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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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9530
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aaronmk
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# to estimate total runtime:
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# bin/psql_vegbien <<<'SELECT COUNT(*) FROM tnrs_input_name'
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# # names from above * 1.5 multiplier for scrubbing accepted names
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# (the test_taxonomic_names sample from Brad produces 8 accepted names for
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# 15 input names)
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# * ((# ms/name from log file * 1 sec/1000 ms) + (# sec to run
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# `SELECT * FROM "tnrs_input_name"` in log file / tnrs.max_names names/batch))
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# * 1 hr / 3600 sec * 1 day / 24 hr = # days
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5079
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aaronmk
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import os.path
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import sys
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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 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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9522
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aaronmk
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cumulative_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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9526
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aaronmk
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stream = tnrs.tnrs_request(names,
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cumulative_profiler=cumulative_tnrs_profiler)
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9515
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aaronmk
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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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