Revision 8774
Added by Aaron Marcuse-Kubitza over 11 years ago
lib/table.run | ||
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#!/bin/bash -e |
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if false; then #### run script template: |
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/table.run |
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import () |
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{ |
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echo_func "$@" |
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before_import_cmds |
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"$(dirname "${BASH_SOURCE[0]}")"/path/to/table.run "$FUNCNAME" "$@" |
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after_import_cmds |
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} |
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fi #### |
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. "$(dirname "${BASH_SOURCE[0]}")"/import.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/local.run |
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if self_not_included; then |
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quote='"' |
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esc_name () { echo "$quote${1//$quote/$quote$quote}$quote"; } |
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mk_esc_name () { set_var "$1"_esc "$(esc_name "${!1}")"; } |
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: "${schema="$(cd "$top_dir"/..; basename "$PWD")"}" |
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mk_esc_name schema |
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: "${table="$( cd "$top_dir" ; basename "$PWD")"}" |
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mk_esc_name table |
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export schema table |
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mysql () |
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{ |
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echo_func "$@" |
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echo_run "$bin_dir"/mysql_bien --database="$schema" --verbose "$@" |
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} |
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mysql_ANSI () |
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{ |
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echo_func "$@" |
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(echo "SET sql_mode = 'ANSI';"; cat)|mysql "$@" |
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} |
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psql () # usage: ([file=...] [dir=...]; self) |
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{ |
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echo_func "$@" |
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local dir="$dir" |
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if test -n "$file"; then |
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set -- --file "$file" "$@" |
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: "${dir:=$(dirname "$file")}" |
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fi |
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: "${dir:=$top_dir}" |
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(cat <<EOF |
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\cd $dir |
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\set schema "$schema" |
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\set table "$table" |
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\set table_str '''"$table"''' |
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SET search_path TO "$schema", util; |
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EOF |
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cat)| |
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echo_run env no_search_path=1 "$bin_dir"/psql_verbose_vegbien "$@" |
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} |
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input_make () |
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{ |
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echo_func "$@" |
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echo_run env make --directory="$top_dir"/.. "${@/#/$table/}" |
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} |
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map_table () |
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{ |
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echo_func "$@" |
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input_make map.csv |
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psql <<EOF |
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SELECT util.reset_map_table('pg_temp.map'); |
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\copy pg_temp.map FROM 'map.csv' CSV HEADER; |
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SELECT util.set_col_names('"$table"', 'pg_temp.map'::regclass); |
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EOF |
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} |
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mk_derived () |
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{ |
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echo_func "$@" |
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"$root_dir"/schemas/VegCore/mk_derived |
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} |
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remake_VegBIEN_mappings () |
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{ |
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echo_func "$@" |
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echo_run rm header.csv map.csv # remake them |
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yes|input_make test |
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} |
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postprocess () # overridable |
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{ |
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echo_func "$@" |
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local file="$top_dir"/postprocess.sql |
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if test -e "$file"; then psql "$@"; fi |
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} |
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import () |
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{ |
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echo_func "$@" |
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map_table |
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postprocess |
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mk_derived |
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} |
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fi |
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lib/util.run | ||
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#!/bin/bash -e |
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# runscripts: a bash-based replacement for make |
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# unlike make, supports full bash functionality including multiline commands |
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# usage: path/to/dir/run cmd args |
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if false; then #### run script template: |
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/util.run or file_including_util.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/other_includes |
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cmd () |
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{ |
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echo_func "$@" |
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"$(dirname "${BASH_SOURCE[0]}")"/path_relative_to_self |
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"$(dirname "${BASH_SOURCE[1]}")"/path_relative_to_caller |
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"$top_dir"/path_relative_to_outermost_script |
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} |
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fi #### |
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: "${verbosity=2}" |
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. "$(dirname "${BASH_SOURCE[0]}")"/util.sh |
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if self_not_included; then |
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# users can override this function to perform other commands (or no commands) |
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# after the script is read |
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on_exit () { run_args_cmd; } |
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trap on_exit EXIT |
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fi |
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lib/import.run | ||
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#!/bin/bash -e |
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if false; then #### run script template: |
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/import.run |
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import () |
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{ |
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echo_func "$@" |
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import_cmds |
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} |
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fi #### |
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. "$(dirname "${BASH_SOURCE[0]}")"/util.run |
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if self_not_included; then |
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import () |
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{ |
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echo_func "$@" |
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} |
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all () |
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{ |
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echo_func "$@" |
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import |
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} |
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fi |
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lib/local.run | ||
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#!/bin/bash -e |
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# links to locally-available resources |
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. "$(dirname "${BASH_SOURCE[0]}")"/util.run |
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if self_not_included; then |
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root_dir="$(dirname "${BASH_SOURCE[0]}")"/.. |
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bin_dir="$root_dir"/bin |
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export PATH="$bin_dir:$PATH" |
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fi |
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inputs/GBIF/table.run | ||
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/table.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run
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if self_not_included; then |
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... | ... | |
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{ |
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echo_func "$@" |
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MySQL_export |
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"$(dirname "${BASH_SOURCE[0]}")"/../../lib/table.run "$FUNCNAME" "$@" |
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"$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/table.run "$FUNCNAME" "$@"
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} |
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fi |
inputs/GBIF/_MySQL/run | ||
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1 | 1 |
#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../../lib/import.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../../lib/runscripts/import.run
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if self_not_included; then |
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inputs/GBIF/run | ||
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1 | 1 |
#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/import.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/import.run
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if self_not_included; then |
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schemas/VegCore/VegCore.ERD.mwb.run | ||
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1 | 1 |
#!/bin/bash -e |
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# syncs VegCore.ERD.mwb's zip file contents |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/util.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/util.run
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if self_not_included; then |
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lib/runscripts/util.run | ||
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#!/bin/bash -e |
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# runscripts: a bash-based replacement for make |
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# unlike make, supports full bash functionality including multiline commands |
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# usage: path/to/dir/run cmd args |
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if false; then #### run script template: |
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/util.run or file_including_util.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/other_includes |
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cmd () |
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{ |
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echo_func "$@" |
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"$(dirname "${BASH_SOURCE[0]}")"/path_relative_to_self |
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"$(dirname "${BASH_SOURCE[1]}")"/path_relative_to_caller |
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"$top_dir"/path_relative_to_outermost_script |
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} |
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fi #### |
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: "${verbosity=2}" |
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. "$(dirname "${BASH_SOURCE[0]}")"/../util.sh |
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if self_not_included; then |
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# users can override this function to perform other commands (or no commands) |
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# after the script is read |
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on_exit () { run_args_cmd; } |
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trap on_exit EXIT |
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fi |
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0 | 32 |
lib/runscripts/table.run | ||
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#!/bin/bash -e |
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if false; then #### run script template: |
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#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/table.run |
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import () |
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{ |
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echo_func "$@" |
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before_import_cmds |
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"$(dirname "${BASH_SOURCE[0]}")"/path/to/table.run "$FUNCNAME" "$@" |
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after_import_cmds |
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} |
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fi #### |
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. "$(dirname "${BASH_SOURCE[0]}")"/import.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/local.run |
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if self_not_included; then |
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quote='"' |
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esc_name () { echo "$quote${1//$quote/$quote$quote}$quote"; } |
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mk_esc_name () { set_var "$1"_esc "$(esc_name "${!1}")"; } |
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: "${schema="$(cd "$top_dir"/..; basename "$PWD")"}" |
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mk_esc_name schema |
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: "${table="$( cd "$top_dir" ; basename "$PWD")"}" |
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mk_esc_name table |
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export schema table |
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mysql () |
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{ |
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echo_func "$@" |
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echo_run "$bin_dir"/mysql_bien --database="$schema" --verbose "$@" |
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} |
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|
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mysql_ANSI () |
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{ |
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echo_func "$@" |
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(echo "SET sql_mode = 'ANSI';"; cat)|mysql "$@" |
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} |
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|
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psql () # usage: ([file=...] [dir=...]; self) |
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{ |
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echo_func "$@" |
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local dir="$dir" |
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if test -n "$file"; then |
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set -- --file "$file" "$@" |
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: "${dir:=$(dirname "$file")}" |
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fi |
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: "${dir:=$top_dir}" |
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|
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(cat <<EOF |
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\cd $dir |
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\set schema "$schema" |
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\set table "$table" |
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\set table_str '''"$table"''' |
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SET search_path TO "$schema", util; |
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EOF |
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cat)| |
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echo_run env no_search_path=1 "$bin_dir"/psql_verbose_vegbien "$@" |
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} |
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input_make () |
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{ |
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echo_func "$@" |
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echo_run env make --directory="$top_dir"/.. "${@/#/$table/}" |
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} |
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map_table () |
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{ |
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echo_func "$@" |
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input_make map.csv |
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psql <<EOF |
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SELECT util.reset_map_table('pg_temp.map'); |
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\copy pg_temp.map FROM 'map.csv' CSV HEADER; |
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SELECT util.set_col_names('"$table"', 'pg_temp.map'::regclass); |
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EOF |
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} |
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mk_derived () |
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{ |
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echo_func "$@" |
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"$root_dir"/schemas/VegCore/mk_derived |
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} |
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remake_VegBIEN_mappings () |
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90 |
{ |
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echo_func "$@" |
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echo_run rm header.csv map.csv # remake them |
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yes|input_make test |
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} |
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95 |
|
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postprocess () # overridable |
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97 |
{ |
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echo_func "$@" |
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local file="$top_dir"/postprocess.sql |
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100 |
if test -e "$file"; then psql "$@"; fi |
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} |
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import () |
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{ |
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echo_func "$@" |
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map_table |
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postprocess |
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mk_derived |
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} |
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fi |
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0 | 112 |
lib/runscripts/import.run | ||
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1 |
#!/bin/bash -e |
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2 |
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if false; then #### run script template: |
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4 |
#!/bin/bash -e |
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. "$(dirname "${BASH_SOURCE[0]}")"/path/to/import.run |
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6 |
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import () |
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8 |
{ |
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echo_func "$@" |
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import_cmds |
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} |
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fi #### |
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13 |
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. "$(dirname "${BASH_SOURCE[0]}")"/util.run |
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if self_not_included; then |
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import () |
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19 |
{ |
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echo_func "$@" |
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} |
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22 |
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all () |
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24 |
{ |
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25 |
echo_func "$@" |
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import |
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} |
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28 |
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fi |
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0 | 30 |
lib/runscripts/local.run | ||
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1 |
#!/bin/bash -e |
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2 |
# links to locally-available resources |
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3 |
. "$(dirname "${BASH_SOURCE[0]}")"/util.run |
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4 |
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5 |
if self_not_included; then |
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root_dir="$(dirname "${BASH_SOURCE[0]}")"/../.. |
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bin_dir="$root_dir"/bin |
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9 |
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export PATH="$bin_dir:$PATH" |
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11 |
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fi |
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0 | 13 |
web/links/index.htm.run | ||
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1 | 1 |
#!/bin/bash -e |
2 | 2 |
# reformats index.htm for display |
3 |
. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/local.run |
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. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/runscripts/local.run
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4 | 4 |
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5 | 5 |
if self_not_included; then |
6 | 6 |
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Also available in: Unified diff
moved lib/*.run into runscripts/ subdir so runscripts are grouped together and easier to find rather than being scattered throughout lib/