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5079
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aaronmk
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#!/usr/bin/env python
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# Scrubs the taxonpaths in VegBIEN using TNRS.
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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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pause = 60 # sec
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max_pause = 2*60*60 # sec; = 2 hr; must be >= max import time of one partition
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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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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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5098
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aaronmk
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tnrs_profiler = profiling.ItersProfiler(iter_text='row')
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try:
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# Iterate over unscrubbed verbatim taxonpaths
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start = 0
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5079
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aaronmk
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total_pause = 0
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5098
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aaronmk
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while True:
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# Fetch next set
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cur = sql.select(db, 'taxonpath', ['taxonomicnamewithauthor'],
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5121
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aaronmk
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[('canon_taxonpath_id', None)], limit=tnrs.max_names,
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5101
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aaronmk
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start=start, cacheable=False)
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5098
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aaronmk
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this_ct = cur.rowcount
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start += this_ct # advance start to fetch next set
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if this_ct == 0:
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total_pause += pause
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if total_pause > max_pause: break
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log('Waited '+str(total_pause)+' sec. Waiting...')
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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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total_pause = 0
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5121
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aaronmk
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names = list(sql.values(cur))
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5098
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aaronmk
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# Run TNRS
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5100
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aaronmk
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log('Processing '+str(this_ct)+' taxonpaths')
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5098
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aaronmk
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log('Making TNRS request')
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tnrs_profiler.start()
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try:
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5121
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aaronmk
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try: stream = tnrs.repeated_tnrs_request(names)
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5098
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aaronmk
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finally: tnrs_profiler.stop(iter_ct=this_ct)
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5099
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aaronmk
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except tnrs.InvalidResponse: pass # skip set in case it caused error
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5098
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aaronmk
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else:
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log('Storing TNRS response data')
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stream_info = csvs.stream_info(stream, parse_header=True)
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stream = streams.ProgressInputStream(stream, sys.stderr, n=1000)
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sql_io.append_csv(db, tnrs_data, stream_info, stream)
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finally:
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log(tnrs_profiler.msg())
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| 82 |
5079
|
aaronmk
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main()
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