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5079
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aaronmk
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#!/usr/bin/env python
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5640
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aaronmk
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# Scrubs the taxonlabels in VegBIEN using TNRS.
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5079
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aaronmk
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# Runs continuously until no new rows are added after max_pause.
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import os.path
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import StringIO
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import sys
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import time
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sys.path.append(os.path.dirname(__file__)+"/../lib")
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import csvs
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import opts
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5098
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aaronmk
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import profiling
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5079
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aaronmk
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import sql
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import sql_gen
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import sql_io
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import streams
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import strings
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import tnrs
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# Config
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5156
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aaronmk
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pause = 2*60*60 # sec; = 2 hr
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max_pause = 9*60*60 # sec; = 9 hr; must be >= max partition import time (1.5 hr)
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5079
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aaronmk
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assert pause <= max_pause
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tnrs_data = sql_gen.Table('tnrs')
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def main():
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# Input
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env_names = []
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db_config = opts.get_env_vars(sql.db_config_names, None, env_names)
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verbosity = float(opts.get_env_var('verbosity', 3, env_names))
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5214
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aaronmk
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wait = opts.env_flag('wait', False, env_names)
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5079
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aaronmk
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if not 'engine' in db_config: raise SystemExit('Usage: '
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+opts.env_usage(env_names)+' '+sys.argv[0]+' 2>>log')
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def log(msg, level=1):
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'''Higher level -> more verbose'''
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if level <= verbosity:
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sys.stderr.write(strings.to_raw_str(msg.rstrip('\n')+'\n'))
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# Connect to DB
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db = sql.connect(db_config, log_debug=log)
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5124
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aaronmk
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tnrs_profiler = profiling.ItersProfiler(iter_text='name')
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5123
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aaronmk
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5640
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aaronmk
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# Iterate over unscrubbed verbatim taxonlabels
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5123
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aaronmk
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total_pause = 0
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5640
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aaronmk
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tables = ['taxonlabel', sql_gen.Join('tnrs',
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5159
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aaronmk
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{'Name_submitted': 'identifyingtaxonomicname'}, sql_gen.filter_out)]
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5643
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aaronmk
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cols = ['identifyingtaxonomicname']
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5159
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aaronmk
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# Has a concatenated name and not already linked to an accepted name
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conds = [('identifyingtaxonomicname', sql_gen.CompareCond(None, '!=')),
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5640
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aaronmk
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('matched_label_id', None)]
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5123
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aaronmk
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while True:
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# Fetch next set
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5643
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aaronmk
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cur = sql.select(db, tables, cols, conds, cols, limit=tnrs.max_names,
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cacheable=False)
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5123
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aaronmk
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this_ct = cur.rowcount
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5640
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aaronmk
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log('Processing '+str(this_ct)+' taxonlabels')
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5123
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aaronmk
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if this_ct == 0:
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5213
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aaronmk
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if not wait: break
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5212
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aaronmk
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log('Waited '+str(total_pause)+' sec total')
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5123
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aaronmk
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total_pause += pause
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if total_pause > max_pause: break
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5212
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aaronmk
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log('Waiting '+str(pause)+' sec...')
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5123
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aaronmk
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time.sleep(pause) # wait for more rows
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continue # try again
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# otherwise, rows found
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5079
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aaronmk
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total_pause = 0
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5123
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aaronmk
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names = list(sql.values(cur))
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# Run TNRS
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log('Making TNRS request')
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tnrs_profiler.start()
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try:
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try: stream = tnrs.repeated_tnrs_request(names)
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finally:
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tnrs_profiler.stop(iter_ct=this_ct)
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log('Cumulatively: '+tnrs_profiler.msg())
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except tnrs.InvalidResponse: pass # skip set in case it caused error
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else:
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log('Storing TNRS response data')
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5590
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aaronmk
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sql_io.append_csv(db, tnrs_data, *csvs.reader_and_header(stream))
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5079
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aaronmk
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main()
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