1
|
#!/usr/bin/env python
|
2
|
# Downloads REMIB data for all nodes
|
3
|
# Usage: env [start=...] [n=...] self
|
4
|
|
5
|
import csv
|
6
|
import itertools
|
7
|
import os.path
|
8
|
import StringIO
|
9
|
import sys
|
10
|
import urllib2
|
11
|
|
12
|
sys.path.append(os.path.dirname(__file__)+"/../../lib")
|
13
|
|
14
|
import exc
|
15
|
import opts
|
16
|
import profiling
|
17
|
import streams
|
18
|
import strings
|
19
|
import timeout
|
20
|
import util
|
21
|
|
22
|
# Config
|
23
|
timeout = 20 # sec
|
24
|
max_consec_empty_responses = 10
|
25
|
|
26
|
alphabet = map(chr, xrange(ord('A'), ord('Z')+1))
|
27
|
|
28
|
class InputException(Exception): pass
|
29
|
|
30
|
class EmptyResponseException(InputException): pass
|
31
|
|
32
|
def is_ignore(line):
|
33
|
line = strings.remove_line_ending(line)
|
34
|
return line == '' or line.startswith('\t') or line.find(',') < 0
|
35
|
|
36
|
def main():
|
37
|
# Get config from env vars
|
38
|
start = util.cast(int, opts.get_env_var('start', 1))
|
39
|
end = util.cast(int, util.none_if(opts.get_env_var('n', None), u''))
|
40
|
if end != None: end += start
|
41
|
|
42
|
log_ = open(sys.argv[0]+'.log', 'a')
|
43
|
def clear_line(): log_.write('\n')
|
44
|
log_indent = 0
|
45
|
def log(msg, line_ending='\n'):
|
46
|
log_.write((' '*log_indent)+msg+line_ending)
|
47
|
|
48
|
os.chdir(os.path.dirname(__file__)) # dir of output files
|
49
|
|
50
|
# Get by family ('familia') because that is the most general level at which
|
51
|
# an identification can be made. This assumes all records have a family.
|
52
|
url_template = ('http://www.conabio.gob.mx/remib/cgi-bin/'
|
53
|
'remib_distribucion.cgi?lengua=EN&niveltax=familia&taxon=[prefix]%25&'
|
54
|
'pais=Todos&pais_otro=&estado=100&formato=csv&mapa=no&mapabase=estados'
|
55
|
'&coleccion=id%3D[node_id]')
|
56
|
|
57
|
if end != None: node_ids = xrange(start, end)
|
58
|
else: node_ids = itertools.count(start)
|
59
|
consec_empty_responses = 0
|
60
|
for node_id in node_ids:
|
61
|
if consec_empty_responses > max_consec_empty_responses: break
|
62
|
|
63
|
log('Processing node #'+str(node_id)+'...')
|
64
|
log_indent += 1
|
65
|
profiler = profiling.ItersProfiler(start_now=True, iter_text='row')
|
66
|
|
67
|
filename = 'node.'+str(node_id)+'.csv'
|
68
|
out = streams.LineCountStream(open(filename, 'w'))
|
69
|
def log_ex(e):
|
70
|
clear_line()
|
71
|
log('! Output line '+str(out.line_num)+': '+exc.str_(e))
|
72
|
start_line_num = out.line_num
|
73
|
node_url_template = url_template.replace('[node_id]', str(node_id))
|
74
|
|
75
|
for prefix_chars in itertools.product(alphabet, repeat=2):
|
76
|
prefix = ''.join(prefix_chars)
|
77
|
log('Processing prefix '+prefix+'...')
|
78
|
row_ct = 0
|
79
|
def print_status(line_ending='\n'):
|
80
|
log('Processed '+str(row_ct)+' row(s)', line_ending)
|
81
|
log_indent += 1
|
82
|
|
83
|
url = node_url_template.replace('[prefix]', prefix)
|
84
|
stream = streams.StreamIter(streams.TimeoutInputStream(
|
85
|
urllib2.urlopen(url), timeout))
|
86
|
|
87
|
is_empty_response = False
|
88
|
try:
|
89
|
util.skip(stream, is_ignore) # skip header
|
90
|
try: metadata_row = csv.reader(stream).next()
|
91
|
except StopIteration: raise EmptyResponseException()
|
92
|
if metadata_row[0] != 'COLLECTION': raise InputException(
|
93
|
'Invalid metadata row: '+str(metadata_row))
|
94
|
|
95
|
# Copy lines
|
96
|
for line in stream:
|
97
|
if is_ignore(line):
|
98
|
error = strings.remove_prefix('\t\t', line)
|
99
|
if len(error) != len(line): raise InputException(error)
|
100
|
break
|
101
|
out.write(line)
|
102
|
|
103
|
row_ct += 1
|
104
|
if row_ct % 100 == 0: print_status('\r')
|
105
|
# CR at end so next print overwrites msg
|
106
|
except EmptyResponseException, e: # must come before InputException
|
107
|
is_empty_response = True
|
108
|
log_ex(e)
|
109
|
break # assume node doesn't exist, so abort node
|
110
|
except InputException, e: log_ex(e)
|
111
|
except timeout.TimeoutException, e:
|
112
|
log_ex(e)
|
113
|
break # assume node is down, so abort node
|
114
|
finally: # still run if break is called
|
115
|
stream.close()
|
116
|
|
117
|
profiler.add_iters(row_ct)
|
118
|
print_status()
|
119
|
log_indent -= 1
|
120
|
|
121
|
if is_empty_response: consec_empty_responses += 1
|
122
|
else: consec_empty_responses = 0 # reset count
|
123
|
|
124
|
profiler.stop()
|
125
|
log(profiler.msg())
|
126
|
log_indent -= 1
|
127
|
|
128
|
main()
|