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Revision 1631

Added inputs/REMIB/src/nodes.all.specimens.csv.make to download REMIB data for all nodes

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inputs/REMIB/src/nodes.all.specimens.csv.make
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#!/usr/bin/env python
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# Downloads REMIB data for all nodes
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# Usage: self
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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 csv
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import profiling
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import streams
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import strings
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import term
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import util
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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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    def clear_line(): sys.stderr.write(term.clear_line)
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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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    stdout = streams.LineCountOutputStream(sys.stdout)
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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(1, 3):
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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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        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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        node_url_template = url_template.replace('[node_id]', str(node_id))
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        for prefix in ['AC']:
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            log('Processing prefix '+prefix+'...')
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            log_indent += 1
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            start_line_num = stdout.line_num
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            url = node_url_template.replace('[prefix]', prefix)
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            stream = streams.StreamIter(urllib2.urlopen(url))
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            util.skip(stream, is_ignore) # skip header
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            metadata_row = csv.reader(stream).next()
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            assert metadata_row[0] == 'COLLECTION'
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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):
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                        clear_line()
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                        log('! Line '+str(stdout.line_num)+': ' +error.rstrip())
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                    break
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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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                stdout.write(line)
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                row_ct += 1
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            stream.close()
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            clear_line()
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            log_indent -= 1
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        profiler.stop(row_ct)
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        print_status()
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        log(profiler.msg())
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        if stdout.line_num == start_line_num: line_range = '<none>'
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        else: line_range = str(start_line_num)+'-'+str(stdout.line_num-1)
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        log('Used output lines '+line_range)
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        log_indent -= 1
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main()
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