def __init__(self, args, opts):
super(Method, self).__init__(args, opts)
self.es_int = ESInterface(host=self.opts.server,
port=self.opts.port,
index_name=self.opts.index_name)
self.regex_citation = re.compile(r"\(\s?(([A-Za-z\-]+\s)+([A-Za-z\-]+\.?)?,?\s\d{2,4}(;\s)?)+\s?\)|"
r"(\[(\d+([,–]\s?)?)+\])|"
r"\[[\d,-]+\]").sub
self.all_digits = re.compile(r"^\d+$").search
if self.opts.remove_stopwords:
with file(self.opts.stopwords_path) as f:
self.stopwords = frozenset([l.strip().lower() for l in f])
else:
self.stopwords = frozenset([])
self.doc_mod = documents_model.DocumentsModel(opts.docs_path)
self.ann_client = AnnotationsClient()
self.reg_apa = re.compile(
# [Chen et al.2000]
r"\(\s?(([A-Za-z\-]+\s)+([A-Za-z\-]+\.?)?,?\s\d{2,4}(;\s)?)+\s?\)|"
r"\(\s?([^ ]+\s?[^ ]*et\sal\.,?\s\d{2,4}(,\s)?)+(\sand\s)?[^ ]+\s?[^ ]*et\sal\.,?\s\d{2,4}\)|"
r"\w+\set al\. \(\d{2,4}\)") # [Chen et al. 200]
self.reg_apa_rare = re.compile(
r"((([A-Z]\w+\set\sal\.,? \d{4})|([A-Z]\w+\sand\s[A-Z]\w+,?\s\d{4}))((,\s)| and )?)+")
self.reg_apa2 = re.compile(
r"\(\s?(\w+\s?\w*et\sal\.,\s\d{2,4}(,\s)?)+(\sand\s)?\w+\s?\w*et\sal\.,\s\d{2,4}\)")
self.reg_ieee = re.compile(r"(\[(\d+([,–]\s?)?)+\])|\[\s?[\d,-]+\]")
self.reg_paranthesis = re.compile(
r"\(\s?\d{1,2}(,\s\d{1,2})*(\sand\s\d{1,2})?\)")
self.nlp_extractor = Extract_NLP_Tags()
self.tokenizer = RegexpTokenizer('[^\w\-\']+', gaps=True)
self.lmtzr = WordNetLemmatizer()
def __init__(self, args, opts):
super(Method, self).__init__(args, opts)
self.es_int = ESInterface(host=self.opts.server,
port=self.opts.port,
index_name=self.opts.index_name)
self.analyzer = self.es_int.get_index_analyzer()
self.regex_citation = re.compile(
r"\(\s?(([A-Za-z\-]+\s)+([A-Za-z\-]+\.?)?,?\s\d{2,4}(;\s)?)+\s?\)|"
r"(\[(\d+([,–]\s?)?)+\])|"
r"\[[\d,-]+\]").sub
self.all_digits = re.compile(r"^\d+$").search
if self.opts.remove_stopwords:
with file(self.opts.stopwords_path) as f:
self.stopwords = frozenset([l.strip().lower() for l in f])
else:
self.stopwords = frozenset([])
self.db = MySQLdb.connect(host=constants.mysql_server,
port=constants.mysql_port,
user=constants.mysql_user,
passwd=constants.mysql_pass,
db=constants.mysql_db)
self.cur = self.db.cursor()
self.ttys = ['SY']
ttygroups = {
"syns": ('AUN', 'EQ', 'SYN', 'MTH'),
"chemicals": ('CCN', 'CSN'),
"drugs": ('BD', 'BN', 'CD', 'DP', 'FBD', 'GN', 'OCD'),
"diseases": ('DI', ),
"findings": ('FI', ),
"hierarchy": ('HS', 'HT', 'HX'),
"related": ('RT', ),
"preferred": ('PTN', 'PT')
}
self.doc_mod = documents_model.DocumentsModel(opts.anns_dir)
# self.ann_client = AnnotationsClient()
self.reg_apa = re.compile(
# [Chen et al.2000]
r"\(\s?(([A-Za-z\-]+\s)+([A-Za-z\-]+\.?)?,?\s\d{2,4}(;\s)?)+\s?\)|"
r"\(\s?([^ ]+\s?[^ ]*et\sal\.,?\s\d{2,4}(,\s)?)+(\sand\s)?[^ ]+\s?[^ ]*et\sal\.,?\s\d{2,4}\)|"
r"\w+\set al\. \(\d{2,4}\)") # [Chen et al. 200]
self.reg_apa_rare = re.compile(
r"((([A-Z]\w+\set\sal\.,? \d{4})|([A-Z]\w+\sand\s[A-Z]\w+,?\s\d{4}))((,\s)| and )?)+"
)
self.reg_apa2 = re.compile(
r"\(\s?(\w+\s?\w*et\sal\.,\s\d{2,4}(,\s)?)+(\sand\s)?\w+\s?\w*et\sal\.,\s\d{2,4}\)"
)
self.reg_ieee = re.compile(r"(\[(\d+([,–]\s?)?)+\])|\[\s?[\d,-]+\]")
self.reg_paranthesis = re.compile(
r"\(\s?\d{1,2}(,\s\d{1,2})*(\sand\s\d{1,2})?\)")
self.nlp_extractor = Extract_NLP_Tags()
self.tokenizer = RegexpTokenizer('[^\w\-\']+', gaps=True)
self.lmtzr = WordNetLemmatizer()
self.stemmer = stem.porter.PorterStemmer()
def __init__(self, args, opts):
super(Method, self).__init__(args, opts)
self.es_int = ESInterface(host=self.opts.server,
port=self.opts.port,
index_name=self.opts.index_name)
self.regex_citation = re.compile(
r"\(\s?(([A-Za-z\-]+\s)+([A-Za-z\-]+\.?)?,?\s\d{2,4}(;\s)?)+\s?\)|"
r"(\[(\d+([,–]\s?)?)+\])|"
r"\[[\d,-]+\]").sub
self.all_digits = re.compile(r"^\d+$").search
if self.opts.remove_stopwords:
with file(self.opts.stopwords_path) as f:
self.stopwords = frozenset([l.strip().lower() for l in f])
else:
self.stopwords = frozenset([])
self.doc_mod = documents_model.DocumentsModel(opts.docs_path)
self.ann_client = AnnotationsClient()