90 |
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{
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| 91 |
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echo_func; set_make_vars
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| 92 |
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| 93 |
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use_local_remote
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| 94 |
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table=herbaria_filter table_esc= mysql_seal_table
|
| 95 |
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}
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| 96 |
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| 97 |
9155
|
aaronmk
|
func_override table.tsv/make__src_table_run
|
| 98 |
9348
|
aaronmk
|
table.tsv/make() # usage: [remake=1] [limit=...] .../run table.tsv/make
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| 99 |
8303
|
aaronmk
|
{
|
| 100 |
9357
|
aaronmk
|
echo_func; set_make_vars
|
| 101 |
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| 102 |
9638
|
aaronmk
|
herbaria_filter/make
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| 103 |
9356
|
aaronmk
|
filter="
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| 104 |
9412
|
aaronmk
|
deleted IS NULL
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| 105 |
9433
|
aaronmk
|
AND institution_code IN (SELECT * FROM herbaria_filter)" \
|
| 106 |
9356
|
aaronmk
|
table.tsv/make__src_table_run
|
| 107 |
8303
|
aaronmk
|
}
|
| 108 |
8705
|
aaronmk
|
|
| 109 |
|
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fi
|
