Project

General

Profile

« Previous | Next » 

Revision 9518

Added by Aaron Marcuse-Kubitza over 11 years ago

bin/tnrs_db: removed no longer used $wait flag (which caused tnrs_db to wait max_pause for new rows to be added), because tnrs_db is now invoked automatically after each import by the import_scrub target (in inputs/input.Makefile) and does not need to run as a daemon. note that when scrub is invoked, it is possible that a previous datasource's import has already scrubbed the names for this import, because tnrs_db runs until all rows in tnrs_input_name are scrubbed.

this also removes clutter in tnrs_db, making it clearer what operations it performs that the library function tnrs.repeated_tnrs_request() does not (namely, interfacing with the DB and profiling the TNRS request).

View differences:

inputs/.TNRS/tnrs/tnrs.make
1 1 
#!/bin/bash
2 2 
# Runs tnrs_db on VegBIEN
3 
# Usage: make inputs/.TNRS/tnrs/tnrs-remake [log=] [wait=1]
3 
# Usage: make inputs/.TNRS/tnrs/tnrs-remake [log=]
4 4 

  		




  5
  5
  
    
# Handle being run as a .make script


  		




  6
  6
  
    
exec >&2


  		












  

    
      bin/tnrs_db
    
  





  1
  1
  
    
#!/usr/bin/env python


  		




  2
  2
  
    
# Scrubs the taxonlabels in VegBIEN using TNRS.


  		




  3
  
  
    
# Runs continuously until no new rows are added after max_pause.


  		




  4
  3
  
    

  		




  5
  4
  
    
import os.path


  		




  6
  5
  
    
import StringIO


  		




  ......




  20
  19
  
    
import strings


  		




  21
  20
  
    
import tnrs


  		




  22
  21
  
    

  		




  23
  
  
    
# Config


  		




  24
  
  
    
pause = 2*60*60 # sec; = 2 hr


  		




  25
  
  
    
max_pause = 9*60*60 # sec; = 9 hr; must be >= max partition import time (1.5 hr)


  		




  26
  
  
    
assert pause <= max_pause


  		




  27
  
  
    

  		




  28
  22
  
    
tnrs_input = sql_gen.Table('tnrs_input_name')


  		




  29
  23
  
    
tnrs_data = sql_gen.Table('tnrs')


  		




  30
  24
  
    

  		




  ......




  33
  27
  
    
    env_names = []


  		




  34
  28
  
    
    db_config = opts.get_env_vars(sql.db_config_names, None, env_names)


  		




  35
  29
  
    
    verbosity = float(opts.get_env_var('verbosity', 3, env_names))


  		




  36
  
  
    
    wait = opts.env_flag('wait', False, env_names)


  		




  37
  30
  
    
    if not 'engine' in db_config: raise SystemExit('Usage: '


  		




  38
  31
  
    
        +opts.env_usage(env_names)+' '+sys.argv[0]+' 2>>log')


  		




  39
  32
  
    
    


  		




  ......




  48
  41
  
    
    tnrs_profiler = profiling.ItersProfiler(iter_text='name')


  		




  49
  42
  
    
    


  		




  50
  43
  
    
    # Iterate over unscrubbed verbatim taxonlabels


  		




  51
  
  
    
    total_pause = 0


  		




  52
  44
  
    
    while True:


  		




  53
  45
  
    
        # Fetch next set


  		




  54
  46
  
    
        cur = sql.select(db, tnrs_input, limit=tnrs.max_names, cacheable=False)


  		




  55
  47
  
    
        this_ct = cur.rowcount


  		




  56
  48
  
    
        log('Processing '+str(this_ct)+' taxonlabels')


  		




  57
  
  
    
        if this_ct == 0:


  		




  58
  
  
    
            if not wait: break


  		




  59
  
  
    
            log('Waited '+str(total_pause)+' sec total')


  		




  60
  
  
    
            total_pause += pause


  		




  61
  
  
    
            if total_pause > max_pause: break


  		




  62
  
  
    
            log('Waiting '+str(pause)+' sec...')


  		




  63
  
  
    
            time.sleep(pause) # wait for more rows


  		




  64
  
  
    
            continue # try again


  		




  
  49
  
    
        if this_ct == 0: break


  		




  65
  50
  
    
        # otherwise, rows found


  		




  66
  
  
    
        total_pause = 0


  		




  67
  51
  
    
        names = list(sql.values(cur))


  		




  68
  52
  
    
        


  		




  69
  53
  
    
        def process():


  		












Also available in:  Unified diff