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#!/usr/bin/env python
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# Downloads REMIB data for all nodes
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# Usage: env [start=...] [n=...] self 2>>log
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import csv
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import itertools
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import os.path
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import StringIO
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import sys
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import urllib2
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sys.path.append(os.path.dirname(__file__)+"/../../../lib")
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import exc
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import opts
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import profiling
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import streams
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import strings
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import timeout
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import util
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timeout_ = 20 # sec
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alphabet = map(chr, xrange(ord('A'), ord('Z')+1))
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class InputException(Exception): pass
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class EmptyResponseException(InputException): pass
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def is_ignore(line):
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line = strings.remove_line_ending(line)
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return line == '' or line.startswith('\t') or line.find(',') < 0
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def main():
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# Get config from env vars
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start = util.cast(int, opts.get_env_var('start', 1))
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end = util.cast(int, util.none_if(opts.get_env_var('n', None), u''))
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if end == None: end = 150 # about 120 nodes listed on the web form
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else: end += start
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def clear_line(): sys.stderr.write('\n')
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log_indent = 0
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def log(msg, line_ending='\n'):
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sys.stderr.write((' '*log_indent)+msg+line_ending)
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os.chdir(os.path.dirname(__file__)) # dir of output files
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# Get by family ('familia') because that is the most general level at which
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# an identification can be made. This assumes all records have a family.
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url_template = ('http://www.conabio.gob.mx/remib/cgi-bin/'
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'remib_distribucion.cgi?lengua=EN&niveltax=familia&taxon=[prefix]%25&'
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'pais=Todos&pais_otro=&estado=100&formato=csv&mapa=no&mapabase=estados'
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'&coleccion=id%3D[node_id]')
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for node_id in xrange(start, end):
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log('Processing node #'+str(node_id)+'...')
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log_indent += 1
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profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
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filename = 'node.'+str(node_id)+'.specimens.csv'
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out = streams.LineCountOutputStream(open(filename, 'w'))
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def log_ex(e):
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clear_line()
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log('! Output line '+str(out.line_num)+': '+exc.str_(e))
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start_line_num = out.line_num
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node_url_template = url_template.replace('[node_id]', str(node_id))
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for prefix_chars in itertools.product(alphabet, repeat=2):
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prefix = ''.join(prefix_chars)
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log('Processing prefix '+prefix+'...')
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row_ct = 0
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def print_status(line_ending='\n'):
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log('Processed '+str(row_ct)+' row(s)', line_ending)
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log_indent += 1
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url = node_url_template.replace('[prefix]', prefix)
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stream = streams.StreamIter(streams.TimeoutInputStream(
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urllib2.urlopen(url), timeout_))
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try:
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util.skip(stream, is_ignore) # skip header
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try: metadata_row = csv.reader(stream).next()
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except StopIteration: raise EmptyResponseException()
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if metadata_row[0] != 'COLLECTION': raise InputException(
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'Invalid metadata row: '+str(metadata_row))
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# Copy lines
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for line in stream:
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if is_ignore(line):
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error = strings.remove_prefix('\t\t', line)
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if len(error) != len(line): raise InputException(error)
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break
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out.write(line)
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row_ct += 1
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if row_ct % 100 == 0: print_status('\r')
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# CR at end so next print overwrites msg
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except EmptyResponseException, e: # must come before InputException
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log_ex(e)
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break # assume node doesn't exist, so abort node
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except InputException, e: log_ex(e)
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except timeout.TimeoutException, e:
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log_ex(e)
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break # assume node is down, so abort node
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finally: # still run if break is called
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stream.close()
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profiler.add_iters(row_ct)
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print_status()
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log_indent -= 1
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profiler.stop()
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log(profiler.msg())
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log_indent -= 1
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main()
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