. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/sh/util.sh

. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/sh/local.sh

. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/sh/local.sh

. "$(dirname "${BASH_SOURCE[0]}")"/lib/sh/local.sh

. "$(dirname "${BASH_SOURCE[0]}")"/../sh/util.sh

. "$(dirname "${BASH_SOURCE[0]}")"/../sh/local.sh

#!/bin/bash -e

# links to locally-available resources

. "$(dirname "${BASH_SOURCE[0]}")"/util.sh

if self_not_included; then

root_dir="$(dirname "${BASH_SOURCE[0]}")"/../..

bin_dir="$root_dir"/bin

bin_dir_abs="$(realpath "$bin_dir")"

export PATH="$bin_dir_abs:$PATH"

#### make

root_make () { echo_func; make --directory="$root_dir" "$@"; }

#### connection vars

: "${remote_server=vegbiendev.nceas.ucsb.edu}"

: "${local_server=localhost}"

: "${local_user=bien}"

: "${local_password="$(cat "$root_dir"/config/bien_password)"}"

#### databases

### MySQL

: "${postgres_compat=1}"

mysqldump_local () { echo_func; use_local_remote; mysqldump_diffable "$@"; }

### PostgreSQL

psql () # usage: [file=...] [dir=...] self

{

	echo_func

	if test -n "$file"; then

		set -- --file "$file" "$@"

		local dir="${dir:-$(dirname "$file")}"

	fi

	local dir="${dir:-$top_dir}"

	local psql_cmd="psql_$(if log_sql; then echo verbose; else echo script; fi)_vegbien"

	(cat <<EOF

\cd $dir

\set schema "$schema"

\set table "$table"

\set table_str '''"$table"'''

SET search_path TO "$schema", util;

EOF

	cat)|

	env no_search_path=1 "$psql_cmd" --output /dev/fd/4 "$@" 4>&1 >&2

}

fi

#!/bin/bash -e

set -o errexit # in case caller did not have -e in #! line

function extern () { (exec "$@") || return; }

isset () { test -n "${!1+isset}"; }

realpath () { readlink -f -- "$1"; }

include_guard_var () { realpath "$1"|"extern" sed 's/[^a-zA-Z0-9_]/_/g'; }

self_not_included () # usage: if self_not_included; then ... fi

{

	test $# -ge 1 || set -- "${BASH_SOURCE[1]}"

	local include_guard="$(include_guard_var "$1")"

	alias self_being_included=false

	! isset "$include_guard" && \

	{ eval "$include_guard"=1; alias self_being_included=true; }

}

# to load newly-defined aliases for use in functions in the same file:

## fi # load new aliases

## if self_being_included; then

# this is needed because aliases defined inside an if statement are not

# available inside that if statement

if self_not_included "${BASH_SOURCE[0]}"; then

shopt -s expand_aliases

unalias () { builtin unalias "$@" 2>&- || true; } # no error if undefined

#### exceptions

alias rethrow='return "$e"'

alias rethrow_subshell='exit "$e"'

fi # load new aliases

if self_being_included; then

# usage: save_e cmd... || use $e (or $?)

function save_e () { "$@"; e=$?; rethrow; } # rethrow because e= clears $?

alias save_e='declare e; save_e ' # last space alias-expands next word

function log_e () # usage: log_e cmd... [ || use $e (or $?) ]

{

	if ! "save_e" "$@"; then

		echo "! $*" >&2

		echo "! command exited with error $e" >&2

		rethrow

	fi

}

alias log_e='declare e; log_e ' # last space alias-expands next word

# usage: try cmd...; ignore status; if catch status; then ...; fi; end_try

function try () { "save_e" "$@" || true; }

alias try='declare e; try ' # last space alias-expands next word

catch () { test "$e" -eq "$1"; e=0; }

ignore () { catch "$@" || true; }

alias end_try='rethrow'

alias end_try_subshell='rethrow_subshell'

#### integers

let () { builtin let "$@" || true; }

	# "If the last ARG evaluates to 0, let returns 1" (`help let`)

bool2int () { save_e test -z "$1"; echo "$e"; } # empty->0; non-empty->1

#### arrays

join () { local IFS="$delim"; echo "$*"; } # usage: delim=... join elems...

reverse () # usage: array=($(reverse args...))

{

	local i

	for (( i=$#; i >= 1; i-- )); do printf '%q ' "${!i}"; done

}

#### verbose output

# usage: (stdout2stderr; cmd...) || return

# `|| return` needed on Mac because of bug where -e doesn't apply to ()

stdout2stderr () { exec >&2; }

# set verbosity

if isset verbose; then : "${verbosity:=$(bool2int "$verbose")}"; fi

: "${verbosity=3}" # default

: "${verbosity:=0}" # ensure non-empty

declare -i verbosity # ensure integer

export verbosity # propagate the verbosity to invoked commands

can_log () { test "$verbosity" -gt 0; } # verbosity=0 turns off all logging

: "${log_indent=  }"

# usage: in func:      inc_log_level; ...

#        outside func: inc_log_level; ...; dec_log_level

alias inc_log_level='declare verbosity="$verbosity" PS4="$log_indent$PS4"

let verbosity--'

alias dec_log_level='declare verbosity="$verbosity" PS4="${PS4#$log_indent}"

let verbosity++'

fi # load new aliases

if self_being_included; then

# usage: (limit_stderr; cmd...) || return

# `|| return` needed on Mac because of bug where -e doesn't apply to ()

limit_stderr () { inc_log_level; if ! can_log; then exec 2>/dev/null; fi; }

limit_stderr_cmd () # usage: [stdout2stderr=1] limit_stderr_cmd cmd...

{

	case "$1" in echo_run) shift; echo_cmd "$@";; esac

	(limit_stderr

		if test -n "$stdout2stderr"; then stdout2stderr; fi

		"$@"

	) || return

}

alias limit_stderr_cmd='limit_stderr_cmd ' # last space alias-expands next word

echo_cmd () { if can_log; then echo "$PS4$*" >&2; fi; }

echo_run () { echo_cmd "$@"; "$@"; }

# auto-echo common external commands

for cmd in rm; do alias "$cmd=echo_run $cmd"; done; unset cmd

# echo all external commands

alias extern="echo_run extern " # last space alias-expands next word

alias self='extern "$FUNCNAME"' # usage: wrapper () { self ...; }

# commands that are always external

for cmd in env; do alias "$cmd=extern $cmd"; done; unset cmd

canon_rel_path ()

{

	local path="$1"

	path="$(realpath "$path")" # canonicalize

	path="${path#$(pwd -P)/}" # remove any shared prefix with the current dir

	echo "$path"

}

fi # load new aliases

if self_being_included; then

function echo_func ()

{

	inc_log_level

	local script="$(canon_rel_path "${BASH_SOURCE[1]}")"

	echo_cmd "$script:${BASH_LINENO[0]}" "${FUNCNAME[1]}" "$@"

}

# usage: cmd1 | { pipe_delay; cmd2; }

alias pipe_delay='sleep 0.1' # s; display after leading output of cmd1

fi # load new aliases

if self_being_included; then

echo_stdin () # usage: input|echo_stdin|cmd

{

	inc_log_level

	if can_log; then

		pipe_delay

		echo ----- >&2

		tee -a /dev/stderr;

		echo ----- >&2

	else cat

	fi

}

echo_vars () # usage: echo_vars var...

{

	inc_log_level; inc_log_level

	if can_log; then

		local var

		for var in "${@%%=*}"; do { echo -n "$PS4"; declare -p "$var";} >&2;done

	fi

}

echo_export ()

{

	builtin export "$@"

	echo_vars "$@"

}

if test "$verbosity" -ge 2; then

	alias export="echo_export" # automatically echo env vars when they are set

fi

usage () { echo "Usage: $1" >&2; (exit 2); }

fi # load new aliases

if self_being_included; then

#### strings

sed_ere_flag="$(test "$(uname)" = Darwin && echo E || echo r)"

sed () { self -"$sed_ere_flag" "$@";}

#### vars

set_var () { eval "$1"'="$2"'; }

set_inv () { set_var no_"$1" "$(test -n "${!1}" || echo 1)"; }

# usage: local var=...; local_inv

alias local_inv='declare "no_$var=$(test -n "${!var}" || echo 1)"'

# usage: local prefix=..._; import_vars

alias import_vars="$(cat <<'EOF'

: "${prefix:?}"

local src_var dest_var

for src_var in $(eval echo '${!'$prefix'*}'); do

	dest_var="${src_var#$prefix}"

	local "$dest_var=${!src_var}"; echo_vars "$dest_var"

done

EOF

)"

#### commands

top_script="$0" # outermost script

top_dir="$(dirname "$top_script")"

# auto-removes a command's output file on error (like make's .DELETE_ON_ERROR)

function to_file () # usage: stdout=... to_file cmd...

{ : "${stdout?}"; log_e "$@" >"$stdout" || { rm "$stdout"; rethrow; }; }

alias to_file='to_file ' # last space alias-expands next word

run_args_cmd () # runs the command line args command

{

	test $? -eq 0 || return

	eval set -- "$(reverse "${BASH_ARGV[@]}")"

	test $# -ge 1 || set -- all

	echo_cmd "$(canon_rel_path "$0")" "$@"; "$@"

}

fwd () # usage: subdirs=(...); fwd "$FUNCNAME" "$@"

{

	echo_func

	: "${subdirs?}"

	for subdir in "${subdirs[@]}"; do

		"$(dirname "${BASH_SOURCE[1]}")"/"$subdir"/run "$@"

	done

}

#### make

# usage: target_filename/command () { echo_func; set_make_vars; ...; }

alias set_make_vars="$(cat <<'EOF'

local command="${FUNCNAME##*/}"; echo_vars command

local target_filename="${FUNCNAME%/*}"; echo_vars target_filename

local target="$top_dir/$target_filename"; echo_vars target

EOF

)"

# usage: set_make_vars; check_target_exists

alias check_target_exists='! test -e "$target" || return 0'

# usage: set_make_vars; to_target cmd...

alias to_target='stdout="$target" to_file ' # last space alias-expands next word

make () { echo_func; stdout2stderr=1 limit_stderr_cmd self "$@"; }

if false; then ## usage:

inline_make 3<<'EOF'

target:

	$(self_dir)/cmd >$@

EOF

# target will be run automatically because it's first in the makefile

fi ##

inline_make ()

{

	echo_func

	local self="$(readlink -f "${BASH_SOURCE[1]}")"

	local self_dir="$(dirname "$self")"

	export self self_dir

	make --makefile=<((

		cat /dev/fd/3

		echo -n "

.SUFFIXES: # turn off built-in suffix rules

.SECONDARY: # don't automatically delete intermediate files

.DELETE_ON_ERROR: # delete target if recipe fails

"

	)|echo_stdin) "$@"

}

#### compression

### zip

zip ()

{

	stdout2stderr=1 try limit_stderr_cmd self "$@"

	ignore 12 # "zip has nothing to do" (`man zip`)

	end_try

}

unzip () { stdout2stderr=1 limit_stderr_cmd self "$@"; }

set_inv force

alias zip_newer='zip ${no_force:+-u }'

alias unzip_newer='unzip ${no_force:+-u }-o'

	# -o is safe because -u only extracts newer files

#### URLs

localize_url () { test _"$1" = _"$(hostname -f)" || echo "$1"; }

#### databases

# using prefixed connection vars

alias use_local='declare prefix=local_; import_vars'

alias use_remote='declare prefix=remote_; import_vars'

alias use_local_remote='use_local; use_remote'

quote='"'

esc_name () { echo "$quote${1//$quote/$quote$quote}$quote"; }

mk_esc_name () { set_var "$1"_esc "$(esc_name "${!1}")"; }

alias mk_schema_esc='declare schema_esc; mk_esc_name schema'

alias mk_table_esc='declare table_esc; mk_esc_name table'

fi # load new aliases

if self_being_included; then

log_sql () { test "$verbosity" -ge 2; }

### MySQL

# auto-adds connection/login opts when specified

mysql_cmd () # usage: mysql* () { ...; mysql_cmd "$@"; }

{

	echo_func

	local ssh_server="$(localize_url "$ssh_server")"

	local server="$(localize_url "$server")"

	if test -n "$ssh_server"; then

		local ssh_dest="${ssh_dest-${ssh_user:+$ssh_user@}$ssh_server}"

	fi

	if test -n "$schema"; then local database="${database-$schema}"; fi

	local var=ssh_dest; local_inv

	extern ${ssh_dest:+ssh "$ssh_dest" }"${FUNCNAME[1]}" \

${server:+ --host="$server" }${user:+--user="$user" } --password\

${password+="$password"} ${database:+--databases "$database" --tables } "$@"

}

mysql () { echo_func; mysql_cmd --verbose "$@"; }

mysql_ANSI ()

{

	echo_func

	(echo "SET sql_mode = 'ANSI';"; cat)|mysql "$@"

}

mysqldump () # usage: [schema=1 | data=1] mysqldump db [table...]

{

	echo_func

	mysql_cmd --quick --lock-tables=false --set-charset \

${postgres_compat:+--compatible=postgresql --add-locks=false }\

${schema:+--no-data }${data:+--no-create-info }"$@"

}

mysqldump_diffable ()

{

	echo_func

	mysqldump "$@"|sed 's/^(-- Dump completed).*$/\1/'

}

### PostgreSQL

pg_copy_to ()

{

	echo_func

	if test -z "$source"; then

		: "${table:?}"; mk_table_esc

		if test -z "$limit"; then local source="$table_esc"

		else local source="(SELECT * FROM $table_esc LIMIT $limit)"

		fi

	fi

	local pg_copy_format="${pg_copy_format-CSV HEADER}"

	psql "$@" <<<"COPY $source TO STDOUT $pg_copy_format;"

}

pg_header ()

{

	echo_func

	local pg_copy_format="CSV HEADER" limit=0

	pg_copy_to "$@"|echo_stdin

}

pg_export_table_no_header ()

{

	echo_func

	local pg_copy_format="CSV"

	pg_copy_to "$@"

}

pg_export_table_to_dir_no_header ()

{

	echo_func

	local table="$1"; shift; mk_table_esc

	local cols="$(pg_header)"

	pg_export_table_no_header "$@" >"$exports_dir/$table.no_header.cols=$cols.csv"

}

fi

. "$(dirname "${BASH_SOURCE[0]}")"/../../lib/sh/local.sh