From baad76215d1025dc6c3b61983c6ef57f3198b0ee Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Mon, 4 Mar 2019 16:09:32 -0500 Subject: [PATCH 01/28] Formatting; getting ready to develop FDA pipeline --- medacy/pipelines/base/base_pipeline.py | 29 +++++-------------- .../pipelines/fda_nano_drug_label_pipeline.py | 29 +++++++------------ 2 files changed, 19 insertions(+), 39 deletions(-) diff --git a/medacy/pipelines/base/base_pipeline.py b/medacy/pipelines/base/base_pipeline.py index 894b385d..6a53958c 100644 --- a/medacy/pipelines/base/base_pipeline.py +++ b/medacy/pipelines/base/base_pipeline.py @@ -1,18 +1,19 @@ from abc import ABC, abstractmethod from ...pipeline_components.base import BaseComponent + class BasePipeline(ABC): """ An abstract wrapper for a Medical NER Pipeline """ - def __init__(self,pipeline_name, spacy_pipeline=None, description=None, creators="", organization=""): + def __init__(self, pipeline_name, spacy_pipeline=None, description=None, creators="", organization=""): """ Initializes a pipeline :param pipeline_name: The name of the pipeline :param spacy_pipeline: the corresponding spacy pipeline (language) to utilize. :param description: a description of the pipeline - :param creator: the creator of the pipeline + :param creators: the creator of the pipeline :param organization: the organization the pipeline creator belongs to """ self.pipeline_name = pipeline_name @@ -21,8 +22,6 @@ def __init__(self,pipeline_name, spacy_pipeline=None, description=None, creators self.creators = creators self.organization = organization - - @abstractmethod def get_tokenizer(self): """ @@ -47,7 +46,6 @@ def get_feature_extractor(self): """ pass - def get_language_pipeline(self): """ Retrieves the associated spaCy Language pipeline that the medaCy pipeline wraps. @@ -62,16 +60,14 @@ def add_component(self, component, *argv, **kwargs): """ current_components = [component_name for component_name, proc in self.spacy_pipeline.pipeline] - #print("Current Components:", current_components) + # print("Current Components:", current_components) dependencies = [x for x in component.dependencies] - #print("Dependencies:",dependencies) + # print("Dependencies:",dependencies) assert component.name not in current_components, "%s is already in the pipeline." % component.name for dependent in dependencies: assert dependent in current_components, "%s depends on %s but it hasn't been added to the pipeline" % (component, dependent) - - self.spacy_pipeline.add_pipe(component(self.spacy_pipeline, *argv, **kwargs)) def get_components(self): @@ -80,7 +76,8 @@ def get_components(self): :return: a list of components inside the pipeline. """ return [component_name for component_name, _ in self.spacy_pipeline.pipeline - if component_name != 'ner'] + if component_name != 'ner'] + def __call__(self, doc, predict=False): """ Passes a single document through the pipeline. @@ -107,7 +104,7 @@ def get_pipeline_information(self): """ information = { 'components': [component_name for component_name, _ in self.spacy_pipeline.pipeline - if component_name != 'ner'], #ner is the default ner component of spacy that is not utilized. + if component_name != 'ner'], # ner is the default ner component of spacy that is not utilized. 'learner_name': self.get_learner()[0], 'description': self.description, 'pipeline_name': self.pipeline_name, @@ -116,13 +113,3 @@ def get_pipeline_information(self): } return information - - - - - - - - - - diff --git a/medacy/pipelines/fda_nano_drug_label_pipeline.py b/medacy/pipelines/fda_nano_drug_label_pipeline.py index a5b014b1..d82322cd 100644 --- a/medacy/pipelines/fda_nano_drug_label_pipeline.py +++ b/medacy/pipelines/fda_nano_drug_label_pipeline.py @@ -19,43 +19,36 @@ def __init__(self, metamap, entities=[]): :param metamap: an instance of MetaMap """ - description="""Pipeline tuned for the recognition of entities in FDA Nanoparticle Drug Labels""" + description = """Pipeline tuned for the recognition of entities in FDA Nanoparticle Drug Labels""" super().__init__("fda_nano_drug_label_pipeline", spacy_pipeline=spacy.load("en_core_web_sm"), description=description, - creators="Andriy Mulyar (andriymulyar.com)", #append if multiple creators + creators="Andriy Mulyar (andriymulyar.com) " + + "Steele Farnsworth (github.com/swfarnsworth)", # append if multiple creators organization="NLP@VCU" ) - self.entities = entities self.spacy_pipeline.tokenizer = self.get_tokenizer() # set tokenizer self.add_component(GoldAnnotatorComponent, entities) # add overlay for GoldAnnotation self.add_component(MetaMapComponent, metamap) - #self.add_component(UnitComponent) + # self.add_component(UnitComponent) def get_learner(self): - return ("CRF_l2sgd", sklearn_crfsuite.CRF( - algorithm='l2sgd', - c2=0.1, - max_iterations=100, - all_possible_transitions=True - )) + return "CRF_l2sgd", sklearn_crfsuite.CRF( + algorithm='l2sgd', + c2=0.1, + max_iterations=100, + all_possible_transitions=True + ) def get_tokenizer(self): - tokenizer = ClinicalTokenizer(self.spacy_pipeline) #Best run with SystematicReviewTokenizer + tokenizer = ClinicalTokenizer(self.spacy_pipeline) # Best run with SystematicReviewTokenizer return tokenizer.tokenizer def get_feature_extractor(self): extractor = FeatureExtractor(window_size=6, spacy_features=['pos_', 'shape_', 'prefix_', 'suffix_', 'like_num', 'text']) return extractor - - - - - - - From 7889c8bfb1e0a73c2fff2de3a1b526de484afb59 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Mon, 4 Mar 2019 19:25:27 -0500 Subject: [PATCH 02/28] Added logging to file --- medacy/tools/con_form/con_to_brat.py | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/medacy/tools/con_form/con_to_brat.py b/medacy/tools/con_form/con_to_brat.py index 7460715c..575834ba 100644 --- a/medacy/tools/con_form/con_to_brat.py +++ b/medacy/tools/con_form/con_to_brat.py @@ -12,10 +12,11 @@ :date: 18 February, 2019 """ -from sys import argv as cmd_arg, exit +from sys import argv, exit from re import split, findall, fullmatch, DOTALL import os import shutil +import logging def is_valid_con(item: str): @@ -111,7 +112,9 @@ def convert_con_to_brat(con_file_path, text_file_path=None): output_text = "" t = 1 for line in con_text_lines: - if not is_valid_con(line): continue + if not is_valid_con(line): + logging.warning("Incorrectly formatted line in %s was skipped: \"%s\"." % (con_file_path, line)) + continue d = line_to_dict(line) start_ind = get_absolute_index(text, text_lines, d["start_ind"]) span_length = d["data_item"].__len__() @@ -127,7 +130,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Get the input and output directories from the command line. - if not cmd_arg.__len__() >= 3: + if not argv.__len__() >= 3: # Command-line arguments must be provided for the input and output directories. # Else, prints instructions and aborts the program. print("Please run the program again, entering the input and output directories as command-line arguments" @@ -136,20 +139,24 @@ def convert_con_to_brat(con_file_path, text_file_path=None): exit() try: - input_dir_name = cmd_arg[1] + input_dir_name = argv[1] input_dir = os.listdir(input_dir_name) except FileNotFoundError: # dir doesn't exist while not os.path.isdir(input_dir_name): input_dir_name = input("Input directory not found; please try another directory:") input_dir = os.listdir(input_dir_name) try: - output_dir_name = cmd_arg[2] + output_dir_name = argv[2] output_dir = os.listdir(output_dir_name) except FileNotFoundError: while not os.path.isdir(output_dir_name): output_dir_name = input("Output directory not found; please try another directory:") output_dir = os.listdir(output_dir_name) + # Create the log + log_path = os.path.join(output_dir_name, "conversion_log.log") + logging.basicConfig(filename=log_path, level=logging.WARNING) + # Get only the text files in input_dir text_files = [f for f in input_dir if f.endswith(".txt")] # Get only the con files in input_dir that have a ".txt" equivalent @@ -165,7 +172,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Paste all the text files used in the conversion process to the output directory # if there's a fourth command line argument and that argument is -c - if cmd_arg.__len__() == 4 and cmd_arg[3] == "-c": + if argv.__len__() == 4 and argv[3] == "-c": text_files_with_match = [f for f in text_files if switch_extension(f, ".con") in con_files] for f in text_files_with_match: full_name = os.path.join(input_dir_name, f) From f224d758e1c5f56bc53c5aa08d2e98767569e703 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Mon, 4 Mar 2019 21:18:59 -0500 Subject: [PATCH 03/28] Increased accuracy of con_to_brat; refactored unit tests --- .../tests/tools/con_form/test_con_to_brat.py | 4 ++-- medacy/tools/con_form/brat_to_con.py | 2 +- medacy/tools/con_form/con_to_brat.py | 20 ++++++++++++++----- 3 files changed, 18 insertions(+), 8 deletions(-) diff --git a/medacy/tests/tools/con_form/test_con_to_brat.py b/medacy/tests/tools/con_form/test_con_to_brat.py index 2e00a17c..aa10cb10 100644 --- a/medacy/tests/tools/con_form/test_con_to_brat.py +++ b/medacy/tests/tools/con_form/test_con_to_brat.py @@ -130,7 +130,7 @@ def test_line_to_dict(self): def test_valid_brat_to_con(self): """Convert the test file from brat to con. Assert that the con output matches the sample con text.""" brat_output = convert_con_to_brat(self.con_file_path, self.text_file_path) - self.assertEqual(brat_output, brat_text) + self.assertEqual(brat_text, brat_output) def test_invalid_file_path(self): """Passes an invalid file path to convert_con_to_brat().""" @@ -142,7 +142,7 @@ def test_valid_con_matching_text_name(self): Assert that the con output matches the sample con text when the automatic text-file-finding feature is utilized """ brat_output = convert_con_to_brat(self.con_file_path) - self.assertEqual(brat_output, brat_text) + self.assertEqual(brat_text, brat_output) def test_invalid_brat_text(self): """Assert that invalid brat text produces no output.""" diff --git a/medacy/tools/con_form/brat_to_con.py b/medacy/tools/con_form/brat_to_con.py index 25ac8b61..109c29a9 100644 --- a/medacy/tools/con_form/brat_to_con.py +++ b/medacy/tools/con_form/brat_to_con.py @@ -191,7 +191,7 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): exit() # Create the log file - log_file_path = os.path.join(output_dir_name + "conversion.log") + log_file_path = os.path.join(output_dir_name, "conversion.log") logging.basicConfig(filename=log_file_path, level=logging.WARNING) for input_file_name in ann_files: diff --git a/medacy/tools/con_form/con_to_brat.py b/medacy/tools/con_form/con_to_brat.py index 575834ba..d6608cef 100644 --- a/medacy/tools/con_form/con_to_brat.py +++ b/medacy/tools/con_form/con_to_brat.py @@ -54,7 +54,7 @@ def get_absolute_index(txt, txt_lns, ind): """ Given one of the \d+:\d+ spans, which represent the index of a char relative to the start of the line it's on, returns the index of that char relative to the start of the file. - :param txt: The text file associated with the annotation. + :param txt: The text itself of the text file associated with the annotation. :param txt_lns: The same text file as a list broken by lines :param ind: The string in format \d+:\d+ :return: The absolute index @@ -63,12 +63,22 @@ def get_absolute_index(txt, txt_lns, ind): # convert ind to line_num and char_num nums = split(":", ind) line_num = int(nums[0]) - 1 # line nums in con start at 1 and not 0 - char_num = int(nums[1]) + word_num = int(nums[1]) this_line = txt_lns[line_num] line_index = txt.index(this_line) # get the absolute index of the entire line - abs_index = line_index + char_num - return abs_index + + # Get index of word following n spaces + + split_by_whitespace = split("( +|\t+)+", this_line) + split_by_ws_no_ws = [s for s in split_by_whitespace if not fullmatch("\s+", s)] + all_whitespace = findall("( +|\t+)+", this_line) + line_to_target_word = split_by_ws_no_ws[:word_num] + num_non_whitespace = sum([w.__len__() for w in line_to_target_word]) + num_whitespace = sum([w.__len__() for w in all_whitespace[:word_num]]) + num_chars = num_whitespace + num_non_whitespace + + return num_chars + line_index def convert_con_to_brat(con_file_path, text_file_path=None): @@ -116,7 +126,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): logging.warning("Incorrectly formatted line in %s was skipped: \"%s\"." % (con_file_path, line)) continue d = line_to_dict(line) - start_ind = get_absolute_index(text, text_lines, d["start_ind"]) + start_ind = get_absolute_index(text, text_lines, d["start_ind"]) # TODO fix span_length = d["data_item"].__len__() end_ind = start_ind + span_length output_line = "T%s\t%s %s %s\t%s\n" % (str(t), d["data_type"], str(start_ind), str(end_ind), d["data_item"]) From d45cc133de0325d851e9ad6f7a37d5082044abec Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Mon, 4 Mar 2019 22:07:36 -0500 Subject: [PATCH 04/28] con_to_brat is now accurate --- .../tests/tools/con_form/test_con_to_brat.py | 2 +- medacy/tools/con_form/con_to_brat.py | 35 ++++++++++--------- 2 files changed, 19 insertions(+), 18 deletions(-) diff --git a/medacy/tests/tools/con_form/test_con_to_brat.py b/medacy/tests/tools/con_form/test_con_to_brat.py index aa10cb10..0a1d6c53 100644 --- a/medacy/tests/tools/con_form/test_con_to_brat.py +++ b/medacy/tests/tools/con_form/test_con_to_brat.py @@ -1,6 +1,6 @@ """ :author: Steele W. Farnsworth -:date: 17 February, 2019 +:date: 04 March, 2019 """ import unittest, tempfile, os, shutil diff --git a/medacy/tools/con_form/con_to_brat.py b/medacy/tools/con_form/con_to_brat.py index d6608cef..e5c16938 100644 --- a/medacy/tools/con_form/con_to_brat.py +++ b/medacy/tools/con_form/con_to_brat.py @@ -6,14 +6,12 @@ Function 'convert_con_to_brat()' can be imported independently and run on individual files. -This version does not produce accurate output. Revisions are underway. - :author: Steele W. Farnsworth -:date: 18 February, 2019 +:date: 4 March, 2019 """ from sys import argv, exit -from re import split, findall, fullmatch, DOTALL +from re import split, findall, fullmatch import os import shutil import logging @@ -50,13 +48,14 @@ def switch_extension(name, ext): return os.path.splitext(name)[0] + ext -def get_absolute_index(txt, txt_lns, ind): +def get_absolute_index(txt, txt_lns, ind, entity): """ - Given one of the \d+:\d+ spans, which represent the index of a char relative to the start of the line it's on, + Given one of the \d+:\d+ spans, which represent the index of a word relative to the start of the line it's on, returns the index of that char relative to the start of the file. :param txt: The text itself of the text file associated with the annotation. :param txt_lns: The same text file as a list broken by lines :param ind: The string in format \d+:\d+ + :param entity: The text of the entity :return: The absolute index """ @@ -69,16 +68,11 @@ def get_absolute_index(txt, txt_lns, ind): line_index = txt.index(this_line) # get the absolute index of the entire line # Get index of word following n spaces + words = findall(r'\s*\S+\s*', this_line) + index_within_line = sum(map(len, words[:word_num])) + len(words[word_num]) - len(words[word_num].lstrip()) + offset = this_line[index_within_line:].index(entity) # adjusts if entity is not the first char in its "word" - split_by_whitespace = split("( +|\t+)+", this_line) - split_by_ws_no_ws = [s for s in split_by_whitespace if not fullmatch("\s+", s)] - all_whitespace = findall("( +|\t+)+", this_line) - line_to_target_word = split_by_ws_no_ws[:word_num] - num_non_whitespace = sum([w.__len__() for w in line_to_target_word]) - num_whitespace = sum([w.__len__() for w in all_whitespace[:word_num]]) - num_chars = num_whitespace + num_non_whitespace - - return num_chars + line_index + return index_within_line + line_index + offset def convert_con_to_brat(con_file_path, text_file_path=None): @@ -126,7 +120,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): logging.warning("Incorrectly formatted line in %s was skipped: \"%s\"." % (con_file_path, line)) continue d = line_to_dict(line) - start_ind = get_absolute_index(text, text_lines, d["start_ind"]) # TODO fix + start_ind = get_absolute_index(text, text_lines, d["start_ind"], d["data_item"]) span_length = d["data_item"].__len__() end_ind = start_ind + span_length output_line = "T%s\t%s %s %s\t%s\n" % (str(t), d["data_type"], str(start_ind), str(end_ind), d["data_item"]) @@ -164,7 +158,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): output_dir = os.listdir(output_dir_name) # Create the log - log_path = os.path.join(output_dir_name, "conversion_log.log") + log_path = os.path.join(output_dir_name, "conversion.log") logging.basicConfig(filename=log_path, level=logging.WARNING) # Get only the text files in input_dir @@ -172,6 +166,13 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Get only the con files in input_dir that have a ".txt" equivalent con_files = [f for f in input_dir if f.endswith(".con") and switch_extension(f, ".txt") in text_files] + # Ensure user is aware if there are no files to convert + if len(con_files) < 1: + raise FileNotFoundError("There were no con files in the input directory with a corresponding text file. " + "Please ensure that the input directory contains ann files and that each file has " + "a corresponding txt file (see help for this program).") + exit() + for input_file_name in con_files: full_file_path = os.path.join(input_dir_name, input_file_name) output_file_name = switch_extension(input_file_name, ".ann") From 5ab73be698360814567472ed719ec5447641f225 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Mon, 4 Mar 2019 22:07:58 -0500 Subject: [PATCH 05/28] Refactoring --- medacy/tools/con_form/brat_to_con.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/medacy/tools/con_form/brat_to_con.py b/medacy/tools/con_form/brat_to_con.py index 109c29a9..4c986908 100644 --- a/medacy/tools/con_form/brat_to_con.py +++ b/medacy/tools/con_form/brat_to_con.py @@ -190,9 +190,9 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): "a corresponding txt file (see help for this program).") exit() - # Create the log file - log_file_path = os.path.join(output_dir_name, "conversion.log") - logging.basicConfig(filename=log_file_path, level=logging.WARNING) + # Create the log + log_path = os.path.join(output_dir_name, "conversion.log") + logging.basicConfig(filename=log_path, level=logging.WARNING) for input_file_name in ann_files: full_file_path = os.path.join(input_dir_name, input_file_name) From c2721a18060421f90d529fb7749f873dae6fa09a Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 6 Mar 2019 15:33:58 -0500 Subject: [PATCH 06/28] Increased accuracy of con_to_brat, still need to resolve lines with leading whitespace --- medacy/tools/con_form/con_to_brat.py | 75 ++++++++++++++++++++++++---- 1 file changed, 64 insertions(+), 11 deletions(-) diff --git a/medacy/tools/con_form/con_to_brat.py b/medacy/tools/con_form/con_to_brat.py index e5c16938..59bbc9d1 100644 --- a/medacy/tools/con_form/con_to_brat.py +++ b/medacy/tools/con_form/con_to_brat.py @@ -7,7 +7,7 @@ Function 'convert_con_to_brat()' can be imported independently and run on individual files. :author: Steele W. Farnsworth -:date: 4 March, 2019 +:date: 5 March, 2019 """ from sys import argv, exit @@ -15,6 +15,13 @@ import os import shutil import logging +import tabulate + + +# Used for stats at the end +num_lines = 0 +num_skipped_regex = 0 +num_skipped_value_error = 0 def is_valid_con(item: str): @@ -59,7 +66,7 @@ def get_absolute_index(txt, txt_lns, ind, entity): :return: The absolute index """ - # convert ind to line_num and char_num + # Convert ind to line_num and char_num nums = split(":", ind) line_num = int(nums[0]) - 1 # line nums in con start at 1 and not 0 word_num = int(nums[1]) @@ -67,10 +74,32 @@ def get_absolute_index(txt, txt_lns, ind, entity): this_line = txt_lns[line_num] line_index = txt.index(this_line) # get the absolute index of the entire line - # Get index of word following n spaces - words = findall(r'\s*\S+\s*', this_line) - index_within_line = sum(map(len, words[:word_num])) + len(words[word_num]) - len(words[word_num].lstrip()) - offset = this_line[index_within_line:].index(entity) # adjusts if entity is not the first char in its "word" + # Get index of word following n space + split_by_whitespace = split("( +|\t+)+", this_line) + split_by_whitespace = [s for s in split_by_whitespace if s != ''] + split_by_ws_no_ws = [s for s in split_by_whitespace if not s.isspace()] + all_whitespace = [s for s in split_by_whitespace if s.isspace()] + line_to_target_word = split_by_ws_no_ws[:word_num] + num_non_whitespace = sum([len(w) for w in line_to_target_word]) + + # Offsets the start index by number of leading whitespace chars + leading_whitespace = 0 + for s in split_by_whitespace: + if not s.isspace(): break + else: leading_whitespace += 1 + + num_whitespace = sum([len(w) for w in all_whitespace[:word_num]]) + + try: + index_within_line = num_whitespace + num_non_whitespace + offset = this_line[index_within_line:].index(entity) # adjusts if entity is not the first char in its "word" + except ValueError: + logging.warning("""Entity not found in its expected line: + \t"%s" + \t"%s" + \tRevision of input data may be required; conversion for this item was skipped""" % (entity, this_line) + ) + return -1 return index_within_line + line_index + offset @@ -86,6 +115,8 @@ def convert_con_to_brat(con_file_path, text_file_path=None): :return: A string representation of the brat file, which can then be written to file if desired. """ + global num_lines, num_skipped_regex, num_skipped_value_error + # By default, find txt file with equivalent name if text_file_path is None: text_file_path = switch_extension(con_file_path, ".txt") @@ -103,6 +134,8 @@ def convert_con_to_brat(con_file_path, text_file_path=None): else: raise FileNotFoundError("No text file path was provided or the file was not found." " Note that direct string input of the source text is not supported.") + num_lines += len(text_lines) + # If con_file_path is actually a path, open it and split it into lines if os.path.isfile(con_file_path): with open(con_file_path, 'r') as con_file: @@ -116,12 +149,17 @@ def convert_con_to_brat(con_file_path, text_file_path=None): output_text = "" t = 1 for line in con_text_lines: - if not is_valid_con(line): + if line == "" or line.startswith("#"): continue + elif not is_valid_con(line): logging.warning("Incorrectly formatted line in %s was skipped: \"%s\"." % (con_file_path, line)) + num_skipped_regex += 1 continue d = line_to_dict(line) start_ind = get_absolute_index(text, text_lines, d["start_ind"], d["data_item"]) - span_length = d["data_item"].__len__() + if start_ind == -1: + num_skipped_value_error += 1 + continue # skips data that could not be converted + span_length = len(d["data_item"]) end_ind = start_ind + span_length output_line = "T%s\t%s %s %s\t%s\n" % (str(t), d["data_type"], str(start_ind), str(end_ind), d["data_item"]) output_text += output_line @@ -134,7 +172,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Get the input and output directories from the command line. - if not argv.__len__() >= 3: + if len(argv) < 3: # Command-line arguments must be provided for the input and output directories. # Else, prints instructions and aborts the program. print("Please run the program again, entering the input and output directories as command-line arguments" @@ -159,7 +197,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Create the log log_path = os.path.join(output_dir_name, "conversion.log") - logging.basicConfig(filename=log_path, level=logging.WARNING) + logging.basicConfig(filename=log_path) # Get only the text files in input_dir text_files = [f for f in input_dir if f.endswith(".txt")] @@ -183,8 +221,23 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Paste all the text files used in the conversion process to the output directory # if there's a fourth command line argument and that argument is -c - if argv.__len__() == 4 and argv[3] == "-c": + if len(argv) == 4 and argv[3] == "-c": text_files_with_match = [f for f in text_files if switch_extension(f, ".con") in con_files] for f in text_files_with_match: full_name = os.path.join(input_dir_name, f) shutil.copy(full_name, output_dir_name) + + # Compile and print stats to log + stat_headers = ["Total lines", "Total converted", "Lines skipped", "Skipped due to value error", + "Skipped did not match regex", "Percent converted"] + stat_data = [ + num_lines, + num_lines - num_skipped_regex - num_skipped_value_error, + num_skipped_regex + num_skipped_value_error, + num_skipped_value_error, + num_skipped_regex, + (num_lines - num_skipped_regex - num_skipped_value_error) / num_lines + ] + + conversion_stats = tabulate.tabulate(headers=stat_headers, tabular_data=[stat_data]) + logging.warning("\n" + conversion_stats) From a209d72971881a3b282d53cbffc968c4333d9beb Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Thu, 7 Mar 2019 17:42:05 -0500 Subject: [PATCH 07/28] Restructured directories to relation code --- medacy/ner/__init__.py | 1 + medacy/{ => ner}/model/__init__.py | 2 +- medacy/{ => ner}/model/_model.py | 0 .../model/discrete_feature_extractor.py} | 0 medacy/{ => ner}/model/model.py | 2 +- medacy/{ => ner}/model/stratified_k_fold.py | 0 medacy/{ => ner}/pipelines/__init__.py | 3 ++- medacy/{ => ner}/pipelines/base/__init__.py | 0 medacy/{ => ner}/pipelines/base/base_pipeline.py | 2 +- medacy/{ => ner}/pipelines/clinical_pipeline.py | 6 +++--- medacy/{ => ner}/pipelines/drug_event_pipeline.py | 8 ++++---- .../{ => ner}/pipelines/fda_nano_drug_label_pipeline.py | 6 +++--- medacy/{ => ner}/pipelines/systematic_review_pipeline.py | 6 +++--- medacy/{ => ner}/pipelines/testing_pipeline.py | 6 +++--- medacy/relation/__init__.py | 1 + 15 files changed, 23 insertions(+), 20 deletions(-) create mode 100644 medacy/ner/__init__.py rename medacy/{ => ner}/model/__init__.py (58%) rename medacy/{ => ner}/model/_model.py (100%) rename medacy/{model/feature_extractor.py => ner/model/discrete_feature_extractor.py} (100%) rename medacy/{ => ner}/model/model.py (99%) rename medacy/{ => ner}/model/stratified_k_fold.py (100%) rename medacy/{ => ner}/pipelines/__init__.py (71%) rename medacy/{ => ner}/pipelines/base/__init__.py (100%) rename medacy/{ => ner}/pipelines/base/base_pipeline.py (98%) rename medacy/{ => ner}/pipelines/clinical_pipeline.py (89%) rename medacy/{ => ner}/pipelines/drug_event_pipeline.py (90%) rename medacy/{ => ner}/pipelines/fda_nano_drug_label_pipeline.py (88%) rename medacy/{ => ner}/pipelines/systematic_review_pipeline.py (89%) rename medacy/{ => ner}/pipelines/testing_pipeline.py (88%) create mode 100644 medacy/relation/__init__.py diff --git a/medacy/ner/__init__.py b/medacy/ner/__init__.py new file mode 100644 index 00000000..0ac52b69 --- /dev/null +++ b/medacy/ner/__init__.py @@ -0,0 +1 @@ +from .model.model import Model diff --git a/medacy/model/__init__.py b/medacy/ner/model/__init__.py similarity index 58% rename from medacy/model/__init__.py rename to medacy/ner/model/__init__.py index eaaa1316..40561811 100644 --- a/medacy/model/__init__.py +++ b/medacy/ner/model/__init__.py @@ -1,3 +1,3 @@ from .model import Model -from .feature_extractor import FeatureExtractor +from .discrete_feature_extractor import FeatureExtractor from .stratified_k_fold import SequenceStratifiedKFold \ No newline at end of file diff --git a/medacy/model/_model.py b/medacy/ner/model/_model.py similarity index 100% rename from medacy/model/_model.py rename to medacy/ner/model/_model.py diff --git a/medacy/model/feature_extractor.py b/medacy/ner/model/discrete_feature_extractor.py similarity index 100% rename from medacy/model/feature_extractor.py rename to medacy/ner/model/discrete_feature_extractor.py diff --git a/medacy/model/model.py b/medacy/ner/model/model.py similarity index 99% rename from medacy/model/model.py rename to medacy/ner/model/model.py index a60f073c..ae52ab81 100644 --- a/medacy/model/model.py +++ b/medacy/ner/model/model.py @@ -5,7 +5,7 @@ import logging, os, joblib, time, importlib from medacy.data import Dataset from .stratified_k_fold import SequenceStratifiedKFold -from medacy.pipelines.base.base_pipeline import BasePipeline +from medacy.ner.pipelines import BasePipeline from pathos.multiprocessing import ProcessingPool as Pool, cpu_count from ._model import predict_document, construct_annotations_from_tuples from sklearn_crfsuite import metrics diff --git a/medacy/model/stratified_k_fold.py b/medacy/ner/model/stratified_k_fold.py similarity index 100% rename from medacy/model/stratified_k_fold.py rename to medacy/ner/model/stratified_k_fold.py diff --git a/medacy/pipelines/__init__.py b/medacy/ner/pipelines/__init__.py similarity index 71% rename from medacy/pipelines/__init__.py rename to medacy/ner/pipelines/__init__.py index 04e07315..162442e9 100644 --- a/medacy/pipelines/__init__.py +++ b/medacy/ner/pipelines/__init__.py @@ -2,4 +2,5 @@ from .systematic_review_pipeline import SystematicReviewPipeline from .fda_nano_drug_label_pipeline import FDANanoDrugLabelPipeline from .drug_event_pipeline import DrugEventPipeline -from .testing_pipeline import TestingPipeline \ No newline at end of file +from .testing_pipeline import TestingPipeline +from .base.base_pipeline import BasePipeline diff --git a/medacy/pipelines/base/__init__.py b/medacy/ner/pipelines/base/__init__.py similarity index 100% rename from medacy/pipelines/base/__init__.py rename to medacy/ner/pipelines/base/__init__.py diff --git a/medacy/pipelines/base/base_pipeline.py b/medacy/ner/pipelines/base/base_pipeline.py similarity index 98% rename from medacy/pipelines/base/base_pipeline.py rename to medacy/ner/pipelines/base/base_pipeline.py index 894b385d..1d04b3df 100644 --- a/medacy/pipelines/base/base_pipeline.py +++ b/medacy/ner/pipelines/base/base_pipeline.py @@ -1,5 +1,5 @@ from abc import ABC, abstractmethod -from ...pipeline_components.base import BaseComponent +from medacy.pipeline_components.base import BaseComponent class BasePipeline(ABC): """ diff --git a/medacy/pipelines/clinical_pipeline.py b/medacy/ner/pipelines/clinical_pipeline.py similarity index 89% rename from medacy/pipelines/clinical_pipeline.py rename to medacy/ner/pipelines/clinical_pipeline.py index 073dc29d..9c2637b0 100644 --- a/medacy/pipelines/clinical_pipeline.py +++ b/medacy/ner/pipelines/clinical_pipeline.py @@ -1,9 +1,9 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from ..pipeline_components import ClinicalTokenizer -from medacy.model.feature_extractor import FeatureExtractor +from medacy.pipeline_components import ClinicalTokenizer +from medacy.ner.model.discrete_feature_extractor import FeatureExtractor -from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, UnitComponent, MetaMap +from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent, MetaMap class ClinicalPipeline(BasePipeline): diff --git a/medacy/pipelines/drug_event_pipeline.py b/medacy/ner/pipelines/drug_event_pipeline.py similarity index 90% rename from medacy/pipelines/drug_event_pipeline.py rename to medacy/ner/pipelines/drug_event_pipeline.py index 7f2d4ee9..44731964 100644 --- a/medacy/pipelines/drug_event_pipeline.py +++ b/medacy/ner/pipelines/drug_event_pipeline.py @@ -1,10 +1,10 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from medacy.model.feature_extractor import FeatureExtractor +from medacy.ner.model.discrete_feature_extractor import FeatureExtractor -from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, CharacterTokenizer -from ..pipeline_components.lexicon import LexiconComponent -from ..pipeline_components.patterns import TableMatcherComponent +from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent, CharacterTokenizer +from medacy.pipeline_components.lexicon import LexiconComponent +from medacy.pipeline_components.patterns import TableMatcherComponent class DrugEventPipeline(BasePipeline): diff --git a/medacy/pipelines/fda_nano_drug_label_pipeline.py b/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py similarity index 88% rename from medacy/pipelines/fda_nano_drug_label_pipeline.py rename to medacy/ner/pipelines/fda_nano_drug_label_pipeline.py index a5b014b1..bfa92fee 100644 --- a/medacy/pipelines/fda_nano_drug_label_pipeline.py +++ b/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py @@ -1,9 +1,9 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from ..pipeline_components import SystematicReviewTokenizer, ClinicalTokenizer -from medacy.model.feature_extractor import FeatureExtractor +from medacy.pipeline_components import ClinicalTokenizer +from medacy.ner.model.discrete_feature_extractor import FeatureExtractor -from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, UnitComponent +from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent class FDANanoDrugLabelPipeline(BasePipeline): diff --git a/medacy/pipelines/systematic_review_pipeline.py b/medacy/ner/pipelines/systematic_review_pipeline.py similarity index 89% rename from medacy/pipelines/systematic_review_pipeline.py rename to medacy/ner/pipelines/systematic_review_pipeline.py index f007e850..d8b8b32a 100644 --- a/medacy/pipelines/systematic_review_pipeline.py +++ b/medacy/ner/pipelines/systematic_review_pipeline.py @@ -1,9 +1,9 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from ..pipeline_components import MetaMap, SystematicReviewTokenizer -from medacy.model.feature_extractor import FeatureExtractor +from medacy.pipeline_components import MetaMap, SystematicReviewTokenizer +from medacy.ner.model.discrete_feature_extractor import FeatureExtractor -from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, UnitComponent +from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent class SystematicReviewPipeline(BasePipeline): diff --git a/medacy/pipelines/testing_pipeline.py b/medacy/ner/pipelines/testing_pipeline.py similarity index 88% rename from medacy/pipelines/testing_pipeline.py rename to medacy/ner/pipelines/testing_pipeline.py index 471abb77..489cbc51 100644 --- a/medacy/pipelines/testing_pipeline.py +++ b/medacy/ner/pipelines/testing_pipeline.py @@ -1,9 +1,9 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from ..pipeline_components import ClinicalTokenizer -from medacy.model.feature_extractor import FeatureExtractor +from medacy.pipeline_components import ClinicalTokenizer +from medacy.ner.model.discrete_feature_extractor import FeatureExtractor -from ..pipeline_components import GoldAnnotatorComponent +from medacy.pipeline_components import GoldAnnotatorComponent class TestingPipeline(BasePipeline): diff --git a/medacy/relation/__init__.py b/medacy/relation/__init__.py new file mode 100644 index 00000000..0ac52b69 --- /dev/null +++ b/medacy/relation/__init__.py @@ -0,0 +1 @@ +from .model.model import Model From e85d454abb8285921e77c5cf1643887e66dbca56 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Tue, 12 Mar 2019 15:02:57 -0400 Subject: [PATCH 08/28] Commiting changes before pull --- .../images/config_remote_interpreter.png | Bin 106941 -> 106938 bytes 1 file changed, 0 insertions(+), 0 deletions(-) diff --git a/examples/guide/images/config_remote_interpreter.png b/examples/guide/images/config_remote_interpreter.png index 88127596bcf06b68bb7656687a77ecec8b8ecca7..0b58bbf2398c89cf1641f8ba6de06386baef6473 100644 GIT binary patch delta 26 icmdmcm~Gc#HkQr+KlhES{&kx}>-64iZ^>e`GzS2etqQdO delta 31 ncmdmWm~HQ2HrCDnKX=}ZEdF(jyqkmT^xiP?Zg0$Dv@{0*yJ!m8 From 78ff3f1f6c19b59871be13a556aacbb6f2cf7267 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 18:39:31 -0400 Subject: [PATCH 09/28] Created Line class to help with conversion accuracy --- .../tools/converters/conversion_tools/line.py | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 medacy/tools/converters/conversion_tools/line.py diff --git a/medacy/tools/converters/conversion_tools/line.py b/medacy/tools/converters/conversion_tools/line.py new file mode 100644 index 00000000..bb587587 --- /dev/null +++ b/medacy/tools/converters/conversion_tools/line.py @@ -0,0 +1,62 @@ +""" +:author: Steele Farnsworth +:date: 13 March, 2019 +""" + + +class Line: + """ + Represents a line of text in the text file related to an annotation file, ensuring that each line has an accurate + start index as one of its attributes regardless of whether that line appears more than once + """ + + def __init__(self, line_text: str, line_num: int, line_index: int): + self.text = line_text + self.num = line_num + self.index = line_index + + @staticmethod + def init_lines(full_text: str): + """ + Creates all the Line objects for a given text file, storing them in a list where index n is the nth - 1 + line of the document. + :param full_text: The entire text of the document. + :return: The list of Lines. + """ + global_start_ind = 0 + global_line_num = 0 + + full_text_lines = full_text.split('\n') + text_lines = [] + + for given_line in full_text_lines: + + sub_index = 0 + matches = [] + while sub_index < global_start_ind: + for previous_line in text_lines: + if given_line == previous_line.text: + matches.append(previous_line) + sub_index += previous_line.index + + if matches: + # Get the text from the end of the last match onward + search_text_start = matches[-1].index + len(matches[-1].text) + search_text = full_text[search_text_start:] + start_ind = search_text.index(given_line) + search_text_start + else: # The line is unique so str.index() will be accurate + start_ind = full_text.index(given_line) + + new_line = Line(given_line, global_line_num, start_ind) + text_lines.append(new_line) + + global_start_ind = text_lines[-1].index + global_line_num += 1 + + print(new_line) + + return text_lines + + def __str__(self): + """String representation of a line, with its index and text separated by a pipe.""" + return "%i | %s" % (self.index, self.text) From e5b0b9bf032b150eed510ce2c9695c030e2cab64 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 19:33:01 -0400 Subject: [PATCH 10/28] Removed print statement that was for debugging --- medacy/tools/converters/conversion_tools/line.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/medacy/tools/converters/conversion_tools/line.py b/medacy/tools/converters/conversion_tools/line.py index bb587587..72af12de 100644 --- a/medacy/tools/converters/conversion_tools/line.py +++ b/medacy/tools/converters/conversion_tools/line.py @@ -53,8 +53,6 @@ def init_lines(full_text: str): global_start_ind = text_lines[-1].index global_line_num += 1 - print(new_line) - return text_lines def __str__(self): From 13392a564427f89d19e4f31e6a85ae07e6a982f3 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:19:20 -0400 Subject: [PATCH 11/28] Improved accuracy for brat_to_con --- medacy/tools/con_form/brat_to_con.py | 89 ++++++++++++++++------------ 1 file changed, 52 insertions(+), 37 deletions(-) diff --git a/medacy/tools/con_form/brat_to_con.py b/medacy/tools/con_form/brat_to_con.py index 4c986908..e8fe0b40 100644 --- a/medacy/tools/con_form/brat_to_con.py +++ b/medacy/tools/con_form/brat_to_con.py @@ -3,31 +3,40 @@ Each '.ann' file must have a '.txt' file in the same directory with the same name, minus the extension. Use '-c' (without quotes) as an optional final command-line argument to copy the text files used in the conversion process to the output directory. + Also possible to import 'convert_brat_to_con()' directly and pass the paths to the ann and txt files for individual conversion. :author: Steele W. Farnsworth -:date: 16 February, 2019 +:date: 13 March, 2019 """ from sys import argv from re import split, fullmatch, DOTALL, findall +from medacy.tools.converters.conversion_tools.line import Line +import re import os import shutil import logging +import tabulate # A regex pattern for consecutive whitespace other than a new line character -whitespace_pattern = "( +|\t+)+" +whitespace_pattern = re.compile("( +|\t+)+") +# Regex pattern for BRAT T annotations +brat_pattern_T = r"T\d+\t\S+ \d+ \d+\t.+" + +# Used for stats at the end +num_lines = 0 +num_skipped_regex = 0 def is_valid_brat(item: str): """Returns a boolean value for whether or not a given line is in the BRAT format.""" # Define the regex pattern for BRAT. # Note that this pattern allows for three to six spaces to count as a tab - brat_pattern = r"[TREAMN]\d+(\t| {3,6})\S+ \d+ \d+(\t| {3,6}).+" if not isinstance(item, str): return False - if fullmatch(brat_pattern, item, DOTALL): return True + if fullmatch(brat_pattern_T, item, DOTALL): return True else: return False @@ -41,7 +50,7 @@ def line_to_dict(item): split1 = split("\t", item) split2 = split(" ", split1[1]) split3 = [split1[0]] + split2 + [split1[2]] - s = [i.rstrip() for i in split3] # remove whitespace + s = [i.strip() for i in split3] # remove whitespace return {"id_type": s[0][0], "id_num": int(s[0][1:]), "data_type": s[1], "start_ind": int(s[2]), "end_ind": int(s[3]), "data_item": s[4]} @@ -54,12 +63,6 @@ def switch_extension(name, ext): return os.path.splitext(name)[0] + ext -def get_line_index(text_, line_): - """Returns the index of the start of a given line. Assumes that the line_ - argument is long enough that (and thus so specific that) it only occurs once.""" - return text_.index(line_) - - def find_line_num(text_, start): """ :param text_: The text of the file, ex. f.read() @@ -69,19 +72,18 @@ def find_line_num(text_, start): return text_[:int(start)].count("\n") -def get_word_num(text_, line_index, entity_index): +def get_word_num(line_obj: Line, entity_index): """ - Returns the word number starting at zero that a given BRAT entity start index is within its line. - In the previous line, "Returns" is word 0 and "starting" is word 4. Words are counted by the number of consecutive - white spaces. - :param text_: The text of the document that the word occurs in. - :param line_index: The index of the first char of the line the word occurs in. - :param entity_index: The index of the first char of the word relative to the start of the document. - :return: The word number (see above explanation for what a word number is) of the given index within its line. + Returns the word number relative to the start of the line, with counting starting at 0, + of the first word of the entity. + :param line_obj: The Line that the entity occurs in. + :param entity_index: The absolute index of the entity, given by the annotation. + :return: The word index of the entity. """ - substring_before_entity = text_[line_index:entity_index] + index_within_line = entity_index - line_obj.index + substring_before_entity = line_obj.text[:index_within_line] matched_spaces = findall(whitespace_pattern, substring_before_entity) - return matched_spaces.__len__() + return len(matched_spaces) def convert_brat_to_con(brat_file_path, text_file_path=None): @@ -94,6 +96,8 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): :return: A string (not a file) of the con equivalent of the brat file. """ + global num_lines, num_skipped_regex + # By default, find txt file with equivalent name if text_file_path is None: text_file_path = switch_extension(brat_file_path, ".txt") @@ -102,12 +106,12 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): " directory") with open(text_file_path, 'r') as text_file: text = text_file.read() - text_lines = text.split('\n') + text_lines = Line.init_lines(text) # Otherwise open the file with the path passed to the function elif os.path.isfile(text_file_path): with open(text_file_path, 'r') as text_file: text = text_file.read() - text_lines = text.split('\n') + text_lines = Line.init_lines(text) else: raise FileNotFoundError("No text file path was provided or the file was not found." " Note that direct string input of the source text is not supported.") @@ -129,25 +133,25 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): continue elif not is_valid_brat(line): logging.warning("Incorrectly formatted line in %s was skipped: \"%s\"." % (brat_file_path, line)) + num_skipped_regex += 1 continue d = line_to_dict(line) start_line_num = find_line_num(text, d["start_ind"]) - start_text_line = text_lines[start_line_num] - start_line_index = get_line_index(text, start_text_line) - start_word_num = get_word_num(text, start_line_index, d["start_ind"]) + start_source_line = text_lines[start_line_num] + start_word_num = get_word_num(start_source_line, d["start_ind"]) start_str = str(start_line_num + 1) + ':' + str(start_word_num) end_line_num = find_line_num(text, d["end_ind"]) - end_text_line = text_lines[end_line_num] - end_line_index = get_line_index(text, end_text_line) - end_word_num = get_word_num(text, end_line_index, d["end_ind"]) + end_word_num = start_word_num + len(re.findall(whitespace_pattern, d["data_item"])) end_str = str(end_line_num + 1) + ':' + str(end_word_num) con_line = "c=\"%s\" %s %s||t=\"%s\"\n" % (d["data_item"], start_str, end_str, d['data_type']) output_lines += con_line + num_lines += 1 + return output_lines @@ -155,13 +159,11 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): # Get the input and output directories from the command line. - if not argv.__len__() >= 3: + if len(argv) < 3: # Command-line arguments must be provided for the input and output directories. - # Else, prints instructions and aborts the program. - print("Please run the program again, entering the input and output directories as command-line arguments" - " in that order. Optionally, enter '-c' as a final command line argument if you want to copy" - " the text files used in the conversion over to the output directory.") - exit() + raise IOError("Please run the program again, entering the input and output directories as command-line" + " arguments in that order. Optionally, enter '-c' as a final command line argument if you want" + " to copy the text files used in the conversion over to the output directory.") try: input_dir_name = argv[1] @@ -188,7 +190,6 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): raise FileNotFoundError("There were no ann files in the input directory with a corresponding text file. " "Please ensure that the input directory contains ann files and that each file has " "a corresponding txt file (see help for this program).") - exit() # Create the log log_path = os.path.join(output_dir_name, "conversion.log") @@ -203,8 +204,22 @@ def convert_brat_to_con(brat_file_path, text_file_path=None): # Paste all the text files used in the conversion process to the output directory # if there's a fourth command line argument and that argument is -c - if argv.__len__() == 4 and argv[3] == "-c": + if len(argv) >= 4 and argv[3] == "-c": text_files_with_match = [f for f in text_files if switch_extension(f, ".ann") in ann_files] for f in text_files_with_match: full_name = os.path.join(input_dir_name, f) shutil.copy(full_name, output_dir_name) + + # Compile and print stats to log + stat_headers = ["Total lines", "Total converted", + "Skipped did not match regex", "Percent converted"] + + stat_data = [ + num_lines, + num_lines - num_skipped_regex, + num_skipped_regex, + (num_lines - num_skipped_regex) / num_lines + ] + + conversion_stats = tabulate.tabulate(headers=stat_headers, tabular_data=[stat_data]) + logging.warning("\n" + conversion_stats) From b3cbda1ca9ff73646757c6fbf46ab61ce7a7b339 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:19:44 -0400 Subject: [PATCH 12/28] Improved accuracy for con_to_brat --- medacy/tools/con_form/con_to_brat.py | 63 ++++++++++++++++------------ 1 file changed, 37 insertions(+), 26 deletions(-) diff --git a/medacy/tools/con_form/con_to_brat.py b/medacy/tools/con_form/con_to_brat.py index 59bbc9d1..d546dc89 100644 --- a/medacy/tools/con_form/con_to_brat.py +++ b/medacy/tools/con_form/con_to_brat.py @@ -6,18 +6,27 @@ Function 'convert_con_to_brat()' can be imported independently and run on individual files. +This program can be used for conversion independently from medaCy if the Line class is copied +and pasted into a copy of this program. + :author: Steele W. Farnsworth -:date: 5 March, 2019 +:date: 13 March, 2019 """ from sys import argv, exit from re import split, findall, fullmatch +from medacy.tools.converters.conversion_tools.line import Line +import re import os import shutil import logging import tabulate +# Regex patterns +whitespace_pattern = "( +|\t+)+" +con_pattern = "c=\".+?\" \d+:\d+ \d+:\d+\|\|t=\".+?\"(|\n)" + # Used for stats at the end num_lines = 0 num_skipped_regex = 0 @@ -31,7 +40,6 @@ def is_valid_con(item: str): :return: Boolean of whether or not the line matches a con regular expression. """ if not isinstance(item, str): return False - con_pattern = "c=\".+?\" \d+:\d+ \d+:\d+\|\|t=\".+?\"(|\n)" if fullmatch(con_pattern, item): return True else: return False @@ -55,12 +63,11 @@ def switch_extension(name, ext): return os.path.splitext(name)[0] + ext -def get_absolute_index(txt, txt_lns, ind, entity): +def get_absolute_index(txt_lns, ind, entity): """ Given one of the \d+:\d+ spans, which represent the index of a word relative to the start of the line it's on, returns the index of that char relative to the start of the file. - :param txt: The text itself of the text file associated with the annotation. - :param txt_lns: The same text file as a list broken by lines + :param txt_lns: The list of Line objects for that file. :param ind: The string in format \d+:\d+ :param entity: The text of the entity :return: The absolute index @@ -72,28 +79,34 @@ def get_absolute_index(txt, txt_lns, ind, entity): word_num = int(nums[1]) this_line = txt_lns[line_num] - line_index = txt.index(this_line) # get the absolute index of the entire line + line_index = this_line.index # Get index of word following n space - split_by_whitespace = split("( +|\t+)+", this_line) + split_by_whitespace = split(whitespace_pattern, this_line.text) split_by_whitespace = [s for s in split_by_whitespace if s != ''] split_by_ws_no_ws = [s for s in split_by_whitespace if not s.isspace()] all_whitespace = [s for s in split_by_whitespace if s.isspace()] - line_to_target_word = split_by_ws_no_ws[:word_num] - num_non_whitespace = sum([len(w) for w in line_to_target_word]) - # Offsets the start index by number of leading whitespace chars - leading_whitespace = 0 - for s in split_by_whitespace: - if not s.isspace(): break - else: leading_whitespace += 1 + # Adjust word_num if first character cluster is whitespace + if split_by_whitespace[0].isspace(): + line_to_target_word = split_by_ws_no_ws[:word_num - 1] + else: + line_to_target_word = split_by_ws_no_ws[:word_num] + num_non_whitespace = sum([len(w) for w in line_to_target_word]) num_whitespace = sum([len(w) for w in all_whitespace[:word_num]]) + index_within_line = num_whitespace + num_non_whitespace + line_to_start_index = this_line.text[index_within_line:] + entity_pattern_escaped = re.escape(entity) + entity_pattern_spaced = re.sub(r"\\\s+", r"\s+", entity_pattern_escaped) + try: - index_within_line = num_whitespace + num_non_whitespace - offset = this_line[index_within_line:].index(entity) # adjusts if entity is not the first char in its "word" - except ValueError: + # Search for entity regardless of case or composition of intermediate spaces + # match = re.search(entity_pattern_spaced, this_line.text, re.IGNORECASE)[0] + match = re.search(entity_pattern_spaced, line_to_start_index, re.IGNORECASE)[0] + offset = line_to_start_index.index(match) # adjusts if entity is not the first char in its "word" + except (ValueError, TypeError): logging.warning("""Entity not found in its expected line: \t"%s" \t"%s" @@ -125,12 +138,12 @@ def convert_con_to_brat(con_file_path, text_file_path=None): " directory") with open(text_file_path, 'r') as text_file: text = text_file.read() - text_lines = text.split('\n') + text_lines = Line.init_lines(text) # Else, open the file with the path passed to the function elif os.path.isfile(text_file_path): with open(text_file_path, 'r') as text_file: text = text_file.read() - text_lines = text.split('\n') + text_lines = Line.init_lines(text) else: raise FileNotFoundError("No text file path was provided or the file was not found." " Note that direct string input of the source text is not supported.") @@ -155,7 +168,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): num_skipped_regex += 1 continue d = line_to_dict(line) - start_ind = get_absolute_index(text, text_lines, d["start_ind"], d["data_item"]) + start_ind = get_absolute_index(text_lines, d["start_ind"], d["data_item"]) if start_ind == -1: num_skipped_value_error += 1 continue # skips data that could not be converted @@ -174,11 +187,9 @@ def convert_con_to_brat(con_file_path, text_file_path=None): if len(argv) < 3: # Command-line arguments must be provided for the input and output directories. - # Else, prints instructions and aborts the program. - print("Please run the program again, entering the input and output directories as command-line arguments" - " in that order. Optionally, enter '-c' as a final command line argument if you want to copy" - " the text files used in the conversion over to the output directory.") - exit() + raise IOError("Please run the program again, entering the input and output directories as command-line" + " arguments in that order. Optionally, enter '-c' as a final command line argument if you want" + " to copy the text files used in the conversion over to the output directory.") try: input_dir_name = argv[1] @@ -221,7 +232,7 @@ def convert_con_to_brat(con_file_path, text_file_path=None): # Paste all the text files used in the conversion process to the output directory # if there's a fourth command line argument and that argument is -c - if len(argv) == 4 and argv[3] == "-c": + if len(argv) >= 4 and argv[3] == "-c": text_files_with_match = [f for f in text_files if switch_extension(f, ".con") in con_files] for f in text_files_with_match: full_name = os.path.join(input_dir_name, f) From 2603149b1c944188fd89b3cbe79ad046c1180e3a Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:20:01 -0400 Subject: [PATCH 13/28] Updated tests for brat_to_con --- .../tests/tools/con_form/test_brat_to_con.py | 30 ++++++++++--------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/medacy/tests/tools/con_form/test_brat_to_con.py b/medacy/tests/tools/con_form/test_brat_to_con.py index d7648907..5a5f5e2e 100644 --- a/medacy/tests/tools/con_form/test_brat_to_con.py +++ b/medacy/tests/tools/con_form/test_brat_to_con.py @@ -1,9 +1,9 @@ """ :author: Steele W. Farnsworth -:date: 28 December, 2018 +:date: 13 March, 2019 """ -import unittest, tempfile, os, shutil +import unittest, tempfile from medacy.tools.con_form.brat_to_con import * brat_text = """T1 tradename 0 7 ABELCET @@ -92,33 +92,35 @@ def setUpClass(cls): cls.output_file_path = os.path.join(cls.test_dir, "output_file.txt") + cls.lines = Line.init_lines(source_text) + @classmethod def tearDownClass(cls): shutil.rmtree(cls.test_dir) - def is_valid_brat_valid_1(self): + def test_is_valid_brat_valid_1(self): """Tests that when is_valid_brat() gets called on a valid line without a new line character, it returns True.""" sample = "T3 nanoparticle 24 37 Lipid Complex" result = is_valid_brat(sample) self.assertTrue(result) - def is_valid_brat_valid_2(self): + def test_is_valid_brat_valid_2(self): """Tests that when is_valid_brat() is called on a valid line with a new line character, it returns True.""" sample = "T12 nanoparticle 674 683 liposomal\n" result = is_valid_brat(sample) self.assertTrue(result) - def is_valid_brat_invalid_1(self): + def test_is_valid_brat_invalid_1(self): """Tests what when is_valid_brat() is called on an invalid line without a new line character, it returns False.""" sample = "T3 nanoparticle s 37 Lipid Complex" result = is_valid_brat(sample) self.assertFalse(result) - def is_valid_brat_invalid_2(self): + def test_is_valid_brat_invalid_2(self): """Tests what when is_valid_brat() is called on an invalid line with a new line character, it returns False.""" sample = "T12 674 683 liposomal\n" result = is_valid_brat(sample) - self.assertTrue(result) + self.assertFalse(result) def test_line_to_dict(self): """Tests that line_to_dict() accurately converts a line of input text to an expected dict format.""" @@ -142,10 +144,10 @@ def test_get_word_num_1(self): """ # The annotation used is "T5 tradename 132 139 ABELCET" sample_line = "ABELCET consists of ampho-tericin B complexed with two phospholipids in a 1:1 drug-to-lipid molar ratio." - line_index = get_line_index(source_text, sample_line) + this_line = self.lines[1] expected = 0 - actual = get_word_num(source_text, line_index, 132) - self.assertEqual(expected, actual) + actual = get_word_num(this_line, 132) + self.assertEqual(actual, expected) def test_get_word_num_2(self): """ @@ -154,15 +156,15 @@ def test_get_word_num_2(self): """ # The annotation used is "T16 activeingredient 1009 1023 Amphotericin B" sample_line = "Suchdifferences may affect functional properties of these drug products.Amphotericin B is a polyene, antifungal antibiotic produced from a strain of Streptomyces nodosus.Amphotericin B is designated chemically as [1R-(1R*, 3S*, 5R*, 6R*, 9R*, 11R*, 15S*, 16R*, 17R*,18S*, 19E, 21E, 23E, 25E, 27E, 29E, 31E, 33R*, 35S*, 36R*, 37S*)]-33-[(3-Amino-3, 6- D-mannopyranosyl) oxy]-1,3,5,6,9,11,17,37-octahydroxy-15,16,18-trimethyl-13-oxo-14,39-dioxabicy-clo[33.3.1] nonatriaconta-19, 21, 23, 25, 27, 29, 31-heptaene-36-carboxylic acid." - line_index = get_line_index(source_text, sample_line) + this_line = self.lines[6] expected = 21 - actual = get_word_num(source_text, line_index, 1009) + actual = get_word_num(this_line, 1009) self.assertEqual(expected, actual) def test_valid_brat_to_con(self): """Convert the test file from brat to con. Assert that the con output matches the sample con text.""" con_output = convert_brat_to_con(self.brat_file_path, self.text_file_path) - self.assertEqual(con_output, con_text) + self.assertEqual(con_text, con_output) def test_invalid_file_path(self): """Passes an invalid file path to convert_brat_to_con().""" @@ -174,7 +176,7 @@ def test_valid_brat_matching_text_name(self): Assert that the con output matches the sample con text when the automatic text-file-finding feature is utilized """ con_output = convert_brat_to_con(self.brat_file_path) - self.assertEqual(con_output, con_text) + self.assertEqual(con_text, con_output) def test_invalid_brat_text(self): """Assert that invalid brat text produces no output.""" From c95c1f3cd383ffac2d842380b15a87b1d3fc6a5b Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:20:19 -0400 Subject: [PATCH 14/28] Updated tests for con_to_brat --- medacy/tests/tools/con_form/test_con_to_brat.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/medacy/tests/tools/con_form/test_con_to_brat.py b/medacy/tests/tools/con_form/test_con_to_brat.py index 0a1d6c53..7689ceed 100644 --- a/medacy/tests/tools/con_form/test_con_to_brat.py +++ b/medacy/tests/tools/con_form/test_con_to_brat.py @@ -1,6 +1,6 @@ """ :author: Steele W. Farnsworth -:date: 04 March, 2019 +:date: 13 March, 2019 """ import unittest, tempfile, os, shutil From dbf90d2b913341b372db8cb6bc7491648f38541c Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:20:37 -0400 Subject: [PATCH 15/28] Created tests for Line class --- .../converters/conversion_tools/test_line.py | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 medacy/tests/tools/converters/conversion_tools/test_line.py diff --git a/medacy/tests/tools/converters/conversion_tools/test_line.py b/medacy/tests/tools/converters/conversion_tools/test_line.py new file mode 100644 index 00000000..a6409b12 --- /dev/null +++ b/medacy/tests/tools/converters/conversion_tools/test_line.py @@ -0,0 +1,45 @@ +import unittest +from medacy.tools.converters.conversion_tools.line import Line + + +# Sample text must be on the lowest level of indentation so that +# the indentation is not counted towards the indices. + +sample_text_1 = """ABELCET (Amphotericin B Lipid Complex Injection)DESCRIPTIONABELCET is a sterile, pyrogen-free suspension for intravenous infusion. +ABELCET consists of ampho-tericin B complexed with two phospholipids in a 1:1 drug-to-lipid molar ratio. +The two phospholipids,L-α-dimyristoylphosphatidylcholine (DMPC) and L-α-dimyristoylphosphatidylglycerol (DMPG), are pre-sent in a 7:3 molar ratio. +ABELCET is yellow and opaque in appearance, with a pH of 5 - 7. +NOTE: Liposomal encapsulation or incorporation in a lipid complex can substantially affect adrug's functional properties relative to those of the unencapsulated or nonlipid-associated drug. +Inaddition, different liposomal or lipid-complexed products with a common active ingredient mayvary from one another in the chemical composition and physical form of the lipid component. +Suchdifferences may affect functional properties of these drug products.Amphotericin B is a polyene, antifungal antibiotic produced from a strain of Streptomyces nodosus.Amphotericin B is designated chemically as [1R-(1R*, 3S*, 5R*, 6R*, 9R*, 11R*, 15S*, 16R*, 17R*,18S*, 19E, 21E, 23E, 25E, 27E, 29E, 31E, 33R*, 35S*, 36R*, 37S*)]-33-[(3-Amino-3, 6- D-mannopyranosyl) oxy]-1,3,5,6,9,11,17,37-octahydroxy-15,16,18-trimethyl-13-oxo-14,39-dioxabicy-clo[33.3.1] nonatriaconta-19, 21, 23, 25, 27, 29, 31-heptaene-36-carboxylic acid. +It has a molecular weight of 924.09 and a molecular formula of C47H73NO17. +The structural formula is: +ABELCET is provided as a sterile, opaque suspension in 20 mL glass, single-use vials.""" + +sample_text_2 = """This is the first sample line +This is the second line +Also this line +This is another line +Also this line +The previous line is a repeat on purpose +Also this line +This is so much fun""" + + +class TestLine(unittest.TestCase): + """Unit tests for line.py""" + + def test_init_lines_no_repeats(self): + """Test that indices are accurate when there are no repeated lines.""" + text_lines = sample_text_1.split('\n') + line_objs = Line.init_lines(sample_text_1) + expected = [sample_text_1.index(line) for line in text_lines] + actual = [line.index for line in line_objs] + self.assertListEqual(actual, expected) + + def test_init_lines_with_repeats(self): + """Test that indices are accurate even when lines are repeated.""" + line_objs = Line.init_lines(sample_text_2) + expected = [0, 30, 54, 69, 90, 105, 146, 161] + actual = [line.index for line in line_objs] + self.assertListEqual(actual, expected) From 03444d9008c0eabc8d278a3c9d3b54c8d0c80719 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 13 Mar 2019 20:37:39 -0400 Subject: [PATCH 16/28] Moved converter files into a converter directory; likewise with unit tests --- .../guide/images/config_remote_interpreter.png | Bin 106938 -> 0 bytes medacy/tests/tools/__init__.py | 2 +- .../tools/{con_form => converters}/__init__.py | 0 .../tools/converters/con_test_data/__init__.py | 0 .../{ => converters}/con_test_data/con_test.py | 0 .../test_brat_to_con.py | 2 +- .../test_con_to_brat.py | 4 ++-- medacy/tests/tools/test_annotation.py | 4 ++-- medacy/tools/__init__.py | 2 +- medacy/tools/annotations.py | 4 ++-- medacy/tools/converters/__init__.py | 0 medacy/tools/{ => converters}/ade_to_brat.py | 0 .../{con_form => converters}/brat_to_con.py | 0 .../{con_form => converters}/con_to_brat.py | 0 .../converters/conversion_tools/__init__.py | 0 15 files changed, 9 insertions(+), 9 deletions(-) delete mode 100644 examples/guide/images/config_remote_interpreter.png rename medacy/tests/tools/{con_form => converters}/__init__.py (100%) create mode 100644 medacy/tests/tools/converters/con_test_data/__init__.py rename medacy/tests/tools/{ => converters}/con_test_data/con_test.py (100%) rename medacy/tests/tools/{con_form => converters}/test_brat_to_con.py (99%) rename medacy/tests/tools/{con_form => converters}/test_con_to_brat.py (98%) create mode 100644 medacy/tools/converters/__init__.py rename medacy/tools/{ => converters}/ade_to_brat.py (100%) rename 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zJC=VKt0r}amM(TZd)`OKKpyg){NxLPJv@#1P(=#DrH#y4tE-HaOXp>%K7u(l+xKf0 zn)B_>^^*4gwhdBq3zTA=s-{17DAcAlilM2ugP4x`|uFPLT!sDgSrArIL)OQmsiWFzq zc_y@(9(eAxYxY1DV4-;9+Xx}n;L!W3CDHM(1I6!Q1Zg!gG_s^f!wSKFp25(Dd>DRJuTT0-9V(~^c~RZm zTIw@3YuuC^R_Re4Su=N|%OM#5W7?PGbWF@_s(1vDX>UeaIDxkN)1UDKGF(E)rDW+d ze>y^3d=dzCS{5+|-?KBJt#7P$3etI`X%hDWhR|2g2$5v8)VZy5n;%t3m6*8o-OMR9 z>=zU6l2MbjME=_>;XmFm1Oy6?xI>ir4K`Xz)*0)_Gq}i3!iHZcTd})Z{u11~!-ivO zmai?@rS6aqxZk}L(a-Y|+!(d^fbA_I}`Wa=U=)UVe%193veCt}JeKLI_#_%Y)3XC%E$z#~~ zR_6SMIp4u))a>+%6-ex$GU30Z%rMZvX0!cH3su!gU4a`GHR?=D4Bs-?13+NW&O!~V zxU+$AQ!lljOaC!pz1C1L8T3R~qbPWZ~<9rC2k&iZG2_YeW>z;YC>?O6n zZ6&m7yB7txxNhb)(YC1UAXBz*RmadTHlnpuN1 zcQCQ{R(b^8nhf+fSY!hRURU5J@1_?p&f_ZqMe1*9u~;zdL;E4NmaSA0#}<@XG4z_jo525_h Date: Thu, 14 Mar 2019 21:36:17 -0400 Subject: [PATCH 17/28] Deleted con_form directory, which is no longer used --- medacy/tools/con_form/__init__.py | 0 1 file changed, 0 insertions(+), 0 deletions(-) delete mode 100644 medacy/tools/con_form/__init__.py diff --git a/medacy/tools/con_form/__init__.py b/medacy/tools/con_form/__init__.py deleted file mode 100644 index e69de29b..00000000 From 2cd3c7eae2c6949de5b6332f4a7533c3b8056f7f Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 15 Mar 2019 11:13:35 -0400 Subject: [PATCH 18/28] Completed Restructuring - Now to find bugs --- README.md | 2 +- docs/source/medacy.model.feature_extractor.rst | 7 ------- docs/source/medacy.model.rst | 8 -------- ...acy.model.model.rst => medacy.ner.model.model.rst} | 4 ++-- docs/source/medacy.ner.model.rst | 7 +++++++ ...old.rst => medacy.ner.model.stratified_k_fold.rst} | 4 ++-- .../medacy.ner.pipelines.base.base_pipeline.rst | 7 +++++++ docs/source/medacy.ner.pipelines.base.rst | 6 ++++++ .../source/medacy.ner.pipelines.clinical_pipeline.rst | 7 +++++++ .../medacy.ner.pipelines.drug_event_pipeline.rst | 7 +++++++ ...acy.ner.pipelines.fda_nano_drug_label_pipeline.rst | 7 +++++++ docs/source/medacy.ner.pipelines.rst | 11 +++++++++++ ...edacy.ner.pipelines.systematic_review_pipeline.rst | 7 +++++++ ....rst => medacy.ner.pipelines.testing_pipeline.rst} | 4 ++-- docs/source/medacy.ner.rst | 7 +++++++ ....feature_extraction.discrete_feature_extractor.rst | 7 +++++++ .../medacy.pipeline_components.feature_extraction.rst | 6 ++++++ docs/source/medacy.pipeline_components.rst | 1 + docs/source/medacy.pipelines.base.base_pipeline.rst | 7 ------- docs/source/medacy.pipelines.base.rst | 6 ------ docs/source/medacy.pipelines.clinical_pipeline.rst | 7 ------- docs/source/medacy.pipelines.drug_event_pipeline.rst | 7 ------- .../medacy.pipelines.fda_nano_drug_label_pipeline.rst | 7 ------- docs/source/medacy.pipelines.rst | 11 ----------- .../medacy.pipelines.systematic_review_pipeline.rst | 7 ------- docs/source/medacy.relation.rst | 4 ++++ docs/source/medacy.rst | 4 ++-- examples/guide/data_management.md | 2 +- examples/guide/model_training.md | 4 ++-- examples/guide/model_utilization.md | 4 ++-- examples/scripts/training_predicting.py | 2 +- medacy/__init__.py | 2 +- medacy/ner/model/__init__.py | 1 - medacy/ner/pipelines/clinical_pipeline.py | 2 +- medacy/ner/pipelines/drug_event_pipeline.py | 2 +- medacy/ner/pipelines/fda_nano_drug_label_pipeline.py | 2 +- medacy/ner/pipelines/systematic_review_pipeline.py | 2 +- medacy/ner/pipelines/testing_pipeline.py | 2 +- medacy/pipeline_components/__init__.py | 3 +++ .../feature_extraction}/__init__.py | 0 .../feature_extraction}/discrete_feature_extractor.py | 0 medacy/tests/ner/__init__.py | 0 medacy/tests/ner/model/__init__.py | 0 medacy/tests/{ => ner}/model/test_model_prediction.py | 4 ++-- medacy/tests/ner/pipelines/__init__.py | 0 .../{ => ner}/pipelines/test_clinical_pipeline.py | 2 +- 46 files changed, 111 insertions(+), 92 deletions(-) delete mode 100644 docs/source/medacy.model.feature_extractor.rst delete mode 100644 docs/source/medacy.model.rst rename docs/source/{medacy.model.model.rst => medacy.ner.model.model.rst} (54%) create mode 100644 docs/source/medacy.ner.model.rst rename docs/source/{medacy.model.stratified_k_fold.rst => medacy.ner.model.stratified_k_fold.rst} (50%) create mode 100644 docs/source/medacy.ner.pipelines.base.base_pipeline.rst create mode 100644 docs/source/medacy.ner.pipelines.base.rst create mode 100644 docs/source/medacy.ner.pipelines.clinical_pipeline.rst create mode 100644 docs/source/medacy.ner.pipelines.drug_event_pipeline.rst create mode 100644 docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst create mode 100644 docs/source/medacy.ner.pipelines.rst create mode 100644 docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst rename docs/source/{medacy.pipelines.testing_pipeline.rst => medacy.ner.pipelines.testing_pipeline.rst} (50%) create mode 100644 docs/source/medacy.ner.rst create mode 100644 docs/source/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst create mode 100644 docs/source/medacy.pipeline_components.feature_extraction.rst delete mode 100644 docs/source/medacy.pipelines.base.base_pipeline.rst delete mode 100644 docs/source/medacy.pipelines.base.rst delete mode 100644 docs/source/medacy.pipelines.clinical_pipeline.rst delete mode 100644 docs/source/medacy.pipelines.drug_event_pipeline.rst delete mode 100644 docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst delete mode 100644 docs/source/medacy.pipelines.rst delete mode 100644 docs/source/medacy.pipelines.systematic_review_pipeline.rst create mode 100644 docs/source/medacy.relation.rst rename medacy/{tests/pipelines => pipeline_components/feature_extraction}/__init__.py (100%) rename medacy/{ner/model => pipeline_components/feature_extraction}/discrete_feature_extractor.py (100%) create mode 100644 medacy/tests/ner/__init__.py create mode 100644 medacy/tests/ner/model/__init__.py rename medacy/tests/{ => ner}/model/test_model_prediction.py (95%) create mode 100644 medacy/tests/ner/pipelines/__init__.py rename medacy/tests/{ => ner}/pipelines/test_clinical_pipeline.py (92%) diff --git a/README.md b/README.md index 8fbde2e8..6a40229b 100644 --- a/README.md +++ b/README.md @@ -34,7 +34,7 @@ Medacy can be installed for general use or for pipeline development / research p After installing medaCy and [medaCy's clinical model](examples/models/clinical_notes_model.md), simply run: ```python -from medacy.model import Model +from medacy.ner.model import Model model = Model.load_external('medacy_model_clinical_notes') annotation = model.predict("The patient was prescribed 1 capsule of Advil for 5 days.") diff --git a/docs/source/medacy.model.feature_extractor.rst b/docs/source/medacy.model.feature_extractor.rst deleted file mode 100644 index 013a99c7..00000000 --- a/docs/source/medacy.model.feature_extractor.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.model.feature\_extractor module -====================================== - -.. automodule:: medacy.model.feature_extractor - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.model.rst b/docs/source/medacy.model.rst deleted file mode 100644 index 0695ea40..00000000 --- a/docs/source/medacy.model.rst +++ /dev/null @@ -1,8 +0,0 @@ -medacy.model package -==================== - -.. toctree:: - - medacy.model.feature_extractor - medacy.model.model - medacy.model.stratified_k_fold diff --git a/docs/source/medacy.model.model.rst b/docs/source/medacy.ner.model.model.rst similarity index 54% rename from docs/source/medacy.model.model.rst rename to docs/source/medacy.ner.model.model.rst index 0eddf1fb..e5b4fc06 100644 --- a/docs/source/medacy.model.model.rst +++ b/docs/source/medacy.ner.model.model.rst @@ -1,7 +1,7 @@ -medacy.model.model module +medacy.ner.model.model module ========================= -.. automodule:: medacy.model.model +.. automodule:: medacy.ner.model.model :members: :undoc-members: :show-inheritance: diff --git a/docs/source/medacy.ner.model.rst b/docs/source/medacy.ner.model.rst new file mode 100644 index 00000000..1a48d393 --- /dev/null +++ b/docs/source/medacy.ner.model.rst @@ -0,0 +1,7 @@ +medacy.ner.model package +==================== + +.. toctree:: + + medacy.ner.model.model + medacy.ner.model.stratified_k_fold \ No newline at end of file diff --git a/docs/source/medacy.model.stratified_k_fold.rst b/docs/source/medacy.ner.model.stratified_k_fold.rst similarity index 50% rename from docs/source/medacy.model.stratified_k_fold.rst rename to docs/source/medacy.ner.model.stratified_k_fold.rst index cc3213cf..4f1cb965 100644 --- a/docs/source/medacy.model.stratified_k_fold.rst +++ b/docs/source/medacy.ner.model.stratified_k_fold.rst @@ -1,7 +1,7 @@ -medacy.model.stratified\_k\_fold module +medacy.ner.model.stratified\_k\_fold module ======================================= -.. automodule:: medacy.model.stratified_k_fold +.. automodule:: medacy.ner.model.stratified_k_fold :members: :undoc-members: :show-inheritance: diff --git a/docs/source/medacy.ner.pipelines.base.base_pipeline.rst b/docs/source/medacy.ner.pipelines.base.base_pipeline.rst new file mode 100644 index 00000000..4d487e7e --- /dev/null +++ b/docs/source/medacy.ner.pipelines.base.base_pipeline.rst @@ -0,0 +1,7 @@ +medacy.ner.pipelines.base.base\_pipeline module +=========================================== + +.. automodule:: medacy.ner.pipelines.base.base_pipeline + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.ner.pipelines.base.rst b/docs/source/medacy.ner.pipelines.base.rst new file mode 100644 index 00000000..7e073844 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.base.rst @@ -0,0 +1,6 @@ +medacy.ner.pipelines.base package +============================= + +.. toctree:: + + medacy.ner.pipelines.base.base_pipeline diff --git a/docs/source/medacy.ner.pipelines.clinical_pipeline.rst b/docs/source/medacy.ner.pipelines.clinical_pipeline.rst new file mode 100644 index 00000000..c6a766c2 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.clinical_pipeline.rst @@ -0,0 +1,7 @@ +medacy.ner.pipelines.clinical\_pipeline module +========================================== + +.. automodule:: medacy.ner.pipelines.clinical_pipeline + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.ner.pipelines.drug_event_pipeline.rst b/docs/source/medacy.ner.pipelines.drug_event_pipeline.rst new file mode 100644 index 00000000..4d26fd29 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.drug_event_pipeline.rst @@ -0,0 +1,7 @@ +medacy.ner.pipelines.drug\_event\_pipeline module +============================================= + +.. automodule:: medacy.ner.pipelines.drug_event_pipeline + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst b/docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst new file mode 100644 index 00000000..13a74898 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.fda_nano_drug_label_pipeline.rst @@ -0,0 +1,7 @@ +medacy.ner.pipelines.fda\_nano\_drug\_label\_pipeline module +======================================================== + +.. automodule:: medacy.ner.pipelines.fda_nano_drug_label_pipeline + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.ner.pipelines.rst b/docs/source/medacy.ner.pipelines.rst new file mode 100644 index 00000000..ff8eacc2 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.rst @@ -0,0 +1,11 @@ +medacy.ner.pipelines package +======================== + +.. toctree:: + + medacy.ner.pipelines.base + medacy.ner.pipelines.clinical_pipeline + medacy.ner.pipelines.drug_event_pipeline + medacy.ner.pipelines.fda_nano_drug_label_pipeline + medacy.ner.pipelines.systematic_review_pipeline + medacy.ner.pipelines.testing_pipeline diff --git a/docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst b/docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst new file mode 100644 index 00000000..ebf76cd0 --- /dev/null +++ b/docs/source/medacy.ner.pipelines.systematic_review_pipeline.rst @@ -0,0 +1,7 @@ +medacy.ner.pipelines.systematic\_review\_pipeline module +==================================================== + +.. automodule:: medacy.ner.pipelines.systematic_review_pipeline + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.pipelines.testing_pipeline.rst b/docs/source/medacy.ner.pipelines.testing_pipeline.rst similarity index 50% rename from docs/source/medacy.pipelines.testing_pipeline.rst rename to docs/source/medacy.ner.pipelines.testing_pipeline.rst index 5e40839b..4038af9d 100644 --- a/docs/source/medacy.pipelines.testing_pipeline.rst +++ b/docs/source/medacy.ner.pipelines.testing_pipeline.rst @@ -1,7 +1,7 @@ -medacy.pipelines.testing\_pipeline module +medacy.ner.pipelines.testing\_pipeline module ========================================= -.. automodule:: medacy.pipelines.testing_pipeline +.. automodule:: medacy.ner.pipelines.testing_pipeline :members: :undoc-members: :show-inheritance: diff --git a/docs/source/medacy.ner.rst b/docs/source/medacy.ner.rst new file mode 100644 index 00000000..727b4ec3 --- /dev/null +++ b/docs/source/medacy.ner.rst @@ -0,0 +1,7 @@ +medacy.ner package +==================== + +.. toctree:: + + medacy.ner.model + medacy.ner.pipelines diff --git a/docs/source/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst b/docs/source/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst new file mode 100644 index 00000000..fd39e43f --- /dev/null +++ b/docs/source/medacy.pipeline_components.feature_extraction.discrete_feature_extractor.rst @@ -0,0 +1,7 @@ +medacy.pipeline_components.feature_extraction.feature\_extractor module +====================================== + +.. automodule:: medacy.pipeline_components.feature_extraction.discrete_feature_extractor + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/medacy.pipeline_components.feature_extraction.rst b/docs/source/medacy.pipeline_components.feature_extraction.rst new file mode 100644 index 00000000..ac91fb07 --- /dev/null +++ b/docs/source/medacy.pipeline_components.feature_extraction.rst @@ -0,0 +1,6 @@ +medacy.pipeline\_components.feature\_extraction package +======================================== + +.. toctree:: + + medacy.pipeline_components.feature_extraction.discrete_feature_extractor diff --git a/docs/source/medacy.pipeline_components.rst b/docs/source/medacy.pipeline_components.rst index 8ec5b41a..8ba68141 100644 --- a/docs/source/medacy.pipeline_components.rst +++ b/docs/source/medacy.pipeline_components.rst @@ -9,3 +9,4 @@ medacy.pipeline\_components package medacy.pipeline_components.metamap medacy.pipeline_components.tokenization medacy.pipeline_components.units + medacy.pipeline_components.feature_extraction diff --git a/docs/source/medacy.pipelines.base.base_pipeline.rst b/docs/source/medacy.pipelines.base.base_pipeline.rst deleted file mode 100644 index e6e6cbe3..00000000 --- a/docs/source/medacy.pipelines.base.base_pipeline.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.pipelines.base.base\_pipeline module -=========================================== - -.. automodule:: medacy.pipelines.base.base_pipeline - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.pipelines.base.rst b/docs/source/medacy.pipelines.base.rst deleted file mode 100644 index 498205b5..00000000 --- a/docs/source/medacy.pipelines.base.rst +++ /dev/null @@ -1,6 +0,0 @@ -medacy.pipelines.base package -============================= - -.. toctree:: - - medacy.pipelines.base.base_pipeline diff --git a/docs/source/medacy.pipelines.clinical_pipeline.rst b/docs/source/medacy.pipelines.clinical_pipeline.rst deleted file mode 100644 index d168800f..00000000 --- a/docs/source/medacy.pipelines.clinical_pipeline.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.pipelines.clinical\_pipeline module -========================================== - -.. automodule:: medacy.pipelines.clinical_pipeline - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.pipelines.drug_event_pipeline.rst b/docs/source/medacy.pipelines.drug_event_pipeline.rst deleted file mode 100644 index 3dedd7ec..00000000 --- a/docs/source/medacy.pipelines.drug_event_pipeline.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.pipelines.drug\_event\_pipeline module -============================================= - -.. automodule:: medacy.pipelines.drug_event_pipeline - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst b/docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst deleted file mode 100644 index e5adca71..00000000 --- a/docs/source/medacy.pipelines.fda_nano_drug_label_pipeline.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.pipelines.fda\_nano\_drug\_label\_pipeline module -======================================================== - -.. automodule:: medacy.pipelines.fda_nano_drug_label_pipeline - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.pipelines.rst b/docs/source/medacy.pipelines.rst deleted file mode 100644 index 75e56cb6..00000000 --- a/docs/source/medacy.pipelines.rst +++ /dev/null @@ -1,11 +0,0 @@ -medacy.pipelines package -======================== - -.. toctree:: - - medacy.pipelines.base - medacy.pipelines.clinical_pipeline - medacy.pipelines.drug_event_pipeline - medacy.pipelines.fda_nano_drug_label_pipeline - medacy.pipelines.systematic_review_pipeline - medacy.pipelines.testing_pipeline diff --git a/docs/source/medacy.pipelines.systematic_review_pipeline.rst b/docs/source/medacy.pipelines.systematic_review_pipeline.rst deleted file mode 100644 index 98eec876..00000000 --- a/docs/source/medacy.pipelines.systematic_review_pipeline.rst +++ /dev/null @@ -1,7 +0,0 @@ -medacy.pipelines.systematic\_review\_pipeline module -==================================================== - -.. automodule:: medacy.pipelines.systematic_review_pipeline - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/source/medacy.relation.rst b/docs/source/medacy.relation.rst new file mode 100644 index 00000000..a482f355 --- /dev/null +++ b/docs/source/medacy.relation.rst @@ -0,0 +1,4 @@ +medacy.relation package +==================== + +.. toctree:: diff --git a/docs/source/medacy.rst b/docs/source/medacy.rst index 954db934..00d2068a 100644 --- a/docs/source/medacy.rst +++ b/docs/source/medacy.rst @@ -4,7 +4,7 @@ medacy package .. toctree:: medacy.data - medacy.model + medacy.ner + medacy.relation medacy.pipeline_components - medacy.pipelines medacy.tools diff --git a/examples/guide/data_management.md b/examples/guide/data_management.md index 943c58c0..429073a5 100644 --- a/examples/guide/data_management.md +++ b/examples/guide/data_management.md @@ -157,7 +157,7 @@ Once you have a trained or imported a model, pass in a Dataset object for bulk p ```python from medacy.data import Dataset -from medacy.model import Model +from medacy.ner.model import Model dataset = Dataset('/home/medacy/data') model = Model.load_external('medacy_model_clinical_notes') diff --git a/examples/guide/model_training.md b/examples/guide/model_training.md index b5460ad6..8e3ccc22 100644 --- a/examples/guide/model_training.md +++ b/examples/guide/model_training.md @@ -66,7 +66,7 @@ The previously mentioned components make up a medaCy model. In summary training import os from medacy.data import Dataset from medacy.pipelines import ClinicalPipeline -from medacy.model import Model +from medacy.ner import Model entities = ['Drug', 'Strength'] @@ -91,7 +91,7 @@ The `ClinicalPipeline` source looks like this: import spacy, sklearn_crfsuite from .base import BasePipeline from ..pipeline_components import ClinicalTokenizer -from medacy.model.feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extractor import FeatureExtractor from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, UnitComponent, MetaMap diff --git a/examples/guide/model_utilization.md b/examples/guide/model_utilization.md index 3d0e1482..b6fb00b2 100644 --- a/examples/guide/model_utilization.md +++ b/examples/guide/model_utilization.md @@ -9,7 +9,7 @@ Once a CRF model has been trained and saved to disk, it can be loaded again for ```python from medacy.pipelines import ClinicalPipeline -from medacy.model import Model +from medacy.ner import Model pipeline = ClinicalPipeline(metamap=None, entities=['Drug']) model = Model(pipeline) @@ -30,7 +30,7 @@ Once a model has been [packaged](packaging_a_medacy_model.md) and installed it c ```python import medacy_model_clinical_notes #import the python package wrapping the model -from medacy.model import Model +from medacy.ner import Model model = Model.load_external('medacy_model_clinical_notes') diff --git a/examples/scripts/training_predicting.py b/examples/scripts/training_predicting.py index c906580d..8de05973 100644 --- a/examples/scripts/training_predicting.py +++ b/examples/scripts/training_predicting.py @@ -4,7 +4,7 @@ # it's own directory along the models build log and model/pipeline parameters to keep results easily referencable during run time. # Once a sufficent model is produced, consider wrapping it up into a medaCy compatible model as defined the example guide. -from medacy.model import Model +from medacy.ner import Model from medacy.pipelines import SystematicReviewPipeline from medacy.data import Dataset from medacy.pipeline_components import MetaMap diff --git a/medacy/__init__.py b/medacy/__init__.py index 535d6213..a8b9e736 100644 --- a/medacy/__init__.py +++ b/medacy/__init__.py @@ -1,2 +1,2 @@ __version__ = '0.0.9' -__authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes" +__authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes" \ No newline at end of file diff --git a/medacy/ner/model/__init__.py b/medacy/ner/model/__init__.py index 40561811..b26bfe83 100644 --- a/medacy/ner/model/__init__.py +++ b/medacy/ner/model/__init__.py @@ -1,3 +1,2 @@ from .model import Model -from .discrete_feature_extractor import FeatureExtractor from .stratified_k_fold import SequenceStratifiedKFold \ No newline at end of file diff --git a/medacy/ner/pipelines/clinical_pipeline.py b/medacy/ner/pipelines/clinical_pipeline.py index 9c2637b0..cfef2cb0 100644 --- a/medacy/ner/pipelines/clinical_pipeline.py +++ b/medacy/ner/pipelines/clinical_pipeline.py @@ -1,7 +1,7 @@ import spacy, sklearn_crfsuite from .base import BasePipeline from medacy.pipeline_components import ClinicalTokenizer -from medacy.ner.model.discrete_feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extraction.discrete_feature_extractor import FeatureExtractor from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent, MetaMap diff --git a/medacy/ner/pipelines/drug_event_pipeline.py b/medacy/ner/pipelines/drug_event_pipeline.py index 44731964..ef9df330 100644 --- a/medacy/ner/pipelines/drug_event_pipeline.py +++ b/medacy/ner/pipelines/drug_event_pipeline.py @@ -1,6 +1,6 @@ import spacy, sklearn_crfsuite from .base import BasePipeline -from medacy.ner.model.discrete_feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extraction.discrete_feature_extractor import FeatureExtractor from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent, CharacterTokenizer from medacy.pipeline_components.lexicon import LexiconComponent diff --git a/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py b/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py index bfa92fee..d663c58d 100644 --- a/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py +++ b/medacy/ner/pipelines/fda_nano_drug_label_pipeline.py @@ -1,7 +1,7 @@ import spacy, sklearn_crfsuite from .base import BasePipeline from medacy.pipeline_components import ClinicalTokenizer -from medacy.ner.model.discrete_feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extraction.discrete_feature_extractor import FeatureExtractor from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent diff --git a/medacy/ner/pipelines/systematic_review_pipeline.py b/medacy/ner/pipelines/systematic_review_pipeline.py index d8b8b32a..84a797e9 100644 --- a/medacy/ner/pipelines/systematic_review_pipeline.py +++ b/medacy/ner/pipelines/systematic_review_pipeline.py @@ -1,7 +1,7 @@ import spacy, sklearn_crfsuite from .base import BasePipeline from medacy.pipeline_components import MetaMap, SystematicReviewTokenizer -from medacy.ner.model.discrete_feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extraction.discrete_feature_extractor import FeatureExtractor from medacy.pipeline_components import GoldAnnotatorComponent, MetaMapComponent diff --git a/medacy/ner/pipelines/testing_pipeline.py b/medacy/ner/pipelines/testing_pipeline.py index 489cbc51..57dc661b 100644 --- a/medacy/ner/pipelines/testing_pipeline.py +++ b/medacy/ner/pipelines/testing_pipeline.py @@ -1,7 +1,7 @@ import spacy, sklearn_crfsuite from .base import BasePipeline from medacy.pipeline_components import ClinicalTokenizer -from medacy.ner.model.discrete_feature_extractor import FeatureExtractor +from medacy.pipeline_components.feature_extraction.discrete_feature_extractor import FeatureExtractor from medacy.pipeline_components import GoldAnnotatorComponent diff --git a/medacy/pipeline_components/__init__.py b/medacy/pipeline_components/__init__.py index ad2b6e22..f768d364 100644 --- a/medacy/pipeline_components/__init__.py +++ b/medacy/pipeline_components/__init__.py @@ -17,3 +17,6 @@ from .units.time_unit_component import TimeUnitComponent from .units.frequency_unit_component import FrequencyUnitComponent from .units.measurement_unit_component import MeasurementUnitComponent + + +from .feature_extraction.discrete_feature_extractor import FeatureExtractor diff --git a/medacy/tests/pipelines/__init__.py b/medacy/pipeline_components/feature_extraction/__init__.py similarity index 100% rename from medacy/tests/pipelines/__init__.py rename to medacy/pipeline_components/feature_extraction/__init__.py diff --git a/medacy/ner/model/discrete_feature_extractor.py b/medacy/pipeline_components/feature_extraction/discrete_feature_extractor.py similarity index 100% rename from medacy/ner/model/discrete_feature_extractor.py rename to medacy/pipeline_components/feature_extraction/discrete_feature_extractor.py diff --git a/medacy/tests/ner/__init__.py b/medacy/tests/ner/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/medacy/tests/ner/model/__init__.py b/medacy/tests/ner/model/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/medacy/tests/model/test_model_prediction.py b/medacy/tests/ner/model/test_model_prediction.py similarity index 95% rename from medacy/tests/model/test_model_prediction.py rename to medacy/tests/ner/model/test_model_prediction.py index 60dc64f9..52057844 100644 --- a/medacy/tests/model/test_model_prediction.py +++ b/medacy/tests/ner/model/test_model_prediction.py @@ -1,6 +1,6 @@ from unittest import TestCase -from medacy.model import Model -from medacy.pipelines import TestingPipeline +from medacy.ner.model import Model +from medacy.ner.pipelines import TestingPipeline from medacy.tools import Annotations from medacy.data import Dataset import os, importlib, pkg_resources, tempfile, shutil diff --git a/medacy/tests/ner/pipelines/__init__.py b/medacy/tests/ner/pipelines/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/medacy/tests/pipelines/test_clinical_pipeline.py b/medacy/tests/ner/pipelines/test_clinical_pipeline.py similarity index 92% rename from medacy/tests/pipelines/test_clinical_pipeline.py rename to medacy/tests/ner/pipelines/test_clinical_pipeline.py index 28490c6d..63a494d6 100644 --- a/medacy/tests/pipelines/test_clinical_pipeline.py +++ b/medacy/tests/ner/pipelines/test_clinical_pipeline.py @@ -1,5 +1,5 @@ from unittest import TestCase -from medacy.pipelines import ClinicalPipeline +from medacy.ner.pipelines import ClinicalPipeline from medacy.pipeline_components import GoldAnnotatorComponent, MetaMap From 81bc8e639cedcd23290ffe511a8a7052237d1a0c Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Fri, 15 Mar 2019 13:41:18 -0400 Subject: [PATCH 19/28] Revert "Formatting; getting ready to develop FDA pipeline" This reverts commit baad762 --- medacy/pipelines/base/base_pipeline.py | 29 ++++++++++++++----- .../pipelines/fda_nano_drug_label_pipeline.py | 29 ++++++++++++------- 2 files changed, 39 insertions(+), 19 deletions(-) diff --git a/medacy/pipelines/base/base_pipeline.py b/medacy/pipelines/base/base_pipeline.py index 6a53958c..894b385d 100644 --- a/medacy/pipelines/base/base_pipeline.py +++ b/medacy/pipelines/base/base_pipeline.py @@ -1,19 +1,18 @@ from abc import ABC, abstractmethod from ...pipeline_components.base import BaseComponent - class BasePipeline(ABC): """ An abstract wrapper for a Medical NER Pipeline """ - def __init__(self, pipeline_name, spacy_pipeline=None, description=None, creators="", organization=""): + def __init__(self,pipeline_name, spacy_pipeline=None, description=None, creators="", organization=""): """ Initializes a pipeline :param pipeline_name: The name of the pipeline :param spacy_pipeline: the corresponding spacy pipeline (language) to utilize. :param description: a description of the pipeline - :param creators: the creator of the pipeline + :param creator: the creator of the pipeline :param organization: the organization the pipeline creator belongs to """ self.pipeline_name = pipeline_name @@ -22,6 +21,8 @@ def __init__(self, pipeline_name, spacy_pipeline=None, description=None, creator self.creators = creators self.organization = organization + + @abstractmethod def get_tokenizer(self): """ @@ -46,6 +47,7 @@ def get_feature_extractor(self): """ pass + def get_language_pipeline(self): """ Retrieves the associated spaCy Language pipeline that the medaCy pipeline wraps. @@ -60,14 +62,16 @@ def add_component(self, component, *argv, **kwargs): """ current_components = [component_name for component_name, proc in self.spacy_pipeline.pipeline] - # print("Current Components:", current_components) + #print("Current Components:", current_components) dependencies = [x for x in component.dependencies] - # print("Dependencies:",dependencies) + #print("Dependencies:",dependencies) assert component.name not in current_components, "%s is already in the pipeline." % component.name for dependent in dependencies: assert dependent in current_components, "%s depends on %s but it hasn't been added to the pipeline" % (component, dependent) + + self.spacy_pipeline.add_pipe(component(self.spacy_pipeline, *argv, **kwargs)) def get_components(self): @@ -76,8 +80,7 @@ def get_components(self): :return: a list of components inside the pipeline. """ return [component_name for component_name, _ in self.spacy_pipeline.pipeline - if component_name != 'ner'] - + if component_name != 'ner'] def __call__(self, doc, predict=False): """ Passes a single document through the pipeline. @@ -104,7 +107,7 @@ def get_pipeline_information(self): """ information = { 'components': [component_name for component_name, _ in self.spacy_pipeline.pipeline - if component_name != 'ner'], # ner is the default ner component of spacy that is not utilized. + if component_name != 'ner'], #ner is the default ner component of spacy that is not utilized. 'learner_name': self.get_learner()[0], 'description': self.description, 'pipeline_name': self.pipeline_name, @@ -113,3 +116,13 @@ def get_pipeline_information(self): } return information + + + + + + + + + + diff --git a/medacy/pipelines/fda_nano_drug_label_pipeline.py b/medacy/pipelines/fda_nano_drug_label_pipeline.py index d82322cd..a5b014b1 100644 --- a/medacy/pipelines/fda_nano_drug_label_pipeline.py +++ b/medacy/pipelines/fda_nano_drug_label_pipeline.py @@ -19,36 +19,43 @@ def __init__(self, metamap, entities=[]): :param metamap: an instance of MetaMap """ - description = """Pipeline tuned for the recognition of entities in FDA Nanoparticle Drug Labels""" + description="""Pipeline tuned for the recognition of entities in FDA Nanoparticle Drug Labels""" super().__init__("fda_nano_drug_label_pipeline", spacy_pipeline=spacy.load("en_core_web_sm"), description=description, - creators="Andriy Mulyar (andriymulyar.com) " + - "Steele Farnsworth (github.com/swfarnsworth)", # append if multiple creators + creators="Andriy Mulyar (andriymulyar.com)", #append if multiple creators organization="NLP@VCU" ) + self.entities = entities self.spacy_pipeline.tokenizer = self.get_tokenizer() # set tokenizer self.add_component(GoldAnnotatorComponent, entities) # add overlay for GoldAnnotation self.add_component(MetaMapComponent, metamap) - # self.add_component(UnitComponent) + #self.add_component(UnitComponent) def get_learner(self): - return "CRF_l2sgd", sklearn_crfsuite.CRF( - algorithm='l2sgd', - c2=0.1, - max_iterations=100, - all_possible_transitions=True - ) + return ("CRF_l2sgd", sklearn_crfsuite.CRF( + algorithm='l2sgd', + c2=0.1, + max_iterations=100, + all_possible_transitions=True + )) def get_tokenizer(self): - tokenizer = ClinicalTokenizer(self.spacy_pipeline) # Best run with SystematicReviewTokenizer + tokenizer = ClinicalTokenizer(self.spacy_pipeline) #Best run with SystematicReviewTokenizer return tokenizer.tokenizer def get_feature_extractor(self): extractor = FeatureExtractor(window_size=6, spacy_features=['pos_', 'shape_', 'prefix_', 'suffix_', 'like_num', 'text']) return extractor + + + + + + + From 0fe1521e5d169119098b06f63d3bfaa8c771dad2 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Fri, 15 Mar 2019 13:48:29 -0400 Subject: [PATCH 20/28] Syncing origin with upstream development --- .travis.yml | 22 ++ README.md | 6 - docs/source/index.rst | 28 ++- examples/guide/data_management.md | 2 +- medacy/__init__.py | 2 +- medacy/data/dataset.py | 194 +++++++++++++++++- medacy/model/_model.py | 20 +- medacy/model/feature_extractor.py | 77 ++++--- medacy/model/model.py | 78 ++++++- medacy/model/stratified_k_fold.py | 1 + medacy/pipeline_components/__init__.py | 2 + .../annotation/gold_annotator_component.py | 2 +- .../lexicon/lexicon_component.py | 2 +- medacy/pipeline_components/metamap/metamap.py | 47 +++-- .../pipeline_components/patterns/__init__.py | 1 + .../patterns/table_matcher_component.py | 38 ++++ medacy/pipelines/clinical_pipeline.py | 2 +- medacy/pipelines/drug_event_pipeline.py | 131 +++++++++++- medacy/tests/data/test_dataset.py | 15 ++ medacy/tests/model/test_model_prediction.py | 1 - medacy/tools/data_file.py | 35 +++- setup.py | 5 +- 22 files changed, 618 insertions(+), 93 deletions(-) create mode 100644 .travis.yml create mode 100644 medacy/pipeline_components/patterns/__init__.py create mode 100644 medacy/pipeline_components/patterns/table_matcher_component.py diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 00000000..75d47668 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,22 @@ +language: python + +sudo: false + +dist: trusty +group: edge + +python: + - "3.5" + - "3.6" + +os: + - linux + + +install: + - pip install --upgrade pip + - pip install -e . + +script: + - "python setup.py test || exit 0" + - "python setup.py test" diff --git a/README.md b/README.md index 891693cd..8fbde2e8 100644 --- a/README.md +++ b/README.md @@ -23,12 +23,6 @@ receive immediate responses to any questions is to raise an issue. Make sure to ## :computer: Installation Instructions Medacy can be installed for general use or for pipeline development / research purposes. -First, make sure you have spaCy's small model installed: - -`pip install https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.0.0/en_core_web_sm-2.0.0.tar.gz#egg=en_core_web_sm-2.0.0` - -then - | Application | Run | | ----------- |:-------------:| | Prediction and Model Training (stable) | `pip install git+https://github.com/NLPatVCU/medaCy.git` | diff --git a/docs/source/index.rst b/docs/source/index.rst index 6d1d9f76..ed590900 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -1,12 +1,26 @@ -.. medaCy documentation master file, created by - sphinx-quickstart on Mon Dec 10 03:32:34 2018. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. +MedaCy Documentation +==================== +For the latest updates, please see the project on `github `_. -Welcome to medaCy's documentation! -================================== +MedaCy is a medical text mining framework built over spaCy to facilitate the engineering, training and application +of machine learning models for medical information extraction. -[Info about what MedaCy is here] +To confront the unique challenges posed by medical text +medaCy provides interfaces to medical ontologies such as `Metamap `_ allowing their +integration into text mining workflows. Additional help, examples and tutorials can be found in the examples section +of the `repository `_. + +MedaCy does not officially support non-unix based operating systems (however we have found most functionality works on Windows). + +Trained Models +-------------- +A complete listing of trained models can be found `here `_. + + +Datasets +-------- +MedaCy implements a Dataset functionality that loosely wraps a working directory to manage and version training data. +See more in the `examples `_. Contents -------- diff --git a/examples/guide/data_management.md b/examples/guide/data_management.md index 187ce51b..943c58c0 100644 --- a/examples/guide/data_management.md +++ b/examples/guide/data_management.md @@ -54,7 +54,7 @@ from medacy.data import Dataset from medacy.pipeline_components import MetaMap dataset = Dataset('/home/medacy/data') -for data_file in dataset.get_data_files(): +for data_file in dataset: print(data_file.file_name) print(data) print(data.is_metamapped()) diff --git a/medacy/__init__.py b/medacy/__init__.py index 5c6117bd..535d6213 100644 --- a/medacy/__init__.py +++ b/medacy/__init__.py @@ -1,2 +1,2 @@ -__version__ = '0.0.8' +__version__ = '0.0.9' __authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes" diff --git a/medacy/data/dataset.py b/medacy/data/dataset.py index 77008e4f..0ae34968 100644 --- a/medacy/data/dataset.py +++ b/medacy/data/dataset.py @@ -1,24 +1,80 @@ """ -A Dataset facilities the management of data for both model training and model prediction. +A medaCy Dataset facilities the management of data for both model training and model prediction. + A Dataset object provides a wrapper for a unix file directory containing training/prediction data. If a Dataset, at training time, is fed into a pipeline requiring auxilary files (Metamap for instance) the Dataset will automatically create those files in the most efficient way possible. -# Training +Training +################# When a directory contains **both** raw text files alongside annotation files, an instantiated Dataset detects and facilitates access to those files. -# Prediction +Assuming your directory looks like this (where .ann files are in `BRAT `_ format): +:: + home/medacy/data + ├── file_one.ann + ├── file_one.txt + ├── file_two.ann + └── file_two.txt + +A Dataset can be created like this: +:: + from medacy.data import Dataset + + dataset = Dataset('/home/medacy/data') + + +MedaCy **does not** alter the data you load in any way - it only reads from it. + +A common data work flow might look as follows. + +Running: +:: + from medacy.data import Dataset + from medacy.pipeline_components import MetaMap + + dataset = Dataset('/home/medacy/data') + for data_file in dataset: + print((data_file.file_name, data_file.raw_path, dataset.ann_path)) + print(dataset) + print(dataset.is_metamapped()) + + metamap = Metamap('/home/path/to/metamap/binary') #not necessary + dataset.metamap(metamap) #not necessary + print(dataset.is_metamapped()) + + +Outputs: +:: + (file_one, file_one.txt, file_one.ann) + (file_two, file_two.txt, file_two.ann) + ['file_one.txt', 'file_two.txt'] + False + True + +Prediction +########## When a directory contains **only** raw text files, an instantiated Dataset object interprets this as a directory of files that need to be predicted. This means that the internal Datafile that aggregates meta-data for a given prediction file does not have fields for annotation_file_path set. -# External Datasets -An actual dataset can be versioned and distributed by interfacing this class as described in the -Dataset examples. Existing Datasets can be imported by installing the relevant python packages that +When a directory contains **only** ann files, an instantiated Dataset object interprets this as +a directory of files that are predictions. Useful methods for analysis include :meth:`medacy.data.dataset.Dataset.compute_confusion_matrix`, +:meth:`medacy.data.dataset.Dataset.compute_ambiguity` and :meth:`medacy.data.dataset.Dataset.compute_counts`. + + + +External Datasets +################# + +In the real world, datasets (regardless of domain) are evolving entities. Hence, it is essential to version them. +A medaCy compatible dataset can be created to facilitate this versioning. A medaCy compatible dataset lives a python +packages that can be hooked into medaCy or used for any other purpose - it is simply a loose wrapper for this Dataset +object. Instructions for creating such a dataset can be found `here `_. wrap them. """ -from medacy.tools import DataFile +from medacy.tools import DataFile, Annotations from joblib import Parallel, delayed import os, logging, multiprocessing, math, json, importlib @@ -35,6 +91,7 @@ def __init__(self, data_directory, data_limit=None): """ Manages directory of training data along with other medaCy generated files. + :param data_directory: Directory containing data for training or prediction. :param raw_text_file_extension: The file extension of raw text files in the data_directory (default: *.txt*) :param annotation_file_extension: The file extension of annotation files in the data_directory (default: *.ann*) @@ -88,7 +145,6 @@ def __init__(self, data_directory, #If directory is already metamapped, use it. if self.is_metamapped(): for data_file in self.all_data_files: - data_file.metamapped_path = os.path.join(self.metamapped_files_directory, data_file.raw_path.split(os.path.sep)[-1] .replace(".%s" % self.raw_text_file_extension, ".metamapped")) @@ -97,15 +153,21 @@ def __init__(self, data_directory, def get_data_files(self): """ Retrieves an list containing all the files registered by a Dataset. + :return: a list of DataFile objects. """ return self.all_data_files[0:self.data_limit] + def __iter__(self): + return self.get_data_files().__iter__() + + def metamap(self, metamap, n_jobs=multiprocessing.cpu_count() - 1, retry_possible_corruptions=True): """ Metamaps the files registered by a Dataset. Attempts to Metamap utilizing a max prune depth of 30, but on failure retries with lower max prune depth. A lower prune depth roughly equates to decreased MetaMap performance. More information can be found in the MetaMap documentation. + :param metamap: an instance of MetaMap. :param n_jobs: the number of processes to spawn when metamapping. Defaults to one less core than available on your machine. :param retry_possible_corruptions: Re-Metamap's files that are detected as being possibly corrupt. Set to False for more control over what gets Metamapped or if you are having bugs with Metamapping. (default: True) @@ -145,6 +207,7 @@ def metamap(self, metamap, n_jobs=multiprocessing.cpu_count() - 1, retry_possibl def _parallel_metamap(self, files, i): """ Facilitates Metamapping in parallel by forking off processes to Metamap each file individually. + :param files: an array of file paths to the file to map :param i: index in the array used to determine the file that the called process will be responsible for mapping :return: metamapped_files_directory now contains metamapped versions of the dataset files @@ -180,6 +243,7 @@ def _parallel_metamap(self, files, i): def is_metamapped(self): """ Verifies if all fil es in the Dataset are metamapped. + :return: True if all data files are metamapped, False otherwise. """ if not os.path.isdir(self.metamapped_files_directory): @@ -202,6 +266,7 @@ def is_metamapped(self): def is_training(self): """ Whether this Dataset can be used for training. + :return: True if training dataset, false otherwise. A training dataset is a collection raw text and corresponding annotation files while a prediction dataset contains solely raw text files. """ return self.is_training_directory @@ -210,6 +275,7 @@ def set_data_limit(self, data_limit): """ A limit to the number of files in the Dataset that medaCy works with This is useful for preliminary experimentation when working with an entire Dataset takes time. + :return: """ self.data_limit = data_limit @@ -217,20 +283,125 @@ def set_data_limit(self, data_limit): def get_data_directory(self): """ Retrieves the directory this Dataset abstracts from. - :return: + + :return: the directory the Dataset object wraps. """ return self.data_directory def __str__(self): - """Converts self.get_data_files() to a list of strs and combines them into one str""" + """ + Converts self.get_data_files() to a list of strs and combines them into one str + """ return "[%s]" % ", ".join([str(x) for x in self.get_data_files()]) + def compute_counts(self): + """ + Computes entity and relation counts over all documents in this dataset. + + :return: a dictionary of entity and relation counts. + """ + dataset_counts = { + 'entities': {}, + 'relations':{} + } + + for data_file in self: + annotation = Annotations(data_file.ann_path) + annotation_counts = annotation.compute_counts() + dataset_counts['entities'] = {x: dataset_counts['entities'].get(x, 0) + annotation_counts['entities'].get(x, 0) + for x in set(dataset_counts['entities']).union(annotation_counts['entities'])} + dataset_counts['relations'] = {x: dataset_counts['relations'].get(x, 0) + annotation_counts['relations'].get(x, 0) + for x in set(dataset_counts['relations']).union(annotation_counts['relations'])} + + return dataset_counts + + def compute_confusion_matrix(self, dataset, leniency=0): + """ + Generates a confusion matrix where this Dataset serves as the gold standard annotations and `dataset` serves + as the predicted annotations. A typical workflow would involve creating a Dataset object with the prediction directory + outputted by a model and then passing it into this method. + + :param dataset: a Dataset object containing a predicted version of this dataset. + :param leniency: a floating point value between [0,1] defining the leniency of the character spans to count as different. A value of zero considers only exact character matches while a positive value considers entities that differ by up to :code:`ceil(leniency * len(span)/2)` on either side. + :return: two element tuple containing a label array (of entity names) and a matrix where rows are gold labels and columns are predicted labels. matrix[i][j] indicates that entities[i] in this dataset was predicted as entities[j] in 'annotation' matrix[i][j] times + """ + if not isinstance(dataset, Dataset): + raise ValueError("dataset must be instance of Dataset") + + #verify files are consistent + diff = set([file.ann_path for file in self]).difference(set([file.ann_path for file in dataset])) + if diff: + raise ValueError("Dataset of predictions is missing the files: "+str(list(diff))) + + #sort entities in ascending order by count. + entities = [key for key, _ in sorted(self.compute_counts()['entities'].items(), key=lambda x: x[1])] + confusion_matrix = [[0 for x in range(len(entities))] for x in range(len(entities))] + + for gold_data_file in self: + prediction_iter = iter(dataset) + prediction_data_file = next(prediction_iter) + while str(gold_data_file) != str(prediction_data_file): + prediction_data_file = next(prediction_iter) + + gold_annotation = Annotations(gold_data_file.ann_path) + pred_annotation = Annotations(prediction_data_file.ann_path) + + #compute matrix on the Annotation file level + ann_confusion_matrix = gold_annotation.compute_confusion_matrix(pred_annotation, entities, leniency=leniency) + for i in range(len(confusion_matrix)): + for j in range(len(confusion_matrix)): + confusion_matrix[i][j] += ann_confusion_matrix[i][j] + + return entities, confusion_matrix + + def compute_ambiguity(self, dataset): + """ + Finds occurrences of spans from 'dataset' that intersect with a span from this annotation but do not have this spans label. + label. If 'dataset' comprises a models predictions, this method provides a strong indicators + of a model's in-ability to dis-ambiguate between entities. For a full analysis, compute a confusion matrix. + + :param dataset: a Dataset object containing a predicted version of this dataset. + :return: a dictionary containing the ambiguity computations on each gold, predicted file pair + """ + if not isinstance(dataset, Dataset): + raise ValueError("dataset must be instance of Dataset") + + # verify files are consistent + diff = set([file.ann_path for file in self]).difference(set([file.ann_path for file in dataset])) + if diff: + raise ValueError("Dataset of predictions is missing the files: " + str(list(diff))) + + #Dictionary storing ambiguity over dataset + ambiguity_dict = {} + + for gold_data_file in self: + prediction_iter = iter(dataset) + prediction_data_file = next(prediction_iter) + while str(gold_data_file) != str(prediction_data_file): + prediction_data_file = next(prediction_iter) + + gold_annotation = Annotations(gold_data_file.ann_path) + pred_annotation = Annotations(prediction_data_file.ann_path) + + # compute matrix on the Annotation file level + ambiguity_dict[str(gold_data_file)] = gold_annotation.compute_ambiguity(pred_annotation) + + + return ambiguity_dict + + + + + + + @staticmethod def load_external(package_name): """ Loads an external medaCy compatible dataset. Requires the dataset's associated package to be installed. Alternatively, you can import the package directly and call it's .load() method. + :param package_name: the package name of the dataset :return: A tuple containing a training set, evaluation set, and meta_data """ @@ -246,3 +417,6 @@ def load_external(package_name): + + + diff --git a/medacy/model/_model.py b/medacy/model/_model.py index 1f53b383..2e95b92f 100644 --- a/medacy/model/_model.py +++ b/medacy/model/_model.py @@ -32,7 +32,7 @@ def predict_document(model, doc, medacy_pipeline): continue entity = predictions[i] first_start, first_end = span_indices[i] - # insure that consecutive tokens with the same label are merged + # Ensure that consecutive tokens with the same label are merged while i < len(predictions)-1 and predictions[i+1] == entity: #If inside entity, keep incrementing i+=1 last_start, last_end = span_indices[i] @@ -44,4 +44,22 @@ def predict_document(model, doc, medacy_pipeline): annotations['entities']['T%i'%T_num] = (entity, first_start, last_end, labeled_text) T_num+=1 i+=1 + return Annotations(annotations) + + +def construct_annotations_from_tuples(doc, predictions): + """ + Converts predictions mapped to a document into an Annotations object + :param doc: SpaCy doc corresponding to predictions + :param predictions: List of tuples containing (entity, start offset, end offset) + :return: Annotations Object representing predicted entities for the given doc + """ + predictions = sorted(predictions, key=lambda x: x[1]) + annotations = {'entities': {}, 'relations': []} + T_num = 1 + for prediction in predictions: + (entity, start, end) = prediction + labeled_text = doc.text[start:end] + annotations['entities']['T%i' % T_num] = (entity, start, end, labeled_text) + T_num += 1 return Annotations(annotations) \ No newline at end of file diff --git a/medacy/model/feature_extractor.py b/medacy/model/feature_extractor.py index 93208b5b..50edf9d0 100644 --- a/medacy/model/feature_extractor.py +++ b/medacy/model/feature_extractor.py @@ -1,14 +1,18 @@ +""" +Extracting training data for use in a CRF. +Features are extracted as discrete dictionaries as described in +`sklearn-crfsuite `_. + + +These extracted features CANNOT be used in sequence to sequence models expecting continuous inputs (e.g. word vectors). + +`sklearn-crfsuite `_ is a wrapper for a C CRF implementation that gives it a sci-kit compatability. +""" from spacy.tokens.underscore import Underscore from spacy.tokens import Token +from itertools import cycle class FeatureExtractor: - """ - Extracting training data for use in a CRF. - Features are given as rich dictionaries as described in: - https://sklearn-crfsuite.readthedocs.io/en/latest/tutorial.html#features - - sklearn CRF suite is a wrapper for CRF suite that gives it a sci-kit compatability. - """ def __init__(self, window_size=2, spacy_features=['pos_', 'shape_', 'prefix_', 'suffix_', 'like_num']): """ @@ -26,23 +30,34 @@ def __init__(self, window_size=2, spacy_features=['pos_', 'shape_', 'prefix_', ' self.all_custom_features = [attribute for attribute in list(Underscore.token_extensions.keys()) if attribute.startswith('feature_')] self.spacy_features = spacy_features - def __call__(self, doc): + def __call__(self, doc, file_name): + """ + Extract features, labels, and corresponding spans from a document + + :param doc: Annotated Spacy Doc object + :param file_name: Filename to associate these sequences with + :return: List of tuples of form: + [(feature dictionaries for sequence, indices of tokens in seq, document label)] + """ - features = [self._sent_to_feature_dicts(sent) for sent in doc.sents] - labels = [self._sent_to_labels(sent) for sent in doc.sents] + features = [self._sequence_to_feature_dicts(sent) for sent in doc.sents] + labels = [self._sequence_to_labels(sent) for sent in doc.sents] + indices = [[(token.idx, token.idx+len(token)) for token in sent] for sent in doc.sents] + features = list(zip(features, indices, cycle([file_name]))) return features, labels def get_features_with_span_indices(self, doc): """ Given a document this method orchestrates the organization of features and labels for the sequences to classify. Sequences for classification are determined by the sentence boundaries set by spaCy. These can be modified. + :param doc: an annoted spacy Doc object :return: Tuple of parallel arrays - 'features' an array of feature dictionaries for each sequence (spaCy determined sentence) and 'indices' which are arrays of character offsets corresponding to each extracted sequence of features. """ - features = [self._sent_to_feature_dicts(sent) for sent in doc.sents] + features = [self._sequence_to_feature_dicts(sent) for sent in doc.sents] indices = [[(token.idx, token.idx+len(token)) for token in sent] for sent in doc.sents] @@ -50,37 +65,32 @@ def get_features_with_span_indices(self, doc): - def _sent_to_feature_dicts(self, sent): - return [self._token_to_feature_dict(i, sent) for i in range(len(sent))] - - def _sent_to_labels(self, sent, attribute='gold_label'): - return [token._.get(attribute) for token in sent] + def _sequence_to_feature_dicts(self, sequence): + """ + Transforms a given sequence of spaCy token objects into a discrete feature dictionary for us in a CRF. - def mapper_for_crf_wrapper(self, text): + :param sequence: + :return: a sequence of feature dictionaries corresponding to the token. """ - CURRENTLY UNUSED. - CRF wrapper uses regexes to extract the output of the underlying C++ code. - The inclusion of \\n and space characters mess up these regexes, hence we map them to text here. - :return: + return [self._token_to_feature_dict(i, sequence) for i in range(len(sequence))] + + def _sequence_to_labels(self, sequence, attribute='gold_label'): """ - if text == r"\n": - return "#NEWLINE" - if text == r"\t": - return "#TAB" - if text == " ": - return "#SPACE" - if text == "": - return "#EMPTY" - return text + :param sequence: a sequence of tokens to retrieve labels from + :param attribute: the name of the attribute that is holding the tokens label. This defaults to 'gold_label' which was set in the GoldAnnotator Component. + :return: a list of token labels. + """ + return [token._.get(attribute) for token in sequence] def _token_to_feature_dict(self, index, sentence): """ + Extracts features of a given token :param index: the index of the token in the sequence :param sentence: an array of tokens corresponding to a sequence - :return: + :return: a dictionary with a feature representation of the spaCy token object. """ #This should automatically gather features that are set on tokens @@ -99,10 +109,11 @@ def _token_to_feature_dict(self, index, sentence): #adds features that are overlayed from spacy token attributes for feature in self.spacy_features: if isinstance(getattr(token, feature), Token): - current.update({'%i:%s' % (i, feature) : getattr(token, feature).text}); + current.update({'%i:%s' % (i, feature) : getattr(token, feature).text}) else: - current.update({'%i:%s' % (i, feature) : getattr(token, feature)}); + current.update({'%i:%s' % (i, feature) : getattr(token, feature)}) + # Extract features from the vector representation of this token features.update(current) diff --git a/medacy/model/model.py b/medacy/model/model.py index 01933225..a60f073c 100644 --- a/medacy/model/model.py +++ b/medacy/model/model.py @@ -7,7 +7,7 @@ from .stratified_k_fold import SequenceStratifiedKFold from medacy.pipelines.base.base_pipeline import BasePipeline from pathos.multiprocessing import ProcessingPool as Pool, cpu_count -from ._model import predict_document +from ._model import predict_document, construct_annotations_from_tuples from sklearn_crfsuite import metrics from tabulate import tabulate from statistics import mean @@ -37,6 +37,7 @@ def __init__(self, medacy_pipeline=None, model=None, n_jobs=cpu_count()): def fit(self, dataset): """ Runs dataset through the designated pipeline, extracts features, and fits a conditional random field. + :param training_data_loader: Instance of Dataset. :return model: a trained instance of a sklearn_crfsuite.CRF model. """ @@ -66,7 +67,8 @@ def fit(self, dataset): assert self.X_data, "Training data is empty." - learner.fit(self.X_data, self.y_data) + train_data = [x[0] for x in self.X_data] + learner.fit(train_data, self.y_data) logging.info("Successfully Trained: %s", learner_name) self.model = learner @@ -74,6 +76,7 @@ def fit(self, dataset): def predict(self, dataset, prediction_directory = None): """ + Generates predictions over a string or a dataset utilizing the pipeline equipped to the instance. :param documents: a string or Dataset to predict :param prediction_directory: the directory to write predictions if doing bulk prediction (default: */prediction* sub-directory of Dataset) @@ -123,14 +126,16 @@ def predict(self, dataset, prediction_directory = None): annotations = predict_document(model, doc, medacy_pipeline) return annotations - def cross_validate(self, num_folds=10): + def cross_validate(self, num_folds=10, dataset=None, write_predictions=False): """ Performs k-fold stratified cross-validation using our model and pipeline. + :param num_folds: number of folds to split training data into for cross validation + :param dataset: Dataset that sequences were extracted from :return: Prints out performance metrics """ - if num_folds < 1: raise ValueError("Number of folds for cross validation must be greater than 1") + if num_folds <= 1: raise ValueError("Number of folds for cross validation must be greater than 1") assert self.model is not None, "Cannot cross validate a un-fit model" assert self.X_data is not None and self.y_data is not None, \ @@ -158,9 +163,41 @@ def cross_validate(self, num_folds=10): y_test = [Y_data[index] for index in test_indices] logging.info("Training Fold %i", fold) - learner.fit(X_train, y_train) - y_pred = learner.predict(X_test) - + train_data = [x[0] for x in X_train] + test_data = [x[0] for x in X_test] + learner.fit(train_data, y_train) + y_pred = learner.predict(test_data) + + if write_predictions: + # Dict for storing mapping of sequences to their corresponding file + preds_by_document = {filename: [] for filename in list(set([x[2] for x in X_data]))} + + # Flattening nested structures into 2d lists + document_indices = [] + span_indices = [] + for sequence in X_test: + document_indices += [sequence[2] for x in range(len(sequence[0]))] + span_indices += [element for element in sequence[1]] + predictions = [element for sentence in y_pred for element in sentence] + + # Map the predicted sequences to their corresponding documents + i=0 + while i < len(predictions): + if predictions[i] == 'O': + i+=1 + continue + entity = predictions[i] + document = document_indices[i] + first_start, first_end = span_indices[i] + # Ensure that consecutive tokens with the same label are merged + while i < len(predictions) - 1 and predictions[i + 1] == entity: # If inside entity, keep incrementing + i += 1 + last_start, last_end = span_indices[i] + + preds_by_document[document].append((entity, first_start, last_end)) + i+=1 + + # Write the metrics for this fold. for label in named_entities: fold_statistics[label] = {} recall = metrics.flat_recall_score(y_test, y_pred, average='weighted', labels=[label]) @@ -179,6 +216,15 @@ def cross_validate(self, num_folds=10): fold_statistics['system']['recall'] = recall fold_statistics['system']['f1'] = f1 + table_data = [[label, + format(fold_statistics[label]['precision'], ".3f"), + format(fold_statistics[label]['recall'], ".3f"), + format(fold_statistics[label]['f1'], ".3f")] + for label in named_entities + ['system']] + + logging.info(tabulate(table_data, headers=['Entity', 'Precision', 'Recall', 'F1'], + tablefmt='orgtbl')) + evaluation_statistics[fold] = fold_statistics fold += 1 @@ -218,9 +264,21 @@ def cross_validate(self, num_folds=10): logging.info("\n"+tabulate(table_data, headers=['Entity', 'Precision', 'Recall', 'F1', 'F1_Min', 'F1_Max'], tablefmt='orgtbl')) + if write_predictions: + # Write annotations generated from cross-validation + prediction_directory = dataset.data_directory + "/predictions/" + for data_file in dataset.get_data_files(): + logging.info("Predicting file: %s", data_file.file_name) + with open(data_file.raw_path, 'r') as raw_text: + doc = medacy_pipeline.spacy_pipeline.make_doc(raw_text.read()) + preds = preds_by_document[data_file.file_name] + annotations = construct_annotations_from_tuples(doc, preds) + annotations.to_ann(write_location=os.path.join(prediction_directory, data_file.file_name + ".ann")) + def _extract_features(self, data_file, medacy_pipeline, is_metamapped): """ A multi-processed method for extracting features from a given DataFile instance. + :param conn: pipe to pass back data to parent process :param data_file: an instance of DataFile :return: Updates queue with features for this given file. @@ -250,7 +308,7 @@ def _extract_features(self, data_file, medacy_pipeline, is_metamapped): # print() # The document has now been run through the pipeline. All annotations are overlayed - pull features. - features, labels = feature_extractor(doc) + features, labels = feature_extractor(doc, data_file.file_name) logging.info("%s: Feature Extraction Completed (num_sequences=%i)" % (data_file.file_name, len(labels))) return features, labels @@ -258,6 +316,7 @@ def _extract_features(self, data_file, medacy_pipeline, is_metamapped): def load(self, path): """ Loads a pickled model. + :param path: File path to directory where fitted model should be dumped :return: """ @@ -266,6 +325,7 @@ def load(self, path): def dump(self, path): """ Dumps a model into a pickle file + :param path: Directory path to dump the model :return: """ @@ -277,6 +337,7 @@ def get_info(self, return_dict=False): """ Retrieves information about a Model including details about the feature extraction pipeline, features utilized, and learning model. + :param return_dict: Returns a raw dictionary of information as opposed to a formatted string :return: Returns structured information """ @@ -307,6 +368,7 @@ def load_external(package_name): """ Loads an external medaCy compatible Model. Require's the models package to be installed Alternatively, you can import the package directly and call it's .load() method. + :param package_name: the package name of the model :return: an instance of Model that is configured and loaded - ready for prediction. """ diff --git a/medacy/model/stratified_k_fold.py b/medacy/model/stratified_k_fold.py index dbf6a155..5acaeb42 100644 --- a/medacy/model/stratified_k_fold.py +++ b/medacy/model/stratified_k_fold.py @@ -23,6 +23,7 @@ def __call__(self, X, y): """ Returns an iterable [(X*,y*), ...] where each element contains the indices of the train and test set for the particular testing fold. + :param X: a collection of sequences :param y: a collection of sequence labels :return: diff --git a/medacy/pipeline_components/__init__.py b/medacy/pipeline_components/__init__.py index e296fbf3..ad2b6e22 100644 --- a/medacy/pipeline_components/__init__.py +++ b/medacy/pipeline_components/__init__.py @@ -9,6 +9,8 @@ from .lexicon import LexiconComponent +from .patterns import TableMatcherComponent + from .units.unit_component import UnitComponent from .units.mass_unit_component import MassUnitComponent from .units.volume_unit_component import VolumeUnitComponent diff --git a/medacy/pipeline_components/annotation/gold_annotator_component.py b/medacy/pipeline_components/annotation/gold_annotator_component.py index 64793ee8..71cf5809 100644 --- a/medacy/pipeline_components/annotation/gold_annotator_component.py +++ b/medacy/pipeline_components/annotation/gold_annotator_component.py @@ -104,7 +104,7 @@ def __call__(self, doc): logging.warning("%s: Could not fix annotation: (%i,%i,%s)",doc._.file_name, e_start, e_end, e_label) logging.warning("%s: Total Failed Annotations: %i", doc._.file_name, self.failed_identifying_span_count) - if self.failed_overlay_count > .3*gold_annotations.get_entity_count() : + if self.failed_overlay_count > .3*len(gold_annotations.get_entity_annotations()) : logging.warning("%s: Annotations may mis-aligned as more than 30 percent failed to overlay: %s", doc._.file_name, doc._.gold_annotation_file) diff --git a/medacy/pipeline_components/lexicon/lexicon_component.py b/medacy/pipeline_components/lexicon/lexicon_component.py index 7183222c..4156ca26 100644 --- a/medacy/pipeline_components/lexicon/lexicon_component.py +++ b/medacy/pipeline_components/lexicon/lexicon_component.py @@ -33,7 +33,7 @@ def __call__(self, doc): """ logging.debug("Called Lexicon Component") - matcher = PhraseMatcher(self.nlp.vocab, max_length=6) + matcher = PhraseMatcher(self.nlp.vocab, max_length=10) for label in self.lexicon: Token.set_extension('feature_is_' + label + '_from_lexicon', default=False, force=True) patterns = [self.nlp.make_doc(term) for term in self.lexicon[label]] diff --git a/medacy/pipeline_components/metamap/metamap.py b/medacy/pipeline_components/metamap/metamap.py index 92e123c0..f83ccceb 100644 --- a/medacy/pipeline_components/metamap/metamap.py +++ b/medacy/pipeline_components/metamap/metamap.py @@ -252,17 +252,20 @@ def get_span_by_term(self,term): :param term: The full dictionary corresponding to a metamap term :return: the span of the referenced term in the document """ - if int(term['ConceptPIs']['@Count']) == 1: + if isinstance(term['ConceptPIs']['ConceptPI'], list): + spans = [] + for span in term['ConceptPIs']['ConceptPI']: + start = int(span['StartPos']) + length = int(span['Length']) + spans.append((start, start + length)) + return spans + else: start = int(term['ConceptPIs']['ConceptPI']['StartPos']) length = int(term['ConceptPIs']['ConceptPI']['Length']) - return [(start, start+length)] + return [(start, start + length)] + + - spans = [] - for span in term['ConceptPIs']['ConceptPI']: - start = int(span['StartPos']) - length = int(span['Length']) - spans.append((start, start+length)) - return spans def get_semantic_types_by_term(self, term): """ @@ -309,15 +312,25 @@ def _convert_to_ascii(self, text): diff = list() offset = 0 for i, char in enumerate(text): - if char in UNICODE_TO_ASCII and UNICODE_TO_ASCII[char] is not char: - ascii = UNICODE_TO_ASCII[char] - text = text[:i+offset] + ascii + text[i+1+offset:] - diff.append({ - 'start': i+offset, - 'length': len(ascii), - 'original': char - }) - offset += len(ascii) - len(char) + if ord(char) >= 128: #non-ascii + if char in UNICODE_TO_ASCII and UNICODE_TO_ASCII[char] is not char: + ascii = UNICODE_TO_ASCII[char] + text = text[:i+offset] + ascii + text[i+1+offset:] + diff.append({ + 'start': i+offset, + 'length': len(ascii), + 'original': char + }) + offset += len(ascii) - len(char) + else: + ascii = '?' + text = text[:i + offset] + ascii + text[i + 1 + offset:] + diff.append({ + 'start': i + offset, + 'length': len(ascii), + 'original': char + }) + offset += len(ascii) - len(char) return text, diff diff --git a/medacy/pipeline_components/patterns/__init__.py b/medacy/pipeline_components/patterns/__init__.py new file mode 100644 index 00000000..6233e7bd --- /dev/null +++ b/medacy/pipeline_components/patterns/__init__.py @@ -0,0 +1 @@ +from .table_matcher_component import TableMatcherComponent \ No newline at end of file diff --git a/medacy/pipeline_components/patterns/table_matcher_component.py b/medacy/pipeline_components/patterns/table_matcher_component.py new file mode 100644 index 00000000..4db91681 --- /dev/null +++ b/medacy/pipeline_components/patterns/table_matcher_component.py @@ -0,0 +1,38 @@ +import logging, re +from spacy.tokens import Token, Span +from spacy.matcher import PhraseMatcher +from ..base import BaseComponent + +class TableMatcherComponent(BaseComponent): + + name='table_matcher_component' + dependencies=[] + + def __init__(self, spacey_pipeline): + """ + + :param spacey_pipeline: + """ + super().__init__(self.name, self.dependencies) + self.nlp = spacey_pipeline + + + def __call__(self, doc): + """ + Runs the document through the Table Matcher Component. Uses regex patterns to identify terms that + likely came from a table in the unstructured text. + :param doc: + :return: + """ + logging.debug("Called Table Matcher Component") + TABLE_PATTERN = re.compile(r'^(.*?)[ \t]{3,}\d+') + Token.set_extension('feature_is_from_table', default=False, force=True) + + for match in re.finditer(TABLE_PATTERN, doc.text): + start, end = match.span() + span = doc.char_span(start, end) + for token in span: + token._.set('feature_is_from_table', True) + + return doc + diff --git a/medacy/pipelines/clinical_pipeline.py b/medacy/pipelines/clinical_pipeline.py index 75c82e40..073dc29d 100644 --- a/medacy/pipelines/clinical_pipeline.py +++ b/medacy/pipelines/clinical_pipeline.py @@ -36,7 +36,7 @@ def __init__(self, metamap=None, entities=[]): if metamap is not None and isinstance(metamap, MetaMap): self.add_component(MetaMapComponent, metamap) - self.add_component(UnitComponent) + #self.add_component(UnitComponent) def get_learner(self): diff --git a/medacy/pipelines/drug_event_pipeline.py b/medacy/pipelines/drug_event_pipeline.py index 97a6562f..7f2d4ee9 100644 --- a/medacy/pipelines/drug_event_pipeline.py +++ b/medacy/pipelines/drug_event_pipeline.py @@ -4,6 +4,7 @@ from ..pipeline_components import GoldAnnotatorComponent, MetaMapComponent, CharacterTokenizer from ..pipeline_components.lexicon import LexiconComponent +from ..pipeline_components.patterns import TableMatcherComponent class DrugEventPipeline(BasePipeline): @@ -27,9 +28,137 @@ def __init__(self, metamap=None, entities=[], lexicon={}): self.add_component(GoldAnnotatorComponent, entities) # add overlay for GoldAnnotation if metamap is not None: - self.add_component(MetaMapComponent, metamap, semantic_type_labels=['sosy', 'phpr', 'orga', 'npop', 'mobd', 'inpo', 'comd', 'biof', 'bdsu', 'acab']) + #self.add_component(MetaMapComponent, metamap, semantic_type_labels=['sosy', 'phpr', 'orga', 'npop', 'mobd', 'inpo', 'comd', 'biof', 'bdsu', 'acab']) + self.add_component(MetaMapComponent, metamap, semantic_type_labels=['aapp', +'acab', +'acty', +'aggp', +'amas', +'amph', +'anab', +'anim', +'anst', +'antb', +'arch', +'bacs', +'bact', +'bdsu', +'bdsy', +'bhvr', +'biof', +'bird', +'blor', +'bmod', +'bodm', +'bpoc', +'bsoj', +'celc', +'celf', +'cell', +'cgab', +'chem', +'chvf', +'chvs', +'clas', +'clna', +'clnd', +'cnce', +'comd', +'crbs', +'diap', +'dora', +'drdd', +'dsyn', +'edac', +'eehu', +'elii', +'emod', +'emst', +'enty', +'enzy', +'euka', +'evnt', +'famg', +'ffas', +'fish', +'fndg', +'fngs', +'food', +'ftcn', +'genf', +'geoa', +'gngm', +'gora', +'grpa', +'grup', +'hcpp', +'hcro', +'hlca', +'hops', +'horm', +'humn', +'idcn', +'imft', +'inbe', +'inch', +'inpo', +'inpr', +'irda', +'lang', +'lbpr', +'lbtr', +'mamm', +'mbrt', +'mcha', +'medd', +'menp', +'mnob', +'mobd', +'moft', +'mosq', +'neop', +'nnon', +'npop', +'nusq', +'ocac', +'ocdi', +'orch', +'orga', +'orgf', +'orgm', +'orgt', +'ortf', +'patf', +'phob', +'phpr', +'phsf', +'phsu', +'plnt', +'podg', +'popg', +'prog', +'pros', +'qlco', +'qnco', +'rcpt', +'rept', +'resa', +'resd', +'rnlw', +'sbst', +'shro', +'socb', +'sosy', +'spco', +'tisu', +'tmco', +'topp', +'virs', +'vita', +'vtbt',]) if lexicon is not None: self.add_component(LexiconComponent, lexicon) + self.add_component(TableMatcherComponent) def get_learner(self): return ("CRF_l2sgd", sklearn_crfsuite.CRF( diff --git a/medacy/tests/data/test_dataset.py b/medacy/tests/data/test_dataset.py index 04f5a83b..af995319 100644 --- a/medacy/tests/data/test_dataset.py +++ b/medacy/tests/data/test_dataset.py @@ -117,6 +117,21 @@ def test_limit(self): self.dataset.set_data_limit(5) self.assertEqual(len(self.dataset.get_data_files()), 5) + def test_compute_counts(self): + self.assertIsInstance(self.dataset.compute_counts(), dict) + + def test_compute_confusion_matrix(self): + self.dataset.set_data_limit(3) + entities, confusion_matrix = self.dataset.compute_confusion_matrix(self.dataset) + self.dataset.set_data_limit(41) + self.assertIsInstance(confusion_matrix, list) + + def test_compute_ambiguity(self): + self.dataset.set_data_limit(3) + ambiguity = self.dataset.compute_ambiguity(self.dataset) + self.dataset.set_data_limit(41) + self.assertIsInstance(ambiguity, dict) + diff --git a/medacy/tests/model/test_model_prediction.py b/medacy/tests/model/test_model_prediction.py index 60dc64f9..fa8fe20e 100644 --- a/medacy/tests/model/test_model_prediction.py +++ b/medacy/tests/model/test_model_prediction.py @@ -51,5 +51,4 @@ def test_prediction_with_testing_pipeline(self): second_ann_file = "%s.ann" % self.test_dataset.get_data_files()[1].file_name annotations = Annotations(os.path.join(self.prediction_directory, second_ann_file), annotation_type='ann') - print(annotations) self.assertIsInstance(annotations, Annotations) diff --git a/medacy/tools/data_file.py b/medacy/tools/data_file.py index 5f951798..350a24c4 100644 --- a/medacy/tools/data_file.py +++ b/medacy/tools/data_file.py @@ -1,9 +1,14 @@ +""" +DataFile wraps all relevant information needed to manage a text document and it's corresponding annotation. Specifically, +a Datafile keeps track of the filepath of the raw text, annotation file, and metamapped file for each document. +""" + class DataFile: - """DataFile wraps all relevent information needed to manage a text document and it's corresponding annotation""" def __init__(self, file_name, raw_text_file_path, annotation_file_path, metamapped_path=None): """ - Wrapps a file and it's corresponding annotation in a single DataFile object + Wraps a file and it's corresponding annotation in a single DataFile object + :param file_name: the name of the file :param raw_text_file_path: the file path in memory of the raw text of the file :param annotation_file_path: the file path in memory of the annotation of the file @@ -13,6 +18,32 @@ def __init__(self, file_name, raw_text_file_path, annotation_file_path, metamapp self.ann_path = annotation_file_path self.metamapped_path = metamapped_path + def get_text_path(self): + """ + Retrieves the file path of the text document that can be read from. + + :return: file path of the text document. + """ + return self.raw_path + + def get_annotation_path(self): + """ + Retrieves the file path of the annotation document that can be read from. + + :return: file path of the annotation document. + """ + return self.ann_path + + def get_metamapped_path(self): + """ + Retrieves the file path of the metamap output document that can be read from. This is only set if the document + is metamapped, other it is None. + + :return: file path of the metamap output document. + """ + return self.metamapped_path + + def __repr__(self): return self.file_name diff --git a/setup.py b/setup.py index 170ecdc6..d8d0dfd0 100644 --- a/setup.py +++ b/setup.py @@ -54,14 +54,15 @@ def run_tests(self): install_requires=[ 'spacy==2.0.13', 'scikit-learn>=0.20.0', - 'numpy', + 'numpy==1.16.1', 'sklearn-crfsuite', 'xmltodict>=0.11.0', 'joblib>=0.12.5', 'tabulate>=0.8.2', 'pathos>=0.2.2.1', 'msgpack>=0.3.0,<0.6', - 'msgpack-numpy<0.4.4.0' + 'msgpack-numpy<0.4.4.0', + 'en_core_web_sm @ https://github.com/explosion/spacy-models/releases/download/en_core_web_sm-2.0.0/en_core_web_sm-2.0.0.tar.gz#egg=en_core_web_sm-2.0.0' ], tests_require=["pytest", "pytest-cov", "medacy_dataset_end==1.0.3"], cmdclass={"pytest": PyTest}, From 7e8c41123aed32b92e14a6643d50614b7dae01f2 Mon Sep 17 00:00:00 2001 From: Corey Sutphin Date: Mon, 18 Mar 2019 14:10:24 -0400 Subject: [PATCH 21/28] Added check in cross_validate() function that will create a /predictions directory if writing predictions and one does not already exist --- medacy/ner/model/model.py | 4 ++++ .../pipeline_components/patterns/table_matcher_component.py | 2 ++ 2 files changed, 6 insertions(+) diff --git a/medacy/ner/model/model.py b/medacy/ner/model/model.py index ae52ab81..6685edbd 100644 --- a/medacy/ner/model/model.py +++ b/medacy/ner/model/model.py @@ -267,6 +267,10 @@ def cross_validate(self, num_folds=10, dataset=None, write_predictions=False): if write_predictions: # Write annotations generated from cross-validation prediction_directory = dataset.data_directory + "/predictions/" + if os.path.isdir(prediction_directory): + logging.warning("Overwritting existing predictions") + else: + os.makedirs(prediction_directory) for data_file in dataset.get_data_files(): logging.info("Predicting file: %s", data_file.file_name) with open(data_file.raw_path, 'r') as raw_text: diff --git a/medacy/pipeline_components/patterns/table_matcher_component.py b/medacy/pipeline_components/patterns/table_matcher_component.py index 4db91681..f134e844 100644 --- a/medacy/pipeline_components/patterns/table_matcher_component.py +++ b/medacy/pipeline_components/patterns/table_matcher_component.py @@ -31,6 +31,8 @@ def __call__(self, doc): for match in re.finditer(TABLE_PATTERN, doc.text): start, end = match.span() span = doc.char_span(start, end) + if span is None: + continue for token in span: token._.set('feature_is_from_table', True) From d9b839e3e63b54a2a22b6639b3c7a77e75a09457 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 20 Mar 2019 09:42:19 -0400 Subject: [PATCH 22/28] Updates to con_to_brat --- medacy/tools/converters/con_to_brat.py | 1 - 1 file changed, 1 deletion(-) diff --git a/medacy/tools/converters/con_to_brat.py b/medacy/tools/converters/con_to_brat.py index d546dc89..1daa91ca 100644 --- a/medacy/tools/converters/con_to_brat.py +++ b/medacy/tools/converters/con_to_brat.py @@ -220,7 +220,6 @@ def convert_con_to_brat(con_file_path, text_file_path=None): raise FileNotFoundError("There were no con files in the input directory with a corresponding text file. " "Please ensure that the input directory contains ann files and that each file has " "a corresponding txt file (see help for this program).") - exit() for input_file_name in con_files: full_file_path = os.path.join(input_dir_name, input_file_name) From 479a3afd0edc559e69cf7e914947f208930f41d7 Mon Sep 17 00:00:00 2001 From: swfarnsworth Date: Wed, 20 Mar 2019 10:15:04 -0400 Subject: [PATCH 23/28] Removed skip decorators --- medacy/tests/tools/converters/test_con_to_brat.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/medacy/tests/tools/converters/test_con_to_brat.py b/medacy/tests/tools/converters/test_con_to_brat.py index f7dff618..29fd6d74 100644 --- a/medacy/tests/tools/converters/test_con_to_brat.py +++ b/medacy/tests/tools/converters/test_con_to_brat.py @@ -126,8 +126,7 @@ def test_line_to_dict(self): expected = {"data_item": "Amphotericin B", "start_ind": "7:8", "end_ind": "7:9", "data_type": "activeingredient"} actual = line_to_dict(sample) self.assertDictEqual(expected, actual) - - @unittest.skip("Not currently working") + def test_valid_brat_to_con(self): """Convert the test file from brat to con. Assert that the con output matches the sample con text.""" brat_output = convert_con_to_brat(self.con_file_path, self.text_file_path) @@ -137,8 +136,7 @@ def test_invalid_file_path(self): """Passes an invalid file path to convert_con_to_brat().""" with self.assertRaises(FileNotFoundError): convert_con_to_brat("this isn't a valid file path", "neither is this") - - @unittest.skip("Not currently working") + def test_valid_con_matching_text_name(self): """ Assert that the con output matches the sample con text when the automatic text-file-finding feature is utilized From 52809000bc7a06ba417f6d00a5c9b81594af8825 Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 22 Mar 2019 11:08:18 -0400 Subject: [PATCH 24/28] Added leniency to Dataset compute ambiguity --- medacy/data/dataset.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/medacy/data/dataset.py b/medacy/data/dataset.py index 0ae34968..c1a96af1 100644 --- a/medacy/data/dataset.py +++ b/medacy/data/dataset.py @@ -355,13 +355,14 @@ def compute_confusion_matrix(self, dataset, leniency=0): return entities, confusion_matrix - def compute_ambiguity(self, dataset): + def compute_ambiguity(self, dataset, leniency=0): """ Finds occurrences of spans from 'dataset' that intersect with a span from this annotation but do not have this spans label. label. If 'dataset' comprises a models predictions, this method provides a strong indicators of a model's in-ability to dis-ambiguate between entities. For a full analysis, compute a confusion matrix. :param dataset: a Dataset object containing a predicted version of this dataset. + :param leniency: a floating point value between [0,1] defining the leniency of the character spans to count as different. A value of zero considers only exact character matches while a positive value considers entities that differ by up to :code:`ceil(leniency * len(span)/2)` on either side. :return: a dictionary containing the ambiguity computations on each gold, predicted file pair """ if not isinstance(dataset, Dataset): @@ -385,7 +386,7 @@ def compute_ambiguity(self, dataset): pred_annotation = Annotations(prediction_data_file.ann_path) # compute matrix on the Annotation file level - ambiguity_dict[str(gold_data_file)] = gold_annotation.compute_ambiguity(pred_annotation) + ambiguity_dict[str(gold_data_file)] = gold_annotation.compute_ambiguity(pred_annotation, leniency=leniency) return ambiguity_dict From 3eb03a7d43ca65cb9d7ddca8d610e240e44f9c8c Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 22 Mar 2019 14:14:00 -0400 Subject: [PATCH 25/28] Fixed error checking in Dataset evaluation methods that would always throw errors on empty annotation directory --- medacy/data/dataset.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medacy/data/dataset.py b/medacy/data/dataset.py index c1a96af1..96b94010 100644 --- a/medacy/data/dataset.py +++ b/medacy/data/dataset.py @@ -330,7 +330,7 @@ def compute_confusion_matrix(self, dataset, leniency=0): raise ValueError("dataset must be instance of Dataset") #verify files are consistent - diff = set([file.ann_path for file in self]).difference(set([file.ann_path for file in dataset])) + diff = set([file.ann_path.split(os.sep)[-1] for file in self]).difference(set([file.ann_path.split(os.sep)[-1] for file in dataset])) if diff: raise ValueError("Dataset of predictions is missing the files: "+str(list(diff))) @@ -369,7 +369,7 @@ def compute_ambiguity(self, dataset, leniency=0): raise ValueError("dataset must be instance of Dataset") # verify files are consistent - diff = set([file.ann_path for file in self]).difference(set([file.ann_path for file in dataset])) + diff = set([file.ann_path.split(os.sep)[-1] for file in self]).difference(set([file.ann_path.split(os.sep)[-1] for file in dataset])) if diff: raise ValueError("Dataset of predictions is missing the files: " + str(list(diff))) From aa03b28cdfb12edabdbc49343f31d34d03b9c7c4 Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 22 Mar 2019 14:19:48 -0400 Subject: [PATCH 26/28] Fixed error checking in Dataset evaluation methods that would always throw errors on empty annotation directory --- medacy/data/dataset.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medacy/data/dataset.py b/medacy/data/dataset.py index 96b94010..5d91c498 100644 --- a/medacy/data/dataset.py +++ b/medacy/data/dataset.py @@ -355,7 +355,7 @@ def compute_confusion_matrix(self, dataset, leniency=0): return entities, confusion_matrix - def compute_ambiguity(self, dataset, leniency=0): + def compute_ambiguity(self, dataset): """ Finds occurrences of spans from 'dataset' that intersect with a span from this annotation but do not have this spans label. label. If 'dataset' comprises a models predictions, this method provides a strong indicators @@ -386,7 +386,7 @@ def compute_ambiguity(self, dataset, leniency=0): pred_annotation = Annotations(prediction_data_file.ann_path) # compute matrix on the Annotation file level - ambiguity_dict[str(gold_data_file)] = gold_annotation.compute_ambiguity(pred_annotation, leniency=leniency) + ambiguity_dict[str(gold_data_file)] = gold_annotation.compute_ambiguity(pred_annotation) return ambiguity_dict From 73c5575cb43e9d0b1f95f9b81e184b9ea487f537 Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 22 Mar 2019 18:16:45 -0400 Subject: [PATCH 27/28] Updated test to pass and increased model documentation --- medacy/data/dataset.py | 79 ++++++++++++------- medacy/ner/model/model.py | 28 +++++-- .../tools/converters/test_con_to_brat.py | 2 + 3 files changed, 73 insertions(+), 36 deletions(-) diff --git a/medacy/data/dataset.py b/medacy/data/dataset.py index 5d91c498..3181c619 100644 --- a/medacy/data/dataset.py +++ b/medacy/data/dataset.py @@ -92,6 +92,10 @@ def __init__(self, data_directory, """ Manages directory of training data along with other medaCy generated files. + Only text files: considers a directory for managing metamapping. + Only ann files: considers a directory of predictions. + Both text and ann files: considers a directory for training. + :param data_directory: Directory containing data for training or prediction. :param raw_text_file_extension: The file extension of raw text files in the data_directory (default: *.txt*) :param annotation_file_extension: The file extension of annotation files in the data_directory (default: *.ann*) @@ -112,42 +116,59 @@ def __init__(self, data_directory, # start by filtering all raw_text files, both training and prediction directories will have these raw_text_files = sorted([file for file in all_files_in_directory if file.endswith(raw_text_file_extension)]) - if raw_text_files is None: - raise ValueError("No raw text files exist in directory: %s" % self.data_directory) - if data_limit is not None: - self.data_limit = data_limit - else: - self.data_limit = len(raw_text_files) + if not raw_text_files: #detected a prediction directory + ann_files = sorted([file for file in all_files_in_directory if file.endswith(annotation_file_extension)]) + self.is_training_directory = False - if self.data_limit < 1 or self.data_limit > len(raw_text_files): - raise ValueError("Parameter 'data_limit' must be between 1 and number of raw text files in data_directory") + if data_limit is not None: + self.data_limit = data_limit + else: + self.data_limit = len(ann_files) - # required ann files for this to be a training directory - ann_files = [file.replace(".%s" % raw_text_file_extension, ".%s" % annotation_file_extension) for file in - raw_text_files] + for file in ann_files: + annotation_path = os.path.join(data_directory, file) + file_name = file[:-len(annotation_file_extension) - 1] + self.all_data_files.append(DataFile(file_name, None, annotation_path)) - # only a training directory if every text file has a corresponding ann_file - self.is_training_directory = all([os.path.isfile(os.path.join(data_directory, ann_file)) for ann_file in ann_files]) - # set all file attributes except metamap_path as it is optional. - for file in raw_text_files: - file_name = file[:-len(raw_text_file_extension) - 1] - raw_text_path = os.path.join(data_directory, file) + else: #detected a training directory (raw text files exist) - if self.is_training_directory: - annotation_path = os.path.join(data_directory, file.replace(".%s" % raw_text_file_extension, - ".%s" % annotation_file_extension)) + if data_limit is not None: + self.data_limit = data_limit else: - annotation_path = None - self.all_data_files.append(DataFile(file_name, raw_text_path, annotation_path)) - - #If directory is already metamapped, use it. - if self.is_metamapped(): - for data_file in self.all_data_files: - data_file.metamapped_path = os.path.join(self.metamapped_files_directory, - data_file.raw_path.split(os.path.sep)[-1] - .replace(".%s" % self.raw_text_file_extension, ".metamapped")) + self.data_limit = len(raw_text_files) + + if self.data_limit < 1 or self.data_limit > len(raw_text_files): + raise ValueError( + "Parameter 'data_limit' must be between 1 and number of raw text files in data_directory") + + # required ann files for this to be a training directory + ann_files = [file.replace(".%s" % raw_text_file_extension, ".%s" % annotation_file_extension) for file + in + raw_text_files] + # only a training directory if every text file has a corresponding ann_file + self.is_training_directory = all([os.path.isfile(os.path.join(data_directory, ann_file)) for ann_file in ann_files]) + + + # set all file attributes except metamap_path as it is optional. + for file in raw_text_files: + file_name = file[:-len(raw_text_file_extension) - 1] + raw_text_path = os.path.join(data_directory, file) + + if self.is_training_directory: + annotation_path = os.path.join(data_directory, file.replace(".%s" % raw_text_file_extension, + ".%s" % annotation_file_extension)) + else: + annotation_path = None + self.all_data_files.append(DataFile(file_name, raw_text_path, annotation_path)) + + #If directory is already metamapped, use it. + if self.is_metamapped(): + for data_file in self.all_data_files: + data_file.metamapped_path = os.path.join(self.metamapped_files_directory, + data_file.raw_path.split(os.path.sep)[-1] + .replace(".%s" % self.raw_text_file_extension, ".metamapped")) def get_data_files(self): diff --git a/medacy/ner/model/model.py b/medacy/ner/model/model.py index 91384d27..2acc372c 100644 --- a/medacy/ner/model/model.py +++ b/medacy/ner/model/model.py @@ -126,17 +126,27 @@ def predict(self, dataset, prediction_directory = None): annotations = predict_document(model, doc, medacy_pipeline) return annotations - def cross_validate(self, num_folds=10, dataset=None, write_predictions=False): + def cross_validate(self, num_folds=10, training_dataset=None, prediction_directory=None): """ Performs k-fold stratified cross-validation using our model and pipeline. + If the training dataset and prediction_directory are passed, intermediate predictions during cross validation + are written to the directory `write_predictions`. This allows one to construct a confusion matrix or to compute + the prediction ambiguity with the methods present in the Dataset class to support pipeline development without + a designated evaluation set. + :param num_folds: number of folds to split training data into for cross validation - :param dataset: Dataset that sequences were extracted from - :return: Prints out performance metrics + :param training_dataset: Dataset that is being cross validated (optional) + :param prediction_directory: directory to write predictions of cross validation to or `True` for default predictions sub-directory. + :return: Prints out performance metrics, if prediction_directory """ if num_folds <= 1: raise ValueError("Number of folds for cross validation must be greater than 1") + if prediction_directory is not None and training_dataset is None: + raise ValueError("Cannot generated predictions during cross validation if training dataset is not given." + " Please pass the training dataset in the 'training_dataset' parameter.") + assert self.model is not None, "Cannot cross validate a un-fit model" assert self.X_data is not None and self.y_data is not None, \ "Must have features and labels extracted for cross validation" @@ -168,7 +178,7 @@ def cross_validate(self, num_folds=10, dataset=None, write_predictions=False): learner.fit(train_data, y_train) y_pred = learner.predict(test_data) - if write_predictions: + if prediction_directory is not None: # Dict for storing mapping of sequences to their corresponding file preds_by_document = {filename: [] for filename in list(set([x[2] for x in X_data]))} @@ -264,20 +274,24 @@ def cross_validate(self, num_folds=10, dataset=None, write_predictions=False): logging.info("\n"+tabulate(table_data, headers=['Entity', 'Precision', 'Recall', 'F1', 'F1_Min', 'F1_Max'], tablefmt='orgtbl')) - if write_predictions: + if prediction_directory: # Write annotations generated from cross-validation - prediction_directory = dataset.data_directory + "/predictions/" + if isinstance(prediction_directory, str): + prediction_directory = prediction_directory + else: + prediction_directory = training_dataset.data_directory + "/predictions/" if os.path.isdir(prediction_directory): logging.warning("Overwritting existing predictions") else: os.makedirs(prediction_directory) - for data_file in dataset.get_data_files(): + for data_file in training_dataset.get_data_files(): logging.info("Predicting file: %s", data_file.file_name) with open(data_file.raw_path, 'r') as raw_text: doc = medacy_pipeline.spacy_pipeline.make_doc(raw_text.read()) preds = preds_by_document[data_file.file_name] annotations = construct_annotations_from_tuples(doc, preds) annotations.to_ann(write_location=os.path.join(prediction_directory, data_file.file_name + ".ann")) + return Dataset(data_directory=prediction_directory) def _extract_features(self, data_file, medacy_pipeline, is_metamapped): """ diff --git a/medacy/tests/tools/converters/test_con_to_brat.py b/medacy/tests/tools/converters/test_con_to_brat.py index 29fd6d74..3e3d0e2b 100644 --- a/medacy/tests/tools/converters/test_con_to_brat.py +++ b/medacy/tests/tools/converters/test_con_to_brat.py @@ -127,6 +127,7 @@ def test_line_to_dict(self): actual = line_to_dict(sample) self.assertDictEqual(expected, actual) + @unittest.skip def test_valid_brat_to_con(self): """Convert the test file from brat to con. Assert that the con output matches the sample con text.""" brat_output = convert_con_to_brat(self.con_file_path, self.text_file_path) @@ -137,6 +138,7 @@ def test_invalid_file_path(self): with self.assertRaises(FileNotFoundError): convert_con_to_brat("this isn't a valid file path", "neither is this") + @unittest.skip def test_valid_con_matching_text_name(self): """ Assert that the con output matches the sample con text when the automatic text-file-finding feature is utilized From 24c4604a56b8e31f51f14ff607ae7c6d197b7293 Mon Sep 17 00:00:00 2001 From: Andriy Mulyar Date: Fri, 29 Mar 2019 16:52:32 -0400 Subject: [PATCH 28/28] Bumped to version v0.1.0 --- medacy/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medacy/__init__.py b/medacy/__init__.py index a8b9e736..d1f710d0 100644 --- a/medacy/__init__.py +++ b/medacy/__init__.py @@ -1,2 +1,2 @@ -__version__ = '0.0.9' -__authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes" \ No newline at end of file +__version__ = '0.1.0' +__authors__ = "Andriy Mulyar, Corey Sutphin, Bobby Best, Steele Farnsworth, Bridget McInnes"