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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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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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5737
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aaronmk
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import dates
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5079
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aaronmk
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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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5669
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aaronmk
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tnrs_input = sql_gen.Table('tnrs_input_name')
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5079
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aaronmk
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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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5124
|
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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9515
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aaronmk
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while True:
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5123
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aaronmk
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# Fetch next set
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5837
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aaronmk
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cur = sql.select(db, tnrs_input, limit=tnrs.max_names, 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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9518
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aaronmk
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if this_ct == 0: break
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5123
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aaronmk
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# otherwise, rows found
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names = list(sql.values(cur))
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9515
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aaronmk
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def process():
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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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9520
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aaronmk
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try: stream = tnrs.tnrs_request(names)
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9515
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aaronmk
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finally:
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9521
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aaronmk
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tnrs_profiler.stop(iter_ct=len(names))
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9515
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aaronmk
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log('Cumulatively: '+tnrs_profiler.msg())
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log('Storing TNRS response data')
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9517
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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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9516
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aaronmk
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# start transaction *before* submitting data, so Time_submitted is
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# correctly set to the submission time rather than the insertion time.
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# these may differ by several minutes if TNRS is slow.
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sql.with_savepoint(db, process)
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5079
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aaronmk
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main()
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