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Revision 14762

Added by Aaron Marcuse-Kubitza over 9 years ago

fix: lib/sh/util.sh: already_exists_msg(): changed calling convention to avoid it seeming like `return 0` is run if already_exists_msg() throws an error, when in fact already_exists_msg() is just a command that should be run before returning/errexiting

View differences:

trunk/inputs/GBIF/raw_occurrence_record_plants/run
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 `institution_code` varchar(255) NOT NULL PRIMARY KEY
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) ENGINE=MyISAM DEFAULT CHARSET=utf8 COMMENT='from IH.vegpath.org?&Index+Herbariorum'
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EOF
31 
) || skip_table || return 0
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) || { skip_table; return 0; }
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	append=1 mysql_import <"$top_dir"/herbaria_filter.ih.csv_
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}
34 34 

  		




  ......




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 KEY `plant_fraction` (`plant_fraction`)


  		




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) ENGINE=MyISAM DEFAULT CHARSET=utf8


  		




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EOF


  		




  48
  
  
    
) || table=plant_fraction skip_table || return 0


  		




  
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) || { table=plant_fraction skip_table; return 0; }


  		




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	mysql <<EOF


  		




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INSERT INTO "plant_fraction"


  		




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SELECT


  		




  ......




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SELECT * FROM `plant_fraction`


  		




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WHERE plant_fraction >= 0.8


  		




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EOF


  		




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) || table=plant_fraction_for_herbaria_filter skip_table || return 0


  		




  
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) || { table=plant_fraction_for_herbaria_filter skip_table; return 0; }


  		




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}


  		




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herbaria_filter/make() # runtime: ~0 ("0m2.235s"): CSV import, index scans only


  		




  ......




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 `institution_code` varchar(255) NOT NULL PRIMARY KEY


  		




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) ENGINE=MyISAM DEFAULT CHARSET=utf8


  		




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EOF


  		




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) || skip_table || return 0


  		




  
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) || { skip_table; return 0; }


  		




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	mysql <<EOF


  		




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INSERT IGNORE INTO $table


  		




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SELECT institution_code FROM ih_herbarium


  		




  ......




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	OR  (family LIKE '%aceae%' OR family IN ('Compositae','Gramineae','Palmae','Guttiferae','Cruciferae','Labiatae','Umbelliferae','Leguminosae'))


  		




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)


  		




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EOF


  		




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) || skip_table || return 0


  		




  
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) || { skip_table; return 0; }


  		




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}


  		




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# table.tsv.gz/upload() runtime: 15 min ("2184253533 100% 2.30MB/s 0:15:03")


  		












  

    
      trunk/lib/runscripts/table.run
    
  





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table_make_install()


  		




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{


  		




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	echo_func


  		




  34
  
  
    
	if ! remaking && pg_table_exists; then skip_table || return 0; fi


  		




  
  34
  
    
	if ! remaking && pg_table_exists; then skip_table; return 0; fi


  		




  35
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	local install_log="${install_log-$top_dir/$install_log_rel}"


  		




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	local verbosity_min= # install logs require default verbosity


  		




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	if ! remaking && test -e "$install_log"; then local_export noclobber=1; fi


  		












  

    
      trunk/lib/sh/util.sh
    
  





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#### commands


  		




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already_exists_msg() # usage: cond || what=... already_exists_msg || return 0


  		




  
  1294
  
    
already_exists_msg()


  		




  
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# usage: cond || { save_e; what=_ already_exists_msg; rethrow; } || return 0


  		




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{


  		




  1296
  
  
    
	save_e # needed because $(mk_hint) resets $?


  		




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	type=info die "$what already exists, skipping


  		




  
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	log_info "$what already exists, skipping


  		




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$(mk_hint 'to force-remake, prepend `rm=1` to the command')"


  		




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}


  		




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  1300
  
    

  		




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require_not_exists() # usage: require_not_exists file || return 0


  		




  1302
  
  
    
{ test ! -e "$1" || what="file \"$1\"" already_exists_msg; }


  		




  
  1302
  
    
{ test ! -e "$1" || { save_e; what="file \"$1\"" already_exists_msg; rethrow;} }


  		




  1303
  1303
  
    

  		




  1304
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function to_file() # usage: stdout=... [if_not_exists=1] [del=] to_file cmd...


  		




  1305
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# auto-removes a command's output file on error (like make's .DELETE_ON_ERROR)


  		












  

    
      trunk/lib/sh/db.sh
    
  





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fi # load new aliases


  		




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if self_being_included; then


  		




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skip_table() # usage: create_table || table=... skip_table || return 0


  		




  
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skip_table() # usage: create_table || { table=... skip_table; return 0; }


  		




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{ what="table $table" already_exists_msg; }


  		




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: "${test=$(isset limit; exit2bool)}" # test mode when using limited # rows


  		












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