# TNRS

import re

import sys

import time

import urllib2

import streams

# Config

initial_pause = 0.35 # sec

pause_growth_factor = 1.3

max_pause = 600 # sec; = 10 min

assert initial_pause <= max_pause

max_taxons = 5000# according to http://tnrs.iplantcollaborative.org/TNRSapp.html

max_taxons = 500 # the maximum above crashes the TNRS server

max_tries = 5

# Protocol params

url_base = 'http://tnrs.iplantcollaborative.org/tnrsdemo/'

url = url_base+'search'

initial_headers = {

    'Content-Type': 'text/x-gwt-rpc; charset=utf-8',

    'X-GWT-Module-Base': url_base,

    'X-GWT-Permutation': '574AA16D15D917C7704646FD92AFF6B3',

}

submission_request_template = ('7|0|7|'+url_base+

'||org.iplantc.tnrs.demo.client.SearchService|doSearch|\

java.lang.String/2004016611|{"sources":"gcc,tropicos,usda", "names":"[taxons]"\

, "type":"matching", "taxonomic":"true", "classification":"tropicos", \

"match_to_rank":"true"}|0.05|1|2|3|4|2|5|5|6|7|')

submission_response_pattern = r'^//OK\[1,\["(\w+)"\],0,7\]$'

retrieval_request_template = ('7|0|15|'+url_base+

'|1E87C78041CEFBF0992F46BDF84D7D60|org.iplantc.tnrs.demo.client.SearchService\

|getRemoteData|com.extjs.gxt.ui.client.data.PagingLoadConfig|\

java.lang.String/2004016611|com.extjs.gxt.ui.client.data.BasePagingLoadConfig/\

2011366567|com.extjs.gxt.ui.client.data.RpcMap/3441186752|sortField|sortDir|\

com.extjs.gxt.ui.client.Style$SortDir/640452531|offset|java.lang.Integer/\

3438268394|limit|{"email":"tnrs@lka5jjs.orv", "key":"[key]", \

"taxonomic_constraint":"false", "source_sorting":"false", "first":"false"}\

|1|2|3|4|2|5|6|7|0|1|8|4|9|0|10|11|0|12|13|0|14|13|100|15|')

retrieval_response_pattern = '^//OK\[.*?\["com.extjs.gxt.ui.client.data.\

BasePagingLoadResult/496878394","java.util.ArrayList/4159755760","org.iplantc.\

tnrs.demo.shared.BeanTNRSEntry/1039545748",".*"\],0,7\]$'

retrieval_response_info_pattern = r'(?ms).*^Set-Cookie: JSESSIONID=(\w+);'

download_request_template = ('7|0|6|'+url_base+

'|1E87C78041CEFBF0992F46BDF84D7D60|org.iplantc.tnrs.demo.client.SearchService|\

downloadRemoteResults|java.lang.String/2004016611|{"name":"tnrs_results.txt", \

"mode":"Best", "type":"Detailed", "encoding":"utf8", "dirty":"false", \

"sources":"false", "taxonomic":"false", "email":"tnrs@lka5jjs.orv", \

"key":"[key]"}|1|2|3|4|1|5|6|')

download_response_pattern = '^//OK\[1,\["(.*)"\],0,7\]$'

download_url_suffix = '&name=tnrs_results.txt&encoding=utf8'

class InvalidResponse(Exception): pass

def gwt_encode(str_): return re.sub(r'[^\w.() -]+', r' ', str_)

def parse_response(name, pattern, str_, response, response_info):

    match = re.match(pattern, str_)

    if not match:

        raise InvalidResponse('Invalid '+name+' response:\n'+response_info+'\n'

            +response)

    return match.groups()

def tnrs_request(taxons, debug=False):

    assert len(taxons) <= max_taxons

    # Logging

    def debug_log(label, str_=''):

        if debug: sys.stderr.write('\n'+label+':\n'+str_+'\n')

    ## HTTP

    headers = initial_headers

    def do_request(request):

        debug_log('request', str(request))

        response = urllib2.urlopen(urllib2.Request(url, request, headers))

        response_str = streams.read_all(response)

        response_info = str(response.info())

        debug_log('response info', response_info)

        debug_log('response str', response_str)

        return response_str, response_info

    def do_repeated_request(request):

        pause = initial_pause

        total_pause = 0

        while True:

            total_pause += pause

            if total_pause > max_pause: raise # error is not temporary

            debug_log('total_pause', str(total_pause)+'s')

            time.sleep(pause) # wait for job to complete

            try: return do_request(request)

            except urllib2.HTTPError: pass # try again

            pause *= pause_growth_factor

    debug_log('Submit')

    request = submission_request_template.replace('[taxons]',

        r'\\n'.join(map(gwt_encode, taxons))) # double-escape \n

    response, response_info = do_request(request)

    key, = parse_response('submission', submission_response_pattern, response,

        response, response_info)

    debug_log('key', key)

    key_enc = gwt_encode(key)

    debug_log('Retrieve')

    request = retrieval_request_template.replace('[key]', key_enc)

    response, response_info = do_repeated_request(request)

    parse_response('retrieval', retrieval_response_pattern, response, response,

        response_info)

    session_id, = parse_response('retrieval info',

        retrieval_response_info_pattern, response_info, response, response_info)

    debug_log('session_id', session_id)

    headers['Cookie'] = 'JSESSIONID='+session_id

    # The output of the retrieve step is unusable because the array has

    # different lengths depending on the taxonomic ranks present in the provided

    # taxon name. The extra download step is therefore necessary.

    debug_log('Prepare download')

    request = download_request_template.replace('[key]', key_enc)

    response, response_info = do_request(request)

    csv_url, = parse_response('download', download_response_pattern, response,

        response, response_info)

    csv_url += download_url_suffix

    debug_log('csv_url', csv_url)

    debug_log('Download')

    response = urllib2.urlopen(urllib2.Request(csv_url))

    debug_log('response info', str(response.info()))

    return response

def repeated_tnrs_request(taxons, debug=False, **kw_args):

    for try_num in xrange(max_tries):

        try: return tnrs_request(taxons, debug, **kw_args)

        except InvalidResponse:

            debug = True # next time, output protocol info for debugging

            # try again

    raise # error is not temporary