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def quadratic_weighted_kappa(rater_a, rater_b, min_rating=None, max_rating=None): """ Calculates kappa correlation between rater_a and rater_b. Kappa measures how well 2 quantities vary together. rater_a is a list of rater a scores rater_b is a list of rater b scores min_rating is an optional ar...
def confusion_matrix(rater_a, rater_b, min_rating=None, max_rating=None): """ Generates a confusion matrix between rater_a and rater_b A confusion matrix shows how often 2 values agree and disagree See quadratic_weighted_kappa for argument descriptions """ assert(len(rater_a) == len(rater_b)) ...
def histogram(ratings, min_rating=None, max_rating=None): """ Generates a frequency count of each rating on the scale ratings is a list of scores Returns a list of frequencies """ ratings = [int(r) for r in ratings] if min_rating is None: min_rating = min(ratings) if max_rating i...
def get_wordnet_syns(word): """ Utilize wordnet (installed with nltk) to get synonyms for words word is the input word returns a list of unique synonyms """ synonyms = [] regex = r"_" pat = re.compile(regex) synset = nltk.wordnet.wordnet.synsets(word) for ss in synset: fo...
def get_separator_words(toks1): """ Finds the words that separate a list of tokens from a background corpus Basically this generates a list of informative/interesting words in a set toks1 is a list of words Returns a list of separator words """ tab_toks1 = nltk.FreqDist(word.lower() for word...
def encode_plus(s): """ Literally encodes the plus sign input is a string returns the string with plus signs encoded """ regex = r"\+" pat = re.compile(regex) return pat.sub("%2B", s)
def getMedian(numericValues): """ Gets the median of a list of values Returns a float/int """ theValues = sorted(numericValues) if len(theValues) % 2 == 1: return theValues[(len(theValues) + 1) / 2 - 1] else: lower = theValues[len(theValues) / 2 - 1] upper = theValue...
def initialize_dictionaries(self, e_set, max_feats2 = 200): """ Initializes dictionaries from an essay set object Dictionaries must be initialized prior to using this to extract features e_set is an input essay set returns a confirmation of initialization """ if(h...
def get_good_pos_ngrams(self): """ Gets a set of gramatically correct part of speech sequences from an input file called essaycorpus.txt Returns the set and caches the file """ if(os.path.isfile(NGRAM_PATH)): good_pos_ngrams = pickle.load(open(NGRAM_PATH, 'rb')) ...
def _get_grammar_errors(self,pos,text,tokens): """ Internal function to get the number of grammar errors in given text pos - part of speech tagged text (list) text - normal text (list) tokens - list of lists of tokenized text """ word_counts = [max(len(t),1) for t...
def gen_length_feats(self, e_set): """ Generates length based features from an essay set Generally an internal function called by gen_feats Returns an array of length features e_set - EssaySet object """ text = e_set._text lengths = [len(e) for e in text] ...
def gen_bag_feats(self, e_set): """ Generates bag of words features from an input essay set and trained FeatureExtractor Generally called by gen_feats Returns an array of features e_set - EssaySet object """ if(hasattr(self, '_stem_dict')): sfeats = se...
def gen_feats(self, e_set): """ Generates bag of words, length, and prompt features from an essay set object returns an array of features e_set - EssaySet object """ bag_feats = self.gen_bag_feats(e_set) length_feats = self.gen_length_feats(e_set) prompt_f...
def gen_prompt_feats(self, e_set): """ Generates prompt based features from an essay set object and internal prompt variable. Generally called internally by gen_feats Returns an array of prompt features e_set - EssaySet object """ prompt_toks = nltk.word_tokenize(...
def gen_feedback(self, e_set, features=None): """ Generate feedback for a given set of essays e_set - EssaySet object features - optionally, pass in a matrix of features extracted from e_set using FeatureExtractor in order to get off topic feedback. Returns a list of list...
def add_essay(self, essay_text, essay_score, essay_generated=0): """ Add new (essay_text,essay_score) pair to the essay set. essay_text must be a string. essay_score must be an int. essay_generated should not be changed by the user. Returns a confirmation that essay was a...
def update_prompt(self, prompt_text): """ Update the default prompt string, which is "". prompt_text should be a string. Returns the prompt as a confirmation. """ if(isinstance(prompt_text, basestring)): self._prompt = util_functions.sub_chars(prompt_text) ...
def generate_additional_essays(self, e_text, e_score, dictionary=None, max_syns=3): """ Substitute synonyms to generate extra essays from existing ones. This is done to increase the amount of training data. Should only be used with lowest scoring essays. e_text is the text of the...
def create(text,score,prompt_string, dump_data=False): """ Creates a machine learning model from input text, associated scores, a prompt, and a path to the model TODO: Remove model path argument, it is needed for now to support legacy code text - A list of strings containing the text of the essays s...
def create_generic(numeric_values, textual_values, target, algorithm = util_functions.AlgorithmTypes.regression): """ Creates a model from a generic list numeric values and text values numeric_values - A list of lists that are the predictors textual_values - A list of lists that are the predictors (...
def create_essay_set(text, score, prompt_string, generate_additional=True): """ Creates an essay set from given data. Text should be a list of strings corresponding to essay text. Score should be a list of scores where score[n] corresponds to text[n] Prompt string is just a string containing the ess...
def get_cv_error(clf,feats,scores): """ Gets cross validated error for a given classifier, set of features, and scores clf - classifier feats - features to feed into the classified and cross validate over scores - scores associated with the features -- feature row 1 associates with score 1, etc. ...
def get_algorithms(algorithm): """ Gets two classifiers for each type of algorithm, and returns them. First for predicting, second for cv error. type - one of util_functions.AlgorithmTypes """ if algorithm == util_functions.AlgorithmTypes.classification: clf = sklearn.ensemble.GradientBoost...
def extract_features_and_generate_model_predictors(predictor_set, algorithm=util_functions.AlgorithmTypes.regression): """ Extracts features and generates predictors based on a given predictor set predictor_set - a PredictorSet object that has been initialized with data type - one of util_functions.Algo...
def extract_features_and_generate_model(essays, algorithm=util_functions.AlgorithmTypes.regression): """ Feed in an essay set to get feature vector and classifier essays must be an essay set object additional array is an optional argument that can specify a numpy array of values to add in return...
def dump_model_to_file(prompt_string, feature_ext, classifier, text, score, model_path): """ Writes out a model to a file. prompt string is a string containing the prompt feature_ext is a trained FeatureExtractor object classifier is a trained classifier model_path is the path of write out the m...
def create_essay_set_and_dump_model(text,score,prompt,model_path,additional_array=None): """ Function that creates essay set, extracts features, and writes out model See above functions for argument descriptions """ essay_set=create_essay_set(text,score,prompt) feature_ext,clf=extract_features_a...
def initialize_dictionaries(self, p_set): """ Initialize dictionaries with the textual inputs in the PredictorSet object p_set - PredictorSet object that has had data fed in """ success = False if not (hasattr(p_set, '_type')): error_message = "needs to be an ...
def gen_feats(self, p_set): """ Generates features based on an iput p_set p_set - PredictorSet """ if self._initialized!=True: error_message = "Dictionaries have not been initialized." log.exception(error_message) raise util_functions.InputErro...
def t_text(self, t): r':\s*<text>' t.lexer.text_start = t.lexer.lexpos - len('<text>') t.lexer.begin('text')
def t_text_end(self, t): r'</text>\s*' t.type = 'TEXT' t.value = t.lexer.lexdata[ t.lexer.text_start:t.lexer.lexpos] t.lexer.lineno += t.value.count('\n') t.value = t.value.strip() t.lexer.begin('INITIAL') return t
def t_KEYWORD_AS_TAG(self, t): r'[a-zA-Z]+' t.type = self.reserved.get(t.value, 'UNKNOWN_TAG') t.value = t.value.strip() return t
def t_LINE_OR_KEYWORD_VALUE(self, t): r':.+' t.value = t.value[1:].strip() if t.value in self.reserved.keys(): t.type = self.reserved[t.value] else: t.type = 'LINE' return t
def tv_to_rdf(infile_name, outfile_name): """ Convert a SPDX file from tag/value format to RDF format. Return True on sucess, False otherwise. """ parser = Parser(Builder(), StandardLogger()) parser.build() with open(infile_name) as infile: data = infile.read() document, erro...
def order_error(self, first_tag, second_tag, line): """Reports an OrderError. Error message will state that first_tag came before second_tag. """ self.error = True msg = ERROR_MESSAGES['A_BEFORE_B'].format(first_tag, second_tag, line) self.logger.log(msg)
def p_lic_xref_1(self, p): """lic_xref : LICS_CRS_REF LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_lic_xref(self.document, value) except OrderError: self.order_er...
def p_lic_comment_1(self, p): """lic_comment : LICS_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_lic_comment(self.document, value) except OrderError: self...
def p_extr_lic_name_1(self, p): """extr_lic_name : LICS_NAME extr_lic_name_value""" try: self.builder.set_lic_name(self.document, p[2]) except OrderError: self.order_error('LicenseName', 'LicenseID', p.lineno(1)) except CardinalityError: self.more_than...
def p_extr_lic_name_value_1(self, p): """extr_lic_name_value : LINE""" if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_extr_lic_text_1(self, p): """extr_lic_text : LICS_TEXT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_lic_text(self.document, value) except OrderError: self.o...
def p_extr_lic_id_1(self, p): """extr_lic_id : LICS_ID LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_lic_id(self.document, value) except SPDXValueError: self.error...
def p_prj_uri_art_3(self, p): """prj_uri_art : ART_PRJ_URI error""" self.error = True msg = ERROR_MESSAGES['ART_PRJ_URI_VALUE'].format(p.lineno(1)) self.logger.log(msg)
def p_prj_home_art_1(self, p): """prj_home_art : ART_PRJ_HOME LINE""" try: self.builder.set_file_atrificat_of_project(self.document, 'home', p[2]) except OrderError: self.order_error('ArtificatOfProjectHomePage', 'FileName', p.lineno(1))
def p_prj_home_art_2(self, p): """prj_home_art : ART_PRJ_HOME UN_KNOWN""" try: self.builder.set_file_atrificat_of_project(self.document, 'home', utils.UnKnown()) except OrderError: self.order_error('ArtifactOfProjectName', 'FileName', p.lineno(1))
def p_prj_name_art_1(self, p): """prj_name_art : ART_PRJ_NAME LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_atrificat_of_project(self.document, 'name', value) except Orde...
def p_file_dep_1(self, p): """file_dep : FILE_DEP LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_file_dep(self.document, value) except OrderError: self.order_error(...
def p_file_contrib_1(self, p): """file_contrib : FILE_CONTRIB LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_file_contribution(self.document, value) except OrderError: ...
def p_file_notice_1(self, p): """file_notice : FILE_NOTICE TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_notice(self.document, value) except OrderError: self....
def p_file_cr_text_1(self, p): """file_cr_text : FILE_CR_TEXT file_cr_value""" try: self.builder.set_file_copyright(self.document, p[2]) except OrderError: self.order_error('FileCopyrightText', 'FileName', p.lineno(1)) except CardinalityError: self.mor...
def p_file_cr_value_1(self, p): """file_cr_value : TEXT""" if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_file_lics_comment_1(self, p): """file_lics_comment : FILE_LICS_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_license_comment(self.document, value) except Or...
def p_file_lics_info_1(self, p): """file_lics_info : FILE_LICS_INFO file_lic_info_value""" try: self.builder.set_file_license_in_file(self.document, p[2]) except OrderError: self.order_error('LicenseInfoInFile', 'FileName', p.lineno(1)) except SPDXValueError: ...
def p_conc_license_3(self, p): """conc_license : LINE""" if six.PY2: value = p[1].decode(encoding='utf-8') else: value = p[1] ref_re = re.compile('LicenseRef-.+', re.UNICODE) if (p[1] in config.LICENSE_MAP.keys()) or (ref_re.match(p[1]) is not None): ...
def p_file_name_1(self, p): """file_name : FILE_NAME LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_name(self.document, value) except OrderError: self.order_er...
def p_spdx_id(self, p): """spdx_id : SPDX_ID LINE""" if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] if not self.builder.doc_spdx_id_set: self.builder.set_doc_spdx_id(self.document, value) else: self.builder.set...
def p_file_comment_1(self, p): """file_comment : FILE_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_comment(self.document, value) except OrderError: s...
def p_file_type_1(self, p): """file_type : FILE_TYPE file_type_value""" try: self.builder.set_file_type(self.document, p[2]) except OrderError: self.order_error('FileType', 'FileName', p.lineno(1)) except CardinalityError: self.more_than_one_error('Fil...
def p_file_chksum_1(self, p): """file_chksum : FILE_CHKSUM CHKSUM""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_file_chksum(self.document, value) except OrderError: sel...
def p_file_conc_1(self, p): """file_conc : FILE_LICS_CONC conc_license""" try: self.builder.set_concluded_license(self.document, p[2]) except SPDXValueError: self.error = True msg = ERROR_MESSAGES['FILE_LICS_CONC_VALUE'].format(p.lineno(1)) self.lo...
def p_file_type_value(self, p): """file_type_value : OTHER | SOURCE | ARCHIVE | BINARY """ if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_pkg_desc_1(self, p): """pkg_desc : PKG_DESC TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_desc(self.document, value) except CardinalityError: self.more_t...
def p_pkg_summary_1(self, p): """pkg_summary : PKG_SUM TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_summary(self.document, value) except OrderError: self.orde...
def p_pkg_cr_text_1(self, p): """pkg_cr_text : PKG_CPY_TEXT pkg_cr_text_value""" try: self.builder.set_pkg_cr_text(self.document, p[2]) except OrderError: self.order_error('PackageCopyrightText', 'PackageFileName', p.lineno(1)) except CardinalityError: ...
def p_pkg_cr_text_value_1(self, p): """pkg_cr_text_value : TEXT""" if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_pkg_lic_comment_1(self, p): """pkg_lic_comment : PKG_LICS_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_license_comment(self.document, value) except OrderErr...
def p_pkg_lic_ff_1(self, p): """pkg_lic_ff : PKG_LICS_FFILE pkg_lic_ff_value""" try: self.builder.set_pkg_license_from_file(self.document, p[2]) except OrderError: self.order_error('PackageLicenseInfoFromFiles', 'PackageName', p.lineno(1)) except SPDXValueError: ...
def p_pkg_lic_ff_value_3(self, p): """pkg_lic_ff_value : LINE""" if six.PY2: value = p[1].decode(encoding='utf-8') else: value = p[1] p[0] = document.License.from_identifier(value)
def p_pkg_src_info_1(self, p): """pkg_src_info : PKG_SRC_INFO TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_source_info(self.document, value) except CardinalityError: ...
def p_pkg_chksum_1(self, p): """pkg_chksum : PKG_CHKSUM CHKSUM""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_chk_sum(self.document, value) except OrderError: self.o...
def p_pkg_home_1(self, p): """pkg_home : PKG_HOME pkg_home_value""" try: self.builder.set_pkg_down_location(self.document, p[2]) except OrderError: self.order_error('PackageHomePage', 'PackageName', p.lineno(1)) except CardinalityError: self.more_than_...
def p_pkg_home_2(self, p): """pkg_home : PKG_HOME error""" self.error = True msg = ERROR_MESSAGES['PKG_HOME_VALUE'] self.logger.log(msg)
def p_pkg_home_value_1(self, p): """pkg_home_value : LINE""" if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_pkg_down_value_1(self, p): """pkg_down_value : LINE """ if six.PY2: p[0] = p[1].decode(encoding='utf-8') else: p[0] = p[1]
def p_pkg_file_name(self, p): """pkg_file_name : PKG_FILE_NAME LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_file_name(self.document, value) except OrderError: ...
def p_package_version_1(self, p): """package_version : PKG_VERSION LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_pkg_vers(self.document, value) except OrderError: ...
def p_package_name(self, p): """package_name : PKG_NAME LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.create_package(self.document, value) except CardinalityError: sel...
def p_review_date_1(self, p): """review_date : REVIEW_DATE DATE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_review_date(self.document, value) except CardinalityError: ...
def p_review_comment_1(self, p): """review_comment : REVIEW_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_review_comment(self.document, value) except CardinalityError:...
def p_annotation_date_1(self, p): """annotation_date : ANNOTATION_DATE DATE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_annotation_date(self.document, value) except CardinalityEr...
def p_annotation_comment_1(self, p): """annotation_comment : ANNOTATION_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_annotation_comment(self.document, value) except C...
def p_annotation_type_1(self, p): """annotation_type : ANNOTATION_TYPE LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.add_annotation_type(self.document, value) except CardinalityEr...
def p_annotation_spdx_id_1(self, p): """annotation_spdx_id : ANNOTATION_SPDX_ID LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_annotation_spdx_id(self.document, value) except C...
def p_doc_comment_1(self, p): """doc_comment : DOC_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_doc_comment(self.document, value) except CardinalityError: ...
def p_doc_name_1(self, p): """doc_name : DOC_NAME LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_doc_name(self.document, value) except CardinalityError: self.more_t...
def p_ext_doc_refs_1(self, p): """ext_doc_ref : EXT_DOC_REF DOC_REF_ID DOC_URI EXT_DOC_REF_CHKSUM""" try: if six.PY2: doc_ref_id = p[2].decode(encoding='utf-8') doc_uri = p[3].decode(encoding='utf-8') ext_doc_chksum = p[4].decode(encoding='utf-...
def p_spdx_version_1(self, p): """spdx_version : DOC_VERSION LINE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_doc_version(self.document, value) except CardinalityError: ...
def p_creator_comment_1(self, p): """creator_comment : CREATOR_COMMENT TEXT""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_creation_comment(self.document, value) except CardinalityE...
def p_created_1(self, p): """created : CREATED DATE""" try: if six.PY2: value = p[2].decode(encoding='utf-8') else: value = p[2] self.builder.set_created_date(self.document, value) except CardinalityError: self.more_...
def write_creation_info(creation_info, out): """ Write the creation info to out. """ out.write('# Creation Info\n\n') # Write sorted creators for creator in sorted(creation_info.creators): write_value('Creator', creator, out) # write created write_value('Created', creation_info....
def write_review(review, out): """ Write the fields of a single review to out. """ out.write('# Review\n\n') write_value('Reviewer', review.reviewer, out) write_value('ReviewDate', review.review_date_iso_format, out) if review.has_comment: write_text_value('ReviewComment', review.com...
def write_annotation(annotation, out): """ Write the fields of a single annotation to out. """ out.write('# Annotation\n\n') write_value('Annotator', annotation.annotator, out) write_value('AnnotationDate', annotation.annotation_date_iso_format, out) if annotation.has_comment: write_...
def write_file(spdx_file, out): """ Write a file fields to out. """ out.write('# File\n\n') write_value('FileName', spdx_file.name, out) write_value('SPDXID', spdx_file.spdx_id, out) if spdx_file.has_optional_field('type'): write_file_type(spdx_file.type, out) write_value('FileCh...
def write_package(package, out): """ Write a package fields to out. """ out.write('# Package\n\n') write_value('PackageName', package.name, out) if package.has_optional_field('version'): write_value('PackageVersion', package.version, out) write_value('PackageDownloadLocation', packag...
def write_extracted_licenses(lics, out): """ Write extracted licenses fields to out. """ write_value('LicenseID', lics.identifier, out) if lics.full_name is not None: write_value('LicenseName', lics.full_name, out) if lics.comment is not None: write_text_value('LicenseComment',...
def write_document(document, out, validate=True): """ Write an SPDX tag value document. - document - spdx.document instance. - out - file like object that will be written to. Optionally `validate` the document before writing and raise InvalidDocumentError if document.validate returns False. ...
def checksum_from_sha1(value): """ Return an spdx.checksum.Algorithm instance representing the SHA1 checksum or None if does not match CHECKSUM_RE. """ # More constrained regex at lexer level CHECKSUM_RE = re.compile('SHA1:\s*([\S]+)', re.UNICODE) match = CHECKSUM_RE.match(value) if matc...
def str_from_text(text): """ Return content of a free form text block as a string. """ REGEX = re.compile('<text>((.|\n)+)</text>', re.UNICODE) match = REGEX.match(text) if match: return match.group(1) else: return None
def set_doc_version(self, doc, value): """ Set the document version. Raise SPDXValueError if malformed value, CardinalityError if already defined """ if not self.doc_version_set: self.doc_version_set = True m = self.VERS_STR_REGEX.match(value) ...
def set_doc_data_lics(self, doc, lics): """Sets the document data license. Raises value error if malformed value, CardinalityError if already defined. """ if not self.doc_data_lics_set: self.doc_data_lics_set = True if validations.validate_data_lics(lics):...
def set_doc_name(self, doc, name): """Sets the document name. Raises CardinalityError if already defined. """ if not self.doc_name_set: doc.name = name self.doc_name_set = True return True else: raise CardinalityError('Document::Nam...