SYMBOL INDEX (182 symbols across 18 files)

FILE: biobert_ner/fast_predict2.py
  class FastPredict (line 20) | class FastPredict:
    method __init__ (line 22) | def __init__(self, estimator, input_fn):
    method _create_generator (line 31) | def _create_generator(self):
    method predict (line 40) | def predict(self, feature_batch):
    method close (line 68) | def close(self):
  function example_input_fn (line 76) | def example_input_fn(generator):

FILE: biobert_ner/modeling.py
  class BertConfig (line 30) | class BertConfig(object):
    method __init__ (line 33) | def __init__(self,
    method from_dict (line 82) | def from_dict(cls, json_object):
    method from_json_file (line 90) | def from_json_file(cls, json_file):
    method to_dict (line 96) | def to_dict(self):
    method to_json_string (line 101) | def to_json_string(self):
  class BertModel (line 106) | class BertModel(object):
    method __init__ (line 130) | def __init__(self,
    method get_pooled_output (line 239) | def get_pooled_output(self):
    method get_sequence_output (line 242) | def get_sequence_output(self):
    method get_all_encoder_layers (line 251) | def get_all_encoder_layers(self):
    method get_embedding_output (line 254) | def get_embedding_output(self):
    method get_embedding_table (line 265) | def get_embedding_table(self):
  function gelu (line 269) | def gelu(input_tensor):
  function get_activation (line 285) | def get_activation(activation_string):
  function get_assignment_map_from_checkpoint (line 322) | def get_assignment_map_from_checkpoint(tvars, init_checkpoint):
  function dropout (line 349) | def dropout(input_tensor, dropout_prob):
  function layer_norm (line 367) | def layer_norm(input_tensor, name=None):
  function layer_norm_and_dropout (line 374) | def layer_norm_and_dropout(input_tensor, dropout_prob, name=None):
  function create_initializer (line 381) | def create_initializer(initializer_range=0.02):
  function embedding_lookup (line 386) | def embedding_lookup(input_ids,
  function embedding_postprocessor (line 435) | def embedding_postprocessor(input_tensor,
  function create_attention_mask_from_input_mask (line 532) | def create_attention_mask_from_input_mask(from_tensor, to_mask):
  function attention_layer (line 566) | def attention_layer(from_tensor,
  function transformer_model (line 763) | def transformer_model(input_tensor,
  function get_shape_list (line 908) | def get_shape_list(tensor, expected_rank=None, name=None):
  function reshape_to_matrix (line 945) | def reshape_to_matrix(input_tensor):
  function reshape_from_matrix (line 959) | def reshape_from_matrix(output_tensor, orig_shape_list):
  function assert_rank (line 972) | def assert_rank(tensor, expected_rank, name=None):

FILE: biobert_ner/ops.py
  function json_to_sent (line 8) | def json_to_sent(data, is_raw_text=False):
  function input_form (line 37) | def input_form(sent_data):
  function isInt (line 66) | def isInt(string):
  function isFloat (line 74) | def isFloat(string):
  function softmax (line 82) | def softmax(logits):
  function CoNLL_tokenizer (line 91) | def CoNLL_tokenizer(text):
  function sentence_split (line 98) | def sentence_split(text):
  function merge_results (line 169) | def merge_results(data, sent_data, predicDict, logitsDict, rep_ent,
  function detokenize (line 479) | def detokenize(tokens, predicts, logits):

FILE: biobert_ner/run_ner.py
  class InputExample (line 113) | class InputExample(object):
    method __init__ (line 116) | def __init__(self, guid, text, label=None):
  class InputFeatures (line 131) | class InputFeatures(object):
    method __init__ (line 134) | def __init__(self, input_ids, input_mask, segment_ids, label_ids,):
  class DataProcessor (line 142) | class DataProcessor(object):
    method get_train_examples (line 145) | def get_train_examples(self, data_dir):
    method get_dev_examples (line 149) | def get_dev_examples(self, data_dir):
    method get_labels (line 153) | def get_labels(self):
    method _read_data (line 158) | def _read_data(cls, data, pmids):
  class NerProcessor (line 193) | class NerProcessor(DataProcessor):
    method get_test_examples (line 194) | def get_test_examples(self, data_dir):
    method get_test_dict_list (line 212) | def get_test_dict_list(self, dict_list, is_raw_text=False):
    method get_labels (line 225) | def get_labels(self):
    method _create_example (line 228) | def _create_example(self, lines, set_type):
  function file_based_input_fn_builder (line 238) | def file_based_input_fn_builder(input_file, seq_length, drop_remainder):
  function create_model (line 272) | def create_model(bert_config, is_training, input_ids, input_mask,
  function model_fn_builder (line 315) | def model_fn_builder(bert_config, num_labels, init_checkpoint, learning_...
  class BioBERT (line 361) | class BioBERT:
    method __init__ (line 362) | def __init__(self, _):
    method recognize (line 447) | def recognize(self, input_dl, is_raw_text=False, thread_id=None,
    method recognize_etype (line 592) | def recognize_etype(self, etype, predict_example_list, tokens, tot_tok...
    method filed_based_convert_examples_to_features (line 663) | def filed_based_convert_examples_to_features(self, examples, max_seq_l...
    method get_input_generator (line 702) | def get_input_generator(self, predict_examples, req_id, mode='test'):
    method get_inputs (line 715) | def get_inputs(self, predict_examples, req_id, mode='test'):
    method fast_input_fn_builder_gen (line 731) | def fast_input_fn_builder_gen(self, gen_predict_examples):
    method fast_input_fn_builder_gen_batch (line 754) | def fast_input_fn_builder_gen_batch(self, gen_predict_examples):
    method convert_single_example (line 785) | def convert_single_example(self, example, max_seq_length, req_id, mode):
    method write_tokens (line 850) | def write_tokens(tokens, mode, req_id):
    method close (line 859) | def close(self):
  function main (line 864) | def main(_):

FILE: biobert_ner/tokenization.py
  function validate_case_matches_checkpoint (line 28) | def validate_case_matches_checkpoint(do_lower_case, init_checkpoint):
  function convert_to_unicode (line 79) | def convert_to_unicode(text):
  function printable_text (line 99) | def printable_text(text):
  function load_vocab (line 122) | def load_vocab(vocab_file):
  function convert_by_vocab (line 137) | def convert_by_vocab(vocab, items):
  function convert_tokens_to_ids (line 145) | def convert_tokens_to_ids(vocab, tokens):
  function convert_ids_to_tokens (line 149) | def convert_ids_to_tokens(inv_vocab, ids):
  function whitespace_tokenize (line 153) | def whitespace_tokenize(text):
  class FullTokenizer (line 162) | class FullTokenizer(object):
    method __init__ (line 165) | def __init__(self, vocab_file, do_lower_case=True):
    method tokenize (line 171) | def tokenize(self, text):
    method convert_tokens_to_ids (line 179) | def convert_tokens_to_ids(self, tokens):
    method convert_ids_to_tokens (line 182) | def convert_ids_to_tokens(self, ids):
  class BasicTokenizer (line 186) | class BasicTokenizer(object):
    method __init__ (line 189) | def __init__(self, do_lower_case=True):
    method tokenize (line 197) | def tokenize(self, text):
    method _run_strip_accents (line 221) | def _run_strip_accents(self, text):
    method _run_split_on_punc (line 232) | def _run_split_on_punc(self, text):
    method _tokenize_chinese_chars (line 252) | def _tokenize_chinese_chars(self, text):
    method _is_chinese_char (line 265) | def _is_chinese_char(self, cp):
    method _clean_text (line 287) | def _clean_text(self, text):
  class WordpieceTokenizer (line 301) | class WordpieceTokenizer(object):
    method __init__ (line 304) | def __init__(self, vocab, unk_token="[UNK]", max_input_chars_per_word=...
    method tokenize (line 309) | def tokenize(self, text):
  function _is_whitespace (line 363) | def _is_whitespace(char):
  function _is_control (line 375) | def _is_control(char):
  function _is_punctuation (line 387) | def _is_punctuation(char):

FILE: biobert_ner/utils.py
  class Profile (line 7) | class Profile(object):
    method __init__ (line 8) | def __init__(self, prefix):
    method __call__ (line 11) | def __call__(self, fn):
  function show_prof_data (line 30) | def show_prof_data():
  function clear_prof_data (line 40) | def clear_prof_data():

FILE: convert.py
  function pubtator2dict_list (line 9) | def pubtator2dict_list(pubtator_file_path, is_raw_text):
  function pubtatorstr2dict_list (line 103) | def pubtatorstr2dict_list(pubtator, is_raw_text):
  function pubtator_biocxml2dict_list (line 201) | def pubtator_biocxml2dict_list(pmids):
  function preprocess (line 301) | def preprocess(text):
  function pubtator2pubannotation (line 351) | def pubtator2pubannotation(pubtator):
  function get_bestplus_spans (line 428) | def get_bestplus_spans(mutations, title_space_abstract):
  function get_pub_annotation (line 467) | def get_pub_annotation(bern_dict, is_raw_text, elapsed_time_dict=None):
  function bern2pub_annotation (line 507) | def bern2pub_annotation(entity_dict):
  function get_pubtator (line 559) | def get_pubtator(bern_dict_list):
  function tmtooljson2bern (line 589) | def tmtooljson2bern(tmtool_res):

FILE: download.py
  function get_pubmed_xml (line 15) | def get_pubmed_xml(pmid, output_path=None):
  function pubmed_xml2pubtator (line 45) | def pubmed_xml2pubtator(pmid, xml_path, output_path=None):
  function get_pmc_xml (line 117) | def get_pmc_xml(pmcid, output_path=None):
  function pmc_xml2pubtator (line 179) | def pmc_xml2pubtator(pmcid, xml_path, output_path=None):
  function get_pmc_archive (line 427) | def get_pmc_archive(non_comm_use_pdf, non_comm_output_dir,
  function download_ftp (line 517) | def download_ftp(url, output_dir, overwrite=True):
  function get_pubmed (line 531) | def get_pubmed(pmid, out_format='json', encoding='unicode'):
  function query_tmtool (line 545) | def query_tmtool(pmids, entity_type='Mutation', out_format='JSON'):
  function query_pubtator2 (line 561) | def query_pubtator2(pmids, out_format='pubtator', escape_html=True):
  function query_pubtator2biocxml (line 581) | def query_pubtator2biocxml(pmids):
  function query_raw_tmtool (line 602) | def query_raw_tmtool(input_str, trigger='tmVar'):
  function query_raw_bern (line 636) | def query_raw_bern(input_str, bern_post_url='https://bern.korea.ac.kr/pl...
  function replace_wspaces (line 654) | def replace_wspaces(t):

FILE: normalize.py
  class Normalizer (line 15) | class Normalizer:
    method __init__ (line 16) | def __init__(self):
    method normalize (line 168) | def normalize(self, base_name, doc_dict_list, cur_thread_name, is_raw_...
    method run_normalizers_wrap (line 291) | def run_normalizers_wrap(self, ent_type, base_name, names, saved_items,
    method run_normalizer (line 298) | def run_normalizer(self, ent_type, base_name, names, saved_items,

FILE: normalizers/chemical_normalizer.py
  function run_server (line 10) | def run_server(logic_func, port):
  function run_normalizer (line 25) | def run_normalizer(data, _):
  function get_tmchem_name (line 64) | def get_tmchem_name(name):

FILE: normalizers/gene_auxiliary_normalizer.py
  function find_best_plus_largest_index (line 7) | def find_best_plus_largest_index(best_plus_dict_path):
  function find_largest_index (line 12) | def find_largest_index(uid_list):
  function make_best_dict (line 15) | def make_best_dict(best_dict_path, start_index, type_code=2):
  function write_auxiliary_dict (line 30) | def write_auxiliary_dict(aux_dict, output_path):
  function load_auxiliary_dict (line 36) | def load_auxiliary_dict(path):
  function make_freq_dict (line 46) | def make_freq_dict(total_sample_path, start_index, threshold, type_code=2):

FILE: normalizers/miRNA_normalizer.py
  class MiRNAFinder (line 4) | class MiRNAFinder:
    method __init__ (line 5) | def __init__(self, dict_path):
    method normalize (line 64) | def normalize(self, miRNA):
    method tag (line 135) | def tag(self, text):

FILE: normalizers/mutation_normalizer.py
  function run_server (line 9) | def run_server(logic_func, port):
  function run_normalizer (line 24) | def run_normalizer(data, _):

FILE: normalizers/pathway_normalizer.py
  class PathwayFinder (line 4) | class PathwayFinder:
    method __init__ (line 5) | def __init__(self, dict_path):
    method tag (line 40) | def tag(self, text):

FILE: normalizers/species_normalizer.py
  function run_server (line 9) | def run_server(logic_func, port):
  function run_normalizer (line 24) | def run_normalizer(data, _):

FILE: server.py
  class GetHandler (line 30) | class GetHandler(BaseHTTPRequestHandler):
    method do_GET (line 34) | def do_GET(self):
    method do_POST (line 262) | def do_POST(self):
    method preprocess_input (line 338) | def preprocess_input(self, text, cur_thread_name):
    method tag_entities (line 372) | def tag_entities(self, text, cur_thread_name, is_raw_text, reuse=False):
    method biobert_recognize (line 486) | def biobert_recognize(self, dict_list, is_raw_text, cur_thread_name):
    method get_err_dict (line 505) | def get_err_dict():
  class ThreadedHTTPServer (line 522) | class ThreadedHTTPServer(ThreadingMixIn, HTTPServer):
  function count_entities (line 526) | def count_entities(data):
  function tell_inputfile (line 541) | def tell_inputfile(host, port, inputfile):
  function delete_files (line 576) | def delete_files(dirname):
  class Main (line 591) | class Main:
    method __init__ (line 592) | def __init__(self, params):

FILE: service_checker.py
  function check_bern (line 13) | def check_bern(from_gmail, to_email, from_google_account, from_google_pa...
  function benchmark (line 49) | def benchmark(tries, batch_size=None, log_interval=100):
  function get_stats (line 174) | def get_stats(lst, batch_size=None):
  function stress_test (line 185) | def stress_test(num_threads, wait_seconds, num_try):

FILE: utils.py
  function query_raw (line 11) | def query_raw(text, url='https://bern.korea.ac.kr/plain'):
  function query (line 15) | def query(pmid, url='https://bern.korea.ac.kr/pubmed', output_format='js...
  function test_bern_get (line 37) | def test_bern_get(num_thread, period_delay_seconds, tries,
  function test_bern_post (line 59) | def test_bern_post(base_text, num_thread, period_delay_seconds, tries,
  function run_command (line 84) | def run_command(command, cwd):
  function ps_grep (line 96) | def ps_grep(q):
  function get_bern_status (line 105) | def get_bern_status(ps_grep_res):
  function send_mail (line 138) | def send_mail(from_addr, to, subject, content, gmail_id, password):
  function is_good (line 155) | def is_good(num_type_set=3, normal_id_cnt=13):
  function is_get_good (line 213) | def is_get_good(pmid, output_format, num_type_set, normal_id_cnt):
  function filter_entities (line 279) | def filter_entities(ner_results, is_raw_text):