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#? name: NucleaRDB
#? www: http://www.receptors.org/
#? urls: http://www.receptors.org/


# encoding: UTF-8

import base64
import common.eutils
import common.utils
import re
import spineapi
import suds.client
import urllib
import utopia.document
import urllib2
from lxml import etree

class NucleaRDBAnnotator(utopia.document.Annotator):
    '''Annotate with NucleaRDB'''

    def getMentions(self, text, pubmedId):
        print 'initialising now ...'

        serviceUrl = 'http://www.receptors.org/nucleardb/webservice'
        wsdlUrl = '%s?wsdl' % serviceUrl
        gc = suds.client.Client(wsdlUrl)
        gs = gc.service

        textBytes = base64.b64encode(text.encode('utf-8'))
        if pubmedId != None:
            pubmedId = pubmedId.encode('utf-8')
        else:
            pubmedId = ''

        #print text
        body = """
        <SOAP-ENV:Envelope
         xmlns:SOAP-ENV="http://schemas.xmlsoap.org/soap/envelope/">
         <SOAP-ENV:Body>
          <ns:getMentions xmlns:ns="http://webservice.web.mcsis.cmbi.ru.nl/">
           <text>{0}</text>
           <pubmedId>{1}</pubmedId>
          </ns:getMentions>
         </SOAP-ENV:Body>
        </SOAP-ENV:Envelope>
        """.format(textBytes, pubmedId).encode('utf8')
        res = urllib2.urlopen(serviceUrl, body, timeout=8)
        res = res.read()
        return gs.getMentions(__inject={'reply': res})

    @utopia.document.buffer
    def on_activate_event(self, document):
        if len(document.annotations('NucleaRDB cache')) == 0:
            print 'annotating stuff . . .'

            pubmedId = common.utils.metadata(document, 'pmid')
            if pubmedId is not None:
                print 'found pubmed id: ' + pubmedId
            else:
                print 'did not find pubmed id'

            ns = {'r': 'GPCR'}

            textMentions = self.getMentions(document.text(), pubmedId)

            objectlist = []
            mention_cache = {}
            for mention in textMentions:
                if mention.mentionType != 'SPECIES':
                    mention_cache.setdefault(mention.html, [])
                    mention_cache[mention.html].append(mention)

            for html, mentions in mention_cache.iteritems():
                annotation = self.createAnnotation(document, html, mentions)
                annotation['displayRelevance']='2000'
                annotation['displayRank']= '2000'
                document.addAnnotation(annotation)

            document.addAnnotation(spineapi.Annotation(), 'NucleaRDB cache')

    def createAnnotation(self, document, html, mentions):
        annotation = spineapi.Annotation()
        annotation['concept'] = 'NucleaRDBInformation'
        annotation['property:name'] = '%s: "%s"' % (mentions[0].mentionType.title(), mentions[0].formalRepresentation)
        annotation['property:description'] = 'NucleaRDB %s record' % mentions[0].mentionType.title()
        annotation['property:sourceDatabase'] = 'nucleardb'
        annotation['property:sourceDescription'] = '<p>The <a href="http://www.receptors.org/nucleardb/">NucleaRDB</a> is a molecular-class information system that collects, combines, validates and stores large amounts of heterogenous data on nuclear hormone receptors.</p>'
        annotation['property:html'] = html

        for mention in mentions:
            #print mention
            start = int(mention.textStart)
            end = int(mention.textEnd)
            match = document.substr(start, end-start)
            annotation.addExtent(match)

        return annotation

class NucleaRDBVisualiser(utopia.document.Visualiser):
    """Viualiser for NucleaRDB entries"""

    def visualisable(self, annotation):
        return annotation.get('concept') == 'NucleaRDBInformation' and 'property:html' in annotation

    def visualise(self, annotation):
        html = annotation['property:html']
        if html.endswith('</tr>'):
            html += '</table>'
        return html

__all__ = ['NucleaRDBAnnotator', 'NucleaRDBVisualiser']