| 1 |
1674
|
aaronmk
|
#!/usr/bin/env python
|
| 2 |
|
|
# A DiGIR client
|
| 3 |
|
|
|
| 4 |
1678
|
aaronmk
|
import os
|
| 5 |
1674
|
aaronmk
|
import os.path
|
| 6 |
|
|
import sys
|
| 7 |
|
|
import urllib
|
| 8 |
|
|
import urllib2
|
| 9 |
1690
|
aaronmk
|
import xml.dom.minidom as minidom
|
| 10 |
1674
|
aaronmk
|
|
| 11 |
|
|
sys.path.append(os.path.dirname(__file__)+"/../lib")
|
| 12 |
|
|
|
| 13 |
1678
|
aaronmk
|
import dates
|
| 14 |
1697
|
aaronmk
|
import http
|
| 15 |
1674
|
aaronmk
|
import opts
|
| 16 |
1699
|
aaronmk
|
import profiling
|
| 17 |
1674
|
aaronmk
|
import streams
|
| 18 |
|
|
import util
|
| 19 |
1709
|
aaronmk
|
import xml_parse
|
| 20 |
1690
|
aaronmk
|
import xpath
|
| 21 |
1674
|
aaronmk
|
|
| 22 |
|
|
# Config
|
| 23 |
|
|
timeout = 20 # sec
|
| 24 |
1692
|
aaronmk
|
default_chunk_size = 10000 # records
|
| 25 |
1674
|
aaronmk
|
|
| 26 |
1692
|
aaronmk
|
schema = 'http://digir.net/schema/conceptual/darwin/full/2003/1.0/darwin2full.xsd'
|
| 27 |
1674
|
aaronmk
|
request_xml_template = '''\
|
| 28 |
|
|
<?xml version="1.0" encoding="UTF-8"?>
|
| 29 |
|
|
<request
|
| 30 |
|
|
xmlns="http://digir.net/schema/protocol/2003/1.0"
|
| 31 |
|
|
xmlns:xsd="http://www.w3.org/2001/XMLSchema"
|
| 32 |
|
|
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
| 33 |
|
|
xmlns:digir="http://digir.net/schema/protocol/2003/1.0"
|
| 34 |
|
|
xmlns:darwin="http://digir.net/schema/conceptual/darwin/2003/1.0"
|
| 35 |
|
|
xmlns:dwc="http://digir.net/schema/conceptual/darwin/2003/1.0"
|
| 36 |
|
|
xsi:schemaLocation="http://digir.net/schema/protocol/2003/1.0
|
| 37 |
|
|
http://digir.sourceforge.net/schema/protocol/2003/1.0/digir.xsd
|
| 38 |
|
|
http://digir.net/schema/conceptual/darwin/2003/1.0
|
| 39 |
|
|
http://digir.sourceforge.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd">
|
| 40 |
|
|
<header>
|
| 41 |
|
|
<version>1.0</version>
|
| 42 |
1678
|
aaronmk
|
<sendTime>[time]</sendTime>
|
| 43 |
|
|
<source>[source]</source>
|
| 44 |
1674
|
aaronmk
|
<destination resource="[resource]">[url]</destination>
|
| 45 |
|
|
<type>search</type>
|
| 46 |
|
|
</header>
|
| 47 |
|
|
<search>
|
| 48 |
|
|
<filter>
|
| 49 |
1675
|
aaronmk
|
<equals>
|
| 50 |
1678
|
aaronmk
|
<darwin:Kingdom>plantae</darwin:Kingdom>
|
| 51 |
1675
|
aaronmk
|
</equals>
|
| 52 |
1674
|
aaronmk
|
</filter>
|
| 53 |
|
|
<records limit="[count]" start="[start]">
|
| 54 |
1679
|
aaronmk
|
<structure schemaLocation="[schema]"/>
|
| 55 |
1674
|
aaronmk
|
</records>
|
| 56 |
|
|
<count>true</count>
|
| 57 |
|
|
</search>
|
| 58 |
|
|
</request>
|
| 59 |
|
|
'''
|
| 60 |
|
|
|
| 61 |
1683
|
aaronmk
|
diags_start = '<diagnostics>'
|
| 62 |
|
|
diags_end = '</diagnostics>'
|
| 63 |
|
|
|
| 64 |
1690
|
aaronmk
|
class InputError(Exception): pass
|
| 65 |
1685
|
aaronmk
|
|
| 66 |
1674
|
aaronmk
|
def main():
|
| 67 |
1690
|
aaronmk
|
# Usage
|
| 68 |
1674
|
aaronmk
|
env_names = []
|
| 69 |
|
|
def usage_err():
|
| 70 |
|
|
raise SystemExit('Usage: '+opts.env_usage(env_names, True)+' '
|
| 71 |
|
|
+sys.argv[0]+' 2>>log')
|
| 72 |
|
|
|
| 73 |
|
|
# Get config from env vars
|
| 74 |
|
|
url = opts.get_env_var('url', None, env_names)
|
| 75 |
|
|
resource = opts.get_env_var('resource', None, env_names)
|
| 76 |
|
|
start = util.cast(int, opts.get_env_var('start', 0, env_names))
|
| 77 |
1690
|
aaronmk
|
count = util.cast(int, opts.get_env_var('n', None, env_names))
|
| 78 |
1692
|
aaronmk
|
chunk_size = util.cast(int, opts.get_env_var('chunk_size',
|
| 79 |
|
|
default_chunk_size, env_names))
|
| 80 |
1678
|
aaronmk
|
debug = opts.env_flag('debug', False, env_names)
|
| 81 |
1674
|
aaronmk
|
if url == None or resource == None: usage_err()
|
| 82 |
|
|
|
| 83 |
1690
|
aaronmk
|
# Logging
|
| 84 |
1678
|
aaronmk
|
def clear_line(): sys.stderr.write('\n')
|
| 85 |
|
|
log_indent = 0
|
| 86 |
1691
|
aaronmk
|
def log(msg, line_ending='\n'): sys.stderr.write(msg+line_ending)
|
| 87 |
1685
|
aaronmk
|
def debug_log(str_, label=None):
|
| 88 |
|
|
if debug:
|
| 89 |
|
|
if label != None: sys.stderr.write(label+':\n')
|
| 90 |
|
|
sys.stderr.write(str_+'\n')
|
| 91 |
1674
|
aaronmk
|
|
| 92 |
1690
|
aaronmk
|
# Request XML
|
| 93 |
1678
|
aaronmk
|
self_dir = os.path.dirname(__file__)
|
| 94 |
|
|
source = os.popen(self_dir+"/local_ip").read().strip()
|
| 95 |
|
|
this_request_xml_template = (request_xml_template
|
| 96 |
|
|
.replace('[source]', source)
|
| 97 |
|
|
.replace('[url]', url)
|
| 98 |
|
|
.replace('[resource]', resource)
|
| 99 |
1679
|
aaronmk
|
.replace('[schema]', schema)
|
| 100 |
1678
|
aaronmk
|
)
|
| 101 |
|
|
|
| 102 |
1690
|
aaronmk
|
# Stats
|
| 103 |
|
|
total = 0
|
| 104 |
|
|
def print_status(line_ending='\n'):
|
| 105 |
|
|
log('Processed '+str(total)+' record(s)', line_ending)
|
| 106 |
|
|
match_ct = None
|
| 107 |
1674
|
aaronmk
|
|
| 108 |
1699
|
aaronmk
|
profiler = profiling.ItersProfiler(start_now=True, iter_text='record')
|
| 109 |
|
|
|
| 110 |
1690
|
aaronmk
|
# Retrieve data
|
| 111 |
|
|
while count == None or total < count:
|
| 112 |
1691
|
aaronmk
|
# Adjust chunk size if last chunk
|
| 113 |
1695
|
aaronmk
|
this_count = chunk_size
|
| 114 |
|
|
if count != None: this_count = min(this_count, count - total)
|
| 115 |
1691
|
aaronmk
|
|
| 116 |
1690
|
aaronmk
|
# Request XML
|
| 117 |
|
|
time = dates.strftime('%Y-%m-%d %H:%M:%S %Z', dates.now())
|
| 118 |
|
|
request_xml = (this_request_xml_template
|
| 119 |
1695
|
aaronmk
|
.replace('[count]', str(this_count))
|
| 120 |
1690
|
aaronmk
|
.replace('[start]', str(start))
|
| 121 |
|
|
.replace('[time]', time)
|
| 122 |
|
|
)
|
| 123 |
|
|
debug_log(request_xml, 'request')
|
| 124 |
|
|
|
| 125 |
|
|
# Send request
|
| 126 |
|
|
this_url = url+'?'+urllib.urlencode({'request': request_xml})
|
| 127 |
|
|
stream = streams.CaptureStream(streams.TimeoutInputStream(
|
| 128 |
|
|
urllib2.urlopen(this_url), timeout), diags_start, diags_end)
|
| 129 |
|
|
|
| 130 |
|
|
# Retrieve response
|
| 131 |
|
|
streams.copy(stream, sys.stdout)
|
| 132 |
1692
|
aaronmk
|
# Make sure output ends in a newline so that consecutive XML documents
|
| 133 |
|
|
# are on different lines
|
| 134 |
|
|
sys.stdout.write('\n')
|
| 135 |
1690
|
aaronmk
|
stream.close()
|
| 136 |
|
|
|
| 137 |
|
|
# Parse diagnostics
|
| 138 |
1706
|
aaronmk
|
diags_str = stream.matches[0]
|
| 139 |
1690
|
aaronmk
|
debug_log(diags_str, 'diagnostics')
|
| 140 |
1709
|
aaronmk
|
diags = xml_parse.parse_str(diags_str)
|
| 141 |
1690
|
aaronmk
|
def get_diag(name):
|
| 142 |
|
|
return xpath.get_value(diags, 'diagnostic[@code='+name+']')
|
| 143 |
|
|
|
| 144 |
|
|
# Process match count
|
| 145 |
|
|
this_match_ct = util.cast(int, get_diag('MATCH_COUNT'))
|
| 146 |
|
|
if this_match_ct != match_ct: # first or updated match count
|
| 147 |
|
|
match_ct = this_match_ct
|
| 148 |
|
|
log('Found '+str(match_ct)+' record(s)')
|
| 149 |
|
|
|
| 150 |
|
|
# Process record count
|
| 151 |
|
|
this_ct = util.cast(int, get_diag('RECORD_COUNT'))
|
| 152 |
|
|
if this_ct == None: raise InputError('Missing RECORD_COUNT diagnostic')
|
| 153 |
|
|
total += this_ct
|
| 154 |
|
|
start += this_ct # advance start to fetch next set
|
| 155 |
|
|
print_status('\r') # CR at end so next print overwrites msg
|
| 156 |
1695
|
aaronmk
|
|
| 157 |
|
|
# Decide if done
|
| 158 |
1690
|
aaronmk
|
if this_ct == 0 or get_diag('END_OF_RECORDS') == 'true': break
|
| 159 |
1687
|
aaronmk
|
|
| 160 |
1690
|
aaronmk
|
print_status()
|
| 161 |
1699
|
aaronmk
|
profiler.stop(total)
|
| 162 |
|
|
log(profiler.msg())
|
| 163 |
1674
|
aaronmk
|
|
| 164 |
|
|
main()
|
