Revision 12968
Added by Aaron Marcuse-Kubitza almost 11 years ago
| trunk/inputs/test_taxonomic_names/_scrub/run | ||
|---|---|---|
| 9 | 9 |
|
| 10 | 10 |
exports/make() |
| 11 | 11 |
{
|
| 12 |
echo_func
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|
| 12 |
begin_target
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|
| 13 | 13 |
(schema=public.$schema |
| 14 | 14 |
cols=(taxonverbatim_id taxonlabel_id taxonname); \ |
| 15 | 15 |
pg_export_tables_to_dir taxonverbatim |
| ... | ... | |
| 23 | 23 |
|
| 24 | 24 |
export_() |
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{
|
| 26 |
echo_func
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|
| 27 |
exports/make |
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| 26 |
begin_target
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|
| 27 |
with_rm exports/make
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|
| 28 | 28 |
} |
| 29 | 29 |
|
| 30 | 30 |
fi |
| trunk/inputs/.geoscrub/geoscrub_output/geoscrub.csv.run | ||
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| 7 | 7 |
|
| 8 | 8 |
export_() # usage: rm=1 .../self.run export_ |
| 9 | 9 |
{
|
| 10 |
echo_func
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|
| 10 |
begin_target
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local_export database=geoscrub table=geoscrub \ |
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cols='decimallatitude,decimallongitude,country,stateprovince,county,countrystd'\ |
| 13 | 13 |
',stateprovincestd,countystd,latlonvalidity,countryvalidity,'\ |
| ... | ... | |
| 17 | 17 |
|
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make() # usage: rm=1 .../self.run make |
| 19 | 19 |
{
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| 20 |
echo_func
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|
| 20 |
begin_target
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|
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local input_path="$(canon_rel_path "$root_dir/exports/geoscrub_input.csv")" |
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DATAFILE="$(basename "$input_path")" command \ |
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"$root_dir/derived/biengeo/geoscrub.sh" \ |
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--geoscrub-input="$(dirname "$input_path")" |
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# runtime: 2.5 h ("21:24:02" - "19:04:58")
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export_ |
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with_rm export_
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|
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} |
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|
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# upload time: 30 s ("0:00:29")
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|
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all() # usage: rm=1 .../self.run |
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{
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echo_func
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| 34 |
make |
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begin_target
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with_rm make
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} |
| 36 | 36 |
|
| 37 | 37 |
fi |
| trunk/inputs/GBIF/_MySQL/run | ||
|---|---|---|
| 16 | 16 |
|
| 17 | 17 |
load_data() # usage: [database=GBIF_new] load_data |
| 18 | 18 |
{
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| 19 |
echo_func
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begin_target
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| 20 | 20 |
|
| 21 | 21 |
use_local_remote |
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database= mysql_root <<EOF |
| ... | ... | |
| 33 | 33 |
|
| 34 | 34 |
import() |
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{
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echo_func
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|
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begin_target
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| 37 | 37 |
top_make |
| 38 | 38 |
} |
| 39 | 39 |
|
| trunk/inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql.run | ||
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| 6 | 6 |
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| 7 | 7 |
cleanup() # makes the SQL suitable for PostgreSQL |
| 8 | 8 |
{
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| 9 |
echo_func
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|
| 9 |
begin_target
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| 10 | 10 |
echo_run in_place "$top_file" $sed_cmd \ |
| 11 | 11 |
-e 's! (BOOLEAN) ! /*\1*/INTEGER !' \ |
| 12 | 12 |
-e 's! (DOUBLE PRECISION) (NULL) ! \1 /*\2*/ !' |
| ... | ... | |
| 14 | 14 |
|
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all() |
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{
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| 17 |
echo_func
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| 18 |
cleanup |
|
| 17 |
begin_target
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with_rm cleanup
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|
| 19 | 19 |
} |
| 20 | 20 |
|
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fi |
| trunk/inputs/FIA/_src/run | ||
|---|---|---|
| 6 | 6 |
|
| 7 | 7 |
import() |
| 8 | 8 |
{
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| 9 |
echo_func
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"$top_dir"/download |
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| 9 |
begin_target
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| 10 |
with_rm "$top_dir"/download
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|
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} |
| 12 | 12 |
|
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fi |
| trunk/inputs/VegBank/verify/input_cols.include.txt.run | ||
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| 6 | 6 |
|
| 7 | 7 |
filter() |
| 8 | 8 |
{
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echo_func
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|
| 9 |
begin_target
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<"${top_file/.include./.}" echo_run filter_out_cs 0 \
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| 11 | 11 |
<(sed 's/ #.*$//' "${top_file/.include./.exclude.}") >"$top_file"
|
| 12 | 12 |
} |
| 13 | 13 |
|
| 14 | 14 |
all() |
| 15 | 15 |
{
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echo_func
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filter |
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begin_target
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with_rm filter
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| 18 | 18 |
} |
| 19 | 19 |
|
| 20 | 20 |
fi |
| trunk/inputs/VegBank/verify/input_cols.exclude.txt.run | ||
|---|---|---|
| 6 | 6 |
|
| 7 | 7 |
filter() |
| 8 | 8 |
{
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| 9 |
echo_func
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|
| 9 |
begin_target
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<"${top_file/.exclude./.}" echo_run grep -F -e '--' -e '#'\
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| 11 | 11 |
|sed 's/^OMIT#.*$/& # included as part of another table/' >"$top_file" |
| 12 | 12 |
} |
| 13 | 13 |
|
| 14 | 14 |
all() |
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{
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echo_func
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| 17 |
filter |
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begin_target
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with_rm filter
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| 18 | 18 |
} |
| 19 | 19 |
|
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fi |
| trunk/schemas/VegCore/VegCore.pg.sql.run | ||
|---|---|---|
| 7 | 7 |
|
| 8 | 8 |
install() |
| 9 | 9 |
{
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| 10 |
echo_func
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begin_target
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|
| 11 | 11 |
root_make schemas/temp/reinstall |
| 12 | 12 |
psql_script_vegbien <"$top_file" |
| 13 | 13 |
} |
| 14 | 14 |
|
| 15 | 15 |
all() |
| 16 | 16 |
{
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| 17 |
echo_func
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| 18 |
install |
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| 17 |
begin_target
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| 18 |
with_rm install
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| 19 | 19 |
} |
| 20 | 20 |
|
| 21 | 21 |
fi |
| trunk/schemas/VegCore/ERD/VegCore.ERD.mwb.run | ||
|---|---|---|
| 31 | 31 |
|
| 32 | 32 |
export_mysql() |
| 33 | 33 |
{
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| 34 |
echo_func
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| 35 |
../VegCore.my.sql/make |
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| 34 |
begin_target
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with_rm ../VegCore.my.sql/make
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} |
| 37 | 37 |
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| 38 | 38 |
../VegCore.pg.sql/make() |
| ... | ... | |
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|
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export_postgres() |
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{
|
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echo_func
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| 47 |
../VegCore.pg.sql/make |
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begin_target
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with_rm ../VegCore.pg.sql/make
|
|
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} |
| 49 | 49 |
|
| 50 | 50 |
export_() |
| 51 | 51 |
{
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| 52 |
echo_func
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|
| 52 |
begin_target
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| 53 | 53 |
(cd "$top_dir"; unzip_newer "$top_filename" document.mwb.xml) |
| 54 |
export_mysql |
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| 55 |
export_postgres |
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| 54 |
with_rm export_mysql
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with_rm export_postgres
|
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} |
| 57 | 57 |
|
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import() |
| 59 | 59 |
{
|
| 60 |
echo_func
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|
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begin_target
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(cd "$top_dir"; zip_newer "$top_filename" document.mwb.xml) |
| 62 | 62 |
} |
| 63 | 63 |
|
| 64 | 64 |
sync() |
| 65 | 65 |
{
|
| 66 |
echo_func
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|
| 67 |
export_ |
|
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begin_target
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| 67 |
with_rm export_
|
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import |
| 69 | 69 |
} |
| 70 | 70 |
|
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all() |
| 72 | 72 |
{
|
| 73 |
echo_func
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| 74 |
sync |
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| 73 |
begin_target
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with_rm sync
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} |
| 76 | 76 |
|
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fi |
| trunk/schemas/VegCore/ERD/VegCore.ERD.png.map.htm.run | ||
|---|---|---|
| 35 | 35 |
|
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all() |
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{
|
| 38 |
echo_func
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|
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cleanup |
|
| 40 |
header.htm/make |
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begin_target
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with_rm cleanup
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with_rm header.htm/make
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} |
| 42 | 42 |
|
| 43 | 43 |
fi |
| trunk/run | ||
|---|---|---|
| 17 | 17 |
|
| 18 | 18 |
export_() |
| 19 | 19 |
{
|
| 20 |
echo_func
|
|
| 21 |
taxon_trait/make |
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| 22 |
"$exports_dir"/geoscrub_input.csv.run export_ |
|
| 20 |
begin_target
|
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with_rm taxon_trait/make
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| 22 |
with_rm "$exports_dir"/geoscrub_input.csv.run export_
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|
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} |
| 24 | 24 |
|
| 25 | 25 |
fi |
| trunk/exports/2013-10-18.Brian_Enquist.Canadensys.csv.run | ||
|---|---|---|
| 5 | 5 |
|
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func_override export___extract_run |
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export_() # runtime: 35 min ("04:08:45" - "03:33:40")
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| 8 |
{ echo_func; export___extract_run "$@"; }
|
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{ begin_target; with_rm export___extract_run "$@"; }
|
|
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|
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on_exit |
| trunk/lib/runscripts/data.pg.sql.run | ||
|---|---|---|
| 7 | 7 |
|
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func_override export___file.pg.sql.run |
| 9 | 9 |
export_() # usage: rm=1 .../file.run export_ |
| 10 |
{ echo_func; data=1 export___file.pg.sql.run; }
|
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| 10 |
{ begin_target; data=1 with_rm export___file.pg.sql.run; }
|
|
| 11 | 11 |
|
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fi |
| trunk/lib/runscripts/util.run | ||
|---|---|---|
| 83 | 83 |
,() # usage: .../run , cmd1 cmd2 ... (like `make cmd1 cmd2 ...`) |
| 84 | 84 |
# treats each of the command-line args as commands the way make does |
| 85 | 85 |
# (instead of as args to the same command, the way runscripts do) |
| 86 |
{ echo_func; for cmd in "$@"; do time echo_run "$cmd"; done; }
|
|
| 86 |
{ begin_target; for cmd in "$@"; do time with_rm echo_run "$cmd"; done; }
|
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| 87 | 87 |
|
| 88 | 88 |
: "${auto_ignore=}" #usage: auto_ignore=1 .../__.run target_that_might_not_exist
|
| 89 | 89 |
unexport auto_ignore # don't pass this to invoked scripts except through fwd() |
| trunk/lib/runscripts/table.run | ||
|---|---|---|
| 7 | 7 |
func_override import__table_run |
| 8 | 8 |
import() |
| 9 | 9 |
{
|
| 10 |
echo_func
|
|
| 10 |
begin_target
|
|
| 11 | 11 |
before_import_cmds |
| 12 | 12 |
with_rm import__table_run "$@" |
| 13 | 13 |
after_import_cmds |
| trunk/lib/runscripts/pg.conf.run | ||
|---|---|---|
| 8 | 8 |
|
| 9 | 9 |
install() |
| 10 | 10 |
{
|
| 11 |
echo_func
|
|
| 11 |
begin_target
|
|
| 12 | 12 |
root_make postgres_reload |
| 13 | 13 |
} |
| 14 | 14 |
|
| trunk/lib/runscripts/mysql.table.run | ||
|---|---|---|
| 38 | 38 |
|
| 39 | 39 |
export_mysql() |
| 40 | 40 |
{
|
| 41 |
echo_func
|
|
| 42 |
table.tsv/make |
|
| 41 |
begin_target
|
|
| 42 |
with_rm table.tsv/make
|
|
| 43 | 43 |
} |
| 44 | 44 |
|
| 45 | 45 |
archive="$top_dir"/_archive/ |
| trunk/lib/runscripts/import_subset.run | ||
|---|---|---|
| 8 | 8 |
|
| 9 | 9 |
all() # usage: inputs=(inputs/{src1,src2,...}/); ...
|
| 10 | 10 |
{
|
| 11 |
echo_func; : "${inputs:?}"
|
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| 11 |
begin_target; : "${inputs:?}"
|
|
| 12 | 12 |
require_dot_script || return |
| 13 | 13 |
|
| 14 | 14 |
backup= . "$bin_dir"/import_all |
| trunk/lib/runscripts/schema.pg.sql.run | ||
|---|---|---|
| 7 | 7 |
|
| 8 | 8 |
func_override export___file.pg.sql.run |
| 9 | 9 |
export_() # usage: rm=1 .../file.run export_ |
| 10 |
{ echo_func; struct=1 export___file.pg.sql.run "$@"; }
|
|
| 10 |
{ begin_target; struct=1 with_rm export___file.pg.sql.run "$@"; }
|
|
| 11 | 11 |
|
| 12 | 12 |
fi |
| trunk/lib/runscripts/install.run | ||
|---|---|---|
| 6 | 6 |
|
| 7 | 7 |
install() |
| 8 | 8 |
{
|
| 9 |
echo_func
|
|
| 9 |
begin_target
|
|
| 10 | 10 |
install_cmds |
| 11 | 11 |
} |
| 12 | 12 |
fi #### |
| ... | ... | |
| 17 | 17 |
|
| 18 | 18 |
install() |
| 19 | 19 |
{
|
| 20 |
echo_func
|
|
| 20 |
begin_target
|
|
| 21 | 21 |
} |
| 22 | 22 |
|
| 23 | 23 |
all() |
| 24 | 24 |
{
|
| 25 |
echo_func
|
|
| 26 |
install |
|
| 25 |
begin_target
|
|
| 26 |
with_rm install
|
|
| 27 | 27 |
} |
| 28 | 28 |
|
| 29 | 29 |
fi |
| trunk/lib/runscripts/extract.run | ||
|---|---|---|
| 12 | 12 |
table="$extract_view" to_top_file pg_export |
| 13 | 13 |
} |
| 14 | 14 |
|
| 15 |
export_sample() { echo_func; n=100 export_; }
|
|
| 15 |
export_sample() { begin_target; n=100 with_rm export_; }
|
|
| 16 | 16 |
|
| 17 | 17 |
fi |
| trunk/lib/runscripts/import.run | ||
|---|---|---|
| 6 | 6 |
|
| 7 | 7 |
import() |
| 8 | 8 |
{
|
| 9 |
echo_func
|
|
| 9 |
begin_target
|
|
| 10 | 10 |
import_cmds |
| 11 | 11 |
} |
| 12 | 12 |
fi #### |
| ... | ... | |
| 17 | 17 |
|
| 18 | 18 |
import() |
| 19 | 19 |
{
|
| 20 |
echo_func
|
|
| 20 |
begin_target
|
|
| 21 | 21 |
} |
| 22 | 22 |
|
| 23 | 23 |
export_() |
| 24 | 24 |
{
|
| 25 |
echo_func
|
|
| 25 |
begin_target
|
|
| 26 | 26 |
} |
| 27 | 27 |
|
| 28 | 28 |
all() |
| 29 | 29 |
{
|
| 30 |
echo_func
|
|
| 30 |
begin_target
|
|
| 31 | 31 |
import |
| 32 |
export_ |
|
| 32 |
with_rm export_
|
|
| 33 | 33 |
} |
| 34 | 34 |
|
| 35 | 35 |
fi |
| trunk/lib/sh/resume_import.sh | ||
|---|---|---|
| 79 | 79 |
|
| 80 | 80 |
resume_import() # usage: [pos=#] resume_import |
| 81 | 81 |
{
|
| 82 |
echo_func; kw_params pos
|
|
| 82 |
begin_target; kw_params pos
|
|
| 83 | 83 |
if ! isset pos; then local pos; pos="$(import_resume_pos)"; fi |
| 84 | 84 |
|
| 85 | 85 |
^.preamble.sql/make |
| trunk/web/links/index.htm.run | ||
|---|---|---|
| 7 | 7 |
|
| 8 | 8 |
clean_up() |
| 9 | 9 |
{
|
| 10 |
echo_func
|
|
| 10 |
begin_target
|
|
| 11 | 11 |
command in_place "$top_file" repl \ |
| 12 | 12 |
"$root_dir"/lib/Firefox_bookmarks.reformat.csv |
| 13 | 13 |
command in_place "$top_file" $sed_cmd \ |
| ... | ... | |
| 18 | 18 |
|
| 19 | 19 |
all() |
| 20 | 20 |
{
|
| 21 |
echo_func
|
|
| 21 |
begin_target
|
|
| 22 | 22 |
clean_up |
| 23 | 23 |
} |
| 24 | 24 |
|
Also available in: Unified diff
*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)