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prepare.py
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#!/usr/bin/env python
from collections import Counter
from urlparse import urlparse
import argparse
import time
import urllib2
import arrow
import sys
import re
import json
from bs4 import BeautifulSoup
from math import radians, cos, sin, asin, sqrt
import os
import sys
from lib.Atlas import ProbeInfo
import fetch_news_sites
# One-off traceroute msm cost
COST_OF_TRACEROUTE = 60
# Number of Alexa top sites to be included in the analysis
# Maximum is 50
TOP_ALEXA_SITES = 25
## find connected probes
MEASUREMENT_TYPES = {
'probe-mesh',
'traceroute',
'http-traceroute',
'https-traceroute',
'local-news-traceroute',
'local-tld-traceroute',
}
GEONAMES_USER=None
authfile = "%s/.geonames/auth" % os.path.dirname(os.path.realpath(__file__) )
if not os.path.exists(authfile):
print >>sys.stderr, ("Geonames authentication file %s not found" % authfile)
sys.exit(1)
auth = open(authfile)
GEONAMES_USER = auth.readline()[:-1]
auth.close()
GEONAMES_USER.rstrip()
sources = {}
dests = {}
def country_stats( cc ):
stats = {}
stats['routed_asns'] = routed_asns_for_country(cc)
# add more stats here?
return stats
def routed_asns_for_country( cc ):
## find country routing stats
routed_asns = None
yyyymmdd = arrow.now().format('YYYY-MM-01')
routed_asns_url = "https://stat.ripe.net/data/country-routing-stats/data.json?resource=%s&starttime=%s&endtime=%s" % (cc, yyyymmdd, yyyymmdd )
try:
conn = urllib2.urlopen( routed_asns_url )
info = json.load (conn )
routed_asns = info['data']['stats'][0]['asns_ris'] # should really be one
except:
print >>sys.stderr, "problem getting routed ASNs for '%s' from RIPEstat" % ( cc )
return routed_asns
def get_asns( cand_list ):
nums = set()
for asn_cand in cand_list:
matched = re.match(r'\s*(?:AS)?(\d+)\s*$', asn_cand.upper())
if matched:
asnum = matched.group(1)
nums.add( int(asnum) )
# some kind of clinchers to distinguish from lists of low numbers
if len(nums) <= len( cand_list ) / 4:
#print "num / cand_list %s/%s : %s" % ( len(nums) , len(cand_list), nums )
return False
# sanity-check, to see if a column is not just something with low numbers. woodynet/AS42 is always there ;)
if max(nums) < 42: return []
return nums
def haversine_km(lat1,lon1,lat2,lon2):
"""
http://stackoverflow.com/questions/4913349/haversine-formula-in-python-bearing-and-distance-between-two-gps-points
Calculate the great circle distance between two points
on the earth (specified in decimal degrees)
"""
# convert decimal degrees to radians
lon1, lat1, lon2, lat2 = map(radians, [lon1, lat1, lon2, lat2])
# haversine formula
dlon = lon2 - lon1
dlat = lat2 - lat1
a = sin(dlat/2)**2 + cos(lat1) * cos(lat2) * sin(dlon/2)**2
c = 2 * asin(sqrt(a))
km = 6367 * c
return km
def find_probes_in_country(cc, eyeball=False, threshold=90):
probes = {}
base_url = (
'http://data.labs.apnic.net/ipv6-measurement/Economies/{}/{}.asns.json'
)
coverage = 0
if cc:
if eyeball:
url = base_url.format(cc, cc)
eyeball_distribution = json.loads(urllib2.urlopen(url).read())
for asn in eyeball_distribution:
if coverage >= threshold:
break
probes.update(ProbeInfo.query(country_code=cc, asn_v4=asn['as'], is_public=True))
probes.update(ProbeInfo.query(country_code=cc, asn_v6=asn['as'], is_public=True))
coverage += asn['percent']
else:
probes = ProbeInfo.query(country_code=cc, is_public=True)
else:
probes = ProbeInfo.query(is_public=True)
'''
asns_v4 = Counter()
asns_v6 = Counter()
for prb_id in probes:
if probes[prb_id]['asn_v4'] != None:
asns_v4[ probes[prb_id]['asn_v4'] ] += 1
if probes[prb_id]['asn_v6'] != None:
asns_v6[ probes[prb_id]['asn_v6'] ] += 1
return asns_v4,asns_v6,probes
'''
return probes
def do_probe_selection_from_tag( tag ):
probes = ProbeInfo.query(tags=tag, status=1)
return map( _to_probedata, probes.values() )
def do_probe_selection_from_ids( ids ):
probes = ProbeInfo.query(id__in=ids, status=1)
return map( _to_probedata, probes.values() )
def do_probe_selection( probes, conf, basedata ):
probes_per_asn={}
for prb_id in probes:
prb_info = probes[prb_id]
print >>sys.stderr, "%s" % (prb_info)
status = prb_info['status']
## down probes are not useful:
if status != 1:
continue
## Exclude probes with system tag IPv4 or IPv4 not working
if("system-ipv4-works" not in probes[prb_id]['tags'] and "system-ipv6-works" not in probes[prb_id]['tags']):
continue
### we want the set of probes that is stable enough
stable_tag_cnt = len( filter( lambda x: x.startswith('system-ipv4-stable-') or x.startswith('system-ipv6-stable-'), probes[prb_id]['tags'] ) )
if stable_tag_cnt == 0:
continue
#if("system-ipv4-stable-1d" not in probes[prb_id]['tags'] and "system-ipv6-stable-1d" not in probes[prb_id]['tags']):
# continue
## probes with auto-geoloc have unreliable geolocation :( :( :(
if 'tags' in prb_info and 'system-auto-geoip-country' in prb_info['tags']:
print >>sys.stderr, "EEPS system-auto-geoip-country %s" % ( prb_id )
continue
dists = {}
loc_close_enough = False ## this is only for location-constrained
for loc in basedata['locations']:
loclat = basedata['locations'][loc]['lat']
loclon = basedata['locations'][loc]['lon']
dists[ loc ] = haversine_km( loclat, loclon, prb_info['latitude'], prb_info['longitude'] )
if 'location-constraint' in basedata:
if dists[ loc ] < basedata['location-constraint']:
loc_close_enough = True
if 'location-constraint' in basedata and loc_close_enough == False:
# don't put this probe in the list of probes to consider
# it is too far from any of the locations we consider
continue
# feed the distance back into the 'probes' data struct too
probes[prb_id]['dists'] = dists
### TODO deal with too far away probes
asn = prb_info['asn_v4']
### TODO fix cases where
if asn == None:
print >>sys.stderr, "no ASN for probe?!,what's up RIPE Atlas backend?. %s" % ( prb_info )
continue
if not asn in probes_per_asn:
probes_per_asn[ asn ] = []
probes_per_asn[ asn ].append({
'dists': dists,
'prb_id': prb_id,
'status': prb_info['status']
})
selected_probes = []
asn_count = 0
asn_multiprobe_count = 0
selected_asn_set = set()
selected_asn_probes = {} ## probe IDs per ASN for selected probes
## stats
prb_per_asn_distr = {}
for asn in probes_per_asn:
asn_count += 1
selected_asn_set.add( asn )
selected_asn_probes[asn] = set()
### in principle this selects the closest and furthest probe for each of the list of locations
if len( probes_per_asn[asn] ) <= 2*len( basedata['locations'] ):
# not enough probes for the fancy selection, just select them all
for prb in probes_per_asn[asn]:
selected_asn_probes[asn].add( prb['prb_id'] )
else: ## we need to do fancy selections
for loc in basedata['locations']:
loc_sorted = sorted( probes_per_asn[asn], key=lambda k: k['dists'][ loc ] )
selected_asn_probes[asn].add(loc_sorted[0]['prb_id'])
selected_asn_probes[asn].add(loc_sorted[-1]['prb_id'])
asn_multiprobe_count += 1
print "AS%s %s" % ( asn, list(selected_asn_probes[asn]) )
prb_per_asn = len(selected_asn_probes[asn])
if not prb_per_asn in prb_per_asn_distr:
prb_per_asn_distr[ prb_per_asn ] = 0
prb_per_asn_distr[ prb_per_asn ] += 1
for p in selected_asn_probes[asn]:
selected_probes.append( p )
'''
print "member ASN set size: %s\n(%s)" % ( len( member_asn_set ), member_asn_set )
overlap_asns = selected_asn_set.intersection( member_asn_set )
print "overlap member+country ASN set: %s\n(%s)" % ( len( overlap_asns ) , overlap_asns )
selected_nonmember_asns = selected_asn_set.difference( member_asn_set )
print "In selection, but not member: %s\n(%s)" % ( len( selected_nonmember_asns ), selected_nonmember_asns )
nonselected_member_asns = member_asn_set.difference( selected_asn_set )
print "Member, but not in selection: %s\n(%s)" % ( len( nonselected_member_asns ), nonselected_member_asns )
print "selected asncount: %s, multiprobe: %s\n(%s)" % ( asn_count, asn_multiprobe_count, selected_asn_set )
print ' '.join(["--add=%s" % (x) for x in selected_probes ])
'''
if len(prb_per_asn_distr.keys()) == 0:
return []
# print some stats
print "distribution of probes per ASN:"
for i in range(1,1+max( prb_per_asn_distr.keys() )):
count = 0
try: count = prb_per_asn_distr[ i ]
except: pass
plural = 's'
if count==1:
plural = ''
print " ASNs with %s probe%s: %s" % ( i , plural, count )
outdata = []
for prb_id in selected_probes:
outdata.append( _to_probedata( probes[prb_id] ) )
return outdata
def _to_probedata( prb_dict ):
struct = {
'probe_id': prb_dict['id'],
'asn_v4': prb_dict['asn_v4'],
'asn_v6': prb_dict['asn_v6'],
'address_v4': prb_dict['address_v4'],
'address_v6': prb_dict['address_v6'],
'country_code': prb_dict['country_code'],
'description': prb_dict['description']
}
try:
if 'latitude' in prb_dict: #v1 api, or a shim pretending to be v1 api:
struct['lat'] = prb_dict['latitude']
struct['lon'] = prb_dict['longitude']
struct['tags'] = prb_dict['tags']
else:
struct['lat'] = prb_dict['geometry']['coordinates'][1]
struct['lon'] = prb_dict['geometry']['coordinates'][0]
struct['tags'] = map(lambda x: x['slug'], prb_dict['tags'] )
if 'dists' in prb_dict:
struct['dists'] = prb_dict['dists']
except:
print prb_dict
raise
return struct
def get_memberlist( murl ):
try:
url = urllib2.Request( murl )
conn = urllib2.urlopen( url )
except:
print "eeps"
if murl.endswith('.json'):
return get_memberlist_json( conn )
else:
return get_memberlist_html_table( conn )
def get_memberlist_json( conn ):
try:
data = json.load( conn )
except:
print >>sys.stderr, "reading json failed"
return None
memberlist = []
if 'member_list' in data:
for mem in data['member_list']:
if 'asnum' in mem:
memberlist.append( mem['asnum'] )
return memberlist
def get_memberlist_html_table( conn ):
soup = BeautifulSoup(conn)
tables = soup.find_all('table')
#print >>sys.stderr, "found %s tables in html" % ( len( tables ) )
max_table=None
max_table_len=0
for t in tables:
if len( str(t) ) > max_table_len:
max_table = t
max_table_len = len( str(t) )
## use the max-size table
rows = max_table.findAll('tr')
col_idx=0
asn_col = None
name_col = None
url_col = None
asns = []
while True:
col_vals = []
# deal with headers properly
#for row in rows[1:]:
for row in rows:
try:
#print row
#print row.findAll('td')
col_val = row.findAll('td')[col_idx].text
col_vals.append( col_val )
except: pass
if len( col_vals ) > 0:
are_asns = get_asns( col_vals )
if are_asns > 0:
asn_col = col_idx
asns = are_asns
#print "asns: %s" % ( are_asns )
#print "len %d" % ( len( are_asns ) )
else:
break
col_idx += 1
return asns
## probably make this blacklist configurable
alexa_blacklist = set([
'xhamster.com',
'pornhub.com',
'xvideos.com',
'xnxx.com',
'bongacams.com'
])
def alexa_country_top25( countries ):
for cc in countries:
targets = []
targetsitenames = []
al_url= "http://www.alexa.com/topsites/countries/%s" % ( cc )
req = urllib2.urlopen( al_url )
# when alexa changes layout this needs to change too
soup = BeautifulSoup( req )
tr = soup.findAll('div', class_='td DescriptionCell')
targetsites = 0
for t in tr:
site = t.find('a').string.lower()
if site in alexa_blacklist:
print >>sys.stderr, "this alexa-top site for country:%s was blocked by ixp-country-jedi blacklist: %s" % ( cc, site )
print >>sys.stderr, "please adapt the blacklist (in source code) if you want this site measured anyways"
continue
# Check if the site is a duplicate (e.g. google.com, google.ru)
site_elements = site.split(".")
sitename = site_elements[0]
if sitename in targetsitenames:
print >>sys.stderr, "this site for country:%s is a duplicate: %s" % ( cc, site )
else:
targetsitenames.append(sitename)
## add 'www'?
if targetsites < TOP_ALEXA_SITES:
targets.append( site )
targetsites = targetsites + 1
print >>sys.stderr, "WARNING: when using alexa-country-top25 lists, some sites may be considered offensive"
print >>sys.stderr, "WARNING: please consider looking at the 'targets' list in basedata.json and see if any of the sites"
print >>sys.stderr, "WARNING: that are going to be measured to might be offensive. Please be considerate to our RIPE Atlas Probe hosts"
print >>sys.stderr, "Targets found: %s\n" % ( '\n'.join( targets ) )
time.sleep( 5 )
return targets
def hitlist_from_websites( urls ):
'''
Get list of hostnames from a list of urls
See for example: http://www.top.ge/cat.php?c=2&where=Government%2C+Ministries%2C+Departments
Or: http://en.wikipedia.org/wiki/List_of_banks_in_Georgia_%28country%29
'''
targets = set()
for url in urls:
req_urlp = urlparse( url )
req = urllib2.urlopen( url )
soup = BeautifulSoup( req )
for link in soup.findAll('a', href=True):
ex_url=link['href']
ex_urlp = urlparse( ex_url )
# remove all but full-qualified urls (get rid of website internal stuff typically)
if not ex_urlp.scheme in ('http','https'):
continue
if ex_urlp.hostname == req_urlp.hostname:
continue
# remove everything that has url-path (typically website internal stuff)
if ex_urlp.path not in ('','/'):
continue
targets.add( ex_urlp.hostname )
print >>sys.stderr, "WARNING: when using alexa-country-top25 lists, some sites may be considered offensive"
print >>sys.stderr, "WARNING: please consider looking at the 'targets' list in basedata.json and see if any of the sites"
print >>sys.stderr, "WARNING: that are going to be measured to might be offensive. Please be considerate to our RIPE Atlas Probe hosts"
print >>sys.stderr, "Targets found: %s\n" % ( '\n'.join( targets ) )
time.sleep( 5 )
return list(targets)
def capital_city_for_country( country_code ):
'''
Use world bank API to return Capital city for a given country-code
Example: returns 'Jakarta,ID' if country_code=='ID'.
'''
try:
#wb_url = "http://api.worldbank.org/countries/%s/?format=json" % ( country_code.lower() )
wb_url = "https://api.worldbank.org/v2/countries/%s/?format=json" % ( country_code.lower() )
req = urllib2.urlopen( wb_url )
resp = json.loads(req.read())
lat = float(resp[1][0]['latitude'])
lon = float(resp[1][0]['longitude'])
name = "%s,%s" % ( resp[1][0]['capitalCity'], country_code )
return (name,lat,lon)
except:
raise ValueError("can't get capital city for '%s' from WorldBank API" % ( country_code ) )
def locstr2latlng( locstring ):
try:
locstr = urllib2.quote( locstring )
geocode_url = "http://api.geonames.org/searchJSON?q=%s&maxRows=10&username=%s" % ( locstr, GEONAMES_USER )
req = urllib2.urlopen(geocode_url)
resp = json.loads(req.read())
if 'error_message' in resp:
raise SystemExit("Maps geocode error: %s" % resp['error_message'])
ll = resp['geonames'][0]
return (float(ll['lat']), float(ll['lng']))
except (ValueError, IndexError):
print "could not determine lat/long for '%s'" % ( locstring )
pass
def extract_websites_in_tld(country_code, max_results=100):
"""Given a TLD, fetch a list of the top websites in this TLD for use as
targets"""
base_url = ("https://domainpunch.com/tlds/topm.php?dtd&draw=3"
"&columns[0][data]=0&columns[0][name]=&columns[0][searchable]=true"
"&columns[0][orderable]=false&columns[0][search][value]="
"&columns[0][search][regex]=false&columns[1][data]=1&columns[1][name]="
"&columns[1][searchable]=true&columns[1][orderable]=true"
"&columns[1][search][value]=&columns[1][search][regex]=false"
"&columns[2][data]=2&columns[2][name]=&columns[2][searchable]=true"
"&columns[2][orderable]=true&columns[2][search][value]="
"&columns[2][search][regex]=false&columns[3][data]=3&columns[3][name]="
"&columns[3][searchable]=true&columns[3][orderable]=true"
"&columns[3][search][value]={}&columns[3][search][regex]=false"
"&columns[4][data]=4&columns[4][name]=&columns[4][searchable]=true"
"&columns[4][orderable]=true&columns[4][search][value]="
"&columns[4][search][regex]=false&order[0][column]=2&order[0][dir]=asc"
"&start=0&length={}&search[value]=&search[regex]=false"
).format(country_code.lower(), max_results)
websites = json.loads(urllib2.urlopen(base_url).read())
return [website['1'] for website in websites['data']]
def calculate_cost_of_measurement(selected_probes):
## Calculate the number of IPv4 and IPv6 addresses
number_of_addresses = {"ipv4" : 0, "ipv6" : 0}
for probe in selected_probes:
if('address_v4' in probe and probe['address_v4'] != None and "system-ipv4-stable-1d" in probe['tags']):
number_of_addresses['ipv4'] += 1
if('address_v6' in probe and probe['address_v6'] != None and "system-ipv6-stable-1d" in probe['tags']):
number_of_addresses['ipv6'] += 1
credits_ipv4 = ( int(number_of_addresses['ipv4']) * (int(number_of_addresses['ipv4'])) ) * COST_OF_TRACEROUTE
credits_ipv6 = ( int(number_of_addresses['ipv6']) * (int(number_of_addresses['ipv6'])) ) * COST_OF_TRACEROUTE
print "* * *\nThe IXP Country Jedi will consume " + str(credits_ipv4+credits_ipv6) + " credits,"
print str(credits_ipv4) + " and " + str(credits_ipv6) + " for IPv4 and IPv6 measurements, respectively. \n * * *"
def main( args ):
member_asn_set = set()
if args.memberlist_url:
member_asn_set = set( get_memberlist( args.memberlist_url ) )
probe_asns_v4,probe_asns_v6,probes = find_probes_in_country( args.country )
selected_probes = do_probe_selection( probes, args, member_asn_set )
if __name__ == '__main__':
with open('./config.json','r') as conffile:
conf = json.load( conffile )
basedata = { # aux info we want saved
'locations': {}, ## locations keyed by name
'ixps': {}, ## IXPs keyed by name
'countries': [], ## countries by iso code
'country-stats': {}, ## various stats per country
'measurement-types': [], ## list of measurements we do
'targets': [], ## list of targets (if not probe-mesh)
} ## auxiliary info that we want saved
####
# country / or other probe selection
####
####### would be nice if we could do both country+probetag
has_sources = False
if 'country' in conf:
# 'list'-ify country
if type( conf['country'] ) != list:
basedata['countries'] = [ conf['country'] ]
else:
basedata['countries'] = conf['country']
# uppercase all
basedata['countries'] = map(lambda x:x.upper(), basedata['countries'])
####
# stats per country
####
for cc in basedata['countries']:
basedata['country-stats'][ cc ] = country_stats( cc )
has_sources = True
if 'probetag' in conf:
# selects probes with certain probetag and looks at their connectivity
basedata['probetag'] = conf['probetag']
has_sources = True
if 'probe_ids' in conf:
basedata['probe_ids'] = conf['probe_ids']
has_sources = True
if not has_sources:
print >>sys.stderr, "need 'country' and/or 'probetag' or a list of probe ids ('probe_ids')"
sys.exit(1)
####
# measurement-types
####
if 'measurement-type' in conf:
if type( conf['measurement-type'] ) != list :
conf['measurement-type'] = [ conf['measurement-type'] ]
for mtype in conf['measurement-type']:
if not mtype in MEASUREMENT_TYPES:
print >> sys.stderr, "measurement-type '%s' not supported (supported types: %s)" % (mtype, MEASUREMENT_TYPES)
sys.exit(1)
else:
basedata['measurement-types'].append( mtype )
### probably need better syntax checking etc. here
else:
## maybe make default 'http-traceroute' if 'targets' is defined?
basedata['measurement-types'] = ['probe-mesh']
####
# targets
####
if 'targets' in conf:
if type( conf['targets'] ) == list:
basedata['targets'] = conf['targets']
else:
print >> sys.stderr, "config has 'targets', but that is not a list"
elif 'target-type' in conf:
if conf['target-type'] == 'alexa-country-top25':
basedata['targets'] = alexa_country_top25( basedata['countries'] )
elif conf['target-type'] == 'local-news-traceroute' in conf['measurement-type']:
pages = fetch_news_sites.fetch_country_pages()
basedata['targets'] = [urlparse(url).hostname for url in
fetch_news_sites.news_sites_for_country(pages[conf['country']])]
elif 'local-tld-traceroute' in conf['measurement-type']:
basedata['targets'] = extract_websites_in_tld(conf['country'])
else:
print >> sys.stderr, "unknown target-type of '%s' in config, bailing out"
sys.exit(1)
elif 'targets-from-websites' in conf:
if type(conf['targets-from-websites']) != list:
print >> sys.stderr, "unknown 'targets-from-websites' needs to be a list, baling out"
sys.exit(1)
basedata['targets'] = hitlist_from_websites( conf['targets-from-websites'] )
####
# locations (only applies when 'countries' is in basedata
####
## If no location present, select the capital of the first country in list
if len(basedata['countries']) > 0:
print basedata
if not 'locations' in conf or len( conf['locations'] ) == 0:
capital_str,lat,lon = capital_city_for_country( basedata['countries'][0] )
print >> sys.stderr, "No location info available for probe selection, defaulting to capital city of country (%s)" % ( capital_str )
basedata['locations'][ capital_str ] = {'lat': lat, 'lon': lon}
else:
for loc in conf['locations']:
lat,lon = locstr2latlng( loc )
basedata['locations'][ loc ] = {'lat': lat, 'lon': lon}
# 'constrain to only the probes X km from the location
if 'location-constraint' in conf:
basedata['location-constraint'] = conf['location-constraint']
### IXPs
if 'ixps' in conf:
for ixp in conf['ixps']:
basedata['ixps'][ ixp['name'] ] = {
'peeringlans': ixp['peeringlans']
}
if 'memberlist' in ixp:
member_asn_set = get_memberlist( ixp['memberlist'] )
print member_asn_set
basedata['ixps'][ ixp['name'] ]['memberlist'] = ixp['memberlist']
basedata['ixps'][ ixp['name'] ]['memberlist_asns'] = sorted( list( member_asn_set ) )
else:
# get them all?
# get them for countries, or if no country specified, get them all?
pass
if os.path.isfile('probeset.json'):
print >>sys.stderr, "probeset.json file exists, not making a new probe selection"
else:
selected_probes = []
if 'probetag' in basedata and len(basedata['countries']) > 0:
## only take probes in these countries
country_set = set( basedata['countries'] )
print >>sys.stderr, "finding probes for tag: %s AND countries: %s" % ( basedata['probetag'], country_set )
selected_probes = do_probe_selection_from_tag( basedata['probetag'] )
selected_probes = filter( lambda x: x['country_code'] in country_set, selected_probes )
elif len(basedata['countries']) > 0:
for country in basedata['countries']:
eyeball_threshold = conf.get('eyeball_threshold')
print >>sys.stderr, "Preparing country: %s" % ( country )
if eyeball_threshold:
probes_cc = find_probes_in_country(country, True, eyeball_threshold)
else:
probes_cc = find_probes_in_country( country )
print >>sys.stderr, "preselected %d probes for %s" % ( len( probes_cc ), country )
sel_probes_for_cc = do_probe_selection( probes_cc, conf, basedata )
print >>sys.stderr, "selected %d probes for %s" % ( len(sel_probes_for_cc), country )
selected_probes += sel_probes_for_cc
print >>sys.stderr, "found: %d probes" % ( len( sel_probes_for_cc ) )
print >>sys.stderr, "END country: %s" % ( country )
# If there are probes manually selected in config.json, add them as well
if 'probe_ids' in basedata:
probes_from_ids = []
selected_probeids = []
print >>sys.stderr, "Adding probes from probe_ids list"
for sel_prb in selected_probes:
selected_probeids.append(sel_prb['probe_id'])
probes_from_ids = do_probe_selection_from_ids( basedata['probe_ids'] )
# Add probes from probe_ids without duplicates
for prb in probes_from_ids:
if prb['probe_id'] not in selected_probeids:
selected_probes.append(prb)
elif 'probetag' in basedata:
print >>sys.stderr, "finding probes for tag: %s" % ( basedata['probetag'] )
selected_probes = do_probe_selection_from_tag( basedata['probetag'] )
elif 'probe_ids' in basedata:
print >>sys.stderr, "finding probes for probe_ids list"
selected_probes = do_probe_selection_from_ids( basedata['probe_ids'] )
print >>sys.stderr, "found %s probes!" % ( len( selected_probes ) )
## estimate the cost of measurement
calculate_cost_of_measurement(selected_probes)
## writing to probeset.json
print "writing probe selection to probeset.json (%s probes)" % ( len( selected_probes ) )
with open('probeset.json','w') as outfile:
json.dump( selected_probes, outfile, indent=2 )
print >>sys.stderr, "writing basedata (locations/ixps) to basedata.json"
with open('./basedata.json','w') as bdfile:
json.dump( basedata, bdfile, indent=2 )